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Summary Understanding RNA processing and turnover requires knowledge of cleavages by major endoribonucleases within a living cell. We have employed TIER-seq (transiently inactivating an endoribonuclease followed by RNA-seq) to profile cleavage products of the essential endoribonuclease RNase E in Salmonella enterica. A dominating cleavage signature is the location of a uridine two nucleotides downstream in a single-stranded segment, which we rationalize structurally as a key recognition determinant that may favor RNase E catalysis. Our results suggest a prominent biogenesis pathway for bacterial regulatory small RNAs whereby RNase E acts together with the RNA chaperone Hfq to liberate stable 3′ fragments from various precursor RNAs. Recapitulating this process in vitro, Hfq guides RNase E cleavage of a representative small-RNA precursor for interaction with a mRNA target. In vivo, the processing is required for target regulation. Our findings reveal a general maturation mechanism for a major class of post-transcriptional regulators., Graphical Abstract, Highlights • TIER-seq precisely maps ∼22,000 endogenous RNase E cleavage sites in Salmonella • Consensus motif of RNase E reveals a 2-nt uridine ruler-and-cut mechanism • RNase E is a central component in both maturation and degradation of small RNAs • There is a general small-RNA biogenesis pathway requiring RNase E and Hfq, Chao et al. discover that the essential bacterial RNase E cleaves numerous transcripts at preferred sites by sensing uridine as a 2-nt ruler. RNase E processing of various precursor RNAs produces many small regulatory RNAs, constituting a major small-RNA biogenesis pathway in bacteria.

Small RNAs (sRNAs) from conserved noncoding genes are crucial regulators in bacterial signaling pathways but have remained elusive in the Cpx response to inner membrane stress. Here we report that an alternative biogenesis pathway releasing the conserved mRNA 3' UTR of stress chaperone CpxP as an ∼60-nt sRNA provides the noncoding arm of the Cpx response. This so-called CpxQ sRNA, generated by general mRNA decay through RNase E, acts as an Hfq-dependent repressor of multiple mRNAs encoding extracytoplasmic proteins. Both CpxQ and the Cpx pathway are required for cell survival under conditions of dissipation of membrane potential. Our discovery of CpxQ illustrates how the conversion of a transcribed 3' UTR into an sRNA doubles the output of a single mRNA to produce two factors with spatially segregated functions during inner membrane stress: a chaperone that targets problematic proteins in the periplasm and a regulatory RNA that dampens their synthesis in the cytosol.

The ubiquitous RNA-binding protein, Hfq, has been shown to be required for the fitness and virulence of an increasing number of bacterial pathogens. Mutants lacking Hfq are often sensitive to host defense mechanisms and highly attenuated in animal models, albeit there is considerable variation in both severity and extent of phenotypes. RNomics and deep sequencing (RNA-seq) approaches discovered the small RNA and mRNA targets of Hfq, and indicated that this protein might impact on the expression of up to 20% of all genes in some organisms, including genes of type 3 secretion systems. Hfq also facilitates post-transcriptional cross-talk between the core and variable genome regions of bacterial pathogens, and might help integrate horizontally acquired virulence genes into existing regulatory networks.

Thirty-eight cows in a herd were determined to be positive for bovine tuberculosis (TB). The bacterial isolation and characterization with multiplex PCR identified six Mycobacterium tuberculosis isolates. The Mycobacterium bovis and M. tuberculosis infection induced comparable pathology in cattle in both gross pathology and histopathology based on the qualitative assessment of the sampled lung tissues. The spoligotyping demonstrated that cow M. tuberculosis isolates belonged to Beijing family strains. Meanwhile, the isolates from tuberculosis patients hospitalized in the local hospitals were assessed. No M. bovis strains were identified in 186 human isolates. Eighty-two percent (153/186) of M. tuberculosis isolates were Beijing-family strains. The 12 loci MIRU genotyping revealed that the first three prevalent patterns were 2232-2517-3533, 2233-2517-3533, and 2223-2517-3533. The bovine M. tuberculosis isolates were the third dominant MIRU pattern. The further 16 loci MIRU-VNTR assay confirmed that the bovine M. tuberculosis strains shared the same pattern suggesting there was a common source causing cow infection and an epidemiological link between cow and human M. tuberculosis infection. On the other hand, the retrospective investigation for the past three years' cases of TB patients from local hospitals revealed 0.34% (17/5011) prevalence of M. bovis infection in local people. In conclusion, in TB high-burden countries like China where bovine and human TB coexists, the fact that cattle maintain both M. bovis and M. tuberculosis would be a potential challenge to both Stop TB Plan of humans and bovine TB eradication scheme.

To understand the nationwide seroprevalence of bovine herpesvirus type 1 (BoHV-1) infection of cows in China, 1344 sera of dairy cows from 29 provinces and 765 sera from 6 herds in Hubei province were collected with stratified random sampling. Another 483 sera from imported cows were included. The serum antibody was tested by BoHV-1 gG ELISA. The results demonstrated that the overall nationwide seroprevalence was 35.8% (481/1344), while the prevalence for individual province ranged from 12.1% to 77.8%. Although each province had positive samples, the prevalence was clustered in areas based on the cow population size. In Hubei Province, the overall seroprevalence was 22.2% (170/765) while the prevalence for individual farms varied greatly from 0.0% to 41.5%. The sera from imported cows had a moderate prevalence of 21.7% (105/483).