Журнал прикладной биоинформатики и вычислительной биологии

Identification and Secondary Structural Investigation of Pseudomonas Putida Strain TB3 Signatures Based on 16S Rrna Gene Obtained From Kolanut Husk

Bukola Temitope Fabunmi and George Oche Ambrose

There is rapid development of drug resistant microorganisms in the environment due to drug abuse and poor environmental sanitation among other factors. Strains of Pseudomonas putida are inhabitants of soil and freshwater that exhibit amazing ability to metabolize a wide range of biogenic and xenobiotic compounds. Some strains are however known to possess plasmid bearing genes that encodes for antibiotic resistant factor which can be transferred to other microorganisms. To inhibit the growth of prokaryotes, antibiotics are prepared to target the ribosomal RNA. In order to make possible discovery of improved antibiotics that can target the ribosomal RNA of P. putida, the secondary and tertiary structures of P. putida strain TB3 16s rRNA is being described. P. putida strain TB3 was isolated following standard procedures from kolanut waste (kolanut husk and testa) obtained from Owena, Ondo State, one of the regions in Nigeria where kolanut is largely cultivated for commercial purposes. The isolates were identified using molecular techniques and Sanger sequencing to identify labeled chain of terminating nucleotides that are incorporated by DNA polymerase during replication of the templates. The secondary structure of the rRNA sequence of the isolate was determined by the interaction between its bases, including hydrogen bonding, base stacking and loops defined as R = r1, r2 . . . ; rN with the indices 1< i < N numbering the nucleotides in the 5l to 3l direction and base pairs were denoted by ri:rj. Nearest- neighbor model was used for the secondary structure prediction and the minimum free energy of the structure was estimated by summing individual energy contributions from base pair stacking, hairpins, bulges, internal loops and multi-branch loops using the function rnafold on Matlab software. An assortment of idiosyncratic chemical and structural properties was observed on the base pairs: they have high affinity for metal ions, they present conformational flexibility to different environments and they are almost thermodynamically unchanging as Watson-Crick base pairs. With the development of new drug discovery technologies, targeting RNA for better antibiotic development is emerging as a new frontier in drug discovery