Dataset Information

Identification and Expression Analysis of Snf2 Family Proteins in Tomato (Solanum lycopersicum).

ABSTRACT: As part of chromatin-remodeling complexes (CRCs), sucrose nonfermenting 2 (Snf2) family proteins alter chromatin structure and nucleosome position by utilizing the energy of ATP, which allows other regulatory proteins to access DNA. Plant genomes encode a large number of Snf2 proteins, and some of them have been shown to be the key regulators at different developmental stages in Arabidopsis. Yet, little is known about the functions of Snf2 proteins in tomato (Solanum lycopersicum). In this study, 45 Snf2s were identified by the homologous search using representative sequences from yeast (S. cerevisiae), fruit fly (D. melanogaster), and Arabidopsis (A. thaliana) against the tomato genome annotation dataset. Tomato Snf2 proteins (also named SlCHRs) could be clustered into 6 groups and distributed on 11 chromosomes. All SlCHRs contained a helicase-C domain with about 80 amino acid residues and a SNF2-N domain with more variable amino acid residues. In addition, other conserved motifs were also identified in SlCHRs by using the MEME program. Expression profile analysis indicated that tomato Snf2 family genes displayed a wide range of expressions in different tissues and some of them were regulated by the environmental stimuli such as salicylic acid, abscisic acid, salt, and cold. Taken together, these results provide insights into the functions of SlCHRs in tomato.

SUBMITTER: Zhang D

PROVIDER: S-EPMC6458923 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundFibrillin (FBN) proteins are widely distributed in the photosynthetic organs. The members of FBN gene family play important roles in plant growth and development, and response to hormone and stresses. Tomato is a vegetable crop with significantly economic value and model plant commonly used in research. However, the FBN family has not been systematical studied in tomato.MethodsIn this study, 14 FBN genes were identified in tomato genome by Pfam and Hmmer 3.0 software. ExPASy, MEGA 6.0, MEME, GSDS, TBtools, PlantCARE and so on were used for physical and chemical properties analysis, phylogenetic analysis, gene structure and conserved motifs analysis, collinearity analysis and cis-acting element analysis of FBN family genes in tomato. Expression characteristics of SlFBNs in different tissues, fruit shape near isogenic lines (NILs), Pst DC3000 and ABA treatments were analyzed based on transcriptome data and quantitative Real-time qPCR (qRT-PCR) analysis.ResultsThe SlFBN family was divided into 11 subgroups. There were 8 FBN homologous gene pairs between tomato and Arabidopsis. All the members of SlFBN family contained PAP conserved domain, but their gene structure and conserved motifs showed apparent differences. The cis-acting elements of light and hormone (especially ethylene, methyl jasmonate (MeJA) and abscisic acid (ABA)) were widely distributed in the SlFBN promoter regions. The expression analysis found that most of SlFBNs were predominantly expressed in leaves of Heinz and S. pimpinellifolium LA1589, and showed higher expressions in mature or senescent leaves than in young leaves. Expression analysis of different tissues and fruit shape NILs indicated SlFBN1, SlFBN2b and SlFBN7a might play important roles during tomato fruit differentiation. All of the SlFBNs responded to Pst DC3000 and ABA treatments. The results of this study contribute to exploring the functions and molecular mechanisms of SlFBNs in leaf development, fruit differentiation, stress and hormone responses.

Project description:Background Alba (Acetylation lowers binding affinity) proteins are an ancient family of nucleic acid-binding proteins that function in gene regulation, RNA metabolism, mRNA translatability, developmental processes, and stress adaptation. However, comprehensive bioinformatics analysis on the Alba gene family of Solanum lycopersicum has not been reported previously. Results In the present study, we undertook the first comprehensive genome-wide characterization of the Alba gene family in tomato (Solanum lycopersicum L.). We identified eight tomato Alba genes, which were classified into two groups: genes containing a single Alba domain and genes with a generic Alba domain and RGG/RG repeat motifs. Cis-regulatory elements and target sites for miRNAs, which function in plant development and stress responses, were prevalent in SlAlba genes. To explore the structure-function relationships of tomato Alba proteins, we predicted their 3D structures, highlighting their likely interactions with several putative ligands. Confocal microscopy revealed that SlAlba–GFP fusion proteins were localized to the nucleus and cytoplasm, consistent with putative roles in various signalling cascades. Expression profiling revealed the differential expression patterns of most SlAlba genes across diverse organs. SlAlba1 and SlAlba2 were predominantly expressed in flowers, whereas SlAlba5 expression peaked in 1 cm-diameter fruits. The SlAlba genes were differentially expressed (up- or downregulated) in response to different abiotic stresses. All but one of these genes were induced by abscisic acid treatment, pointing to their possible regulatory roles in stress tolerance via an abscisic acid-dependent pathway. Furthermore, co-expression of SlAlba genes with multiple genes related to several metabolic pathways spotlighted their crucial roles in various biological processes and signalling. Conclusions Our characterization of SlAlba genes should facilitate the discovery of additional genes associated with organ and fruit development as well as abiotic stress adaptation in tomato. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-021-03310-0.

Dataset Information

Identification and Expression Analysis of Snf2 Family Proteins in Tomato (Solanum lycopersicum).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets