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  • Crops, Nitrogen, Water: Are Legumes Friend, Foe, or Misunderstood Ally?
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-03-17
    Mark A. Adams, Nina Buchmann, Janet Sprent, Thomas N. Buckley, Tarryn L. Turnbull

    Biological nitrogen fixation (BNF) by crop legumes reduces demand for industrial nitrogen fixation (INF). Nonetheless, rates of BNF in agriculture remain low, with strong negative feedback to BNF from reactive soil nitrogen (N) and drought. We show that breeding for yield has resulted in strong relationships between photosynthesis and leaf N in non-leguminous crops, whereas grain legumes show strong relations between leaf N and water use efficiency (WUE). We contrast these understandings with other studies that draw attention to the water costs of grain legume crops, and their potential for polluting the biosphere with N. We propose that breeding grain legumes for reduced stomatal conductance can increase WUE without compromising production or BNF. Legume crops remain a better bet than relying on INF.

  • Translating High-Throughput Phenotyping into Genetic Gain
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-03-16
    José Luis Araus, Shawn C. Kefauver, Mainassara Zaman-Allah, Mike S. Olsen, Jill E. Cairns

    Inability to efficiently implement high-throughput field phenotyping is increasingly perceived as a key component that limits genetic gain in breeding programs. Field phenotyping must be integrated into a wider context than just choosing the correct selection traits, deployment tools, evaluation platforms, or basic data-management methods. Phenotyping means more than conducting such activities in a resource-efficient manner; it also requires appropriate trial management and spatial variability handling, definition of key constraining conditions prevalent in the target population of environments, and the development of more comprehensive data management, including crop modeling. This review will provide a wide perspective on how field phenotyping is best implemented. It will also outline how to bridge the gap between breeders and ‘phenotypers’ in an effective manner.

  • Illuminating the Nucleus: UVR8 Interacts with More
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-03-16
    Kaiwen Sun, Ziqiang Zhu

    Ultraviolet-B (UV-B) light suppresses hypocotyl elongation. Although UV-B photo-perception mechanisms have been well investigated, the signaling events from UV-B photoreceptor to downstream transcription are largely unknown. Two recent papers illustrate that the UV-B photoreceptor directly inhibits its interacting transcription factors and reveal the missing link between UV-B perception and transcriptional regulation.

  • Gibberellin Localization and Transport in Plants
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-03-09
    Jenia Binenbaum, Roy Weinstain, Eilon Shani

    Distribution patterns and finely-tuned concentration gradients of plant hormones govern plant growth and development. Gibberellin (GA) is a plant hormone regulating key processes in plants; many of them are of significant agricultural importance, such as seed germination, root and shoot elongation, flowering, and fruit patterning. Although studies have demonstrated that GA movement is essential for multiple developmental aspects, how GAs are transported throughout the plant and where exactly they accumulate remain largely unknown. Here, we summarize recent findings from studies of GA movement and localization, and discuss the importance of GA intermediates in long- and short-distance movement. We further review recently identified Arabidopsis GA transporters and highlight their complex specialization and robust functional redundancy in GA transport activity.

  • A Bypass in Jasmonate Biosynthesis – the OPR3-independent Formation
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-03-09
    Claus Wasternack, Bettina Hause

    For the first time in 25 years, a new pathway for biosynthesis of jasmonic acid (JA) has been identified. JA production takes place via 12-oxo-phytodienoic acid (OPDA) including reduction by OPDA reductases (OPRs). A loss-of-function allele, opr3-3, revealed an OPR3-independent pathway converting OPDA to JA.

  • The Hidden Face of Rubisco
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-03-07
    Mathieu Pottier, Dimitri Gilis, Marc Boutry

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) fixes atmospheric CO2 into organic compounds and is composed of eight copies each of a large subunit (RbcL) and a small subunit (RbcS). Recent reports have revealed unusual RbcS, which are expressed in particular tissues and confer higher catalytic rate, lesser affinity for CO2, and a more acidic profile of the activity versus pH. The resulting Rubisco was proposed to be adapted to a high CO2 environment and recycle CO2 generated by the metabolism. These RbcS belong to a cluster named T (for trichome), phylogenetically distant from cluster M, which gathers well-characterized RbcS expressed in mesophyll or bundle-sheath tissues. Cluster T is largely represented in different plant phyla, including pteridophytes and bryophytes, indicating an ancient origin.

  • The C/S1 bZIP Network: A Regulatory Hub Orchestrating Plant Energy Homeostasis
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-03-07
    Wolfgang Dröge-Laser, Christoph Weiste

    Sustaining energy homeostasis is crucial to every living being. To balance energy supply and demand, plants make use of an evolutionarily conserved management system consisting of two counteracting kinases, TOR (TARGET OF RAPAMYCIN) and SnRK1 (Snf1-RELATED PROTEIN KINASE 1). SnRK1 is involved in reorganizing enzymatic and transcriptional responses to survive energy-limiting conditions. Recently, members of the bZIP (basic leucine zipper) transcription factor family have been established as SnRK1 downstream mediators. We review here current knowledge on the functional impact of these group C and S1 bZIPs, and analyze their regulation by environmental and endogenous cues. Given their specific homo- and heterodimerization, the so-called C/S1 bZIP network is proposed to act as a signaling hub that coordinates plant development and stress responses.

  • Peptide Aptamers to Inhibit Protein Function in Plants
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-03-05
    Zhenzhen Hao, Pichang Gong, Chaoying He, Jinxing Lin

    Peptide aptamers – artificial short peptides with specific binding affinity for target molecules – can be used to interfere with protein functions and protein–protein interactions in plant cells. Therefore, peptide aptamers have emerged as a new, powerful tool with high efficiency and specificity and wide applications in functional genomics and plant biotechnology.

  • The Root Transition Zone: A Hot Spot for Signal Crosstalk
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-02-27
    Xiangpei Kong, Guangchao Liu, Jiajia Liu, Zhaojun Ding

    The root transition zone (TZ), located between the apical meristem and basal elongation region, has a unique role in root growth and development. The root TZ is not only the active site for hormone crosstalk, but also the perception site for various environmental cues, such as aluminum (Al) stress and low phosphate (Pi) stress. We propose that the root TZ is a hot spot for the integration of diverse inputs from endogenous (hormonal) and exogenous (sensorial) stimuli to control root growth.

  • Triterpene Messages from the EU-FP7 Project TriForC
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-02-23
    Alain Goossens, Anne Osbourn, Franck Michoux, Søren Bak

    TriForC is an innovative EU-funded collaborative project that has established an integrative pipeline for the exploitation of plant triterpenes for commercialization in agriculture and pharmacology. We discuss the main outcomes of TriForC and reflect on its potential long-term impact and on the importance of EU projects for science, industry, and society.

  • BRexit: Possible Brassinosteroid Export and Transport Routes
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-02-17
    Nemanja Vukašinović, Eugenia Russinova

    The movement and differential distribution of endogenous plant hormones are the determining factors for many developmental processes. Brassinosteroids (BRs) are a group of plant steroidal hormones that promote growth and development. Although synthesis and signalling of BRs are well described and characterized, the exit mechanism of these compounds from the cell remains uncharacterizd. Whether BRs are able to move within the apoplast and whether the BR synthesis in one cell can trigger the signalling in its neighbours is also unknown. Here, we draw the attention to these aspects of the BR biology, propose several BR cell export routes and discuss possible consequences of local BR hormonal gradients, resulting from localized biosynthesis and a short-distance transport, for plant development.

  • Gene Expression Dominance in Allopolyploids: Hypotheses and Models
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-02-09
    Samuel Bottani, Nicolae Radu Zabet, Jonathan F. Wendel, Reiner A. Veitia

    The classical example of nonadditive contributions of the two parents to allopolyploids is nucleolar dominance, which entails silencing of one parental set of ribosomal RNA genes. This has been observed for many other loci. The prevailing explanation for this genome-wide expression disparity is that the two merged genomes differ in their transposable element (TE) complement and in their level of TE-mediated repression of gene expression. Alternatively, and not exclusively, gene expression dominance may arise from mismatches between trans effectors and their targets. Here, we explore quantitative models of regulatory mismatches leading to gene expression dominance. We also suggest that, when pairs of merged genomes are similar from one allopolyploidization event to another, gene-level and genome dominance patterns should also be similar.

  • Plant Ribonomics: Proteins in Search of RNA Partners
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-02-09
    Tino Köster, Katja Meyer

    Research into the regulation of gene expression underwent a shift from focusing on DNA-binding proteins as key transcriptional regulators to RNA-binding proteins (RBPs) that come into play once transcription has been initiated. RBPs orchestrate all RNA-processing steps in the cell. To obtain a global view of in vivo targets, the RNA complement associated with particular RBPs is determined via immunoprecipitation of the RBP and subsequent identification of bound RNAs via RNA-seq. Here, we describe technical advances in identifying RBP in vivo targets and their binding motifs. We provide an up-to-date view of targets of nucleocytoplasmic RBPs collected in arabidopsis. We also discuss current experimental limitations and provide an outlook on how the approaches may advance our understanding of post-transcriptional networks.

  • Fruit Softening: Revisiting the Role of Pectin
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-02-09
    Duoduo Wang, Trevor H. Yeats, Selman Uluisik, Jocelyn K.C. Rose, Graham B. Seymour

    Fruit softening, which is a major determinant of shelf life and commercial value, is the consequence of multiple cellular processes, including extensive remodeling of cell wall structure. Recently, it has been shown that pectate lyase (PL), an enzyme that degrades de-esterified pectin in the primary wall, is a major contributing factor to tomato fruit softening. Studies of pectin structure, distribution, and dynamics have indicated that pectins are more tightly integrated with cellulose microfibrils than previously thought and have novel structural features, including branches of the main polymer backbone. Moreover, recent studies of the significance of pectinases, such as PL and polygalacturonase, are consistent with a causal relationship between pectin degradation and a major effect on fruit softening.

  • The Pivotal Role of Ethylene in Plant Growth
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-02-07
    Marieke Dubois, Lisa Van den Broeck, Dirk Inzé

    Being continuously exposed to variable environmental conditions, plants produce phytohormones to react quickly and specifically to these changes. The phytohormone ethylene is produced in response to multiple stresses. While the role of ethylene in defense responses to pathogens is widely recognized, recent studies in arabidopsis and crop species highlight an emerging key role for ethylene in the regulation of organ growth and yield under abiotic stress. Molecular connections between ethylene and growth-regulatory pathways have been uncovered, and altering the expression of ethylene response factors (ERFs) provides a new strategy for targeted ethylene-response engineering. Crops with optimized ethylene responses show improved growth in the field, opening new windows for future crop improvement. This review focuses on how ethylene regulates shoot growth, with an emphasis on leaves.

  • Fast-Forwarding Genetic Gain
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-02-06
    Huihui Li, Awais Rasheed, Lee T. Hickey, Zhonghu He

    ‘Speed breeding’ enables scientists to exploit gene bank accessions and mutant collections for an unparalleled rapid gene discovery and gene deployment. Combining speed breeding and other leading-edge plant breeding technologies with strategic global partnerships, has the potential to achieve the genetic gain targets required to deliver our future crops.

  • Hacking an Algal Transcription Factor for Lipid Biosynthesis
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-02-03
    Xiulai Chen, Guipeng Hu, Liming Liu

    Transcriptional engineering is a viable means for engineering microalgae to produce lipid, but it often results in a trade-off between production and growth. A recent study shows that engineering a single transcriptional regulator enables efficient carbon partitioning to lipid biosynthesis with high biomass productivity.

  • MTPSLs: New Terpene Synthases in Nonseed Plants
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-20
    Qidong Jia, Tobias G. Köllner, Jonathan Gershenzon, Feng Chen

    Terpenes constitute a large class of plant secondary metabolites. It was once presumed that these compounds are biosynthesized by typical plant terpene synthases in all land plants. This view has changed with the identification of a new group of terpene synthase genes called MTPSLs for microbial terpene synthase-like genes. MTPSLs are structurally and phylogenetically more related to bacterial and fungal terpene synthases than to typical plant terpene synthases. They are widely distributed in nonseed plants but absent in seed plants and green algae. Much of the terpene diversity in nonseed plants is presumed to be determined by MTPSLs. Phylogenetic analysis suggests that ancestral MTPSL genes were acquired by early land plants from bacteria and fungi through horizontal gene transfer.

  • Capacitation in Plant and Animal Fertilization
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-11-20
    Subramanian Sankaranarayanan, Tetsuya Higashiyama

    Sexual reproduction relies on the successful fusion of the sperm and egg cell. Despite the vast differences between plants and animals, there are similarities at a molecular level between plant and animal reproduction. While the molecular basis of fertilization has been extensively studied in plants, the process of capacitation has received little attention until recently. Recent research has started to uncover the molecular basis of plant capacitation. Furthermore, recent studies suggest that the key molecules in plants and animal fertilization are functionally conserved. Here, we review new insights for our understanding of capacitation of pollen tube and fertilization in plants and also propose that there are commonalities in the process of sexual reproduction between plants and animals.

  • Alternative Splicing Control of Abiotic Stress Responses
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-23
    Tom Laloum, Guiomar Martín, Paula Duque

    Alternative splicing, which generates multiple transcripts from the same gene, is an important modulator of gene expression that can increase proteome diversity and regulate mRNA levels. In plants, this post-transcriptional mechanism is markedly induced in response to environmental stress, and recent studies have identified alternative splicing events that allow rapid adjustment of the abundance and function of key stress-response components. In agreement, plant mutants defective in splicing factors are severely impaired in their response to abiotic stress. Notably, mounting evidence indicates that alternative splicing regulates stress responses largely by targeting the abscisic acid (ABA) pathway. We review here current understanding of post-transcriptional control of plant stress tolerance via alternative splicing and discuss research challenges for the near future.

  • Class VIIIb APETALA2 Ethylene Response Factors in Plant Development
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-23
    John W. Chandler

    The APETALA2 (AP2) transcription factor superfamily in many plant species is extremely large. In addition to well-documented roles in stress responses, some AP2 members in arabidopsis, such as those of subgroup VIIIb, which includes DORNRÖSCHEN, DORNRÖSCHEN-LIKE, PUCHI, and LEAFY PETIOLE, are also important developmental regulators throughout the plant life cycle. Information is accumulating from orthologs of these proteins in important crop species that they influence key agronomic traits, such as the release of bud-burst in woody perennials and floral meristem identity and branching in cereals, and thereby represent potential for agronomic improvement. Given the increasing recognition of their developmental significance, this review highlights the function of these proteins and addresses their phylogenetic and evolutionary relationships.

  • Evolution of Sucrose Metabolism: The Dichotomy of Invertases and Beyond
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-11-25
    Hongjian Wan, Limin Wu, Yuejian Yang, Guozhi Zhou, Yong-Ling Ruan

    In higher plants, invertases hydrolyze sucrose (Suc), the major end product of photosynthesis, into glucose (Glc) and fructose (Fru), which are used as nutrients, energy sources, and signaling molecules for plant growth, yield formation, and stress responses. The invertase enzymes, named CWINs, VINs, and CINs, are located in the cell wall, vacuole, and cytosol, respectively. We hypothesize, based on their distinctive subcellular locations and physiological roles, that invertases may have undergone different modes during evolution with important functional implications. Here, we provide phylogenetic and functional genomic evidence that CINs are evolutionarily and functionally more stable compared with CWINs and VINs, possibly reflecting their roles in maintaining cytosolic sugar homeostasis for cellular function, and that CWINs have coevolved with the vasculature, likely as a functional component of phloem unloading.

  • Oxygen, Energy, and Light Signalling Direct Meristem Fate
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-10
    Michael J. Considine

    Light, nutrition, and oxygen are each important cues for developmental transitions in plants. A small number of recent studies have converged to give the first indication of how these environmental cues act together and independently via auxin, cytokinin, and ethylene to regulate cell proliferation in the root and shoot meristems.

  • Database Taxonomics as Key to Modern Plant Biology
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-11-13
    Marcus A. Koch, Dmitry A. German, Markus Kiefer, Andreas Franzke

    The advent of omic technologies opened new and multiple avenues to access higher levels of complexity. Taxonomy – discovering and naming biodiversity – has also entered a taxonomics epoch and serves as a tool not only to name biological diversity, but also to fully explore biological knowledge and to build bridges between disciplines.

  • Dimensionless Numbers for Plant Biology
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-11-05
    Joseph K.E. Ortega

    Dimensionless numbers are ubiquitous in the physical sciences because they provide insight into physical processes, organize large quantities of data, facilitate ‘scale analysis’ and establish ‘similarity’. Here I explore the use of dimensionless numbers in plant biology, focusing on the expansive growth rate of plant, fungal, and algal cells.

  • Are GM Crops for Yield and Resilience Possible?
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-09-29
    Matthew J. Paul, Michael L. Nuccio, Shib Sankar Basu

    Crop yield improvements need to accelerate to avoid future food insecurity. Outside Europe, genetically modified (GM) crops for herbicide- and insect-resistance have been transformative in agriculture; other traits have also come to market. However, GM of yield potential and stress resilience has yet to impact on food security. Genes have been identified for yield such as grain number, size, leaf growth, resource allocation, and signaling for drought tolerance, but there is only one commercialized drought-tolerant GM variety. For GM and genome editing to impact on yield and resilience there is a need to understand yield-determining processes in a cell and developmental context combined with evaluation in the grower environment. We highlight a sugar signaling mechanism as a paradigm for this approach.

  • Soil Biodiversity Effects from Field to Fork
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-11-13
    Matthias C. Rillig, Anika Lehmann, Johannes Lehmann, Tessa Camenzind, Cornelia Rauh

    Our knowledge of soil biodiversity in agriculture in general is currently increasing rapidly. However, almost all studies have stopped with the quantification of soil biodiversity effects on crops at harvest time, ignoring subsequent processes along the agrifood chain until food arrives on our plates. Here we develop a conceptual framework for the study of such postharvest effects. We present the main mechanisms (direct and indirect) via which soil biodiversity can influence crop quality aspects and give examples of how effects at harvest time may become attenuated through postharvest operations and how biodiversity may also affect some of these operations (i.e., storage) themselves. Future research with a broader focus has the potential to unveil how soil biodiversity may benefit from what ends up on our forks.

  • Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-17
    Joelle Sasse, Enrico Martinoia, Trent Northen

    Plant health in natural environments depends on interactions with complex and dynamic communities comprising macro- and microorganisms. While many studies have provided insights into the composition of rhizosphere microbiomes (rhizobiomes), little is known about whether plants shape their rhizobiomes. Here, we discuss physiological factors of plants that may govern plant–microbe interactions, focusing on root physiology and the role of root exudates. Given that only a few plant transport proteins are known to be involved in root metabolite export, we suggest novel families putatively involved in this process. Finally, building off of the features discussed in this review, and in analogy to well-known symbioses, we elaborate on a possible sequence of events governing rhizobiome assembly.

  • Translational Research: Exploring and Creating Genetic Diversity
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-11-07
    Pierre Jacob, Adi Avni, Abdelhafid Bendahmane

    The crop selection process has created a genetic bottleneck ultimately restricting breeding output. Wild relatives of major crops as well as the so-called ‘neglected plant’ species represent a reservoir of genetic diversity that remains underutilized. These species could be used as a tool to discover new alleles of agronomic interest or could be the target of breeding programs. Targeted induced local lesions in the genome (TILLING) can be used to translate in neglected crops what has been discovered in major crops and reciprocally. However, random mutagenesis, used in TILLING approaches, provides only a limited density of mutational events at a defined target locus. Alternatively, clustered regularly interspaced short palindromic repeats (CRISPR) associated 9 (Cas9) fused to a cytidine deaminase could serve as a localized mutagenic agent to produce high-density mutant populations. Artificial evolution is at hand.

  • Molecular Control of Male Fertility for Crop Hybrid Breeding
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-11-07
    Yu-Jin Kim, Dabing Zhang

    In many plant species, male-sterile female lines with cytoplasmic male sterility (CMS) or nuclear-controlled environment-sensitive genic male sterility (EGMS) have long been used to efficiently produce hybrids that harness hybrid vigor or heterosis. However, the underlying molecular mechanisms for these applications have only recently been uncovered in a few species. We provide here an update on the understanding of cytoplasmic–nuclear communication based on the discovery of mitochondrial CMS genes and their corresponding nuclear fertility determinants. Recent findings that uncover diverse mechanisms such as epigenetic, transcriptional, and post-transcriptional controls of EGMS by temperature and photoperiod signals are also reviewed. Furthermore, translational research that applies basic knowledge of plant male fertility control to hybrid seed production practice is highlighted.

  • Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-19
    Carla P. Coelho, Pu Huang, Dong-Yeon Lee, Thomas P. Brutnell

    The INDETERMINATE DOMAIN (IDD) family of transcriptional regulators controls a diversity of processes in a variety of plant tissues and organs and at different stages of plant development. Several recent reports describe the genetic characterization of IDD family members, including those that are likely to regulate C4 kranz anatomy, with implications for the engineering of C4 traits into C3 crops. In this review we summarize the reported functions of IDD members in the regulation of metabolic sensing and leaf, root, seed, and inflorescence development. We also provide an IDD phylogeny for the grasses and suggest future directions and strategies to define the function of IDDs in C4 photosynthesis and other developmental processes.

  • Genetic Control of Root System Development in Maize
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-11-20
    Frank Hochholdinger, Peng Yu, Caroline Marcon

    The maize root system comprises structurally and functionally different root types. Mutant analyses have revealed that root-type-specific genetic regulators intrinsically determine the maize root system architecture. Molecular cloning of these genes has demonstrated that key elements of auxin signal transduction, such as LOB domain (LBD) and Aux/IAA proteins, are instrumental for seminal, shoot-borne, and lateral root initiation. Moreover, genetic analyses have demonstrated that genes related to exocytotic vesicle docking, cell wall loosening, and cellulose synthesis and organization control root hair elongation. The identification of upstream regulators, protein interaction partners, and downstream targets of these genes together with cell-type-specific transcriptome analyses have provided novel insights into the regulatory networks controlling root development and architecture in maize.

  • Stabilizing the Transcription Factors by E3 Ligase COP1
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-04
    Ying Pan, Hui Shi

    Photomorphogenesis is oppositely regulated by two groups of transcription factors. CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1) degrades the positive factors but stabilizes the negative ones to predominantly repress photomorphogenesis. It is known that COP1 degrades substrates as an E3 ligase. Two recent studies unraveled the long-sought mechanisms of how COP1 stabilizes the negative transcription factors.

  • Bridging Scales in Plant Biology Using Network Science
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-10
    Salva Duran-Nebreda, George W. Bassel

    Three recent studies have captured the organizational properties of plants at each the cellular, organ, and whole organism level. Data abstraction into networks enabled topological analyses to be performed, identifying optimizations within each scale. Multiscale network analysis provides the opportunity to integrate these levels, and quantitatively link genotype to phenotype.

  • Dancing with the Stars: An Asterid NLR Family
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-10
    John P. Rathjen, Peter N. Dodds

    Wu and co-workers show how a network of sensor and helper NOD-like receptor proteins (NLRs) act together to confer robust resistance to diverse plant pathogens.

  • Can Peroxisomes Inform Cellular Response to Drought?
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-11-05
    Andrei Smertenko

    Although plant germplasm contains numerous unknown traits for drought-tolerance, the ability to phenotype this material remains challenging. I propose that peroxisome abundance may be a viable parameter for the evaluation of drought response at the cellular level, and hence could be useful to improve phenotyping efforts.

  • Epicormic Resprouting in Fire-Prone Ecosystems
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-09-17
    Juli G. Pausas, Jon E. Keeley

    Many plants resprout from basal buds after disturbance, and this is common in shrublands subjected to high-intensity fires. However, resprouting after fire from epicormic (stem) buds is globally far less common. Unlike basal resprouting, post-fire epicormic resprouting is a key plant adaptation for retention of the arborescent skeleton after fire, allowing rapid recovery of the forest or woodland and leading to greater ecosystem resilience under recurrent high-intensity fires. Here we review the biogeography of epicormic resprouting, the mechanisms of protection, the fire regimes where it occurs, and the evolutionary drivers that shaped this trait. We propose that epicormic resprouting is adaptive in ecosystems with high fire frequency and relatively high productivity, at moderate–high fire intensities.

  • New Molecular Mechanisms to Reduce Arsenic in Crops
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-19
    Emma R. Lindsay, Frans J.M. Maathuis

    Arsenic is toxic to all life forms and is a potent carcinogen. Its accumulation in crop plants and subsequent consumption poses a serious threat to public health worldwide. Recent developments have enhanced our understanding of the molecular mechanisms governing arsenic uptake, detoxification, and accumulation in plants. In particular, the identification of plant arsenate reductase enzymes and emerging details of the processes underlying arsenic distribution and deposition in the seed will prove invaluable in the development of new strategies to mitigate this threat. Here we provide an outline of these recent developments and suggest new molecular mechanisms that could be employed to reduce arsenic in crops.

  • Plant Phospholipid Diversity: Emerging Functions in Metabolism and Protein–Lipid Interactions
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-06
    Yuki Nakamura

    Phospholipids are essential components of biological membranes and signal transduction cascades in plants. In recent years, plant phospholipid research was greatly advanced by the characterization of numerous mutants affected in phospholipid biosynthesis and the discovery of a number of functionally important phospholipid-binding proteins. It is now accepted that most phospholipids to some extent have regulatory functions, including those that serve as constituents of biological membranes. Phospholipids are more than an inert end product of lipid biosynthesis. This review article summarizes recent advances on phospholipid biosynthesis with a particular focus on polar head group synthesis, followed by a short overview on protein–phospholipid interactions as an emerging regulatory mechanism of phospholipid function in arabidopsis (Arabidopsis thaliana).

  • Mixed-Ploidy Species: Progress and Opportunities in Polyploid Research
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-17
    Filip Kolář, Martin Čertner, Jan Suda, Peter Schönswetter, Brian C. Husband

    Mixed-ploidy species harbor a unique form of genomic and phenotypic variation that influences ecological interactions, facilitates genetic divergence, and offers insights into the mechanisms of polyploid evolution. However, there have been few attempts to synthesize this literature. We review here research on the cytotype distribution, diversity, and dynamics of intensively studied mixed-ploidy species and consider the implications for understanding mechanisms of polyploidization such as cytotype formation, establishment, coexistence, and post-polyploid divergence. In general, mixed-ploidy species are unevenly represented among families: they exhibit high cytotype diversity, often within populations, and frequently comprise rare and odd-numbered ploidies. Odd-ploidies often occur in association with asexuality. We highlight research hypotheses and opportunities that take advantage of the unique properties of ploidy variation.

  • Small RNAs: Big Impact on Plant Development
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-12
    Marco D’Ario, Sam Griffiths-Jones, Minsung Kim

    While the role of proteins in determining cell identity has been extensively studied, the contribution of small noncoding RNA molecules such as miRNAs and siRNAs has been also recognised. miRNAs bind to complementary sites in target mRNA molecules to trigger the degradation or translational inhibition of those targets. Recent studies have revealed that miRNAs play pivotal roles in key developmental processes such as patterning of the embryo, meristem, leaf, and flower. Furthermore, these miRNAs have been recruited throughout plant evolution into pathways that create diverse plant organ forms and shapes. This review focuses on the roles of miRNAs in establishing plant cell identity during key plant development processes and creating morphological diversity during plant evolution.

  • Balancing Immunity and Yield in Crop Plants
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-10-14
    Yuese Ning, Wende Liu, Guo-Liang Wang

    Crop diseases cause enormous yield losses and threaten global food security. The use of highly resistant cultivars can effectively control plant diseases, but in crops, genetic immunity to disease often comes with an unintended reduction in growth and yield. Here, we review recent advances in understanding how nucleotide-binding domain, leucine-rich repeat (NLR) receptors and cell wall-associated kinase (WAK) proteins function in balancing immunity and yield. We also discuss the role of plant hormones and transcription factors in regulating the trade-offs between plant growth and immunity. Finally, we describe how a novel mechanism of translational control of defense proteins can enhance immunity without the reduction in fitness.

  • Phytochrome Responses: Think Globally, Act Locally
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-09-21
    Carlos L. Ballaré

    Localized responses to changes in the red to far-red ratio (R:FR) allow plants to efficiently forage for light in patchy canopies, and to fine-tune physiological activities to the local light environment. Recent studies are elucidating the molecular mechanisms that mediate localized responses to R:FR and the functional implications of these responses.

  • Pearl Millet Genome: Lessons from a Tough Crop
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-09-19
    Marilyne Debieu, Ghislain Kanfany, Laurent Laplaze

    Pearl millet is an important cereal for food security in the arid regions of Africa and India. The recently published genome of this tough cereal crop has shed new light on its history and adaptation to dry, hot climates and paves the way for much-needed genomic-based breeding efforts.

  • Novel Stress in Plants by Altering the Photoperiod
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-09-29
    Silvia Nitschke, Anne Cortleven, Thomas Schmülling

    Recent work has shown that changing the photoperiod induces stress in Arabidopsis thaliana. It has particularly dramatic consequences in cytokinin-deficient plants and clock mutants. Here, we argue that studying the impact of an altered photoperiod will provide novel insights into the circadian clock, factors regulating it, and pathways under its control.

  • Challenges towards Revitalizing Hemp: A Multifaceted Crop
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-09-05
    Craig Schluttenhofer, Ling Yuan

    Hemp has been an important crop throughout human history for food, fiber, and medicine. Despite significant progress made by the international research community, the basic biology of hemp plants remains insufficiently understood. Clear objectives are needed to guide future research. As a semi-domesticated plant, hemp has many desirable traits that require improvement, including eliminating seed shattering, enhancing the quantity and quality of stem fiber, and increasing the accumulation of phytocannabinoids. Methods to manipulate the sex of hemp plants will also be important for optimizing yields of seed, fiber, and cannabinoids. Currently, research into trait improvement is hindered by the lack of molecular techniques adapted to hemp. Here we review how addressing these limitations will help advance our knowledge of plant biology and enable us to fully domesticate and maximize the agronomic potential of this promising crop.

  • Combinatorial Transcriptional Control of Plant Specialized Metabolism
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-01-31
    Maite Colinas, Alain Goossens

    Plants produce countless specialized compounds of diverse chemical nature and biological activities. Their biosynthesis often exclusively occurs either in response to environmental stresses or is limited to dedicated anatomical structures. In both scenarios, regulation of biosynthesis appears to be mainly controlled at the transcriptional level, which is generally dependent on a combined interplay of DNA-related mechanisms and the activity of transcription factors that may act in a combinatorial manner. How environmental and developmental cues are integrated into a coordinated cell type-specific stress response has only partially been unraveled so far. Building on the available examples from (metabolic) gene expression, here we propose theoretical models of how this integration of signals may occur at the level of transcriptional control.

  • lncRNAs in Plant and Animal Sexual Reproduction
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-01-31
    Agnieszka A. Golicz, Prem L. Bhalla, Mohan B. Singh

    Long noncoding RNAs (lncRNAs) are transcripts over 200 base pairs in length with no discernible protein-coding potential. Multiple lines of evidence point to lncRNAs as master regulators, controlling the expression of protein-coding genes. Studies in plants and animals consistently show high expression of lncRNAs in reproductive organs in a cell- and tissue-specific manner. Sexual reproduction is a complex process that involves cell fate specification and specialized cell division requiring precise coordination of gene expression in response to intrinsic and extrinsic signals. The roles of lncRNAs as master regulators of gene expression and chromatin organization might make them particularly suited for coordination and control of molecular processes involved in sexual reproduction.

  • Signaling Peptides and Receptors Coordinating Plant Root Development
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-01-30
    Eunkyoo Oh, Pil Joon Seo, Jungmook Kim

    Small peptides mediate cell–cell communication to coordinate a variety of plant developmental processes. Signaling peptides specifically bind to the extracellular domains of receptors that belong to the receptor-like kinase family, and the peptide–receptor interaction activates a range of biochemical and physiological processes. The plant root is crucial for the anchorage of plants in soil as well as for the uptake of water and nutrients. Over recent years great progress has been made in the identification of receptors, structural analysis of peptide–receptor pairs, and characterization of their signaling pathways during plant root development. We review here recent advances in the elucidation of the functions and molecular mechanisms of signaling peptides, the peptide–receptor pairs that activate signal initiation, and their signaling pathways during root development.

  • CHASEing Cytokinin Receptors in Plants, Bacteria, Fungi, and Beyond
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-01-20
    Samar Kabbara, Thomas Schmülling, Nicolas Papon

    Cytokinin (CK) signaling pathways were believed to be restricted to terrestrial plants. However, the identification of CK receptor homologs in phytopathogenic bacteria, cyanobacteria, and early diverging fungi has recently been reported. CK signaling in prokaryotic and non-plant eukaryotic organisms sheds new light on the dissemination and evolution of this hormone.

  • Dynamic Epigenetic Changes during Plant Regeneration
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-01-12
    Kyounghee Lee, Pil Joon Seo

    Plants have the remarkable ability to drive cellular dedifferentiation and regeneration. Changes in epigenetic landscapes accompany the cell fate transition. Notably, modifications of chromatin structure occur primarily during callus formation via an in vitro tissue culture process and, thus, pluripotent callus cells have unique epigenetic signatures. Here, we highlight the latest progress in epigenetic regulation of callus formation in plants, which addresses fundamental questions related to cell fate changes and pluripotency establishment. Global and local modifications of chromatin structure underlie callus formation, and the combination and sequence of epigenetic modifications further shape intricate cell fate changes. This review illustrates how a series of chromatin marks change dynamically during callus formation and their biological relevance in plant regeneration.

  • Venus Flytrap: How an Excitable, Carnivorous Plant Works
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-01-11
    Rainer Hedrich, Erwin Neher

    The carnivorous plant Dionaea possesses very sensitive mechanoreceptors. Upon contact with prey an action potential is triggered which, via an electrical network – comparable to the nervous system of vertebrates – rapidly closes its bivalved trap. The ‘hunting cycle’ comprises a constitutively activated mechanism for the rapid capture of prey, followed by a well-orchestrated sequence of activation of genes responsible for tight trap closure, digestion of the prey, and uptake of nutrients. Decisions on the step-by-step activation are based on ‘counting’ the number of stimulations of sensory organs. These remarkable animal-like skills in the carnivore are achieved not by taking over genes from its prey but by modifying and rearranging the functions of genes that are ubiquitous in plants.

  • Plant Flowering: Imposing DNA Specificity on Histone-Fold Subunits
    Trends Plant Sci. (IF 11.911) Pub Date : 2018-01-10
    Nerina Gnesutta, Roberto Mantovani, Fabio Fornara

    CONSTANS (CO) is a master regulator of flowering time, although the mechanisms underlying its role as a transcriptional regulator are not well understood. The DNA-binding domain of CO shares homology with that of NUCLEAR FACTOR YA (NF-YA), a subunit of the CCAAT-binding trimer NF-Y. Recent publications indicate that CO and its rice homolog HEADING DATE 1 (Hd1) form heterotrimers with the histone-fold subunits of NF-Y to efficiently bind promoter elements in the florigen genes. Differences in the DNA-binding specificities of NF-Y and NF-CO can be conceptualized based on our knowledge of the 3D structure of the NF-Y/CCAAT complex. Here we discuss the modes of assembly of NF-Y-like heterotrimers and possible models for their activity as flexible sequence-specific transcriptional regulators.

  • PIF3 Integrates Light and Low Temperature Signaling
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-12-27
    Li Lin, Xiaorui Liu, Ruohe Yin

    PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) is a basic ​helix–loop–helix transcription factor with critical roles in light signaling. Recent work identified PIF3 as a negative regulator of arabidopsis (Arabidopsis thaliana) freezing tolerance.

  • Plant–Pesticide Interactions and the Global Chloromethane Budget
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-12-26
    Françoise Bringel, Ivan Couée

    Ecological, signaling, metabolic, and chemical processes in plant–microorganism systems and in plant-derived material may link the use of chlorinated pesticides in the environment with plant chloromethane emission. This neglected factor should be taken into account to assess global planetary budgets of chloromethane and impacts on atmospheric ozone depletion.

  • An In Vivo Perspective of the Role(s) of the Alternative Oxidase Pathway
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-12-18
    Néstor Fernández Del-Saz, Miquel Ribas-Carbo, Allison E. McDonald, Hans Lambers, Alisdair R. Fernie, Igor Florez-Sarasa

    Despite intense research on the in vitro characterization of regulatory factors modulating the alternative oxidase (AOX) pathway, the regulation of its activity in vivo is still not fully understood. Advances concerning in vivo regulation of AOX based on the oxygen-isotope fractionation technique are reviewed, and regulatory factors that merit future research are highlighted. In addition, we review and discuss the main biological functions assigned to the plant AOX, and suggest future experiments involving in vivo activity measurements to test different hypothesized physiological roles.

  • MAPping Kinase Regulation of ICE1 in Freezing Tolerance
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-12-14
    Yukun Liu, Jun Zhou

    Mitogen-activated protein kinase (MAPK) signaling has important roles in plant stress responses. Two recent reports showed how MAPK signaling regulates the response to cold stress through the Inducer of CBF expression 1 (ICE1)-CBF-cold-responsive (COR) transcriptional pathway in Arabidopsis thaliana, expanding our understanding of cold stress signaling and regulation in plants.

  • Coping with ‘Dark Sides of the Sun’ through Photoreceptor Signaling
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-12-09
    Emilie Demarsy, Michel Goldschmidt-Clermont, Roman Ulm

    Plants grow in constantly changing environments, including highly variable light intensities. Sunlight provides the energy that drives photosynthesis and is thus of the utmost importance for plant growth and the generation of oxygen, which the majority of life on Earth depends on. However, exposure to either insufficient or excess levels of light can have detrimental effects and cause light stress. Whereas exposure to insufficient light limits photosynthetic activity, resulting in ‘energy starvation’, exposure to excess light can damage the photosynthetic apparatus. Furthermore, strong sunlight is associated with high levels of potentially damaging UV-B radiation. Different classes of photoreceptors play important roles in coping with the negative aspects of sunlight, for which specific mechanisms are emerging that are reviewed here.

  • Plant Volatiles as Mate-Finding Cues for Insects
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-12-08
    Hao Xu, Ted C.J. Turlings

    Plant volatiles are used not only by herbivorous insects to find their host plants, but also by the natural enemies of the herbivores to find their prey. There is also increasing evidence that plant volatiles, in addition to species-specific pheromones, help these insects to find mating partners. Plant structures such as flowers, fruit, and leaves are frequently rendezvous sites for mate-seeking insects. Here we propose that the combined use of plant volatiles and pheromones can efficiently guide insects to these sites, where they will have access to both mates and food. This notion is supported by the fact that plant volatiles can stimulate the release of sex pheromones and can render various insects more receptive to potential mates.

  • UTR-Dependent Control of Gene Expression in Plants
    Trends Plant Sci. (IF 11.911) Pub Date : 2017-12-06
    Ashish Kumar Srivastava, Yuming Lu, Gaurav Zinta, Zhaobo Lang, Jian-Kang Zhu

    Throughout their lives, plants sense many developmental and environmental stimuli, and activation of optimal responses against these stimuli requires extensive transcriptional reprogramming. To facilitate this activation, plant mRNA contains untranslated regions (UTRs) that significantly increase the coding capacity of the genome by producing multiple mRNA variants from the same gene. In this review we compare UTRs of arabidopsis (Arabidopsis thaliana) and rice (Oryza sativum) at the genome scale to highlight their complexity in crop plants. We discuss different modes of UTR-based regulation with emphasis on genes that regulate multiple plant processes, including flowering, stress responses, and nutrient homeostasis. We demonstrate functional specificity in genes with variable UTR length and propose future research directions.

Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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