CellBioNewsFeb 8, 2024

First molecular insights into the #degradation of the #ribosomal #30S subunit.

#RNase_R

https://phys.org/news/2024-02-molecular-insights-degradation-ribosomal-30s.html

First molecular insights into the degradation of the ribosomal 30S subunit

A research team from the Department of Chemistry at the Universität Hamburg has succeeded for the first time in identifying at the molecular level the dynamic mechanism used by the enzyme RNase R to degrade the ribosomal 30S subunit. The results of the study were published in the scientific journal Nature.

Phys.org
Scientific FrontlineDec 14, 2023
The discovery that a #ribosomal #protein exhibits a remarkable evolutionary transformation, with its three-dimensional structure changing drastically while its sequence remains relatively conserved.
#Biology #Microbiology #sflorg
https://www.sflorg.com/2023/12/bio12142301.html
Ribosomal protein exhibits remarkable evolutionary transformation

The protein, known as msL1/msL2, is found in ribosomes of parasitic microorganisms called microsporidia

Cosmin SaveanuOct 5, 2023

Comet barplots are an interesting way to underline quantitative changes (I don't know if this is how they are called). Found in a fantastic paper published last year by the Kressler group about the importance of chaperones and CCR4/NOT in correct folding and formation of #ribosomal proteins. A "tour de force" of #genetics and molecular biology in #yeast.

https://pubmed.ncbi.nlm.nih.gov/35357307/

Dedicated chaperones coordinate co-translational regulation of ribosomal protein production with ribosome assembly to preserve proteostasis - PubMed

The biogenesis of eukaryotic ribosomes involves the ordered assembly of around 80 ribosomal proteins. Supplying equimolar amounts of assembly-competent ribosomal proteins is complicated by their aggregation propensity and the spatial separation of their location of synthesis and pre-ribosome incorpo …

PubMed
CellBioNewsJun 23, 2023

#Ribosomal gatekeepers: Study sheds light on molecular control centers of #eukaryote #protein factories.

#METAP1 #SRP

https://phys.org/news/2023-06-ribosomal-gatekeepers-molecular-centers-eukaryote.html

Ribosomal gatekeepers: Study sheds light on molecular control centers of eukaryote protein factories

Based on genetic blueprints, individual amino acids are assembled into long amino acid chains, the proteins, in the protein factories of our cells, the ribosomes. Each newly formed protein starts with the amino acid methionine. This amino acid is often split off again during protein synthesis, as soon as the growing amino acid chain leaves the protein factory through the "ribosomal tunnel." In these cases, the excision of methionine is essential to ensure the subsequent function of the corresponding proteins in the cell.

Cosmin SaveanuJun 1, 2023

As someone who identified twenty years ago some of the factors involved in the assembly of the yeast 60S #ribosomal subunit, it is fantastic to see now a structure of a pre-60S particle at its exit from the nucleus through the nuclear pore complex.

Just for fun, the name of one of the proteins that is involved in the pre-60S export is Alb1, a name that comes from "Arx1's little brother" as it is in contact with Arx1.

https://pubmed.ncbi.nlm.nih.gov/37258668/

Nuclear export of pre-60S particles through the nuclear pore complex - PubMed

The nuclear pore complex (NPC) is the bidirectional gate that mediates the exchange of macromolecules or their assemblies between nucleus and cytoplasm<sup>1-3</sup>. The assembly intermediates of the ribosomal subunits, pre-60S and pre-40S particles, are among the largest cargoes of the NPC and the …

PubMed
Cosmin SaveanuMay 30, 2023

When individual deletion #yeast strains cannot grow alone, some can be rescued by neighbouring strains producing a critical #metabolite. A search for cross-complementation by co-culture of mutants identified interesting links between, mostly, aminoacid synthesis pathways.

Some of the genetic interaction remain mysterious, such as those involving the deletion of #ribosomal protein genes RPS24B or RPL27A.

https://pubmed.ncbi.nlm.nih.gov/37248413/

Spontaneously established syntrophic yeast communities improve bioproduction - PubMed

Nutritional codependence (syntrophy) has underexplored potential to improve biotechnological processes by using cooperating cell types. So far, design of yeast syntrophic communities has required extensive genetic manipulation, as the co-inoculation of most eukaryotic microbial auxotrophs does not r …

PubMed
Cosmin SaveanuApr 23, 2023

A real challenging idea from the Katrin Karbstein's lab: #ribosomal proteins damaged by oxidation are replaced with "fresh" ones to maintain #ribosomes functional. For Rpl10, its association and dissociation from mature ribosomes in the cytoplasm was already known, so it is not clear if the hypothesis put forward in the paper is not a consequence of the shuttling ability of some #proteins assisted by assembly chaperones.

https://pubmed.ncbi.nlm.nih.gov/37086725/

Chaperone-directed ribosome repair after oxidative damage - PubMed

Because of the central role ribosomes play for protein translation and ribosome-mediated mRNA and protein quality control (RQC), the ribosome pool is surveyed and dysfunctional ribosomes degraded both during assembly, as well as the functional cycle. Oxidative stress downregulates translation and da …

PubMed
CellBioNewsApr 5, 2023

Researchers discover new class of #ribosomal #peptide with #hemolytic activity.

#RiPP #genomics

https://phys.org/news/2023-04-class-ribosomal-peptide-hemolytic.html

Researchers discover new class of ribosomal peptide with hemolytic activity

Living organisms produce a myriad of natural products which can be used in modern medicine and therapeutics. Bacteria and other microbes have become the main source for natural products, including a growing family called ribosomally synthesized and post-translationally modified peptides, or RiPPs. The labs of Douglas Mitchell (MMG), John and Margaret Witt Professor of Chemistry, and Huimin Zhao (CABBI/BSD/GSE/MMG), Steven L. Miller Chair of Chemical and Biomolecular Engineering, at the University of Illinois Urbana-Champaign have been working in tandem to identify and analyze new RiPPs that could be good candidates for drug development and therapeutics.

Phys.org
PLOS BiologyJan 6, 2023
Physically separating early steps in #ribosome assembly in the #Ecoli nucleoid from the RNA #degradosome attached to the inner cytoplasmic membrane protects precursor #ribosomal RNA in immature particles from degradation @Lydia_LH17 &co #PLOSBiology https://plos.io/3Qj1x2O
Attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA in ribosome assembly intermediates

RNA processing and degradation shape the transcriptome by generating stable molecules that are necessary for translation (rRNA and tRNA) and by facilitating the turnover of mRNA, which is necessary for the posttranscriptional control of gene expression. In bacteria and the plant chloroplast, RNA degradosomes are multienzyme complexes that process and degrade RNA. In many bacterial species, the endoribonuclease RNase E is the central component of the RNA degradosome. RNase E-based RNA degradosomes are inner membrane proteins in a large family of gram-negative bacteria (β- and γ-Proteobacteria). Until now, the reason for membrane localization was not understood. Here, we show that a mutant strain of Escherichia coli, in which the RNA degradosome is localized to the interior of the cell, has high levels of 20S and 40S particles that are defective intermediates in ribosome assembly. These particles have aberrant protein composition and contain rRNA precursors that have been cleaved by RNase E. After RNase E cleavage, rRNA fragments are degraded to nucleotides by exoribonucleases. In vitro, rRNA in intact ribosomes is resistant to RNase E cleavage, whereas protein-free rRNA is readily degraded. We conclude that RNA degradosomes in the nucleoid of the mutant strain interfere with cotranscriptional ribosome assembly. We propose that membrane-attached RNA degradosomes in wild-type cells control the quality of ribosome assembly after intermediates are released from the nucleoid. That is, the compact structure of mature ribosomes protects rRNA against cleavage by RNase E. Turnover of a proportion of intermediates in ribosome assembly explains slow growth of the mutant strain. Competition between mRNA and rRNA degradation could be the cause of slower mRNA degradation in the mutant strain. We conclude that attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA precursors, thus explaining the reason for conservation of membrane-attached RNA degradosomes throughout the β- and γ-Proteobacteria.

PLOS BiologyJan 6, 2023
Physically separating early steps in #ribosome assembly in the #Ecoli nucleoid from the RNA #degradosome attached to the inner cytoplasmic membrane protects precursor #ribosomal RNA in immature particles from degradation @Lydia_LH17 &co #PLOSBiology https://plos.io/3Qj1x2O
Attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA in ribosome assembly intermediates

RNA processing and degradation shape the transcriptome by generating stable molecules that are necessary for translation (rRNA and tRNA) and by facilitating the turnover of mRNA, which is necessary for the posttranscriptional control of gene expression. In bacteria and the plant chloroplast, RNA degradosomes are multienzyme complexes that process and degrade RNA. In many bacterial species, the endoribonuclease RNase E is the central component of the RNA degradosome. RNase E-based RNA degradosomes are inner membrane proteins in a large family of gram-negative bacteria (β- and γ-Proteobacteria). Until now, the reason for membrane localization was not understood. Here, we show that a mutant strain of Escherichia coli, in which the RNA degradosome is localized to the interior of the cell, has high levels of 20S and 40S particles that are defective intermediates in ribosome assembly. These particles have aberrant protein composition and contain rRNA precursors that have been cleaved by RNase E. After RNase E cleavage, rRNA fragments are degraded to nucleotides by exoribonucleases. In vitro, rRNA in intact ribosomes is resistant to RNase E cleavage, whereas protein-free rRNA is readily degraded. We conclude that RNA degradosomes in the nucleoid of the mutant strain interfere with cotranscriptional ribosome assembly. We propose that membrane-attached RNA degradosomes in wild-type cells control the quality of ribosome assembly after intermediates are released from the nucleoid. That is, the compact structure of mature ribosomes protects rRNA against cleavage by RNase E. Turnover of a proportion of intermediates in ribosome assembly explains slow growth of the mutant strain. Competition between mRNA and rRNA degradation could be the cause of slower mRNA degradation in the mutant strain. We conclude that attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA precursors, thus explaining the reason for conservation of membrane-attached RNA degradosomes throughout the β- and γ-Proteobacteria.