Prediction and identification of novel sRNAs involved inAgrobacteriumstrains by integrated genome-wide and transcriptome-based methods
| Autor: | Vikram Kumar, K. Rajendran, Hariharan Sabapathy, Ilamathi Raja, Manoharan Kumariah, Jebasingh Tennyson |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Agrobacterium 030106 microbiology Virulence Computational biology Real-Time Polymerase Chain Reaction Microbiology Genome Transcriptome 03 medical and health sciences Ti plasmid Sigma factor Genetics Gene Silencing Molecular Biology Gene biology Gene Expression Profiling Computational Biology Gene Expression Regulation Bacterial Genomics biology.organism_classification Transformation (genetics) RNA Small Untranslated Genome Bacterial |
| Zdroj: | FEMS Microbiology Letters. 365 |
| ISSN: | 1574-6968 |
| DOI: | 10.1093/femsle/fny247 |
| Popis: | Small RNAs (sRNAs) are a class of gene regulators in bacteria, playing a central role in their response to environmental changes. Bioinformatic prediction facilitates the identification of sRNAs expressed under different conditions. We propose a novel method of prediction of sRNAs from the genome of Agrobacterium based on a positional weight matrix of conditional sigma factors. sRNAs predicted from the genome are integrated with the virulence-specific transcriptome data to identify putative sRNAs that are overexpressed during Agrobacterial virulence induction. A total of 384 sRNAs are predicted from transcriptome data analysis of Agrobacterium fabrum and 100-500 sRNAs from the genome of different Agrobacterial strains. In order to refine our study, a final set of 10 novel sRNAs with best features across different replicons targeting virulence genes were experimentally identified using semi-quantitative polymerase chain reaction. Since Ti plasmid plays a major role in virulence, out of 10 sRNAs across the replicons, 4 novel sRNAs differentially expressed under virulence induced and non-induced conditions are predicted to be present in the Ti plasmid T-DNA region flanking virulence-related genes like agrocinopine synthase, indole 3-lactate synthase, mannopine synthase and tryptophan monooxygenase. Further validation of the function of these sRNAs in conferring virulence would be relevant to explore their role in Agrobacterium-mediated plant transformation. |
| Databáze: | OpenAIRE |
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