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.

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 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 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 Gene expression profiling of adp-glucose pyrophosphorylase (AGPase) in sink and source organs of some cassava varieties with different starch contents in Vietnam

2018 ◽  
Vol 14 (4) ◽  
pp. 673-682
Author(s):  
Nguyen Thi Minh Hong ◽  
Le Thu Ngoc ◽  
Nguyen Mau Hung ◽  
Pham Bich Ngoc ◽  
Chu Hoang Ha
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Transcript Level ◽  
Starch Biosynthesis ◽  
Storage Roots ◽  
Genes Encoding ◽  
Adp Glucose Pyrophosphorylase ◽  
Level Analysis ◽  
Starch Production ◽  
Cassava Varieties

Starch is the most widespread and abundant storage carbohydrate in plants. We depend upon starch for our nutrition, exploit its unique properties in industry, and use it as a feedstock for bio-ethanol production. Starch is stored in the form of osmotically inactive, water-insoluble granules in amyloplasts (storage starch) and chloroplasts (transitory starch). The biosynthesis of starch involves not only the production of the composite glucans but also their arrangement into an organized form within the starch granule. Understanding the specific functions played by individual isoforms of enzymes involved in starch biosynthesis pathways will provide important basis for regulation of starch production in plant. A transcript-level analysis of the genes which encode starch-synthesis enzymes is fundamental for assessment of enzyme function and the regulatory mechanism for starch biosynthesis in source and sink organs. In this work, the expression level of the genes encoding ADP-glucose pyrophosphorylase (AGPase) in two local varieties Do Dia Phuong (Do DF) and Trang Hoa Binh (Trang HB) as well as two imported varieties KM94 (Rayong1 X Rayong 90) and KM140 (KM98-1 x KM36) with different starch contents were evaluated by quantitative real-time PCR method. The result of transcript level analysis made the expression profiles of cassava AGPS and AGPL genes (encoding AGPase small and large subunits) during three development periods, 90, 180 and 270 DAP (day after planting). The transcriptional activities of these genes exhibited tissue-specific expression patterns. In particular, AGPS2 and AGPL1 transcripts were predominant in leaves, whereas expression of AGPS1, AGPL2, and AGPL3 appeared to be mostly confined to storage roots. Despite of having disparities between development stages, expression patterns of both AGPS2 and AGPL1 in leaves did not show significant differences amongst investigated cassava varieties. In contrast, transcriptional activities of AGPS1 and AGPL3 in tubers had patterns directly related to the starch contents of the cultivars. These results indicated that AGPS1 and AGPL3 genes likely play an important role in the starch biosynthesis pathway and have potential for regulation of starch production in cassava.

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 Evidence Supporting the Regulatory Relationships through a Paracrine Pathway between the Sternum and Pectoral Muscles in Ducks

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 463
Author(s):  
Yanying Li ◽  
Hehe Liu ◽  
Lei Wang ◽  
Yang Xi ◽  
Jiwen Wang ◽  
...  
Keyword(s):  
Muscle Development ◽  
Regulatory Mechanism ◽  
Expression Patterns ◽  
Pectoral Muscle ◽  
Scientific Data ◽  
Secreted Proteins ◽  
Rna Seq ◽  
Genes Encoding ◽  
Key Genes ◽  
Bone Calcification

Muscles and bones are anatomically closely linked, and they can conduct communication by mechanical and chemical signals. However, the specific regulatory mechanism between the pectoral muscle and sternum in birds was largely unknown. The present study explored the potential relationship between them in ducks. The result of the sections showed that more nuclei in proliferate states were observed in the pectoral muscle fibers attached to the calcified sternum, than those attached to the un-calcified sternum. The RNA-seq identified 328 differentially expressed genes (DEGs) in the sternum between the calcified and un-calcified groups. Gene ontology (GO) showed that the DEGs were mainly enriched in pathways associated with calcification. In addition, DEGs in the muscles between the calcified and un-calcified sternum groups were mainly annotated to signal transduction receptor pathways. The expression patterns of genes encoding for secreted proteins, in bone (CXCL12, BMP7 and CTSK) and muscle (LGI1), were clustered with muscle development (MB) and bone calcification (KCNA1, OSTN, COL9A3, and DCN) related genes, respectively, indicating the regulatory relationships through a paracrine pathway existing between the sternum and pectoral muscles in ducks. Together, we demonstrated that the pectoral muscle development was affected by the sternal ossification states in ducks. The VEGFA, CXCL12, SPP1, NOG, and BMP7 were possibly the key genes to participate in the ossification of the duck sternum. We firstly listed evidence supporting the regulatory relationships through a paracrine pathway between the sternum and pectoral muscles in ducks, which provided scientific data for the study of the synergistic development of bone and skeletal muscle.

scholarly journals Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types

2021 ◽  
Vol 12 ◽  
Author(s):  
Natalia Petrova ◽  
Alsu Nazipova ◽  
Oleg Gorshkov ◽  
Natalia Mokshina ◽  
Olga Patova ◽  
...  
Keyword(s):  
Cell Wall ◽  
Higher Plants ◽  
Expression Patterns ◽  
Transcript Level ◽  
Genome Wide ◽  
Distinct Cell ◽  
A Genome ◽  
Genes Encoding ◽  
Genome Wide Search ◽  
Encoding Genes

The genomes of higher plants encode a variety of proteins with lectin domains that are able to specifically recognize certain carbohydrates. Plants are enriched in a variety of potentially complementary glycans, many of which are located in the cell wall. We performed a genome-wide search for flax proteins with lectin domains and compared the expression of the encoding genes in different stem tissues that have distinct cell wall types with different sets of major polysaccharides. Over 400 genes encoding proteins with lectin domains that belong to different families were revealed in the flax genome; three quarters of these genes were expressed in stem tissues. Hierarchical clustering of the data for all expressed lectins grouped the analyzed samples according to their characteristic cell wall type. Most lectins differentially expressed in tissues with primary, secondary, and tertiary cell walls were predicted to localize at the plasma membrane or cell wall. These lectins were from different families and had various architectural types. Three out of four flax genes for proteins with jacalin-like domains were highly upregulated in bast fibers at the stage of tertiary cell wall deposition. The dynamic changes in transcript level of many genes for lectins from various families were detected in stem tissue over the course of gravitropic response induced by plant gravistimulation. The data obtained in this study indicate a large number of lectin-mediated events in plants and provide insight into the proteins that take part in tissue specialization and reaction to abiotic stress.

scholarly journals Molecular and Functional Analysis of U-box E3 Ubiquitin Ligase Gene Family in Rice (Oryza sativa)

2021 ◽  
Vol 22 (21) ◽  
pp. 12088
Author(s):  
Me-Sun Kim ◽  
Kwon-Kyoo Kang ◽  
Yong-Gu Cho
Keyword(s):  
Functional Analysis ◽  
Drought Stress ◽  
Gene Family ◽  
Ubiquitin Ligase ◽  
Expression Patterns ◽  
E3 Ubiquitin Ligase ◽  
Sequencing Analysis ◽  
Abiotic And Biotic Stresses ◽  
Cis Acting ◽  
Biotic Stresses

Proteins encoded by U-box type ubiquitin ligase (PUB) genes in rice are known to play an important role in plant responses to abiotic and biotic stresses. Functional analysis has revealed a detailed molecular mechanism involving PUB proteins in relation to abiotic and biotic stresses. In this study, characteristics of 77 OsPUB genes in rice were identified. Systematic and comprehensive analyses of the OsPUB gene family were then performed, including analysis of conserved domains, phylogenetic relationships, gene structure, chromosome location, cis-acting elements, and expression patterns. Through transcriptome analysis, we confirmed that 16 OsPUB genes show similar expression patterns in drought stress and blast infection response pathways. Numerous cis-acting elements were found in promoter sequences of 16 OsPUB genes, indicating that the OsPUB genes might be involved in complex regulatory networks to control hormones, stress responses, and cellular development. We performed qRT-PCR on 16 OsPUB genes under drought stress and blast infection to further identify the reliability of transcriptome and cis-element analysis data. It was confirmed that the expression pattern was similar to RNA-sequencing analysis results. The transcription of OsPUB under various stress conditions indicates that the PUB gene might have various functions in the responses of rice to abiotic and biotic stresses. Taken together, these results indicate that the genome-wide analysis of OsPUB genes can provide a solid basis for the functional analysis of U-box E3 ubiquitin ligase genes. The molecular information of the U-box E3 ubiquitin ligase gene family in rice, including gene expression patterns and cis-acting regulatory elements, could be useful for future crop breeding programs by genome editing.

scholarly journals Characterization of histone deacetylases and their roles in response to abiotic and PAMPs stresses in Sorghum bicolor

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Qiaoli Du ◽  
Yuanpeng Fang ◽  
Junmei Jiang ◽  
Meiqing Chen ◽  
Xiaodong Fu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Family ◽  
Histone Deacetylases ◽  
Molecular Model ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Abiotic And Biotic Stresses ◽  
Systematic Analysis ◽  
Biotic Stresses ◽  
Biological Stress

Abstract Background Histone deacetylases (HDACs) play an important role in the regulation of gene expression, which is indispensable in plant growth, development, and responses to environmental stresses. In Arabidopsis and rice, the molecular functions of HDACs have been well-described. However, systematic analysis of the HDAC gene family and gene expression in response to biotic and abiotic stresses has not been reported for sorghum. Results We conducted a systematic analysis of the sorghum HDAC gene family and identified 19 SbHDACs mainly distributed on eight chromosomes. Phylogenetic tree analysis of SbHDACs showed that the gene family was divided into three subfamilies: RPD3/HDA1, SIR2, and HD2. Tissue-specific expression results showed that SbHDACs displayed different expression patterns in different tissues, indicating that these genes may perform different functions in growth and development. The expression pattern of SbHDACs under different stresses (high and low temperature, drought, osmotic and salt) and pathogen-associated molecular model (PAMPs) elf18, chitin, and flg22) indicated that SbHDAC genes may participate in adversity responses and biological stress defenses. Overexpression of SbHDA1, SbHDA3, SbHDT2 and SbSRT2 in Escherichia coli promoted the growth of recombinant cells under abiotic stress. Interestingly, we also showed that the sorghum acetylation level was enhanced when plants were under cold, heat, drought, osmotic and salt stresses. The findings will help us to understand the HDAC gene family in sorghum, and illuminate the molecular mechanism of the responses to abiotic and biotic stresses. Conclusion We have identified and classified 19 HDAC genes in sorghum. Our data provides insights into the evolution of the HDAC gene family and further support the hypothesis that these genes are important for the plant responses to abiotic and biotic stresses.

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 ◽  
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 7 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 Cs WRKY genes in improving abiotic and biotic stress resistance in cucumber.

Sign in / Sign up

Export Citation Format

Share Document