A developmentally regulated Streptomyces endoribonuclease resembles ribonuclease E of Escherichia coli

Abstract

SummaryWe report that the Streptomyces species S. lividans and S. coelicolor, morphologically complex Grampositive soil bacteria, contain a developmentally regulated endoribonuclease activity (here named RNase ES) that functionally and immunologically resembles Escherichia coli RNase E. In Streptomyces cells, RNA I -the antisense repressor of replication of ColE1-type plasmids -is cleaved at sites attacked by RNase E. A Mg 2þ -dependent endonuclease that produces RNase E-like cleavages in RNA I and 9S ribosomal RNA was identified in S. lividans cell extracts. A Streptomyces peptide migrating at 70 kDa in SDS/polyacrylamide gels binds to RNase E substrates and reacts with three separate anti-RNase E monoclonal antibodies; the endonucleolytic cleavage activity co-purified with the immunoreactive 70 kDa peptide. We show that RNase ES activity is regulated during the Streptomyces life cycle: activity increased as cells progressed from exponential growth to stationary phase in liquid culture, or from mycelial growth to sporulation on solid media. While mutations that interfere with S. coelicolor development late in its life cycle did not prevent this developmentally associated increase in RNase ES activity, the increase was blocked by a mutation (bldA) that interferes early with both morphological and physiological differentiation.

Identification of the gene encoding the 5S ribosomal RNA maturase in Bacillus subtilis: Mature 5S rRNA is dispensable for ribosome function

“…The eubacterial kingdom is mostly split between those organisms that have RNase E or RNase EG and those that have RNase M5+ We have identified only a few organisms in the various databases that have neither type of enzyme and some, members of the clostridial family, that have both+ Most organisms that have RNase E have CafA/RNase G as well, whereas most of those with RNase EG have no other close homologs on their chromosomes+ Given the almost equal evolutionary distance between RNase EG and RNase E and RNase G, it is possible that the latter nucleases arose by duplication of the gene encoding RNase EG and subsequent divergent evolution+ Interestingly, none of the bacteria having an RNase EG enzyme, and some bacterial species that have RNase E, do not possess an obvious RNase T homolog to perform the trimming reaction+ Recent evidence has suggested that, in vitro at least, RNase E and RNase G have overlapping substrate specificity (Tock et al+, 2000)+ It thus seems likely that RNase EG will behave similarly+ Indeed, an enzyme that cleaves E. coli 9S rRNA with the same specificity as RNase E has been identified in Streptomyces coelicolor (Hagege & Cohen, 1997), a high G ϩ C Grampositive bacterium+ Its roughly equal homology to RNase E and RNase G suggests it is an RNase EG-type nuclease+ Curiously, however, although this protein is similar in size to E. coli RNase E, it is a central portion of the enzyme that shows homology to the N-terminal catalytic domain of RNase E+ A similar situation is found in the closely related bacterium, Mycobacterium tuberculosis+ Most eubacteria having neither RNase E nor RNase EG, that is, the low G ϩ C Gram-positive group and B. burgdorferi, have an rnmV gene instead+ RNase M5 activity has also been demonstrated in extracts of two other Bacillus strains, Bacillus Q and Bacillus licheniformis (Stiekema et al+, 1980a(Stiekema et al+, , 1980b)+ Why the low G ϩ C Gram-positive bacteria should have RNase M5 and high G ϩ C Gram-positive organisms, RNase EG, is not immediately obvious+…”

An Oligoribonuclease Gene in Streptomyces griseus

“…Little is known about RNA decay in members of Streptomyces with a complex life cycle, and only a few ribonucleases have been identified. RNase ES that resembles E. coli RNase E and is produced at a late stage in S. coelicolor A3(2) and S. lividans (10) and RNase III that is involved in actinorhodin production in S. coelicolor A3(2) (1, 25) are examples. Because of the complex life cycle of Streptomyces species, a variety of developmentally regulated ribonucleases are presumably present to degrade specific transcripts differentially during various growth stages.…”

Overexpression of the polynucleotide phosphorylase gene (pnp) of Streptomyces antibioticus affects mRNA stability and poly(A) tail length but not ppGpp levels

“…Three enzymes involved in RNA decay and processing have been identified in Streptomyces. An RNase E homologue has been found in Streptomyces coelicolor (Hagege & Cohen, 1997). RNase E is a single-strand-specific endoribonuclease which in E. coli is thought to be the key enzyme involved in the initiation of mRNA decay (Coburn & Mackie, 1999;Rauhut & Klug, 1999;Regnier & Arraiano, 2000).…”