The Metallo-β-Lactamase Family of Ribonucleases

Homologs of Phycobilisome Abundance Regulator PsoR Are Widespread across Cyanobacteria

During chromatic acclimation (CA), cyanobacteria undergo shifts in their physiology and metabolism in response to changes in their light environment. Various forms of CA, which involves the tuning of light-harvesting accessory complexes known as phycobilisomes (PBS) in response to distinct wavelengths of light, have been recognized. Recently, a negative regulator of PBS abundance, PsoR, about which little was known, was identified. We used sequence analyses and bioinformatics to predict the role of PsoR in cyanobacteria and PBS regulation and to examine its presence in a diverse range of cyanobacteria. PsoR has sequence similarities to the β-CASP family of proteins involved in DNA and RNA processing. PsoR is a putative nuclease widespread across Cyanobacteria, of which over 700 homologs have been observed. Promoter analysis suggested that psoR is co-transcribed with upstream gene tcpA. Multiple transcription factors involved in global gene regulation and stress responses were predicted to bind to the psoR-tcpA promoter. The predicted protein–protein interactions with PsoR homologs included proteins involved in DNA and RNA metabolism, as well as a phycocyanin-associated protein predicted to interact with PsoR from Fremyella diplosiphon (FdPsoR). The widespread presence of PsoR homologs in Cyanobacteria and their ties to DNA- and RNA-metabolizing proteins indicated a potentially unique role for PsoR in CA and PBS abundance regulation.

Tips and tricks to probe the RNA-degrading activities of hyperthermophilic archaeal β-CASP ribonucleases

The importance of ribonucleases in posttranscriptional control of gene expression has been established in Eukarya and Bacteria for over a decade. However, this process has been overlooked in Archaea, which are of universal importance to elucidate fundamental biological mechanisms and to study the evolution of life on Earth. Very few ribonucleolytic activities have been reported in Archaea, and RNA metabolism pathways wait to be described. Recently we have identified two major groups of archaeal ribonucleases, aCPSF1 and aRNase J, which are members of the β-CASP metallo-β-lactamase family. Here, we describe in vitro methods to characterize the endo- and exoribonucleolytic activities of hyperthermophilic archaeal β-CASP ribonucleases. The use of various labeled RNA substrates allows defining the specificity of RNA cleavage and the directionality of the exoribonucleolytic trimming activity of the archaeal enzymes which work at high temperature. Elucidating in vitro ribonucleolytic activities is one step toward the understanding of the role of β-CASP ribonucleases in RNA metabolism pathways in archaeal cells.

Bacillus subtilis mutants with knockouts of the genes encoding ribonucleases RNase Y and RNase J1 are viable, with major defects in cell morphology, sporulation, and competence

The genes encoding the ribonucleases RNase J1 and RNase Y have long been considered essential for Bacillus subtilis cell viability, even before there was concrete knowledge of their function as two of the most important enzymes for RNA turnover in this organism. Here we show that this characterization is incorrect and that ΔrnjA and Δrny mutants are both viable. As expected, both strains grow relatively slowly, with doubling times in the hour range in rich medium. Knockout mutants have major defects in their sporulation and competence development programs. Both mutants are hypersensitive to a wide range of antibiotics and have dramatic alterations to their cell morphologies, suggestive of cell envelope defects. Indeed, RNase Y mutants are significantly smaller in diameter than wild-type strains and have a very disordered peptidoglycan layer. Strains lacking RNase J1 form long filaments in tight spirals, reminiscent of mutants of the actin-like proteins (Mre) involved in cell shape determination. Finally, we combined the rnjA and rny mutations with mutations in other components of the degradation machinery and show that many of these strains are also viable. The implications for the two known RNA degradation pathways of B. subtilis are discussed.