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Genome-Wide Identification of the VQ Protein Gene Family of Tobacco (Nicotiana tabacum L.) and Analysis of Its Expression in Response to Phytohormones and Abiotic and Biotic Stresses.

ABSTRACT: VQ motif-containing proteins (VQ proteins) are transcriptional regulators that work independently or in combination with other transcription factors (TFs) to control plant growth and development and responses to biotic and abiotic stresses. VQ proteins contain a conserved FxxhVQxhTG amino acid motif that is the main element of its interaction with WRKY TFs. We identified 59 members of the tobacco (Nicotiana tabacum L.) NtVQ gene family by in silico analysis and examined their differential expression in response to phytohormonal treatments and following exposure to biotic and abiotic stressors. NtVQ proteins clustered into eight groups based upon their amino acid sequence and presence of various conserved domains. Groups II, IV, V, VI, and VIII contained the largest proportion of NtVQ gene family members differentially expressed in response to one or more phytohormone, and NtVQ proteins with similar domain structures had similar patterns of response to different phytohormones. NtVQ genes differentially expressed in response to temperature alterations and mechanical wounding were also identified. Over half of the NtVQ genes were significantly induced in response to Ralstonia solanacearum infection. This first comprehensive characterization of the NtVQ genes in tobacco lays the foundation for further studies of the NtVQ-mediated regulatory network in plant growth, developmental, and stress-related processes.

SUBMITTER: Liu C

PROVIDER: S-EPMC7140788 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundAlcohol dehydrogenases (ADHs) are the crucial enzymes that can convert ethanol into acetaldehyde. In tobacco, members of ADH gene family are involved in various stresses tolerance reactions, lipid metabolism and pathways related to plant development. It will be of great application significance to analyze the ADH gene family and expression profile under various stresses in tobacco.ResultsA total of 53 ADH genes were identified in tobacco (Nicotiana tabacum L.) genome and were grouped into 6 subfamilies based on phylogenetic analysis. Gene structure (exon/intron) and protein motifs were highly conserved among the NtADH genes, especially the members within the same subfamily. A total of 5 gene pairs of tandem duplication, and 3 gene pairs of segmental duplication were identified based on the analysis of gene duplication events. Cis-regulatory elements of the NtADH promoters participated in cell development, plant hormones, environmental stress, and light responsiveness. The analysis of expression profile showed that NtADH genes were widely expressed in topping stress and leaf senescence. However, the expression patterns of different members appeared to be diverse. The qRT-PCR analysis of 13 NtADH genes displayed their differential expression pattern in response to the bacterial pathogen Ralstonia solanacearum L.InfectionMetabolomics analysis revealed that NtADH genes were primarily associated with carbohydrate metabolism, and moreover, four NtADH genes (NtADH20/24/48/51) were notably involved in the pathway of alpha-linolenic acid metabolism which related to the up-regulation of 9-hydroxy-12-oxo-10(E), 15(Z)-octadecadienoic acid and 9-hydroxy-12-oxo-15(Z)-octadecenoic acid.ConclusionThe genome-wide identification, evolutionary analysis, expression profiling, and exploration of related metabolites and metabolic pathways associated with NtADH genes have yielded valuable insights into the roles of these genes in response to various stresses. Our results could provide a basis for functional analysis of NtADH gene family under stressful conditions.

Project description:Melatonin plays key roles in development and confers stress tolerance to plants. Serotonin N-acetyltransferase (SNAT) is either the enzyme involved in the last step or the penultimate enzyme of phytomelatonin biosynthesis. To date, SNAT genes have not been characterized in tobacco (Nicotiana tabacum), an economically important plant species. The sequence of the Acetyltransf_7 conserved domain was used as a query sequence, and 12 NtSNAT candidate genes were in turn identified in the genome of tobacco. These NtSNATs could be divided into two groups based on the phylogenetic tree. NtSNAT1 and NtSNAT2 clustered together with the other typical SNATs, but the other 10 NtSNATs separately clustered outside of the typical SNATs. These 10 NtSNATs have only motif 1, whereas representative SNATs, such as NtSNAT1 and NtSNAT2 or a SNAT from cyanobacteria, have five motifs. In addition, NtSNAT1 and NtSNAT2 are highly homologous to the characterized OsSNAT1, 62.95 and 71.36%, respectively; however, the homology between the other 10 NtSNAT genes and OsSNAT1 is low. Concomitantly, it is hypothesized that NtSNAT1 and NtSNAT2 are the homolog of SNATs, whereas the other 10 candidates could be considered NtSNAT-like genes. Furthermore, both Nicotiana tomentosiformis and Nicotiana sylvestris, two diploid ancestor species of N. tabacum, have two SNAT candidates; therefore, it is speculated that gene rearrangement or deletion during the process of genomic stabilization after whole-genome duplication or polyploidization led to the preservation of NtSNAT1 and NtSNAT2 during the evolution of tobacco from the ancestral diploid to the allotetraploid. NtSNAT and NtSNAT-like genes were differentially expressed in all organs under different stress conditions, indicating that these genes potentially associated with plant growth and development and stress resistance. Under different stress conditions, the expression of NtSNAT1 was significantly upregulated upon high-temperature and cadmium stresses, while the expression of NtSNAT2 did not significantly increase under any of the tested stress treatments. These results provide valuable information for elucidating the evolutionary relationship of SNAT genes in tobacco and genetic resources for improving tobacco production in the future.

Project description:The Hsp20 genes are involved in the response of plants to environment stresses including heat shock and also play a vital role in plant growth and development. They represent the most abundant small heat shock proteins (sHsps) in plants, but little is known about this family in tomato (Solanum lycopersicum), an important vegetable crop in the world. Here, we characterized heat shock protein 20 (SlHsp20) gene family in tomato through integration of gene structure, chromosome location, phylogenetic relationship, and expression profile. Using bioinformatics-based methods, we identified at least 42 putative SlHsp20 genes in tomato. Sequence analysis revealed that most of SlHsp20 genes possessed no intron or a relatively short intron in length. Chromosome mapping indicated that inter-arm and intra-chromosome duplication events contributed remarkably to the expansion of SlHsp20 genes. Phylogentic tree of Hsp20 genes from tomato and other plant species revealed that SlHsp20 genes were grouped into 13 subfamilies, indicating that these genes may have a common ancestor that generated diverse subfamilies prior to the mono-dicot split. In addition, expression analysis using RNA-seq in various tissues and developmental stages of cultivated tomato and the wild relative Solanum pimpinellifolium revealed that most of these genes (83%) were expressed in at least one stage from at least one genotype. Out of 42 genes, 4 genes were expressed constitutively in almost all the tissues analyzed, implying that these genes might have specific housekeeping function in tomato cell under normal growth conditions. Two SlHsp20 genes displayed differential expression levels between cultivated tomato and S. pimpinellifolium in vegetative (leaf and root) and reproductive organs (floral bud and flower), suggesting inter-species diversification for functional specialization during the process of domestication. Based on genome-wide microarray analysis, we showed that the transcript levels of SlHsp20 genes could be induced profusely by abiotic and biotic stresses such as heat, drought, salt, Botrytis cinerea, and Tomato Spotted Wilt Virus (TSWV), indicating their potential roles in mediating the response of tomato plants to environment stresses. In conclusion, these results provide valuable information for elucidating the evolutionary relationship of Hsp20 gene family and functional characterization of the SlHsp20 gene family in the future.

Dataset Information

Genome-Wide Identification of the VQ Protein Gene Family of Tobacco (Nicotiana tabacum L.) and Analysis of Its Expression in Response to Phytohormones and Abiotic and Biotic Stresses.

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