Functional Characterization of VDACs in Grape and Its Putative Role in Response to Pathogen Stress

Voltage-dependent anion channels (VDACs) are the most abundant proteins in the mitochondrial outer membranes of all eukaryotic cells. They participate in mitochondrial energy metabolism, mitochondria-mediated apoptosis, and cell growth and reproduction. Here, the chromosomal localizations, gene structure, conserved domains, and phylogenetic relationships were analyzed. The amino acid sequences of VDACs were found to be highly conserved. The tissue-specific transcript analysis from transcriptome data and qRT-PCR demonstrated that grapevine VDACs might play an important role in plant growth and development. It was also speculated that VDAC3 might be a regulator of modulated leaf and berry development as the expression patterns during these developmental stages are up-regulated. Further, we screened the role of all grape VDACs’ response to pathogen stress and found that VDAC3 from downy mildew Plasmopara viticola-resistant Chinese wild grapevine species Vitis piasezkii “Liuba-8” had a higher expression than the downy mildew susceptible species Vitis vinifera cv. “Thompson Seedless” after inoculation with P. viticola. Overexpression of VpVDAC3 resulted in increased resistance to pathogens, which was found to prevent VpVDAC3 protein accumulation through protein post-transcriptional regulation. Taken together, these data indicate that VpVDAC3 plays a role in P. viticola defense and provides the evidence with which to understand the mechanism of grape response to pathogen stress.

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Genome-wide Identification and Abiotic Stress Response Pattern Analysis of NF-Y Gene Family in Peanut (Arachis Hypogaea L.)

Tropical Plant Biology ◽

10.1007/s12042-021-09295-2 ◽

2021 ◽

Author(s):

Qian Wan ◽

Lu Luo ◽

Xiurong Zhang ◽

Yuying Lv ◽

Suqing Zhu ◽

...

Keyword(s):

Abiotic Stress ◽

Stress Response ◽

Gene Family ◽

Developmental Stages ◽

Expression Patterns ◽

Regulatory Region ◽

Amino Acid Sequences ◽

Start Codon ◽

Abiotic Stress Response ◽

Specific Expression

AbstractThe nuclear factor Y (NF-Y) transcription factor (TF) family consists of three subfamilies NF-YA, NF-YB and NF-YC. Many studies have proven that NF-Y complex plays multiple essential roles in stress response in Arabidopsis and other plant species. However, little attention has been given to these genes in peanut. In this study, thirty-three AhNF-Y genes were identified in cultivated peanut and they were distributed on 16 chromosomes. A phylogenetic analysis of the NF-Y amino acid sequences indicated that the peanut NF-Y proteins were clustered in pairs at the end of the branches and showed high conservation with previous reported plant NF-Ys. Evolutionary history analysis showed that only segmental duplication contributed to expansion of this gene family. Analysis of the 1500-bp regulatory regions upstream the start codon showed that, except for AhNF-YB6, peanut NF-Ys contained at least one abiotic stress response element in their regulatory region. Expression patterns of peanut NF-Ys in 22 tissues and developmental stages were analyzed. A few NF-Ys showed universal expression patterns, while most NF-Ys showed specific expression patterns. Through RNA-seq and qRT-PCR analyses, expression of six AhNF-Y genes was induced under salt stress in leaves or roots. In addition, AhNF-YA4/8/11, NF-YB4 and NF-YC2/8 also responded to osmotic stress, ABA (abscisic acid) and salicylic acid (SA) treatment.

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Genome-Wide Identification and Expression Profiling of the Polygalacturonase (PG) and Pectin Methylesterase (PME) Genes in Grapevine (Vitis vinifera L.)

International Journal of Molecular Sciences ◽

10.3390/ijms20133180 ◽

2019 ◽

Vol 20 (13) ◽

pp. 3180 ◽

Cited By ~ 6

Author(s):

Nadeem Khan ◽

Fizza Fatima ◽

Muhammad Salman Haider ◽

Hamna Shazadee ◽

Zhongjie Liu ◽

...

Keyword(s):

Expression Profiling ◽

Developmental Stages ◽

Expression Patterns ◽

Functional Characterization ◽

Vitis Vinifera L ◽

Specific Response ◽

Gene Duplications ◽

Crop Species ◽

Specific Expression ◽

Tissue Specific

In pectin regulation, polygalacturonases (PGs) and pectin methylesterases (PMEs) are critical components in the transformation, disassembly network, and remodeling of plant primary cell walls. In the current study, we identified 36 PG and 47 PME genes using the available genomic resources of grapevine. Herein, we provide a comprehensive overview of PGs and PMEs, including phylogenetic and collinearity relationships, motif and gene structure compositions, gene duplications, principal component analysis, and expression profiling during developmental stages. Phylogenetic analysis of PGs and PMEs revealed similar domain composition patterns with Arabidopsis. The collinearity analysis showed high conservation and gene duplications with purifying selection. The type of duplications also varied in terms of gene numbers in PGs (10 dispersed, 1 proximal, 12 tandem, and 13 segmental, respectively) and PMEs (23 dispersed, 1 proximal, 16 tandem, and 7 segmental, respectively). The tissue-specific response of PG and PME genes based on the reported transcriptomic data exhibited diverged expression patterns in various organs during different developmental stages. Among PGs, VvPG8, VvPG10, VvPG13, VvPG17, VvPG18, VvPG19, VvPG20, VvPG22, and VvPG23 showed tissue- or organ-specific expression in majority of the tissues during development. Similarly, in PMEs, VvPME3, VvPME4, VvPME5, VvPME6, VvPME19, VvPME21, VvPME23, VvPME29, VvPME31, and VvPME32 suggested high tissue-specific response. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomics (KEGG) enrichment, and cis-elements prediction analysis also suggested the putative functions of PGs and PMEs in plant development, such as pectin and carbohydrate metabolism, and stress activities. Moreover, qRT-PCR validation of 32 PG and PME genes revealed their role in various organs of grapevines (i.e., root, stem, tendril, inflorescence, flesh, skins, and leaves). Therefore, these findings will lead to novel insights and encourage cutting-edge research on functional characterization of PGs and PMEs in fruit crop species.

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β-Aminobutyric Acid-Induced Resistance Against Downy Mildew in Grapevine Acts Through the Potentiation of Callose Formation and Jasmonic Acid Signaling

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-18-0819 ◽

2005 ◽

Vol 18 (8) ◽

pp. 819-829 ◽

Cited By ~ 158

Author(s):

Mollah Md. Hamiduzzaman ◽

Gabor Jakab ◽

Laurent Barnavon ◽

Jean-Marc Neuhaus ◽

Brigitte Mauch-Mani

Keyword(s):

Jasmonic Acid ◽

Downy Mildew ◽

Induced Resistance ◽

Defense Mechanisms ◽

Expression Patterns ◽

Plasmopara Viticola ◽

Aminobutyric Acid ◽

Marker Genes ◽

Synthesis Inhibitor ◽

Callose Deposition

β-Aminobutyric acid (BABA) was used to induce resistance in grapevine, (Vitis vinifera) against downy mildew (Plasmopara viticola). This led to a strong reduction of mycelial growth and sporulation in the susceptible cv. Chasselas. Comparing different inducers, the best protection was achieved with BABA followed by jasmonic acid (JA), whereas benzo (1,2,3)-thiadiazole-7-carbothionic acid-Smethyl ester (a salicylic acid [SA] analog) and abscisic acid (ABA) treatment did not increase the resistance significantly. Marker genes for the SA and JA pathways showed potentiated expression patterns in BABA-treated plants following infection. The callose synthesis inhibitor 2-deoxy- D-glucose partially suppressed BABA- and JA-induced resistance against P. viticola in Chasselas. Application of the phenylalanine ammonia lyase inhibitor 2-aminoindan-2- phosphonic acid and the lipoxygenase (LOX) inhibitor 5, 8, 11, 14-eicosatetraynoic acid (ETYA) also led to a reduction of BABA-induced resistance (BABA-IR), suggesting that callose deposition as well as defense mechanisms depending on phenylpropanoids and the JA pathways all contribute to BABA-IR. The similar phenotype of BABA- and JA-induced resistance, the potentiated expression pattern of JA-regulated genes (LOX-9 and PR-4) following BABA treatment, and the suppression of BABA-IR with ETYA suggest an involvement of the JA pathway in BABA-IR of grapevine leading to a primed deposition of callose and lignin around the infection sites.

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In silico identification, characterization and expression profile of WUSCHEL-related homeobox (WOX) gene family in Vanilla planifolia

Plant Science Today ◽

10.14719/pst.2020.7.2.722 ◽

2020 ◽

Vol 7 (2) ◽

pp. 206-213

Author(s):

Thiveyarajan Victorathisayam ◽

Madhvi Kanchan ◽

` Himani ◽

Thandullu R. Suriyanarayanan ◽

Jaspreet K. Sembi ◽

...

Keyword(s):

Gene Family ◽

Expression Profile ◽

Developmental Stages ◽

Expression Patterns ◽

Functional Characterization ◽

Alpha Helix ◽

Vanilla Planifolia ◽

In Planta ◽

Specific Expression ◽

Spatio Temporal

Vanilla planifolia is an economically important orchid, which is being commercially exploited by the food industry for the highly valued secondary metabolite vanillin. WUSCHEL-related homeobox (WOX) gene family encodes for WUSCHEL-related homeobox (WOX) transcription factors that participate in embryogenesis, organogenesis and florigenesis and in diverse plant developmental processes as well. In the present study, we analysed V. planifolia transcriptome and identified 6 WOX (VpWOX) transcripts, that encode putative WOX (VpWOX) transcription factor proteins. Domain analysis was done which indicates the presence of helix-loop-helix-turn-helix which is identifying feature of WOX gene family proteins. We executed phylogenetic clustering for the VpWOX proteins with their counterpart from the model plant Arabidopsis thaliana (AtWOX) and other closely related orchid species, Phalaenopsis equestris (PeWOX), Dendrobium catenatum (DcWOX) and Apostasia shenzhenica (AsWOX) and established their clade specific grouping. Spatio-temporal expression profile for VpWOX genes was analysed for different plant developmental stages which shows that VpWOX13 is expressing uniformly in all the developmental stages whereas, other genes have tissue specific expression. Based on gene expression patterns, we selected four VpWOX proteins and carried out secondary and tertiary structural analysis which indicates the presence of alpha helix and beta turn in the protein structure. The present study provides basic understanding of the functioning of WOX gene family in V. planifolia and paves the path for functional characterization of selected VpWOX genes in planta and in heterologous system in future for commercial utilization.

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Functional Characterization of BrF3'H, Which Determines the Typical Flavonoid Profile of Purple Chinese Cabbage

Frontiers in Plant Science ◽

10.3389/fpls.2021.793589 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sangkyu Park ◽

Hyo Lee ◽

Myung Ki Min ◽

Jihee Ha ◽

Jaeeun Song ◽

...

Keyword(s):

Chinese Cabbage ◽

Expression Patterns ◽

Functional Characterization ◽

Phenylpropanoid Pathway ◽

Amino Acid Sequences ◽

In Planta ◽

Normal Green ◽

Wide Range

Flavonols and anthocyanins are the two major classes of flavonoids in Brassica rapa. To elucidate the flavonoid biosynthetic pathway in Chinese cabbage (B. rapa L. subsp. pekinensis), we analyzed flavonoid contents in two varieties of Chinese cabbage with normal green (5546) and purple (8267) leaves. The 8267 variety accumulates significantly higher levels of quercetin, isorhamnetin, and cyanidin than the 5546 variety, indicating that 3′-dihydroxylated flavonoids are more prevalent in the purple than in the green variety. Gene expression analysis showed that the expression patterns of most phenylpropanoid pathway genes did not correspond to the flavonoid accumulation patterns in 5546 and 8267 varieties, except for BrPAL1.2 while most early and late flavonoid biosynthetic genes are highly expressed in 8267 variety. In particular, the flavanone 3′-hydroxylase BrF3′H (Bra009312) is expressed almost exclusively in 8267. We isolated the coding sequences of BrF3′H from the two varieties and found that both sequences encode identical amino acid sequences and are highly conserved with F3'H genes from other species. An in vitro enzymatic assay demonstrated that the recombinant BrF3′H protein catalyzes the 3′-hydroxylation of a wide range of 4′-hydroxylated flavonoid substrates. Kinetic analysis showed that kaempferol is the most preferred substrate and dihydrokaempferol (DHK) is the poorest substrate for recombinant BrF3′H among those tested. Transient expression of BrF3′H in Nicotiana benthamiana followed by infiltration of naringenin and DHK as substrates resulted in eriodictyol and quercetin production in the infiltrated leaves, demonstrating the functionality of BrF3′H in planta. As the first functional characterization of BrF3′H, our study provides insight into the molecular mechanism underlying purple coloration in Chinese cabbage.

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Genome-Wide Identification and Function of Aquaporin Genes During Dormancy and Sprouting Periods of Kernel-Using Apricot (Prunus armeniaca L.)

Frontiers in Plant Science ◽

10.3389/fpls.2021.690040 ◽

2021 ◽

Vol 12 ◽

Author(s):

Shaofeng Li ◽

Lin Wang ◽

Yaoxiang Zhang ◽

Gaopu Zhu ◽

Xuchun Zhu ◽

...

Keyword(s):

Cold Stress ◽

Cold Tolerance ◽

Resistance Genes ◽

Stress Responses ◽

Expression Patterns ◽

Functional Characterization ◽

Regulatory Elements ◽

Prunus Armeniaca ◽

Protein Accumulation ◽

Flower Buds

Aquaporins (AQPs) are essential channel proteins that play a major role in plant growth and development, regulate plant water homeostasis, and transport uncharged solutes across biological membranes. In this study, 33 AQP genes were systematically identified from the kernel-using apricot (Prunus armeniaca L.) genome and divided into five subfamilies based on phylogenetic analyses. A total of 14 collinear blocks containing AQP genes between P. armeniaca and Arabidopsis thaliana were identified by synteny analysis, and 30 collinear blocks were identified between P. armeniaca and P. persica. Gene structure and conserved functional motif analyses indicated that the PaAQPs exhibit a conserved exon-intron pattern and that conserved motifs are present within members of each subfamily. Physiological mechanism prediction based on the aromatic/arginine selectivity filter, Froger’s positions, and three-dimensional (3D) protein model construction revealed marked differences in substrate specificity between the members of the five subfamilies of PaAQPs. Promoter analysis of the PaAQP genes for conserved regulatory elements suggested a greater abundance of cis-elements involved in light, hormone, and stress responses, which may reflect the differences in expression patterns of PaAQPs and their various functions associated with plant development and abiotic stress responses. Gene expression patterns of PaAQPs showed that PaPIP1-3, PaPIP2-1, and PaTIP1-1 were highly expressed in flower buds during the dormancy and sprouting stages of P. armeniaca. A PaAQP coexpression network showed that PaAQPs were coexpressed with 14 cold resistance genes and with 16 cold stress-associated genes. The expression pattern of 70% of the PaAQPs coexpressed with cold stress resistance genes was consistent with the four periods [Physiological dormancy (PD), ecological dormancy (ED), sprouting period (SP), and germination stage (GS)] of flower buds of P. armeniaca. Detection of the transient expression of GFP-tagged PaPIP1-1, PaPIP2-3, PaSIP1-3, PaXIP1-2, PaNIP6-1, and PaTIP1-1 revealed that the fusion proteins localized to the plasma membrane. Predictions of an A. thaliana ortholog-based protein–protein interaction network indicated that PaAQP proteins had complex relationships with the cold tolerance pathway, PaNIP6-1 could interact with WRKY6, PaTIP1-1 could interact with TSPO, and PaPIP2-1 could interact with ATHATPLC1G. Interestingly, overexpression of PaPIP1-3 and PaTIP1-1 increased the cold tolerance of and protein accumulation in yeast. Compared with wild-type plants, PaPIP1-3- and PaTIP1-1-overexpressing (OE) Arabidopsis plants exhibited greater tolerance to cold stress, as evidenced by better growth and greater antioxidative enzyme activities. Overall, our study provides insights into the interaction networks, expression patterns, and functional analysis of PaAQP genes in P. armeniaca L. and contributes to the further functional characterization of PaAQPs.

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The Desaturase Gene Family is Crucially Required for Fatty Acid Metabolism and Survival of the Brown Planthopper, Nilaparvata lugens

International Journal of Molecular Sciences ◽

10.3390/ijms20061369 ◽

2019 ◽

Vol 20 (6) ◽

pp. 1369 ◽

Cited By ~ 3

Author(s):

Jia-mei Zeng ◽

Wen-feng Ye ◽

Ali Noman ◽

Ricardo Machado ◽

Yong-gen Lou

Keyword(s):

Fatty Acid ◽

Developmental Stages ◽

Rice Variety ◽

Expression Patterns ◽

Brown Planthopper ◽

Functional Characterization ◽

Nilaparvata Lugens ◽

Resistant Variety ◽

Mrna Levels ◽

Desaturase Gene

Desaturases are essentially required for unsaturated fatty acid (UFA) biosynthesis. We identified 10 genes encoding putative desaturases in the transcriptome database of the brown planthopper (BPH), Nilaparvata lugens. These include eight First Desaturase family genes, one cytochrome b5 fused desaturase gene (Nlug-Cytb5r) and one Sphingolipid Desaturase gene (Nlug-ifc). Transcript level profiling revealed significant variation in the expression patterns of these genes across tissues and developmental stages, which occur in a gene-specific manner. Interestingly, their expression was also modulated by the insect food source: the mRNA levels of Nlug-desatC and Nlug-Cytb5r were down-regulated, but the expression level of Nlug-desatA1-b and Nlug-desatA1-c were elevated in the BPH fed on the resistant rice variety Babawee as compared to the non-resistant variety Taichun Native 1 (TN1). Silencing Nlug-desatA1-b, Nlug-desatA1-c, or Nlug-Ifc reduced fatty acid composition and abundance in female BPH 1-d-old-adults compared to controls. Whereas, single knockdown of all ten desaturase genes significantly increased mortality of BPH nymphs compared with controls. Of the ten desaturase genes, knockdown of Nlug-desatA1-b and Nlug-desatA2 caused the highest mortality in BPH (91% and 97%, respectively). Our findings offer a base for expression and functional characterization of newly identified desaturase genes in BPH, and may contribute to RNA interference-based pest management strategies.

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Genome-Wide Identification and Characterization of Polygalacturonase Gene Family in Maize (Zea mays L.)

International Journal of Molecular Sciences ◽

10.3390/ijms221910722 ◽

2021 ◽

Vol 22 (19) ◽

pp. 10722

Author(s):

Lu Lu ◽

Quancan Hou ◽

Linlin Wang ◽

Tianye Zhang ◽

Wei Zhao ◽

...

Keyword(s):

Zea Mays ◽

Gene Family ◽

Zea Mays L ◽

Developmental Stages ◽

Expression Profiles ◽

Functional Divergence ◽

Expression Patterns ◽

Functional Characterization ◽

Evolutionary Relationship ◽

Segmental Duplications

Polygalacturonase (PG, EC 3.2.1.15) is a crucial enzyme for pectin degradation and is involved in various developmental processes such as fruit ripening, pollen development, cell expansion, and organ abscission. However, information on the PG gene family in the maize (Zea mays L.) genome and the specific members involved in maize anther development are still lacking. In this study, we identified 55 PG family genes from the maize genome and further characterized their evolutionary relationship and expression patterns. Phylogenetic analysis revealed that ZmPGs are grouped into six Clades, and gene structures of the same Clade are highly conserved, suggesting their functional conservation. The ZmPGs are randomly distributed across maize chromosomes, and collinearity analysis showed that many ZmPGs might be derived from tandem duplications and segmental duplications, and these genes are under purifying selection. Furthermore, gene expression analysis provided insights into possible functional divergence among ZmPGs. Based on the RNA-seq data analysis, we found that many ZmPGs are expressed in various tissues while 18 ZmPGs are highly expressed in maize anther, and their detailed expression profiles in different anther developmental stages were further investigated by using RT-qPCR analysis. These results provide valuable information for further functional characterization and application of the ZmPGs in maize.

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Genome-Wide Identification and Expression Profiling of 2OGD Superfamily Genes from Three Brassica Plants

Genes ◽

10.3390/genes12091399 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1399

Author(s):

Ding Jiang ◽

Guangguang Li ◽

Guoju Chen ◽

Jianjun Lei ◽

Bihao Cao ◽

...

Keyword(s):

Developmental Stages ◽

Expression Profiles ◽

Expression Patterns ◽

Functional Characterization ◽

Gene Families ◽

Plant Genome ◽

Valuable Insight ◽

Systematic Analysis ◽

Brassica Plants ◽

Root Tissues

The 2-oxoglutarate and Fe(II)-dependent dioxygenase (2OGD) superfamily is the second largest enzyme family in the plant genome, and its members are involved in various oxygenation and hydroxylation reactions. Due to their important biochemical significance in metabolism, a systematic analysis of the plant 2OGD genes family is necessary. Here, we identified 160, 179, and 337 putative 2OGDs from Brassica rapa, Brassica oleracea, and Brassica napus. According to their gene structure, domain, phylogenetic features, function, and previous studies, we also divided 676 2OGDs into three subfamilies: DOXA, DOXB, and DOXC. Additionally, homologous and phylogenetic comparisons of three subfamily genes provided valuable insight into the evolutionary characteristics of the 2OGD genes from Brassica plants. Expression profiles derived from the transcriptome and Genevestigator database exhibited distinct expression patterns of the At2OGD, Br2OGD, and Bo2OGD genes in different developmental stages, tissues, or anatomical parts. Some 2OGD genes showed high expression levels in various tissues, such as callus, seed, silique, and root tissues, while other 2OGD genes were expressed at very low levels in other tissues. Analysis of six Bo2OGD genes in different tissues by qRT-PCR indicated that these genes are involved in the metabolism of gibberellin, which in turn regulates plant growth and development. Our working system analysed 2OGD gene families of three Brassica plants and laid the foundation for further study of their functional characterization.

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Callose Synthase Family Genes Involved in the Grapevine Defense Response to Downy Mildew Disease

Phytopathology ◽

10.1094/phyto-07-15-0166-r ◽

2016 ◽

Vol 106 (1) ◽

pp. 56-64 ◽

Cited By ~ 13

Author(s):

Ying Yu ◽

Li Jiao ◽

Shufang Fu ◽

Ling Yin ◽

Yali Zhang ◽

...

Keyword(s):

Downy Mildew ◽

Defense Response ◽

Promoter Activity ◽

Expression Patterns ◽

Plasmopara Viticola ◽

Transient Expression Assay ◽

Callose Synthase ◽

Oomycete Pathogen ◽

Muscadinia Rotundifolia ◽

Common Plant

The deposition of callose is a common plant defense response to intruding pathogens and part of the plant’s innate immunity. In this study, eight grapevine callose synthase (CalS) genes were identified and characterized. To investigate biological function of CalS in grapevine against the infection of Plasmopara viticola, expression patterns of grapevine CalS family genes were analyzed among resistant/susceptible cultivars. After P. viticola infection, expression of CalS1, 3, 7, 8, 9, 10, and 11 were significantly modified among the grapevine cultivars. For example, the expression of CalS1 and CalS10 were greatly increased in downy mildew (DM)-immune Muscadinia rotundifolia ‘Carlos’ and ‘Noble’. Transient expression assay with promoters of the CalS1 and CalS10 genes confirmed that they were regulated by the oomycete pathogen P. viticola. CalS1 promoter activity was also significantly up-regulated by ABA in DM-immune M. rotundifolia ‘Noble’, but down-regulated in DM-susceptible Vitis vinifera ‘Chardonnay’. The CalS1 promoter, however, was also down-regulated by GA in ‘Chardonnay’, but not affected in ‘Noble’. The promoter activity of CalS10 was significantly up-regulated by GA in ‘Chardonnay’, but not regulated by ABA at all. It is proposed that CalS1 and CalS10 were involved in grapevine defense against DM disease.

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