RtcB is involved in transfer RNA (tRNA) splicing in archaeal and eukaryotic organisms. However, most RtcBs are found in bacteria, whose tRNAs have no introns. Because tRNAs are the substrates of archaeal and eukaryotic RtcB, it is assumed that bacterial RtcBs are for repair of damaged tRNAs. Here, we show that a subset of bacterial RtcB, denoted RtcB2 herein, specifically repair ribosomal damage in the decoding center. To access the damage site for repair, however, the damaged 70S ribosome needs to be dismantled first, and this is accomplished by bacterial PrfH. Peptide-release assays revealed that PrfH is only active with the damaged 70S ribosome but not with the intact one. A 2.55-Å cryo-electron microscopy structure of PrfH in complex with the damaged 70S ribosome provides molecular insight into PrfH discriminating between the damaged and the intact ribosomes via specific recognition of the cleaved 3′-terminal nucleotide. RNA repair assays demonstrated that RtcB2 efficiently repairs the damaged 30S ribosomal subunit but not the damaged tRNAs. Cell-based assays showed that the RtcB2–PrfH pair reverse the damage inflicted by ribosome-specific ribotoxins in vivo. Thus, our combined biochemical, structural, and cell-based studies have uncovered a bacterial defense system specifically evolved to reverse the lethal ribosomal damage in the decoding center for cell survival.

In bacteria, rescue of stalled ribosomes due to 3′-truncated mRNAs is carried out by the ubiquitous trans-translation system as well as alternative ribosome-rescue factors such as ArfA and ArfB. It is unclear, however, how the stalled ribosomes caused by ribosomal damages are rescued. Here, we report that a bacterial system composed of PrfH and RtcB not only rescues a stalled ribosome resulting from a specific damage in the decoding center but also repairs the damage afterwards. Peptide release assays reveal that PrfH is only active with the damaged ribosome, but not with the intact one. A 2.55-angstrom cryo-EM structure of PrfH in complex with the damaged 70S ribosome provides molecular insight into specific recognition of the damage site by PrfH. RNA repair assays demonstrate that PrfH-coupled RtcB efficiently repairs the damaged 30S ribosomal subunit, but not the damaged tRNAs. Thus, our studies have uncovered a biological operation by a pair of bacterial enzymes, aiming to reverse the potentially lethal damage inflicted by an invading ribotoxin for cell survival.

Lignin is a complex natural polysaccharide primarily present in secondary wood or secondary xylem and phloem elements of the plant body. It constitutes one-fourth to one-third of the dry mass of wood and also, provides rigidity and strength. Lignin lacks a defined primary structure and is a heterogeneous biopolymer. Lignin-degradation is a major challenge because it can be a potential source of edible polysaccharide including glucose. In this investigation, commercial coir was considered as the source of isolating lignin-degrading fungus. A simple bioassay was carried out in coconut fibre (coir) and wood. In case of the fungal sample, the coir was inoculated in dry and wet conditions which resulted in 5.63% and 48.35% degradation respectively. On the basis of this, different lignin-degrading enzymes were assayed and purified. The fungus was identified as Microascus sp. on the basis of colony morphology, spore structure and perithecium formation. Further studies were conducted on the degraded coir and scanning electron microscope (SEM) images were taken. In future, these organisms can be a potential source of ligninolytic enzymes useful in different activities.