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Cheng A, Wan D, Ghatak A, Wang C, Feng D, Fondell JD, Ebright RH, Fan H. Identification and Structural Modeling of the RNA Polymerase Omega Subunits in Chlamydiae and Other Obligate Intracellular Bacteria. mBio 2023; 14:e0349922. [PMID: 36719197 PMCID: PMC9973325 DOI: 10.1128/mbio.03499-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/04/2023] [Indexed: 02/01/2023] Open
Abstract
Gene transcription in bacteria is carried out by the multisubunit RNA polymerase (RNAP), which is composed of a catalytic core enzyme and a promoter-recognizing σ factor. The core enzyme comprises two α subunits, one β subunit, one β' subunit, and one ω subunit. The ω subunit plays critical roles in the assembly of the core enzyme and other cellular functions, including the regulation of bacterial growth, the stress response, and biofilm formation. However, the identity of an ω subunit for the obligate intracellular bacterium Chlamydia has not previously been determined. Here, we report the identification of the hypothetical protein CTL0286 as the probable chlamydial ω subunit based on sequence, synteny, and AlphaFold and AlphaFold-Multimer three-dimensional-structure predictions. Our findings indicate that CTL0286 functions as the missing ω subunit of chlamydial RNAP. Our extended analysis also indicates that all obligate intracellular bacteria have ω orthologs. IMPORTANCE Chlamydiae are obligate intracellular bacteria that replicate only inside eukaryotic cells. Previously, it has not been possible to identify a candidate gene encoding the chlamydial RNA polymerase ω subunit, and it has been hypothesized that the chlamydial RNA polymerase ω subunit was lost in the evolutionary process through which Chlamydiae reduced their genome size and proteome sizes to adapt to an obligate intracellular lifestyle. Here, we report the identification of the chlamydial RNA polymerase ω subunit, based on conserved sequence, conserved synteny, AlphaFold-predicted conserved three-dimensional structure, and AlfaFold-Multimer-predicted conserved interactions. Our identification of the previously elusive chlamydial RNA polymerase ω subunit sets the stage for investigation of its roles in regulation of gene expression during chlamydial growth, development, and stress responses, and sets the stage for preparation and study of the intact chlamydial RNA polymerase and its interactions with inhibitors.
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Affiliation(s)
- Andrew Cheng
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Danny Wan
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
- Graduate Program in Physiology and Integrative Biology, Rutgers School of Graduate Studies, Piscataway, New Jersey, USA
| | - Arkaprabha Ghatak
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Chengyuan Wang
- Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Deyu Feng
- Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Joseph D. Fondell
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Richard H. Ebright
- Waksman Institute, Rutgers University, Piscataway, New Jersey, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA
| | - Huizhou Fan
- Department of Pharmacology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
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Park J, Yim SS, Wang HH. High-Throughput Transcriptional Characterization of Regulatory Sequences from Bacterial Biosynthetic Gene Clusters. ACS Synth Biol 2021; 10:1859-1873. [PMID: 34288650 DOI: 10.1021/acssynbio.0c00639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Recent efforts to sequence, survey, and functionally characterize the diverse biosynthetic capabilities of bacteria have identified numerous Biosynthetic Gene Clusters (BGCs). Genes found within BGCs are typically transcriptionally silent, suggesting their expression is tightly regulated. To better elucidate the underlying mechanisms and principles that govern BGC regulation on a DNA sequence level, we employed high-throughput DNA synthesis and multiplexed reporter assays to build and to characterize a library of BGC-derived regulatory sequences. Regulatory sequence transcription levels were measured in the Actinobacteria Streptomyces albidoflavus J1074, a popular model strain from a genus rich in BGC diversity. Transcriptional activities varied over 1000-fold in range and were used to identify key features associated with expression, including GC content, transcription start sites, and sequence motifs. Furthermore, we demonstrated that transcription levels could be modulated through coexpression of global regulatory proteins. Lastly, we developed and optimized a S. albidoflavus cell-free expression system for rapid characterization of regulatory sequences. This work helps to elucidate the regulatory landscape of BGCs and provides a diverse library of characterized regulatory sequences for rational engineering and activation of cryptic BGCs.
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Affiliation(s)
- Jimin Park
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
- Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Sung Sun Yim
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Harris H. Wang
- Department of Systems Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York 10032, United States
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3
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Villegas Kcam MC, Tsong AJ, Chappell J. Rational engineering of a modular bacterial CRISPR-Cas activation platform with expanded target range. Nucleic Acids Res 2021; 49:4793-4802. [PMID: 33823546 PMCID: PMC8096225 DOI: 10.1093/nar/gkab211] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 11/14/2022] Open
Abstract
CRISPR-Cas activator (CRISPRa) systems that selectively turn on transcription of a target gene are a potentially transformative technology for programming cellular function. While in eukaryotes versatile CRISPRa systems exist, in bacteria these systems suffer from a limited ability to activate different genes due to strict distance-dependent requirements of functional target binding sites, and require greater customization to optimize performance in different genetic and cellular contexts. To address this, we apply a rational protein engineering approach to create a new CRISPRa platform that is highly modular to allow for easy customization and has increased targeting flexibility through harnessing engineered Cas proteins. We first demonstrate that transcription activation domains can be recruited by CRISPR-Cas through noncovalent protein-protein interactions, which allows each component to be encoded on separate and easily interchangeable plasmid elements. We then exploit this modularity to rapidly screen a library of different activation domains, creating new systems with distinct regulatory properties. Furthermore, we demonstrate that by harnessing a library of circularly permuted Cas proteins, we can create CRISPRa systems that have different target binding site requirements, which together, allow for expanded target range.
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Affiliation(s)
| | - Annette J Tsong
- Department of BioSciences, Rice University, 6100 Main Street, MS 140, Houston, TX 77005, USA
| | - James Chappell
- Department of BioSciences, Rice University, 6100 Main Street, MS 140, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, 6100 Main Street, MS 142, Houston, TX 77005, USA
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4
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Kurkela J, Fredman J, Salminen TA, Tyystjärvi T. Revealing secrets of the enigmatic omega subunit of bacterial RNA polymerase. Mol Microbiol 2021; 115:1-11. [PMID: 32920946 DOI: 10.1111/mmi.14603] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/14/2022]
Abstract
The conserved omega (ω) subunit of RNA polymerase (RNAP) is the only nonessential subunit of bacterial RNAP core. The small ω subunit (7 kDa-11.5 kDa) contains three conserved α helices, and helices α2 and α3 contain five fully conserved amino acids of ω. Four conserved amino acids stabilize the correct folding of the ω subunit and one is located in the vicinity of the β' subunit of RNAP. Otherwise ω shows high variation between bacterial taxa, and although the main interaction partner of ω is always β', many interactions are taxon-specific. ω-less strains show pleiotropic phenotypes, and based on in vivo and in vitro results, a few roles for the ω subunits have been described. Interactions of the ω subunit with the β' subunit are important for the RNAP core assembly and integrity. In addition, the ω subunit plays a role in promoter selection, as ω-less RNAP cores recruit fewer primary σ factors and more alternative σ factors than intact RNAP cores in many species. Furthermore, the promoter selection of an ω-less RNAP holoenzyme bearing the primary σ factor seems to differ from that of an intact RNAP holoenzyme.
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Affiliation(s)
- Juha Kurkela
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
| | - Julia Fredman
- Faculty of Science and Engineering/Biochemistry/Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, Finland
| | - Tiina A Salminen
- Faculty of Science and Engineering/Biochemistry/Structural Bioinformatics Laboratory, Åbo Akademi University, Turku, Finland
| | - Taina Tyystjärvi
- Department of Biochemistry/Molecular Plant Biology, University of Turku, Turku, Finland
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5
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Cui Y, Schmid BV, Cao H, Dai X, Du Z, Ryan Easterday W, Fang H, Guo C, Huang S, Liu W, Qi Z, Song Y, Tian H, Wang M, Wu Y, Xu B, Yang C, Yang J, Yang X, Zhang Q, Jakobsen KS, Zhang Y, Stenseth NC, Yang R. Evolutionary selection of biofilm-mediated extended phenotypes in Yersinia pestis in response to a fluctuating environment. Nat Commun 2020; 11:281. [PMID: 31941912 PMCID: PMC6962365 DOI: 10.1038/s41467-019-14099-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 12/04/2019] [Indexed: 12/16/2022] Open
Abstract
Yersinia pestis is transmitted from fleas to rodents when the bacterium develops an extensive biofilm in the foregut of a flea, starving it into a feeding frenzy, or, alternatively, during a brief period directly after feeding on a bacteremic host. These two transmission modes are in a trade-off regulated by the amount of biofilm produced by the bacterium. Here by investigating 446 global isolated Y. pestis genomes, including 78 newly sequenced isolates sampled over 40 years from a plague focus in China, we provide evidence for strong selection pressures on the RNA polymerase ω-subunit encoding gene rpoZ. We demonstrate that rpoZ variants have an increased rate of biofilm production in vitro, and that they evolve in the ecosystem during colder and drier periods. Our results support the notion that the bacterium is constantly adapting-through extended phenotype changes in the fleas-in response to climate-driven changes in the niche.
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Affiliation(s)
- Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Boris V Schmid
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Blindern, N-0316, Oslo, Norway
| | - Hanli Cao
- The Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, 830002, China
| | - Xiang Dai
- The Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, 830002, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - W Ryan Easterday
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Blindern, N-0316, Oslo, Norway
| | - Haihong Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Chenyi Guo
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Shanqian Huang
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, 100875, China
| | - Wanbing Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Zhizhen Qi
- Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Diseases Prevention and Control, Xining, 811602, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, 100875, China
| | - Min Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Yarong Wu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Bing Xu
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, 100875, China
| | - Chao Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jing Yang
- State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, 100875, China
| | - Xianwei Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Qingwen Zhang
- Key Laboratory for Plague Prevention and Control of Qinghai Province, Qinghai Institute for Endemic Diseases Prevention and Control, Xining, 811602, China
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Blindern, N-0316, Oslo, Norway.
| | - Yujiang Zhang
- The Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi, 830002, China.
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Blindern, N-0316, Oslo, Norway. .,Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing, 100084, China.
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
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Kurkela J, Hakkila K, Antal T, Tyystjärvi T. Acclimation to High CO 2 Requires the ω Subunit of the RNA Polymerase in Synechocystis. PLANT PHYSIOLOGY 2017; 174:172-184. [PMID: 28351910 PMCID: PMC5411146 DOI: 10.1104/pp.16.01953] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/23/2017] [Indexed: 06/06/2023]
Abstract
Inactivation of the nonessential ω-subunit of the RNA polymerase core in the ΔrpoZ strain of the model cyanobacterium Synechocystis sp. PCC 6803 leads to a unique high-CO2-sensitive phenotype. Supplementing air in the growth chamber with 30 mL L-1 (3%) CO2 accelerated the growth rate of the control strain (CS) 4-fold, whereas ΔrpoZ did not grow faster than under ambient air. The slow growth of ΔrpoZ during the first days in high CO2 was due to the inability of the mutant cells to adjust photosynthesis to high CO2 The light-saturated photosynthetic activity of ΔrpoZ in high CO2 was only half of that measured in CS, Rubisco content was one-third lower, and cells of ΔrpoZ were not able to increase light-harvesting phycobilisome antenna like CS upon high-CO2 treatment. In addition, altered structural and functional organization of photosystem I and photosystem II were detected in the ΔrpoZ strain compared with CS when cells were grown in high CO2 but not in ambient air. Moreover, respiration of ΔrpoZ did not acclimate to high CO2 Unlike the photosynthetic complexes, the RNA polymerase complex and ribosomes were produced in high CO2 similarly as in CS Our results indicate that the deletion of the ω-subunit specifically affects photosynthesis and respiration, but transcription and translation remain active. Thus, the specific effect of the ω-subunit on photosynthesis but not on all household processes suggests that the ω-subunit might have a regulatory function in cyanobacteria.
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Affiliation(s)
- Juha Kurkela
- Department of Biochemistry/Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland (J.K., K.H., T.T.); and
- Biological Faculty, Moscow State University, Vorobyevi Gory 119992, Moscow, Russia (T.A.)
| | - Kaisa Hakkila
- Department of Biochemistry/Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland (J.K., K.H., T.T.); and
- Biological Faculty, Moscow State University, Vorobyevi Gory 119992, Moscow, Russia (T.A.)
| | - Taras Antal
- Department of Biochemistry/Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland (J.K., K.H., T.T.); and
- Biological Faculty, Moscow State University, Vorobyevi Gory 119992, Moscow, Russia (T.A.)
| | - Taina Tyystjärvi
- Department of Biochemistry/Molecular Plant Biology, University of Turku, FI-20014 Turku, Finland (J.K., K.H., T.T.); and
- Biological Faculty, Moscow State University, Vorobyevi Gory 119992, Moscow, Russia (T.A.)
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7
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The ω Subunit Governs RNA Polymerase Stability and Transcriptional Specificity in Staphylococcus aureus. J Bacteriol 2016; 199:JB.00459-16. [PMID: 27799328 DOI: 10.1128/jb.00459-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/26/2016] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen that causes infection in a wide variety of sites within the human body. Its ability to adapt to the human host and to produce a successful infection requires precise orchestration of gene expression. While DNA-dependent RNA polymerase (RNAP) is generally well characterized, the roles of several small accessory subunits within the complex have yet to be fully explored. This is particularly true for the omega (ω or RpoZ) subunit, which has been extensively studied in Gram-negative bacteria but largely neglected in Gram-positive counterparts. In Escherichia coli, it has been shown that ppGpp binding, and thus control of the stringent response, is facilitated by ω. Interestingly, key residues that facilitate ppGpp binding by ω are not conserved in S. aureus, and consequently, survival under starvation conditions is unaffected by rpoZ deletion. Further to this, ω-lacking strains of S. aureus display structural changes in the RNAP complex, which result from increased degradation and misfolding of the β' subunit, alterations in δ and σ factor abundance, and a general dissociation of RNAP in the absence of ω. Through RNA sequencing analysis we detected a variety of transcriptional changes in the rpoZ-deficient strain, presumably as a response to the negative effects of ω depletion on the transcription machinery. These transcriptional changes translated to an impaired ability of the rpoZ mutant to resist stress and to fully form a biofilm. Collectively, our data underline, for the first time, the importance of ω for RNAP stability, function, and cellular physiology in S. aureus IMPORTANCE: In order for bacteria to adjust to changing environments, such as within the host, the transcriptional process must be tightly controlled. Transcription is carried out by DNA-dependent RNA polymerase (RNAP). In addition to its major subunits (α2ββ') a fifth, smaller subunit, ω, is present in all forms of life. Although this small subunit is well studied in eukaryotes and Gram-negative bacteria, only limited information is available for Gram-positive and pathogenic species. In this study, we investigated the structural and functional importance of ω, revealing key roles in subunit folding/stability, complex assembly, and maintenance of transcriptional integrity. Collectively, our data underline, for the first time, the importance of ω for RNAP function and cellular harmony in S. aureus.
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Zhu C, Kang Q, Bai L, Cheng L, Deng Z. Identification and engineering of regulation-related genes toward improved kasugamycin production. Appl Microbiol Biotechnol 2015; 100:1811-1821. [PMID: 26521251 DOI: 10.1007/s00253-015-7082-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/06/2015] [Accepted: 10/12/2015] [Indexed: 10/22/2022]
Abstract
Kasugamycin, produced by Streptomyces kasugaensis and Streptomyces microaureus, is an important amino-glycoside family antibiotic and widely used for veterinary and agricultural applications. In the left flanking region of the previously reported kasugamycin gene cluster, four additional genes (two-component system kasW and kasX, MerR-family kasV, and isoprenylcysteine carboxyl methyltransferase kasS) were identified both in the low-yielding S. kasugaensis BCRC12349 and high-yielding S. microaureus XM301. Deletion of regulatory gene kasT abolished kasugamycin production, and its overexpression in BCRC12349 resulted in an increased titer by 186 %. Deletion of kasW, kasX, kasV, and kasS improved kasugamycin production by 12, 19, 194, and 22 %, respectively. qRT-PCR analysis demonstrated that the transcription of kas genes was significantly increased in all the four mutants. Similar gene inactivation was performed in the high-yielding strain S. microaureus XM301. As expected, the deletion of kasW/X resulted in a 58 % increase of the yield from 6 to 9.5 g/L. However, the deletion of kasV and over-expression of kasT had no obvious effect, and the disruption of kasS surprisingly decreased kasugamycin production. In addition, trans-complementation of the kasS mutant with a TTA codon-mutated kasS increased the kasugamycin yield by 20 %. A much higher transcription of kas genes was detected in the high-yielding XM301 than in the low-yielding BCRC12349, which may partially account for the discrepancy of gene inactivation effects between them. Our work not only generated engineered strains with improved kasugamycin yield, but also pointed out that different strategies on manipulating regulatory-related genes should be considered for low-yielding or high-yielding strains.
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Affiliation(s)
- Chenchen Zhu
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Lin Cheng
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China.
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.,School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China
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Weiss A, Shaw LN. Small things considered: the small accessory subunits of RNA polymerase in Gram-positive bacteria. FEMS Microbiol Rev 2015; 39:541-54. [PMID: 25878038 DOI: 10.1093/femsre/fuv005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2015] [Indexed: 01/21/2023] Open
Abstract
The DNA-dependent RNA polymerase core enzyme in Gram-positive bacteria consists of seven subunits. Whilst four of them (α2ββ(')) are essential, three smaller subunits, δ, ε and ω (∼9-21.5 kDa), are considered accessory. Both δ and ω have been viewed as integral components of RNAP for several decades; however, ε has only recently been described. Functionally these three small subunits carry out a variety of tasks, imparting important, supportive effects on the transcriptional process of Gram-positive bacteria. While ω is thought to have a wide range of roles, reaching from maintaining structural integrity of RNAP to σ factor recruitment, the only suggested function for ε thus far is in protecting cells from phage infection. The third subunit, δ, has been shown to have distinct influences in maintaining transcriptional specificity, and thus has a key role in cellular fitness. Collectively, all three accessory subunits, although dispensable under laboratory conditions, are often thought to be crucial for proper RNAP function. Herein we provide an overview of the available literature on each subunit, summarizing landmark findings that have deepened our understanding of these proteins and their function, and outline future challenges in understanding the role of these small subunits in the transcriptional process.
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Affiliation(s)
- Andy Weiss
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL 33620, USA
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10
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Gunnelius L, Kurkela J, Hakkila K, Koskinen S, Parikainen M, Tyystjärvi T. The ω subunit of RNA polymerase is essential for thermal acclimation of the cyanobacterium Synechocystis sp. PCC 6803. PLoS One 2014; 9:e112599. [PMID: 25386944 PMCID: PMC4227741 DOI: 10.1371/journal.pone.0112599] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/09/2014] [Indexed: 01/26/2023] Open
Abstract
The rpoZ gene encodes the small ω subunit of RNA polymerase. A ΔrpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions (constant illumination at 40 µmol photons m−2 s−1; 32°C; ambient CO2) but was heat sensitive and died at 40°C. In the control strain, 71 genes were at least two-fold up-regulated and 91 genes down-regulated after a 24-h treatment at 40°C, while in ΔrpoZ 394 genes responded to heat. Only 62 of these heat-responsive genes were similarly regulated in both strains, and 80% of heat-responsive genes were unique for ΔrpoZ. The RNA polymerase core and the primary σ factor SigA were down-regulated in the control strain at 40°C but not in ΔrpoZ. In accordance with reduced RNA polymerase content, the total RNA content of mild-heat-stress-treated cells was lower in the control strain than in ΔrpoZ. Light-saturated photosynthetic activity decreased more in ΔrpoZ than in the control strain upon mild heat stress. The amounts of photosystem II and rubisco decreased at 40°C in both strains while PSI and the phycobilisome antenna protein allophycocyanin remained at the same level as in standard conditions. The phycobilisome rod proteins, phycocyanins, diminished during the heat treatment in ΔrpoZ but not in the control strain, and the nblA1 and nblA2 genes (encode NblA proteins required for phycobilisome degradation) were up-regulated only in ΔrpoZ. Our results show that the ω subunit of RNAP is essential in heat stress because it is required for heat acclimation of diverse cellular processes.
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Affiliation(s)
- Liisa Gunnelius
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Juha Kurkela
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Kaisa Hakkila
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Satu Koskinen
- Department of Biochemistry, University of Turku, Turku, Finland
| | | | - Taina Tyystjärvi
- Department of Biochemistry, University of Turku, Turku, Finland
- * E-mail:
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11
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Gunnelius L, Hakkila K, Kurkela J, Wada H, Tyystjärvi E, Tyystjärvi T. The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria. Nucleic Acids Res 2014; 42:4606-14. [PMID: 24476911 PMCID: PMC3985657 DOI: 10.1093/nar/gku084] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The eubacterial RNA polymerase core, a transcription machinery performing DNA-dependent RNA polymerization, consists of two α subunits and β, β' and ω subunits. An additional σ subunit is recruited for promoter recognition and transcription initiation. Cyanobacteria, a group of eubacteria characterized by oxygenic photosynthesis, have a unique composition of the RNA polymerase (RNAP) core due to splitting of the β' subunit to N-terminal γ and C-terminal β' subunits. The physiological roles of the small ω subunit of RNAP, encoded by the rpoZ gene, are not yet completely understood in any bacteria. We found that although ω is non-essential in cyanobacteria, it has a major impact on the overall gene expression pattern. In ΔrpoZ strain, recruitment of the primary σ factor into the RNAP holoenzyme is inefficient, which causes downregulation of highly expressed genes and upregulation of many low-expression genes. Especially, genes encoding proteins of photosynthetic carbon concentrating and carbon fixing complexes were down, and the ΔrpoZ mutant showed low light-saturated photosynthetic activity and accumulated photoprotective carotenoids and α-tocopherol. The results indicate that the ω subunit facilitates the association of the primary σ factor with the RNAP core, thereby allowing efficient transcription of highly expressed genes.
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Affiliation(s)
- Liisa Gunnelius
- Department of Biochemistry, University of Turku, FIN-20014 Turku, Finland and Department of Life Sciences, University of Tokyo, Komaba 3-8-1, Meguro-ku, Tokyo 153-8902, Japan
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The RNA polymerase omega factor RpoZ is regulated by PhoP and has an important role in antibiotic biosynthesis and morphological differentiation in Streptomyces coelicolor. Appl Environ Microbiol 2011; 77:7586-94. [PMID: 21908625 DOI: 10.1128/aem.00465-11] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The RNA polymerase (RNAP) omega factor (ω) forms a complex with the α₂ββ' core of this enzyme in bacteria. We have characterized the rpoZ gene of Streptomyces coelicolor, which encodes a small protein (90 amino acids) identified as the omega factor. Deletion of the rpoZ gene resulted in strains with a slightly reduced growth rate, although they were still able to sporulate. The biosynthesis of actinorhodin and, particularly, that of undecylprodigiosin were drastically reduced in the ΔrpoZ strain, suggesting that expression of these secondary metabolite biosynthetic genes is dependent upon the presence of RpoZ in the RNAP complex. Complementation of the ΔrpoZ mutant with the wild-type rpoZ allele restored both phenotype and antibiotic production. Interestingly, the rpoZ gene contains a PHO box in its promoter region. DNA binding assays showed that the phosphate response regulator PhoP binds to such a region. Since luciferase reporter studies showed that rpoZ promoter activity was increased in a ΔphoP background, it can be concluded that rpoZ is controlled negatively by PhoP, thus connecting phosphate depletion regulation with antibiotic production and morphological differentiation in Streptomyces.
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Doherty GP, Fogg MJ, Wilkinson AJ, Lewis PJ. Small subunits of RNA polymerase: localization, levels and implications for core enzyme composition. Microbiology (Reading) 2010; 156:3532-3543. [DOI: 10.1099/mic.0.041566-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial RNA polymerases (RNAPs) contain several small auxiliary subunits known to co-purify with the core α, β and β′ subunits. The ω subunit is conserved between Gram-positive and Gram-negative bacteria, while the δ subunit is conserved within, but restricted to, Gram-positive bacteria. Although various functions have been assigned to these subunits via in vitro assays, very little is known about their in vivo roles. In this work we constructed a pair of vectors to investigate the subcellular localization of the δ and ω subunits in Bacillus subtilis with respect to the core RNAP. We found these subunits to be closely associated with RNAP involved in transcribing both mRNA and rRNA operons. Quantification of these subunits revealed δ to be present at equimolar levels with RNAP and ω to be present at around half the level of core RNAP. For comparison, the localization and quantification of RNAP β′ and ω subunits in Escherichia coli was also investigated. Similar to B. subtilis, β′ and ω closely associated with the nucleoid and formed subnucleoid regions of high green fluorescent protein intensity, but, unlike ω in B. subtilis, ω levels in E. coli were close to parity with those of β′. These results indicate that δ is likely to be an integral RNAP subunit in Gram-positives, whereas ω levels differ substantially between Gram-positives and -negatives. The ω subunit may be required for RNAP assembly and subsequently be turned over at different rates or it may play roles in Gram-negative bacteria that are performed by other factors in Gram-positives.
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Affiliation(s)
- Geoff P. Doherty
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Mark J. Fogg
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
| | - Anthony J. Wilkinson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK
| | - Peter J. Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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Vrentas CE, Gaal T, Burgess RR, Gourse RL. An improved procedure for the purification of the Escherichia coli RNA polymerase ω subunit. Protein Expr Purif 2010; 71:190-4. [DOI: 10.1016/j.pep.2009.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 11/30/2009] [Accepted: 11/30/2009] [Indexed: 11/28/2022]
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Machida K, Aritoku Y, Tsuchida T. One-pot fermentation of pladienolide D by Streptomyces platensis expressing a heterologous cytochrome P450 gene. J Biosci Bioeng 2009; 107:596-8. [DOI: 10.1016/j.jbiosc.2009.01.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 01/29/2009] [Accepted: 01/30/2009] [Indexed: 11/30/2022]
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Mathew R, Chatterji D. The evolving story of the omega subunit of bacterial RNA polymerase. Trends Microbiol 2006; 14:450-5. [PMID: 16908155 DOI: 10.1016/j.tim.2006.08.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2006] [Revised: 07/10/2006] [Accepted: 08/02/2006] [Indexed: 10/24/2022]
Abstract
Omega (omega) is the smallest subunit of bacterial RNA polymerase (RNAP). Although identified early in RNAP research, its function remained ambiguous and shrouded by controversy for a considerable period. It has subsequently been shown that the protein has a structural role in maintenance of the conformation of the largest subunit, beta', and recruitment of beta' to the enzyme assembly. Conservation of this function across all forms of life indicates the importance of its role. Several recent observations have suggested additional functional roles for this protein and have settled some long-standing controversies surrounding it. In this context, revisiting the omega subunit story is especially interesting; here, we review the progress of omega research since its discovery and highlight the importance of these recent observations.
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Affiliation(s)
- Renjith Mathew
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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Mathew R, Mukherjee R, Balachandar R, Chatterji D. Deletion of the rpoZ gene, encoding the ω subunit of RNA polymerase, results in pleiotropic surface-related phenotypes in Mycobacterium smegmatis. Microbiology (Reading) 2006; 152:1741-1750. [PMID: 16735737 DOI: 10.1099/mic.0.28879-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Theωsubunit, the smallest subunit of bacterial RNA polymerase, is known to be involved in maintaining the conformation of theβ′ subunit and aiding its recruitment to the rest of the core enzyme assembly inEscherichia coli. It has recently been shown inMycobacterium smegmatis, by creating a deletion mutation of therpoZgene encodingω, that the physiological role of theωsubunit also includes providing physical protection toβ′. Interestingly, the mutant had altered colony morphology. This paper demonstrates that the mutant mycobacterium has pleiotropic phenotypes including reduced sliding motility and defective biofilm formation. Analysis of the spatial arrangement of biofilms by electron microscopy suggests that the altered phenotype of the mutant arises from a deficiency in generation of extracellular matrix. Complementation of the mutant strain with a copy of the wild-typerpoZgene integrated in the bacterial chromosome restored both sliding motility and biofilm formation to the wild-type state, unequivocally proving the role ofωin the characteristics observed for the mutant bacterium. Analysis of the cell wall composition demonstrated that the mutant bacterium had an identical glycopeptidolipid profile to the wild-type, but failed to synthesize the short-chain mycolic acids characteristic of biofilm growth inM. smegmatis.
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Affiliation(s)
- Renjith Mathew
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Raju Mukherjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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Ikeno S, Aoki D, Hamada M, Hori M, Tsuchiya KS. DNA sequencing and transcriptional analysis of the kasugamycin biosynthetic gene cluster from Streptomyces kasugaensis M338-M1. J Antibiot (Tokyo) 2006; 59:18-28. [PMID: 16568715 DOI: 10.1038/ja.2006.4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Streptomyces kasugaensis M338-M1 produces the aminoglycoside antibiotic kasugamycin (KSM). We previously cloned, sequenced and characterized the KSM acetyltransferase, transporter, and some of the biosynthetic genes from this strain. To identify other potential genes in a chromosome walk experiment, a 6.8-kb EcoRI-PstI region immediately downstream from the KSM transporter genes was sequenced. Five open reading frames (designated as kasN, kasO, kasP, kasQ, kasR) and the 5' region of kasA were found in this region. The genes are apparently co-transcribed as bicistrons, all of which are co-directional except for the kasPQ transcript. Homology analysis of the deduced products of kasN, kasP, kasQ and kasR revealed similarities with known enzymes: KasN, D-amino acid oxidase from Pseudomonas aeruginosa (35% identity); KasP, F420-dependent H4MPT reductase from Streptomyces lavendulae (33% identity); KasQ, UDP-N-acetylglucosamine 2-epimerase from Streptomyces verticillus (45% identity); and KasR, NDP-hexose 3,4-dehydratase from Streptomyces cyanogenus (38% identity); respectively. A gel retardation assay showed that KasT, a putative pathway-specific regulator for this gene cluster, bound to the upstream region of kasN and to the intergenic region of kasQ-kasR, suggesting that the expression of these operons is under the control of the regulator protein.
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Affiliation(s)
- Souichi Ikeno
- Showa Pharmaceutical University, 3-3165 Higashi Tamagawagakuen, Machida-shi, Tokyo 194-8543, Japan.
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Wang HA, Qin L, Lu P, Pang ZX, Deng ZX, Zhao GP. cvhA gene of Streptomyces hygroscopicus 10-22 encodes a negative regulator for mycelia development. Acta Biochim Biophys Sin (Shanghai) 2006; 38:271-80. [PMID: 16604267 DOI: 10.1111/j.1745-7270.2006.00160.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
A five-gene cluster cvhABCDE was identified from Streptomyces hygroscopicus 10-22. As the first gene of this cluster, cvhA encoded a putative sensor histidine kinase with a predicted sensor domain consisting of two trans-membrane segments at the N-terminus and a conserved HATPase_c domain at the C-terminus. The C-terminus polypeptide of CvhA expressed in Escherichia coli was purified and shown to be autophosphorylated with [gamma-32P]ATP in vitro. The phosphoryl group was acid-labile and basic-stable, which supported histidine as the phosphorylation residue. No obvious difference of mycelia development was observed between the null mutant of cvhA generated by targeted gene replacement and the wild-type parental strain 10-22 grown on solid soya flour medium with 2%-8% glucose or sucrose, but the cvhA mutant could form much more abundant aerial mycelia and spores than the wild-type strain on solid soya flour medium supplemented with 6%-8% mannitol, 6%-8% sorbitol, 4%-6% mannose, or 4%-6% fructose. This phenotype was complemented by the cloned wild-type cvhA gene, and no difference was observed for growth curves of the cvhA mutant and the wild strain in liquid minimal medium with the tested sugars at a concentration of 4%, 6% and 8%. We thus propose that CvhA is likely a sensor histidine kinase and negatively regulates the morphological differentiation in a sugar-dependent manner in S. hygroscopicus 10-22.
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Affiliation(s)
- Heng-An Wang
- Biotechnology Institute, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai 201101, China
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Vrentas CE, Gaal T, Ross W, Ebright RH, Gourse RL. Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA. Genes Dev 2005; 19:2378-87. [PMID: 16204187 PMCID: PMC1240046 DOI: 10.1101/gad.1340305] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Previous studies have come to conflicting conclusions about the requirement for the omega subunit of RNA polymerase in bacterial transcription regulation. We demonstrate here that purified RNAP lacking omega does not respond in vitro to the effector of the stringent response, ppGpp. DksA, a transcription factor that works in concert with ppGpp to regulate rRNA expression in vivo and in vitro, fully rescues the ppGpp-unresponsiveness of RNAP lacking omega, likely explaining why strains lacking omega display a stringent response in vivo. These results demonstrate that omega plays a role in RNAP function (in addition to its previously reported role in RNAP assembly) and highlight the importance of inclusion of omega in RNAP purification protocols. Furthermore, these results suggest that either one or both of two short segments in the beta' subunit that physically link omega to the ppGpp-binding region of the enzyme may play crucial roles in ppGpp and DksA function.
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Affiliation(s)
- Catherine E Vrentas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Mathew R, Ramakanth M, Chatterji D. Deletion of the gene rpoZ, encoding the omega subunit of RNA polymerase, in Mycobacterium smegmatis results in fragmentation of the beta' subunit in the enzyme assembly. J Bacteriol 2005; 187:6565-70. [PMID: 16159791 PMCID: PMC1236636 DOI: 10.1128/jb.187.18.6565-6570.2005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A deletion mutation in the gene rpoZ of Mycobacterium smegmatis causes reduced growth rate and a change in colony morphology. During purification of RNA polymerase from the mutant strain, the beta' subunit undergoes fragmentation but the fragments remain associated with the enzyme and maintain it in an active state until the whole destabilized assembly breaks down in the final step of purification. Complementation of the mutant strain with an integrated copy of the wild-type rpoZ brings back the wild-type colony morphology and improves the growth rate and activity of the enzyme, and the integrity of the beta' subunit remains unaffected.
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Affiliation(s)
- Renjith Mathew
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Cloning System for Streptomyces kasugaensis Using the Hybrid Melanin-Synthesizing Gene melE as a Chromogenic Marker. ACTA ACUST UNITED AC 2003. [DOI: 10.3209/saj.17_27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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