Post-transcriptional gene regulation (PTGR) concerns processes involved in the maturation, transport, stability and translation of coding and non-coding RNAs. RNA-binding proteins (RBPs) and ribonucleoproteins coordinate RNA processing and PTGR. The introduction of large-scale quantitative methods, such as next-generation sequencing and modern protein mass spectrometry, has renewed interest in the investigation of PTGR and the protein factors involved at a systems-biology level. Here, we present a census of 1,542 manually curated RBPs that we have analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression. Our analysis is a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism.

/pdf/a-census-of-human-rna-binding-proteins-1mii7pfs5y.pdf

A census of human RNA-binding proteins.

https://www.cell.com/cell/pdf/S0092-8674(05)00442-3.pdf

RNA degradation by the exosome is promoted by a nuclear polyadenylation complex

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli

The synthesis of ribosomes is one of the major metabolic pathways in all cells. In addition to around 75 individual ribosomal proteins and 4 ribosomal RNAs, synthesis of a functional eukaryotic ribosome requires a remarkable number of trans-acting factors. Here, we will discuss the recent, and often surprising, advances in our understanding of ribosome synthesis in the yeast Saccharomyces cerevisiae. These will underscore the unexpected complexity of eukaryotic ribosome synthesis.

Ribosome synthesis in Saccharomyces cerevisiae.

tRNA biology has come of age, revealing an unprecedented level of understanding and many unexpected discoveries along the way. This review highlights new findings on the diverse pathways of tRNA maturation, and on the formation and function of a number of modifications. Topics of special focus include the regulation of tRNA biosynthesis, quality control tRNA turnover mechanisms, widespread tRNA cleavage pathways activated in response to stress and other growth conditions, emerging evidence of signaling pathways involving tRNA and cleavage fragments, and the sophisticated intracellular tRNA trafficking that occurs during and after biosynthesis.

/pdf/trna-biology-charges-to-the-front-4a28s6q74p.pdf

tRNA biology charges to the front

In Escherichia coli , rRNA operons are transcribed as 30S precursor molecules that must be extensively processed to generate mature 16S, 23S and 5S rRNA. While it is known that RNase III cleaves the primary transcript to separate the individual rRNAs, there is little information about the secondary processing reactions needed to form their mature 3′ and 5′ termini. We have now found that inactivation of the endoribonuclease RNase E slows down in vivo maturation of 16S RNA from the 17S RNase III cleavage product. Moreover, in the absence of CafA protein, a homolog of RNase E, formation of 16S RNA also slows down, but in this case a 16.3S intermediate accumulates. When both RNase E and CafA are inactivated, 5′ maturation of 16S rRNA is completely blocked. In contrast, 3′ maturation is essentially unaffected. The 5′ unprocessed precursor that accumulates in the double mutant can be assembled into 30S and 70S ribosomes. Precursors also can be processed in vitro by RNase E and CafA. These data indicate that both RNase E and CafA protein are required for a two step, sequential maturation of the 5′ end of 16S rRNA, and that CafA protein is a new ribonuclease. We propose that it be renamed RNase G.

/pdf/rnase-g-cafa-protein-and-rnase-e-are-both-required-for-the-5-2vruniapmx.pdf

RNase G (CafA protein) and RNase E are both required for the 5′ maturation of 16S ribosomal RNA

Conversion of tRNA precursors to their mature forms requires the action of both endo- and exoribonucleases. Although studies over many years identified the endoribonuclease, RNase P, and several exoribonucleases as the enzymes responsible for generating the mature 5' and 3' termini, respectively, of Escherichia coli tRNAs, relatively little is known about how tRNAs are separated from long multimeric or multifunction transcripts, or from long leader and trailer sequences. To examine this question, the tRNA products that accumulate in mutant strains devoid of multiple exoribonucleases plus one or several endoribonucleases were analyzed by northern analysis. We find that the multifunction tyrT transcript, which contains two tRNA(Tyr)1 sequences separated by a 209-nt spacer region plus a downstream mRNA, is cleaved at three sites in the spacer region by the endoribonuclease, RNase E. When both RNase E and RNase P are absent, a product containing both tRNAs accumulates. Two multimeric tRNA transcripts, those for tRNA Arg-His-Leu-Pro and tRNA Gly-Cys-Leu also require RNase E for maturation. For the former transcript, products with long 3' extensions on tRNA(Arg), tRNA(His), and tRNA(Pro), as well as the primary transcript, accumulate in the absence of RNase E. For the latter transcript, RNase E cleaves downstream of each tRNA. Little processing of either multimeric transcript occurs in the absence of both RNase E and RNase P. These data indicate that RNase E is a major contributor to the initial processing of E. coli tRNA transcripts, providing substrates for final maturation by RNase P and the 3' exoribonucleases. Based on this new information, a detailed model for tRNA maturation is proposed.

/pdf/rnase-e-plays-an-essential-role-in-the-maturation-of-3ih5alifvx.pdf

RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors.

In addition to tRNA and 5S RNA, Escherichia coli contains several other small, stable RNA species; these are M1, 10Sa, 6S, and 4.5S RNA. Although these RNAs are initially synthesized as precursor molecules, relatively little is known about their maturation. The data presented here show that 3′ exoribonucleolytic trimming is required for the final maturation of each of these molecules. As found previously with tRNA, but not 5S RNA, any one of a number of exoribonucleases can carry out the trimming reaction in vivo, although RNases T and PH are most effective. In their absence, large amounts of immature molecules accumulate for most of the RNAs, and these can be converted to the mature forms in vitro by the purified RNases. A model is proposed that identifies a structural feature present in all the small, stable RNAs of E. coli, and describes how this structure together with the RNases influences the common mechanism for 3′ maturation.

3‧ Exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli

The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R.

In recent years there has been a dramatic shift in our thinking about ribonucleases (RNases). Although they were once considered to be nonspecific, degradative enzymes, it is now clear that RNases play a central role in every aspect of cellular RNA metabolism, including decay of mRNA, conversion of RNA precursors to their mature forms, and end-turnover of certain RNAs. Recognition of the importance of this class of enzymes has led to an explosion of work and the establishment of significant new concepts. Thus, we now realize that RNases, both endoribonucleases and exoribonucleases, can be highly specific for particular sequences or structures. It has also become apparent that a single cell can contain a large number of distinct RNases, approaching as many as 20 members, often with overlapping specificities. Some RNases also have been found to be components of supramolecular complexes and to function in concert with other enzymes to carry out their role in RNA metabolism. This review focuses on the exoribonucleases, both prokaryotic and eukaryotic, and details their structure, catalytic properties, and physiological function.

Zhongwei Li

Papers

RNase G (CafA protein) and RNase E are both required for the 5′ maturation of 16S ribosomal RNA

RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors.

3‧ Exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli

The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R.

Exoribonucleases and their multiple roles in RNA metabolism.