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Diversification of the Rho transcription termination factor in bacteria

Affiliations
  • 1Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand.
  • 2Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA.
  • 3Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY 12222, USA.
  • 4Genetics Otago, University of Otago, Dunedin, Otago 9054, New Zealand.

Published on:

July 5, 2024

Abstract

Correct termination of transcription is essential for gene expression. In bacteria, factor-dependent termination relies on the Rho factor, that classically has three conserved domains. Some bacteria also have a functional insertion region. However, the variation in Rho structure among bacteria has not been analyzed in detail. This study determines the distribution, sequence conservation, and predicted features of Rho factors with diverse domain architectures by analyzing 2730 bacterial genomes. About half (49.8%) of the species analyzed have the typical Escherichia coli like Rho while most of the other species (39.8%) have diverse, atypical forms of Rho. Besides conservation of the main domains, we describe a duplicated RNA-binding domain present in specific species and novel variations in the bicyclomycin binding pocket. The additional regions observed in Rho proteins exhibit remarkable diversity. Commonly, however, they have exceptional amino acid compositions and are predicted to be intrinsically disordered, to undergo phase separation, or have prion-like behavior. Phase separation has recently been shown to play roles in Rho function and bacterial fitness during harsh conditions in one species and this study suggests a more widespread role. In conclusion, diverse atypical Rho factors are broadly distributed among bacteria, suggesting additional cellular roles.

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