More Transporters, More Substrates: The Arabidopsis Major Facilitator Superfamily Revisited Mol. Plant (IF 10.812) Pub Date : 2019-07-19 María Niño-González, Esther Novo-Uzal, Dale N. Richardson, Pedro M. Barros, Paula Duque
The Major Facilitator Superfamily (MFS) is ubiquitous in living organisms and represents the largest group of secondary active membrane transporters. In plants, significant research efforts have focused on the role of specific families within the MFS, particularly those transporting macronutrients (C, N and P) that comprise the vast majority of the members of this superfamily. Other MFS families remain less explored, though a plethora of additional substrates and physiological functions have been uncovered. Nevertheless, the lack of a systematic approach to the analysis of the MFS as a whole has obscured the high diversity and versatility of these transporters. Here, we present a phylogenetic analysis of all annotated MFS domain-containing proteins encoded in the Arabidopsis thaliana genome and propose that this superfamily of transporters consists of 218 members, clustered in 22 families. In reviewing the available information regarding the diversity in biological functions and substrates of arabidopsis MFS members, we provide arguments for intensified research on these membrane transporters to unveil the breadth of their physiological relevance, disclose the molecular mechanisms underlying their mode of action, and explore their biotechnological potential.
Nucleocytoplasmic Trafficking of the Arabidopsis WD40 Repeat Protein XIW1 Regulates ABI5 Stability and Abscisic Acid Responses Mol. Plant (IF 10.812) Pub Date : 2019-07-08 Xuezhong Xu, Wang Wan, Guobin Jiang, Yue Xi, Haijian Huang, Jiajia Cai, Yanan Chang, Cheng-Guo Duan, Satendra K. Mangrauthia, Xinxiang Peng, Jian-Kang Zhu, Guohui Zhu
WD40 repeat-containing proteins (WD40 proteins) serve as versatile scaffolds for protein-protein interactions, modulating a variety of cellular processes such as plant stress and hormone responses. Here, we describe a WD40 protein, XIW1 (for XPO1-Interacting WD40 protein 1), that positively regulates the Abscisic acid (ABA) response in Arabidopsis. XIW1 is located in the cytoplasm and nucleus. It interacts with the nuclear transport receptor XPO1 and is exported by XPO1 from the nucleus. Mutation of XIW1 reduces the induction of ABA-responsive genes and the accumulation of ABA Insensitive 5 (ABI5), leading to ABA-insensitive phenotypes during seed germination and seedling growth, and decreased drought stress resistance. ABA treatment upregulates the expression of XIW1, and both ABA and abiotic stresses promote the nuclear accumulation of the XIW1 protein. In the nucleus, XIW1 interacts with ABI5, and loss of XIW1 results in rapid proteasomal degradation of ABI5. Taken together, these data suggest that XIW1 is a nucleocytoplasmic shuttling protein that has a positive role in ABA responses by interacting with and maintaining the stability of ABI5 in the nucleus.
GTR-mediated radial import directs accumulation of defensive glucosinolates to sulfur-rich cells (S-cells) in phloem cap of inflorescence stem of Arabidopsis thaliana Mol. Plant (IF 10.812) Pub Date : 2019-06-29 Deyang Xu, Pascal Hunziker, Olga Koroleva, Andreas Blennow, Christoph Crocoll, Alexander Schulz, Hussam Hassan Nour-Eldin, Barbara Ann Halkier
In the phloem cap region of Arabidopsis, sulfur-rich cells (S-cells) accumulate >100 mM glucosinolates (GLS), but are biosynthetically inactive. The source and route of S-cell-bound GLS remain elusive. Here we used single-cell sampling and scanning electron microscopy with Energy-dispersive X-ray analysis to show that the GLS importers NPF2.10/GTR1 and NPF2.11/GTR2 are critical for GLS accumulation in S-cells, although not localized to the S-cells. Analysis of S-cell GLS in homo- and heterografts of gtr1 gtr2, and biosynthetic null mutant on wild type indicate that S-cells accumulate GLS via symplasmic connections either directly from neighboring biosynthetic cells or indirectly to non-neighboring cells expressing GTRs. Distinct sources and transport routes exist for different types of GLS, and vary dependent on the position of S-cells in the inflorescence stem. Based on our data, we propose a model for GLS transport routes either directly from biosynthetic cells or via GTR-mediated import from apoplastic space radially into a symplasmic domain wherein the S-cells are the ultimate sink. Similarly, we observed accumulation of the cyanogenic glucoside defense compounds in high-turgor cells in phloem cap of Lotus japonicus, suggesting that storage of defense compounds in high-turgor cells may be a general mechanism for chemical protection of the phloem cap.
Perspectives on the application of genome editing technologies in crop breeding Mol. Plant (IF 10.812) Pub Date : 2019-06-28 Kai Hua, Jinshan Zhang, Jose Ramon Botella, Changle Ma, Fanjiang Kong, Baohui Liu, Jian-Kang Zhu
Most conventional and modern crop improvement methods exploit natural or artificially induced genetic variations and require laborious characterization of multiple generations of time-consuming genetic crosses. Genome editing systems, in contrast, provide the means to rapidly modify genomes in a precise and predictable way, making it possible to introduce improvements directly into elite varieties. Here, we describe the range of applications available to agricultural researchers using existing genome editing tools. In addition to providing examples of genome editing applications in crop breeding, we discuss the technical and social challenges faced by breeders using genome editing tools for crop improvement.
BZR1 Family Transcription Factors Function Redundantly and Indispensably in BR Signaling but Exhibit BRI1-Independent Function in Regulating Anther Development in Arabidopsis Mol. Plant (IF 10.812) Pub Date : 2019-06-21 Lian-Ge Chen, Zhihua Gao, Zhiying Zhao, Xinye Liu, Yongpeng Li, Yuxiang Zhang, Xigang Liu, Yu Sun, Wenqiang Tang
BRASSINAZOLE RESISTANT 1 family proteins (BZRs) are central transcription factors that govern brassinosteroid (BR)-regulated gene expression and plant growth. However, it is unclear whether there exists a BZRs-independent pathway that mediates BR signaling. In this study, we found that knocking out the expression of all BZRs in Arabidopsis generated a hextuple mutant (bzr-h) displays vegetative growth phenotypes that were almost identical to those of the BR receptors null mutant bri1brl1brl3 (bri-t). By RNA sequencing, we found that global gene expression in bzr-h was unaffected by 2 h of BR treatment. The anthers of bzr-h plants were loculeless, but a similar phenotype was not observed in bri-t, suggesting that BZRs have a BR signaling-independent regulatory role in anther development. By real-time PCR and in situ hybridization, we found that the expression of SPOROCYTELESS (SPL), a transcription factor gene that is essential for anther locule development, was barely detectable in the bzr-h mutant, suggesting that BZRs regulate locule development by regulating SPL expression. Together, our findings not only demonstrate that BZRs are indispensable transcription factors for the regulation of both BR signaling and anther locule development, but also provide new insight into the molecular mechanisms that control microsporogenesis process in Arabidopsis.
Elimination of a retrotransposon for quenching genome instability in modern rice Mol. Plant (IF 10.812) Pub Date : 2019-06-20 Yu Peng, Yingying Zhang, Yijie Gui, Dong An, Junzhong Liu, Xun Xu, Qun Li, Junmin Wang, Wen Wang, Chunhai Shi, Longjiang Fan, Baorong Lu, Yiwen Deng, Sheng Teng, Zuhua He
Transposable elements (TEs) constitute the most abundant portions of plant genomes and can dramatically shape host genomes during plant evolution. They also play important roles in crop domestication. However, whether TEs themselves are also selected during crop domestication remained unknown. Here, we identify an active long terminal repeat (LTR) retrotransposon, HUO, as a potential selection target during rice domestication and breeding. HUO is a low-copy-number LTR retrotransposon, and displays transposition activity under the natural growth conditions and transmits transpositions through male gametogenesis, preferentially inserting into genomic regions capable of transcription. HUO exists in all wild rice accessions, about half of the archaeological rice grains (1200-7000 years ago) and landraces, but is absent in almost all modern varieties, indicating its gradual elimination during rice domestication and breeding. Our data hints that HUO is subjected to strict gene silencing through the RNA-directed DNA methylation (RdDM) pathway. Our study also suggests that HUO may trigger genomic defense through altering genome-wide DNA methylation and small RNA biogenesis, and changing global gene expression, resulting in decreased disease resistance and yield, which may explain its elimination in rice breeding. Thus, our study reveals that negative selection of an active retrotransposon may be important for genome stability during crop domestication and breeding.
Whole-plant live imaging of reactive oxygen species Mol. Plant (IF 10.812) Pub Date : 2019-06-18 Yosef Fichman, Gad Miller, Ron Mittler
Reactive oxygen species (ROS) are key regulators of numerous subcellular, cellular and systemic signals. They function in plants as an integral part of many different hormonal, physiological and developmental pathways, as well as play a critical role in defense and acclimation responses to different biotic and abiotic conditions. Although many ROS imaging techniques have been developed and utilized in plants, a whole-plant imaging platform for the dynamic detection of ROS in mature plants is lacking. Here we describe a robust and straightforward method for the whole-plant live imaging of ROS in mature plants grown in soil. The new method could be used to study local and systemic ROS signals in different genetic variants, conduct phenotyping studies to identify new pathways for ROS signaling, monitor the stress level of different plants and mutants, and unravel novel routes of ROS integration into stress, growth regulation and development in plants. We demonstrate the utility of the new method for the study of systemic ROS signals in different mutants of Arabidopsis thaliana, as well as for the study of wound responses in wheat and corn.
A GmNINa-miR172c-NNC1 Regulatory Network Coordinates the Nodulation and Autoregulation of Nodulation Pathways in Soybean Mol. Plant (IF 10.812) Pub Date : 2019-06-13 Lixiang Wang, Zhengxi Sun, Chao Su, Yongliang Wang, Qiqi Yan, Jiahuan Chen, Thomas Ott, Xia Li
Symbiotic root nodules are root lateral organs of plants in which nitrogen-fixing bacteria (rhizobia) convert atmospheric nitrogen to ammonia. The formation and number of nodules in legumes are precisely controlled by a rhizobia-induced signal cascade and host-controlled autoregulation of nodulation (AON). However, how these pathways are integrated and their underlying mechanisms are unclear. Here, we report that the microRNA172c (miR172c) activates soybean (Glycine max) Rhizobia-Induced CLE1 (GmRIC1) and GmRIC2 by removing the transcriptional repression of these genes by soybean Nodule Number Control 1 (NNC1), thereby activating the AON pathway. NNC1 interacts with GmNINa, the soybean ortholog of Lotus NODULE INCEPTION (NIN) and hampers its transcriptional activation of GmRIC1 and GmRIC2. Importantly, GmNINa acts as a transcriptional activator of miR172c. Intriguingly, NNC1 can transcriptionally repress miR172c expression, introducing a novel negative feedback loop into the NNC1 regulatory network. Moreover, GmNINa interacts with NNC1 and can relieve the NNC1-mediated repression of miR172c transcription. Thus, the GmNINa/miR172c/NNC1 network is a master switch that coordinately regulates and optimizes NF and AON signaling, supporting the balance between nodulation and AON in soybean.
OsBRXL4 Regulates Shoot Gravitropism and Rice Tiller Angle through Affecting LAZY1 Nuclear Localization Mol. Plant (IF 10.812) Pub Date : 2019-06-12 Zhen Li, Yan Liang, Yundong Yuan, Lei Wang, Xiangbing Meng, Guosheng Xiong, Jie Zhou, Yueyue Cai, Ningpei Han, Lekai Hua, Guifu Liu, Jiayang Li, Yonghong Wang
Rice tiller angle is a key agronomic trait that contributes to ideal plant architecture and grain production. Our previous study showed that LAZY1 (LA1) controls tiller angle via affecting shoot gravitropism, but the molecular mechanism remains largely unknown. Here, we identified a LA1-interacting protein named Brevis Radix Like 4 (OsBRXL4). We showed that the interaction between OsBRXL4 and LA1 occurs at the plasma membrane and that their interaction determines LA1 nuclear localization. We found that LA1 nuclear localization is essential for LA1 function, which is different from AtLA1, the ortholog in Arabidopsis. Overexpression of OsBRXL4 leads to a prostrate growth phenotype, whereas OsBRXLs RNAi plants, in which the expression levels of OsBRXL1, OsBRXL4, and OsBRXL5 were decreased, display a compact phenotype. Further genetic evidence confirmed that OsBRXL4 controls rice tiller angle by affecting LA1 nuclear localization. Consistent with this, OsBRXL4 regulates the shoot gravitropism through affecting polar auxin transport as did LA1. Therefore, our study not only identifies OsBRXL4 as a regulatory component of rice tiller angle, but also provides a new insight into our understanding of rice plant architecture.
The Structure and Function of Major Plant Metabolite Modifications Mol. Plant (IF 10.812) Pub Date : 2019-06-11 Shouchuang Wang, Saleh Alseekh, Alisdair R. Fernie, Jie Luo
Plants produce myriad structurally and functionally diverse metabolites that play many different roles in growth and development and in response to continually changing environmental conditions and abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress and challenges that have been achieved in the field. We cover both technical and functional aspects focusing on the influence that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, emerging insight into the evolution of metabolic pathways and metabolite functionality will be described.
Wxlv, the ancestral allele of rice Waxy gene Mol. Plant (IF 10.812) Pub Date : 2019-06-08 Changquan Zhang, Jihui Zhu, Shengjie Chen, Xiaolei Fan, Qianfeng Li, Yan Lu, Min Wang, Hengxiu Yu, Chuandeng Yi, Shuzhu Tang, Minghong Gu, Qiaoquan Liu
In rice grains, the Waxy (Wx) gene is responsible for the synthesis of amylose, the most important determinant for eating and cooking quality. Up to now, several Wx alleles have been elucidated on their effects of amylose content as well as the taste of cooked rice. However, the relationships between artificial selection and the evolution as well as distribution of various Wx alleles remain unclear. Herein, we report the cloning of the ancestral allele Wxlv of the Wx locus, which dramatically affects the mouthfeel of rice grains by modulating the size of amylose molecules. We demonstrated that Wxlv originated directly from wild rice, and the three major Wx alleles in cultivated rice (Wxb, Wxa, and Wxin) differentiated after the substitution of one base pair at the functional sites. These data indicate that the Wxlv allele played an important role in artificial selection and domestication. The findings also shed light on the evolution of various Wx alleles, which have greatly contributed to improving the eating and cooking quality of rice.
Wound-induced shoot-to-root relocation of JA-Ile precursors coordinates Arabidopsis growth Mol. Plant (IF 10.812) Pub Date : 2019-06-08 Adina Schulze, Marlene Zimmer, Stefan Mielke, Hagen Stellmach, Charles W. Melnyk, Bettina Hause, Debora Gasperini
Multicellular organisms rely upon the movement of signaling molecules across cells, tissues and organs to communicate among distal sites. In plants, localized leaf damage activates jasmonate (JA)-dependent transcriptional reprogramming in both harmed and unharmed tissues. Although previous evidence indicated that JA species can translocate from damaged into distal sites, the identity of the mobile compound(s), the tissues through which they translocate and the impact of their relocation remain unknown. Here, we found that following shoot wounding, the relocation of endogenous jasmonates through the phloem is essential to initiate JA signaling and stunt growth in unharmed roots of Arabidopsis thaliana. By coupling grafting experiments to hormone profiling, we uncovered that the hormone precursor OPDA and its derivatives, but not the bioactive JA-Ile conjugate, translocate from wounded shoots into undamaged roots. Upon root relocation, the mobile precursors cooperatively regulated JA responses through their conversion into JA-Ile and JA signaling activation. Collectively, our findings demonstrate the existence of long-distance translocation of endogenous OPDA and its derivatives which serve as communication molecules to coordinate shoot-to-root responses, and highlight the importance of a controlled re-distribution of hormone precursors among organs during plant stress acclimation.
ETR1 Integrates Response to Ethylene and Cytokinins into a Single Multistep Phosphorelay Pathway to Control Root Growth Mol. Plant (IF 10.812) Pub Date : 2019-06-07 Marketa Zdarska, Abigail Rubiato Cuyacot, Paul T. Tarr, Amel Yamoune, Agnieszka Szmitkowska, Vendula Hrdinová, Zuzana Gelová, Elliot M. Meyerowitz, Jan Hejátko
Cytokinins and ethylene control plant development via sensors from the histidine kinase (HK) family. However, downstream signaling pathways for the key phytohormones are distinct. Here we report not only cytokinin but also ethylene is able to control root apical meristem (RAM) size through activation of the multistep phosphorelay (MSP) pathway. We find both cytokinin and ethylene-dependent RAM shortening requires ethylene binding to ETR1 and its HK activity. The receiver domain of ETR1 interacts with MSP signaling intermediates acting downstream of cytokinin receptors, further substantiating the role of ETR1 in MSP signaling. Our studies find both cytokinin and ethylene induce the MSP in similar and distinct cell types with ETR1-mediated ethylene signaling controlling MSP output specifically in the root transition zone. We identified members of the MSP pathway specific and common to both hormones and show that ETR1-regulated ARR3 controls RAM size. ETR1-mediated MSP spatially differs from canonical CTR1/EIN2/EIN3 ethylene signaling and is independent of EIN2, indicating that both pathways can be spatially and functionally separated. Furthermore, we demonstrate that canonical ethylene signaling controls MSP responsiveness to cytokinin specifically in the root transition zone, presumably via regulation of ARR10, one of the positive regulators of MSP signaling in Arabidopsis.
A Post-domestication Mutation Dt2 Triggers Systemic Modification of Divergent and Convergent Pathways Modulating Multiple Agronomic Traits in Soybean Mol. Plant (IF 10.812) Pub Date : 2019-05-29 Dajian Zhang, Xutong Wang, Shuo Li, Chaofan Wang, Michael J. Gosney, Michael V. Mickelbart, Jianxin Ma
The semi-determinate stem growth habit in leguminous crops, similar to the “green revolution” semi-dwarf trait in cereals, is a key plant architecture trait that affects several other traits determining grain yield. In soybean, semi-determinacy is modulated by a post-domestication gain-of-function mutation, Dt2, that encodes a MADS-domain transcription factor. However, its role in systemic modification of stem growth and other traits is unknown. Here, we show that Dt2 functions not only as a direct repressor of Dt1 that prevents terminal flowering, but also as a direct activator of putative floral integrator/identity genes including GmSOC1, GmAP1, and GmFUL that may promote flowering. We also demonstrate that Dt2 functions as a direct repressor of putative drought responsive transcription factor gene GmDREB1D, and as a direct activator of GmSPCH and GmGRP7 that are potentially associated with asymmetric young epidermal cell division and stomatal opening, respectively, which may affect the plant’s water-use efficiency (WUE). More intriguingly, Dt2 was found to be a direct activator or repressor of the precursors of eight miRNAs targeting genes potentially associated with meristem maintenance, flowering time, stomatal density, WUE, and/or stress responses. This study, thus, reveals the molecular basis of pleiotropy associated with plant productivity, adaptability, and environmental resilience.
Phosphorylation of LTF1, A MYB Transcription Factor in Populus, Acts as a Sensory Switch Regulating Lignin Biosynthesis in Wood Cells Mol. Plant (IF 10.812) Pub Date : 2019-05-27 Jinshan Gui, Laifu Luo, Yu Zhong, Jiayan Sun, Toshiaki Umezawa, Laigeng Li
Lignin is specifically deposited in plant secondary cell walls and initiation of lignin biosynthesis is regulated by a variety of developmental and environmental signals. However, the mechanism governing the regulation of lignin biosynthesis remains to be elucidated. Here, we identified a lignin biosynthesis associated transcription factor (LTF) from Populus, LTF1, which binds to the promoter of 4-coumarate-CoA ligase (4CL), a key lignin biosynthetic gene. We showed that LTF1 in its unphosphorylated state functions as a regulator to restrain lignin biosynthesis. When LTF1 becomes phosphorylated by PdMPK6 in response to external stimuli such as wounding, it underwent degradation through a proteasome pathway, resulting in activation of lignification. Expression of the LTF1 phosphorylation-null mutation led to stable LTF1 accumulation and persistent attenuation of lignification in wood cells. The study reveals a mechanism where LTF1 phosphorylation acts as a sensory switch to regulate lignin biosynthesis in response to environmental stimuli. The discovery of novel modulators and mechanisms to modify lignin biosynthesis has important implications for improving the utilization of cell wall biomass.
Genome sequences provide insights into the reticulate origin and unique traits of woody bamboos Mol. Plant (IF 10.812) Pub Date : 2019-05-27 Zhen-Hua Guo, Peng-Fei Ma, Guo-Qian Yang, Jin-Yong Hu, Yun-Long Liu, En-Hua Xia, Mi-Cai Zhong, Lei Zhao, Gui-Ling Sun, Yu-Xing Xu, You-Jie Zhao, Yi-Chi Zhang, Yu-Xiao Zhang, Xue-Mei Zhang, Meng-Yuan Zhou, Ying Guo, Cen Guo, Jing-Xia Liu, De-Zhu Li
Polyploidization is a major driver of speciation and its importance to plant evolution has been well recognized. Bamboos comprise of one diploid herbaceous and three polyploid woody lineages, and are the only major subfamily in grasses which diversified in forests with tree-like lignified culm for its woody members. Here we generated four draft genomes of major bamboo lineages at three different ploidy levels (diploid, tetraploid and hexaploid). We also constructed a high-density genetic linkage map of bamboo for a hexaploid species, providing a linkage-map-based strategy for assembly and identification of subgenomes in polyploids. Further phylogenomic analyses based on a large dataset of syntenic genes with expected copies revealed that woody bamboos originated subsequent to the divergence of the herbaceous bamboo lineage, and experienced complex reticulate evolution by three independent allopolyploid events involving four extinct diploid ancestors. A shared but distinct subgenome was identified in all polyploid forms, and its progenitor could be critical in ancient polyploidizations and origin of woody bamboos. We also found important genetic clues to the unique flowering behavior and woody trait in bamboos. Taken together, our study provides significant insights into ancient reticulate evolution at the subgenome level in the absence of extant donor species, and offers a potential model scenario for a broad-scale study of plant origins by allopolyploidization in angiosperms.
Systems biology of plant microbiome interactions Mol. Plant (IF 10.812) Pub Date : 2019-05-23 Patricia A. Rodriguez, Michael Rothballer, Soumitra Paul Chowdhury, Thomas Nussbaumer, Caroline Gutjahr, Pascal Falter-Braun
In natural environments plants are exposed to diverse microbiota that they interact with in complex ways. While plant-pathogen interactions have been intensely studied to understand defense mechanisms in plants, many microbes and microbial communities can have substantial beneficial effects on their plant host. Such beneficial effects include improved acquisition of nutrients, accelerated growth, resilience against pathogens, and improved resistance against abiotic stress conditions such as heat, drought, and salinity. However, the beneficial effects of bacterial strains or consortia on their host are often cultivar- and species-specific posing an obstacle to their general application. Remarkably many of the signals that trigger plant immune responses are molecularly highly similar and often identical in pathogenic and beneficial microbes. Thus, it is unclear what determines the outcome of a particular microbe-host interaction and which factors enable plants to distinguish beneficials from pathogens. To unravel the complex network of genetic, microbial, and metabolic interactions including the signaling events mediating microbe-host interactions, comprehensive quantitative systems biology approaches will be needed.
Systems biology approach pinpoints minimum requirements for auxin distribution during fruit opening Mol. Plant (IF 10.812) Pub Date : 2019-05-23 Xin-Ran Li, Renske M.A. Vroomans, Samantha Fox, Verônica A. Grieneisen, Lars Østergaard, Athanasius F.M. Marée
The phytohormone auxin is implied in steering various developmental decisions during plant morphogenesis in a concentration-dependent manner. Auxin maxima have been shown to maintain meristematic activity, for example of the root apical meristem, and position new sites of outgrowth, such as during lateral root initiation and phyllotaxis. More recently, it has been demonstrated that sites of auxin minima also provide positional information. In the developing Arabidopsis fruit, auxin minima are required for correct differentiation of the valve margin. It remains unclear, however, how this auxin minimum is generated and maintained. Here we employ a systems biology approach to model auxin transport based on experimental observations. This allows us to determine the minimal requirements for its establishment. Our simulations reveal that two alternative processes — which we coin “flux-barrier” and “flux-passage” — are both able to generate an auxin minimum, but under different parameter settings. Both models are in principle able to yield similar auxin profiles but present qualitatively distinct patterns of auxin flux. The models were tested by tissue-specific inducible ablation, revealing that the auxin minimum in the fruit is most likely generated by a flux-passage process. Model predictions were further supported through 3D PIN-localisation imaging and implementing experimentally observed transporter localisation. Through such an experimental-modelling cycle, we predict how the auxin minimum gradually matures during fruit development to ensure timely fruit opening and seed dispersal.
mTERF5 Acts as a Transcriptional Pausing Factor to Positively Regulate Transcription of Chloroplast psbEFLJ Mol. Plant (IF 10.812) Pub Date : 2019-05-22 Shunhua Ding, Yi Zhang, Zhi Hu, Xiahe Huang, Bohan Zhang, Qingtao Lu, Xiaogang Wen, Yingchun Wang, Congming Lu
RNA polymerase transcriptional pausing represents a major checkpoint in transcription in bacteria and metazoans, but it is unknown whether this phenomenon occurs in plant organelles. Here, we report that transcriptional pausing occurs in chloroplasts. We found that mTERF5 specifically and positively regulates the transcription of chloroplast psbEFLJ (encoding four key subunits of photosystem II) in Arabidopsis thaliana. mTERF5 causes the plastid-encoded RNA polymerase (PEP) complex to pause at psbEFLJ by binding to the +30 to +51 position of double-stranded DNA. Moreover, mTERF5 interacts with pTAC6, an essential subunit of the PEP complex, although pTAC6 is not involved in the transcriptional pausing at psbEFLJ. mTERF5 recruits additional pTAC6 to the transcriptionally paused region of psbEFLJ and this recruited pTAC6 can be assembled into the PEP complex to regulate psbEFLJ transcription. Our findings shed light on the role of transcriptional pausing in chloroplast transcription in plants.
De Novo Domestication: An Alternative Route toward New Crops for the Future Mol. Plant (IF 10.812) Pub Date : 2019-04-15 Alisdair R. Fernie, Jianbing Yan
Current global agricultural production must feed over 7 billion people. However, productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental deterioration. Moreover, the increase in human population size and dietary changes are putting an ever greater burden on agriculture. The majority of this burden is met by the cultivation of a very small number of species, largely in locations that differ from their origin of domestication. Recent technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable low-input agriculture. Here we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.
Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game Mol. Plant (IF 10.812) Pub Date : 2019-01-30 Jian Sun, Dianrong Ma, Liang Tang, Minghui Zhao, Guangchen Zhang, Wenjia Wang, Jiayu Song, Xiang Li, Zimeng Liu, Wenxing Zhang, Quan Xu, Yuncheng Zhou, Jianzhong Wu, Toshio Yamamoto, Fei Dai, Yan Lei, Song Li, Gang Zhou, Wenfu Chen
Crop weediness, especially that of weedy rice (Oryza sativa f. spontanea), remains mysterious. Weedy rice possesses robust ecological adaptability; however, how this strain originated and gradually formed proprietary genetic features remains unclear. Here, we demonstrate that weedy rice at Asian high latitudes (WRAH) is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice. We also identified novel quantitative trait loci underlying weedy-specific traits, and revealed that a genome block on the end of chromosome 1 is associated with rice weediness. To identify the genomic modifications underlying weedy rice evolution, we generated the first de novo assembly of a high-quality weedy rice genome (WR04-6), and conducted a comparative genomics study between WR04-6 with other rice reference genomes. Multiple lines of evidence, including the results of demographic scenario comparisons, suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication. A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity.
A Single-Cell RNA Sequencing Profiles the Developmental Landscape of Arabidopsis Root Mol. Plant (IF 10.812) Pub Date : 2019-04-17 Tian-Qi Zhang, Zhou-Geng Xu, Guan-Dong Shang, Jia-Wei Wang
Cells of eukaryotic multicellular organisms have inherent heterogeneity. Recent advances in single-cell gene expression studies enable us to explore transcriptional regulation in dynamic development processes and highly heterogeneous cell populations. In this study, using a high-throughput single-cell RNA-sequencing assay, we found that the cells in Arabidopsis root are highly heterogeneous in their transcriptomes. A total of 24 putative cell clusters and the cluster-specific marker genes were identified. The spatial distribution and temporal ordering of the individual cells at different developmental stages illustrate their hierarchical structures and enable the reconstruction of continuous differentiation trajectory of root development. Moreover, we found that each root cell cluster exhibits distinct patterns of ion assimilation and hormonal responses. Collectively, our study reveals a high degree of heterogeneity of root cells and identifies the expression signatures of intermediate states during root cell differentiation at single-cell resolution. We also established a web server (http://wanglab.sippe.ac.cn/rootatlas/) to facilitate the use of the datasets generated in this study.
Lower Temperature 1 Enhances Aba Responses And Plant Drought Tolerance By Modulating The Stability And Localization Of C2-Domain Aba-Related Proteins In Arabidopsis Mol. Plant (IF 10.812) Pub Date : 2019-05-16 Tao Qin, Qiuzhen Tian, Guifeng Wang, Liming Xiong
Plasma membrane associated abscisic acid (ABA) signal transduction is an integral part of ABA signaling. The C2-domain ABA-related (CAR) proteins play important roles in the recruitment of ABA receptors to the plasma membrane to facilitate ABA signaling yet how CAR proteins are regulated is unclear. In this study, we conducted a genetic screen for leaf transpiration mutants and identified an uncharacterized protein, LOT1 (LOWER TEMPERATURE 1), that regulates the dynamic localization and stability of CAR proteins. The lot1 mutant had a lower leaf temperature relative to the wild type due to higher transpiration. We found that LOT1 interacts with CAR9 in yeast and in planta. ABA reduces LOT1-CAR9 interaction in the nucleus likely via Ca2+, which results in increased distribution of CAR9 to the plasma membrane. We further found that the stability of CAR9 is affected by LOT1. Less CAR9 protein was accumulated and more was ubiquitinated in lot1. While lot1, car9 and lot1 car9 double mutant were hyposensitive to ABA, the hyposensitive phenotype of lot1 could be rescued by overexpressing CAR9. Our study characterized a new protein that regulates plant tolerance to drought stress by affecting ABA signaling through regulating the stability and dynamic localization of CAR9.
Natural Variation in CCD4 Promoter Underpins Species-specific Evolution of Red Coloration in Citrus Peel Mol. Plant (IF 10.812) Pub Date : 2019-05-16 Xiongjie Zheng, Kaijie Zhu, Quan Sun, Weiyi Zhang, Xia Wang, Hongbo Cao, Meilian Tan, Zongzhou Xie, Yunliu Zeng, Junli Ye, Lijun Chai, Qiang Xu, Zhiyong Pan, Shunyuan Xiao, Paul D. Fraser, Xiuxin Deng
Carotenoids and apocarotenoids can act as phytohormones and volatile precursors that influence plant development and confer aesthetic and nutritional value critical to consumer preference. Citrus fruits display considerable natural variation for carotenoid and apocarotenoid pigments. A multifaceted genetic approach revealed that a 5´cis-regulatory change at CCD4b encoding CAROTENOID CLEAVAGE DIOXYGENASE 4b is a major genetic determinant for the natural variation of C30 apocarotenoids responsible for the red coloration of citrus peel. Functional analyses demonstrated that besides its known role in synthesizing β-citraurin, CCD4b is also responsible for the production of another important C30 apocarotenoid pigment, β-citraurinene. Furthermore, promoter and transcript analyses for CCD4b among citrus germplasm accessions established a tight correlation between presence of a putative 5´ cis-regulatory enhancer within a MITE transposon and the enhanced allelic expression of CCD4b in C30 apocarotenoid-rich red-peeled accessions. A phylogenetic analysis provides evidence that functional diversification and naturally occurring promoter variation of CCD4b constituted the stepwise evolution of red peels in mandarins and their hybrids. Our findings provide insight into the genetic and evolutionary basis of apocarotenoid diversity in plants and may also facilitate breeding efforts that aim to improve the nutritional and aesthetic value of citrus and perhaps other fruit crops.
Maize Carbohydrate partitioning defective33 encodes a MCTP protein and functions in sucrose export from leaves Mol. Plant (IF 10.812) Pub Date : 2019-05-16 Thu M. Tran, Tyler J. McCubbin, Saadia Bihmidine, Benjamin T. Julius, R. Frank Baker, Martin Schauflinger, Clifford Weil, Nathan Springer, Paul Chomet, Ruth Wagner, Jeff Woessner, Karen Grote, Jeanette Peevers, Thomas L. Slewinski, David M. Braun
To sustain plant growth, development, and crop yield, sucrose must be transported from leaves to distant parts of the plant, such as seeds and roots. To identify genes that regulate sucrose accumulation and transport in maize (Zea mays), we isolated carbohydrate partitioning defective33 (cpd33), a recessive mutant that accumulated excess starch and soluble sugars in mature leaves. The cpd33 mutants also exhibited chlorosis in the leaf blades, greatly diminished plant growth, and reduced fertility. Cpd33 encodes a protein containing multiple C2 domains and transmembrane regions. Subcellular localization experiments showed the CPD33 protein localized to plasmodesmata (PD), the plasma membrane, and the endoplasmic reticulum. We also found that a loss-of-function-mutant of the CPD33 homolog in Arabidopsis, QUIRKY, had a similar carbohydrate hyperaccumulation phenotype. Radioactively labeled sucrose transport assays showed that sucrose export was significantly lower in cpd33 mutant leaves relative to wild-type leaves. However, PD transport in the adaxial-abaxial direction was unaffected in cpd33 mutant leaves. Intriguingly, transmission electron microscopy revealed fewer PD at the companion cell – sieve element interface in mutant phloem tissue, providing a possible explanation for the reduced sucrose export in mutant leaves. Collectively, our results suggest that CPD33 functions to promote symplastic transport into sieve elements.
Folate Metabolism Interferes Plant Immunity through 1C Methionine Synthase-directed Genome-wide DNA Methylation Enhancement Mol. Plant (IF 10.812) Pub Date : 2019-05-09 Beatriz González, Pablo Vera
Plants rely on primary metabolism for flexible adaptation to environmental changes. Here, through a combination of chemical genetics and forward genetic studies in Arabidopsis plants we identified that the essential folate metabolic pathway exerts a salicylic acid (SA)-independent negative control on plant immunity. Disruption of the folate pathway promotes enhanced resistance to Pseudomonas syringae DC3000 via activation of a primed immune state in the plant, and its implementation results in enhanced susceptibility. Comparative proteomics analysis using immune-defective mutants identified a methionine synthase (METS1), in charge of the synthesis of Met through the folate-dependent 1C metabolism, acting as a nexus between the folate pathway and plant immunity. Overexpression of METS1 represses plant immunity and is accompanied by genome-wide global increase in DNA methylation, revealing that imposing a methylation pressure at the genome level compromises plant immunity. These observations therefore provide evidences indicating that the folate pathway represents a new layer of complexity in the regulation of plant defense responses.
Translational Regulation of Plant Response to High Temperature by a Dual Function tRNAHis Guanylyltransferase in Rice Mol. Plant (IF 10.812) Pub Date : 2019-05-07 Ke Chen, Tao Guo, Xin-Min Li, Yi-Min Zhang, Yi-Bing Yang, Wang-Wei Ye, Nai-Qian Dong, Chuan-Lin Shi, Yi Kan, You-Huang Xiang, Hai Zhang, Ya-Chao Li, Ji-Ping Gao, Xuehui Huang, Qiang Zhao, Bin Han, Jun-Xiang Shan, Hong-Xuan Lin
Plants are sessile organisms, and have thus evolved numerous strategies to acclimate to changes in environmental temperature. There is emerging evidence to describe the molecular basis of this acclimation. In this study, we identified a tRNAHis guanylyltransferase, AET1, that contributes to the modification of pre-tRNAHis and is required for normal growth under high temperature conditions in rice. Interestingly, AET1 possibly interacts with both RACK1A and eIF3h in the ER (endoplasmic reticulum). Notably, AET1 can directly bind to the OsARF mRNAs including the uORFs of OsARF19 and OsARF23, indicating that AET1 is associated with translation regulation. Furthermore, polysome profiling assays suggest that the translational status remains unaffected in the aet1 mutant, but that the translational efficiency of OsARF19 and OsARF23 is reduced; moreover, the OsARF23 protein levels are obviously decreased in the aet1 mutant under high temperature, implying that AET1 regulates auxin signaling in response to high temperature. Our findings provide new insights into the molecular mechanisms that AET1 plays a dual function in tRNA modification and translational control involved in the regulation of the environmental temperature response in rice.
Transcriptional regulation of miR528 by OsSPL9 orchestrates antiviral response in rice Mol. Plant (IF 10.812) Pub Date : 2019-05-03 Shengze Yao, Zhirui Yang, Rongxin Yang, Yu Huang, Ge Guo, Xiangyue Kong, Ying Lan, Tong Zhou, He Wang, Wenming Wang, Xiaofeng Cao, Jianguo Wu, Yi Li
Many microRNAs (miRNAs) are critical regulators of plant antiviral defense. However, little is known as to how these miRNAs respond to virus invasion at the transcriptional level. We established previously that defense to Rice stripe virus (RSV) invasion entailed a reduction of miR528 accumulation in rice, thus alleviating miR528-mediated degradation of L-Ascorbate Oxidase (AO) mRNA, bolstering the antiviral activity of AO. Here we show that this miR528-AO defense module is also regulated by the transcription factor SPL9. SPL9 displayed high affinity binding to specific motifs within the promoter region of miR528 and activated the transcription of miR528 promoter in vivo assay. Loss-of-function mutations in SPL9 correlated with a significant reduction of miR528 but a substantial increase of AO mRNA, enhancing rice resistance to RSV. Conversely, transgenic overexpression of SPL9 stimulated the expression of miR528, hence lowering the level of AO mRNA and compromising rice defense to RSV. Importantly, gain in RSV susceptibility did not occur when SPL9 overexpression was attempted in mir528 loss-of-function mutants, or in transgenic rice expressing a miR528-resistant AO. In conclusion, SPL9-mediated transcriptional activation of miR528 expression adds a novel layer of regulation of the miR528-AO antiviral defense.
Fine-Tuning of MiR528 Accumulation Modulates Flowering Time in Rice Mol. Plant (IF 10.812) Pub Date : 2019-05-03 Rongxin Yang, Pingchuan Li, Hailiang Mei, Dong Wang, Jing Sun, Chao Yang, Lili Hao, Shouyun Cao, Chengcai Chu, Songnian Hu, Xianwei Song, Xiaofeng Cao
In plants, microRNA (miRNA) functions in the post-transcriptional repression of target mRNAs are well-explored, but the mechanisms regulating the accumulation of miRNAs remain poorly understood. Here, we report that distinct mechanisms regulate accumulation of a monocot-specific miRNA, rice (Oryza sativa) miR528. At the transcriptional level, miR528 accumulated in older plants and exhibited diurnal rhythms; at the post-transcriptional level, aging modulated miR528 levels by enhancing pri-miR528 alternative splicing. In addition, miR528 promoted flowering under long-day conditions by targeting RED AND FAR-RED INSENSITIVE 2 (OsRFI2). Moreover, natural variation in the MIR528 promoter region caused differences in miR528 expression among rice varieties, potentially due to differences in the binding strength of the transcription factor OsSPL9. Together, our findings show evidence for fine-tuning of miR528 levels in rice and provide insight into the mechanisms that regulate MIRNA expression in plants.
SERK Receptor-Like Kinases Control Division Patterns of Vascular Precursors and Ground Tissue Stem Cells during Embryo Development in Arabidopsis Mol. Plant (IF 10.812) Pub Date : 2019-05-03 Huiqiang Li, Zeping Cai, Xiaojuan Wang, Meizhen Li, Yanwei Cui, Nan Cui, Fei Yang, Mingsong Zhu, Junxiang Zhao, Wenbin Du, Kai He, Jing Yi, Frans E. Tax, Suiwen Hou, Jia Li, Xiaoping Gou
During embryo development, the vascular precursors and the ground tissue stem cells divide to renew themselves and produce the vascular tissue, endodermal cells and cortical cells. However, the molecular mechanisms regulating division of these stem cells have remained largely elusive. In this study, we show that loss function of SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) genes results in aberrant embryo development. Fewer cortical, endodermal and vascular cells are generated in the embryo of serk1 serk2 bak1 triple mutants. WUSCHEL RELATED HOMEOBOX 5 (WOX5) is ectopically expressed in vascular cells of serk1 serk2 bak1 embryos. The first transverse division of the vascular precursors in mid-globular embryos and the second asymmetric division of the ground tissue stem cells in early-heart embryos are abnormally altered to a longitudinal division. The embryo defects can be partially rescued by constitutively activated mitogen-activated protein kinase (MAPK) kinase kinase YODA (YDA) and MAPK kinase MKK5. Our results revealed that SERK-mediated signals regulate division patterns of the vascular precursors and the ground tissue stem cells likely via the YDA-MKK4/5 cascade during embryo development.
Origin and evolution of core components responsible for monitoring light environment changes during plant terrestrialization Mol. Plant (IF 10.812) Pub Date : 2019-04-19 Xue Han, Xin Chang, Zhenhua Zhang, Haodong Chen, Hang He, Bojian Zhong, Xing Wang Deng
Light serves as the source of energy as well as information signals for photosynthetic plants. During evolution, plants have acquired the ability to monitor environmental light radiation and adjust their developmental patterns to optimally utilize light energy for photosynthesis. The mechanisms of light perception and signal transduction have been comprehensively studied in the past decades, mostly in a few model plants, including Arabidopsis thaliana. However, systematic analyses of the origin and evolution of core components involved in light perception and signal transduction are still lacking. Herein, we took advantages of the recently sequenced genomes and transcriptomes covering all the main Archaeplastida clades in the public domains to identify orthologous genes of the core components involved in light perception and signal transduction and to reconstruct their evolutionary history. Our analyses suggested that the acclimation to different distributions of light quality in new environments led to the origination of specific light signaling pathways in plants. The UVR8 (UV Resistance Locus 8) signaling pathway originated during the movement of plants from the deeper sea to shallow water to deal with ultraviolet B light (UV-B). After acquisition of the UV-B adaptation, origination of the phytochrome signaling pathway helped plants to colonize the water surface where red light became the prominent light energy source. The pathway of seedling emergence, which is mediated by the combination of light and phytohormone signals to orchestrate plant growth pattern transitions, originated before the emergence of seed plants. Although cryptochromes and some key components of E3 ubiquitin ligase systems already existed before the divergence of plant and animal kingdoms, the coevolution and optimization of light perception and their downstream signal transduction components, including key transcription factors and E3 ubiquitin ligase systems, are evident during plant terrestrialization.
Tiller Bud Formation Regulators MOC3 and MOC1 Cooperatively Promote Tiller Bud Outgrowth by Activating FON1 Expression in Rice Mol. Plant (IF 10.812) Pub Date : 2019-04-29 Gaoneng Shao, Zefu Lu, Jinsong Xiong, Bing Wang, Yanhui Jing, Xiangbing Meng, Guifu Liu, Haiyan Ma, Yan Liang, Fan Chen, Yonghong Wang, Jiayang Li, Hong Yu
Tillering in rice is one of the most important agronomic traits. Rice tiller development can be divided into two main processes: the formation of the axillary bud and its subsequent outgrowth. Several genes critical for bud formation in rice have been identified by genetic studies, however, their molecular function and relationships are still largely unknown. Here, we report that MONOCULM1 (MOC1) and MONOCULM 3/TILLERS ABSENT 1/STERILE AND REDUCED TILLERING 1 (MOC3/TAB1/SRT1), two vital regulators for tiller formation in rice, could physically interact to regulate tiller bud outgrowth through upregulating the expression of FLORAL ORGAN NUMBER1 (FON1), the homolog of CLAVATA1 in rice. MOC3 could directly bind to the promoter of FON1 and subsequently activate FON1 expression. MOC1 functions as a co-activator of MOC3, which did not directly bind to the FON1 promoter, but could further activate the FON1 expression in the presence of MOC3. Accordingly, FON1 is highly expressed at axillary meristems and shows remarkable decreased expression levels in moc1 and moc3 mutants. Loss-of-function mutants of FON1 exhibit normal bud formation, but deficient bud outgrowth and reduced tiller number. Collectively, these results shed lights on the joint transcriptional regulation by MOC1 and MOC3, and establish a new framework for the control of tiller bud formation and outgrowth.
Two RING-Finger Ubiquitin E3 Ligases Regulate the Degradation of SPX4, An Internal Phosphate Sensor, for Phosphate Homeostasis and Signaling in Rice Mol. Plant (IF 10.812) Pub Date : 2019-04-17 Wenyuan Ruan, Meina Guo, Xueqing Wang, Zhenhui Guo, Zhuang Xu, Lei Xu, Hongyu Zhao, Haiji Sun, Chengqi Yan, Keke Yi
SPX-domain-containing proteins (SPXs) play an important role in inorganic phosphate (Pi) sensing, signaling, and transport in eukaryotes. In plants, SPXs are known to integrate cellular Pi status and negatively regulate the activity of Pi central regulators, the PHOSPATE STARVATION RESPONSE proteins (PHRs). The stability of SPXs, such as SPX4, is reduced under Pi-deficient conditions. However, the mechanisms by which SPXs are degraded remain unclear. In this study, using a yeast-two-hybrid screen we identified two RING-finger ubiquitin E3 ligases regulating SPX4 degradation, designated SDEL1 and SDEL2, which were post-transcriptionally induced by Pi starvation. We found that both SDELs were located in the nucleus and cytoplasm, had ubiquitin E3 ligase activity, and directly ubiquitinated the K213 and K299 lysine residues in SPX4 to regulate its stability. Furthermore, we found that PHR2, a Pi central regulator in rice, could compete with SDELs by interacting with SPX4 under Pi-sufficient conditions, which protected SPX4 from ubiquitination and degradation. Consistent with the biochemical function of SDEL1 and SDEL2, overexpression of SDEL1 or SDEL2 resulted in Pi overaccumulation and induced Pi-starvation signaling even under Pi-sufficient conditions. Conversely, their loss-of-function mutants displayed decreased Pi accumulation and reduced Pi-starvation signaling. Collectively, our study revealed that SDEL1 and SDEL2 facilitate the degradation of SPX4 to modulate PHR2 activity and regulate Pi homeostasis and Pi signaling in response to external Pi availability in rice.
Natural Variations at TIG1 Encoding a TCP Transcription Factor Contribute to Plant Architecture Domestication in Rice Mol. Plant (IF 10.812) Pub Date : 2019-04-16 Weifeng Zhang, Lubin Tan, Hongying Sun, Xinhui Zhao, Fengxia Liu, Hongwei Cai, Yongcai Fu, Xianyou Sun, Ping Gu, Zuofeng Zhu, Chuanqing Sun
The modification of plant architecture was a crucial target in rice domestication and modern genetic improvement. Although a fraction of genes regulating rice plant architecture have been characterized, the molecular mechanisms underlying rice plant architecture domestication has not been elucidated. Here we show that the phenotype of inclined growth tiller in wild rice is controlled by a single dominant gene, TILLER INCLINED GROWTH 1 (TIG1), which is on chromosome 8 and encodes a TCP transcriptional activator. The TIG1 mRNA is primarily enriched in the far-land side of tiller base, promotes cell elongation and enlarges the tiller angle in wild rice. Variations in the tig1 promoter of indica cultivars led to decreased expression of TIG1 in the far-land side of tiller base, reduced cell length and tiller angle, which led to the transition from inclined growth tiller of wild rice to the erect growth tiller during rice domestication. The TIG1 protein activates the expression of EXPA3, EXPB5 and SAUR39 to regulate cell elongation and increase the tiller angle. Selective sweep analysis revealed that the tig1 allele had been selected in indica cultivars by human beings. The cloning of TIG1 supports a new scenario of plant architecture evolution in rice.
The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis Mol. Plant (IF 10.812) Pub Date : 2019-04-15 Qing Zhao, Jun Yang, Meng-Ying Cui, Jie Liu, Yumin Fang, Mengxiao Yan, Wenqing Qiu, Huiwen Shang, Zhicheng Xu, Reheman Yidiresi, Jing-Ke Weng, Tomáš Pluskal, Marielle Vigouroux, Burkhard Steuernagel, Yukun Wei, Lei Yang, Yonghong Hu, Xiao-Ya Chen, Cathie Martin
Scutellaria baicalensis Georgi is important in Chinese Traditional Medicine where preparations of dried roots, ‘Huang Qin’, are used for liver and lung complaints including complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14 Mb genome has been assembled into 9 pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence to those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed how the specialised metabolic pathway for the synthesis of 4’deoxyflavone bioactives evolved in the genus, Scutellaria. We found that the gene encoding a specific cinnamate CoA ligase likely obtained its new function following recent mutations, and four genes encoding enzymes in the 4’deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification and point mutations coupled to gene neo- and sub-functionalizations were involved in the evolution of 4’deoxyflavone synthesis in the genus, Scutellaria. The reference genome of S. baicalensis will facilitate the development of improved assemblies of genome sequences for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in members of the mint family, Lamiaceae, but also would facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants.
The Systems Biology of Lateral Root Formation: Connecting the dots Mol. Plant (IF 10.812) Pub Date : 2019-04-03 J.A.Santos Teixeira, K.H.Ten Tusscher
The root system is a major determinant of a plant’s access to water and nutrients. The architecture of this root system to a large extent depends on the repeated formation of new lateral roots. In this review we discuss lateral root development from a systems biology perspective. We focus on studies combining experiments with computational modelling which have advanced our understanding of how the auxin-centred regulatory modules involved in different stages of lateral root development exert their specific functions. Next, we discuss how these regulatory networks may enable robust transitions from one developmental stage to the next, a subject that thus far has received limited attention. Additionally, we describe how environmental factors impinge on these modules, and the different manners in which these environmental signals are being integrated to enable coordinated developmental decision making. We end with suggestions for extending current models of lateral root development to incorporate multiple processes and stages. Only through such more comprehensive models can we fully elucidate the cooperative effects of multiple processes, and how one stage drives the transition to the next.
Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula Mol. Plant (IF 10.812) Pub Date : 2019-04-03 Beatriz Lagunas, Mingkee Achom, Roxanna Bonyadi-Pour, Alonso J. Pardal, Bethany L. Richmond, Chrysi Sergaki, Saúl Vázquez, Patrick Schäfer, Sascha Ott, John Hammond, Miriam L. Gifford
Understanding how plants respond to nitrogen in their environment is crucial for determining how they use it and how the nitrogen use affects other processes related to plant growth and development. Under nitrogen limitation the activity and affinity of uptake systems is increased in roots, and lateral root formation is regulated in order to adapt to low nitrogen levels and scavenge from the soil. Plants in the legume family can form associations with rhizobial nitrogen-fixing bacteria, and this association is tightly regulated by nitrogen levels. The effect of nitrogen on nodulation has been extensively investigated, but the effects of nodulation on plant nitrogen responses remain largely unclear. In this study, we integrated molecular and phenotypic data in the legume Medicago truncatula and determined that genes controlling nitrogen influx are differently expressed depending on whether plants are mock or rhizobia inoculated. We found that a functional autoregulation of nodulation pathway is required for roots to perceive, take up, and mobilize nitrogen as well as for normal root development. Our results together revealed that autoregulation of nodulation, root development, and the location of nitrogen are processes balanced by the whole plant system as part of a resource-partitioning mechanism.
Two Arabidopsis Receptor-like Cytoplasmic Kinases SZE1 and SZE2 Associate with the ZAR1–ZED1 Complex and Are Required for Effector-Triggered Immunity Mol. Plant (IF 10.812) Pub Date : 2019-04-01 Cheng Liu, Dayong Cui, Jingbo Zhao, Na Liu, Bo Wang, Jing Liu, Enjun Xu, Zhubing Hu, Dongtao Ren, Dingzhong Tang, Yuxin Hu
Plants utilize intracellular nucleotide-binding leucine-rich repeat domain-containing receptors (NLRs) to recognize pathogen effectors and induce a robust defense response named effector-triggered immunity (ETI). The Arabidopsis NLR protein HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) forms a precomplex with HOPZ-ETI-DEFICIENT 1 (ZED1), a receptor-like cytoplasmic kinase (RLCK) XII-2 subfamily member, to recognize the Pseudomonas syringae effector HopZ1a. We previously described a dominant mutant of Arabidopsis ZED1, zed1-D, which displays temperature-sensitive autoimmunity in a ZAR1-dependent manner. Here, we report that the RLCKs SUPPRESSOR OF ZED1-D1 (SZE1) and SZE2 associate with the ZAR1–ZED1 complex and are required for the ZED1-D-activated autoimmune response and HopZ1a-triggered immunity. We show that SZE1 but not SZE2 has autophosphorylation activity, and that the N-terminal myristoylation of both SZE1 and SZE2 is critical for their plasma membrane localization and ZED1-D-activated autoimmunity. Furthermore, we demonstrate that SZE1 and SZE2 both interact with ZAR1 to form a functional complex and are required for resistance against P. syringae pv. tomato DC3000 expressing HopZ1a. We also provide evidence that SZE1 and SZE2 interact with HopZ1a and function together with ZED1 to change the intramolecular interactions of ZAR1, leading to its activation. Taken together, our results reveal SZE1 and SZE2 as critical signaling components of HopZ1a-triggered immunity.
Genome Engineering in Rice Using Cas9 Variants that Recognize NG PAM Sequences Mol. Plant (IF 10.812) Pub Date : 2019-03-27 Kai Hua, Xiaoping Tao, Peijin Han, Rui Wang, Jian-Kang Zhu
CRISPR/Cas9 genome editing relies on sgRNA-target DNA base pairing and a short downstream PAM sequence to recognize target DNA. The strict protospacer adjacent motif (PAM) requirement hinders applications of the CRISPR/Cas9 system since it restricts the targetable sites in the genomes. xCas9 and SpCas9-NG are two recently engineered SpCas9 variants that can recognize more relaxed NG PAMs, implying a great potential in addressing the issue of PAM constraint. Here we use stable transgenic lines to evaluate the efficacies of xCas9 and SpCas9-NG in performing gene editing and base editing in rice. We found that xCas9 can efficiently induce mutations at target sites with NG and GAT PAM sequences in rice. However, base editors containing xCas9 failed to edit most of the tested target sites. SpCas9-NG exhibited a robust editing activity at sites with various NG PAMs without showing any preference for the third nucleotide after NG. Moreover, we showed that xCas9 and SpCas9-NG have higher specificity than SpCas9 at the CGG PAM site. We further demonstrated that different forms of cytosine or adenine base editors containing SpCas9-NG worked efficiently in rice with broadened PAM compatibility. Taken together, our work has yielded versatile genome-engineering tools that will significantly expand the target scope in rice and other crops.
Improving Plant Genome Editing with High-Fidelity xCas9 and Non-canonical PAM-Targeting Cas9-NG Mol. Plant (IF 10.812) Pub Date : 2019-03-27 Zhaohui Zhong, Simon Sretenovic, Qiurong Ren, Lijia Yang, Yu Bao, Caiyan Qi, Mingzhu Yuan, Yao He, Shishi Liu, Xiaopei Liu, Jiaheng Wang, Lan Huang, Yan Wang, Dibin Baby, David Wang, Tao Zhang, Yiping Qi, Yong Zhang
Two recently engineered SpCas9 variants, namely xCas9 and Cas9-NG, show promising potential in improving targeting specificity and broadening the targeting range. In this study, we evaluated these Cas9 variants in the model and crop plant, rice. We first tested xCas9-3.7, the most effective xCas9 variant in mammalian cells, for targeted mutagenesis at 16 possible NGN PAM (protospacer adjacent motif) combinations in duplicates. xCas9 exhibited nearly equivalent editing efficiency to wild-type Cas9 (Cas9-WT) at most canonical NGG PAM sites tested, whereas it showed limited activity at non-canonical NGH (H = A, C, T) PAM sites. High editing efficiency of xCas9 at NGG PAMs was further demonstrated with C to T base editing by both rAPOBEC1 and PmCDA1 cytidine deaminases. With mismatched sgRNAs, we found that xCas9 had improved targeting specificity over the Cas9-WT. Furthermore, we tested two Cas9-NG variants, Cas9-NGv1 and Cas9-NG, for targeting NGN PAMs. Both Cas9-NG variants showed higher editing efficiency at most non-canonical NG PAM sites tested, and enabled much more efficient editing than xCas9 at AT-rich PAM sites such as GAT, GAA, and CAA. Nevertheless, we found that Cas9-NG variants showed significant reduced activity at the canonical NGG PAM sites. In stable transgenic rice lines, we demonstrated that Cas9-NG had much higher editing efficiency than Cas9-NGv1 and xCas9 at NG PAM sites. To expand the base-editing scope, we developed an efficient C to T base-editing system by making fusion of Cas9-NG nickase (D10A version), PmCDA1, and UGI. Taken together, our work benchmarked xCas9 as a high-fidelity nuclease for targeting canonical NGG PAMs and Cas9-NG as a preferred variant for targeting relaxed PAMs for plant genome editing.
Cas9-NG Greatly Expands the Targeting Scope of the Genome-Editing Toolkit by Recognizing NG and Other Atypical PAMs in Rice Mol. Plant (IF 10.812) Pub Date : 2019-03-27 Bin Ren, Lang Liu, Shaofang Li, Yongjie Kuang, Jingwen Wang, Dawei Zhang, Xueping Zhou, Honghui Lin, Huanbin Zhou
CRISPR technologies enabling precise genome manipulation are valuable for gene function studies and molecular crop breeding. However, the requirement of a protospacer adjacent motif (PAM), such as NGG and TTN, for Cas protein recognition restricts the selection of targetable genomic loci in practical applications of CRISPR technologies. Recently Cas9-NG, which recognizes a minimal NG PAM, was reported to expand the targeting space of genome editing in human cells, but it remains unclear whether this Cas9 variant can be used in plants. In this study, we evaluated the nuclease activity of Cas9-NG toward various NGN PAMs by targeting endogenous genes in transgenic rice. We found that Cas9-NG edits all NGG, NGA, NGT, and NGC sites with impaired activity, while the gene-edited plants were dominated by monoallelic mutations. Cas9-NG-engineered base editors were then developed and used to generate OsBZR1 gain-of-function plants that can not be created by other available Cas9-engineered base editors. Moreover, we showed that a Cas9-NG-based transcriptional activator efficiently upregulated the expression of endogenous target genes in rice. In addition, we discovered that Cas9-NG recognizes NAC, NTG, NTT, and NCG apart from NG PAM. Together, these findings demonstrate that Cas9-NG can greatly expand the targeting scope of genome-editing tools, showing great potential for targeted genome editing, base editing, and genome regulation in plants.
Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement Mol. Plant (IF 10.812) Pub Date : 2019-03-19 Xiaoping Chen, Qing Lu, Hao Liu, Jianan Zhang, Yanbin Hong, Haofa Lan, Haifen Li, Jinpeng Wang, Haiyan Liu, Shaoxiong Li, Manish K. Pandey, Zhikang Zhang, Guiyuan Zhou, Jigao Yu, Guoqiang Zhang, Jiaqing Yuan, Xingyu Li, Shijie Wen, Xuanqiang Liang
Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.
Molecular Mechanism of the Specificity of Protein Import into Chloroplasts and Mitochondria in Plant Cells Mol. Plant (IF 10.812) Pub Date : 2019-03-16 Dong Wook Lee, Sumin Lee, Junho Lee, Seungjin Woo, Md. Abdur Razzak, Alessandro Vitale, Inhwan Hwang
Plants possess both types of endosymbiotic organelles, chloroplasts and mitochondria. Transit peptides and presequences function as signal sequences for specific import into chloroplasts and mitochondria, respectively. However, how these highly similar signal sequences confer the protein import specificity remains elusive. Here, we show that mitochondrial- or chloroplast-specific import involves two distinct steps, specificity determination and translocation across envelopes, which are mediated by the N-terminal regions and functionally interchangeable C-terminal regions, respectively, of transit peptides and presequences. A domain harboring multiple-arginine and hydrophobic sequence motifs in the N-terminal regions of presequences was identified as the mitochondrial specificity factor. The presence of this domain and the absence of arginine residues in the N-terminal regions of otherwise common targeting signals confers specificity of protein import into mitochondria and chloroplasts, respectively. AtToc159, a chloroplast import receptor, also contributes to determining chloroplast import specificity. We propose that common ancestral sequences were functionalized into mitochondrial- and chloroplast-specific signal sequences by the presence and absence, respectively, of multiple-arginine and hydrophobic sequence motifs in the N-terminal region.
MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis Mol. Plant (IF 10.812) Pub Date : 2019-01-09 Rainer Schwacke, Gabriel Y. Ponce-Soto, Kirsten Krause, Anthony M. Bolger, Borjana Arsova, Asis Hallab, Kristina Gruden, Mark Stitt, Marie E. Bolger, Björn Usadel
Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.
Development of a Haploid-Inducer Mediated Genome Editing (IMGE) System for Accelerating Maize Breeding Mol. Plant (IF 10.812) Pub Date : 2019-03-19 Baobao Wang, Lei Zhu, Binbin Zhao, Yongping Zhao, Yurong Xie, Zhigang Zheng, Yaoyao Li, Juan Sun, Haiyang Wang
Crop breeding aims to generate pure inbred lines with multiple desired traits. Doubled haploid (DH) and genome editing using CRISPR/Cas9 are two powerful game-changing technologies in crop breeding. However, both of them still fall short in rapid generation of pure elite inbred lines with integrated favorable traits. We report here the development of a Haploid-Inducer Mediated Genome Editing approach (IMGE for short), which utilizes a maize haploid inducer (HI) line carrying a CRISPR/Cas9 cassette targeting for a desired agronomic trait to pollinate an elite maize inbred line, and to generate genome edited haploids in the elite maize background. Homozygous pure DH lines with the desired trait improvement could be generated within two generations, thus bypassing the lengthy procedure of repeated crossing and backcrossing used in conventional breeding for integrating a desirable trait into elite commercial backgrounds. We envisage that this technology could be widely used to accelerate crop breeding.
Artemisinin biosynthesis in non-glandular trichome cells of Artemisia annua Mol. Plant (IF 10.812) Pub Date : 2019-03-06 Rika Judd, M.Caleb Bagley, Mingzhuo Li, Yue Zhu, Caiyan Lei, Seyit Yuzuak, Måns Ekelöf, Gaobin Pu, Xiting Zhao, David C. Muddiman, De-Yu Xie
Artemisinin-based combination therapy (ACT) forms the first line of malaria treatment. However, the yield fluctuation of artemisinin has been an unsolved problem for the global ACT demand. This problem is mainly caused by the sole glandular trichome (GT) specificity of artemisinin biosynthesis in all current Artemisia annua crops. Herein, we report that non-GT cells express the artemisinin biosynthetic pathway. Gene expression analysis demonstrates the transcripts of six known pathway genes in GT-free leaves and calli of a novel inbred A. annua cultivar. LC-qTOF-MS/MS analysis shows that these two types of GT-free materials produce artemisinin, artemisinic acid, and arteannuin B. Detailed IR-MALDESI imaging profiling discloses that these three metabolites and dihydroartemisinin are localized in non-GT cells of leaves. All data demonstrate that non-GT cells of inbred A. annua biosynthesize artemisinin and its derivatives. Moreover, we employ all developed approaches to understand artemisinin biosynthesis in the reported glandless (gl) mutant lacking artemisinin. The resulting data demonstrate that leaves of regenerated gl plantlets biosynthesize artemisinin. These findings not only adds new knowledge to revise the current dogma of the artemisinin biosynthesis, but also expedites innovation of novel metabolic engineering technologies for high and stable production of artemisinin in the future.
Diverse chromatic acclimation regulating phycoerythrocyanin and rod-shaped phycobilisome in cyanobacteria Mol. Plant (IF 10.812) Pub Date : 2019-02-26 Yuu Hirose, Song Chihong, Mai Watanabe, Chinatsu Yonekawa, Kazuyoshi Murata, Masahiko Ikeuchi, Toshihiko Eki
Cyanobacteria have evolved various photoacclimation processes to perform oxygenic photosynthesis under different light environments. Chromatic acclimation (CA) is widely recognized and ecologically important photoacclimation, where cyanobacteria alter the absorbing light colors of their supermolecular antenna complex called phycobilisome. To date, several CA variants have been characterized that regulate the green-absorbing phycoerythrin (PE) and/or the red-absorbing phycocyanin (PC), within the hemi-discoidal form of phycobilisome. Here we identify a unique CA regulatory gene cluster encoding yellow-green-absorbing phycoerythrocyanin (PEC) and a rod-membrane linker protein (CpcL) for the rod-shaped form of phycobilisome. Using the cyanobacterium Leptolyngbya sp. PCC 6406, we revealed novel CA variants regulating PEC (CA7) and the rod-shaped phycobilisome (CA0), which maximizes yellow-green light−harvesting capacity and balances the excitation of photosystems, respectively. The distributions of CA gene clusters in 455 cyanobacteria genomes revealed eight CA variants responding to green and red light, which are classified based on the presence of PEC, PE, CpcL and CA photosensors. Phylogenetic analysis of the components suggested that the emergence of CA7 was a single event and preceded that of heterocystous strains, whereas the acquisition of CA0 occurred multiple times. These results offer novel insights into the diversity and evolution of the complex cyanobacterial photoacclimation mechanisms.
A Chromosome-Scale Genome Assembly of Paper Mulberry (Broussonetia papyrifera) Provides New Insights into Its Forage and Papermaking Usage Mol. Plant (IF 10.812) Pub Date : 2019-02-26 Xianjun Peng, Hui Liu, Peilin Chen, Feng Tang, Yanmin Hu, Fenfen Wang, Zhi Pi, Meiling Zhao, Naizhi Chen, Hui Chen, Xiaokang Zhang, Xueqing Yan, Min Liu, Xiaojun Fu, Guofeng Zhao, Pu Yao, Lili Wang, He Dai, Shihua Shen
Paper mulberry (Broussonetia papyrifera) is a well-known woody tree historically used for Cai Lun papermaking, one of the four great inventions of ancient China. More recently, Paper mulberry has also been used as forage to address the shortage of feedstuff because of its digestible crude fiber and high protein contents. In this study, we obtained a chromosome-scale genome assembly for Paper mulberry using integrated approaches, including Illumina and PacBio sequencing platform as well as Hi-C, optical, and genetic maps. The assembled Paper mulberry genome consists of 386.83 Mb, which is close to the estimated size, and 99.25% (383.93 Mb) of the assembly was assigned to 13 pseudochromosomes. Comparative genomic analysis revealed the expansion and contraction in the flavonoid and lignin biosynthetic gene families, respectively, accounting for the enhanced flavonoid and decreased lignin biosynthesis in Paper mulberry. Moreover, the increased ratio of syringyl-lignin to guaiacyl-lignin in Paper mulberry underscores its suitability for use in medicine, forage, papermaking, and barkcloth making. We also identified the root-associated microbiota of Paper mulberry and found that Pseudomonas and Rhizobia were enriched in its roots and may provide the source of nitrogen for its stems and leaves via symbiotic nitrogen fixation. Collectively, these results suggest that Paper mulberry might have undergone adaptive evolution and recruited nitrogen-fixing microbes to promote growth by enhancing flavonoid production and altering lignin monomer composition. Our study provides significant insights into genetic basis of the usefulness of Paper mulberry in papermaking and barkcloth making, and as forage. These insights will facilitate further domestication and selection as well as industrial utilization of Paper mulberry worldwide.
Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants Mol. Plant (IF 10.812) Pub Date : 2018-11-15 Xuelei Lai, Arnaud Stigliani, Gilles Vachon, Cristel Carles, Cezary Smaczniak, Chloe Zubieta, Kerstin Kaufmann, François Parcy
Transcription factors (TFs) are key cellular components that control gene expression. They recognize specific DNA sequences, the TF binding sites (TFBSs), and thus are targeted to specific regions of the genome where they can recruit transcriptional co-factors and/or chromatin regulators to fine-tune spatiotemporal gene regulation. Therefore, the identification of TFBSs in genomic sequences and their subsequent quantitative modeling is of crucial importance for understanding and predicting gene expression. Here, we review how TFBSs can be determined experimentally, how the TFBS models can be constructed in silico, and how they can be optimized by taking into account features such as position interdependence within TFBSs, DNA shape, and/or by introducing state-of-the-art computational algorithms such as deep learning methods. In addition, we discuss the integration of context variables into the TFBS modeling, including nucleosome positioning, chromatin states, methylation patterns, 3D genome architectures, and TF cooperative binding, in order to better predict TF binding under cellular contexts. Finally, we explore the possibilities of combining the optimized TFBS model with technological advances, such as targeted TFBS perturbation by CRISPR, to better understand gene regulation, evolution, and plant diversity.
Tension and Resolution: Dynamic, Evolving Populations of Organelle Genomes within Plant Cells Mol. Plant (IF 10.812) Pub Date : 2018-11-13 Iain G. Johnston
Mitochondria and plastids form dynamic, evolving populations physically embedded in the fluctuating environment of the plant cell. Their evolutionary heritage has shaped how the cell controls the genetic structure and the physical behavior of its organelle populations. While the specific genes involved in these processes are gradually being revealed, the governing principles underlying this controlled behavior remain poorly understood. As the genetic and physical dynamics of these organelles are central to bioenergetic performance and plant physiology, this challenges both fundamental biology and strategies to engineer better-performing plants. This article reviews current knowledge of the physical and genetic behavior of mitochondria and chloroplasts in plant cells. An overarching hypothesis is proposed whereby organelles face a tension between genetic robustness and individual control and responsiveness, and different species resolve this tension in different ways. As plants are immobile and thus subject to fluctuating environments, their organelles are proposed to favor individual responsiveness, sacrificing genetic robustness. Several notable features of plant organelles, including large genomes, mtDNA recombination, fragmented organelles, and plastid/mitochondrial differences may potentially be explained by this hypothesis. Finally, the ways that quantitative and systems biology can help shed light on the plethora of open questions in this field are highlighted.
The Auxin-Regulated Protein ZmAuxRP1 Coordinates the Balance between Root Growth and Stalk Rot Disease Resistance in Maize Mol. Plant (IF 10.812) Pub Date : 2018-10-25 Jianrong Ye, Tao Zhong, Dongfeng Zhang, Chuanyu Ma, Lina Wang, Lishan Yao, Qianqian Zhang, Mang Zhu, Mingliang Xu
To optimize fitness, plants must efficiently allocate their resources between growth and defense. Although phytohormone crosstalk has emerged as a major player in balancing growth and defense, the genetic basis by which plants manage this balance remains elusive. We previously identified a quantitative disease-resistance locus, qRfg2, in maize (Zea mays) that protects against the fungal disease Gibberella stalk rot. Here, through map-based cloning, we demonstrate that the causal gene at qRfg2 is ZmAuxRP1, which encodes a plastid stroma-localized auxin-regulated protein. ZmAuxRP1 responded quickly to pathogen challenge with a rapid yet transient reduction in expression that led to arrested root growth but enhanced resistance to Gibberella stalk rot and Fusarium ear rot. ZmAuxRP1 was shown to promote the biosynthesis of indole-3-acetic acid (IAA), while suppressing the formation of benzoxazinoid defense compounds. ZmAuxRP1 presumably acts as a resource regulator modulating indole-3-glycerol phosphate and/or indole flux at the branch point between the IAA and benzoxazinoid biosynthetic pathways. The concerted interplay between IAA and benzoxazinoids can regulate the growth–defense balance in a timely and efficient manner to optimize plant fitness.
Capturing Auxin Response Factors Syntax Using DNA Binding Models Mol. Plant (IF 10.812) Pub Date : 2018-10-15 Arnaud Stigliani, Raquel Martin-Arevalillo, Jérémy Lucas, Adrien Bessy, Thomas Vinos-Poyo, Victoria Mironova, Teva Vernoux, Renaud Dumas, François Parcy
Auxin is a key hormone performing a wealth of functions throughout the life cycle of plants. It acts largely by regulating genes at the transcriptional level through a family of transcription factors called auxin response factors (ARFs). Even though all ARF monomers analyzed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here, we report the use of position weight matrices (PWMs) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We found that the genome binding of two ARFs (ARF2 and ARF5/Monopteros [MP]) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrated why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrated their power with biochemical experiments in the identification of the regulatory regions of IAA19, an well-characterized auxin-responsive gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin-upregulated genes, thus deciphering the ARFbs syntax functional for regulation. Our study provides a general method to exploit the potential of genome-wide DNA binding assays and to decode gene regulation.
The HuangZaoSi maize genome provides insights into genomic variation and improvement history of maize Mol. Plant (IF 10.812) Pub Date : 2019-02-23 Chunhui Li, Wei Song, Yingfeng Luo, Shenghan Gao, Ruyang Zhang, Zi Shi, Xiaqing Wang, Ronghuan Wang, Fengge Wang, Jidong Wang, Yanxin Zhao, Aiguo Su, Shuai Wang, Xin Li, Meijie Luo, Shuaishuai Wang, Yunxia Zhang, Jianrong Ge, Jiuran Zhao
Maize (Zea mays L. subsp. mays) is a globally important crop and a classic genetic model plant. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS), which hybrids bred from HZS improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of 6 completed sequenced maize genomes show that 638 proteins fall into 264 HZS specific gene families with majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZS related lines reveals the breeding history of HZS improved lines (HILs). More than 60% of identified selective sweeps were clustered in identity-by-descent (IBD) conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions (CSRs). Furthermore, we demonstrated that HZS-specific family genes were not uniformly distributed in the genome, but enriched in improvement/function-related genomic regions. This study provides an important and novel resource for the maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize.
TIR-Learner, a new ensemble method for TIR Transposable Element annotation, provides evidence for abundant new transposable elements in maize genome Mol. Plant (IF 10.812) Pub Date : 2019-02-23 Weijia Su, Xun Gu, Thomas Peterson
Transposable elements (TEs) make up a large and rapidly evolving proportion of plant genomes. Among Class II DNA TEs, TIR elements are flanked by characteristic terminal inverted repeat sequences (TIRs). TIR TEs may play important roles in genome evolution, including generating allelic diversity, inducing structural variation, and regulating gene expression. However, TIR TE identification and annotation has been hampered by the lack of effective tools, resulting in erroneous TE annotations and a significant underestimation of the proportion of TIR elements in the maize genome. This problem has largely limited our understanding of the impact of TIR elements on plant genome structure and evolution. In this paper, we propose a new method of TIR element detection and annotation. This new pipeline combines the advantages of current homology-based annotation methods with powerful de novo machine-learning approaches, resulting in greatly increased efficiency and accuracy of TIR element annotation. The results show that the copy number and genome proportion of TIR elements in maize is much larger than that of current annotations. Additionally, the distribution of some TIR superfamily elements is reduced in centromeric and pericentromeric positions, while others do not show a similar bias. Finally, the incorporation of machine learning techniques has enabled the identification of large numbers of new DTA (hAT) family elements which have all the hallmarks of bona fide TEs, yet which lack high homology with currently-known DTA elements. Together these results provide new tools for TE research and new insight into the impact of TIR elements on maize genome diversity.
Multicellular systems biology: quantifying cellular patterning and function in plant organs using network science Mol. Plant (IF 10.812) Pub Date : 2019-02-20 George W. Bassel
Organ function is at least partially shaped and constrained by the organization of their constituent cells. Extensive investigation has revealed mechanisms explaining how these patterns are generated, with less being known about their functional relevance. In this paper, a methodology to discretize and quantitatively analyze cellular patterning is described. By performing global organ-scale cellular interaction mapping, the organization of cells can be extracted and analyzed using network science. This provides a means to take the developmental analysis of cellular organization in complex organisms beyond qualitative descriptions, and provides data-driven approaches to inferring cellular function. The bridging of a structure-function relationship in hypocotyl epidermal cell patterning through global topological analysis provides support for this approach. The analysis of cellular topologies from patterning mutants further enables the contribution of gene activity towards the organizational properties of tissues to be linked, bridging molecular and tissue scales. This systems-based approach to investigate multicellular complexity paves the way to uncovering the principles of complex organ design, and achieving predictive genotype-phenotype mapping.
PBS3 protects EDS1 from proteasome-mediated degradation in plant immunity Mol. Plant (IF 10.812) Pub Date : 2019-02-11 Ming Chang, Jinping Zhao, Huan Chen, Guangyong Li, Jian Chen, Min Li, Ian A. Palmer, Junqi Song, James R. Alfano, Fengquan Liu, Zheng Qing Fu
Plant immunity is mediated by the positive regulators PBS3 and EDS1 and the negative regulators NPR3 and NPR4. However, the relationships among these important immune regulators remain elusive. Here, we show that PBS3 interacts with EDS1 in both the cytoplasm and the nucleus and is required for EDS1 protein accumulation. NPR3 and NPR4, which function as SA receptors and adaptors of Cullin3-based E3 ligase, interact with and mediate the degradation of EDS1 via the 26S proteasome. We prove that PBS3 inhibits the poly-ubiquitination and subsequent degradation of EDS1 by reducing the association of EDS1 with the Cullin3 adaptors NPR3 and NPR4. Furthermore, we show that PBS3 and EDS1 also contribute to PAMP-triggered immunity (PTI) in addition to effector-triggered immunity (ETI). Our study reveals a novel mechanism, in which plants fine-tune defense responses by inhibiting the degradation of a positive player in plant immunity.
The Blue Light Receptor CRY1 Interacts with BZR1 and BIN2 to Modulate the Phosphorylation and Nuclear Function of BZR1 in Repressing BR Signaling in Arabidopsis Mol. Plant (IF 10.812) Pub Date : 2019-02-11 Guanhua He, Jie Liu, Huixue Dong, Jiaqiang Sun
The blue light receptor cryptochrome 1 (CRY1) primarily mediates blue-light inhibition of hypocotyl elongation. However, the underlying mechanisms remain largely elusive. We report here that CRY1 inhibits hypocotyl elongation by repressing BR signaling. Genetic interaction assay reveals a negative regulatory effect of CRY1 on the function of BZR1, a core transcription factor in the BR signaling pathway. We show that CRY1 interacts with the DNA-binding domain of BZR1 to interfere with the DNA-binding ability of BZR1 and represses its transcriptional activity. Further, we show that CRY1 promotes the phosphorylation of BZR1 and inhibits the nuclear accumulation of BZR1. Significantly, we demonstrates that CRY1 interacts with the GSK3-like kinase BIN2 and enhances the interaction of BIN2 and BZR1 in a light-dependent way. Our findings reveal that CRY1 negatively regulates the function of BZR1 through at least two mechanisms: interfering with the DNA-binding ability of BZR1 and promoting the phosphorylation of BZR1. Therefore, we uncover a novel CRY1-BIN2-BZR1 regulatory module that mediates crosstalk between blue light and BR signaling to coordinate plant growth in Arabidopsis.
A novel chimeric mitochondrial gene confers cytoplasmic effects on seed oil content in polyploid rapeseed (Brassica napus L.) Mol. Plant (IF 10.812) Pub Date : 2019-01-28 Jun Liu, Wanjun Hao, Jing Liu, Shihang Fan, Wei Zhao, Linbing Deng, Xinfa Wang, Zhiyong Hu, Wei Hua, Hanzhong Wang
Cytoplasmic effects (CE) are discovered to influence a diverse array of agronomic traits in crops, and understanding the underlying mechanisms can help accelerate breeding programs. Seed oil content (SOC) is of great agricultural, nutritional and economic importance. However, the genetic basis of CE on SOC (CE-SOC) remains enigmatic. Here we employ an optimized approach to sequence cytoplasmic (plastid and mitochondrial) genomes of allotetraploid oilseed rape (Brassica napus L.) 51218 and 56366 cultivars that bear contrasting CE-SOC. By combining comparative genomics and genome-wide transcriptome analysis, we identify mitochondria-encoded orf188 as a potential CE-SOC determinant gene. Functional transgenic analyses in the model system Arabidopsis thaliana and rapeseed indicate that orf188 governs CE-SOC and can significantly increase SOC, strikingly, through promoting the yield of ATP. Further transcriptional profiling with microarray and RNA-Seq consistently reveal transcriptional reprogramming of mitochondrial energy metabolism to facilitate ATP production. Intriguingly, orf188 is a previously uncharacterized chimeric gene in the evolution of genetic novelty that endows rapeseed with positive CE-SOC. Our results sheds light on the molecular basis of CE contributing to a key quantitative trait in polyploidy crops and enrich the theory on maternal control of oil content, providing new scientific guidance for creation of high-oil germplasm resources.
A Phytophthora capsici effector targets ACD11 binding partners that regulate ROS-mediated defense response in Arabidopsis thaliana Mol. Plant (IF 10.812) Pub Date : 2019-01-28 Qi Li, Gan Ai, Danyu Shen, Fen Zou, Ji Wang, Tian Bai, Yanyu Chen, Shutian Li, Meixiang Zhang, Maofeng Jing, Daolong Dou
Reactive oxygen species (ROS) play a vital role in plant immune response, but the genes involved in regulation of ROS are scantily reported. Phytophthora pathogens produce a large number of effectors to promote infection, but the modes of action adopted are largely unknown. Here, we found RxLR207 could activate ROS-mediated cell death in Nicotiana benthamiana and was essential for virulence of P. capsici. Then we demonstrated that this effector targeted to BPA1 (binding partner of ACD11) and 4 members of BPLs (BPA1 Like proteins) in Arabidopsis, and the corresponding mutants resulted in enhanced ROS accumulation and cell death under biotic or abiotic stresses. Furthermore, we showed that BPA1 and several BPLs had functional redundancy in plant immunity to P. capsici. Finally, we uncovered that BPA1 and all 6 members of BPLs interacted with ACD11, and stabilization of ACD11 was impaired in mutants of bpa1, bpl2, bpl3 and bpl4. RxLR207 could promote the degradation of BPA1 and BPL1, BPL2, and BPL4 to disrupt ACD11 stabilization in a 26S proteasome-dependent manner. Our findings indicate important roles of Arabidopsis BPA1 and its homologs in ROS homeostasis and defense response, highlighting a promising strategy to use pathogen effector-directed approach in discovery of novel plant immune regulators.
Phytophthora sojae effector PsAvh240 inhibits a host aspartic protease secretion to promote infection Mol. Plant (IF 10.812) Pub Date : 2019-01-28 Baodian Guo, Haonan Wang, Bo Yang, Wenjing Jiang, Maofeng Jing, Haiyang Li, Yeqiang Xia, Yuanpeng Xu, Qinli Hu, Fangfang Wang, Feng Yu, Yan Wang, Wenwu Ye, Suomeng Dong, Weiman Xing, Yuanchao Wang
Plants secrete defence molecules into the extracellular space (the apoplast) to combat attacking microbes. Thus far, the mechanisms by which successful pathogens subvert plant apoplastic immunity remain poorly known. In this study, we show that PsAvh240, a membrane-localised effector of the soybean pathogen Phytophthora sojae, promote P. sojae infection in the soybean hairy roots. PsAvh240 interacts with a soybean resistant aspartic protease GmAP1 in planta and suppresses the secretion of GmAP1 to the apoplast. The crystal structure reveals that PsAvh240 comprises six α-helices and two WY motifs. The first two α-helices of PsAvh240 are responsible for plasma membrane localisation of the effector, which are required for PsAvh240 interaction with GmAP1. The second WY motifs of two PsAvh240 molecules form a handshake arrangement resulting in a handshake-like dimer. This dimerization is required for the effector's repression of GmAP1 secretion. Taken together, these data revealed that PsAvh240 localises at the plasma membrane to interfere with GmAP1 secretion, which presents an effective mechanism by which effector proteins suppress plant apoplastic immunity.
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- Prog. Solid State Chem.