Genera specific distribution of DEAD-box RNA helicases in cyanobacteria

Abstract

Although RNA helicases are essentially ubiquitous and perform roles in all stages of RNA metabolism, phylogenetic analysis of the DEAD (Asp-Glu-Ala-Asp)-box RNA helicase family in a single phylum has not been performed. Here, we performed a phylogenetic analysis on DEAD-box helicases from all currently available cyanobacterial genomes, comprising a total of 362 helicase protein sequences from 280 strains. DEAD-box helicases belonging to three distinct clades were observed. Two clades, the CsdA (cold shock DEAD-box A)-like and RhlE (RNA helicase E)-like helicases, cluster with the homologous proteins from Escherichia coli . The third clade, the CrhR (cyanobacterial RNA helicase Redox)-like helicases, is unique to cyanobacteria and characterized by a conserved sequence motif in the C-terminal extension. Restricted distribution is observed across cyanobacterial diversity with respect to both helicase type and strain. CrhR-like and CsdA-like helicases essentially never occur together, while RhlE always occurs with either a CrhR-like or CsdA-like helicase. CrhR-like and RhlE-like proteins occurred in filamentous cyanobacteria of the orders Nostocales , Oscillatoriales and Synechococcales . Similarly, CsdA- and RhlE-like proteins are restricted to unicellular cyanobacteria of the genera Cyanobium and Synechococcus . In addition, the unexpected occurrence of RhlE in two Synechococcus strains suggests recent acquisition and evolutionary divergence. This study, therefore, raises physiological and evolutionary questions as to why DEAD-box RNA helicases encoded in cyanobacterial lineages display restricted distributions, suggesting niches that require either CrhR or CsdA RNA helicase activity but not both. Extensive conservation of gene synteny surrounding the previously described rimO–crhR operon is also observed, indicating a role in the maintenance of photosynthesis. The analysis provides insights into the evolution, origin and dissemination of sequences within a single gene family to yield divergent functional roles.

The temperature-regulated DEAD-box RNA helicase CrhR interactome: autoregulation and photosynthesis-related transcripts

“…PCC 6803 (from here: Synechocystis) encodes the DEAD-box RNA helicase CrhR, for cyanobacterial RNA helicase redox (Rosana et al, 2012a). As defined by a 50 amino acids sequence motif, CrhR is the archetype protein of a new clade within the DEAD-box RNA helicase family (Whitford et al, 2021). In contrast to the situation in plants and also in many other bacteria, CrhR (crhR/slr0083) is the only DEAD-box RNA helicase encoded in Synechocystis (Redder et al, 2015).…”

“Life is short, and art is long”: RNA degradation in cyanobacteria and model bacteria

“…For instance, E. coli and B. subtilis have five and four DEAD‐box proteins, respectively. Cyanobacteria usually have 1 to 3 genes encoding DEAD‐box helicases, except that Synechococcus PCC 7942 and a few other species have no such genes 157 . According to their sequence similarity, cyanobacterial DEAD‐box helicases have been classified into three groups: CsdA‐like, RhlE‐like, and CrhR‐like 157 .…”