This indicates that the operon cluster could be a remnant of a primordial operon cluster encoding the full transcriptional and translational machinery. 2014), three of the five translation initiation and elongation factors (IF-1, EF-Tu, and EF-G) ( Ramakrishnan 2002), and two subunits of the Sec translocase ( du Plessis et al. 1999), up to 31 out of the 33 universal ribosomal proteins ( Ban et al. The potential ancestral operon cluster included the genes encoding the main subunits of the RNA polymerase (RpoA, RpoB, and RpoC) ( Zhang et al. At least part of this operon cluster is similarly organized in archaea indicating that it might have been present in the last common ancestor of bacteria and archaea ( Coenye and Vandamme 2005). In the Proteobacteria, this cluster is ∼33 kb long and contains seven operons ( tufB, secE, rpoBC, str, S10, spc, and alpha) that encode up to 50 genes of the transcriptional and translational machinery (precise numbers vary between species) and operon concatenation is maintained due to operon coregulation ( Brandis et al. 2001 Coenye and Vandamme 2005 Brandis et al. 1997 Wachtershauser 1998 Barloy-Hubler et al. Conservation on a higher order, operon synteny, is virtually absent in bacteria ( Tamames 2001).Ī prominent exception to this rule is the secE- rpoBC- str- S10- spc- alpha operon cluster ( Watanabe et al. These genes are generally organized within operons and gene synteny could be driven by selection for coregulation and/or the ability of horizontal transfer of fully functional units ( Moreno-Hagelsieb et al. This higher degree of synteny has been used to identify functional groups of genes, to supplement traditional phylogenetic analysis methods, and to reconstruct the organization of ancestral genomes ( Overbeek et al. Despite this general trend there are a few genes that display a significant degree of synteny across the bacterial domain of life which suggests that this gene order was present in at least the last common ancestor of all bacteria. As life evolved, the order of genes on the chromosome changed over time until selection, genetic drift and horizontal gene transfer (HGT) removed almost all traces of the last common gene order from modern chromosomes ( Koonin et al. It is generally accepted that all life on earth has evolved from a universal common ancestor which would entail that all life forms share a single ancestral gene order ( Woese 2000 Koonin 2003, 2014 Forterre 2015 Booth et al. The analysis of the alternation events indicates that segmental genome duplications and/or transposon-directed recombination play a crucial role in rearrangements of the operon cluster.
This indicates the recurrence of relaxed selection on the gene order within bacterial chromosomes. While there is a general trend for loss of gene synteny over time, there are examples of increased alteration rates at specific branch points or within specific bacterial orders.
Initially, a small number of genes is inserted between the operons breaking the concatenation followed by a second event that fully disconnects the operons. Further examination showed that the process of disconnecting two operons generally follows the same pattern. A total of 163 independent evolutionary events were identified in which the operon cluster was altered. Using 204 whole genome sequences, ∼2 Gy of evolution of the operon cluster were reconstructed back to the last common ancestors of the Gammaproteobacteria and of the Bacilli. Previous studies have indicated that at least part of this operon cluster might have been present in the last common ancestor of bacteria and archaea. A prominent exception to this rule is a >40 kb long cluster of five core operons ( secE- rpoBC- str- S10- spc- alpha) and three variable adjacent operons ( cysS, tufB, and ecf) that together contain 57 genes of the transcriptional and translational machinery. Closely related species can have almost no conservation in long-range gene order. The evolution of gene order rearrangements within bacterial chromosomes is a fast process.
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