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• 1. [Article] Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution

  Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We ...

  Citation × Citation Citation Abstract Copy Title: Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution Author: Kacharia, Fenil R., Millar, Jess A., Raghavan, Rahul Year: 2017 Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks. Furthermore, it has previously been difficult to trace the evolutionary histories of sRNAs because rapid evolution obscures their original sources. We overcame this challenge by identifying a recently evolved sRNA in Escherichia coli, which allowed us to determine that novel sRNAs could emerge from vestigial bacteriophage genes, the first known source for sRNA origination. Title: Emergence of New sRNAs in Enteric Bacteria is Associated with Low Expression and Rapid Evolution Author: Kacharia, Fenil R., Millar, Jess A., Raghavan, Rahul Year: 2017 Non-coding small RNAs (sRNAs) are critical to post-transcriptional gene regulation in bacteria. However, unlike for protein-coding genes, the evolutionary forces that shape sRNAs are not understood. We investigated sRNAs in enteric bacteria and discovered that recently emerged sRNAs evolve at significantly faster rates than older sRNAs. Concomitantly, younger sRNAs are expressed at significantly lower levels than older sRNAs. This process could potentially facilitate the integration of newly emerged sRNAs into bacterial regulatory networks. Furthermore, it has previously been difficult to trace the evolutionary histories of sRNAs because rapid evolution obscures their original sources. We overcame this challenge by identifying a recently evolved sRNA in Escherichia coli, which allowed us to determine that novel sRNAs could emerge from vestigial bacteriophage genes, the first known source for sRNA origination. Close

• 2. [Article] Genome Rearrangements Can Make and Break Small RNA Genes

  Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are ...

  Citation × Citation Citation Abstract Copy Title: Genome Rearrangements Can Make and Break Small RNA Genes Author: Raghavan, Rahul, Kacharia, Fenil R., Millar, Jess A, Sislak, Christine Demko, Ochman, Howard Year: 2015 Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are conserved among enteric bacteria, but because of the regulatory roles of sRNAs, differences in sRNA repertoires might be responsible for features that differentiate closely related species. We scanned the E. coli MG1655 and Salmonella enterica Typhimurium genomes for nonsyntenic IGRs as a potential source of uncharacterized, species-specific sRNAs and found that genome rearrangements have reconfigured several IGRs causing the disruption and formation of sRNAs. Within an IGR that is present in E. coli but was disrupted in Salmonella by a translocation event is an sRNA that is associated with the FNR/CRP global regulators and influences E. coli biofilm formation. A Salmonella-specific sRNA evolved de novo through point mutations that generated a σ70 promoter sequence in an IGR that arose through genome rearrangement events. The differences in the sRNA pools among bacterial species have previously been ascribed to duplication, deletion, or horizontal acquisition. Here, we show that genomic rearrangements also contribute to this process by either disrupting sRNA-containing IGRs or creating IGRs in which novel sRNAs may evolve. Title: Genome Rearrangements Can Make and Break Small RNA Genes Author: Raghavan, Rahul, Kacharia, Fenil R., Millar, Jess A, Sislak, Christine Demko, Ochman, Howard Year: 2015 Small RNAs (sRNAs) are short, transcribed regulatory elements that are typically encoded in the intergenic regions (IGRs) of bacterial genomes. Several sRNAs, first recognized in Escherichia coli, are conserved among enteric bacteria, but because of the regulatory roles of sRNAs, differences in sRNA repertoires might be responsible for features that differentiate closely related species. We scanned the E. coli MG1655 and Salmonella enterica Typhimurium genomes for nonsyntenic IGRs as a potential source of uncharacterized, species-specific sRNAs and found that genome rearrangements have reconfigured several IGRs causing the disruption and formation of sRNAs. Within an IGR that is present in E. coli but was disrupted in Salmonella by a translocation event is an sRNA that is associated with the FNR/CRP global regulators and influences E. coli biofilm formation. A Salmonella-specific sRNA evolved de novo through point mutations that generated a σ70 promoter sequence in an IGR that arose through genome rearrangement events. The differences in the sRNA pools among bacterial species have previously been ascribed to duplication, deletion, or horizontal acquisition. Here, we show that genomic rearrangements also contribute to this process by either disrupting sRNA-containing IGRs or creating IGRs in which novel sRNAs may evolve. Close