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Comparative Genomics Analysis of Translational Frameshifting in Aerobic Cobalt Chelatase Genes

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Comparative Genomics Analysis of Translational Frameshifting in Aerobic Cobalt Chelatase Genes Comparative genomics analysis of translational frameshifting in aerobic cobalt chelatase genes Ivan Antonov Institute of Bioengineering, Research Centre of Biotechnology, RAS, Moscow, Russia, [email protected] Maria Zamkova Russian N.N.Blokhin Cancer Research Center, Moscow, Russia, [email protected] Cobalt chelatase CobNST is one of about 25 enzymes required for aerobic biosynthesis of cobalamin (vitamin B12) in prokaryotes. It has been shown that the large, medium and small subunits of this enzyme are encoded by the cobN, cobT and cobS genes, respectively [1]. A later computational study has revealed a number of prokaryotic genomes where the cobT and cobS genes are missing from the cobalamin biosynthesis pathway. Instead these genomes contain the chlD and chlI genes encoding the medium and small subunits of the magnesium chelatase chlIDH - the enzyme required for chlorophyll biosynthesis. Given the high similarity between the magnesium and cobalt chelatases, the authors have hypothesized that the products of the chlD and chlI genes can replace the missing subunits of the cobNST enzyme. Recently, we have discovered a functional programmed ribosomal frameshifting (PRF) signal located inside the cobT gene from diverse bacteria and archea that efficiently diverts translation to the -1 reading frame [3]. The goal of the present study is to determine the possible biological function of this conserved recoding event. For this purpose we performed a comparative genomics analysis of the PRF-utilization by the cobalt and magnesium chelatase genes from more than 1200 prokaryotic genomes. In total, there were 135 and 36 cobT genes with putative -1 and +1 frameshifting, respectively. Given the high similarity between the CobS protein and the N-terminal part of the CobT protein, we hypothesized that translational frameshifting may allow cobT mRNA to produce two cobaltochelatase subunits. Indeed, the phylogenetic analysis of proteobacteria revealed a strong correlation between the presence of the PRF signal in the cobT gene and the absence of a separate cobS gene in the genome. Particularly, the cobS gene is missing in the genome of the cobalamin synthesizing pathogenic bacteria P.aeruginosa while its cobT gene contains a typical -1 PRF signal. Thus, it may have a potential to produce the missing small chelatase subunit via premature termination of the cobT translation. Therefore, we describe yet another case where translational frameshifting allows mRNA to produce two different proteins. This mechanism is highly conserved and can be found in both archaea and bacteria. Our results may also provide some useful information to the evolution of chlorophyll and/or cobalamin biosynthesis pathways. We would like to thank Pavel Baranov and Mark Borodovsky for the important contributions to the original discovery of the PRF in the chelatase gene. This work was supported by the RFBR grant № 18-34-00589 to IA. References [1] Debussche L, Couder M, Thibaut D, Cameron B, Crouzet J, Blanche F. Assay, purification, and characterization of cobaltochelatase, a unique complex enzyme catalyzing cobalt insertion in hydrogenobyrinic acid a,c-diamide during coenzyme B12 biosynthesis in Pseudomonas denitrificans. J Bacteriol. 1992 Nov;174(22):7445-51. [2] Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J Biol Chem. 2003 Oct 17;278(42): 41148-59. [3] Antonov I, Coakley A, Atkins JF, Baranov PV, Borodovsky M. Identification of the nature of reading frame transitions observed in prokaryotic genomes. Nucleic Acids Res. 2013 Jul; 41(13):6514-30..
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