Preliminary Prediction And Identification Of The SRNAs In The Mesorhizobium Huakuii7653R

With the development of biotechnology and genomics, research on small RNAs (sRNAs) is becoming a hot spot in this field, it has been reported that more and more sRNAs are present in the genomes of plants、animals and microorganisms. sRNA databases have been established and it provides a large amount of sRNA information which is useful for the biological function analysis. Bioinformatics is an important amd powerful approach to predict sRNA and now being widely used. The recognized mature sRNA prediction methods are QRNA or deepBase-based. The realiability of predicted sRNA can be verified by laboratory experiments such as Northern hybridization or biochip.In this work, by using QRNA software package,9candidate sRNAs were identified from the non-coding regions of Mesorhizbium huakuii7653R completed genome. They are SraG RNA, CsrB RNA, SraC RNA, MicF RNA, RsmYRNA, HgcC RNA, RtT RNA, ISO61RNA and Qrr RNA. In combination with the literature mining, we have analyzed the putative biological functions of9no-coding RNAs and localized the upstream and downstream of structure genetic information for individual sRNA predicted.To obtain direct experimental evidences to verify the authenticity of9predicting sRNAs, RT-PCR experiments were conducted to confirm that9no-codeng RNAs were present in the transcription products of7653R. Northern hybridization and real time RT-PCR experiments were carried out to investigate the biological process for which individual sRNA possibly is involved in. The results showed that9predicted no-coding RNAs were confirmed to be small RNA, and each own expression and level can be induced by some specific stress conditions such as symbiosis, anaerobic cultivation, H2O2,4M NaCl, differernt pH and temperature treatments. Among them, it was found that SraG RNA, HgcC RNA and RtT RNA had the highest expression levels under symbiosis. CsrB RNA had the highest expression level under37℃. SraC RNA and ISO61RNA showed the highest expression level under10℃. While MicF RNA, RsmYRNA and Qrr RNA had the highest expression level under H2O2treatment condition. According to the targeted genes prediction and theoretical analysis based on publications, it is hypothesized that Qrr RNA, MicF RNA and RtT RNA are possibly directly participate the rhizobial symbiotic nitrogen fixation, while RsmY RNA, HgcC RNA and SraG RNA may be indirectly involved in the same process.