scholarly journals Comprehensive Analysis of the Cadmium Tolerance of Abscisic Acid-, Stress- and Ripening-Induced Proteins (ASRs) in Maize

2019 ◽  
Vol 20 (1) ◽  
pp. 133 ◽  
Author(s):  
Jie Zhang ◽  
Qiusha Zhu ◽  
Haijuan Yu ◽  
Liang Li ◽  
Guoqiang Zhang ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Expression Patterns ◽  
Acid Stress ◽  
In Silico Analysis ◽  
Screening Strategy ◽  
Functional Domain ◽  
In Planta ◽  
Specific Expression ◽  
Tobacco Leaves ◽  
Cd Tolerance

In plants, abscisic acid-, stress-, and ripening-induced (ASR) proteins have been shown to impart tolerance to multiple abiotic stresses such as drought and salinity. However, their roles in metal stress tolerance are poorly understood. To screen plant Cd-tolerance genes, the yeast-based gene hunting method which aimed to screen Cd-tolerance colonies from maize leaf cDNA library hosted in yeast was carried out. Here, maize ZmASR1 was identified to be putative Cd-tolerant through this survival screening strategy. In silico analysis of the functional domain organization, phylogenetic classification and tissue-specific expression patterns revealed that maize ASR1 to ASR5 are typical ASRs with considerable expression in leaves. Further, four of them were cloned for testifying Cd tolerance using yeast complementation assay. The results indicated that they all confer Cd tolerance in Cd-sensitive yeast. Then they were transiently expressed in tobacco leaves for subcellular localization analysis and for Cd-challenged lesion assay, continuously. The results demonstrated that all 4 maize ASRs tested are localized to the cell nucleus and cytoplasm in tobacco leaves. Moreover, they were confirmed to be Cd-tolerance genes in planta through lesion analysis in Cd-infiltrated leaves transiently expressing them. Taken together, our results demonstrate that maize ASRs play important roles in Cd tolerance, and they could be used as promising candidate genes for further functional studies toward improving the Cd tolerance in plants.

scholarly journals A network of transcriptional repressors mediates auxin response specificity

2018 ◽  
Author(s):  
Jekaterina Truskina ◽  
Jingyi Han ◽  
Carlos S. Galvan-Ampudia ◽  
Stéphanie Lainé ◽  
Géraldine Brunoud ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Open Chromatin ◽  
Transcriptional Repressors ◽  
In Planta ◽  
Auxin Response ◽  
Specific Expression ◽  
Developmental Patterns ◽  
Auxin Signalling ◽  
Response Specificity

INTRODUCTORY PARAGRAPHThe regulation of signalling capacity plays a pivotal role in setting developmental patterns in both plants and animals (1). The hormone auxin is a key signal for plant growth and development that acts through the AUXIN RESPONSE FACTOR (ARF) transcription factors (2). A subset of these ARFs comprises transcriptional activators of target genes in response to auxin, and are essential for regulating auxin signalling throughout the plant lifecycle (3). While ARF activators show tissue-specific expression patterns, it is unknown how their expression patterns are established. Chromatin modifications and accessibility studies revealed the chromatin of loci encoding ARF activators is constitutively open for transcription. Using a high-throughput yeast one-hybrid (Y1H) approach, we discovered a network of transcriptional regulators of ARF activator genes from Arabidopsis thaliana. Expression analyses demonstrated that the majority of these regulators act as repressors of ARF transcription in planta. Our observations support a scenario where the default configuration of open chromatin enables a network of transcriptional repressors to shape the expression pattern of ARF activators and provide specificity in auxin signalling output throughout development.

scholarly journals Characterization and abiotic stress-responsive expression analysis of SGT1 genes in Brassica oleracea

Genome ◽  
2016 ◽  
Vol 59 (4) ◽  
pp. 243-251 ◽  
Author(s):  
Ashokraj Shanmugam ◽  
Senthil Kumar Thamilarasan ◽  
Jong-In Park ◽  
Mi Young Jung ◽  
Ill-Sup Nou
Keyword(s):  
Brassica Oleracea ◽  
Expression Analysis ◽  
Abiotic Stresses ◽  
Target Genes ◽  
Expression Patterns ◽  
Strong Association ◽  
Stress Conditions ◽  
Plant Responses ◽  
Functional Domain ◽  
Specific Expression

SGT1 genes are involved in enhancing plant responses to various biotic and abiotic stresses. Brassica oleracea is known to contain two types of SGT1 genes, namely suppressor of G2 allele of SKP1 and suppressor of GCR2. In this study, through systematic analysis, four putative SGT1 genes were identified and characterized in B. oleracea. In phylogenetic analysis, the genes clearly formed separate groups, namely BolSGT1a, BolSGT1b (both suppressor of G2 allele of SKP1 types), and BolSGT1 (suppressor of GCR2). Functional domain analysis and organ-specific expression patterns suggested possible roles for BolSGT1 genes during stress conditions. BolSGT1 genes showed significant changes in expression in response to heat, cold, drought, salt, or ABA treatment. Interaction network analysis supported the expression analysis, and showed that the BolSGT1a and BolSGT1b genes are strongly associated with co-regulators during stress conditions. However, the BolSGT1 gene did not show any strong association. Hence, BolSGT1 might be a stress resistance-related gene that functions without a co-regulator. Our results show that BolSGT1 genes are potential target genes to improve B. oleracea resistance to abiotic stresses such as heat, cold, and salt.

scholarly journals Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7510 ◽  
Author(s):  
Yanan Shi ◽  
Huanlong Liu ◽  
Yameng Gao ◽  
Yujiao Wang ◽  
Min Wu ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Moso Bamboo ◽  
Bimolecular Fluorescence Complementation ◽  
Pcr Analysis ◽  
Hormone Regulation ◽  
In Planta ◽  
Phyllostachys Edulis ◽  
Specific Expression

Growth-regulating factor (GRF), a small plant-specific transcription factor (TF) family, is extensively involved in the regulation of growth and developmental processes. However, the GRF family has not been comprehensively studied in moso bamboo (Phyllostachys edulis), a typical non-timber forest member. Here, 18 GRF genes were identified and characterized from the moso bamboo genome, and they clustered into three subfamilies (A, B and C). PeGRF genes were analyzed to determine their gene structures, conserved motifs and promoter. The non-synonymous/synonymous substitution ratios of paralogous and orthologous were less than 1, indicating that the GRF family mainly experienced purifying selection during evolution. According to the analysis of tissue-specific expression patterns, the participation of moso bamboo GRFs might be required during the formation and development of these five tissues. Moreover, PeGRF proteins might be involved in the regulation of plant development in biological processes. The qRT-PCR analysis demonstrated that PeGRF genes played essential roles in combating hormonal stresses and they might be involved in hormone regulation. PeGRF11, a nuclear localized protein as assessed by a subcellular localization assay, could interact with PeGIF3 in yeast and in planta according to yeast two-hybridization and bimolecular fluorescence complementation assays (BiFC) assays. But PeGRF11, as a TF, had no transcriptional activity in yeast. These results provide useful information for future functional research on the GRF genes in moso bamboo.

scholarly journals Genome-wide characterization and expression patterns of chitinase genes in the pigeonpea (Cajanus cajan (L.) Millsp.) genome

Plant Omics ◽  
2019 ◽  
pp. 109-119
Author(s):  
Ajay Kumar Mahato ◽  
Ajay Kumar Sharm ◽  
Nagendra Kumar Singh
Keyword(s):  
Developmental Stages ◽  
Insect Pests ◽  
Expression Patterns ◽  
Functional Domain ◽  
Specific Expression ◽  
Genome Wide ◽  
Wide Range ◽  
Version 2.0 ◽  
Chitinase Genes ◽  
Plant Chitinases

Plant chitinases are involved in defense as well as a wide range of physiological functions in plants, including germination, embryogenesis, flowering, and senescence. This study was conducted to identify and annotate the chitinase-related genes from the pigeonpea genome version 2.0, their chromosomal localization and phylogenetic relationship with chitinase genes from 13 different plant species. Here, we report the identification of 34 putative chitinase genes in the pigeonpea genome. These 34 genes encode proteins belonging to two functional domain families, and are subdivided into four classes matching four of the five chitinase classes in Arabidopsis. These chitinase genes are present in clusters on the chromosome. We investigated the expression patterns of these chitinases in 29 different tissues at five developmental stages. There was clear clustering of the chitinase genes into three groups based on their expression patterns in tissues. We identified two chitinase genes C_caj-24 and C_caj-25 that were highly expressed in all tissues as well as other chitinase genes with tissue-specific expression, which suggests that they play important roles in plant defense at specific developmental stages. This information on pigeonpea chitinases could be useful for the development of pigeonpea varieties that are resistant to insect pests and fungal diseases.

scholarly journals Abscisic Acid, Stress, and Ripening (TtASR1) Gene as a Functional Marker for Salt Tolerance in Durum Wheat

2020 ◽  
Vol 2020 ◽  
pp. 1-10 ◽  
Author(s):  
Karama Hamdi ◽  
Faiçal Brini ◽  
Najla Kharrat ◽  
Khaled Masmoudi ◽  
Inès Yakoubi
Keyword(s):  
Abscisic Acid ◽  
Salt Tolerance ◽  
Durum Wheat ◽  
Stress Responses ◽  
Expression Patterns ◽  
Acid Stress ◽  
Wheat Breeding ◽  
Functional Marker ◽  
Environmental Signals ◽  
Heat And Cold Stress

In semiarid Mediterranean agroecosystems, drought and salinity are the main abiotic stresses hampering wheat productivity and yield instability. Abscisic acid, stress, and ripening (ASR) are small plant proteins and play important roles in different biological processes. In the present study, the TtASR1 gene was isolated and characterized for the first time from durum wheat (Tritucum turgidum L. subsp. durum). TtASR1 is a small gene, about 684 bp long, located on chromosome 4AL, encoding a protein of 136 amino acid residues consisting of a histidine-rich N terminus and C-terminal conserved ABA-WDS domain (Pfam PF02496). Our results showed that TtASR1 protein could function as a chaperone-like protein and improve the viability of E. coli under heat and cold stress and increase the Saccharomyces cerevisiae tolerance under salt and osmotic stress. Transcript expression patterns of TtASR1 revealed that ASRs play important roles in abiotic stress responses in diverse organs. Indeed, TtASR1 was upregulated in leaves by different developmental (ABA) and environmental signals (PEG, salt). In cv. Mahmoudi (salt-tolerant Tunisian durum landraces) roots, TtASR1 was upregulated by salt stress, while it was downregulated in cv. Azizi (salt-sensitive Tunisian durum landraces), supporting the implication of this gene in the salt tolerance mechanism. Taken together and after validation in the plant system, the TtASR1 gene may provide a potential functional marker for marker-assisted selection in a durum wheat breeding program for salt tolerance.

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

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.

scholarly journals In silico analysis of maize HDACs with an emphasis on their response to biotic and abiotic stresses

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8539 ◽  
Author(s):  
Kang Zhang ◽  
Lu Yu ◽  
Xi Pang ◽  
Hongzhe Cao ◽  
Helong Si ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Gene Family ◽  
Histone Deacetylases ◽  
Expression Patterns ◽  
In Silico Analysis ◽  
Hormone Treatment ◽  
Specific Expression ◽  
Systematic Analysis ◽  
Biotic Stresses

Histone deacetylases (HDACs) are key epigenetic factors in regulating chromatin structure and gene expression in multiple aspects of plant growth, development, and response to abiotic or biotic stresses. Many studies on systematic analysis and molecular function of HDACs in Arabidopsis and rice have been conducted. However, systematic analysis of HDAC gene family and gene expression in response to abiotic and biotic stresses has not yet been reported. In this study, a systematic analysis of the HDAC gene family in maize was performed and 18 ZmHDACs distributed on nine chromosomes were identified. Phylogenetic analysis of ZmHDACs showed that this gene family could be divided into RPD3/HDA1, SIR2, and HD2 groups. Tissue-specific expression results revealed that ZmHDACs exhibited diverse expression patterns in different tissues, indicating that these genes might have diversified functions in growth and development. Expression pattern of ZmHDACs in hormone treatment and inoculation experiment suggested that several ZmHDACs might be involved in jasmonic acid or salicylic acid signaling pathway and defense response. Interestingly, HDAC genes were downregulated under heat stress, and immunoblotting results demonstrated that histones H3K9ac and H4K5ac levels were increased under heat stress. These results provide insights into ZmHDACs, which could help to reveal their functions in controlling maize development and responses to abiotic or biotic stresses.

Contact Chemosensory Genes Identified in Leg Transcriptome of Apis cerana cerana (Hymenoptera: Apidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2015-2029 ◽  
Author(s):  
Yali Du ◽  
Kai Xu ◽  
Weihua Ma ◽  
Wenting Su ◽  
Miaomiao Tai ◽  
...  
Keyword(s):  
Honey Bees ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Apis Cerana ◽  
In Silico Analysis ◽  
Apis Cerana Cerana ◽  
Specific Expression ◽  
Genes Encoding ◽  
Honey Bee Workers ◽  
Selection Of

Abstract Correct gustatory recognition and selection of foods both within and outside the hive by honey bee workers are fundamental to the maintenance of colonies. The tarsal chemosensilla located on the legs of workers are sensitive to nonvolatile compounds and proposed to be involved in gustatory detection. However, little is known about the molecular mechanisms underlying the gustatory recognition of foods in honey bees. In the present study, RNA-seq was performed with RNA samples extracted from the legs of 1-, 10-, and 20-d-old workers of Apis cerana cerana Fabricius, a dominant indigenous crop pollinator with a keen perception ability for phytochemicals. A total of 124 candidate chemosensory proteins (CSPs), including 15 odorant-binding proteins (OBPs), 5 CSPs, 7 gustatory receptors (GRs), 2 sensory neuron membrane proteins (SNMPs), and 95 odorant receptors (ORs), were identified from the assembled leg transcriptome. In silico analysis of expression showed that 36 of them were differentially expressed among the three different ages of A. c. cerana workers. Overall, the genes encoding OBPs and CSPs had great but extremely variable FPKM values and thus were highly expressed in the legs of workers, whereas the genes encoding ORs, GRs, and SNMPs (except SNMP2) were expressed at low levels. Tissue-specific expression patterns indicated that two upregulated genes, AcerOBP15 and AcerCSP3, were predominately expressed in the legs of 20-d-old foragers, suggesting they may play an essential role in gustatory recognition and selection of plant nectars and pollens. This study lays a foundation for further research on the feeding preferences of honey bees.

scholarly journals The two paralogous kiwellin proteins KWL1 and KWL1-b from maize are structurally related and have overlapping functions in plant defense

2020 ◽  
Vol 295 (23) ◽  
pp. 7816-7825
Author(s):  
Florian Altegoer ◽  
Paul Weiland ◽  
Pietro Ivan Giammarinaro ◽  
Sven-Andreas Freibert ◽  
Lynn Binnebesel ◽  
...  
Keyword(s):  
Plant Defense ◽  
Pathogenic Bacteria ◽  
Expression Patterns ◽  
Defense Responses ◽  
Effector Proteins ◽  
Chorismate Mutase ◽  
Carbohydrate Binding ◽  
In Planta ◽  
Specific Expression ◽  
Defense Proteins

Many plant-pathogenic bacteria and fungi deploy effector proteins that down-regulate plant defense responses and reprogram plant metabolism for colonization and survival in planta. Kiwellin (KWL) proteins are a widespread family of plant-defense proteins that target these microbial effectors. The KWL1 protein from maize (corn, Zea mays) specifically inhibits the enzymatic activity of the secreted chorismate mutase Cmu1, a virulence-promoting effector of the smut fungus Ustilago maydis. In addition to KWL1, 19 additional KWL paralogs have been identified in maize. Here, we investigated the structure and mechanism of the closest KWL1 homolog, KWL1-b (ZEAMA_GRMZM2G305329). We solved the Cmu1–KWL1-b complex to 2.75 Å resolution, revealing a highly symmetric Cmu1–KWL1-b heterotetramer in which each KWL1-b monomer interacts with a monomer of the Cmu1 homodimer. The structure also revealed that the overall architecture of the heterotetramer is highly similar to that of the previously reported Cmu1–KWL1 complex. We found that upon U. maydis infection of Z. mays, KWL1-b is expressed at significantly lower levels than KWL1 and exhibits differential tissue-specific expression patterns. We also show that KWL1-b inhibits Cmu1 activity similarly to KWL1. We conclude that KWL1 and KWL1-b are part of a redundant defense system that tissue-specifically targets Cmu1. This notion was supported by the observation that both KWL proteins are carbohydrate-binding proteins with distinct and likely tissue-related specificities. Moreover, binding by Cmu1 modulated the carbohydrate-binding properties of both KWLs. These findings indicate that KWL proteins are part of a spatiotemporally coordinated, plant-wide defense response comprising proteins with overlapping activities.

scholarly journals Evolution and regulation of a large effector family of Pyricularia oryzae

2020 ◽  
Author(s):  
Daniel J Ebbole ◽  
Meilian Chen ◽  
Zhenhui Zhong ◽  
Nicholas Farmer ◽  
Wenhui Zheng ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Family Members ◽  
Allelic Diversity ◽  
Sequence Divergence ◽  
Pyricularia Oryzae ◽  
Sequence Diversity ◽  
Null Alleles ◽  
In Planta ◽  
Specific Expression

Plant pathogen effectors play important roles in parasitism, including countering plant immunity. However, investigations of the emergence and diversification of fungal effectors across host-adapted populations has been limited. We previously identified a gene encoding a suppressor of plant cell death in Pyricularia oryzae (Syn. Magnaporthe oryzae). Here we report the gene is one of a 21-member gene family and we characterize sequence diversity in different populations. Within the rice pathogen population, nucleotide diversity is low, however, the majority of gene family members display presence-absence polymorphism or other null alleles. Gene family allelic diversity is greater between host-adapted populations and we thus named them host adapted genes (HAGs). Multiple copies of HAGs were found in some genome assemblies and sequence divergence between the alleles in two cases suggested they were the result of repeat-induced point mutagenesis. Transfer of family members between populations and novel HAG haplotypes resulting from apparent recombination were observed. HAG family transcripts were induced in planta and a subset of HAGs are dependent on a key regulator of pathogenesis, PMK1. We also found differential intron splicing for some HAGs that would prevent ex planta protein expression. For some genes, spliced transcript was expressed in anti-phase with an overlapping antisense transcript. Characterization of HAG expression patterns and allelic diversity reveal novel mechanisms for HAG regulation and mechanisms generating sequence diversity and novel allele combinations. This evidence of strong in planta-specific expression and selection operating on the HAG family is suggestive of a role in parasitism.

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