1
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Jiang R, Yuan S, Zhou Y, Wei Y, Li F, Wang M, Chen B, Yu H. Strategies to overcome the challenges of low or no expression of heterologous proteins in Escherichia coli. Biotechnol Adv 2024; 75:108417. [PMID: 39038691 DOI: 10.1016/j.biotechadv.2024.108417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024]
Abstract
Protein expression is a critical process in diverse biological systems. For Escherichia coli, a widely employed microbial host in industrial catalysis and healthcare, researchers often face significant challenges in constructing recombinant expression systems. To maximize the potential of E. coli expression systems, it is essential to address problems regarding the low or absent production of certain target proteins. This article presents viable solutions to the main factors posing challenges to heterologous protein expression in E. coli, which includes protein toxicity, the intrinsic influence of gene sequences, and mRNA structure. These strategies include specialized approaches for managing toxic protein expression, addressing issues related to mRNA structure and codon bias, advanced codon optimization methodologies that consider multiple factors, and emerging optimization techniques facilitated by big data and machine learning.
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Affiliation(s)
- Ruizhao Jiang
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China
| | - Shuting Yuan
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China
| | - Yilong Zhou
- Tanwei College, Tsinghua University, Beijing 100084, China
| | - Yuwen Wei
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China
| | - Fulong Li
- Beijing Evolyzer Co.,Ltd., 100176, China
| | | | - Bo Chen
- Beijing Evolyzer Co.,Ltd., 100176, China
| | - Huimin Yu
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Key Laboratory of Industrial Biocatalysis (Tsinghua University), the Ministry of Education, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China.
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2
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Sharma N, van Oijen AM, Spenkelink LM, Mueller SH. Insight into Single-Molecule Imaging Techniques for the Study of Prokaryotic Genome Maintenance. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:595-614. [PMID: 39328428 PMCID: PMC11423410 DOI: 10.1021/cbmi.4c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 09/28/2024]
Abstract
Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.
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Affiliation(s)
- Nischal Sharma
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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3
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Molodtsov V, Wang C, Zhang J, Kaelber JT, Blaha G, Ebright RH. Structural basis of RfaH-mediated transcription-translation coupling. Nat Struct Mol Biol 2024:10.1038/s41594-024-01372-w. [PMID: 39117885 DOI: 10.1038/s41594-024-01372-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
The NusG paralog RfaH mediates bacterial transcription-translation coupling in genes that contain a DNA sequence element, termed an ops site, required for pausing RNA polymerase (RNAP) and for loading RfaH onto the paused RNAP. Here, we report cryo-electron microscopy structures of transcription-translation complexes (TTCs) containing Escherichia coli RfaH. The results show that RfaH bridges RNAP and the ribosome, with the RfaH N-terminal domain interacting with RNAP and the RfaH C-terminal domain interacting with the ribosome. The results show that the distribution of translational and orientational positions of RNAP relative to the ribosome in RfaH-coupled TTCs is more restricted than in NusG-coupled TTCs because of the more restricted flexibility of the RfaH interdomain linker. The results further suggest that the structural organization of RfaH-coupled TTCs in the 'loading state', in which RNAP and RfaH are located at the ops site during formation of the TTC, is the same as the structural organization of RfaH-coupled TTCs in the 'loaded state', in which RNAP and RfaH are located at positions downstream of the ops site during function of the TTC. The results define the structural organization of RfaH-containing TTCs and set the stage for analysis of functions of RfaH during translation initiation and transcription-translation coupling.
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Affiliation(s)
- Vadim Molodtsov
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
- Research Institute for Systems Biology and Medicine, Moscow, Russia
| | - Chengyuan Wang
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
- Center for Microbes, Development and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jing Zhang
- Center for Microbes, Development and Health, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jason T Kaelber
- Rutgers CryoEM and Nanoimaging Facility and Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, USA
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA.
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4
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Xie Y, Shu T, Liu T, Spindler MC, Mahamid J, Hocky GM, Gresham D, Holt LJ. Polysome collapse and RNA condensation fluidize the cytoplasm. Mol Cell 2024; 84:2698-2716.e9. [PMID: 39059370 DOI: 10.1016/j.molcel.2024.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 03/25/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024]
Abstract
The cell interior is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cellular physiology. Cellular stress responses almost universally lead to inhibition of translation, resulting in polysome collapse and release of mRNA. The released mRNA molecules condense with RNA-binding proteins to form ribonucleoprotein (RNP) condensates known as processing bodies and stress granules. Here, we show that polysome collapse and condensation of RNA transiently fluidize the cytoplasm, and coarse-grained molecular dynamic simulations support this as a minimal mechanism for the observed biophysical changes. Increased mesoscale diffusivity correlates with the efficient formation of quality control bodies (Q-bodies), membraneless organelles that compartmentalize misfolded peptides during stress. Synthetic, light-induced RNA condensation also fluidizes the cytoplasm. Together, our study reveals a functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to enable efficient response of cells to stress conditions.
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Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Tong Shu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA
| | - Tiewei Liu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Marie-Christin Spindler
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Glen M Hocky
- Department of Chemistry and Simons Center for Computational Physical Chemistry, New York University, New York, NY, USA
| | - David Gresham
- Department of Biology, New York University, New York, NY, USA.
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY, USA.
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5
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Sun X, Singla-Rastogi M, Wang J, Zhao C, Wang X, Li P. The uS10c-BPG2 module mediates ribosomal RNA processing in chloroplast nucleoids. Nucleic Acids Res 2024; 52:7893-7909. [PMID: 38686791 PMCID: PMC11260468 DOI: 10.1093/nar/gkae339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/09/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
In plant chloroplasts, certain ribosomal proteins (RPs) and ribosome biogenesis factors (RBFs) are present in nucleoids, implying an association between nucleoids and ribosome biogenesis. In Arabidopsis, the YqeH-type GTPase Brassinazole-Insensitive Pale Green2 (BPG2) is a chloroplast nucleoid-associated RBF. Here, we investigated the relationship between nucleoids and BPG2-involved ribosome biogenesis steps by exploring how BPG2 targets ribosomes. Our findings demonstrate that BPG2 interacts with an essential plastid RP, uS10c, in chloroplast nucleoids in a ribosomal RNA (rRNA)-independent manner. We also discovered that uS10c is a haploinsufficient gene, as the heterozygous deletion of this gene leads to variegated shoots and chlorophyll aggregation. uS10c is integrated into 30S ribosomal particles when rRNA is relatively exposed and also exists in polysome fractions. In contrast, BPG2 exclusively associates with 30S ribosomal particles. Notably, the interaction between BPG2 and 30S particles is influenced by the absence of uS10c, resulting in BPG2 diffusing in chloroplasts instead of targeting nucleoids. Further, our results reveal that the loss of BPG2 function and the heterozygous deletion of uS10c impair the processing of 16S and 23S-4.5S rRNAs, reduce plastid protein accumulation, and trigger the plastid signaling response. Together, these findings indicate that the uS10c-BPG2 module mediates ribosome biogenesis in chloroplast nucleoids.
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Affiliation(s)
- Xueping Sun
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | | | - Jingwen Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, PR China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
| | - Pengcheng Li
- Institute of Crop Germplasm Resources (Biotechnology Research Center), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, Shandong 250100, PR China
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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6
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Wang C, Molodtsov V, Kaelber JT, Blaha G, Ebright RH. Structural basis of long-range transcription-translation coupling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.20.604413. [PMID: 39071276 PMCID: PMC11275968 DOI: 10.1101/2024.07.20.604413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Structures recently have been reported of molecular assemblies that mediate transcription-translation coupling in Escherichia coli . In these molecular assemblies, termed "coupled transcription-translation complexes" or "TTC-B", RNA polymerase (RNAP) interacts directly with the ribosome, the transcription elongation factor NusG or its paralog RfaH forms a bridge between RNAP and ribosome, and the transcription elongation factor NusA optionally forms a second bridge between RNAP and ribosome. Here, we have determined structures of coupled transcription-translation complexes having mRNA spacers between RNAP and ribosome longer than the maximum-length mRNA spacer compatible with formation of TTC-B. The results define a new class of coupled transcription-translation complex, termed "TTC-LC," where "LC" denotes "long-range coupling." TTC-LC differs from TTC-B by a ∼60° rotation and ∼70 Å translation of RNAP relative to ribosome, resulting in loss of direct interactions between RNAP and ribosome and creation of a ∼70 Å gap between RNAP and ribosome. TTC-LC accommodates long mRNA spacers by looping out mRNA from the gap between RNAP and ribosome. We propose that TTC-LC is an intermediate in assembling and disassembling TTC-B, mediating pre-TTC-B transcription-translation coupling before a ribosome catches up to RNAP, and mediating post-TTC-B transcription-translation coupling after a ribosome stops moving and RNAP continues moving.
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7
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Humphrey ED, Sukhodolets MV. Isolation and Partial Characterization of Novel, Structurally Uniform (Hfq 6) n≥8 Assemblies Carrying Accessory Transcription and Translation Factors. Biochemistry 2024; 63:1647-1662. [PMID: 38869079 DOI: 10.1021/acs.biochem.3c00728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
In growing E. coli cells, the transcription-translation complexes (TTCs) form characteristic foci; however, the exact molecular composition of these superstructures is not known with certainty. Herein, we report that, during our recently developed "fast" procedures for purification of E. coli RNA polymerase (RP), a fraction of the RP's α/RpoA subunits is displaced from the core RP complexes and copurifies with multiprotein superstructures carrying the nucleic acid-binding protein Hfq and the ribosomal protein S6. We show that the main components of these large multiprotein assemblies are fixed protein copy-number (Hfq6)n≥8 complexes; these complexes have a high level of structural uniformity and are distinctly unlike the previously described (Hfq6)n "head-to-tail" polymers. We describe purification of these novel, structurally uniform (Hfq6)n≥8 complexes to near homogeneity and show that they also contain small nonprotein molecules and accessory S6. We demonstrate that Hfq, S6, and RP have similar solubility profiles and present evidence pointing to a role of the Hfq C-termini in superstructure formation. Taken together, our data offer new insights into the composition of the macromolecular assemblies likely acting as scaffolds for transcription complexes and ribosomes during bacterial cells' active growth.
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Affiliation(s)
- Elijah D Humphrey
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
| | - Maxim V Sukhodolets
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, Texas 77710, United States
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8
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Hustmyer CM, Landick R. Bacterial chromatin proteins, transcription, and DNA topology: Inseparable partners in the control of gene expression. Mol Microbiol 2024; 122:81-112. [PMID: 38847475 PMCID: PMC11260248 DOI: 10.1111/mmi.15283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
DNA in bacterial chromosomes is organized into higher-order structures by DNA-binding proteins called nucleoid-associated proteins (NAPs) or bacterial chromatin proteins (BCPs). BCPs often bind to or near DNA loci transcribed by RNA polymerase (RNAP) and can either increase or decrease gene expression. To understand the mechanisms by which BCPs alter transcription, one must consider both steric effects and the topological forces that arise when DNA deviates from its fully relaxed double-helical structure. Transcribing RNAP creates DNA negative (-) supercoils upstream and positive (+) supercoils downstream whenever RNAP and DNA are unable to rotate freely. This (-) and (+) supercoiling generates topological forces that resist forward translocation of DNA through RNAP unless the supercoiling is constrained by BCPs or relieved by topoisomerases. BCPs also may enhance topological stress and overall can either inhibit or aid transcription. Here, we review current understanding of how RNAP, BCPs, and DNA topology interplay to control gene expression.
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Affiliation(s)
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison
- Department of Bacteriology, University of Wisconsin-Madison
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9
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Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer KM. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nat Rev Mol Cell Biol 2024; 25:534-554. [PMID: 38509203 PMCID: PMC11199108 DOI: 10.1038/s41580-024-00706-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/22/2024]
Abstract
Many steps of RNA processing occur during transcription by RNA polymerases. Co-transcriptional activities are deemed commonplace in prokaryotes, in which the lack of membrane barriers allows mixing of all gene expression steps, from transcription to translation. In the past decade, an extraordinary level of coordination between transcription and RNA processing has emerged in eukaryotes. In this Review, we discuss recent developments in our understanding of co-transcriptional gene regulation in both eukaryotes and prokaryotes, comparing methodologies and mechanisms, and highlight striking parallels in how RNA polymerases interact with the machineries that act on nascent RNA. The development of RNA sequencing and imaging techniques that detect transient transcription and RNA processing intermediates has facilitated discoveries of transcription coordination with splicing, 3'-end cleavage and dynamic RNA folding and revealed physical contacts between processing machineries and RNA polymerases. Such studies indicate that intron retention in a given nascent transcript can prevent 3'-end cleavage and cause transcriptional readthrough, which is a hallmark of eukaryotic cellular stress responses. We also discuss how coordination between nascent RNA biogenesis and transcription drives fundamental aspects of gene expression in both prokaryotes and eukaryotes.
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Affiliation(s)
- Morgan Shine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jackson Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dagmar Zigackova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lydia Herzel
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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10
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Saba J, Flores K, Marshall B, Engstrom MD, Peng Y, Garje AS, Comstock L, Landick R. Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.599965. [PMID: 38948710 PMCID: PMC11213015 DOI: 10.1101/2024.06.21.599965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Human gut Bacteroides species encode numerous (eight or more) tightly regulated capsular polysaccharides (CPS). Specialized paralogs of the universal transcription elongation factor NusG, called UpxY (Y), and an anti-Y UpxZ (Z) are encoded by the first two genes of each CPS operon. The Y-Z regulators combine with promoter inversions to limit CPS transcription to a single operon in most cells. Y enhances transcript elongation whereas Z inhibits noncognate Ys. How Y distinguishes among cognate CPS operons and how Z inhibits only noncognate Ys are unknown. Using in-vivo nascent-RNA sequencing and promoter-less in vitro transcription (PIVoT), we establish that Y recognizes a paused RNA polymerase via sequences in both the exposed non-template DNA and the upstream duplex DNA. Y association is aided by novel 'pause-then-escape' nascent RNA hairpins. Z binds non-cognate Ys to directly inhibit Y association. This Y-Z hierarchical regulatory program allows Bacteroides to create CPS subpopulations for optimal fitness.
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Affiliation(s)
- Jason Saba
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Katia Flores
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Bailey Marshall
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Cell and Molecular Biology Training Program, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Michael D. Engstrom
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Yikai Peng
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Atharv S. Garje
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Genetics Training Program, University of Wisconsin–Madison, Madison, WI 53706, USA
| | - Laurie Comstock
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706, USA
- Department of Bacteriology, University of Wisconsin–Madison, Madison, WI 53706, USA
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11
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Kim S, Wang YH, Hassan A, Kim S. Re-defining how mRNA degradation is coordinated with transcription and translation in bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.588412. [PMID: 38659903 PMCID: PMC11042359 DOI: 10.1101/2024.04.18.588412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
In eukaryotic cells, transcription, translation, and mRNA degradation occur in distinct subcellular regions. How these mRNA processes are organized in bacteria, without employing membrane-bound compartments, remains unclear. Here, we present generalizable principles underlying coordination between these processes in bacteria. In Escherichia coli, we found that co-transcriptional degradation is rare for mRNAs except for those encoding inner membrane proteins, due to membrane localization of the main ribonuclease, RNase E. We further found, by varying ribosome binding sequences, that translation affects mRNA stability not because ribosomes protect mRNA from degradation, but because low translation leads to premature transcription termination in the absence of transcription-translation coupling. Extending our analyses to Bacillus subtilis and Caulobacter crescentus, we established subcellular localization of RNase E (or its homolog) and premature transcription termination in the absence of transcription-translation coupling as key determinants that explain differences in transcriptional and translational coupling to mRNA degradation across genes and species.
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Affiliation(s)
- Seunghyeon Kim
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yu-Huan Wang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Albur Hassan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sangjin Kim
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801, USA
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12
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Kuzminov A. Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma. J Bacteriol 2024; 206:e0021123. [PMID: 38358278 PMCID: PMC10994824 DOI: 10.1128/jb.00211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Bacterial chromosome, the nucleoid, is traditionally modeled as a rosette of DNA mega-loops, organized around proteinaceous central scaffold by nucleoid-associated proteins (NAPs), and mixed with the cytoplasm by transcription and translation. Electron microscopy of fixed cells confirms dispersal of the cloud-like nucleoid within the ribosome-filled cytoplasm. Here, I discuss evidence that the nucleoid in live cells forms DNA phase separate from riboprotein phase, the "riboid." I argue that the nucleoid-riboid interphase, where DNA interacts with NAPs, transcribing RNA polymerases, nascent transcripts, and ssRNA chaperones, forms the transcription zone. An active part of phase separation, transcription zone enforces segregation of the centrally positioned information phase (the nucleoid) from the surrounding action phase (the riboid), where translation happens, protein accumulates, and metabolism occurs. I speculate that HU NAP mostly tiles up the nucleoid periphery-facilitating DNA mobility but also supporting transcription in the interphase. Besides extruding plectonemically supercoiled DNA mega-loops, condensins could compact them into solenoids of uniform rings, while HU could support rigidity and rotation of these DNA rings. The two-phase cytoplasm arrangement allows the bacterial cell to organize the central dogma activities, where (from the cell center to its periphery) DNA replicates and segregates, DNA is transcribed, nascent mRNA is handed over to ribosomes, mRNA is translated into proteins, and finally, the used mRNA is recycled into nucleotides at the inner membrane. The resulting information-action conveyor, with one activity naturally leading to the next one, explains the efficiency of prokaryotic cell design-even though its main intracellular transportation mode is free diffusion.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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13
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Greiss F, Lardon N, Schütz L, Barak Y, Daube SS, Weinhold E, Noireaux V, Bar-Ziv R. A genetic circuit on a single DNA molecule as an autonomous dissipative nanodevice. Nat Commun 2024; 15:883. [PMID: 38287055 PMCID: PMC10825189 DOI: 10.1038/s41467-024-45186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Realizing genetic circuits on single DNA molecules as self-encoded dissipative nanodevices is a major step toward miniaturization of autonomous biological systems. A circuit operating on a single DNA implies that genetically encoded proteins localize during coupled transcription-translation to DNA, but a single-molecule measurement demonstrating this has remained a challenge. Here, we use a genetically encoded fluorescent reporter system with improved temporal resolution and observe the synthesis of individual proteins tethered to a DNA molecule by transient complexes of RNA polymerase, messenger RNA, and ribosome. Against expectations in dilute cell-free conditions where equilibrium considerations favor dispersion, these nascent proteins linger long enough to regulate cascaded reactions on the same DNA. We rationally design a pulsatile genetic circuit by encoding an activator and repressor in feedback on the same DNA molecule. Driven by the local synthesis of only several proteins per hour and gene, the circuit dynamics exhibit enhanced variability between individual DNA molecules, and fluctuations with a broad power spectrum. Our results demonstrate that co-expressional localization, as a nonequilibrium process, facilitates single-DNA genetic circuits as dissipative nanodevices, with implications for nanobiotechnology applications and artificial cell design.
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Affiliation(s)
- Ferdinand Greiss
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Nicolas Lardon
- Department of Chemical Biology, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Yoav Barak
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shirley S Daube
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, 52056, Aachen, Germany
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Roy Bar-Ziv
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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14
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Oelschlaeger P. Molecular Mechanisms and the Significance of Synonymous Mutations. Biomolecules 2024; 14:132. [PMID: 38275761 PMCID: PMC10813300 DOI: 10.3390/biom14010132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Synonymous mutations result from the degeneracy of the genetic code. Most amino acids are encoded by two or more codons, and mutations that change a codon to another synonymous codon do not change the amino acid in the gene product. Historically, such mutations have been considered silent because they were assumed to have no to very little impact. However, research in the last few decades has produced several examples where synonymous mutations play important roles. These include optimizing expression by enhancing translation initiation and accelerating or decelerating translation elongation via codon usage and mRNA secondary structures, stabilizing mRNA molecules and preventing their breakdown before translation, and faulty protein folding or increased degradation due to enhanced ubiquitination and suboptimal secretion of proteins into the appropriate cell compartments. Some consequences of synonymous mutations, such as mRNA stability, can lead to different outcomes in prokaryotes and eukaryotes. Despite these examples, the significance of synonymous mutations in evolution and in causing disease in comparison to nonsynonymous mutations that do change amino acid residues in proteins remains controversial. Whether the molecular mechanisms described by which synonymous mutations affect organisms can be generalized remains poorly understood and warrants future research in this area.
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Affiliation(s)
- Peter Oelschlaeger
- Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
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15
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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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16
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Tare P, Bhowmick T, Katagi G, China A, Nagaraja V. Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time. ACS OMEGA 2023; 8:47510-47519. [PMID: 38144119 PMCID: PMC10733919 DOI: 10.1021/acsomega.3c04754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/11/2023] [Indexed: 12/26/2023]
Abstract
RNA polymerases (RNAPs) across the bacterial kingdom have retained a conserved structure and function. In spite of the remarkable similarity of the enzyme in different bacteria, a wide variation is found in the promoter-polymerase interaction, transcription initiation, and termination. However, the transcription elongation was considered to be a monotonic process, although the rate of elongation could vary in different bacteria. Such variations in RNAP elongation rates could be important to fine-tune the transcription, which in turn would influence cellular metabolism and growth rates. Here, we describe a quantitative study to measure the transcription rates for the RNAPs from three bacteria, namely, Mycobacterium tuberculosis, Mycobacterium smegmatis, and Escherichia coli, which exhibit different growth kinetics. The RNA synthesis rates of the RNAPs were calculated from the real-time elongation kinetic profile using surface plasmon resonance through a computational flux flow model. The computational model revealed the modular process of elongation, with different rate profiles for the three RNAPs. Notably, the transcription elongation rates of these RNAPs followed the trend in the growth rates of these bacteria.
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Affiliation(s)
- Priyanka Tare
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
| | - Tuhin Bhowmick
- Department
of Physics, Indian Institute of Science, Bangalore 560012, India
- Centre
for Cellular and Molecular Platforms, NCBS-TIFR, Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Gurunath Katagi
- Centre
for Cellular and Molecular Platforms, NCBS-TIFR, Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Arnab China
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
| | - Valakunja Nagaraja
- Department
of Microbiology and Cell Biology, Indian
Institute of Science, Bangalore 560012, India
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17
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Molodtsov V, Wang C, Kaelber JT, Blaha G, Ebright RH. Structural basis of RfaH-mediated transcription-translation coupling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.05.565726. [PMID: 37986937 PMCID: PMC10659316 DOI: 10.1101/2023.11.05.565726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The NusG paralog RfaH mediates bacterial transcription-translation coupling on genes that contain a DNA sequence element, termed an ops site, required for pausing RNA polymerase (RNAP) and for loading RfaH onto the paused RNAP. Here we report cryo-EM structures of transcription-translation complexes (TTCs) containing RfaH. The results show that RfaH bridges RNAP and the ribosome, with the RfaH N-terminal domain interacting with RNAP, and with the RfaH C-terminal domain interacting with the ribosome. The results show that the distribution of translational and orientational positions of RNAP relative to the ribosome in RfaH-coupled TTCs is more restricted than in NusG-coupled TTCs, due to the more restricted flexibility of the RfaH interdomain linker. The results further show that the structural organization of RfaH-coupled TTCs in the "loading state," in which RNAP and RfaH are located at the ops site during formation of the TTC, is the same as the structural organization of RfaH-coupled TTCs in the "loaded state," in which RNAP and RfaH are located at positions downstream of the ops site during function of the TTC. The results define the structural organization of RfaH-containing TTCs and set the stage for analysis of functions of RfaH during translation initiation and transcription-translation coupling. One sentence summary Cryo-EM reveals the structural basis of transcription-translation coupling by RfaH.
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18
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Woodgate J, Zenkin N. Transcription-translation coupling: Recent advances and future perspectives. Mol Microbiol 2023; 120:539-546. [PMID: 37856403 PMCID: PMC10953045 DOI: 10.1111/mmi.15076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 10/21/2023]
Abstract
The flow of genetic information from the chromosome to protein in all living organisms consists of two steps: (1) copying information coded in DNA into an mRNA intermediate via transcription by RNA polymerase, followed by (2) translation of this mRNA into a polypeptide by the ribosome. Unlike eukaryotes, where transcription and translation are separated by a nuclear envelope, in bacterial cells, these two processes occur within the same compartment. This means that a pioneering ribosome starts translation on nascent mRNA that is still being actively transcribed by RNA polymerase. This tethering via mRNA is referred to as 'coupling' of transcription and translation (CTT). CTT raises many questions regarding physical interactions and potential mutual regulation between these large (ribosome is ~2.5 MDa and RNA polymerase is 0.5 MDa) and powerful molecular machines. Accordingly, we will discuss some recently discovered structural and functional aspects of CTT.
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Affiliation(s)
- Jason Woodgate
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle Upon TyneUK
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19
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Xie Y, Liu T, Gresham D, Holt LJ. mRNA condensation fluidizes the cytoplasm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542963. [PMID: 37398029 PMCID: PMC10312499 DOI: 10.1101/2023.05.30.542963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The intracellular environment is packed with macromolecules of mesoscale size, and this crowded milieu significantly influences cell physiology. When exposed to stress, mRNAs released after translational arrest condense with RNA binding proteins, resulting in the formation of membraneless RNA protein (RNP) condensates known as processing bodies (P-bodies) and stress granules (SGs). However, the impact of the assembly of these condensates on the biophysical properties of the crowded cytoplasmic environment remains unclear. Here, we find that upon exposure to stress, polysome collapse and condensation of mRNAs increases mesoscale particle diffusivity in the cytoplasm. Increased mesoscale diffusivity is required for the efficient formation of Q-bodies, membraneless organelles that coordinate degradation of misfolded peptides that accumulate during stress. Additionally, we demonstrate that polysome collapse and stress granule formation has a similar effect in mammalian cells, fluidizing the cytoplasm at the mesoscale. We find that synthetic, light-induced RNA condensation is sufficient to fluidize the cytoplasm, demonstrating a causal effect of RNA condensation. Together, our work reveals a new functional role for stress-induced translation inhibition and formation of RNP condensates in modulating the physical properties of the cytoplasm to effectively respond to stressful conditions.
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Affiliation(s)
- Ying Xie
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
- Department of Biology, New York University, New York, New York, United States
| | - Tiewei Liu
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
| | - David Gresham
- Department of Biology, New York University, New York, New York, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York, United States
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20
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Gerber A, van Otterdijk S, Bruggeman FJ, Tutucci E. Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. Transcription 2023; 14:105-126. [PMID: 37050882 PMCID: PMC10807504 DOI: 10.1080/21541264.2023.2199669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/14/2023] Open
Abstract
Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.
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Affiliation(s)
- Alan Gerber
- Amsterdam UMC, Location Vrije Universiteit Amsterdam, Department of Neurosurgery, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Brain Tumor Center Amsterdam, Amsterdam, The Netherlands
| | - Sander van Otterdijk
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J. Bruggeman
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Evelina Tutucci
- Systems Biology Lab, A-LIFE department, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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21
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Gor K, Duss O. Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly. Biomolecules 2023; 13:866. [PMID: 37238735 PMCID: PMC10216711 DOI: 10.3390/biom13050866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Ribosome assembly is one of the most fundamental processes of gene expression and has served as a playground for investigating the molecular mechanisms of how protein-RNA complexes (RNPs) assemble. A bacterial ribosome is composed of around 50 ribosomal proteins, several of which are co-transcriptionally assembled on a ~4500-nucleotide-long pre-rRNA transcript that is further processed and modified during transcription, the entire process taking around 2 min in vivo and being assisted by dozens of assembly factors. How this complex molecular process works so efficiently to produce an active ribosome has been investigated over decades, resulting in the development of a plethora of novel approaches that can also be used to study the assembly of other RNPs in prokaryotes and eukaryotes. Here, we review biochemical, structural, and biophysical methods that have been developed and integrated to provide a detailed and quantitative understanding of the complex and intricate molecular process of bacterial ribosome assembly. We also discuss emerging, cutting-edge approaches that could be used in the future to study how transcription, rRNA processing, cellular factors, and the native cellular environment shape ribosome assembly and RNP assembly at large.
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Affiliation(s)
- Kavan Gor
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany;
- Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69117 Heidelberg, Germany
| | - Olivier Duss
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany;
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22
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Wee LM, Tong AB, Florez Ariza AJ, Cañari-Chumpitaz C, Grob P, Nogales E, Bustamante CJ. A trailing ribosome speeds up RNA polymerase at the expense of transcript fidelity via force and allostery. Cell 2023; 186:1244-1262.e34. [PMID: 36931247 PMCID: PMC10135430 DOI: 10.1016/j.cell.2023.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 03/18/2023]
Abstract
In prokaryotes, translation can occur on mRNA that is being transcribed in a process called coupling. How the ribosome affects the RNA polymerase (RNAP) during coupling is not well understood. Here, we reconstituted the E. coli coupling system and demonstrated that the ribosome can prevent pausing and termination of RNAP and double the overall transcription rate at the expense of fidelity. Moreover, we monitored single RNAPs coupled to ribosomes and show that coupling increases the pause-free velocity of the polymerase and that a mechanical assisting force is sufficient to explain the majority of the effects of coupling. Also, by cryo-EM, we observed that RNAPs with a terminal mismatch adopt a backtracked conformation, while a coupled ribosome allosterically induces these polymerases toward a catalytically active anti-swiveled state. Finally, we demonstrate that prolonged RNAP pausing is detrimental to cell viability, which could be prevented by polymerase reactivation through a coupled ribosome.
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Affiliation(s)
- Liang Meng Wee
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alexander B Tong
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Alfredo Jose Florez Ariza
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Cristhian Cañari-Chumpitaz
- QB3-Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patricia Grob
- QB3-Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Carlos J Bustamante
- QB3-Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, USA; Department of Physics, University of California Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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23
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Kaval KG, Chimalapati S, Siegel SD, Garcia N, Jaishankar J, Dalia AB, Orth K. Membrane-localized expression, production and assembly of Vibrio parahaemolyticus T3SS2 provides evidence for transertion. Nat Commun 2023; 14:1178. [PMID: 36859532 PMCID: PMC9977878 DOI: 10.1038/s41467-023-36762-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/15/2023] [Indexed: 03/03/2023] Open
Abstract
It has been proposed that bacterial membrane proteins may be synthesized and inserted into the membrane by a process known as transertion, which involves membrane association of their encoding genes, followed by coupled transcription, translation and membrane insertion. Here, we provide evidence supporting that the pathogen Vibrio parahaemolyticus uses transertion to assemble its type III secretion system (T3SS2), to inject virulence factors into host cells. We propose a two-step transertion process where the membrane-bound co-component receptor (VtrA/VtrC) is first activated by bile acids, leading to membrane association and expression of its target gene, vtrB, located in the T3SS2 pathogenicity island. VtrB, the transmembrane transcriptional activator of T3SS2, then induces the localized expression and membrane assembly of the T3SS2 structural components and its effectors. We hypothesize that the proposed transertion process may be used by other enteric bacteria for efficient assembly of membrane-bound molecular complexes in response to extracellular signals.
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Affiliation(s)
- Karan Gautam Kaval
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Sara D Siegel
- Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27606, USA
| | - Nalleli Garcia
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Jananee Jaishankar
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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24
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Sarmah P, Shang W, Origi A, Licheva M, Kraft C, Ulbrich M, Lichtenberg E, Wilde A, Koch HG. mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria. Cell Rep 2023; 42:112140. [PMID: 36842086 PMCID: PMC10066597 DOI: 10.1016/j.celrep.2023.112140] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 01/10/2023] [Accepted: 02/02/2023] [Indexed: 02/26/2023] Open
Abstract
Signal-sequence-dependent protein targeting is essential for the spatiotemporal organization of eukaryotic and prokaryotic cells and is facilitated by dedicated protein targeting factors such as the signal recognition particle (SRP). However, targeting signals are not exclusively contained within proteins but can also be present within mRNAs. By in vivo and in vitro assays, we show that mRNA targeting is controlled by the nucleotide content and by secondary structures within mRNAs. mRNA binding to bacterial membranes occurs independently of soluble targeting factors but is dependent on the SecYEG translocon and YidC. Importantly, membrane insertion of proteins translated from membrane-bound mRNAs occurs independently of the SRP pathway, while the latter is strictly required for proteins translated from cytosolic mRNAs. In summary, our data indicate that mRNA targeting acts in parallel to the canonical SRP-dependent protein targeting and serves as an alternative strategy for safeguarding membrane protein insertion when the SRP pathway is compromised.
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Affiliation(s)
- Pinku Sarmah
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University Freiburg, 79104 Freiburg, Germany
| | - Maximilian Ulbrich
- Internal Medicine IV, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | | | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
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25
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Hadjeras L, Bouvier M, Canal I, Poljak L, Morin-Ogier Q, Froment C, Burlet-Schlitz O, Hamouche L, Girbal L, Cocaign-Bousquet M, Carpousis AJ. Attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA in ribosome assembly intermediates. PLoS Biol 2023; 21:e3001942. [PMID: 36603027 PMCID: PMC9848016 DOI: 10.1371/journal.pbio.3001942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/18/2023] [Accepted: 12/01/2022] [Indexed: 01/06/2023] Open
Abstract
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.
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Affiliation(s)
- Lydia Hadjeras
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
| | - Marie Bouvier
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
| | - Isabelle Canal
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
| | - Leonora Poljak
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
| | | | - Carine Froment
- IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Infrastructure Nationale de Protéomique, ProFI, Toulouse, France
| | - Odile Burlet-Schlitz
- IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Infrastructure Nationale de Protéomique, ProFI, Toulouse, France
| | - Lina Hamouche
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
| | - Laurence Girbal
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Agamemnon J. Carpousis
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- * E-mail:
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26
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Li X, Chou T. Stochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling. Biophys J 2023; 122:254-266. [PMID: 36199250 PMCID: PMC9822797 DOI: 10.1016/j.bpj.2022.09.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 01/11/2023] Open
Abstract
Under certain cellular conditions, transcription and mRNA translation in prokaryotes appear to be "coupled," in which the formation of mRNA transcript and production of its associated protein are temporally correlated. Such transcription-translation coupling (TTC) has been evoked as a mechanism that speeds up the overall process, provides protection against premature termination, and/or regulates the timing of transcript and protein formation. What molecular mechanisms underlie ribosome-RNAP coupling and how they can perform these functions have not been explicitly modeled. We develop and analyze a continuous-time stochastic model that incorporates ribosome and RNAP elongation rates, initiation and termination rates, RNAP pausing, and direct ribosome and RNAP interactions (exclusion and binding). Our model predicts how distributions of delay times depend on these molecular features of transcription and translation. We also propose additional measures for TTC: a direct ribosome-RNAP binding probability and the fraction of time the translation-transcription process is "protected" from attack by transcription-terminating proteins. These metrics quantify different aspects of TTC and differentially depend on parameters of known molecular processes. We use our metrics to reveal how and when our model can exhibit either acceleration or deceleration of transcription, as well as protection from termination. Our detailed mechanistic model provides a basis for designing new experimental assays that can better elucidate the mechanisms of TTC.
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Affiliation(s)
- Xiangting Li
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California
| | - Tom Chou
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, California; Department of Mathematics, University of California, Los Angeles, Los Angeles, California.
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27
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Abstract
In bacteria, transcription and translation take place in the same cellular compartment. Therefore, a messenger RNA can be translated as it is being transcribed, a process known as transcription-translation coupling. This process was already recognized at the dawn of molecular biology, yet the interplay between the two key players, the RNA polymerase and ribosome, remains elusive. Genetic data indicate that an RNA sequence can be translated shortly after it has been transcribed. The closer both processes are in time, the less accessible the RNA sequence is between the RNA polymerase and ribosome. This temporal coupling has important consequences for gene regulation. Biochemical and structural studies have detailed several complexes between the RNA polymerase and ribosome. The in vivo relevance of this physical coupling has not been formally demonstrated. We discuss how both temporal and physical coupling may mesh to produce the phenomenon we know as transcription-translation coupling.
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Affiliation(s)
- Gregor M Blaha
- Department of Biochemistry, University of California, Riverside, California, USA;
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA;
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
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28
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Chandra S, Gupta K, Khare S, Kohli P, Asok A, Mohan SV, Gowda H, Varadarajan R. The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality. Mol Biol Evol 2022; 39:msac187. [PMID: 36069948 PMCID: PMC9555053 DOI: 10.1093/molbev/msac187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Deep mutational scanning studies suggest that synonymous mutations are typically silent and that most exposed, nonactive-site residues are tolerant to mutations. Here, we show that the ccdA antitoxin component of the Escherichia coli ccdAB toxin-antitoxin system is unusually sensitive to mutations when studied in the operonic context. A large fraction (∼80%) of single-codon mutations, including many synonymous mutations in the ccdA gene shows inactive phenotype, but they retain native-like binding affinity towards cognate toxin, CcdB. Therefore, the observed phenotypic effects are largely not due to alterations in protein structure/stability, consistent with a large region of CcdA being intrinsically disordered. E. coli codon preference and strength of ribosome-binding associated with translation of downstream ccdB gene are found to be major contributors of the observed ccdA mutant phenotypes. In select cases, proteomics studies reveal altered ratios of CcdA:CcdB protein levels in vivo, suggesting that the ccdA mutations likely alter relative translation efficiencies of the two genes in the operon. We extend these results by studying single-site synonymous mutations that lead to loss of function phenotypes in the relBE operon upon introduction of rarer codons. Thus, in their operonic context, genes are likely to be more sensitive to both synonymous and nonsynonymous point mutations than inferred previously.
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Affiliation(s)
- Soumyanetra Chandra
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kritika Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Pehu Kohli
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aparna Asok
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Harsha Gowda
- Institute of Bioinformatics, Bangalore 560100, India
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29
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Dash S, Palma CSD, Baptista ISC, Almeida BLB, Bahrudeen MNM, Chauhan V, Jagadeesan R, Ribeiro AS. Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes of E. coli. Nucleic Acids Res 2022; 50:8512-8528. [PMID: 35920318 PMCID: PMC9410904 DOI: 10.1093/nar/gkac643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/07/2022] [Accepted: 07/20/2022] [Indexed: 11/14/2022] Open
Abstract
Cold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while their single-cell protein numbers' variability increases after cold shock. We hypothesized that some cold shock repressed genes could be triggered by high propensity for transcription locking due to changes in DNA supercoiling (likely due to DNA relaxation caused by an overall reduction in negative supercoiling). Concomitantly, we found that nearly half of cold shock repressed genes are also highly responsive to gyrase inhibition (albeit most genes responsive to gyrase inhibition are not cold shock responsive). Further, their response strengths to cold shock and gyrase inhibition correlate. Meanwhile, under cold shock, nucleoid density increases, and gyrases and nucleoid become more colocalized. Moreover, the cellular energy decreases, which may hinder positive supercoils resolution. Overall, we conclude that sensitivity to diminished negative supercoiling is a core feature of E. coli's short-term, cold shock transcriptional program, and could be used to regulate the temperature sensitivity of synthetic circuits.
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Affiliation(s)
- Suchintak Dash
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Cristina S D Palma
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Ines S C Baptista
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Bilena L B Almeida
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Mohamed N M Bahrudeen
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Vatsala Chauhan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Rahul Jagadeesan
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Andre S Ribeiro
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland.,Center of Technology and Systems (CTS-Uninova), NOVA University of Lisbon 2829-516, Monte de Caparica, Portugal
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30
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Xiong HB, Pan HM, Long QY, Wang ZY, Qu WT, Mei T, Zhang N, Xu XF, Yang ZN, Yu QB. AtNusG, a chloroplast nucleoid protein of bacterial origin linking chloroplast transcriptional and translational machineries, is required for proper chloroplast gene expression in Arabidopsis thaliana. Nucleic Acids Res 2022; 50:6715-6734. [PMID: 35736138 PMCID: PMC9262611 DOI: 10.1093/nar/gkac501] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 05/25/2022] [Accepted: 06/20/2022] [Indexed: 12/24/2022] Open
Abstract
In Escherichia coli, transcription-translation coupling is mediated by NusG. Although chloroplasts are descendants of endosymbiotic prokaryotes, the mechanism underlying this coupling in chloroplasts remains unclear. Here, we report transcription-translation coupling through AtNusG in chloroplasts. AtNusG is localized in chloroplast nucleoids and is closely associated with the chloroplast PEP complex by interacting with its essential component PAP9. It also comigrates with chloroplast ribosomes and interacts with their two components PRPS5 (uS5c) and PRPS10 (uS10c). These data suggest that the transcription and translation machineries are coupled in chloroplasts. In the atnusg mutant, the accumulation of chloroplast-encoded photosynthetic gene transcripts, such as psbA, psbB, psbC and psbD, was not obviously changed, but that of their proteins was clearly decreased. Chloroplast polysomic analysis indicated that the decrease in these proteins was due to the reduced efficiency of their translation in this mutant, leading to reduced photosynthetic efficiency and enhanced sensitivity to cold stress. These data indicate that AtNusG-mediated coupling between transcription and translation in chloroplasts ensures the rapid establishment of photosynthetic capacity for plant growth and the response to environmental changes. Therefore, our study reveals a conserved mechanism of transcription-translation coupling between chloroplasts and E. coli, which perhaps represents a regulatory mechanism of chloroplast gene expression. This study provides insights into the underlying mechanisms of chloroplast gene expression in higher plants.
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Affiliation(s)
| | | | | | - Zi-Yuan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Wan-Tong Qu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Tong Mei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Nan Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Xiao-Feng Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Zhong-Nan Yang
- Correspondence may also be addressed to Zhong-Nan Yang. Tel: +86 21 64324650;
| | - Qing-Bo Yu
- To whom correspondence should be addressed. Tel: +86 21 64324812;
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31
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Suenaga Y, Kato M, Nagai M, Nakatani K, Kogashi H, Kobatake M, Makino T. Open reading frame dominance indicates protein‐coding potential of RNAs. EMBO Rep 2022; 23:e54321. [PMID: 35438231 PMCID: PMC9171421 DOI: 10.15252/embr.202154321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Recent studies have identified numerous RNAs with both coding and noncoding functions. However, the sequence characteristics that determine this bifunctionality remain largely unknown. In the present study, we develop and test the open reading frame (ORF) dominance score, which we define as the fraction of the longest ORF in the sum of all putative ORF lengths. This score correlates with translation efficiency in coding transcripts and with translation of noncoding RNAs. In bacteria and archaea, coding and noncoding transcripts have narrow distributions of high and low ORF dominance, respectively, whereas those of eukaryotes show relatively broader ORF dominance distributions, with considerable overlap between coding and noncoding transcripts. The extent of overlap positively and negatively correlates with the mutation rate of genomes and the effective population size of species, respectively. Tissue‐specific transcripts show higher ORF dominance than ubiquitously expressed transcripts, and the majority of tissue‐specific transcripts are expressed in mature testes. These data suggest that the decrease in population size and the emergence of testes in eukaryotic organisms allowed for the evolution of potentially bifunctional RNAs.
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Affiliation(s)
- Yusuke Suenaga
- Department of Molecular Carcinogenesis Chiba Cancer Centre Research Institute Chiba Japan
| | - Mamoru Kato
- Division of Bioinformatics National Cancer Centre Research Institute Tokyo Japan
| | - Momoko Nagai
- Division of Bioinformatics National Cancer Centre Research Institute Tokyo Japan
| | - Kazuma Nakatani
- Department of Molecular Carcinogenesis Chiba Cancer Centre Research Institute Chiba Japan
- Department of Molecular Biology and Oncology Chiba University School of Medicine Chiba Japan
- Innovative Medicine CHIBA Doctoral WISE Program Chiba University School of Medicine Chiba Japan
| | - Hiroyuki Kogashi
- Department of Molecular Carcinogenesis Chiba Cancer Centre Research Institute Chiba Japan
- Department of Molecular Biology and Oncology Chiba University School of Medicine Chiba Japan
| | - Miho Kobatake
- Department of Molecular Carcinogenesis Chiba Cancer Centre Research Institute Chiba Japan
| | - Takashi Makino
- Laboratory of Evolutionary Genomics Graduate School of Life Sciences Tohoku University Sendai Japan
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32
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Carpousis AJ, Campo N, Hadjeras L, Hamouche L. Compartmentalization of RNA Degradosomes in Bacteria Controls Accessibility to Substrates and Ensures Concerted Degradation of mRNA to Nucleotides. Annu Rev Microbiol 2022; 76:533-552. [PMID: 35671533 DOI: 10.1146/annurev-micro-041020-113308] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA degradosomes are multienzyme complexes composed of ribonucleases, RNA helicases, and metabolic enzymes. RNase E-based degradosomes are widespread in Proteobacteria. The Escherichia coli RNA degradosome is sequestered from transcription in the nucleoid and translation in the cytoplasm by localization to the inner cytoplasmic membrane, where it forms short-lived clusters that are proposed to be sites of mRNA degradation. In Caulobacter crescentus, RNA degradosomes localize to ribonucleoprotein condensates in the interior of the cell [bacterial ribonucleoprotein-bodies (BR-bodies)], which have been proposed to drive the concerted degradation of mRNA to nucleotides. The turnover of mRNA in growing cells is important for maintaining pools of nucleotides for transcription and DNA replication. Membrane attachment of the E. coli RNA degradosome is necessary to avoid wasteful degradation of intermediates in ribosome assembly. Sequestering RNA degradosomes to C. crescentus BR-bodies, which exclude structured RNA, could have a similar role in protecting intermediates in ribosome assembly from degradation. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Agamemnon J Carpousis
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , , .,TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nathalie Campo
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , ,
| | - Lydia Hadjeras
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , , .,Current affiliation: IMIB, University of Würzburg, Würzburg, Germany;
| | - Lina Hamouche
- LMGM, Université de Toulouse, CNRS, UPS, CBI, Toulouse, France; , ,
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33
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How to save a bacterial ribosome in times of stress. Semin Cell Dev Biol 2022; 136:3-12. [PMID: 35331628 DOI: 10.1016/j.semcdb.2022.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/01/2022] [Accepted: 03/11/2022] [Indexed: 11/21/2022]
Abstract
Biogenesis of ribosomes is one of the most cost- and resource-intensive processes in all living cells. In bacteria, ribosome biogenesis is rate-limiting for growth and must be tightly coordinated to yield maximum fitness of the cells. Since bacteria are continuously facing environmental changes and stress conditions, they have developed sophisticated systems to sense and regulate their nutritional status. Amino acid starvation leads to the synthesis and accumulation of the nucleotide-based second messengers ppGpp and pppGpp [(p)ppGpp], which in turn function as central players of a pleiotropic metabolic adaptation mechanism named the stringent response. Here, we review our current knowledge on the multiple roles of (p)ppGpp in the stress-related modulation of the prokaryotic protein biosynthesis machinery with the ribosome as its core constituent. The alarmones ppGpp/pppGpp act as competitors of their GDP/GTP counterparts, to affect a multitude of ribosome-associated P-loop GTPases involved in the translation cycle, ribosome biogenesis and hibernation. A similar mode of inhibition has been found for the GTPases of the proteins involved in the SRP-dependent membrane-targeting machinery present in the periphery of the ribosome. In this sense, during stringent conditions, binding of (p)ppGpp restricts the membrane insertion and secretion of proteins. Altogether, we highlight the enormously resource-intensive stages of ribosome biogenesis as a critical regulatory hub of the stringent response that ultimately tunes the protein synthesis capacity and consequently the survival of the cell.
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Chen PH, Sung LK, Hegemann JD, Chu J. Disrupting transcription and folate biosynthesis leads to synergistic suppression of Escherichia coli growth. ChemMedChem 2022; 17:e202200075. [PMID: 35201676 PMCID: PMC9314896 DOI: 10.1002/cmdc.202200075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 11/12/2022]
Abstract
The use of synergistic antibiotic combinations has emerged as a viable approach to contain the rapid spread of antibiotic‐resistant pathogens. Here we report the discovery of a new strongly synergistic pair – microcin J25 and sulfamonomethoxine. The former is a lasso peptide that inhibits the function of RNA polymerase and the latter is a sulfonamide antibacterial agent that disrupts the folate pathway. Key to our discovery was a screening strategy that focuses on an antibiotic (microcin J25) that targets a hub (transcription) in the densely interconnected network of cellular pathways. The rationale was that disrupting such a hub likely weakens the entire network, generating weak links that potentiate the growth inhibitory effect of other antibiotics. We found that MccJ25 potentiates five other antibiotics as well. These results showcase the merit of taking a more targeted approach in the search and study of synergistic antibiotic pairs.
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Affiliation(s)
- Pei-Hsin Chen
- National Taiwan University, Chemistry, No. 1, Sec. 4, Roosevelt Rd., 10617, Taipei, TAIWAN
| | | | - Julian D Hegemann
- Helmholtz Centre for Infection Research: Helmholtz-Zentrum fur Infektionsforschung GmbH, Helmholtz Institute for Pharmaceutical Research Saarland, GERMANY
| | - John Chu
- National Taiwan University, Chemistry, No.1, Sec.4, Roosevelt Road, Deptartment of Chemistry, Rm A521, 106319, Taipei, TAIWAN
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35
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Dai W, Darst SA, Dunham CM, Landick R, Petsko G, Weixlbaumer A. Seeing gene expression in cells: the future of structural biology. Fac Rev 2022; 10:79. [PMID: 35146496 DOI: 10.12703/r-01-000004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Although much is known about the machinery that executes fundamental processes of gene expression in cells, much also remains to be learned about how that machinery works. A recent paper by O'Reilly et al. reports a major step forward in the direct visualization of central dogma processes at submolecular resolution inside bacterial cells frozen in a native state. The essential methodologies involved are cross-linking mass spectrometry (CLMS) and cryo-electron tomography (cryo-ET). In-cell CLMS provides in vivo protein interaction maps. Cryo-ET allows visualization of macromolecular complexes in their native environment. These methods have been integrated by O'Reilly et al. to describe a dynamic assembly in situ between a transcribing RNA polymerase (RNAP) and a translating ribosome - a complex known as the expressome - in the model bacterium Mycoplasma pneumoniae 1. With the application of improved data processing and classification capabilities, this approach has allowed unprecedented insights into the architecture of this molecular assembly line, confirming the existence of a physical link between RNAP and the ribosome and identifying the transcription factor NusA as the linking molecule, as well as making it possible to see the structural effects of drugs that inhibit either transcription or translation. The work provides a glimpse into the future of integrative structural cell biology and can serve as a roadmap for the study of other molecular machineries in their native context.
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Affiliation(s)
- Wei Dai
- Institute for Quantitative Biomedicine, Rutgers University
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36
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Seale JSW, Feng Y, Feng L, Astumian RD, Stoddart JF. Polyrotaxanes and the pump paradigm. Chem Soc Rev 2022; 51:8450-8475. [DOI: 10.1039/d2cs00194b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The year 2022 marks the 30th anniversary of the first reports of polyrotaxanes in the scientific literature.
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Affiliation(s)
- James S. W. Seale
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Yuanning Feng
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Liang Feng
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - R. Dean Astumian
- Department of Physics and Astronomy, University of Maine, Orono, Maine 04469, USA
| | - J. Fraser Stoddart
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
- Stoddart Institute of Molecular Science, Department of Chemistry, Zhejiang University, Hangzhou 310021, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311215, China
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37
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Sattler L, Graumann PL. Real-Time Messenger RNA Dynamics in Bacillus subtilis. Front Microbiol 2021; 12:760857. [PMID: 34867890 PMCID: PMC8637298 DOI: 10.3389/fmicb.2021.760857] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Messenger RNA molecules have been localized to different positions in cells and have been followed by time-lapse microscopy. We have used MS2-mVenus-labeled mRNA and single-particle tracking to obtain information on the dynamics of single-mRNA molecules in real time. Using single-molecule tracking, we show that several mRNA molecules visualized via two MS2-binding sites and MS2-mVenus expressed in Bacillus subtilis cells show free diffusion through the entire cell and constrained motion predominantly close to the cell membrane and at the polar regions of the cells. Because constrained motion of mRNAs likely reflects molecules complexed with ribosomes, our data support the idea that translation occurs at sites surrounding the nucleoids. Squared displacement analyses show the existence of at least two distinct populations of molecules with different diffusion constants or possibly of three populations, for example, freely mobile mRNAs, mRNAs in transition complexes, or in complex with polysomes. Diffusion constants between differently sized mRNAs did not differ dramatically and were much lower than that of cytosolic proteins. These data agree with the large size of mRNA molecules and suggest that, within the viscous cytoplasm, size variations do not translate into mobility differences. However, at observed diffusion constants, mRNA molecules would be able to reach all positions within cells in a frame of seconds. We did not observe strong differences in the location of confined motion for mRNAs encoding mostly soluble or membrane proteins, indicating that there is no strong bias for localization of membrane protein-encoding transcripts for the cell membrane.
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Affiliation(s)
- Laura Sattler
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Peter L Graumann
- Centre for Synthetic Microbiology (SYNMIKRO) and Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
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38
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Zhu M, Mu H, Han F, Wang Q, Dai X. Quantitative analysis of asynchronous transcription-translation and transcription processivity in Bacillus subtilis under various growth conditions. iScience 2021; 24:103333. [PMID: 34805793 PMCID: PMC8586808 DOI: 10.1016/j.isci.2021.103333] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 10/25/2022] Open
Abstract
Tight coordination between transcription and translation has long been recognized as the hallmark of gene expression in bacteria. In Escherichia coli cells, disruption of the transcription-translation coordination leads to the loss of transcription processivity via triggering Rho-mediated premature transcription termination. Here we quantitatively characterize the transcription and translation kinetics in Gram-positive model bacterium Bacillus subtilis. We found that the speed of transcription elongation is much faster than that of translation elongation in B. subtilis under various growth conditions. Moreover, a Rho-independent loss of transcription processivity occurs constitutively in several genes/operons but is not subject to translational control. When the transcription elongation is decelerated under poor nutrients, low temperature, or nucleotide depletion, the loss of transcription processivity is strongly enhanced, suggesting that its degree is modulated by the speed of transcription elongation. Our study reveals distinct design principles of gene expression in E. coli and B. subtilis.
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Affiliation(s)
- Manlu Zhu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Haoyan Mu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Fei Han
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Qian Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
| | - Xiongfeng Dai
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, Hubei Province, China
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39
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Troung SF, Sukhodolets MV. The bacterial protein Hfq: Stable modifications and growth phase-dependent changes in SPAM profiles. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1183:122958. [PMID: 34628185 DOI: 10.1016/j.jchromb.2021.122958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 11/25/2022]
Abstract
In bacteria transcription is coupled to translation, and while it is broadly accepted that transcription-translation complexes (TTCs) are formed in growing bacterial cells, the exact spatial organization of these macromolecular assemblies is not known with certainty. Recent studies indicated the formation of orderly cytosolic superstructures in growing E. coli cells. The bacterial nucleic acid (NA)-binding protein Hfq has been shown to function at the interface of RNA synthesis-degradation machinery; multiple, independent studies link Hfq to orderly cytosolic assemblies. In this work, using fast cell lysis/2D-PAGE and in vitro reconstitution analyses we studied the Hfq modifications and small protein-associated molecules (SPAM). We demonstrate that native Hfq carries stable modifications and simulate 2D patterns of native Hfq-SPAM complexes in reconstitution experiments with purified Hfq and synthetic NA probes. We also demonstrate that genetically engineered Hfq lacking the conserved arginine residues positioned near the rim of the disc formed by the subunits' N-terminal domains binds DNA with a reduced affinity in comparison with wild-type Hfq. These results are consistent with the proposed Hfq-mediated DNA remodeling and point to the involvement of this patch of conserved arginines in interactions with DNA.
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Affiliation(s)
- Stanley F Troung
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, TX 77710, United States
| | - Maxim V Sukhodolets
- Department of Chemistry and Biochemistry, Lamar University, Beaumont, TX 77710, United States.
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40
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Webster MW, Weixlbaumer A. Macromolecular assemblies supporting transcription-translation coupling. Transcription 2021; 12:103-125. [PMID: 34570660 DOI: 10.1080/21541264.2021.1981713] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Coordination between the molecular machineries that synthesize and decode prokaryotic mRNAs is an important layer of gene expression control known as transcription-translation coupling. While it has long been known that translation can regulate transcription and vice-versa, recent structural and biochemical work has shed light on the underlying mechanistic basis. Complexes of RNA polymerase linked to a trailing ribosome (expressomes) have been structurally characterized in a variety of states at near-atomic resolution, and also directly visualized in cells. These data are complemented by recent biochemical and biophysical analyses of transcription-translation systems and the individual components within them. Here, we review our improved understanding of the molecular basis of transcription-translation coupling. These insights are discussed in relation to our evolving understanding of the role of coupling in cells.
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Affiliation(s)
- Michael W Webster
- Department of Integrated Structural Biology, Institut de Gé né tique et de Biologie Molé culaire et Cellulaire (IGBMC), Illkirch Cedex, France.,Université de Strasbourg, Strasbourg, France.,CNRS Umr 7104, Illkirch Cedex.,Inserm U1258, Illkirch Cedex, France
| | - Albert Weixlbaumer
- Department of Integrated Structural Biology, Institut de Gé né tique et de Biologie Molé culaire et Cellulaire (IGBMC), Illkirch Cedex, France.,Université de Strasbourg, Strasbourg, France.,CNRS Umr 7104, Illkirch Cedex.,Inserm U1258, Illkirch Cedex, France
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41
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The intricate relationship between transcription and translation. Proc Natl Acad Sci U S A 2021; 118:2106284118. [PMID: 33958445 DOI: 10.1073/pnas.2106284118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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42
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Weixlbaumer A, Grünberger F, Werner F, Grohmann D. Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World. Front Microbiol 2021; 12:661827. [PMID: 33995325 PMCID: PMC8116511 DOI: 10.3389/fmicb.2021.661827] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 03/30/2021] [Indexed: 01/07/2023] Open
Abstract
The lack of a nucleus is the defining cellular feature of bacteria and archaea. Consequently, transcription and translation are occurring in the same compartment, proceed simultaneously and likely in a coupled fashion. Recent cryo-electron microscopy (cryo-EM) and tomography data, also combined with crosslinking-mass spectrometry experiments, have uncovered detailed structural features of the coupling between a transcribing bacterial RNA polymerase (RNAP) and the trailing translating ribosome in Escherichia coli and Mycoplasma pneumoniae. Formation of this supercomplex, called expressome, is mediated by physical interactions between the RNAP-bound transcription elongation factors NusG and/or NusA and the ribosomal proteins including uS10. Based on the structural conservation of the RNAP core enzyme, the ribosome, and the universally conserved elongation factors Spt5 (NusG) and NusA, we discuss requirements and functional implications of transcription-translation coupling in archaea. We furthermore consider additional RNA-mediated and co-transcriptional processes that potentially influence expressome formation in archaea.
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Affiliation(s)
- Albert Weixlbaumer
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France
- Université de Strasbourg, Strasbourg, France
- CNRS UMR7104, Illkirch, France
- INSERM U1258, Illkirch, France
| | - Felix Grünberger
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
| | - Finn Werner
- RNAP Lab, Division of Biosciences, Institute for Structural and Molecular Biology, London, United Kingdom
| | - Dina Grohmann
- Institute of Microbiology and Archaea Centre, University of Regensburg, Regensburg, Germany
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
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43
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Yang J, Han YH, Im J, Seo SW. Synthetic protein quality control to enhance full-length translation in bacteria. Nat Chem Biol 2021; 17:421-427. [PMID: 33542534 DOI: 10.1038/s41589-021-00736-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/08/2021] [Indexed: 01/30/2023]
Abstract
Coupled transcription and translation processes in bacteria cause indiscriminate translation of intact and truncated messenger RNAs, inevitably generating nonfunctional polypeptides. Here, we devised a synthetic protein quality control (ProQC) system that enables translation only when both ends of mRNAs are present and followed by circularization based on sequence-specific RNA-RNA hybridization. We demonstrate that the ProQC system dramatically improved the fraction of full-length proteins among all synthesized polypeptides by selectively translating intact mRNA and reducing abortive translation. As a result, full-length protein synthesis increased up to 2.5-fold without changing the transcription or translation efficiency. Furthermore, we applied the ProQC system for 3-hydroxypropionic acid, violacein and lycopene production by ensuring full-length expression of enzymes in biosynthetic pathways, resulting in 1.6- to 2.3-fold greater biochemical production. We believe that our ProQC system can be universally applied to improve not only the quality of recombinant protein production but also efficiencies of metabolic pathways.
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Affiliation(s)
- Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea.,Institute of Chemical Processes, Seoul National University, Seoul, Korea
| | - Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea
| | - Jongwon Im
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea. .,Institute of Chemical Processes, Seoul National University, Seoul, Korea. .,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Korea. .,Bio-MAX Institute, Seoul National University, Seoul, Korea. .,Institute of Engineering Research, Seoul National University, Seoul, Korea.
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44
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Schärfen L, Neugebauer KM. Transcription Regulation Through Nascent RNA Folding. J Mol Biol 2021; 433:166975. [PMID: 33811916 DOI: 10.1016/j.jmb.2021.166975] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022]
Abstract
Folding of RNA into secondary structures through intramolecular base pairing determines an RNA's three-dimensional architecture and associated function. Simple RNA structures like stem loops can provide specialized functions independent of coding capacity, such as protein binding, regulation of RNA processing and stability, stimulation or inhibition of translation. RNA catalysis is dependent on tertiary structures found in the ribosome, tRNAs and group I and II introns. While the extent to which non-coding RNAs contribute to cellular maintenance is generally appreciated, the fact that both non-coding and coding RNA can assume relevant structural states has only recently gained attention. In particular, the co-transcriptional folding of nascent RNA of all classes has the potential to regulate co-transcriptional processing, RNP (ribonucleoprotein particle) formation, and transcription itself. Riboswitches are established examples of co-transcriptionally folded coding RNAs that directly regulate transcription, mainly in prokaryotes. Here we discuss recent studies in both prokaryotes and eukaryotes showing that structure formation may carry a more widespread regulatory logic during RNA synthesis. Local structures forming close to the catalytic center of RNA polymerases have the potential to regulate transcription by reducing backtracking. In addition, stem loops or more complex structures may alter co-transcriptional RNA processing or its efficiency. Several examples of functional structures have been identified to date, and this review provides an overview of physiologically distinct processes where co-transcriptionally folded RNA plays a role. Experimental approaches such as single-molecule FRET and in vivo structural probing to further advance our insight into the significance of co-transcriptional structure formation are discussed.
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Affiliation(s)
- Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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45
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Steinberg R, Koch HG. The largely unexplored biology of small proteins in pro- and eukaryotes. FEBS J 2021; 288:7002-7024. [PMID: 33780127 DOI: 10.1111/febs.15845] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 12/29/2022]
Abstract
The large abundance of small open reading frames (smORFs) in prokaryotic and eukaryotic genomes and the plethora of smORF-encoded small proteins became only apparent with the constant advancements in bioinformatic, genomic, proteomic, and biochemical tools. Small proteins are typically defined as proteins of < 50 amino acids in prokaryotes and of less than 100 amino acids in eukaryotes, and their importance for cell physiology and cellular adaptation is only beginning to emerge. In contrast to antimicrobial peptides, which are secreted by prokaryotic and eukaryotic cells for combatting pathogens and competitors, small proteins act within the producing cell mainly by stabilizing protein assemblies and by modifying the activity of larger proteins. Production of small proteins is frequently linked to stress conditions or environmental changes, and therefore, cells seem to use small proteins as intracellular modifiers for adjusting cell metabolism to different intra- and extracellular cues. However, the size of small proteins imposes a major challenge for the cellular machinery required for protein folding and intracellular trafficking and recent data indicate that small proteins can engage distinct trafficking pathways. In the current review, we describe the diversity of small proteins in prokaryotes and eukaryotes, highlight distinct and common features, and illustrate how they are handled by the protein trafficking machineries in prokaryotic and eukaryotic cells. Finally, we also discuss future topics of research on this fascinating but largely unexplored group of proteins.
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Affiliation(s)
- Ruth Steinberg
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
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46
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Irastortza-Olaziregi M, Amster-Choder O. Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises. Front Microbiol 2021; 11:624830. [PMID: 33552035 PMCID: PMC7858274 DOI: 10.3389/fmicb.2020.624830] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/18/2020] [Indexed: 01/17/2023] Open
Abstract
Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes associate with and initiate translation of mRNAs whose transcription has not yet concluded, therefore forming "RNAP.mRNA.ribosome" complexes. CTT is a well-documented phenomenon that is involved in important gene regulation processes, such as attenuation and operon polarity. Despite the progress in our understanding of the cellular signals that coordinate CTT, certain aspects of its molecular architecture remain controversial. Additionally, new information on the spatial segregation between the transcriptional and the translational machineries in certain species, and on the capability of certain mRNAs to localize translation-independently, questions the unanimous occurrence of CTT. Furthermore, studies where transcription and translation were artificially uncoupled showed that transcription elongation can proceed in a translation-independent manner. Here, we review studies supporting the occurrence of CTT and findings questioning its extent, as well as discuss mechanisms that may explain both coupling and uncoupling, e.g., chromosome relocation and the involvement of cis- or trans-acting elements, such as small RNAs and RNA-binding proteins. These mechanisms impact RNA localization, stability, and translation. Understanding the two options by which genes can be expressed and their consequences should shed light on a new layer of control of bacterial transcripts fate.
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Affiliation(s)
- Mikel Irastortza-Olaziregi
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, Faculty of Medicine, IMRIC, The Hebrew University of Jerusalem, Jerusalem, Israel
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47
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Wang B, Artsimovitch I. NusG, an Ancient Yet Rapidly Evolving Transcription Factor. Front Microbiol 2021; 11:619618. [PMID: 33488562 PMCID: PMC7819879 DOI: 10.3389/fmicb.2020.619618] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022] Open
Abstract
Timely and accurate RNA synthesis depends on accessory proteins that instruct RNA polymerase (RNAP) where and when to start and stop transcription. Among thousands of transcription factors, NusG/Spt5 stand out as the only universally conserved family of regulators. These proteins interact with RNAP to promote uninterrupted RNA synthesis and with diverse cellular partners to couple transcription to RNA processing, modification or translation, or to trigger premature termination of aberrant transcription. NusG homologs are present in all cells that utilize bacterial-type RNAP, from endosymbionts to plants, underscoring their ancient and essential function. Yet, in stark contrast to other core RNAP components, NusG family is actively evolving: horizontal gene transfer and sub-functionalization drive emergence of NusG paralogs, such as bacterial LoaP, RfaH, and UpxY. These specialized regulators activate a few (or just one) operons required for expression of antibiotics, capsules, secretion systems, toxins, and other niche-specific macromolecules. Despite their common origin and binding site on the RNAP, NusG homologs differ in their target selection, interacting partners and effects on RNA synthesis. Even among housekeeping NusGs from diverse bacteria, some factors promote pause-free transcription while others slow the RNAP down. Here, we discuss structure, function, and evolution of NusG proteins, focusing on unique mechanisms that determine their effects on gene expression and enable bacterial adaptation to diverse ecological niches.
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Affiliation(s)
- Bing Wang
- Department of Microbiology and the Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Irina Artsimovitch
- Department of Microbiology and the Center for RNA Biology, The Ohio State University, Columbus, OH, United States
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48
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Steinberg R, Origi A, Natriashvili A, Sarmah P, Licheva M, Walker PM, Kraft C, High S, Luirink J, Shi WQ, Helmstädter M, Ulbrich MH, Koch HG. Posttranslational insertion of small membrane proteins by the bacterial signal recognition particle. PLoS Biol 2020; 18:e3000874. [PMID: 32997663 PMCID: PMC7549839 DOI: 10.1371/journal.pbio.3000874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 10/12/2020] [Accepted: 09/02/2020] [Indexed: 01/05/2023] Open
Abstract
Small membrane proteins represent a largely unexplored yet abundant class of proteins in pro- and eukaryotes. They essentially consist of a single transmembrane domain and are associated with stress response mechanisms in bacteria. How these proteins are inserted into the bacterial membrane is unknown. Our study revealed that in Escherichia coli, the 27-amino-acid-long model protein YohP is recognized by the signal recognition particle (SRP), as indicated by in vivo and in vitro site-directed cross-linking. Cross-links to SRP were also observed for a second small membrane protein, the 33-amino-acid-long YkgR. However, in contrast to the canonical cotranslational recognition by SRP, SRP was found to bind to YohP posttranslationally. In vitro protein transport assays in the presence of a SecY inhibitor and proteoliposome studies demonstrated that SRP and its receptor FtsY are essential for the posttranslational membrane insertion of YohP by either the SecYEG translocon or by the YidC insertase. Furthermore, our data showed that the yohP mRNA localized preferentially and translation-independently to the bacterial membrane in vivo. In summary, our data revealed that YohP engages an unique SRP-dependent posttranslational insertion pathway that is likely preceded by an mRNA targeting step. This further highlights the enormous plasticity of bacterial protein transport machineries. Small membrane proteins represent a largely unexplored yet abundant class of proteins, but how they are inserted into the bacterial membrane is unknown. This study identifies a novel posttranslational protein transport pathway that relies on the signal recognition particle and the SecYEG translocon/YidC insertase.
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Affiliation(s)
- Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Ana Natriashvili
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Pinku Sarmah
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Princess M. Walker
- Department of Chemistry, Ball State University, Muncie, Indiana, United States of America
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Stephen High
- School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | - Joen Luirink
- Molecular Microbiology, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Wei. Q. Shi
- Department of Chemistry, Ball State University, Muncie, Indiana, United States of America
| | - Martin Helmstädter
- Internal Medicine IV, Department of Medicine, Medical Center − University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian H. Ulbrich
- Internal Medicine IV, Department of Medicine, Medical Center − University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- * E-mail:
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49
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Irastortza-Olaziregi M, Amster-Choder O. RNA localization in prokaryotes: Where, when, how, and why. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1615. [PMID: 32851805 DOI: 10.1002/wrna.1615] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/27/2020] [Accepted: 06/02/2020] [Indexed: 12/27/2022]
Abstract
Only recently has it been recognized that the transcriptome of bacteria and archaea can be spatiotemporally regulated. All types of prokaryotic transcripts-rRNAs, tRNAs, mRNAs, and regulatory RNAs-may acquire specific localization and these patterns can be temporally regulated. In some cases bacterial RNAs reside in the vicinity of the transcription site, but in many others, transcripts show distinct localizations to the cytoplasm, the inner membrane, or the pole of rod-shaped species. This localization, which often overlaps with that of the encoded proteins, can be achieved either in a translation-dependent or translation-independent fashion. The latter implies that RNAs carry sequence-level features that determine their final localization with the aid of RNA-targeting factors. Localization of transcripts regulates their posttranscriptional fate by affecting their degradation and processing, translation efficiency, sRNA-mediated regulation, and/or propensity to undergo RNA modifications. By facilitating complex assembly and liquid-liquid phase separation, RNA localization is not only a consequence but also a driver of subcellular spatiotemporal complexity. We foresee that in the coming years the study of RNA localization in prokaryotes will produce important novel insights regarding the fundamental understanding of membrane-less subcellular organization and lead to practical outputs with biotechnological and therapeutic implications. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Mikel Irastortza-Olaziregi
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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50
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Washburn RS, Zuber PK, Sun M, Hashem Y, Shen B, Li W, Harvey S, Acosta Reyes FJ, Gottesman ME, Knauer SH, Frank J. Escherichia coli NusG Links the Lead Ribosome with the Transcription Elongation Complex. iScience 2020; 23:101352. [PMID: 32726726 PMCID: PMC7390762 DOI: 10.1016/j.isci.2020.101352] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/04/2020] [Accepted: 07/03/2020] [Indexed: 02/07/2023] Open
Abstract
It has been known for more than 50 years that transcription and translation are physically coupled in bacteria, but whether or not this coupling may be mediated by the two-domain protein N-utilization substance (Nus) G in Escherichia coli is still heavily debated. Here, we combine integrative structural biology and functional analyses to provide conclusive evidence that NusG can physically link transcription with translation by contacting both RNA polymerase and the ribosome. We present a cryo-electron microscopy structure of a NusG:70S ribosome complex and nuclear magnetic resonance spectroscopy data revealing simultaneous binding of NusG to RNAP and the intact 70S ribosome, providing the first direct structural evidence for NusG-mediated coupling. Furthermore, in vivo reporter assays show that recruitment of NusG occurs late in transcription and strongly depends on translation. Thus, our data suggest that coupling occurs initially via direct RNAP:ribosome contacts and is then mediated by NusG.
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Affiliation(s)
- Robert S Washburn
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Philipp K Zuber
- Biochemistry IV - Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany
| | - Ming Sun
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Yaser Hashem
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Bingxin Shen
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Wen Li
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Sho Harvey
- University of Michigan, Ann Arbor, MI 48109, USA
| | - Francisco J Acosta Reyes
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA
| | - Max E Gottesman
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
| | - Stefan H Knauer
- Biochemistry IV - Biopolymers, University of Bayreuth, 95447 Bayreuth, Germany.
| | - Joachim Frank
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA.
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