Versatile physiological functions of the Nudix Hydrolase family in berry development and stress response in grapevine

2020 ◽  
Author(s):  
Zhaoke Wang ◽  
Peipei Wang ◽  
Le Guan ◽  
Muhammad Salman Haider ◽  
Maazullah Nasim ◽  
...  
Keyword(s):  
Stress Response ◽  
Expression Patterns ◽  
Leaf Roll ◽  
Pcr Analysis ◽  
Berry Development ◽  
Abiotic And Biotic Stresses ◽  
Physiological Functions ◽  
Biotic Stresses ◽  
Wide Range ◽  
Nudix Hydrolases

Abstract Background Nudix hydrolases are widely distributed across all classes of organisms and provide the potential capacity to hydrolyze a wide range of organic pyrophosphates. Although Nudix hydrolases are involved in plants detoxification processes in response to abiotic and biotic stresses, the biological functions of Nudix hydrolases remain largely unclear in grapevine. Results A total of 25 putative grapevine Nudix hydrolases ( VvNUDXs ) were identified by bioinformatics analysis and classified into eight subfamilies based to their preferred substrates. Both tandem and segmental duplications were responsible for the evolution and expansion of NUDX gene family in grapevine. To investigate into their regulatory roles of VvNUDX genes during growth and development as well as in response to abiotic and biotic stress in grapevine, the expression patterns were revealed in publicly available microarray data. The spatial and temporal expression patterns of VvNUDX genes indicated that these genes might play important roles in multiple developmental processes. Transcriptome and qRT-PCR analysis exhibited that ten VvNUDX genes were specifically expressed in grapevine berries, suggesting the potential roles in grapevine berry development. Expression and phylogenetic analysis demonstrated that VvNUDX1 and VvNUDX3 might be involved in terpenoid biosynthesis in grapevine. Futhermore, most VvNUDX genes toward the ADP-ribose/NADH were different patterns in response to various abiotic and biotic stresses, such as salinity and drought, as well as different types of biotic treatments, such as Erysiphe necator , Bois Noir phytoplasma and leaf-roll-associated virus-3 (GLRaV-3). Conclusions These results showed that VvNUDX were associated with plant detoxification processes in response to abiotic and biotic stresses, and regulate disease immunity and resistance pathways. The present informations may provide good opportunities to explore the physiological functions of VvNUDX genes in berry development and stress response networks in grapevine.

scholarly journals VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development

2020 ◽  
Author(s):  
Haley S. Toups ◽  
Noé Cochetel ◽  
Dennis Gray ◽  
Grant R. Cramer
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Berry Development ◽  
Rna Seq ◽  
Abiotic And Biotic Stresses ◽  
Vitis Species ◽  
Biotic Stresses ◽  
Similar Expression

Abstract Background: VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. To better understand this highly duplicated, conserved clade, additional members of the clade were identified in four Vitis genotypes. A meta-data analysis was performed on publicly available microarray and RNA-Seq data (confirmed and expanded with RT-qPCR), and Vitis VviERF6L1 overexpression lines were established and characterized with phenotyping and RNA-Seq. Results: A total of 18 PN40024 VviERF6Ls were identified; additional VviERF6Ls were identified in Cabernet Sauvignon, Chardonnay, and Carménère. The amino acid sequences of VviERF6Ls were found to be highly conserved. VviERF6L transcripts were detected in numerous plant organs and were differentially expressed in response to numerous abiotic stresses including water deficit, salinity, and cold as well as biotic stresses such as red blotch virus, N. parvum , and E. necator . VviERF6Ls were differentially expressed across stages of berry development, peaking in the pre-veraison/veraison stage and retaining conserved expression patterns across different vineyards, years, and Vitis cultivars. Co-expression network analysis identified a scarecrow-like transcription factor and a calmodulin-like gene with highly similar expression profiles to the VviERF6L clade. Overexpression of VviERF6L1 in a Seyval Blanc background did not result in detectable morphological phenotypes. Genes differentially expressed in response to VviERF6L1 overexpression were associated with abiotic and biotic stress responses. Conclusions: VviERF6Ls represent a large and distinct clade of ERF transcription factors in grapevine. The high conservation of protein sequence between these 18 transcription factors may indicate these genes originate from a duplication event in Vitis . Despite high sequence similarity and similar expression patterns, VviERF6Ls demonstrate unique levels of expression supported by similar but heterogeneous promoter sequences. VviERF6L gene expression differed between Vitis species, cultivars and organs including roots, leaves and berries. These genes respond to berry development and abiotic and biotic stresses. VviERF6L1 overexpression in Vitis vinifera results in differential expression of genes related to phytohormone and immune system signaling. Further investigation of this interesting gene family is warranted.

scholarly journals VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development

2020 ◽  
Author(s):  
Haley S. Toups ◽  
Noé Cochetel ◽  
Dennis Gray ◽  
Grant R. Cramer
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Berry Development ◽  
Rna Seq ◽  
Abiotic And Biotic Stresses ◽  
Vitis Species ◽  
Biotic Stresses ◽  
Similar Expression

Abstract Background VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. To better understand this highly duplicated, conserved clade, additional members of the clade were identified in four Vitis genotypes. A meta-data analysis was performed on publicly available microarray and RNA-Seq data (confirmed and expanded with RT-qPCR), and a Vitis VviERF6L1 overexpression line was established and characterized with phenotyping and RNA-Seq. Results A total of 18 PN40024 VviERF6Ls were identified; additional VviERF6Ls were identified in Cabernet Sauvignon, Chardonnay, and Carménère. The amino acid sequences of VviERF6Ls were found to be highly conserved. VviERF6L transcripts were detected in numerous plant organs and were differentially expressed in response to numerous abiotic stresses including water deficit, salinity, and cold as well as biotic stresses such as red blotch virus, N. parvum , and E. necator . VviERF6Ls were differentially expressed across stages of berry development, peaking in the pre-veraison/veraison stage, and retaining conserved expression patterns across different vineyards, years, and Vitis cultivars. Co-expression network analysis identified a scarecrow-like transcription factor and a calmodulin-like gene with highly similar expression profiles to the VviERF6L clade. Overexpression of VviERF6L1 in a Seyval Blanc background did not result in detectable morphological phenotypes. Genes differentially expressed in response to VviERF6L1 overexpression were associated with abiotic and biotic stress responses. Conclusions VviERF6Ls represent a large and distinct clade of ERF transcription factors in grapevine. The high conservation of protein sequence between these 18 transcription factors may indicate these genes originate from a duplication event in Vitis . Despite high sequence similarity and similar expression patterns, VviERF6Ls demonstrate unique levels of expression supported by similar but heterogeneous promoter sequences. VviERF6L gene expression differed between Vitis species, cultivars and organs including roots, leaves and berries. These genes respond to berry development and abiotic and biotic stresses. VviERF6L1 overexpression in Vitis vinifera results in differential expression of genes related to phytohormone and immune system signaling. Further investigation of this interesting gene family is warranted.

scholarly journals Recent Development on Plant Aldehyde Dehydrogenase Enzymes and Their Functions in Plant Development and Stress Signaling

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 51
Author(s):  
Adesola J. Tola ◽  
Amal Jaballi ◽  
Hugo Germain ◽  
Tagnon D. Missihoun
Keyword(s):  
Plant Development ◽  
Critical Analysis ◽  
Current Knowledge ◽  
Stress Signaling ◽  
Oxygen Species ◽  
Abiotic And Biotic Stresses ◽  
Aldehyde Dehydrogenases ◽  
Biotic Stresses ◽  
Wide Range ◽  
Excessive Accumulation

Abiotic and biotic stresses induce the formation of reactive oxygen species (ROS), which subsequently causes the excessive accumulation of aldehydes in cells. Stress-derived aldehydes are commonly designated as reactive electrophile species (RES) as a result of the presence of an electrophilic α, β-unsaturated carbonyl group. Aldehyde dehydrogenases (ALDHs) are NAD(P)+-dependent enzymes that metabolize a wide range of endogenous and exogenous aliphatic and aromatic aldehyde molecules by oxidizing them to their corresponding carboxylic acids. The ALDH enzymes are found in nearly all organisms, and plants contain fourteen ALDH protein families. In this review, we performed a critical analysis of the research reports over the last decade on plant ALDHs. Newly discovered roles for these enzymes in metabolism, signaling and development have been highlighted and discussed. We concluded with suggestions for future investigations to exploit the potential of these enzymes in biotechnology and to improve our current knowledge about these enzymes in gene signaling and plant development.

scholarly journals Expression Patterns of Convergently Overlapping Arabidopsis Thaliana Gene Pairs OHP-NDP1 and OHP2-MES14

2014 ◽  
Vol 56 (1) ◽  
pp. 80-89 ◽  
Author(s):  
Karol Stawski ◽  
Mariusz Banach ◽  
Anna Goc
Keyword(s):  
Regulatory Mechanism ◽  
Expression Patterns ◽  
Transcript Level ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Gene Pairs ◽  
Etiolated Seedlings ◽  
Genes Encoding ◽  
Prolonged Heat ◽  
Prolonged Heat Treatment

Abstract The function of one-helix proteins (OHPs) in the thylakoid membrane remains poorly understood but may be linked to plant photosystem protection. In Arabidopsis, the 3'UTRs of the genes encoding OHP and OHP2 partially overlap with NDP1 and MES14 respectively. Antisense orientation of genes has the potential to form double-stranded transcript (dsRNA) molecules which can be processed to siRNA and trigger RNA interference (RNAi). Natural siRNAs are induced by abiotic and biotic stresses. We examined whether the expression of the OHP-NDP1 and OHP2-MES14 gene pairs is regulated in this way. Both OHP genes, but neither NDP1 nor MES14, were activated by light in etiolated seedlings, whereas cold and prolonged heat treatment elevated the OHP transcript level. Expression of OHP2 was down-regulated after 2 h of osmotic and heat stress, while salt and osmotic stress increased MES14 transcript levels. No inverse regulation of these overlapping gene pairs was observed, excluding RNAi as a regulatory mechanism in the tested conditions. The presence of alternatively polyadenylat-ed transcripts of the studied genes raises the possibility of another regulatory mechanism of 3'UTR overlap.

scholarly journals Molecular Diversity of The Tidal Swamp Rice (Oryza sativa L.) Germplasm of The South Kalimantan, Indonesia

2018 ◽  
Author(s):  
Dindin H. Mursyidin ◽  
Purnomo Purnomo ◽  
Issirep Sumardi ◽  
Budi S. Daryono
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Phylogenetic Reconstruction ◽  
Intergenic Spacer ◽  
The South ◽  
Abiotic And Biotic Stresses ◽  
Intergenic Spacer Region ◽  
Biotic Stresses ◽  
Tidal Swamp ◽  
Wide Range

Tidal swamp rice has long been cultivated by the local people of the South Kalimantan, Indonesia. This germplasm possess some important traits for adapted to a wide range of abiotic and biotic stresses. In this study, a total of sixteen cultivars of this germplasm, consisting of fifteen of the South Kalimantan Province and one of Sumatera Island, Indonesia (an outgroup) were analyzed, phylogenetically based on the chloroplast trnL-F and nuclear intergenic spacer region (IGS). The results showed that this germplasm has a relatively more extraordinary genetic diversity than other local rice germplasm. In a nucleotide level, this germplasm showed a genetic diversity of 0.61 for nuclear IGS and 0.58 for trnL-F. The phylogenetic reconstruction also exhibited that this germplasm has the unique illustration of phylogenetic trees, particularly for the combined sequence datasets. Thus, the results of our study would provide useful information for further understanding of evolutionary relationships of this germplasm and facilitate the efficient utilization of valuable genes for genetic improvement, particularly in the tidal swamp areas.

scholarly journals Genome-Wide Identification, Phylogenetic and Expression Pattern Analysis of GATA Family Genes in Cucumber (Cucumis sativus L.)

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1626
Author(s):  
Kaijing Zhang ◽  
Li Jia ◽  
Dekun Yang ◽  
Yuchao Hu ◽  
Martin Kagiki Njogu ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Constitutive Expression ◽  
Regulatory Elements ◽  
Homologous Gene ◽  
Abiotic And Biotic Stresses ◽  
Characteristic Type ◽  
Biotic Stresses ◽  
Gata Family

GATA transcription factors are a class of transcriptional regulatory proteins that contain a characteristic type-IV zinc finger DNA-binding domain, which play important roles in plant growth and development. The GATA gene family has been characterized in various plant species. However, GATA family genes have not been identified in cucumber. In this study, 26 GATA family genes were identified in cucumber genome, whose physicochemical characteristics, chromosomal distributions, phylogenetic tree, gene structures conserved motifs, cis-regulatory elements in promoters, homologous gene pairs, downstream target genes were analyzed. Tissue expression profiles of cucumber GATA family genes exhibited that 17 GATA genes showed constitutive expression, and some GATA genes showed tissue-specific expression patterns. RNA-seq analysis of green and virescent leaves revealed that seven GATA genes might be involved in the chloroplast development and chlorophyll biosynthesis. Importantly, expression patterns analysis of GATA genes in response to abiotic and biotic stresses indicated that some GATA genes respond to either abiotic stress or biotic stress, some GATA genes such as Csa2G162660, Csa3G017200, Csa3G165640, Csa4G646060, Csa5G622830 and Csa6G312540 were simultaneously functional in resistance to abiotic and biotic stresses. Overall, this study will provide useful information for further analysis of the biological functions of GATA factors in cucumber.

scholarly journals Identification and Expression Analysis of Two allene oxide cyclase (AOC) Genes in Watermelon

Agriculture ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 225 ◽  
Author(s):  
Jingwen Li ◽  
Yelan Guang ◽  
Youxin Yang ◽  
Yong Zhou
Keyword(s):  
Functional Divergence ◽  
Expression Patterns ◽  
Red Light ◽  
Pcr Analysis ◽  
Infected Leaf ◽  
Allene Oxide ◽  
Primary Role ◽  
Root Knot Nematode ◽  
Allene Oxide Cyclase ◽  
Wide Range

Allene oxide cyclase (AOC, EC 5.3.99.6) catalyzes the most important step in the jasmonic acid (JA) biosynthetic pathway and mediates plant defense response to a wide range of biotic and abiotic stresses. In this study, two AOC genes were identified from watermelon. Sequence analysis revealed that each of ClAOC1 and ClAOC2 contained an allene oxide cyclase domain and comprised eight highly conserved β-strands, which are the typical characteristics of AOC proteins. Phylogenetic analysis showed that ClAOC1 and ClAOC2 were clustered together with AOCs from dicotyledon, with the closest relationships with JcAOC from Jatropha curcas and Ljaoc1 from Lotus japonicus. Different intron numbers were observed in ClAOC1 and ClAOC2, which may result in their functional divergence. qRT-PCR analysis revealed that ClAOC1 and ClAOC2 have specific and complex expression patterns in multiple organs and under hormone treatments. Both ClAOC1 and ClAOC2 displayed the highest transcriptional levels in stem apex and fruit and exhibited relatively lower expression in stem. JA, salicylic acid (SA), and ethylene (ET) could enhance the expression of ClAOC1 and ClAOC2, particularly that of ClAOC2. Red light could induce the expression of ClAOC2 in root-knot nematode infected leaf and root of watermelon, indicating that ClAOC2 might play a primary role in red light-induced resistance against root-knot nematodes through JA signal pathway. These findings provide important information for further research on AOC genes in watermelon.

scholarly journals Genome-wide analysis of the WRKY gene family in the cucumber genome and transcriptome-wide identification of WRKY transcription factors that respond to biotic and abiotic stresses

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Chunhua Chen ◽  
Xueqian Chen ◽  
Jing Han ◽  
Wenli Lu ◽  
Zhonghai Ren
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Biotic Stress ◽  
Abiotic Stresses ◽  
Expression Patterns ◽  
Wrky Transcription Factors ◽  
Biotic And Abiotic Stresses ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Cucumber Genome

Abstract Background Cucumber (Cucumis sativus L.) is an economically important vegetable crop species. However, it is susceptible to various abiotic and biotic stresses. WRKY transcription factors play important roles in plant growth and development, particularly in the plant response to biotic and abiotic stresses. However, little is known about the expression pattern of WRKY genes under different stresses in cucumber. Results In the present study, an analysis of the new assembly of the cucumber genome (v3.0) allowed the identification of 61 cucumber WRKY genes. Phylogenetic and synteny analyses were performed using related species to investigate the evolution of the cucumber WRKY genes. The 61 CsWRKYs were classified into three main groups, within which the gene structure and motif compositions were conserved. Tissue expression profiles of the WRKY genes demonstrated that 24 CsWRKY genes showed constitutive expression (FPKM > 1 in all samples), and some WRKY genes showed organ-specific expression, suggesting that these WRKYs might be important for plant growth and organ development in cucumber. Importantly, analysis of the CsWRKY gene expression patterns revealed that five CsWRKY genes strongly responded to both salt and heat stresses, 12 genes were observed to be expressed in response to infection from downy mildew and powdery mildew, and three CsWRKY genes simultaneously responded to all treatments analysed. Some CsWRKY genes were observed to be induced/repressed at different times after abiotic or biotic stress treatment, demonstrating that cucumber WRKY genes might play different roles during different stress responses and that their expression patterns vary in response to stresses. Conclusions Sixty-one WRKY genes were identified in cucumber, and insight into their classification, evolution, and expression patterns was gained in this study. Responses to different abiotic and biotic stresses in cucumber were also investigated. Our results provide a better understanding of the function of CsWRKY genes in improving abiotic and biotic stress resistance in cucumber.

scholarly journals Genome-wide identification of ZmSnRK2 genes and functional analysis of ZmSnRK2.10 in ABA signaling pathway in maize (Zea mays L)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Tiandan Long ◽  
Binjie Xu ◽  
Yufeng Hu ◽  
Yayun Wang ◽  
Changqing Mao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Patterns ◽  
Functional Study ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Aba Signaling ◽  
Genome Database ◽  
Wide Range ◽  
Duplication Events ◽  
Aba Insensitive

Abstract Background Phytohormone abscisic acid (ABA) is involved in the regulation of a wide range of biological processes. In Arabidopsis, it has been well-known that SnRK2s are the central components of the ABA signaling pathway that control the balance between plant growth and stress response, but the functions of ZmSnRK2 in maize are rarely reported. Therefore, the study of ZmSnRK2 is of great importance to understand the ABA signaling pathways in maize. Results In this study, 14 ZmSnRK2 genes were identified in the latest version of maize genome database. Phylogenetic analysis revealed that ZmSnRK2s are divided into three subclasses based on their diversity of C-terminal domains. The exon-intron structures, phylogenetic, synteny and collinearity analysis indicated that SnRK2s, especially the subclass III of SnRK2, are evolutionally conserved in maize, rice and Arabidopsis. Subcellular localization showed that ZmSnRK2 proteins are localized in the nucleus and cytoplasm. The RNA-Seq datasets and qRT-PCR analysis showed that ZmSnRK2 genes exhibit spatial and temporal expression patterns during the growth and development of different maize tissues, and the transcript levels of some ZmSnRK2 genes in kernel are significantly induced by ABA and sucrose treatment. In addition, we found that ZmSnRK2.10, which belongs to subclass III, is highly expressed in kernel and activated by ABA. Overexpression of ZmSnRK2.10 partially rescued the ABA-insensitive phenotype of snrk2.2/2.3 double and snrk2.2/2.3/2.6 triple mutants and led to delaying plant flowering in Arabidopsis. Conclusion The SnRK2 gene family exhibits a high evolutionary conservation and has expanded with whole-genome duplication events in plants. The ZmSnRK2s expanded in maize with whole-genome and segmental duplication, not tandem duplication. The expression pattern analysis of ZmSnRK2s in maize offers important information to study their functions. Study of the functions of ZmSnRK.10 in Arabidopsis suggests that the ABA-dependent members of SnRK2s are evolutionarily conserved in plants. Our study elucidated the structure and evolution of SnRK2 genes in plants and provided a basis for the functional study of ZmSnRK2s protein in maize.

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