Research paperGenome-wide identification and analysis of the sucrose synthase gene family in cassava (Manihot esculenta Crantz)
Introduction
Sucrose is an essential carbon and energy source in the life cycle of various unicellular and multicellular organisms (Lunn, 2002). In higher plants, it is one of the most important carbohydrates produced by photosynthesis in source leaves and is involved in various fundamental pathways of plant growth and development, such as cell division (Gaudin et al., 2000), flowering induction (Ohto et al., 2001), vascular tissue differentiation (Uggla et al., 2001), seed germination (Iraqi and Tremblay, 2001), and accumulation of storage products (Rook et al., 2001). Additionally, in the event of abiotic stresses (e.g., cold, drought, and salt stress), sucrose biosynthesis protects the stability of membranes and proteins and increases metabolism in response to these stresses (Yang et al., 2001, Strand et al., 2003, Fernandes et al., 2004). Meanwhile, early studies have demonstrated the role of sucrose as a signaling molecule, whereby it regulates the expression of genes, encoded enzymes, and can influence a wide range of metabolic pathways (Ciereszko et al., 2001, Stitt et al., 2002, Vaughn et al., 2002, Zourelidou et al., 2002). Sucrose is hydrolyzed by two key enzymes before it is exported to sink tissues in plants. One enzyme is invertase (INV, EC 3.2.1.26), which hydrolyzes sucrose into glucose and fructose, and the other is sucrose synthase (SUS, EC 2.4.1.13), which catalyzes the reversible reaction of sucrose and uridine diphosphate (UDP) into UDP-glucose and fructose (Chourey et al., 1998, Kleczkowski et al., 2010). SUS activity plays a pivotal role in a wide range of important metabolic pathways, such as regulating sucrose partitioning between source and sink tissues (Haigler et al., 2001, Hockema and Etxeberria, 2001), starch biosynthesis (Tang and Sturm, 1999, Barratt et al., 2001), cellulose synthesis in secondary cell walls (Albrecht and Mustroph, 2003, Fujii et al., 2010, Baroja-Fernández et al., 2012), nitrogen fixation (Hohnjec et al., 2003, Baier et al., 2010), and survival following exposure to environmental stresses (Albrecht and Mustroph, 2003, Harada et al., 2005).
Previous studies revealed that SUSs are encoded by a small multi-gene family. Recently, the increasing identification and characterization of SUS gene families in many plant species has revealed variations in the number of members. For instance, the pea and maize SUS gene families contain three divergent genes (Barratt et al., 2001, Duncan et al., 2006), while the model species, Arabidopsis, rice, and Lotus japonicas, have at least six distinct SUS genes (Bieniawska et al., 2007, Hirose et al., 2008, Horst et al., 2007). Moreover, 15 SUS genes were identified in genomes of tetraploid cotton (G. Hirsutum) (Zou et al., 2013) and poplar (Populus trichocarpa) (An et al., 2014), and 30 members were isolated from pear (Pyrus bretschneideri), which is presently regarded as the largest SUS gene family (Abdullah et al., 2018). The members of the SUS gene family from individual species revealed functional and structural divergence, and differential gene expression patterns during different stages of plant growth and development. For example, three divergent SUS isoforms (SUS1, SUS2, and SUS3) displayed distinct expression patterns during organ development in different pea organs. SUS1 was expressed in a wide range of tissues and was abundantly expressed in the developing seeds, whereas SUS2 was strongly expressed in older testas and leaves. Conversely, SUS3 was only weakly expressed in flowers and young testas (Barratt et al., 2001). Another sucrose synthase gene (Sh1) —linked to cell wall synthesis— was abundant in the developing maize endosperm, while the SUS1 was widely expressed and had a central role in starch synthesis (Duncan et al., 2006). The six AtSUS genes also showed differential expression in Arabidopsis, but a partial overlap has been noted. Their specific roles have been extensively investigated in studies that involving knockout mutants (Bieniawska et al., 2007, Baud et al., 2004). In other plant species, such as L. japonicas, Citrus unshiu, cotton, poplar, and grape, SUS genes have also revealed tissue-specific and development-dependent expression patterns, suggesting that they may have evolved specialized physiological functions (Horst et al., 2007, Zou et al., 2013, An et al., 2014, Komatsu et al., 2002, Zhu et al., 2017). Overall, SUS genes have been extensively explored in a variety of species, but there remains a dearth of knowledge on these genes in cassava (Manihot esculenta Crantz).
Cassava is one of the highest yielding food crops and is widely cultivated worldwide, mostly in tropical and subtropical regions (e.g., Africa, Asia, South America etc.). Owing to the high starch content, cassava storage roots are the main calorie source for more than 800 million people globally (Consortium, 2015). In addition to being an important nutritional source, the jhigh starch content of storage roots makes them potential candidates for bioethanol production, which is an important alternative to fossil fuels (Jasson et al., 2009, Nguyun et al., 2007). Starch accumulation in cassava storage roots begins with the hydrolysis of sucrose into UDP-glucose by the sucrose synthase. Since UDP-glucose is the immediate precursor of starch synthesis, understanding the functions of sucrose synthase in sucrose metabolism and starch accumulation is important for improving the productivity of cassava storage roots. Previous studies mostly concentrated on the physiological functions of SUS isozymes (Cruz et al., 2003) or simply focused on the expression of SUS genes (Liao et al., 2017, Liu et al., 2018). To date, the number of genome-wide studies and comprehensive analysis of the SUS gene family in cassava have been limited.
In the present work, the members of SUS gene family were identified and characterized from cassava, using a previous genomic database. The investigation mainly focused on the identification, chromosomal localization, exon/intron organization and structural analysis of conserved motifs in SUS genes. In addition, their evolutionary relationships, expression profiles (in different tissues and developmental stages) and stress inducibility (to cold and drought stress) were examined. To further investigate their potential roles in abiotic stress tolerance, the activities of encoded enzymes were determined under drought and cold stress. Overall, our results could facilitate a more comprehensive understanding of the function of SUS genes in cassava.
Section snippets
Identification of the SUS genes from the cassava genome
To identify the SUS genes, the whole-genome sequence of cassava (Manihot esculenta v6.1) was downloaded from EnsemblPlants (http://plants.ensembl.org/index.html). Annotated protein databases were scanned using HMMER 3.0 (http://hmmer.org/) with the Hidden Markov model (HMM) of Sucrose_synth domain (PF00862), which was downloaded from Pfam (http://pfam.xfam.org/). A high-quality (E-value < 1e−20) protein set was used to construct a cassava-specific Sucrose_synth HMM. Then this new
Identification of sucrose synthase gene family in cassava
A total of seven non-redundant sucrose synthase genes were identified (simply designated as MeSUS 1–7) from the cassava genome database (their nucleotide and amino acid sequences are summarized in Supplementary data S1). Their physical and chemical characteristics were listed in Table 1. As results showed that the open reading frames (ORF) of MeSUS genes ranged from 2418 to 2523 bp in length, while the predicted Mw for the encoded proteins were between 92.57 kDa and 95.97 kDa (806 to 841 amino
Discussion
In higher plants, SUS is encoded by a small multigene family, and plays a crucial role in regulating sucrose metabolism (Chourey et al., 1998, Kleczkowski et al., 2010). Recently, due to a growing number of high-quality whole genome sequences, various SUS family isoforms have been comprehensively investigated from different plant species (e.g., Arabidopsis, rice, and L. japonicas) (Bieniawska et al., 2007, Hirose et al., 2008, Horst et al., 2007). However, the prevalence and functional
Conclusions
In the present study, we identified and analyzed seven non-redundant SUS genes from cassava. Phylogenetic analysis showed that these genes clustered into three different groups, named as SUS I, SUS II, and SUS III, respectively. Their spatio-temporal expression in various tissues and developmental stages indicated that the expression of MeSUS3, and 5–7 was pronounced in the source leaves, whereas that of MeSUS1, 2, and 4 was in the sink tissues (storage roots). The expression of MeSUS2, MeSUS4,
Funding
This study was supported by the National Grand Fundamental Research 937 Program (No. 2010CB126601), Open Sciences Fund Project of State Key Laboratory for Conservation and Utilization of subtropical Agro-Bioresources (No. SKLCOSA-b201609; SKLCUSA-b201704; SKLCUSA-a201802), Guangxi Science and Technology Plan Project (No. 2018AB46010), and the Key Project of the Natural Sciences Fund of Guangxi (No. 2010GXNSFD013025).
CRediT authorship contribution statement
Tangwei Huang: Conceptualization, Data curation, Investigation, Software, Writing - original draft. Xinglu Luo: Conceptualization, Funding acquisition, Project administration, Writing - review & editing. Zhupeng Fan: Methodology, Investigation. Yanni Yang: Methodology, Investigation. Wen Wan: Methodology, Investigation.
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
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