Abstract
When bacteria diverge, they need to adapt to the new environments, such as new hosts or different tissues of the same host, by accumulating beneficial genomic variations, but a general scenario is unknown due to the lack of appropriate methods. Here we profiled the ACTAGT sequence and its degenerated forms (i.e., hexa-nucleotide sequences with one of the six nucleotides different from ACTAGT) in Salmonella to estimate the nucleotide amelioration processes of bacterial genomes. ACTAGT was mostly located in coding sequences but was also found in several intergenic regions, with its degenerated forms widely scattered throughout the bacterial genomes. We speculated that the distribution of ACTAGT and its degenerated forms might be lineage-specific as a consequence of different selection pressures imposed on ACTAGT at different genomic locations (in genes or intergenic regions) among different Salmonella lineages. To validate this speculation, we modelled the secondary structures of the ACTAGT-containing sequences conserved across Salmonella and many other enteric bacteria. Compared to ACTAGT at conserved regions, the degenerated forms were distributed throughout the bacterial genomes, with the degeneration patterns being highly similar among bacteria of the same phylogenetic lineage but radically different across different lineages. This finding demonstrates biased amelioration under distinct selection pressures among the bacteria and provides insights into genomic evolution during bacterial divergence.
Highlights
Bacteria constantly accumulate genomic changes to become increasingly better fit to the changing environment, such as in acquiring new capabilities to exploit nature for available resources, including laterally transferred DNA (LTD, e.g., prophages, genomic islands, etc.) and nucleotide variations (NVs, e.g., base substitutions, short insertion or deletions, etc.)
Whereas the XbaI cleavage sequence patterns, profiled by either bioinformatics[15] or pulsed field gel electrophoresis (PFGE) analysis[16, 17], are lineage-specific among Salmonella as a result of independent divergence of the ancestral CTAG sequences, information provided by XbaI profiling is limited due to the facts that several XbaI cleavage sites are normally methylated and so are not cleavable by the XbaI enzyme[17] and that several cleavage sites are located within rrn operons and so are often translocated or even removed when the genome is rearranged by recombination between rrn genes[2, 3, 18, 19]
We first profiled the ACTAGT sequences in S. typhimurium LT2 and identified their counterparts in other representative strains of Salmonella and E. coli K12; in addition, we profiled the degenerated forms of ACTAGT in the compared genomes based on their homology to the ACTAGT sequences in S. typhimurium LT2 (Supplementary Table 1)
Summary
Bacteria constantly accumulate genomic changes to become increasingly better fit to the changing environment, such as in acquiring new capabilities to exploit nature for available resources, including laterally transferred DNA (LTD, e.g., prophages, genomic islands, etc.) and nucleotide variations (NVs, e.g., base substitutions, short insertion or deletions, etc.). Novel and effective approaches are needed to systematically analyze NVs and reveal general patterns of nucleotide divergence between biologically different bacterial relatives. To look into this issue, we have recently profiled evolutionarily conserved short genomic sequences and inspected their degeneration patterns among closely related bacteria. We profiled the SpeI cleavage sequence ACTAGT and its degenerated forms in the genome of representative Salmonella lineages to obtain a snapshot of the genome optimization processes through NV during bacterial evolution. A very special finding is that some degenerated forms of ACTAGT were highly conserved, pointing to an adaptive nucleotide substitution event, in which an alternative nucleotide replaces one of the six nucleotides ACTAGT, maintaining the function and in the meantime minimizing the number of the CTAG sequence in the genome, toward an optimal genome construction
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