bims-tricox 2022-12-25 papers

Issue of 2022‒12‒25
three papers selected by
Yash Verma
University of Delhi South Campus

Biochem Biophys Res Commun. 2022 Dec 08. pii: S0006-291X(22)01687-4. [Epub ahead of print]641 110-115

Sarah Takallou, Nathalie Puchacz, Danielle Allard, Kamaledin B Said, Mohammad Reza Nokhbeh, Bahram Samanfar, Ashkan Golshani.

Despite the similarity in fundamental goals of translation initiation between different domains of life, it is one of the most phylogenetically diverse steps of the central dogma of molecular biology. In a classical view, the translation signals for prokaryotes and eukaryotes are distinct from each other. This idea was challenged by the finding that the Internal Ribosome Entry Site (IRES) belonging to Plautia stali intestine virus (PSIV) could bypass the domain-specific boundaries and effectively initiate translation in E. coli. This finding led us to investigate whether the ability of PSIV IRES to initiate translation in E. coli is specific to this IRES and also to study features that allow this viral IRES to mediate prokaryotic translation initiation. We observed that certain IRESs may also possess the ability to initiate E. coli translation. Our results also indicated that the structural integrity of the PSIV IRES in translation in prokaryotes does not appear to be as critical as it is in eukaryotes. We also demonstrated that two regions of the PSIV IRES with complementarity to 16S ribosomal RNA are important for the ability of this IRES to initiate translation in E. coli.

Keywords: E.coli; IRES; Prokaryotic translation; Sequence complementarity; Translation initiation; rRNA

DOI: https://doi.org/10.1016/j.bbrc.2022.12.022

Nat Struct Mol Biol. 2022 Dec 19.

A single 2'-O-methylation of ribosomal RNA gates assembly of a functional ribosome.

James N Yelland, Jack P K Bravo, Joshua J Black, David W Taylor, Arlen W Johnson.

RNA modifications are widespread in biology and abundant in ribosomal RNA. However, the importance of these modifications is not well understood. We show that methylation of a single nucleotide, in the catalytic center of the large subunit, gates ribosome assembly. Massively parallel mutational scanning of the essential nuclear GTPase Nog2 identified important interactions with rRNA, particularly with the 2'-O-methylated A-site base Gm2922. We found that methylation of G2922 is needed for assembly and efficient nuclear export of the large subunit. Critically, we identified single amino acid changes in Nog2 that completely bypass dependence on G2922 methylation and used cryoelectron microscopy to directly visualize how methylation flips Gm2922 into the active site channel of Nog2. This work demonstrates that a single RNA modification is a critical checkpoint in ribosome biogenesis, suggesting that such modifications can play an important role in regulation and assembly of macromolecular machines.

DOI: https://doi.org/10.1038/s41594-022-00891-8

Cells. 2022 Dec 12. pii: 4014. [Epub ahead of print]11(24):

Accelerated Evolution of Cytochrome c in Higher Primates, and Regulation of the Reaction between Cytochrome c and Cytochrome Oxidase by Phosphorylation.

Sue Ellen Brand, Martha Scharlau, Lois Geren, Marissa Hendrix, Clayre Parson, Tyler Elmendorf, Earl Neel, Kaila Pianalto, Jennifer Silva-Nash, Bill Durham, Francis Millett.

Cytochrome c (Cc) underwent accelerated evolution from the stem of the anthropoid primates to humans. Of the 11 amino acid changes that occurred from horse Cc to human Cc, five were at Cc residues near the binding site of the Cc:CcO complex. Single-point mutants of horse and human Cc were made at each of these positions. The Cc:CcO dissociation constant KD of the horse mutants decreased in the order: T89E > native horse Cc > V11I Cc > Q12M > D50A > A83V > native human. The largest effect was observed for the mutants at residue 50, where the horse Cc D50A mutant decreased KD from 28.4 to 11.8 μM, and the human Cc A50D increased KD from 4.7 to 15.7 μM. To investigate the role of Cc phosphorylation in regulating the reaction with CcO, phosphomimetic human Cc mutants were prepared. The Cc T28E, S47E, and Y48E mutants increased the dissociation rate constant kd, decreased the formation rate constant kf, and increased the equilibrium dissociation constant KD of the Cc:CcO complex. These studies indicate that phosphorylation of these residues plays an important role in regulating mitochondrial electron transport and membrane potential ΔΨ.

Keywords: Cytochrome c; Cytochrome c oxidase; electron transfer; phosphorylation

DOI: https://doi.org/10.3390/cells11244014