In-silico specificity comparison between GMF-GMR and JMF-JMR primers for detecting moaC genes of food spoilage bacteria pseudomonas spp

Abstract

Pseudomonas spp. have been known as notorious food spoilage bacteria with ability to produce thermo-tolerant enzymes. They pose serious risk to public health as its most pathogenic member, P. aeruginosa, could cause nosocomial infections affecting peoplewith immunodeficiency. The use of GMF-GMR primers had been reported capable for detecting bacterial moaC of Alcaligenes javaensis JG3. The gene is suspected to be related with dormancy of pathogenic bacteria. This study aimed to investigate specificity of the GMR-GMF as well as a newly designed JMF-JMR pairs of primers (JMF: 5'-GGCGTACATCATCCACACTG-3' and JMR: 5'-GGCGTTGACCATCTATGACA-3') for detecting moaC genes of 57 members of Pseudomonas spp. retrieved from http://insilico.ehu.eus/database using in silico PCR (Polymerase Chain Reaction). The results showed that GMF-GMR primers could selectively amplify 271-bp in silico PCR products from 14 out of 57 members of Pseudomonas spp. tested. However, BLASTn analysis on these 14 amplified DNA sequences showed that they were not part of moaC, yet glpK gene fragment sequences. Meanwhile, the newly designed primers from moaC sequence of strain JG3, JMFJMR, could specifically amplify 214-bp in silico PCR products from 2 out of 57 members of Pseudomonas spp. matched to bacterial moaC gene fragment sequences. As conclusion, based on in silico study JMF-JMR primers are more specific than GMF-GMR ones for detecting moaC gene fragments of members of Pseudomonas spp. studied.