Structure and regulation of the Asr gene family in banana.
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ABSTRACT:
SUBMITTER: Henry IM
PROVIDER: S-EPMC3180632 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Tomato ABSCISIC ACID RIPENING 1 (ASR1) was the first cloned plant ASR gene. ASR orthologs were then cloned from a large number of monocot, dicot and gymnosperm plants, where they are mostly involved in response to abiotic (drought and salinity) stress and fruit ripening. The tomato genome encodes five ASR genes: ASR1, 2, 3 and 5 encode low-molecular-weight proteins (ca. 110 amino acid residues each), whereas ASR4 encodes a 297-residue polypeptide. Information on the expression of the tomato ASR gene family is scarce. We used quantitative RT-PCR to assay the expression of this gene family in plant development and in response to salt and osmotic stresses. ASR1 and ASR4 were the main expressed genes in all tested organs and conditions, whereas ASR2 and ASR3/5 expression was two to three orders of magnitude lower (with the exception of cotyledons). ASR1 is expressed in all plant tissues tested whereas ASR4 expression is limited to photosynthetic organs and stamens. Essentially, ASR1 accounted for most of ASR gene expression in roots, stems and fruits at all developmental stages, whereas ASR4 was the major gene expressed in cotyledons and young and fully developed leaves. Both ASR1 and ASR4 were expressed in flower organs, with ASR1 expression dominating in stamens and pistils, ASR4 in sepals and petals. Steady-state levels of ASR1 and ASR4 were upregulated in plant vegetative organs following exposure to salt stress, osmotic stress or the plant abiotic stress hormone abscisic acid (ABA). Tomato plants overexpressing ASR1 displayed enhanced survival rates under conditions of water stress, whereas ASR1-antisense plants displayed marginal hypersensitivity to water withholding.
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Project description:Abscisic acid (ABA)-, stress-, and ripening-induced (ASR) proteins are reported to be involved in drought stress responses. However, the function of maize ASR genes in enhancing drought tolerance is not known. Here, nine maize ASR members were cloned, and the molecular features of these genes were analyzed. Phenotype results of overexpression of maize ZmASR3 gene in Arabidopsis showed lower malondialdehyde (MDA) levels and higher relative water content (RWC) and proline content than the wild type under drought conditions, demonstrating that ZmASR3 can improve drought tolerance. Further experiments showed that ZmASR3-overexpressing transgenic lines displayed increased stomatal closure and reduced reactive oxygen species (ROS) accumulation by increasing the enzyme activities of superoxide dismutase (SOD) and catalase (CAT) under drought conditions. Moreover, overexpression of ZmASR3 in Arabidopsis increased ABA content and reduced sensitivity to exogenous ABA in both the germination and post-germination stages. In addition, the ROS-related, stress-responsive, and ABA-dependent pathway genes were activated in transgenic lines under drought stress. Taken together, these results suggest that ZmASR3 acts as a positive regulator of drought tolerance in plants.
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Project description:BackgroundThe classification of the Musaceae (banana) family species and their phylogenetic inter-relationships remain controversial, in part due to limited nucleotide information to complement the morphological and physiological characters. In this work the evolutionary relationships within the Musaceae family were studied using 13 species and DNA sequences obtained from a set of 19 unlinked nuclear genes.ResultsThe 19 gene sequences represented a sample of ~16 kb of genome sequence (~73% intronic). The sequence data were also used to obtain estimates for the divergence times of the Musaceae genera and Musa sections. Nucleotide variation within the sample confirmed the close relationship of Australimusa and Callimusa sections and showed that Eumusa and Rhodochlamys sections are not reciprocally monophyletic, which supports the previous claims for the merger between the two latter sections. Divergence time analysis supported the previous dating of the Musaceae crown age to the Cretaceous/Tertiary boundary (~ 69 Mya), and the evolution of Musa to ~50 Mya. The first estimates for the divergence times of the four Musa sections were also obtained.ConclusionsThe gene sequence-based phylogeny presented here provides a substantial insight into the course of speciation within the Musaceae. An understanding of the main phylogenetic relationships between banana species will help to fine-tune the taxonomy of Musaceae.
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Project description:Recently there has been much interest in the Regulators of Calcineurin (RCAN) proteins which are important endogenous modulators of the calcineurin-NFATc signalling pathway. They have been shown to have a crucial role in cellular programmes such as the immune response, muscle fibre remodelling and memory, but also in pathological processes such as cardiac hypertrophy and neurodegenerative diseases. In vertebrates, the RCAN family form a functional subfamily of three members RCAN1, RCAN2 and RCAN3 whereas only one RCAN is present in the rest of Eukarya. In addition, RCAN genes have been shown to collocate with RUNX and CLIC genes in ACD clusters (ACD21, ACD6 and ACD1). How the RCAN genes and their clustering in ACDs evolved is still unknown. After analysing RCAN gene family evolution using bioinformatic tools, we propose that the three RCAN vertebrate genes within the ACD clusters, which evolved from single copy genes present in invertebrates and lower eukaryotes, are the result of two rounds of whole genome duplication, followed by a segmental duplication. This evolutionary scenario involves the loss or gain of some RCAN genes during evolution. In addition, we have analysed RCAN gene structure and identified the existence of several characteristic features that can be involved in RCAN evolution and gene expression regulation. These included: several transposable elements, CpG islands in the 5' region of the genes, the existence of antisense transcripts (NAT) associated with the three human genes, and considerable evidence for bidirectional promoters that regulate RCAN gene expression. Furthermore, we show that the CpG island associated with the RCAN3 gene promoter is unmethylated and transcriptionally active. All these results provide timely new insights into the molecular mechanisms underlying RCAN function and a more in depth knowledge of this gene family whose members are obvious candidates for the development of future therapies.
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Project description:BACKGROUND:Abscisic acid-, stress-, and ripening-induced (ASR) genes are a class of plant specific transcription factors (TFs), which play important roles in plant development, growth and abiotic stress responses. The wheat ASRs have not been described in genome-wide yet. METHODS:We predicted the transmembrane regions and subcellular localization using the TMHMM server, and Plant-mPLoc server and CELLO v2.5, respectively. Then the phylogeny tree was built by MEGA7. The exon-intron structures, conserved motifs and TFs binding sites were analyzed by GSDS, MEME program and PlantRegMap, respectively. RESULTS:In wheat, 33ASR genes were identified through a genome-wide survey and classified into six groups. Phylogenetic analyses revealed that the TaASR proteins in the same group tightly clustered together, compared with those from other species. Duplication analysis indicated that the TaASR gene family has expanded mainly through tandem and segmental duplication events. Similar gene structures and conserved protein motifs of TaASRs in wheat were identified in the same groups. ASR genes contained various TF binding cites associated with the stress responses in the promoter region. Gene expression was generally associated with the expected group-specific expression pattern in five tissues, including grain, leaf, root, spike and stem, indicating the broad conservation of ASR genes function during wheat evolution. The qRT-PCR analysis revealed that several ASRs were up-regulated in response to NaCl and PEG stress. CONCLUSION:We identified ASR genes in wheat and found that gene duplication events are the main driving force for ASR gene evolution in wheat. The expression of wheat ASR genes was modulated in responses to multiple abiotic stresses, including drought/osmotic and salt stress. The results provided important information for further identifications of the functions of wheat ASR genes and candidate genes for high abiotic stress tolerant wheat breeding.
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Project description:BackgroundThe major intrinsic protein (MIP) family is a family of proteins, including aquaporins, which facilitate water and small molecule transport across plasma membranes. In plants, MIPs function in a huge variety of processes including water transport, growth, stress response, and fruit development. In this study, we characterize the structure and transcriptional regulation of the MIP family in grapevine, describing the putative genome duplication events leading to the family structure and characterizing the family's tissue and developmental specific expression patterns across numerous preexisting microarray and RNAseq datasets. Gene co-expression network (GCN) analyses were carried out across these datasets and the promoters of each family member were analyzed for cis-regulatory element structure in order to provide insight into their transcriptional regulation.ResultsA total of 29 Vitis vinifera MIP family members (excluding putative pseudogenes) were identified of which all but two were mapped onto Vitis vinifera chromosomes. In this study, segmental duplication events were identified for five plasma membrane intrinsic protein (PIP) and four tonoplast intrinsic protein (TIP) genes, contributing to the expansion of PIPs and TIPs in grapevine. Grapevine MIP family members have distinct tissue and developmental expression patterns and hierarchical clustering revealed two primary groups regardless of the datasets analyzed. Composite microarray and RNA-seq gene co-expression networks (GCNs) highlighted the relationships between MIP genes and functional categories involved in cell wall modification and transport, as well as with other MIPs revealing a strong co-regulation within the family itself. Some duplicated MIP family members have undergone sub-functionalization and exhibit distinct expression patterns and GCNs. Cis-regulatory element (CRE) analyses of the MIP promoters and their associated GCN members revealed enrichment for numerous CREs including AP2/ERFs and NACs.ConclusionsCombining phylogenetic analyses, gene expression profiling, gene co-expression network analyses, and cis-regulatory element enrichment, this study provides a comprehensive overview of the structure and transcriptional regulation of the grapevine MIP family. The study highlights the duplication and sub-functionalization of the family, its strong coordinated expression with genes involved in growth and transport, and the putative classes of TFs responsible for its regulation.
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Project description:The LOX genes have been identified and characterized in many plant species, but studies on the banana LOX genes are very limited. In this study, we respectively identified 18 MaLOX, 11 MbLOX, and 12 MiLOX genes from the Musa acuminata, M. balbisiana and M. itinerans genome data, investigated their gene structures and characterized the physicochemical properties of their encoded proteins. Banana LOXs showed a preference for using and ending with G/C and their encoded proteins can be classified into 9-LOX, Type I 13-LOX and Type II 13-LOX subfamilies. The expansion of the MaLOXs might result from the combined actions of genome-wide, tandem, and segmental duplications. However, tandem and segmental duplications contribute to the expansion of MbLOXs. Transcriptome data based gene expression analysis showed that MaLOX1, 4, and 7 were highly expressed in fruit and their expression levels were significantly regulated by ethylene. And 11, 12 and 7 MaLOXs were found to be low temperature-, high temperature-, and Fusarium oxysporum f. sp. Cubense tropical race 4 (FocTR4)-responsive, respectively. MaLOX8, 9 and 13 are responsive to all the three stresses, MaLOX4 and MaLOX12 are high temperature- and FocTR4-responsive; MaLOX6 and MaLOX17 are significantly induced by low temperature and FocTR4; and the expression of MaLOX7 and MaLOX16 are only affected by high temperature. Quantitative real-time PCR (qRT-PCR) analysis revealed that the expression levels of several MaLOXs are regulated by MeJA and FocTR4, indicating that they can increase the resistance of banana by regulating the JA pathway. Additionally, the weighted gene co-expression network analysis (WGCNA) of MaLOXs revealed 3 models respectively for 5 (MaLOX7-11), 3 (MaLOX6, 13, and 17), and 1 (MaLOX12) MaLOX genes. Our findings can provide valuable information for the characterization, evolution, diversity and functionality of MaLOX, MbLOX and MiLOX genes and are helpful for understanding the roles of LOXs in banana growth and development and adaptations to different stresses.
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Project description:Src-family kinases are modular signaling proteins involved in a diverse array of cellular processes. All members of the Src family share the same domain organization, with modular SH3, SH2 and kinase domains followed by a C-terminal negative regulatory tail. X-ray crystallographic analyses of several Src family members have revealed critical roles for the SH3 and SH2 domains in the down-regulation of the kinase domain. This review focuses on biological, biophysical, and computational studies that reveal conformationally distinct active states within this unique kinase family.
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