NLM DIR Seminar Schedule

Abstract:

The 2021 release of the COG database, https://www.ncbi.nlm.nih.gov/research/COG, covers 1,309 complete prokaryotic genomes, usually with a single genome per bacterial or archaeal genus. One of the most useful features of the COGs is the availability of COG-specific patterns of the gene presence/absence, which allows straightforward identification of the genomes that do not encode the selected gene. We have used this feature to examine the distribution of the ribosomal genes in bacterial and archaeal genomes and the conservation of sporulation genes among various lineages of the Firmicutes. While some genes turned out to be missing because of the problems in genome sequencing, assembly, and gene calling, these studies allowed us to compile the lists of essential and auxiliary components of the ribosomal and sporulation machineries. Similar approaches were used to analyze cell division genes in planctomycetes and c-di-AMP- and c-di-GMP-related proteins, including c-di-GMP receptors with PilZ and MshEN domains. We also used them in the characterization of two emerging pathogens. One of them, Shewanella algae, an opportunistic pathogen that causes skin and soft tissue infections, was found to encode several c-di-GMP-related enzymes with novel N-terminal sensor domains. Another one, Paenibacillus thiaminolyticus, was isolated in the cases of neonatal sepsis and postinfectious hydrocephalus in newborns in Mbale, Uganda. Genomic sequencing of the P. thiaminolyticus type strain and the clinical isolates showed that the pathogenic strains carried several mobile genetic elements, including potential prophages. One of these elements included an operon encoding type IV pili, whose production was subsequently shown to be an important virulence factor and predicted to be regulated by c-di-GMP. Further characterization of the signaling systems of these pathogens could pave the way to controlling their virulence and biofilm formation. Based on PMIDs 33167031, 33753464, 35638784, 31740763, 32095817, 32472931, 34928179, 31740493, 34351223, 35311563, 32273361, 32998967, 30187651, and 33356690.