A conserved Histophilus somni 23S intervening sequence yields functional, fragmented 23S rRNA

Authors: Harhay, Gregory; Harhay, Dayna; Brader, Kerry; Smith, Timothy - Tim

Submitted to: Microbiology Spectrum
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/12/2021
Publication Date: 12/1/2021
Citation: Harhay, G.P., Harhay, D.M., Brader, K.D., Smith, T.P.L. 2021. A conserved Histophilus somni 23S intervening sequence yields functional, fragmented 23S rRNA. Microbiology Spectrum. 9(3). Article e0143121. https://doi.org/10.1128/Spectrum.01431-21.
DOI: https://doi.org/10.1128/Spectrum.01431-21

Interpretive Summary: Histophilus somni is a bacterial pathogen causing disease in respiratory, reproductive, cardiac, and other tissues affecting cattle health and wellbeing worldwide. This pathogen contributes to bovine respiratory disease complex, the primary driver for the theraputic use of antibiotics in livestock production systems. Because this pathogen is widespread, it has a significant economic impact on the cattle industry when production losses and treatments are considered. To develop rational treatment strategies that reduce antibiotic use, improve animal health and wellbeing, and reduce the pathogen’s economic impact on the cattle industry, veterinary practitioners require a better understanding of Histophilus somni biology. In this study, we show for the first time that a component of this pathogen’s protein-synthesizing machinery is unusually fragmented in two pieces, with a central portion of the intact component cut out. It is unknown if this fragmentation affects the pathogen’s ability to cause disease in single or multiple tissues. More generally, it is unknown how this fragmentation affects the pathogen’s biology. However, new hypotheses can be formulated to control the pathogen considering this newly discovered fragmentation of a component of its protein-synthesizing machinery.

Technical Abstract: Histophilus somni is a Gram-negative bacterial organism that acts as an opportunistic pathogen and is a fastidious member of the Pasteurellaceae family associated with diseases of respiratory, reproductive, cardiac, and other tissues of ruminants. We identified an intervening sequence (IVS) embedded in all five copies of the 23S rRNA gene in the closed genome sequence of the H. somni isolate USDA-ARS-USMARC-63250 that may play an important role in affecting the biology of the organism. Sequencing the RNA from this isolate shows that most of the IVS is cleaved from the transcript, resulting in independent fragments of this structural rRNA that remain functional within the bacterial ribosome. The IVS lies between positions 1170 and 1278 bp of the 3,017-bp gene and exhibits self-complementarity between its 5' and 3' ends that predicts a stem-loop structure interrupting helix-45 in the transcribed 23S rRNA. Excision removes a 94-nucleotide (nt) stem-loop structure that displays an unusual 1-nt 3' end overhang instead of the more typical 2-nt overhang commonly observed at the ends of other excised IVS stem-loops. A comparison with genomes of other H. somni isolates indicates that this IVS is highly conserved, with 31 of 32 complete genomes having similar interruptions of canonical 23S rRNA genes. The potential biological effects of either the released IVS or the fragmentation of the functional 23S rRNA are unknown, but fragmentation may enhance rRNA degradation in ways that contribute to the regulation of gene expression. IMPORTANCE The genome biology underlying H. somni virulence, pathogenicity, environmental adaptability, and broad tissue tropism is understood poorly. We identified a novel H. somni 109-nt IVS stem-loop structure, of which the central portion is excised from the 23S rRNA transcript, resulting in the fragmentation of this rRNA in the H. somni isolate USDA-ARS-USMARC-63250 and the release of a 94-nt structured RNA of unknown function. We determined that this peculiar rRNA biology is widespread among sequenced H. somni isolates, suggesting it has importance to organism biology. The fragmented 23S rRNA molecules remain functional in the ribosome, given that the isolate grows in culture. The structured excised portion of the IVS, presumably due to the action of the endoribonuclease III, has an unusual 1-nt 3' end overhang. This newly discovered H. somni 23S rRNA fragmentation may enhance rRNA degradation providing a previously unrecognized avenue for regulating H. somni biological processes.