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Viruses Dec 2021Plant RNA viruses encode essential viral proteins that depend on the host translation machinery for their expression. However, genomic RNAs of most plant RNA viruses... (Review)
Review
Plant RNA viruses encode essential viral proteins that depend on the host translation machinery for their expression. However, genomic RNAs of most plant RNA viruses lack the classical characteristics of eukaryotic cellular mRNAs, such as mono-cistron, 5' cap structure, and 3' polyadenylation. To adapt and utilize the eukaryotic translation machinery, plant RNA viruses have evolved a variety of translation strategies such as cap-independent translation, translation recoding on initiation and termination sites, and post-translation processes. This review focuses on advances in cap-independent translation and translation recoding in plant viruses.
Topics: Enhancer Elements, Genetic; Frameshifting, Ribosomal; Plant Viruses; Protein Biosynthesis; RNA Caps; RNA Viruses; Viral Proteins
PubMed: 34960768
DOI: 10.3390/v13122499 -
Cells Mar 2020Mechanical forces acting on biological systems, at both the macroscopic and microscopic levels, play an important part in shaping cellular phenotypes. There is a growing... (Review)
Review
Mechanical forces acting on biological systems, at both the macroscopic and microscopic levels, play an important part in shaping cellular phenotypes. There is a growing realization that biomolecules that respond to force directly applied to them, or via mechano-sensitive signalling pathways, can produce profound changes to not only transcriptional pathways, but also in protein translation. Forces naturally occurring at the molecular level can impact the rate at which the bacterial ribosome translates messenger RNA (mRNA) transcripts and influence processes such as co-translational folding of a nascent protein as it exits the ribosome. In eukaryotes, force can also be transduced at the cellular level by the cytoskeleton, the cell's internal filamentous network. The cytoskeleton closely associates with components of the translational machinery such as ribosomes and elongation factors and, as such, is a crucial determinant of localized protein translation. In this review we will give (1) a brief overview of protein translation in bacteria and eukaryotes and then discuss (2) how mechanical forces are directly involved with ribosomes during active protein synthesis and (3) how eukaryotic ribosomes and other protein translation machinery intimately associates with the mechanosensitive cytoskeleton network.
Topics: Eukaryotic Cells; Humans; Phenotype; Protein Biosynthesis; Proteins; RNA, Messenger; Ribosomes
PubMed: 32156009
DOI: 10.3390/cells9030650 -
Cell Feb 2023Curtailed protein translation ensures stemness and multipotency in embryonic and adult tissue-specific stem cells. In this issue of Cell, a study led by Zhao and...
Curtailed protein translation ensures stemness and multipotency in embryonic and adult tissue-specific stem cells. In this issue of Cell, a study led by Zhao and colleagues uncovered increased susceptibility of hematopoietic stem cells (HSC) to iron-dependent programmed necrotic cell death (ferroptosis) as a consequence of low protein synthesis.
Topics: Cell Proliferation; Ferroptosis; Hematopoietic Stem Cells; Protein Biosynthesis
PubMed: 36803600
DOI: 10.1016/j.cell.2023.01.010 -
Methods in Enzymology 2023
Topics: Peptides; Ribosomes; Protein Biosynthesis
PubMed: 37230595
DOI: 10.1016/S0076-6879(23)00179-9 -
Methods in Molecular Biology (Clifton,... 2024The endoplasmic reticulum takes care of the folding, assembly, and quality control of thousands of proteins destined to the different compartments of the endomembrane...
The endoplasmic reticulum takes care of the folding, assembly, and quality control of thousands of proteins destined to the different compartments of the endomembrane system or to be secreted in the apoplast. Here we describe how these early events in the life of all these proteins can be followed biochemically by using velocity or isopycnic ultracentrifugation, metabolic labelling with radioactive amino acids, drug treatments, and immunoselection in various conditions and, in certain cases, predicted in silico by algorithms.
Topics: Protein Biosynthesis; Algorithms; Amino Acids; Biological Transport; Endoplasmic Reticulum
PubMed: 38411815
DOI: 10.1007/978-1-0716-3710-4_14 -
ACS Synthetic Biology Nov 2023With the advantages of simple genetic composition, low metabolic background, low energy waste, and high genetic stability, genome-reduced strains, as promising...
With the advantages of simple genetic composition, low metabolic background, low energy waste, and high genetic stability, genome-reduced strains, as promising functional chassis, have become an intensive direction for constructing potent biosynthesis factories. Herein, an innovative Genome-Reduced strain-based Active Cell-free Easy-to-make-protein (GRACE) system is built as minimal transcription-translation machinery. In this study, two genome-reduced strains, ΔW3110 and ΔMG1655, with genome reduction of 11.53% and 37.85%, are fused with the cell-free transcription-translation (CFTT) system. The GRACE systems perform better than the corresponding CFTT systems derived from their parental strains in representative valuable applications, such as the expression and solubilization of membrane proteins or protein polymers, biosensing of inorganic or organic molecules based on different principles, and unnatural amino acid embedding. Obviously, the GRACE system has provided a brand-new enabling platform for cell-free transcription-translation basic and applied studies and also would inspire the potential of genome-reduced strains for versatile applications.
Topics: Escherichia coli; Escherichia coli Proteins; Genome, Bacterial; Protein Biosynthesis; Cell-Free System
PubMed: 37852206
DOI: 10.1021/acssynbio.3c00324 -
Trends in Cell Biology Aug 2020During mRNA translation, the genetic information stored in mRNA is translated into a protein sequence. It is imperative that the genetic information is translated with... (Review)
Review
During mRNA translation, the genetic information stored in mRNA is translated into a protein sequence. It is imperative that the genetic information is translated with high precision. Surprisingly, however, recent experimental evidence has demonstrated that translation can be highly heterogeneous, even among different mRNA molecules derived from a single gene in an individual cell; multiple different polypeptides can be produced from a single mRNA molecule and the rate of translation can vary in both space and time. However, whether translational heterogeneity serves an important cellular function, or rather predominantly represents gene expression 'noise' remains an open question. In this review, we discuss the molecular basis and potential functions of such translational heterogeneity.
Topics: Amino Acid Sequence; Animals; Humans; Models, Biological; Protein Biosynthesis; RNA, Messenger; RNA-Binding Proteins; Ribosomes
PubMed: 32461030
DOI: 10.1016/j.tcb.2020.04.008 -
Science (New York, N.Y.) Jun 2023A new method maps the location of thousands of translating RNAs in cells and tissues.
A new method maps the location of thousands of translating RNAs in cells and tissues.
Topics: Gene Expression Regulation; Protein Biosynthesis; RNA, Messenger; Gene Expression Profiling
PubMed: 37384700
DOI: 10.1126/science.adi6844 -
Chemical Communications (Cambridge,... Jun 2022Posttranslational modifications, typically small chemical tags attached on amino acids following protein biosynthesis, have a profound effect on protein structure and... (Review)
Review
Posttranslational modifications, typically small chemical tags attached on amino acids following protein biosynthesis, have a profound effect on protein structure and function. Numerous chemically and structurally diverse posttranslational modifications, including methylation, acetylation, hydroxylation, and ubiquitination, have been identified and characterised on lysine residues in proteins. In this feature article, we focus on chemical tools that rely on the site-specific incorporation of unnatural amino acids into peptides and proteins to probe posttranslational modifications of lysine. We highlight that simple amino acid mimics enable detailed mechanistic and functional assignment of enzymes that install and remove such modifications, and proteins that specifically recognise lysine posttranslational modifications.
Topics: Acetylation; Amino Acids; Lysine; Protein Processing, Post-Translational; Proteins; Ubiquitination
PubMed: 35678513
DOI: 10.1039/d2cc00708h -
Annual Review of Biomedical Data Science Aug 2022The formation of protein complexes is crucial to most biological functions. The cellular mechanisms governing protein complex biogenesis are not yet well understood, but... (Review)
Review
The formation of protein complexes is crucial to most biological functions. The cellular mechanisms governing protein complex biogenesis are not yet well understood, but some principles of cotranslational and posttranslational assembly are beginning to emerge. In bacteria, this process is favored by operons encoding subunits of protein complexes. Eukaryotic cells do not have polycistronic mRNAs, raising the question of how they orchestrate the encounter of unassembled subunits. Here we review the constraints and mechanisms governing eukaryotic co- and posttranslational protein folding and assembly, including the influence of elongation rate on nascent chain targeting, folding, and chaperone interactions. Recent evidence shows that mRNAs encoding subunits of oligomeric assemblies can undergo localized translation and form cytoplasmic condensates that might facilitate the assembly of protein complexes. Understanding the interplay between localized mRNA translation and cotranslational proteostasis will be critical to defining protein complex assembly in vivo.
Topics: Molecular Chaperones; Protein Biosynthesis; Protein Folding; RNA, Messenger; Saccharomyces cerevisiae
PubMed: 35472290
DOI: 10.1146/annurev-biodatasci-121721-095858