1
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Pedraza-Reyes M, Abundiz-Yañez K, Rangel-Mendoza A, Martínez LE, Barajas-Ornelas RC, Cuéllar-Cruz M, Leyva-Sánchez HC, Ayala-García VM, Valenzuela-García LI, Robleto EA. Bacillus subtilis stress-associated mutagenesis and developmental DNA repair. Microbiol Mol Biol Rev 2024; 88:e0015823. [PMID: 38551349 PMCID: PMC11332352 DOI: 10.1128/mmbr.00158-23] [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: 04/04/2024] Open
Abstract
SUMMARYThe metabolic conditions that prevail during bacterial growth have evolved with the faithful operation of repair systems that recognize and eliminate DNA lesions caused by intracellular and exogenous agents. This idea is supported by the low rate of spontaneous mutations (10-9) that occur in replicating cells, maintaining genome integrity. In contrast, when growth and/or replication cease, bacteria frequently process DNA lesions in an error-prone manner. DNA repairs provide cells with the tools needed for maintaining homeostasis during stressful conditions and depend on the developmental context in which repair events occur. Thus, different physiological scenarios can be anticipated. In nutritionally stressed bacteria, different components of the base excision repair pathway may process damaged DNA in an error-prone approach, promoting genetic variability. Interestingly, suppressing the mismatch repair machinery and activating specific DNA glycosylases promote stationary-phase mutations. Current evidence also suggests that in resting cells, coupling repair processes to actively transcribed genes may promote multiple genetic transactions that are advantageous for stressed cells. DNA repair during sporulation is of interest as a model to understand how transcriptional processes influence the formation of mutations in conditions where replication is halted. Current reports indicate that transcriptional coupling repair-dependent and -independent processes operate in differentiating cells to process spontaneous and induced DNA damage and that error-prone synthesis of DNA is involved in these events. These and other noncanonical ways of DNA repair that contribute to mutagenesis, survival, and evolution are reviewed in this manuscript.
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Affiliation(s)
- Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Karen Abundiz-Yañez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Alejandra Rangel-Mendoza
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Lissett E. Martínez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Rocío C. Barajas-Ornelas
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Mayra Cuéllar-Cruz
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | | | | | - Luz I. Valenzuela-García
- Department of Sustainable Engineering, Advanced Materials Research Center (CIMAV), Arroyo Seco, Durango, Mexico
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2
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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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3
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García-Lozano M, Henzler C, Porras MÁG, Pons I, Berasategui A, Lanz C, Budde H, Oguchi K, Matsuura Y, Pauchet Y, Goffredi S, Fukatsu T, Windsor D, Salem H. Paleocene origin of a streamlined digestive symbiosis in leaf beetles. Curr Biol 2024; 34:1621-1634.e9. [PMID: 38377997 DOI: 10.1016/j.cub.2024.01.070] [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: 12/18/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024]
Abstract
Timing the acquisition of a beneficial microbe relative to the evolutionary history of its host can shed light on the adaptive impact of a partnership. Here, we investigated the onset and molecular evolution of an obligate symbiosis between Cassidinae leaf beetles and Candidatus Stammera capleta, a γ-proteobacterium. Residing extracellularly within foregut symbiotic organs, Stammera upgrades the digestive physiology of its host by supplementing plant cell wall-degrading enzymes. We observe that Stammera is a shared symbiont across tortoise and hispine beetles that collectively comprise the Cassidinae subfamily, despite differences in their folivorous habits. In contrast to its transcriptional profile during vertical transmission, Stammera elevates the expression of genes encoding digestive enzymes while in the foregut symbiotic organs, matching the nutritional requirements of its host. Despite the widespread distribution of Stammera across Cassidinae beetles, symbiont acquisition during the Paleocene (∼62 mya) did not coincide with the origin of the subfamily. Early diverging lineages lack the symbiont and the specialized organs that house it. Reconstructing the ancestral state of host-beneficial factors revealed that Stammera encoded three digestive enzymes at the onset of symbiosis, including polygalacturonase-a pectinase that is universally shared. Although non-symbiotic cassidines encode polygalacturonase endogenously, their repertoire of plant cell wall-degrading enzymes is more limited compared with symbiotic beetles supplemented with digestive enzymes from Stammera. Highlighting the potential impact of a symbiotic condition and an upgraded metabolic potential, Stammera-harboring beetles exploit a greater variety of plants and are more speciose compared with non-symbiotic members of the Cassidinae.
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Affiliation(s)
- Marleny García-Lozano
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Christine Henzler
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | | | - Inès Pons
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Aileen Berasategui
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany; Amsterdam Institute for Life and Environment, Vrije Universiteit, Amsterdam 1081 HV, the Netherlands
| | - Christa Lanz
- Genome Center, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Heike Budde
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen 72076, Germany
| | - Kohei Oguchi
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan; Misaki Marine Biological Station, The University of Tokyo, Miura 238-0225, Japan
| | - Yu Matsuura
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 903-0213, Japan
| | - Yannick Pauchet
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Shana Goffredi
- Department of Biology, Occidental College, Los Angeles, CA 90041, USA
| | - Takema Fukatsu
- National Institute for Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
| | - Donald Windsor
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama
| | - Hassan Salem
- Mutualisms Research Group, Max Planck Institute for Biology, Tübingen 72076, Germany; Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama.
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4
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Furumo Q, Meyer M. PIPETS: A statistically robust, gene-annotation agnostic analysis method to study bacterial termination using 3'-end sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585559. [PMID: 38562853 PMCID: PMC10983905 DOI: 10.1101/2024.03.18.585559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
We present PIPETS, an R package available on Bioconductor that provides a novel analysis approach to study 3'-end sequencing data. PIPETS statistically robust, gene-annotation agnostic methodology identified more significant 3'-end termination signal across a wider range of genomic contexts than existing analysis tools. PIPETS provides a broadly applicable platform to compare data sets across different organisms.
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Affiliation(s)
- Quinlan Furumo
- Department of Biology, Boston College, Chestnut Hill, MA, 02135, United States
| | - Michelle Meyer
- Department of Biology, Boston College, Chestnut Hill, MA, 02135, United States
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5
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Gupta S, Pal D. Utilizing RNA-seq Data to Infer Bacterial Transcription Termination Sites and Validate Predictions. Methods Mol Biol 2024; 2812:345-365. [PMID: 39068372 DOI: 10.1007/978-1-0716-3886-6_19] [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] [Indexed: 07/30/2024]
Abstract
The transcription termination process is an important part of the gene expression process in the cell. It has been studied extensively, but many aspects of the mechanism are not well understood. The widespread availability of experimental RNA-seq data from high-throughput experiments provides a unique opportunity to infer the end of the transcription units genome wide. This data is available for both Rho-dependent and Rho-independent termination pathways that drive transcription termination in bacteria. Our book chapter gives an overview of the current knowledge of Rho-independent transcription termination mechanisms and the prediction approaches currently deployed to infer the termination sites. Thereafter, we describe our method that uses cluster hairpins to detect Rho-independent transcription termination sites. These clusters are a group of hairpins that lies at <15 bp from each other and are together capable of enforcing the termination process. The idea of a group of hairpins being extensively used for transcription termination is new, and results show that at least 52% of the total cases are of this type, while in the remaining cases, a single strong hairpin is capable of driving transcription termination. The reads derived from the RNA-seq data for corresponding bacteria have been used to validate the predicted sites. The predictions that match these RNA-seq derived sites have higher confidence, and we find almost 98% of the predicted sites, including alternate termination sites, to match the RNA-seq data. We discuss the features of predicted hairpins in detail for a better understanding of the Rho-independent transcription termination mechanism in bacteria. We also explain how users can use the tools developed by us to do transcription terminator predictions and design their experiments through genome-level visualization of the transcription termination sites from the precomputed INTERPIN database.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, Karnataka, India.
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6
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Cui W, Lin Q, Wu Y, Wang X, Zhang Y, Lin X, Zhang L, Liu X, Han L, Zhou Z. Creation of Architecturally Minimal Transcriptionally Activating Riboswitches Responsive to Theophylline Reveals an Unconventional Design Strategy. ACS Synth Biol 2023; 12:3716-3729. [PMID: 38052004 DOI: 10.1021/acssynbio.3c00519] [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] [Indexed: 12/07/2023]
Abstract
Riboswitches are noncoding RNA switches that are largely utilized in bacteria and play a significant role in synthetic biology. Nonetheless, their natural counterparts possess lengthy sequences and intricate structures, posing challenges for their modular integration into complex gene circuits. Consequently, it is imperative to develop simplified synthetic riboswitches that can be effortlessly incorporated into gene circuits. The conventional approach to generate synthetic riboswitches entails tedious library construction and extensive screening, which frequently yields suboptimal performance. To overcome this obstacle, alternative methods are urgently needed. In this study, we created a novel approach to designing a diverse set of transcription-activating riboswitches that exhibit high performance and broad compatibility. The strategy involved starting with a synthetic theophylline RNA aptamer and designing an expression platform that forms a transcriptional terminator in its inactive state but switches to an antiterminator when it is activated. Several sequences were designed, constructed, and subjected to virtual screening, resulting in the identification of two transcription-activating riboswitches. These riboswitches were then engineered to reduce the basal leakage and increase the activation level through extending the hairpin region using a screened random sequence. These architecturally minimal synthetic riboswitches were highly adapted to different constitutive promoters in a modular manner, generating a differentially responsive output to theophylline. As a proof-of-principle, the synthetic riboswitches were applied to rewire a synthetic quorum-sensing circuit (QSC). The reprogrammed QSC successfully modulated the temporal responsive profile against the activation. This strategy is expected to expand the variety of high-performance riboswitches that are responsive to different ligands, thereby further facilitating the design of complex genetic circuits.
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Affiliation(s)
- Wenjing Cui
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, MOE, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qiao Lin
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yi Wu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinran Wang
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yuqing Zhang
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xinyu Lin
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Linpei Zhang
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, MOE, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xu Liu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Laichuang Han
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, MOE, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhemin Zhou
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, MOE, Jiangnan University, Wuxi, Jiangsu 214122, China
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7
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Gupta S, Padmashali N, Pal D. INTERPIN: A repository for intrinsic transcription termination hairpins in bacteria. Biochimie 2023; 214:228-236. [PMID: 37499897 DOI: 10.1016/j.biochi.2023.07.018] [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: 03/09/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
The large-scale detection of putative intrinsic transcription terminators is limited to only a few bacteria currently. We discovered a group of hairpins, called cluster hairpins, present within 15 nucleotides from each other. These are expected to work in tandem to cause intrinsic transcription termination (ITT), while the single hairpin can do the same alone. Therefore, exploring these ITT sites and the hairpins across bacterial genomes becomes highly desirable. INTERPIN is the largest archived collection of in silico inferred ITT hairpins in bacteria, covering 12745 bacterial genomes and encompassing ten bacterial phyla for ∼25 million hairpins. Users can obtain details on operons, individual cluster, and single ITT hairpins that were screened therein. Integrated Genome Viewer (IGV) software interactively visualizes hairpin secondary and tertiary structures in the genomic context. We also discuss statistics for the occurrence of cluster or single hairpins and other termination alternatives while showing the validation of predicted hairpins against in vivo detected hairpins. The database is freely available at http://pallab.cds.iisc.ac.in/INTERPIN/. INTERPIN (database and software) can make predictions for both AT and GC-rich genomes, which has not been achieved by any other program so far. It can also be used to improve genome annotation as well as to get predictions to improve the understanding of the ITT pathway by further analysis.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Namrata Padmashali
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bengaluru, 560012, Karnataka, India.
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8
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Miguel-Arribas A, Martín-María A, Alaerds ECW, Val-Calvo J, Yuste L, Rojo F, Abia D, Wu L, Meijer WJJ. Extraordinary long-stem confers resistance of intrinsic terminators to processive antitermination. Nucleic Acids Res 2023; 51:6073-6086. [PMID: 37125647 PMCID: PMC10325885 DOI: 10.1093/nar/gkad333] [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: 10/06/2022] [Revised: 03/14/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023] Open
Abstract
Many prokaryotic operons encode a processive antitermination (P-AT) system. Transcription complexes associated with an antitermination factor can bypass multiple transcription termination signals regardless of their sequences. However, to avoid compromising transcriptional regulation of downstream regions, the terminator at the end of the operon needs to be resistant to antitermination. So far, no studies on the mechanism of resistance to antitermination have been reported. The recently discovered conAn P-AT system is composed of two components that are encoded at the start of many conjugation operons on plasmids of Gram-positive bacteria. Here we report the identification of a conAn-resistant terminator, named TerR, in the conjugation operon of the Bacillus subtilis plasmid pLS20, re-defining the end of the conjugation operon. We investigated the various characteristics of TerR and show that its extraordinary long stem is the determining feature for resistance to antitermination. This is the first P-AT resistance mechanism to be reported.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Ana Martín-María
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Eef C W Alaerds
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Luis Yuste
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, C. Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, C. Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa”, (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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9
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Petroni E, Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi. Nat Commun 2023; 14:3931. [PMID: 37402717 DOI: 10.1038/s41467-023-39576-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023] Open
Abstract
Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. Here, we use several RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi - the etiological agent of Lyme disease. We identify complex gene arrangements and operons, untranslated regions and small RNAs. We predict intrinsic terminators and experimentally test examples of Rho-dependent transcription termination. Remarkably, 63% of RNA 3' ends map upstream of or internal to open reading frames (ORFs), including genes involved in the unique infectious cycle of B. burgdorferi. We suggest these RNAs result from premature termination, processing and regulatory events such as cis-acting regulation. Furthermore, the polyamine spermidine globally influences the generation of truncated mRNAs. Collectively, our findings provide insights into transcription termination and uncover an abundance of potential RNA regulators in B. burgdorferi.
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Affiliation(s)
- Emily Petroni
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Daniel Tetreault
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Ryan K Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA
| | - Philip P Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA.
- Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD, 20892, USA.
- Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD, 20892, USA.
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10
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Zhang Y, Han W, Wang L, Wang H, Jia Q, Chen T, Wang S, Li M. Correlative Escherichia coli Transcription Rate and Bubble Conformation Remodeled by NusA and NusG. J Phys Chem B 2023; 127:2909-2917. [PMID: 36977198 DOI: 10.1021/acs.jpcb.2c08771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Transcription is highly regulated by a variety of transcription factors, among which NusA and NusG act contradictorily in Escherichia coli (E. coli) that NusA stabilizes a paused RNA polymerase (RNAP) and NusG suppresses it. The mechanism of the NusA and NusG regulations on RNAP transcription has been addressed, but their effect on the conformational changes of the transcription bubble correlated with transcription kinetics remains elusive. By using single-molecule magnetic trap, we identify a reduction in the transcription rate of ∼40% events by NusA. Although the rest ∼60% of transcription events exhibit unaffected transcription rates, a NusA-enhanced standard deviation of the transcription rate is observed. NusA remodeling also increases the extent of DNA unwinding in the transcription bubble by 1-2 base pairs, which can be reduced by NusG. The NusG remodeling is more significant on the RNAP molecules with reduced transcription rates rather than those without. Our results provide a quantitative view on the mechanisms of transcriptional regulation by NusA and NusG factors.
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Affiliation(s)
- Yuqiong Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Weijing Han
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Lisha Wang
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Hao Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qi Jia
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
| | - Tongsheng Chen
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong 510631, China
| | - Shuang Wang
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ming Li
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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11
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Ahmad E, Mitra A, Ahmed W, Mahapatra V, Hegde SR, Sala C, Cole ST, Nagaraja V. Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194923. [PMID: 36822574 DOI: 10.1016/j.bbagrm.2023.194923] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Abstract
Intrinsic and Rho-dependent transcription termination mechanisms regulate gene expression and recycle RNA polymerase in bacteria. Both the modes are well studied in Escherichia coli, and a few other organisms. The understanding of Rho function is limited in most other bacteria including mycobacteria. Here, we highlight the dominance of Rho-dependent termination in mycobacteria and validate Rho as a key regulatory factor. The lower abundance of intrinsic terminators, high cellular levels of Rho, and its genome-wide association with a majority of transcriptionally active genes indicate the pronounced role of Rho-mediated termination in Mycobacterium tuberculosis (Mtb). Rho modulates the termination of RNA synthesis for both protein-coding and stable RNA genes in Mtb. Concordantly, the depletion of Rho in mycobacteria impact its growth and enhances the transcription read-through at 3' ends of the transcription units. We demonstrate that MtbRho is catalytically active in the presence of RNA with varied secondary structures. These properties suggest an evolutionary adaptation of Rho as the efficient and preponderant mode of transcription termination in mycobacteria.
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Affiliation(s)
- Ezaz Ahmad
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Anirban Mitra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Wareed Ahmed
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Varsha Mahapatra
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India
| | - Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru 560100, India
| | - Claudia Sala
- Monoclonal Antibody Discovery Laboratory, Fondazione Toscana Life Sciences, 53100 Siena, Italy
| | | | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru 560012, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru 560064, India.
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12
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Allosteric mechanism of transcription inhibition by NusG-dependent pausing of RNA polymerase. Proc Natl Acad Sci U S A 2023; 120:e2218516120. [PMID: 36745813 PMCID: PMC9963633 DOI: 10.1073/pnas.2218516120] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
NusG is a transcription elongation factor that stimulates transcription pausing in Gram+ bacteria including B. subtilis by sequence-specific interaction with a conserved pause-inducing -11TTNTTT-6 motif found in the non-template DNA (ntDNA) strand within the transcription bubble. To reveal the structural basis of NusG-dependent pausing, we determined a cryo-EM structure of a paused transcription complex (PTC) containing RNA polymerase (RNAP), NusG, and the TTNTTT motif in the ntDNA strand. The interaction of NusG with the ntDNA strand rearranges the transcription bubble by positioning three consecutive T residues in a cleft between NusG and the β-lobe domain of RNAP. We revealed that the RNAP swivel module rotation (swiveling), which widens (swiveled state) and narrows (non-swiveled state) a cleft between NusG and the β-lobe, is an intrinsic motion of RNAP and is directly linked to trigger loop (TL) folding, an essential conformational change of all cellular RNAPs for the RNA synthesis reaction. We also determined cryo-EM structures of RNAP escaping from the paused transcription state. These structures revealed the NusG-dependent pausing mechanism by which NusG-ntDNA interaction inhibits the transition from swiveled to non-swiveled states, thereby preventing TL folding and RNA synthesis allosterically. This motion is also reduced by the formation of an RNA hairpin within the RNA exit channel. Thus, the pause half-life can be modulated by the strength of the NusG-ntDNA interaction and/or the stability of the RNA hairpin. NusG residues that interact with the TTNTTT motif are widely conserved in bacteria, suggesting that NusG-dependent pausing is widespread.
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13
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Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase. PLoS Genet 2023; 19:e1010618. [PMID: 36735730 PMCID: PMC9931155 DOI: 10.1371/journal.pgen.1010618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/15/2023] [Accepted: 01/14/2023] [Indexed: 02/04/2023] Open
Abstract
Transcription termination factor Rho is known for its ubiquitous role in suppression of pervasive, mostly antisense, transcription. In the model Gram-positive bacterium Bacillus subtilis, de-repression of pervasive transcription by inactivation of rho revealed the role of Rho in the regulation of post-exponential differentiation programs. To identify other aspects of the regulatory role of Rho during adaptation to starvation, we have constructed a B. subtilis strain (Rho+) that expresses rho at a relatively stable high level in order to compensate for its decrease in the wild-type cells entering stationary phase. The RNAseq analysis of Rho+, WT and Δrho strains (expression profiles can be visualized at http://genoscapist.migale.inrae.fr/seb_rho/) shows that Rho over-production enhances the termination efficiency of Rho-sensitive terminators, thus reducing transcriptional read-through and antisense transcription genome-wide. Moreover, the Rho+ strain exhibits global alterations of sense transcription with the most significant changes observed for the AbrB, CodY, and stringent response regulons, forming the pathways governing the transition to stationary phase. Subsequent physiological analyses demonstrated that maintaining rho expression at a stable elevated level modifies stationary phase-specific physiology of B. subtilis cells, weakens stringent response, and thereby negatively affects the cellular adaptation to nutrient limitations and other stresses, and blocks the development of genetic competence and sporulation. These results highlight the Rho-specific termination of transcription as a novel element controlling stationary phase. The release of this control by decreasing Rho levels during the transition to stationary phase appears crucial for the functionality of complex gene networks ensuring B. subtilis survival in stationary phase.
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14
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Petroni E, Esnault C, Tetreault D, Dale RK, Storz G, Adams PP. Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen B. burgdorferi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522626. [PMID: 36712141 PMCID: PMC9881889 DOI: 10.1101/2023.01.04.522626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. We employed complementary RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi - the etiological agent of Lyme disease. By systematically mapping B. burgdorferi RNA ends at single nucleotide resolution, we delineated complex gene arrangements and operons and mapped untranslated regions (UTRs) and small RNAs (sRNAs). We experimentally tested modes of B. burgdorferi transcription termination and compared our findings to observations in E. coli , P. aeruginosa , and B. subtilis . We discovered 63% of B. burgdorferi RNA 3' ends map upstream or internal to open reading frames (ORFs), suggesting novel mechanisms of regulation. Northern analysis confirmed the presence of stable 5' derived RNAs from mRNAs encoding gene products involved in the unique infectious cycle of B. burgdorferi . We suggest these RNAs resulted from premature termination and regulatory events, including forms of cis- acting regulation. For example, we documented that the polyamine spermidine globally influences the generation of truncated mRNAs. In one case, we showed that high spermidine concentrations increased levels of RNA fragments derived from an mRNA encoding a spermidine import system, with a concomitant decrease in levels of the full- length mRNA. Collectively, our findings revealed new insight into transcription termination and uncovered an abundance of potential RNA regulators.
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Affiliation(s)
- Emily Petroni
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Caroline Esnault
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Daniel Tetreault
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Ryan K. Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Philip P. Adams
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.,Postdoctoral Research Associate Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD 20892, USA.,Independent Research Scholar Program, Intramural Research Program, National Institutes of Health, Bethesda, MD 20892, USA.,correspondence:
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15
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Mandell ZF, Vishwakarma RK, Yakhnin H, Murakami KS, Kashlev M, Babitzke P. Comprehensive transcription terminator atlas for Bacillus subtilis. Nat Microbiol 2022; 7:1918-1931. [PMID: 36192538 PMCID: PMC10024249 DOI: 10.1038/s41564-022-01240-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/26/2022] [Indexed: 01/12/2023]
Abstract
The transcriptome-wide contributions of Rho-dependent and intrinsic (Rho-independent) transcription termination mechanisms in bacteria are unclear. By sequencing released transcripts in a wild-type strain and strains containing deficiencies in NusA, NusG and/or Rho (10 strains), we produced an atlas of terminators for the model Gram-positive bacterium Bacillus subtilis. We found that NusA and NusG stimulate 77% and 19% of all intrinsic terminators, respectively, and that both proteins participate in Rho-dependent termination. We also show that Rho stimulates termination at 10% of the intrinsic terminators in vivo. We recapitulated Rho-stimulated intrinsic termination at 5 terminators in vitro and found that Rho requires the KOW domain of NusG to stimulate this process at one of these terminators. Computational analyses of our atlas using RNAstructure, MEME suite and DiffLogo, combined with in vitro transcription experiments, revealed that Rho stimulates intrinsic terminators with weak hairpins and/or U-rich tracts by remodelling the RNA upstream of the intrinsic terminator to prevent the formation of RNA structures that could otherwise compete with the terminator hairpin. We also identified 56 putative examples of 'hybrid Rho-dependent termination', wherein classical Rho-dependent termination occurs after readthrough of a Rho-stimulated intrinsic terminator.
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Affiliation(s)
- Zachary F Mandell
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Molecular Biology and Genetics and Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Rishi K Vishwakarma
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Helen Yakhnin
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Katsuhiko S Murakami
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Mikhail Kashlev
- NCI RNA Biology Laboratory, Center for Cancer Research, NCI, Frederick, MD, USA
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA.
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16
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Mandell ZF, Zemba D, Babitzke P. Factor-stimulated intrinsic termination: getting by with a little help from some friends. Transcription 2022; 13:96-108. [PMID: 36154805 PMCID: PMC9715273 DOI: 10.1080/21541264.2022.2127602] [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: 07/11/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 01/12/2023] Open
Abstract
Transcription termination is known to occur via two mechanisms in bacteria, intrinsic termination (also frequently referred to as Rho-independent or factor-independent termination) and Rho-dependent termination. Based primarily on in vitro studies using Escherichia coli RNA polymerase, it was generally assumed that intrinsic termination and Rho-dependent termination are distinct mechanisms and that the signals required for intrinsic termination are present primarily within the nucleic acids. In this review, we detail recent findings from studies in Bacillus subtilis showing that intrinsic termination in this organism is highly stimulated by NusA, NusG, and even Rho. In NusA-stimulated intrinsic termination, NusA facilitates the formation of weak terminator hairpins and compensates for distal U-rich tract interruptions. In NusG-stimulated intrinsic termination, NusG stabilizes a sequence-dependent pause at the point of termination, which extends the time frame for RNA hairpins with weak terminal base pairs to form in either a NusA-stimulated or a NusA-independent fashion. In Rho-stimulated intrinsic termination, Rho prevents the formation of antiterminator-like RNA structures that could otherwise compete with the terminator hairpin. Combined, NusA, NusG, and Rho stimulate approximately 97% of all intrinsic terminators in B. subtilis. Thus, the general view that intrinsic termination is primarily a factor-independent process needs to be revised to account for recent findings. Moreover, the historical distinction between Rho-dependent and intrinsic termination is overly simplistic and needs to be modernized.
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Affiliation(s)
- Zachary F. Mandell
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States
- Department of Molecular Biology and Genetics and Department of Biology, Johns Hopkins University, Baltimore, MD, United State
| | - Dani Zemba
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, United States
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17
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Takada H, Mandell ZF, Yakhnin H, Glazyrina A, Chiba S, Kurata T, Wu KJY, Tresco BIC, Myers AG, Aktinson GC, Babitzke P, Hauryliuk V. Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp. Nucleic Acids Res 2022; 50:6174-6189. [PMID: 35699226 PMCID: PMC9226507 DOI: 10.1093/nar/gkac497] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/22/2022] [Accepted: 05/26/2022] [Indexed: 12/14/2022] Open
Abstract
Since antibiotic resistance is often associated with a fitness cost, bacteria employ multi-layered regulatory mechanisms to ensure that expression of resistance factors is restricted to times of antibiotic challenge. In Bacillus subtilis, the chromosomally-encoded ABCF ATPase VmlR confers resistance to pleuromutilin, lincosamide and type A streptogramin translation inhibitors. Here we show that vmlR expression is regulated by translation attenuation and transcription attenuation mechanisms. Antibiotic-induced ribosome stalling during translation of an upstream open reading frame in the vmlR leader region prevents formation of an anti-antiterminator structure, leading to the formation of an antiterminator structure that prevents intrinsic termination. Thus, transcription in the presence of antibiotic induces vmlR expression. We also show that NusG-dependent RNA polymerase pausing in the vmlR leader prevents leaky expression in the absence of antibiotic. Furthermore, we demonstrate that induction of VmlR expression by compromised protein synthesis does not require the ability of VmlR to rescue the translational defect, as exemplified by constitutive induction of VmlR by ribosome assembly defects. Rather, the specificity of induction is determined by the antibiotic's ability to stall the ribosome on the regulatory open reading frame located within the vmlR leader. Finally, we demonstrate the involvement of (p)ppGpp-mediated signalling in antibiotic-induced VmlR expression.
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Affiliation(s)
- Hiraku Takada
- Faculty of Life Sciences, Kyoto Sangyo University and Institute for Protein Dynamics, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden
| | - Zachary F Mandell
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Helen Yakhnin
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Anastasiya Glazyrina
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University and Institute for Protein Dynamics, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Tatsuaki Kurata
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Kelvin J Y Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ben I C Tresco
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Andrew G Myers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gemma C Aktinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, 90187 Umeå, Sweden
- University of Tartu, Institute of Technology, 50411, Tartu, Estonia
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18
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Chhabra S, Mandell ZF, Liu B, Babitzke P, Bechhofer DH. Analysis of mRNA Decay Intermediates in Bacillus subtilis 3' Exoribonuclease and RNA Helicase Mutant Strains. mBio 2022; 13:e0040022. [PMID: 35311531 PMCID: PMC9040804 DOI: 10.1128/mbio.00400-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 02/28/2022] [Indexed: 12/22/2022] Open
Abstract
The Bacillus subtilis genome encodes four 3' exoribonucleases: polynucleotide phosphorylase (PNPase), RNase R, RNase PH, and YhaM. Previous work showed that PNPase, encoded by the pnpA gene, is the major 3' exonuclease involved in mRNA turnover; in a pnpA deletion strain, numerous mRNA decay intermediates accumulate. Whether B. subtilis mRNA decay occurs in the context of a degradosome complex is controversial. In this study, global mapping of mRNA decay intermediate 3' ends within coding sequences was performed in strains that were either deleted for or had an inactivating point mutation in the pnpA gene. The patterns of 3'-end accumulation in these strains were highly similar, which may have implications for the role of a degradosome in mRNA decay. A comparison with mapped 3' ends in a strain lacking CshA, the major RNA helicase, indicated that many mRNAs require both PNPase and CshA for efficient decay. Transcriptome sequencing (RNA-seq) analysis of strains lacking RNase R suggested that this enzyme did not play a major role in mRNA turnover in the wild-type strain. Strains were constructed that contained only one of the four known 3' exoribonucleases. When RNase R was the only 3' exonuclease present, it was able to degrade a model mRNA efficiently, showing processive decay even through a strong stem-loop structure that inhibits PNPase processivity. Strains containing only RNase PH or only YhaM were also insensitive to this RNA secondary structure, suggesting the existence of another, as-yet-unidentified, 3' exoribonuclease. IMPORTANCE The ability to rapidly change bacterial gene expression programs in response to environmental conditions is highly dependent on the efficient turnover of mRNA. While much is known about the regulation of gene expression at the transcriptional and translational levels, much less is known about the intermediate step of mRNA decay. Here, we mapped the 3' ends of mRNA decay intermediates in strains that were missing the major 3' exoribonuclease PNPase or the RNA helicase CshA. We also assessed the roles of three other B. subtilis 3' exonucleases in the mRNA decay process. The data confirm the primary role of PNPase in mRNA turnover and suggest the involvement of one or more unknown RNases.
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Affiliation(s)
- Shivani Chhabra
- Icahn School of Medicine at Mount Sinai, Department of Pharmacological Sciences, New York, New York, USA
| | - Zachary F. Mandell
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, University Park, Pennsylvania, USA
| | - Bo Liu
- Icahn School of Medicine at Mount Sinai, Department of Pharmacological Sciences, New York, New York, USA
| | - Paul Babitzke
- The Pennsylvania State University, Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, University Park, Pennsylvania, USA
| | - David H. Bechhofer
- Icahn School of Medicine at Mount Sinai, Department of Pharmacological Sciences, New York, New York, USA
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19
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Cheng L, White EN, Brandt NL, Yu AM, Chen AA, Lucks J. Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch. Nucleic Acids Res 2022; 50:12001-12018. [PMID: 35348734 PMCID: PMC9756952 DOI: 10.1093/nar/gkac102] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/17/2022] [Accepted: 02/02/2022] [Indexed: 12/24/2022] Open
Abstract
RNA folds cotranscriptionally to traverse out-of-equilibrium intermediate structures that are important for RNA function in the context of gene regulation. To investigate this process, here we study the structure and function of the Bacillus subtilis yxjA purine riboswitch, a transcriptional riboswitch that downregulates a nucleoside transporter in response to binding guanine. Although the aptamer and expression platform domain sequences of the yxjA riboswitch do not completely overlap, we hypothesized that a strand exchange process triggers its structural switching in response to ligand binding. In vivo fluorescence assays, structural chemical probing data and experimentally informed secondary structure modeling suggest the presence of a nascent intermediate central helix. The formation of this central helix in the absence of ligand appears to compete with both the aptamer's P1 helix and the expression platform's transcriptional terminator. All-atom molecular dynamics simulations support the hypothesis that ligand binding stabilizes the aptamer P1 helix against central helix strand invasion, thus allowing the terminator to form. These results present a potential model mechanism to explain how ligand binding can induce downstream conformational changes by influencing local strand displacement processes of intermediate folds that could be at play in multiple riboswitch classes.
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Affiliation(s)
- Luyi Cheng
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Elise N White
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Naomi L Brandt
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Angela M Yu
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alan A Chen
- Correspondence may also be addressed to Alan A. Chen. Tel: +1 518 437 4420;
| | - Julius B Lucks
- To whom correspondence should be addressed. Tel: +1 847 467 2943;
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20
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Transcriptome-Wide Effects of NusA on RNA Polymerase Pausing in Bacillus subtilis. J Bacteriol 2022; 204:e0053421. [PMID: 35258320 DOI: 10.1128/jb.00534-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Transcription elongation is a highly processive process that is punctuated by RNA polymerase (RNAP) pausing. Long-lived pauses can provide time for diverse regulatory events to occur, which play important roles in modulating gene expression. Transcription elongation factors can dramatically affect RNAP pausing in vitro. The genome-wide role of such factors in pausing in vivo has been examined only for NusG in Bacillus subtilis. NusA is another transcription elongation factor known to stimulate pausing of B. subtilis and Escherichia coli RNAP in vitro. Here, we present the first in vivo study to identify the genome-wide role of NusA in RNAP pausing. Using native elongation transcript sequencing followed by RNase digestion (RNET-seq), we analyzed factor-dependent RNAP pausing in B. subtilis and found that NusA has a relatively minor role in RNAP pausing compared to NusG. We demonstrate that NusA has both stimulating and suppressing effects on pausing in vivo. Based on our thresholding criteria on in vivo data, NusA stimulates pausing at 129 pause peaks in 93 different genes or 5' untranslated regions (5' UTRs). Putative pause hairpins were identified for 87 (67%) of the 129 NusA-stimulated pause peaks, suggesting that RNA hairpins are a common component of NusA-stimulated pause signals. However, a consensus sequence was not identified as a NusA-stimulated pause motif. We further demonstrate that NusA stimulates pausing in vitro at some of the pause sites identified in vivo. IMPORTANCE NusA is an essential transcription elongation factor that was assumed to play a major role in RNAP pausing. NusA stimulates pausing in vitro; however, the essential nature of NusA had prevented an assessment of its role in pausing in vivo. Using a NusA depletion strain and RNET-seq, we identified a similar number of NusA-stimulated and NusA-suppressed pause peaks throughout the genome. NusA-stimulated pausing was confirmed at several sites in vitro. However, NusA did not always stimulate pausing at sites identified in vivo, while in other instances NusA stimulated pausing at sites not observed in vivo. We found that NusA has only a minor role in stimulating RNAP pausing in B. subtilis.
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21
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Gupta S, Pal D. Clusters of hairpins induce intrinsic transcription termination in bacteria. Sci Rep 2021; 11:16194. [PMID: 34376740 PMCID: PMC8355165 DOI: 10.1038/s41598-021-95435-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 07/20/2021] [Indexed: 01/13/2023] Open
Abstract
Intrinsic transcription termination (ITT) sites are currently identified by locating single and double-adjacent RNA hairpins downstream of the stop codon. ITTs for a limited number of genes/operons in only a few bacterial genomes are currently known. This lack of coverage is a lacuna in the existing ITT inference methods. We have studied the inter-operon regions of 13 genomes covering all major phyla in bacteria, for which good quality public RNA-seq data exist. We identify ITT sites in 87% of cases by predicting hairpin(s) and validate against 81% of cases for which the RNA-seq derived sites could be calculated. We identify 72% of these sites correctly, with 98% of them located ≤ 80 bases downstream of the stop codon. The predicted hairpins form a cluster (when present < 15 bases) in two-thirds of the cases, the remaining being single hairpins. The largest number of clusters is formed by two hairpins, and the occurrence decreases exponentially with an increasing number of hairpins in the cluster. Our study reveals that hairpins form an effective ITT unit when they act in concert in a cluster. Their pervasiveness along with single hairpin terminators corroborates a wider utilization of ITT mechanisms for transcription control across bacteria.
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Affiliation(s)
- Swati Gupta
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Debnath Pal
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka, 560012, India.
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22
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Abstract
Cellular life depends on transcription of DNA by RNA polymerase to express genetic information. RNA polymerase has evolved not just to read information from DNA and write it to RNA but also to sense and process information from the cellular and extracellular environments. Much of this information processing occurs during transcript elongation, when transcriptional pausing enables regulatory decisions. Transcriptional pauses halt RNA polymerase in response to DNA and RNA sequences and structures at locations and times that help coordinate interactions with small molecules and transcription factors important for regulation. Four classes of transcriptional pause signals are now evident after decades of study: elemental pauses, backtrack pauses, hairpin-stabilized pauses, and regulator-stabilized pauses. In this review, I describe current understanding of the molecular mechanisms of these four classes of pause signals, remaining questions about how RNA polymerase responds to pause signals, and the many exciting directions now open to understand pausing and the regulation of transcript elongation on a genome-wide scale. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Robert Landick
- Department of Biochemistry and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
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23
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Abstract
Bacterial protein synthesis rates have evolved to maintain preferred stoichiometries at striking precision, from the components of protein complexes to constituents of entire pathways. Setting relative protein production rates to be well within a factor of two requires concerted tuning of transcription, RNA turnover, and translation, allowing many potential regulatory strategies to achieve the preferred output. The last decade has seen a greatly expanded capacity for precise interrogation of each step of the central dogma genome-wide. Here, we summarize how these technologies have shaped the current understanding of diverse bacterial regulatory architectures underpinning stoichiometric protein synthesis. We focus on the emerging expanded view of bacterial operons, which encode diverse primary and secondary mRNA structures for tuning protein stoichiometry. Emphasis is placed on how quantitative tuning is achieved. We discuss the challenges and open questions in the application of quantitative, genome-wide methodologies to the problem of precise protein production. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- James C Taggart
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; ,
| | - Jean-Benoît Lalanne
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; , .,Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Current affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA;
| | - Gene-Wei Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA; ,
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Mandell ZF, Oshiro RT, Yakhnin AV, Vishwakarma R, Kashlev M, Kearns DB, Babitzke P. NusG is an intrinsic transcription termination factor that stimulates motility and coordinates gene expression with NusA. eLife 2021; 10:e61880. [PMID: 33835023 PMCID: PMC8060035 DOI: 10.7554/elife.61880] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/08/2021] [Indexed: 12/21/2022] Open
Abstract
NusA and NusG are transcription factors that stimulate RNA polymerase pausing in Bacillus subtilis. While NusA was known to function as an intrinsic termination factor in B. subtilis, the role of NusG in this process was unknown. To examine the individual and combinatorial roles that NusA and NusG play in intrinsic termination, Term-seq was conducted in wild type, NusA depletion, ΔnusG, and NusA depletion ΔnusG strains. We determined that NusG functions as an intrinsic termination factor that works alone and cooperatively with NusA to facilitate termination at 88% of the 1400 identified intrinsic terminators. Our results indicate that NusG stimulates a sequence-specific pause that assists in the completion of suboptimal terminator hairpins with weak terminal A-U and G-U base pairs at the bottom of the stem. Loss of NusA and NusG leads to global misregulation of gene expression and loss of NusG results in flagella and swimming motility defects.
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Affiliation(s)
- Zachary F Mandell
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Reid T Oshiro
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Alexander V Yakhnin
- NCI RNA Biology Laboratory, Center for Cancer Research, NCIFrederickUnited States
| | - Rishi Vishwakarma
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Mikhail Kashlev
- NCI RNA Biology Laboratory, Center for Cancer Research, NCIFrederickUnited States
| | - Daniel B Kearns
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Paul Babitzke
- Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
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