The E. coli RhlE RNA helicase regulates the function of related RNA helicases during ribosome assembly

Abstract

Escherichia coli contains five members of the DEAD-box RNA helicase family, a ubiquitous class of proteins characterized by their ability to unwind RNA duplexes. Although four of these proteins have been implicated in RNA turnover or ribosome biogenesis, no cellular function for the RhlE DEAD-box protein has been described as yet. During an analysis of the coldsensitive growth defect of a strain lacking the DeaD/CsdA RNA helicase, rhlE plasmids were identified from a chromosomal library as multicopy suppressors of the growth defect. Remarkably, when tested for allele specificity, RhlE overproduction was found to exacerbate the cold-sensitive growth defect of a strain that lacks the SrmB RNA helicase. Moreover, the absence of RhlE exacerbated or alleviated the cold-sensitive defect of deaD or srmB strains, respectively. Primer extension and ribosome analysis indicated that RhlE regulates the accumulation of immature ribosomal RNA or ribosome precursors when deaD or srmB strains are grown at low temperatures. By using an epitope-tagged version of RhlE, the majority of RhlE in cell extracts was found to cosediment with ribosome-containing fractions. Since both DeaD and SrmB have been recently shown to function in ribosome assembly, these findings suggests that rhlE genetically interacts with srmB and deaD to modulate their function during ribosome maturation. On the basis of the available evidence, I propose that RhlE is a novel ribosome assembly factor, which plays a role in the interconversion of ribosomal RNA-folding intermediates that are further processed by DeaD or SrmB during ribosome maturation.

Functional and molecular analysis of Escherichia coli strains lacking multiple DEAD-box helicases

“…Cells were lysed by sonication, and ribosome profiles were generated by sucrose density gradient ultracentrifugation, as described previously (Jain 2008). Each ribosome profile experiment was repeated three to eight times.…”

“…SrmB and DeaD are implicated in ribosome biogenesis as assembly factors and the absence of either confers (Charollais et al 2003(Charollais et al , 2004. No role for RhlE has been established, though it was recently shown to modulate the function of SrmB and DeaD (Jain 2008).…”

DEAD-Box RNA Helicases in Gram-Positive RNA Decay

“…Finally, RhlE is the least-characterized RNA helicase in E. coli. Genetic data indicate that RhlE might be involved in ribosome biogenesis together with CsdA and SrmB ( Jain, 2008). Other data show that RhlE is also able to associate with the degradosome (Khemici et al, 2004).…”

Time course of large ribosomal subunit assembly in E. coli cells overexpressing a helicase inactive DbpA protein

“…In order to fulfill the cell's demand for new proteins and to avoid wasting valuable cellular energy, ribosome assembly needs to occur rapidly and accurately. To ensure this, cells use a number of different protein and RNA maturation factors (El Hage et al 2001;Charollais et al 2003Charollais et al , 2004El Hage and Alix 2004;Jain 2008). One class of RNA maturation factors used by the cell during ribosome assembly is DEAD-box RNA helicases (Cordin et al 2006;Linder 2006;Pyle 2008;Pan and Russell 2010;Shajani et al 2011;Henn et al 2012;Putnam and Jankowsky 2013).…”

“…In vivo, this unwinding activity is believed to facilitate RNA structural rearrangements during the ribosome assembly process (Shajani et al 2011). E. coli contains five DEAD-box RNA helicases, with four of them (SrmB, DeaD, RhlE, and DbpA) involved in ribosome assembly (Iost and Dreyfus 2006;Jain 2008;Iost et al 2013).…”