scholarly journals Investigation and Computational Analysis of Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum): Insights Into Sulfur Adjustment for Proper Development and Stimuli Responses

2021 ◽  
Author(s):  
Sahar Faraji ◽  
Parviz Heidari ◽  
Hoorieh Amouei ◽  
Ertugrul Filiz ◽  
Abdullah . ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Active Sites ◽  
Sulfur Metabolism ◽  
Solanum Tuberosum L ◽  
Functional Characterization ◽  
The Other ◽  
Protein Motifs ◽  
A Genome

Various kinds of primary metabolisms in plants are modulated through sulfate assimilation that the uptake of this inorganic compound can be regulated via the sulfate transporters, such as sulfotransfer-ases (SOTs), engaged in the sulfur metabolism. In the current study a genome-wide approach has been utilized for recognition and characterization of SOT family genes in the significant nutritional crop po-tato (Solanum tuberosum L.). As a result, 29 StSOT genes were identified in the potato genome, which were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure demonstrated two highly conserved 5' PSB region and 3' PB motif that are essential for sulfotransferase and catalytic ac-tivities. The protein-protein interaction networks also significantly demonstrated an interesting collabo-ration between SOTs and the other genes, such as PRTase, APS-kinase, protein phosphatase and APRs, in sulfur compounds biosynthesis and regulation of the flavonoid and brassinosteroid metabolic pro-cesses, which clearly detected the importance of sulfotransferases for potato proper growth/development and stress dealing. Notably, the homology modeling of StSOT proteins and dock-ing analysis of their ligand-binding sites revealed the presence of some stress-responsive residues, such as proline, glycine, serine and lysine, in their active sites. The expression assay of StSOT genes via the potato RNA-seq data clearly suggested the engagements of these gene family members in plants growth and extension as well as responses to various hormones and biotic/abiotic stimulus circum-stances. Our predictions can be informative for the functional characterization of the SOT genes in po-tato and may the other nutritional crops.

scholarly journals Investigation and Computational Analysis of the Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum): Insights into Sulfur Adjustment for Proper Development and Stimuli Responses

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2597
Author(s):  
Sahar Faraji ◽  
Parviz Heidari ◽  
Hoorieh Amouei ◽  
Ertugrul Filiz ◽  
Abdullah ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Stress Responses ◽  
Active Sites ◽  
Sulfur Metabolism ◽  
Functional Characterization ◽  
Phosphate Binding ◽  
Protein Motifs ◽  
A Genome

Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the significant nutritional crop potato (Solanum tuberosum L.). Twenty-nine putative StSOT genes were identified in the potato genome and were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure revealed two highly conserved 5′-phosphosulfate-binding (5′ PSB) regions and a 3′-phosphate-binding (3′ PB) motif that are essential for sulfotransferase activities. The protein–protein interaction networks also revealed an interesting interaction between SOTs and other proteins, such as PRTase, APS-kinase, protein phosphatase, and APRs, involved in sulfur compound biosynthesis and the regulation of flavonoid and brassinosteroid metabolic processes. This suggests the importance of sulfotransferases for proper potato growth and development and stress responses. Notably, homology modeling of StSOT proteins and docking analysis of their ligand-binding sites revealed the presence of proline, glycine, serine, and lysine in their active sites. An expression essay of StSOT genes via potato RNA-Seq data suggested engagement of these gene family members in plants’ growth and extension and responses to various hormones and biotic or abiotic stimuli. Our predictions may be informative for the functional characterization of the SOT genes in potato and other nutritional crops.

Functional characterization of the pollen-specific SBgLR promoter from potato (Solanum tuberosum L.)

Planta ◽  
2007 ◽  
Vol 227 (2) ◽  
pp. 387-396 ◽  
Author(s):  
Zhihong Lang ◽  
Peng Zhou ◽  
Jingjuan Yu ◽  
Guangming Ao ◽  
Qian Zhao
Keyword(s):  
Solanum Tuberosum ◽  
Solanum Tuberosum L ◽  
Functional Characterization

scholarly journals Genome-Wide Identification and Analysis of VQ Motif-containing Gene Family in Brassica napus and Functional Characterization of BnMKS1 in Response to Leptosphaeria maculans

2020 ◽  
Author(s):  
Zhongwei Zou ◽  
Fei Liu ◽  
Shuanglong Huang ◽  
DILANTHA GERARD FERNANDO
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Functional Characterization ◽  
Leptosphaeria Maculans ◽  
Defense Responses ◽  
Marker Genes ◽  
Blackleg Disease ◽  
Genome Wide ◽  
A Genome

Proteins containing Valine-glutamine (VQ) motifs play important roles in plant growth and development, as well as in defense responses to both abiotic and biotic stresses. Blackleg disease, which is caused by Leptosphaeria maculans, is the most important disease in canola (Brassica napus L.) worldwide. H; however, the identification of B. napus VQs and their functions in response to blackleg disease have not yet been reported. In this study, we conducted a genome genome-wide identification and characterization of the VQ gene family in B. napus, including chromosome location, phylogenetic relations, gene structure, motif domain, synteny analysis, and cis-elements categorization of their promoter regions. To understand B. napus VQ gene function in response to blackleg disease, we overexpressed BnVQ7 (BnaA01g36880D, also known as the mitogen-activated protein kinase4 substrate1 (MKS1) gene) in a blackleg-susceptible canola variety Westar. Overexpression The overexpression of BnMKS1 in canola did not improve its resistance to blackleg disease at the seedling stage. H; however, transgenic canola plants overexpressing BnMKS1 displayed an enhanced resistance to L. maculans infection at the adult plant stage. Expression levels of downstream and defense marker genes in cotyledons increased significantly at the necrotrophic stage of L. maculans infection in the overexpression line of BnMKS1, suggesting that the SA salicylic acid (SA)- and jasmonic acid (JA )-mediated signaling pathways were both involved in the defense responses. Together, these results suggest that BnMKS1 might play an important role in the defense against L. maculans.

Isolation and functional characterization of a stolon specific promoter from potato (Solanum tuberosum L.)

Gene ◽  
2003 ◽  
Vol 303 ◽  
pp. 77-87 ◽  
Author(s):  
Luisa M Trindade ◽  
Beatrix Horvath ◽  
Christian Bachem ◽  
Evert Jacobsen ◽  
Richard G.F Visser
Keyword(s):  
Solanum Tuberosum ◽  
Solanum Tuberosum L ◽  
Functional Characterization

scholarly journals Comprehensive Genome-Wide Identification and Transcript Profiling of GABA Pathway Gene Family in Apple (Malus domestica)

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1973
Author(s):  
Qingbo Zheng ◽  
Shenghui Su ◽  
Zhe Wang ◽  
Yongzhang Wang ◽  
Xiaozhao Xu
Keyword(s):  
Amino Acid ◽  
Gene Family ◽  
Alternative Pathway ◽  
Functional Characterization ◽  
Gaba Shunt ◽  
Gaba Transporters ◽  
Pathway Gene ◽  
Genome Wide ◽  
A Genome

γ-Aminobutyric Acid (GABA), a four-carbon non-protein amino acid, is a significant component of the free amino acid pool in most prokaryotic and eukaryotic organisms. GABA is involved in pH regulation, maintaining C/N balance, plant development and defence, as well as a compatible osmolyte and an alternative pathway for glutamate utilization via anion flux. Glutamate decarboxylase (GAD, EC 4.1.1.15) and GABA transaminase (GABA-T, EC 2.6.1.19) are two key enzymes involved in the synthesis and metabolism of GABA. Recently, GABA transporters (GATs), protein and aluminium-activated malate transporter (ALMT) proteins which function as GABA receptors, have been shown to be involved in GABA regulation. However, there is no report on the characterization of apple GABA pathway genes. In this study, we performed a genome-wide analysis and expression profiling of the GABA pathway gene family in the apple genome. A total of 24 genes were identified including five GAD genes (namely MdGAD 1–5), two GABA-T genes (namely MdGABA-T 1,2), 10 GAT genes (namely GAT 1–10) and seven ALMT genes (namely MdALMT1–7). These genes were randomly distributed on 12 chromosomes. Phylogenetic analyses grouped GABA shunt genes into three clusters—cluster I, cluster II, and cluster III—which had three, four, and five genes, respectively. The expression profile analysis revealed significant MdGAD4 expression levels in both fruit and flower organs, except pollen. However, there were no significant differences in the expression of other GABA shunt genes in different tissues. This work provides the first characterization of the GABA shunt gene family in apple and suggests their importance in apple response to abiotic stress. These results can serve as a guide for future studies on the understanding and functional characterization of these gene families.

scholarly journals Genome-Wide Identification and Expression Analysis of the Class III Peroxidase Gene Family in Potato (Solanum tuberosum L.)

2020 ◽  
Vol 11 ◽  
Author(s):  
Xuanshong Yang ◽  
Jiazheng Yuan ◽  
Wenbin Luo ◽  
Mingyue Qin ◽  
Jiahan Yang ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Solanum Tuberosum L ◽  
Pcr Analysis ◽  
Class Iii ◽  
Protein Motifs ◽  
Real Time Quantitative Pcr ◽  
Gene Pairs ◽  
Genome Wide ◽  
Class Iii Peroxidases

Class III peroxidases (PRXs) are plant-specific enzymes and play important roles in plant growth, development and stress response. In this study, a total of 102 non-redundant PRX gene members (StPRXs) were identified in potato (Solanum tuberosum L.). They were divided into 9 subfamilies based on phylogenetic analysis. The members of each subfamily were found to contain similar organizations of the exon/intron structures and protein motifs. The StPRX genes were not equally distributed among chromosomes. There were 57 gene pairs of segmental duplication and 26 gene pairs of tandem duplication. Expression pattern analysis based on the RNA-seq data of potato from public databases indicated that StPRX genes were expressed differently in various tissues and responded specifically to heat, salt and drought stresses. Most of the StPRX genes were expressed at significantly higher levels in root than in other tissues. In addition, real-time quantitative PCR (qRT-PCR) analysis for 7 selected StPRX genes indicated that these genes displayed various expression levels under abiotic stresses. Our results provide valuable information for better understanding the evolution of StPRX gene family in potato and lay the vital foundation for further exploration of PRX gene function in plants.

Characterization of three members of the ACC synthase gene family in Solanum tuberosum L.

1995 ◽  
Vol 246 (4) ◽  
pp. 496-508 ◽  
Author(s):  
Luis J. C. Destéfano-Beltrán ◽  
Wim Van Caeneghem ◽  
Jan Gielen ◽  
Luc Richard ◽  
Marc Van Montagu ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Gene Family ◽  
Solanum Tuberosum L ◽  
Acc Synthase

Isolation and molecular characterization of a new vegetative MADS-box gene from Solanum tuberosum L.

Planta ◽  
1998 ◽  
Vol 207 (2) ◽  
pp. 181-188 ◽  
Author(s):  
María José Carmona ◽  
Nely Ortega ◽  
Federico Garcia-Maroto
Keyword(s):  
Solanum Tuberosum ◽  
Molecular Characterization ◽  
Solanum Tuberosum L ◽  
Mads Box ◽  
Mads Box Gene
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