Phyletic distribution and conservation of the bacterial transcription termination factor Rho

Abstract

Transcription termination factor Rho is a ring-shaped, ATP-dependent molecular motor that targets hundreds of transcription units in Escherichia coli. Interest in Rho was renewed recently on the realization that this essential factor is involved in multiple interactions and cellular processes that protect the E. coli genome and regulate its expression on a global scale. Yet it is currently unknown if (and how) Rho-dependent mechanisms are conserved throughout the bacterial kingdom. Here, we mined public databases to assess the distribution, expression and structural conservation of Rho across bacterial phyla. We found that rho is present in more than 90 % of sequenced bacterial genomes, although Cyanobacteria, Mollicutes and a fraction of Firmicutes are totally devoid of rho. Genomes lacking rho tend to be small and AT-rich and often belong to species with parasitic/symbiotic lifestyles (such as Mollicutes). By contrast, large GCrich genomes, such as those of Actinobacteria, often contain rho duplicates and/or encode Rho proteins that bear insertion domains of unknown function(s). Notwithstanding, most Rho sequences across taxa contain canonical RNA-binding and ATP hydrolysis signature motifs, a feature suggestive of largely conserved mechanism(s) of action. Mutations that impair binding of bicyclomycin are present in~5 % of rho sequences, implying that species from diverse ecosystems have developed resistance against this natural antibiotic. Altogether, these findings assert that Rho function is widespread among bacteria and suggest that it plays a particularly relevant role in the expression of complex genomes and/or bacterial adaptation to changing environments.

Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death

“…In addition, approximately a third of Rho proteins, including Rho from M. tuberculosis , contain a large extra N-terminal sequence of unknown function40. The first experiments that analysed transcription termination by M. tuberculosis Rho suggested it to not require ATP hydrolysis to terminate transcription41.…”

Mycobacterium tuberculosis Rho Is an NTPase with Distinct Kinetic Properties and a Novel RNA-Binding Subdomain

“…However, the E. coli AMO14 competent cells, transformed with pTrc99C- mtbrho , showed no growth at non-permissive temperature (Figure 6A) [22]. Since the presence of the N-terminal subdomain makes MtbRho a larger protein (602residues) than EcRho (419residues) (Figure S1B) [21], [43], it seemed plausible that this additional region of MtbRho could be a hindrance to complementation. However, a deletant of the MtbRho gene which lacked the 158-amino acid region (residues 87–241) also failed to complement(data not shown).…”

“…Several studies on EcRho have unraveled the biochemical and structural basis for its preference for C-rich RNA [15], [16], [17], [18], [19], [20]. However, in spite of its key cellular role and its presence in a large number of diverse bacterial families [21], very few Rho homologs have been studied. Characterization of the properties and understanding Rho-mediated termination is of paramount importance in organisms such as Mycobacterium tuberculosis ( Mtb ) [22] which is the causative agent of the number-one killer disease worldwide.…”

“…Notably, sequence analysis showed that the Rho homologs in Mycobacterium species and other actinobacteria are larger than EcRho mainly due to an ‘extra-stretch’ of ∼150–200 residues in their RNA-binding domains [5], [7], [21], [22], [42], [43]. In this manuscript, we present results demonstrating that purified M. tuberculosis Rho (MtbRho) can hydrolyse purine nucleoside triphosphates(NTP) – ATP and GTP-in presence of mycobacterial RNA.…”

NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble

“…NusG and its paralog RfaH have also been proposed to mediate transcription-translation coupling via direct contacts with S10 (Burmann et al., 2010, Burmann and Rösch, 2011). However, the CTD contacts are not universally conserved: Rho is absent in eukaryotes and even some Bacteria (D’Heygère et al, 2013), whereas S10 and RNAP are separated by a nuclear membrane in eukaryotes, where CTD interacts with proteins involved in splicing, polyadenylation, and other RNA processing pathways.…”