scholarly journals Expansion and Evolutionary Patterns of Glycosyltransferase Family 8 in Gramineae Crop Genomes and Their Expression under Salt and Cold Stresses in Oryza sativa ssp. japonica

Biomolecules ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 188 ◽  
Author(s):  
Weilong Kong ◽  
Ziyun Gong ◽  
Hua Zhong ◽  
Yue Zhang ◽  
Gangqing Zhao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Brachypodium Distachyon ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Oryza Rufipogon ◽  
Potential Candidate ◽  
Evolutionary Patterns

Plant cell walls play a fundamental role in several ways, providing structural support for cells, resistance against pathogens and facilitating the communication between cells. The glycosyltransferase family 8 (GT8) is involved in the formation of the plant cell wall. However, the evolutionary relationship and the functional differentiation of this important gene family remain obscure in Gramineae crop genomes. In the present investigation, we identified 269 GT8 genes in the seven Gramineae representative crop genomes, namely, 33 in Hordeum vulgare, 37 in Brachypodium distachyon, 40 in Oryza sativa ssp. japonica, 41 in Oryza rufipogon, 36 in Setaria italica, 37 in Sorghum bicolor, and 45 in Zea mays. Phylogenetic analysis suggested that all identified GT8 proteins belonged to seven subfamilies: galacturonosyltransferase (GAUT), galacturonosyltransferase-like (GATL), GATL-related (GATR), galactinol synthase (GolS), and plant glycogenin-like starch initiation proteins A (PGSIP-A), PGSIP-B, and PGSIP-C. We estimated that the GAUT subfamily might be further divided into four subgroups (I–IV) due to differentiation of gene structures and expression patterns. Our orthogroup analysis identified 22 orthogroups with different sizes. Of these orthogroups, several orthogroups were lost in some species, such as S. italica and Z. mays. Moreover, lots of duplicate pairs and collinear pairs were discovered among these species. These results indicated that multiple duplication modes led to the expansion of this important gene family and unequal loss of orthogroups and subfamilies might have happened during the evolutionary process. RNA-seq, microarray analysis, and qRT-PCR analyses indicated that GT8 genes are critical for plant growth and development, and for stresses responses. We found that OsGolS1 was significantly up-regulated under salt stress, while OsGAUT21, OsGATL2, and OsGATL5 had remarkable up-regulation under cold stress. The current study highlighted the expansion and evolutionary patterns of the GT8 gene family in these seven Gramineae crop genomes and provided potential candidate genes for future salt- and cold- resistant molecular breeding studies in O. sativa.

scholarly journals Plant Cell Wall Proteomics: A Focus on Monocot Species, Brachypodium distachyon, Saccharum spp. and Oryza sativa

2019 ◽  
Vol 20 (8) ◽  
pp. 1975 ◽  
Author(s):  
Maria Juliana Calderan-Rodrigues ◽  
Juliana Guimarães Fonseca ◽  
Fabrício Edgar de Moraes ◽  
Laís Vaz Setem ◽  
Amanda Carmanhanis Begossi ◽  
...  
Keyword(s):  
Cell Wall ◽  
Oryza Sativa ◽  
Plant Cell ◽  
Cell Walls ◽  
Plant Cell Wall ◽  
Developmental Stages ◽  
Brachypodium Distachyon ◽  
Cell Types ◽  
Biofuel Production ◽  
Saccharum Spp

Plant cell walls mostly comprise polysaccharides and proteins. The composition of monocots’ primary cell walls differs from that of dicots walls with respect to the type of hemicelluloses, the reduction of pectin abundance and the presence of aromatic molecules. Cell wall proteins (CWPs) differ among plant species, and their distribution within functional classes varies according to cell types, organs, developmental stages and/or environmental conditions. In this review, we go deeper into the findings of cell wall proteomics in monocot species and make a comparative analysis of the CWPs identified, considering their predicted functions, the organs analyzed, the plant developmental stage and their possible use as targets for biofuel production. Arabidopsis thaliana CWPs were considered as a reference to allow comparisons among different monocots, i.e., Brachypodium distachyon, Saccharum spp. and Oryza sativa. Altogether, 1159 CWPs have been acknowledged, and specificities and similarities are discussed. In particular, a search for A. thaliana homologs of CWPs identified so far in monocots allows the definition of monocot CWPs characteristics. Finally, the analysis of monocot CWPs appears to be a powerful tool for identifying candidate proteins of interest for tailoring cell walls to increase biomass yield of transformation for second-generation biofuels production.

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

scholarly journals A new insight into the evolution and functional divergence of FRK genes in Pyrus bretschneideri

2018 ◽  
Vol 5 (7) ◽  
pp. 171463 ◽  
Author(s):  
Yunpeng Cao ◽  
Shumei Li ◽  
Yahui Han ◽  
Dandan Meng ◽  
Chunyan Jiao ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Structure ◽  
Functional Divergence ◽  
Sugar Content ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
World Market ◽  
Pear Fruit ◽  
Rosaceae Species ◽  
Chinese White

In plants, plant fructokinases (FRKs) are considered to be the main gateway of fructose metabolism as they can phosphorylate fructose to fructose-6-phosphate. Chinese white pears ( Pyrus bretschneideri ) are one of the popular fruits in the world market; sugar content is an important factor affecting the quality of the fruit. We identified 49 FRKs from four Rosaceae species; 20 of these sequences were from Chinese white pear. Subsequently, phylogenic relationship, gene structure and micro-collinearity were analysed. Phylogenetic and exon–intron analysis classified these FRK s into 10 subfamilies, and it was aimed to further reveal the variation of the gene structure and the evolutionary relationship of this gene family. Remarkably, gene expression patterns in different tissues or different development stages of the pear fruit suggested functional redundancy for PbFRKs derived from segmental duplication or genome-wide duplication and sub-functionalization for some of them. Additionally, PbFRK11 , PbFRK13 and PbFRK16 were found to play important roles in regulating the sugar content in the fruit. Overall, this study provided important insights into the evolution of the FRK gene family in four Rosaceae species, and highlighted its roles in both pear tissue and fruits. Results presented here provide the appropriate candidate of PbFRK s that might contribute to fructose efflux in the pear fruit.

scholarly journals The Role of Brachypodium distachyon Wall-Associated Kinases (WAKs) in Cell Expansion and Stress Responses

Cells ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 2478
Author(s):  
Xingwen Wu ◽  
Antony Bacic ◽  
Kim L. Johnson ◽  
John Humphries
Keyword(s):  
Cell Wall ◽  
Stress Response ◽  
Plant Cell ◽  
Stress Responses ◽  
Cell Expansion ◽  
Plant Cell Wall ◽  
Brachypodium Distachyon ◽  
Critical Role ◽  
Cell Integrity

The plant cell wall plays a critical role in signaling responses to environmental and developmental cues, acting as both the sensing interface and regulator of plant cell integrity. Wall-associated kinases (WAKs) are plant receptor-like kinases located at the wall—plasma membrane—cytoplasmic interface and implicated in cell wall integrity sensing. WAKs in Arabidopsis thaliana have been shown to bind pectins in different forms under various conditions, such as oligogalacturonides (OG)s in stress response, and native pectin during cell expansion. The mechanism(s) WAKs use for sensing in grasses, which contain relatively low amounts of pectin, remains unclear. WAK genes from the model monocot plant, Brachypodium distachyon were identified. Expression profiling during early seedling development and in response to sodium salicylate and salt treatment was undertaken to identify WAKs involved in cell expansion and response to external stimuli. The BdWAK2 gene displayed increased expression during cell expansion and stress response, in addition to playing a potential role in the hypersensitive response. In vitro binding assays with various forms of commercial polysaccharides (pectins, xylans, and mixed-linkage glucans) and wall-extracted fractions (pectic/hemicellulosic/cellulosic) from both Arabidopsis and Brachypodium leaf tissues provided new insights into the binding properties of BdWAK2 and other candidate BdWAKs in grasses. The BdWAKs displayed a specificity for the acidic pectins with similar binding characteristics to the AtWAKs.

scholarly journals Identification, Evolutionary and Expression Analysis of PYL-PP2C-SnRK2s Gene Families in Soybean

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1356
Author(s):  
Zhaohan Zhang ◽  
Shahid Ali ◽  
Tianxu Zhang ◽  
Wanpeng Wang ◽  
Linan Xie
Keyword(s):  
Gene Family ◽  
Higher Plants ◽  
Expression Patterns ◽  
Family Members ◽  
Evolutionary Relationship ◽  
Gene Families ◽  
Class Iii ◽  
Sequencing Data ◽  
Entire Genome ◽  
Core Components

Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway.

scholarly journals Genome-Wide Identification, Evolutionary Patterns, and Expression Analysis of bZIP Gene Family in Olive (Olea europaea L.)

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 510
Author(s):  
Siyu Rong ◽  
Zhiyang Wu ◽  
Zizhang Cheng ◽  
Shan Zhang ◽  
Huan Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Analysis ◽  
Fruit Development ◽  
Leucine Zipper ◽  
Expression Patterns ◽  
Lipid Synthesis ◽  
Structural Features ◽  
Oil Accumulation ◽  
Evolutionary Patterns ◽  
Bzip Family

Olive (Olea europaea.L) is an economically important oleaginous crop and its fruit cold-pressed oil is used for edible oil all over the world. The basic region-leucine zipper (bZIP) family is one of the largest transcription factors families among eukaryotic organisms; its members play vital roles in environmental signaling, stress response, plant growth, seed maturation, and fruit development. However, a comprehensive report on the bZIP gene family in olive is lacking. In this study, 103 OebZIP genes from the olive genome were identified and divided into 12 subfamilies according to their genetic relationship with 78 bZIPs of A. thaliana. Most OebZIP genes are clustered in the subgroup that has a similar gene structure and conserved motif distribution. According to the characteristics of the leucine zipper region, the dimerization characteristics of 103 OebZIP proteins were predicted. Gene duplication analyses revealed that 22 OebZIP genes were involved in the expansion of the bZIP family. To evaluate the expression patterns of OebZIP genes, RNA-seq data available in public databases were analyzed. The highly expressed OebZIP genes and several lipid synthesis genes (LPGs) in fruits of two varieties with different oil contents during the fast oil accumulation stage were examined via qRT-PCR. By comparing the dynamic changes of oil accumulation, OebZIP1, OebZIP7, OebZIP22, and OebZIP99 were shown to have a close relationship with fruit development and lipid synthesis. Additionally, some OebZIP had a significant positive correlation with various LPG genes. This study gives insights into the structural features, evolutionary patterns, and expression analysis, laying a foundation to further reveal the function of the 103 OebZIP genes in olive.

scholarly journals The Spatio-Temporal Distribution of Cell Wall-Associated Glycoproteins During Wood Formation in Populus

2020 ◽  
Vol 11 ◽  
Author(s):  
Tayebeh Abedi ◽  
Romain Castilleux ◽  
Pieter Nibbering ◽  
Totte Niittylä
Keyword(s):  
Gene Expression ◽  
Cell Wall ◽  
Plant Cell ◽  
Cell Walls ◽  
Plant Cell Wall ◽  
Expression Patterns ◽  
Wood Formation ◽  
Cell Type Specificity ◽  
Spatio Temporal ◽  
Ray Cell

Plant cell wall associated hydroxyproline-rich glycoproteins (HRGPs) are involved in several aspects of plant growth and development, including wood formation in trees. HRGPs such as arabinogalactan-proteins (AGPs), extensins (EXTs), and proline rich proteins (PRPs) are important for the development and architecture of plant cell walls. Analysis of publicly available gene expression data revealed that many HRGP encoding genes show tight spatio-temporal expression patterns in the developing wood of Populus that are indicative of specific functions during wood formation. Similar results were obtained for the expression of glycosyl transferases putatively involved in HRGP glycosylation. In situ immunolabelling of transverse wood sections using AGP and EXT antibodies revealed the cell type specificity of different epitopes. In mature wood AGP epitopes were located in xylem ray cell walls, whereas EXT epitopes were specifically observed between neighboring xylem vessels, and on the ray cell side of the vessel walls, likely in association with pits. Molecular mass and glycan analysis of AGPs and EXTs in phloem/cambium, developing xylem, and mature xylem revealed clear differences in glycan structures and size between the tissues. Separation of AGPs by agarose gel electrophoresis and staining with β-D-glucosyl Yariv confirmed the presence of different AGP populations in phloem/cambium and xylem. These results reveal the diverse changes in HRGP-related processes that occur during wood formation at the gene expression and HRGP glycan biosynthesis levels, and relate HRGPs and glycosylation processes to the developmental processes of wood formation.

scholarly journals Genome-wide identification, phylogeny and expression analysis of G6PC gene family in common carp, Cyprinus carpio

2020 ◽  
Vol 45 (2) ◽  
Author(s):  
Sijia Liu ◽  
Fei Tian ◽  
Cunfang Zhang ◽  
Zhigang Qiao ◽  
Kai Zhao
Keyword(s):  
Gene Family ◽  
Common Carp ◽  
Cyprinus Carpio ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Critical Role ◽  
Cold Treatment ◽  
Evolutionary Relationship ◽  
Whole Genome Sequence ◽  
Evolutionary Analysis

AbstractObjectiveThe Glucose 6-phosphatase (G6Pase) catalytic subunit (G6PC) catalyzes glucose 6-phosphate (G6P) to inorganic phosphate and glucose, playing a critical role in endogenous energy supply. Here, the G6PC gene family was investigated and characterized in common carp (Cyprinus carpio).MethodsSequence alignment and phylogenetic analysis were performed using MEGA5. The HMM profiles, motif structure were analyzed using Pfam and MEME, respectively. Quantitative real-time PCR was used to test the expression profiles.ResultsFour assumptive members of G6PC family in common carp whole-genome sequence were identified as cg6pca.1, cg6pca.2a, cg6pca.2b and cg6pcb which were classified into g6pca and g6pcb subtypes, respectively. Evolutionary analysis revealed that cg6pca.2a and cg6pca.2b have a closer evolutionary relationship, and the same subtype members have higher homology among different species. A classical PAP2-glucose phosphates domain is found in four genes and were highly conserved. The expression patterns revealed that only cg6pca.2a elevated significantly after 12 and 24 h of both starvation and cold treatment (p < 0.05).ConclusionsThis study performed a comprehensive analysis of G6PC gene family in common carp. Moreover, cg6pca.2 may be the major functional gene in cold and fasting stress. And the transfactors, PLAG1 and Sox8, may be concerned with expression regulation of cg6pca.2.

scholarly journals Induction of Genes Encoding Plant Cell Wall-Degrading Carbohydrate-Active Enzymes by Lignocellulose-Derived Monosaccharides and Cellobiose in the White-Rot FungusDichomitus squalens

2018 ◽  
Vol 84 (11) ◽  
Author(s):  
Sara Casado López ◽  
Mao Peng ◽  
Tedros Yonatan Issak ◽  
Paul Daly ◽  
Ronald P. de Vries ◽  
...  
Keyword(s):  
Cell Wall ◽  
Plant Cell ◽  
Plant Cell Wall ◽  
Plant Biomass ◽  
Expression Patterns ◽  
Fine Tuning ◽  
White Rot ◽  
White Rot Fungus ◽  
Content Type ◽  
Dichomitus Squalens

ABSTRACTFungi can decompose plant biomass into small oligo- and monosaccharides to be used as carbon sources. Some of these small molecules may induce metabolic pathways and the production of extracellular enzymes targeted for degradation of plant cell wall polymers. Despite extensive studies in ascomycete fungi, little is known about the nature of inducers for the lignocellulolytic systems of basidiomycetes. In this study, we analyzed six sugars known to induce the expression of lignocellulolytic genes in ascomycetes for their role as inducers in the basidiomycete white-rot fungusDichomitus squalensusing a transcriptomic approach. This identified cellobiose andl-rhamnose as the main inducers of cellulolytic and pectinolytic genes, respectively, ofD. squalens. Our results also identified differences in gene expression patterns between dikaryotic and monokaryotic strains ofD. squalenscultivated on plant biomass-derived monosaccharides and the disaccharide cellobiose. This suggests that despite conservation of the induction between these two genetic forms ofD. squalens, the fine-tuning in the gene regulation of lignocellulose conversion is differently organized in these strains.IMPORTANCEWood-decomposing basidiomycete fungi have a major role in the global carbon cycle and are promising candidates for lignocellulosic biorefinery applications. However, information on which components trigger enzyme production is currently lacking, which is crucial for the efficient use of these fungi in biotechnology. In this study, transcriptomes of the white-rot fungusDichomitus squalensfrom plant biomass-derived monosaccharide and cellobiose cultures were studied to identify compounds that induce the expression of genes involved in plant biomass degradation.

scholarly journals Genome-Wide Identification and Characterization of the SHI-Related Sequence Gene Family in Rice

2020 ◽  
Vol 16 ◽  
pp. 117693432094149
Author(s):  
Jun Yang ◽  
Peng Xu ◽  
Diqiu Yu
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Brachypodium Distachyon ◽  
Functional Divergence ◽  
Japonica Rice ◽  
Segmental Duplications ◽  
Related Sequence ◽  
Genome Wide ◽  
A Genome

Rice ( Oryza sativa) yield is correlated to various factors. Transcription regulators are important factors, such as the typical SHORT INTERNODES-related sequences (SRSs), which encode proteins with single zinc finger motifs. Nevertheless, knowledge regarding the evolutionary and functional characteristics of the SRS gene family members in rice is insufficient. Therefore, we performed a genome-wide screening and characterization of the OsSRS gene family in Oryza sativa japonica rice. We also examined the SRS proteins from 11 rice sub-species, consisting of 3 cultivars, 6 wild varieties, and 2 other genome types. SRS members from maize, sorghum, Brachypodium distachyon, and Arabidopsis were also investigated. All these SRS proteins exhibited species-specific characteristics, as well as monocot- and dicot-specific characteristics, as assessed by phylogenetic analysis, which was further validated by gene structure and motif analyses. Genome comparisons revealed that segmental duplications may have played significant roles in the recombination of the OsSRS gene family and their expression levels. The family was mainly subjected to purifying selective pressure. In addition, the expression data demonstrated the distinct responses of OsSRS genes to various abiotic stresses and hormonal treatments, indicating their functional divergence. Our study provides a good reference for elucidating the functions of SRS genes in rice.

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