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The Journal of Biological Chemistry Sep 2023Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria.... (Review)
Review
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
Topics: Adaptation, Psychological; Escherichia coli; Escherichia coli Proteins; Heat-Shock Proteins; Protein Biosynthesis; Protein Transport
PubMed: 37586589
DOI: 10.1016/j.jbc.2023.105163 -
BioRxiv : the Preprint Server For... Oct 2023RNAs can fold into compact three-dimensional structures, and most RNAs undergo protein interactions in the cell. These compact and occluded environments can block the...
RNAs can fold into compact three-dimensional structures, and most RNAs undergo protein interactions in the cell. These compact and occluded environments can block the ability of structure-probing agents to provide useful data about the folding and modification of the underlying RNA. The development of probes that can analyze structure in crowded settings, and differentiate the proximity of interactions, can shed new light on RNA biology. To this end, here we employ 2'-OH-reactive probes that are small enough to access folded RNA structure underlying many close molecular contacts within cells, providing considerably broader coverage for intracellular RNA structural analysis. We compare reverse transcriptase stops in RNA-Seq data from probes of small and standard size to assess RNA-protein proximity and evaluate solvent-exposed tunnels adjacent to RNA. The data are analyzed first with structurally characterized complexes (human 18S and 28S RNA), and then applied transcriptome-wide to polyadenylated transcripts in HEK293 cells. In our transcriptome profile, the smallest probe acetylimidazole (AcIm) yields 80% greater structural coverage than larger conventional reagent NAIN3, providing enhanced structural information in hundreds of transcripts. We further show that acetyl probes provide superior signals for identifying mA modification sites in transcripts, and provide information regarding methylation sites that are inaccessible to a larger standard probe. RNA infrastructure profiling (RISP) enables enhanced analysis of transcriptome structure, modification, and interactions in living cells, especially in spatially crowded settings.
PubMed: 37873487
DOI: 10.1101/2023.10.09.561413 -
Cell Chemical Biology Jan 2024tRNAs are among the most abundant and essential biomolecules in cells. These spontaneously folding, extensively structured yet conformationally flexible anionic polymers... (Review)
Review
tRNAs are among the most abundant and essential biomolecules in cells. These spontaneously folding, extensively structured yet conformationally flexible anionic polymers literally bridge the worlds of RNAs and proteins, and serve as Rosetta stones that decipher and interpret the genetic code. Their ubiquitous presence, functional irreplaceability, and privileged access to cellular compartments and ribosomes render them prime targets for both endogenous regulation and exogenous manipulation. There is essentially no part of the tRNA that is not touched by another interaction partner, either as programmed or imposed by an external adversary. Recent progresses in genetic, biochemical, and structural analyses of the tRNA interactome produced a wealth of new knowledge into their interaction networks, regulatory functions, and molecular interfaces. In this review, I describe and illustrate the general principles of tRNA recognition by proteins and other RNAs, and discuss the underlying molecular mechanisms that deliver affinity, specificity, and functional competency.
Topics: Nucleic Acid Conformation; RNA, Transfer; RNA; Genetic Code; Ribosomes
PubMed: 38159570
DOI: 10.1016/j.chembiol.2023.12.008 -
RNA (New York, N.Y.) Jan 2024The structure of an RNA, and even more so its interactions with other RNAs, provide valuable information about its function. Secondary structure-based tools for RNA-RNA...
The structure of an RNA, and even more so its interactions with other RNAs, provide valuable information about its function. Secondary structure-based tools for RNA-RNA interaction predictions provide a quick way to identify possible interaction targets and structures. However, these tools ignore the effect of steric hindrance on the tertiary (3D) structure level, and do not consider whether a suitable folding pathway exists to form the interaction. As a consequence, these tools often predict interactions that are unrealistically long and could be formed (in three dimensions) only by going through highly entangled intermediates. Here, we present a computational pipeline to assess whether a proposed secondary (2D) structure interaction is sterically feasible and reachable along a plausible folding pathway. To this end, we simulate the folding of a series of 3D structures along a given 2D folding path. To avoid the complexity of large-scale atomic resolution simulations, our pipeline uses coarse-grained 3D modeling and breaks up the folding path into small steps, each corresponding to the extension of the interaction by 1 or 2 bp. We apply our pipeline to analyze RNA-RNA interaction formation for three selected RNA-RNA complexes. We find that kissing hairpins, in contrast to interactions in the exterior loop, are difficult to extend and tend to get stuck at an interaction length of 6 bp. Our tool, including source code, documentation, and sample data, is available at www.github.com/irenekb/RRI-3D.
Topics: RNA; Nucleic Acid Conformation; Feasibility Studies; RNA Folding; Software
PubMed: 38071473
DOI: 10.1261/rna.079756.123 -
BioRxiv : the Preprint Server For... Mar 2024Riboswitches are ligand-responsive gene-regulatory RNA elements that perform key roles in maintaining cellular homeostasis. Understanding how riboswitch sensitivity is...
Riboswitches are ligand-responsive gene-regulatory RNA elements that perform key roles in maintaining cellular homeostasis. Understanding how riboswitch sensitivity is controlled is critical to understanding how highly conserved aptamer domains are deployed in a variety of contexts with different sensitivity demands. Here we uncover new roles by which RNA folding dynamics control riboswitch sensitivity in cells. By investigating the ZTP riboswitch, we identify multiple mechanistic routes of altering expression platform sequence and structure to slow RNA folding, all of which enhance riboswitch sensitivity. Applying these methods to riboswitches with diverse aptamer architectures that regulate transcription and translation with ON and OFF logic demonstrates the generality of our findings, indicating that any riboswitch that operates in a kinetic regime can be sensitized by slowing expression platform folding. Comparison of the most sensitized versions of these switches to equilibrium aptamer:ligand dissociation constants suggests a limit to the sensitivities achievable by kinetic RNA switches. Our results add to the growing suite of knowledge and approaches that can be used to rationally program cotranscriptional RNA folding for biotechnology applications, and suggest general RNA folding principles for understanding dynamic RNA systems in other areas of biology.
PubMed: 38585885
DOI: 10.1101/2024.03.29.587317 -
Viruses Feb 2024Theodor ("Ted") Otto Diener (* 28 February 1921 in Zürich, Switzerland; † 28 March 2023 in Beltsville, MD, USA) pioneered research on viroids while working at the...
Theodor ("Ted") Otto Diener (* 28 February 1921 in Zürich, Switzerland; † 28 March 2023 in Beltsville, MD, USA) pioneered research on viroids while working at the Plant Virology Laboratory, Agricultural Research Service, USDA, in Beltsville. He coined the name viroid and defined viroids' important features like the infectivity of naked single-stranded RNA without protein-coding capacity. During scientific meetings in the 1970s and 1980s, viroids were often discussed at conferences together with other "subviral pathogens". This term includes what are now called satellite RNAs and prions. Satellite RNAs depend on a helper virus and have linear or, in the case of virusoids, circular RNA genomes. Prions, proteinaceous infectious particles, are the agents of scrapie, kuru and some other diseases. Many satellite RNAs, like viroids, are non-coding and exert their function by thermodynamically or kinetically controlled folding, while prions are solely host-encoded proteins that cause disease by misfolding, aggregation and transmission of their conformations into infectious prion isoforms. In this memorial, we will recall the work of Ted Diener on subviral pathogens.
Topics: Animals; Viroids; Prions; RNA, Satellite; Nucleic Acids; RNA, Viral; Plant Diseases
PubMed: 38543726
DOI: 10.3390/v16030360 -
The Journal of International Advanced... Oct 2023As the most common cause of speech disorders, the etiological study of deafness is important for the diagnosis and treatment of deafness. The mitochondrial genome has... (Review)
Review
As the most common cause of speech disorders, the etiological study of deafness is important for the diagnosis and treatment of deafness. The mitochondrial genome has gradually become a hotspot for deafness genetic research. Mitochondria are the core organelles of energy and material metabolism in eukaryotic cells. Human mitochondria contain 20 amino acids, except for tRNALeu and tRNASer, which have 2 iso-receptors, the other 18 amino acids correspond to unique tRNAs one by one, so mutations in any one tRNA may lead to protein translation defects in mitochondria and thus affect their oxidative phosphorylation process resulting in the corresponding disease phenotype. Mitochondrial tRNAs are extensively modified with base modifications that contribute to the correct folding of tRNAs and maintain their stability. Defective mitochondrial tRNA modifications are closely associated with the development of mitochondrial diseases. The in-depth study found that modification defects of mammalian mitochondrial tRNAs are associated with deafness, especially the nucleotide modification defect of mt-tRNA-37. This article reviews the research on mitochondrial tRNAs, nucleotide modification structure of mitochondrial tRNA-37, and nuclear genes related to modification defects to provide new ideas for the etiological study of deafness.
Topics: Animals; Humans; Mitochondria; RNA, Transfer; Mutation; Amino Acids; Nucleotides; Deafness; Mammals
PubMed: 37789629
DOI: 10.5152/iao.2023.231107 -
Blood Advances Sep 2023Impaired protein homeostasis, though well established in age-related disorders, has been recently linked with the pathogenesis of myeloproliferative neoplasms (MPNs)....
Impaired protein homeostasis, though well established in age-related disorders, has been recently linked with the pathogenesis of myeloproliferative neoplasms (MPNs). However, little is known about MPN-specific modulators of proteostasis, thus impeding our ability for increased mechanistic understanding and discovery of additional therapeutic targets. Loss of proteostasis, in itself, is traced to dysregulated mechanisms in protein folding and intracellular calcium signaling at the endoplasmic reticulum (ER). Here, using ex vivo and in vitro systems (including CD34+ cultures from patient bone marrow and healthy cord/peripheral blood specimens), we extend our prior data from platelet RNA sequencing in patients with MPN and discover select proteostasis-associated markers at RNA and/or protein levels in each of platelet, parent megakaryocyte, and whole blood specimens. Importantly, we identify a novel role in MPNs for enkurin (ENKUR), a calcium mediator protein originally implicated only in spermatogenesis. Our data reveal consistent ENKUR downregulation at both RNA and protein levels across specimens from patients with MPN and experimental models (including upon treatment with thapsigargin, an agent that causes protein misfolding in the ER by selective loss of calcium), with a concomitant upregulation of a cell cycle marker, CDC20. Silencing of ENKUR using short hairpin RNA in CD34+-derived megakaryocytes further confirms this association with CDC20 at both RNA and protein levels and indicates a likely role for the PI3K/Akt pathway. Together, our work sheds light on enkurin as a novel marker of MPN pathogenesis and indicates further mechanistic investigation into a role for dysregulated calcium homeostasis and ER and protein folding stress in MPN transformation.
Topics: Male; Humans; Megakaryocytes; Phosphatidylinositol 3-Kinases; Calcium; Blood Platelets; Myeloproliferative Disorders; Antigens, CD34; Neoplasms; Calmodulin-Binding Proteins; Adaptor Proteins, Signal Transducing
PubMed: 37315179
DOI: 10.1182/bloodadvances.2022008939 -
IEEE/ACM Transactions on Computational... 2023We propose a new deterministic methodology to predict the secondary structure of RNA sequences. What information of stem is important for structure prediction, and is it...
We propose a new deterministic methodology to predict the secondary structure of RNA sequences. What information of stem is important for structure prediction, and is it enough ? The proposed simple deterministic algorithm uses minimum stem length, Stem-Loop score, and co-existence of stems, to give good structure predictions for short RNA and tRNA sequences. The main idea is to consider all possible stem with certain stem loop energy and strength to predict RNA secondary structure. We use graph notation, where stems are represented as vertexes, and co-existence between stems as edges. This full Stem-graph presents all possible folding structure, and we pick sub-graph(s) which give the best matching energy for structure prediction. Stem-Loop score adds structure information and speeds up the computation. The proposed method can predict secondary structure even with pseudo knots. One of the strengths of this approach is the simplicity and flexibility of the algorithm, and it gives a deterministic answer. Numerical experiments are done on various sequences from Protein Data Bank and the Gutell Lab using a laptop and results take only a few seconds.
Topics: RNA; Protein Structure, Secondary; Base Sequence; Algorithms; Nucleic Acid Conformation
PubMed: 37028040
DOI: 10.1109/TCBB.2023.3253049 -
Proteomics Dec 2023Proteins with up to 100 amino acids have been largely overlooked due to the challenges associated with predicting and identifying them using traditional methods. Recent... (Review)
Review
Proteins with up to 100 amino acids have been largely overlooked due to the challenges associated with predicting and identifying them using traditional methods. Recent advances in bioinformatics and machine learning, DNA sequencing, RNA and Ribo-seq technologies, and mass spectrometry (MS) have greatly facilitated the detection and characterisation of these elusive proteins in recent years. This has revealed their crucial role in various cellular processes including regulation, signalling and transport, as toxins and as folding helpers for protein complexes. Consequently, the systematic identification and characterisation of these proteins in bacteria have emerged as a prominent field of interest within the microbial research community. This review provides an overview of different strategies for predicting and identifying these proteins on a large scale, leveraging the power of these advanced technologies. Furthermore, the review offers insights into the future developments that may be expected in this field.
Topics: Proteins; Mass Spectrometry; Computational Biology
PubMed: 37609810
DOI: 10.1002/pmic.202200421