1
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Chen H, Zhou X, Dai W. Identification of antimicrobial-susceptible Pseudomonas aeruginosa RpoA variant strains through positional conservation pattern. J Antimicrob Chemother 2024; 79:2298-2305. [PMID: 38990679 DOI: 10.1093/jac/dkae228] [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: 04/12/2024] [Accepted: 06/18/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Bacterial RNA polymerase (RNAP) is a promising target for antimicrobial chemotherapy due to its indispensable role in bacterial growth and survival. Among its components, only the rpoB gene encoding the β-subunit is known for its association with rifampicin resistance. We recently identified a variant of the RNAP α-subunit (RpoA) in Pseudomonas aeruginosa, conferring heightened bacterial susceptibility to antimicrobials. This susceptibility was attributed to the specific down-regulation of the MexEF-OprN efflux pump. OBJECTIVES We asked how to distinguish antimicrobial-susceptible variant strains from clinical isolates. METHODS In this study, we identified various P. aeruginosa RpoA variants from clinical sources. Using the sequence alignment of different bacterial RpoA species, we computed the positional conservation of substitutions in RpoA variants using Shannon Entropy. RESULTS Our findings revealed that selective RpoA variant strains exhibited distinct profiles of antimicrobial susceptibility. Notably, RpoA variant strains, containing single-substitutions in the C-terminal domain (α-CTD) but not the N-terminal domain (α-NTD), showed attenuated MexEF-OprN expression and increased susceptibility to MexEF-OprN-specific antibiotics. Furthermore, we observed a close correlation between the susceptibility of these α-CTD RpoA variant strains to antibiotics and the conservation degrees of positional substitutions. CONCLUSIONS Our findings demonstrate the prevalence of antimicrobial-susceptible RpoA variant strains among P. aeruginosa clinical isolates. The identified positional conservation pattern in our study facilitates the rapid classification of RpoA variant strains with distinct drug resistances. Given the high conservation of RNAP across bacterial species, our findings open a new therapeutic perspective for precisely and efficiently combating pathogenic RpoA variant strains with specific antimicrobials.
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Affiliation(s)
- Huali Chen
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoqing Zhou
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Weijun Dai
- Integrative Microbiology Research Center, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
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2
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He C, He G, Feng Y. Structural basis of phage transcriptional regulation. Structure 2024; 32:1031-1039. [PMID: 39067444 DOI: 10.1016/j.str.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/03/2024] [Accepted: 07/02/2024] [Indexed: 07/30/2024]
Abstract
Phages are the most prevalent and diverse entities in the biosphere and represent the simplest systems that are capable of self-replication. Many fundamental concepts of transcriptional regulation were revealed through phage studies. The replication of phages within bacteria entails the hijacking of the host transcription machinery. Typically, this is accomplished through proteins and RNAs encoded by the phage genome that bind to the host RNA polymerase and modify its characteristics. Understanding these processes offers valuable insights into the mechanisms of bacterial transcription itself. Historically, X-ray crystallography has been the major tool for elucidating the structural basis of phage transcriptional regulation. In recent years, the application of cryoelectron microscopy has not only allowed the exploration of protein-protein and protein-nucleic acid interactions at near-atomic resolution but also captured transient intermediate states, further expanding our mechanistic understanding of phage transcriptional regulation.
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Affiliation(s)
- Chuchu He
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guanchen He
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Key Laboratory for Diagnosis and Treatment of Physic-Chemical and Aging Injury Diseases of Zhejiang Province, Hangzhou 310003, China.
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3
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Hou MH, Chen CJ, Yang CS, Wang YC, Chen Y. Structural and functional characterization of cyclic pyrimidine-regulated anti-phage system. Nat Commun 2024; 15:5634. [PMID: 38965224 PMCID: PMC11224242 DOI: 10.1038/s41467-024-49861-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 06/21/2024] [Indexed: 07/06/2024] Open
Abstract
3',5'-cyclic uridine monophosphate (cUMP) and 3',5'-cyclic cytidine monophosphate (cCMP) have been established as bacterial second messengers in the phage defense system, named pyrimidine cyclase system for anti-phage resistance (Pycsar). This system consists of a pyrimidine cyclase and a cyclic pyrimidine receptor protein. However, the molecular mechanism underlying cyclic pyrimidine synthesis and recognition remains unclear. Herein, we determine the crystal structures of a uridylate cyclase and a cytidylate cyclase, revealing the conserved residues for cUMP and cCMP production, respectively. In addition, a distinct zinc-finger motif of the uridylate cyclase is identified to confer substantial resistance against phage infections. Furthermore, structural characterization of cUMP receptor protein PycTIR provides clear picture of specific cUMP recognition and identifies a conserved N-terminal extension that mediates PycTIR oligomerization and activation. Overall, our results contribute to the understanding of cyclic pyrimidine-mediated bacterial defense.
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Affiliation(s)
- Mei-Hui Hou
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Chao-Jung Chen
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, 40447, Taiwan
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, 40447, Taiwan
| | - Chia-Shin Yang
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Yu-Chuan Wang
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Yeh Chen
- Department of Food Science and Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan.
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4
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Posfai A, Zhou J, McCandlish DM, Kinney JB. Gauge fixing for sequence-function relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593772. [PMID: 38798671 PMCID: PMC11118547 DOI: 10.1101/2024.05.12.593772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Quantitative models of sequence-function relationships are ubiquitous in computational biology, e.g., for modeling the DNA binding of transcription factors or the fitness landscapes of proteins. Interpreting these models, however, is complicated by the fact that the values of model parameters can often be changed without affecting model predictions. Before the values of model parameters can be meaningfully interpreted, one must remove these degrees of freedom (called "gauge freedoms" in physics) by imposing additional constraints (a process called "fixing the gauge"). However, strategies for fixing the gauge of sequence-function relationships have received little attention. Here we derive an analytically tractable family of gauges for a large class of sequence-function relationships. These gauges are derived in the context of models with all-order interactions, but an important subset of these gauges can be applied to diverse types of models, including additive models, pairwise-interaction models, and models with higher-order interactions. Many commonly used gauges are special cases of gauges within this family. We demonstrate the utility of this family of gauges by showing how different choices of gauge can be used both to explore complex activity landscapes and to reveal simplified models that are approximately correct within localized regions of sequence space. The results provide practical gauge-fixing strategies and demonstrate the utility of gauge-fixing for model exploration and interpretation.
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Affiliation(s)
- Anna Posfai
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
| | - Juannan Zhou
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
- Department of Biology, University of Florida, Gainesville, FL, 32611
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
| | - Justin B Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724
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5
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Shi J, Feng Z, Song Q, Wang F, Zhang Z, Liu J, Li F, Wen A, Liu T, Ye Z, Zhang C, Das K, Wang S, Feng Y, Lin W. Structural and functional insights into transcription activation of the essential LysR-type transcriptional regulators. Protein Sci 2024; 33:e5012. [PMID: 38723180 PMCID: PMC11081524 DOI: 10.1002/pro.5012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024]
Abstract
The enormous LysR-type transcriptional regulators (LTTRs), which are diversely distributed amongst prokaryotes, play crucial roles in transcription regulation of genes involved in basic metabolic pathways, virulence and stress resistance. However, the precise transcription activation mechanism of these genes by LTTRs remains to be explored. Here, we determine the cryo-EM structure of a LTTR-dependent transcription activation complex comprising of Escherichia coli RNA polymerase (RNAP), an essential LTTR protein GcvA and its cognate promoter DNA. Structural analysis shows two N-terminal DNA binding domains of GcvA (GcvA_DBD) dimerize and engage the GcvA activation binding sites, presenting the -35 element for specific recognition with the conserved σ70R4. In particular, the versatile C-terminal domain of α subunit of RNAP directly interconnects with GcvA_DBD, σ70R4 and promoter DNA, providing more interfaces for stabilizing the complex. Moreover, molecular docking supports glycine as one potential inducer of GcvA, and single molecule photobleaching experiments kinetically visualize the occurrence of tetrameric GcvA-engaged transcription activation complex as suggested for the other LTTR homologs. Thus, a general model for tetrameric LTTR-dependent transcription activation is proposed. These findings will provide new structural and functional insights into transcription activation of the essential LTTRs.
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Affiliation(s)
- Jing Shi
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Zhenzhen Feng
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Qian Song
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Fulin Wang
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Zhipeng Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal UniversityGuangzhouGuangdongChina
- Guangdong Key Laboratory of Laser Life ScienceCollege of Biophotonics, South China Normal UniversityGuangzhouGuangdongChina
- Songshan Lake Materials LaboratoryDongguanGuangdongChina
| | - Jian Liu
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Fangfang Li
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Aijia Wen
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Tianyu Liu
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Zonghang Ye
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Chao Zhang
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
| | - Kalyan Das
- Rega Institute for Medical Research, Department of MicrobiologyImmunology and Transplantation, KU LeuvenLeuvenBelgium
| | - Shuang Wang
- Songshan Lake Materials LaboratoryDongguanGuangdongChina
- Beijing National Laboratory for Condensed Matter PhysicsInstitute of Physics, Chinese Academy of SciencesBeijingChina
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouChina
| | - Wei Lin
- Department of Pathogen BiologySchool of Medicine, Nanjing University of Chinese MedicineNanjingChina
- State Key Laboratory of Bioreactor EngineeringEast China University of Science and TechnologyShanghaiChina
- Nanjing Drum Tower Hospital Clinical College, Nanjing University of Chinese MedicineNanjingChina
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6
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Hammond-Weinberger DR, Lennon CW. Understanding operon architecture using LEGO bricks. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2024; 25:e0003424. [PMID: 38661411 PMCID: PMC11044628 DOI: 10.1128/jmbe.00034-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 04/26/2024]
Abstract
Many undergraduates struggle to interpret abstract concepts in molecular biology. Modeling can facilitate learning by making these abstract concepts tangible. Here, we present an exercise based on the lac operon designed for undergraduate students using LEGO bricks. The lac operon is a classic example of transcriptional regulation taught in a variety of undergraduate biology courses and is fundamental to understanding the regulation of gene expression. This easy-to-implement active learning exercise demonstrates how the various components of the lac operon are oriented under a variety of nutritional conditions to control gene expression. In addition, higher-order concepts, such as the effect of mutation on lac operon expression, can be readily modeled. Overall, students not only found this exercise to be enjoyable but also helpful as a tool to engage with this course material.
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7
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Kompaniiets D, Wang D, Yang Y, Hu Y, Liu B. Structure and molecular mechanism of bacterial transcription activation. Trends Microbiol 2024; 32:379-397. [PMID: 37903670 DOI: 10.1016/j.tim.2023.10.001] [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: 06/23/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 11/01/2023]
Abstract
Transcription activation is an important checkpoint of regulation of gene expression which occurs in response to different intracellular and extracellular signals. The key elements in this signal transduction process are transcription activators, which determine when and how gene expression is activated. Recent structural studies on a considerable number of new transcription activation complexes (TACs) revealed the remarkable mechanistic diversity of transcription activation mediated by different factors, necessitating a review and re-evaluation of the transcription activation mechanisms. In this review, we present a comprehensive summary of transcription activation mechanisms and propose a new, elaborate, and systematic classification of transcription activation mechanisms, primarily based on the structural features of diverse TAC components.
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Affiliation(s)
- Dmytro Kompaniiets
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Dong Wang
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Bin Liu
- Section of Transcription and Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
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8
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Schubert C, Unden G. Regulation of Aerobic Succinate Transporter dctA of E. coli by cAMP-CRP, DcuS-DcuR, and EIIAGlc: Succinate as a Carbon Substrate and Signaling Molecule. Microb Physiol 2024; 34:108-120. [PMID: 38432210 DOI: 10.1159/000538095] [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: 01/17/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
INTRODUCTION C4-dicarboxylates (C4-DC) have emerged as significant growth substrates and signaling molecules for various Enterobacteriaceae during their colonization of mammalian hosts. Particularly noteworthy is the essential role of fumarate respiration during colonization of pathogenic bacteria. To investigate the regulation of aerobic C4-DC metabolism, the study explored the transcriptional control of the main aerobic C4-DC transporter, dctA, under different carbohydrate conditions. In addition, mutants related to carbon catabolite repression (CCR) and C4-DC regulation (DcuS-DcuR) were examined to better understand the regulatory integration of aerobic C4-DC metabolism into CCR. For initial insight into posttranslational regulation, the interaction between the aerobic C4-DC transporter DctA and EIIAGlc from the glucose-specific phosphotransferase system was investigated. METHODS The expression of dctA was characterized in the presence of various carbohydrates and regulatory mutants affecting CCR. This was accomplished by fusing the dctA promoter (PdctA) to the lacZ reporter gene. Additionally, the interaction between DctA and EIIAGlc of the glucose-specific phosphotransferase system was examined in vivo using a bacterial two-hybrid system. RESULTS The dctA promoter region contains a class I cAMP-CRP-binding site at position -81.5 and a DcuR-binding site at position -105.5. DcuR, the response regulator of the C4-DC-activated DcuS-DcuR two-component system, and cAMP-CRP stimulate dctA expression. The expression of dctA is subject to the influence of various carbohydrates via cAMP-CRP, which differently modulate cAMP levels. Here we show that EIIAGlc of the glucose-specific phosphotransferase system strongly interacts with DctA, potentially resulting in the exclusion of C4-DCs when preferred carbon substrates, such as sugars, are present. In contrast to the classical inducer exclusion known for lactose permease LacY, inhibition of C4-DC uptake into the cytoplasm affects only its role as a substrate, but not as an inducer since DcuS detects C4-DCs in the periplasmic space ("substrate exclusion"). The work shows an interplay between cAMP-CRP and the DcuS-DcuR regulatory system for the regulation of dctA at both transcriptional and posttranslational levels. CONCLUSION The study highlights a hierarchical interplay between global (cAMP-CRP) and specific (DcuS-DcuR) regulation of dctA at the transcriptional and posttranslational levels. The integration of global and specific transcriptional regulation of dctA, along with the influence of EIIAGlc on DctA, fine-tunes C4-DC catabolism in response to the availability of other preferred carbon sources. It attributes DctA a central role in the control of aerobic C4-DC catabolism and suggests a new role to EIIAGlc on transporters (control of substrate uptake by substrate exclusion).
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Affiliation(s)
- Christopher Schubert
- Institute for Molecular Physiology (IMP), Microbiology and Wine Research, Johannes Gutenberg-University, Mainz, Germany
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Gottfried Unden
- Institute for Molecular Physiology (IMP), Microbiology and Wine Research, Johannes Gutenberg-University, Mainz, Germany,
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9
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Mishra A, Hughes AC, Amon JD, Rudner DZ, Wang X, Kearns DB. SwrA-mediated Multimerization of DegU and an Upstream Activation Sequence Enhance Flagellar Gene Expression in Bacillus subtilis. J Mol Biol 2024; 436:168419. [PMID: 38141873 DOI: 10.1016/j.jmb.2023.168419] [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: 08/30/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
The earliest genes in bacterial flagellar assembly are activated by narrowly-conserved proteins called master regulators that often act as heteromeric complexes. A complex of SwrA and the response-regulator transcription factor DegU is thought to form the master flagellar regulator in Bacillus subtilis but how the two proteins co-operate to activate gene expression is poorly-understood. Here we find using ChIP-Seq that SwrA interacts with a subset of DegU binding sites in the chromosome and does so in a DegU-dependent manner. Using this information, we identify a DegU-specific inverted repeat DNA sequence in the Pflache promoter region and show that SwrA synergizes with DegU phosphorylation to increase binding affinity. We further demonstrate that the SwrA/DegU footprint extends from the DegU binding site towards the promoter, likely through SwrA-induced DegU multimerization. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription by disrupting a previously-unrecognized upstream activation sequence (UAS). Thus, the SwrA-DegU heteromeric complex likely enables both remote binding and interaction between the activator and RNA polymerase. Small co-activator proteins like SwrA may allow selective activation of subsets of genes where activator multimerization is needed. Why some promoters require activator multimerization and some require UAS sequences is unknown.
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Affiliation(s)
- Ayushi Mishra
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Anna C Hughes
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Jeremy D Amon
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - David Z Rudner
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47408, USA
| | - Daniel B Kearns
- Department of Biology, Indiana University, Bloomington, IN 47408, USA.
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10
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Kompaniiets D, He L, Wang D, Zhou W, Yang Y, Hu Y, Liu B. Structural basis for transcription activation by the nitrate-responsive regulator NarL. Nucleic Acids Res 2024; 52:1471-1482. [PMID: 38197271 PMCID: PMC10853779 DOI: 10.1093/nar/gkad1231] [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: 09/25/2023] [Revised: 12/10/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024] Open
Abstract
Transcription activation is a crucial step of regulation during transcription initiation and a classic check point in response to different stimuli and stress factors. The Escherichia coli NarL is a nitrate-responsive global transcription factor that controls the expression of nearly 100 genes. However, the molecular mechanism of NarL-mediated transcription activation is not well defined. Here we present a cryo-EM structure of NarL-dependent transcription activation complex (TAC) assembled on the yeaR promoter at 3.2 Å resolution. Our structure shows that the NarL dimer binds at the -43.5 site of the promoter DNA with its C-terminal domain (CTD) not only binding to the DNA but also making interactions with RNA polymerase subunit alpha CTD (αCTD). The key role of these NarL-mediated interactions in transcription activation was further confirmed by in vivo and in vitro transcription assays. Additionally, the NarL dimer binds DNA in a different plane from that observed in the structure of class II TACs. Unlike the canonical class II activation mechanism, NarL does not interact with σ4, while RNAP αCTD is bound to DNA on the opposite side of NarL. Our findings provide a structural basis for detailed mechanistic understanding of NarL-dependent transcription activation on yeaR promoter and reveal a potentially novel mechanism of transcription activation.
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Affiliation(s)
- Dmytro Kompaniiets
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Lina He
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Wang
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Wei Zhou
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
- Hubei JiangXia Laboratory, Wuhan 430071, China
| | - Bin Liu
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN 55912, USA
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11
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Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ. DNA looping mediates cooperative transcription activation. Nat Struct Mol Biol 2024; 31:293-299. [PMID: 38177666 DOI: 10.1038/s41594-023-01149-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/04/2023] [Indexed: 01/06/2024]
Abstract
Transcription factors respond to multilevel stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator, NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by ∼50°, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a 'DNA looping' mechanism of cooperative transcription activation in bacteria.
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Affiliation(s)
- Shu-Jing Han
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yong-Liang Jiang
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China.
| | - Lin-Lin You
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Li-Qiang Shen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoxian Wu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Feng Yang
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Ning Cui
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Wen-Wen Kong
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Hui Sun
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Ke Zhou
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Hui-Chao Meng
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Zhi-Peng Chen
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yuxing Chen
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Cong-Zhao Zhou
- School of Life Sciences and Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, China.
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Shimada T, Ogasawara H, Kobayashi I, Ishihama A. Genomic SELEX Screening of Regulatory Targets of Transcription Factors. Methods Mol Biol 2024; 2819:77-102. [PMID: 39028503 DOI: 10.1007/978-1-0716-3930-6_5] [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: 07/20/2024]
Abstract
The genome of Escherichia coli K-12 is transcribed by a single species of RNA polymerase. The selectivity of transcriptional targets is determined via interaction with one of seven species of the sigma subunit and a total of approximately 300 species of transcription factor (TFs). For comprehensive identification of the regulatory targets of these two groups of regulatory proteins on the genome, we developed an in vitro approach, "Genomic SELEX" (gSELEX) screening. Here we describe a detailed protocol of the gSELEX screening system, which uses purified regulatory proteins and fragments of genomic DNA from E. coli. Moreover, we describe methods and examples of results using cell-free synthetic proteins.
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Affiliation(s)
- Tomohiro Shimada
- Meiji University, School of Agriculture, Kawasaki, Kanagawa, Japan.
| | - Hiroshi Ogasawara
- Research Center for Advanced Science and technology, Division of Gene Research, Shinshu University, Ueda, Nagano, Japan
| | - Ikki Kobayashi
- Meiji University, School of Agriculture, Kawasaki, Kanagawa, Japan
| | - Akira Ishihama
- Research Center for Micro-Nano Technology, Hosei University, Koganei, Tokyo, Japan
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13
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Tewary A, Prajapati RK, Mukhopadhyay J. Mechanism of δ Mediated Transcription Activation in Bacillus subtilis: Interaction with α CTD of RNA Polymerase Stabilizes δ and Successively Facilitates the Open Complex Formation. J Mol Biol 2023; 435:168366. [PMID: 37972688 DOI: 10.1016/j.jmb.2023.168366] [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: 07/05/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The α CTD (C-terminal domain of the α subunit) of RNA polymerase (RNAP) is a target for transcriptional regulators. In the transcription activation at Class I, Class II, and Class III promoters of bacteria, the transcriptional regulator, binds to DNA at different sites and interacts with the α CTD to stabilize the RNAP at the promoter or it binds to the α CTD to form a prerecruitment complex that searches for its cognate binding site. This 'simple recruitment mechanism' of the transcriptional machinery at the promoter is responsible for the activation of transcription. Strikingly, in B. subtilis the binding of RNAP at the promoter stabilizes the transcriptional regulator, δ at the -41 site of the promoter DNA through an interaction with its α CTD and successively facilitates the open complex formation. Two residues R293 and K294 of α CTD (equivalent to K297 and K298 of E. coli) are involved in the interactions with δ and essential for the activation of transcription. R293 is responsible for the stabilization of δ, while K294 is responsible for facilitating the open complex formation. Based on our data we propose a new model of transcription activation by δ of B. subtilis that is similar to (its binding location and interaction with α CTD), but distinct from (the recruitment of transcription factor by RNAP at the DNA, and enhancement of the open complex formation) the model Class II promoters in bacteria.
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Affiliation(s)
- Aniruddha Tewary
- Department of Chemical Science, Bose Institute, EN80 Sector V, Kolkata 700091, India.
| | | | - Jayanta Mukhopadhyay
- Department of Chemical Science, Bose Institute, EN80 Sector V, Kolkata 700091, India.
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14
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Chubiz LM. The Mar, Sox, and Rob Systems. EcoSal Plus 2023; 11:eesp00102022. [PMID: 37220096 PMCID: PMC10729928 DOI: 10.1128/ecosalplus.esp-0010-2022] [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: 09/14/2022] [Accepted: 03/03/2023] [Indexed: 01/28/2024]
Abstract
Environments inhabited by Enterobacteriaceae are diverse and often stressful. This is particularly true for Escherichia coli and Salmonella during host association in the gastrointestinal systems of animals. There, E. coli and Salmonella must survive exposure to various antimicrobial compounds produced or ingested by their host. A myriad of changes to cellular physiology and metabolism are required to achieve this feat. A central regulatory network responsible for sensing and responding to intracellular chemical stressors like antibiotics are the Mar, Sox, and Rob systems found throughout the Enterobacteriaceae. Each of these distinct regulatory networks controls expression of an overlapping set of downstream genes whose collective effects result in increased resistance to a wide array of antimicrobial compounds. This collection of genes is known as the mar-sox-rob regulon. This review will provide an overview of the mar-sox-rob regulon and molecular architecture of the Mar, Sox, and Rob systems.
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Affiliation(s)
- Lon M. Chubiz
- Department of Biology, University of Missouri–St. Louis, St. Louis, Missouri, USA
- Biochemistry and Biotechnology Program, University of Missouri–St. Louis, St. Louis, Missouri, USA
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15
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He H, Yang M, Li S, Zhang G, Ding Z, Zhang L, Shi G, Li Y. Mechanisms and biotechnological applications of transcription factors. Synth Syst Biotechnol 2023; 8:565-577. [PMID: 37691767 PMCID: PMC10482752 DOI: 10.1016/j.synbio.2023.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 08/15/2023] [Accepted: 08/27/2023] [Indexed: 09/12/2023] Open
Abstract
Transcription factors play an indispensable role in maintaining cellular viability and finely regulating complex internal metabolic networks. These crucial bioactive functions rely on their ability to respond to effectors and concurrently interact with binding sites. Recent advancements have brought innovative insights into the understanding of transcription factors. In this review, we comprehensively summarize the mechanisms by which transcription factors carry out their functions, along with calculation and experimental-based methods employed in their identification. Additionally, we highlight recent achievements in the application of transcription factors in various biotechnological fields, including cell engineering, human health, and biomanufacturing. Finally, the current limitations of research and provide prospects for future investigations are discussed. This review will provide enlightening theoretical guidance for transcription factors engineering.
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Affiliation(s)
- Hehe He
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Mingfei Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Siyu Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Gaoyang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
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16
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Lamoureux CR, Decker KT, Sastry AV, Rychel K, Gao Y, McConn J, Zielinski D, Palsson BO. A multi-scale expression and regulation knowledge base for Escherichia coli. Nucleic Acids Res 2023; 51:10176-10193. [PMID: 37713610 PMCID: PMC10602906 DOI: 10.1093/nar/gkad750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/02/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023] Open
Abstract
Transcriptomic data is accumulating rapidly; thus, scalable methods for extracting knowledge from this data are critical. Here, we assembled a top-down expression and regulation knowledge base for Escherichia coli. The expression component is a 1035-sample, high-quality RNA-seq compendium consisting of data generated in our lab using a single experimental protocol. The compendium contains diverse growth conditions, including: 9 media; 39 supplements, including antibiotics; 42 heterologous proteins; and 76 gene knockouts. Using this resource, we elucidated global expression patterns. We used machine learning to extract 201 modules that account for 86% of known regulatory interactions, creating the regulatory component. With these modules, we identified two novel regulons and quantified systems-level regulatory responses. We also integrated 1675 curated, publicly-available transcriptomes into the resource. We demonstrated workflows for analyzing new data against this knowledge base via deconstruction of regulation during aerobic transition. This resource illuminates the E. coli transcriptome at scale and provides a blueprint for top-down transcriptomic analysis of non-model organisms.
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Affiliation(s)
- Cameron R Lamoureux
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine T Decker
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ye Gao
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - John Luke McConn
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
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17
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Lou YC, Huang HY, Yeh HH, Chiang WH, Chen C, Wu KP. Structural basis of transcriptional activation by the OmpR/PhoB-family response regulator PmrA. Nucleic Acids Res 2023; 51:10049-10058. [PMID: 37665001 PMCID: PMC10570014 DOI: 10.1093/nar/gkad724] [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: 07/27/2022] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
PmrA, an OmpR/PhoB-family response regulator, triggers gene transcription responsible for polymyxin resistance in bacteria by recognizing promoters where the canonical-35 element is replaced by the pmra-box, representing the PmrA recognition sequence. Here, we report a cryo-electron microscopy (cryo-EM) structure of a bacterial PmrA-dependent transcription activation complex (TAC) containing a PmrA dimer, an RNA polymerase σ70 holoenzyme (RNAPH) and the pbgP promoter DNA. Our structure reveals that the RNAPH mainly contacts the PmrA C-terminal DNA-binding domain (DBD) via electrostatic interactions and reorients the DBD three base pairs upstream of the pmra-box, resulting in a dynamic TAC conformation. In vivo assays show that the substitution of the DNA-recognition residue eliminated its transcriptional activity, while variants with altered RNAPH-interacting residues resulted in enhanced transcriptional activity. Our findings suggest that both PmrA recognition-induced DNA distortion and PmrA promoter escape play crucial roles in its transcriptional activation.
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Affiliation(s)
- Yuan-Chao Lou
- Biomedical Translation Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hsuan-Yu Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-Hong Yeh
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Wei-Hung Chiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chinpan Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
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18
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Dayarathne K, Ishikawa T, Watanabe S, Ishikawa Y, Aikeranmu K, Kitagawaa H, Komatsubara N, Yamaguchi M, Kawai-Yamada M. Heterologous expression of mtf and mtc genes of Pseudanabaena foetida var. intermedia is sufficient to produce 2-methylisoborneol in Escherichia coli. Microbiol Spectr 2023; 11:e0256123. [PMID: 37732762 PMCID: PMC10580876 DOI: 10.1128/spectrum.02561-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/31/2023] [Indexed: 09/22/2023] Open
Abstract
Microbial volatile metabolite 2-methylisoborneol (2-MIB) causes odor and taste issues in drinking water, making it unappealing for human consumption. It has been suggested that 2-MIB biosynthesis consists of two main steps, namely, methylation of geranyl diphosphate into 2-methyl geranyl diphosphate by geranyl diphosphate methyl transferase (GPPMT) and subsequent cyclization into 2-MIB by 2-MIB synthase (MIBS). Pseudanabaena foetida var. intermedia is a 2-MIB-producing cyanobacterium whose GPPMT and MIBS enzymes are encoded by adjacent mtf and mtc genes. The present study identified a 2-MIB-related gene cluster composed of cnbA, mtf, mtc, and cnbB genes in P. foetida var. intermedia. The two homologous cyclic nucleotide-binding protein genes, cnbA and cnbB, were detected adjacent to the mtf and mtc genes, respectively. The nucleotide sequence of the cnbA-mtf-mtc-cnbB gene cluster showed 99.55% identity with 2-MIB synthesis-associated gene cluster of Pseudanabaena sp. dqh15. RT-PCR results revealed that mtf and mtc genes are co-expressed, while cnbA and cnbB genes are expressed independently in P. foetida var. intermedia. To investigate whether only mtf and mtc genes are sufficient for 2-MIB synthesis, the two-gene unit (mtf-mtc) was introduced into Escherichia coli strain JM109 via overexpression vector pYS1C. Gas chromatograph-mass spectrometry results showed that the E. coli strain transformed with mtf-mtc was able to produce 2-MIB. The intracellular 2-MIB level in P. foetida var. intermedia was higher than the extracellular 2-MIB level, while the transformed E. coli strain showed an opposite trend. Growth inhibition was observed in the 2-MIB-producing transformed E. coli strain. IMPORTANCE Contamination of drinking water with odiferous microbial metabolite 2-MIB is a worldwide concern. Removal of 2-MIB from drinking water burdens the water purification process. Therefore, it is important to search for alternative methods, such as suppressing the production of 2-MIB by aquatic microorganisms. For that, it is necessary to expand the current knowledge about the mechanism of 2-MIB synthesis at the genetic level. This study revealed that mtf and mtc genes of the 2-MIB-related gene cluster are transcribed as a single unit in P. foetida var. intermedia, and the expression of both mtf and mtc genes is essential and sufficient for 2-MIB synthesis in E. coli heterologous gene expression system.
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Affiliation(s)
- Kaushalya Dayarathne
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, 1-chōme-1-1 Sakuragaoka, Setagaya-city, Tokyo, Japan
| | - Yuuma Ishikawa
- Institute for Molecular Physiology, Heinrich-Heine-Universität, Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Kadeer Aikeranmu
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Hina Kitagawaa
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Natsumi Komatsubara
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Masatoshi Yamaguchi
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, Japan
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19
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Mishra A, Hughes AC, Amon JD, Rudner DZ, Wang X, Kearns DB. SwrA extends DegU over an UP element to activate flagellar gene expression in Bacillus subtilis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552067. [PMID: 37577504 PMCID: PMC10418190 DOI: 10.1101/2023.08.04.552067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
SwrA activates flagellar gene expression in Bacillus subtilis to increase the frequency of motile cells in liquid and elevate flagellar density to enable swarming over solid surfaces. Here we use ChIP-seq to show that SwrA interacts with many sites on the chromosome in a manner that depends on the response regulator DegU. We identify a DegU-specific inverted repeat DNA sequence and show that SwrA synergizes with phosphorylation to increase DegU DNA binding affinity. We further show that SwrA increases the size of the DegU footprint expanding the region bound by DegU towards the promoter. The location of the DegU inverted repeat was critical and moving the binding site closer to the promoter impaired transcription more that could be explained by deactivation. We conclude that SwrA/DegU forms a heteromeric complex that enables both remote binding and interaction between the activator and RNA polymerase in the context of an interceding UP element. We speculate that multimeric activators that resolve cis-element spatial conflicts are common in bacteria and likely act on flagellar biosynthesis loci and other long operons of other multi-subunit complexes. IMPORTANCE In Bacteria, the sigma subunit of RNA polymerase recognizes specific DNA sequences called promoters that determine where gene transcription begins. Some promoters also have sequences immediately upstream called an UP element that is bound by the alpha subunit of RNA polymerase and is often necessary for transcription. Finally, promoters may be activated by transcription factors that bind DNA specific sequences and help recruit RNA polymerase to weak promoter elements. Here we show that the promoter for the 32 gene long flagellar operon in Bacillus subtilis requires an UP element and is activated by a heteromeric transcription factor of DegU and SwrA. Our evidence suggests that SwrA oligomerizes DegU over the DNA to allow RNA polymerase to interact with DegU and the UP element simultaneously. Heteromeric activator complexes are known but poorly-understood in bacteria and we speculate they may be needed to resolve spatial conflicts in the DNA sequence.
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Zhao M, Gao B, Wen A, Feng Y, Lu YQ. Structural basis of λCII-dependent transcription activation. Structure 2023; 31:968-974.e3. [PMID: 37269829 DOI: 10.1016/j.str.2023.05.008] [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: 12/13/2022] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 06/05/2023]
Abstract
The CII protein of bacteriophage λ activates transcription from the phage promoters PRE, PI, and PAQ by binding to two direct repeats that straddle the promoter -35 element. Although genetic, biochemical, and structural studies have elucidated many aspects of λCII-mediated transcription activation, no precise structure of the transcription machinery in the process is available. Here, we report a 3.1-Å cryo-electron microscopy (cryo-EM) structure of an intact λCII-dependent transcription activation complex (TAC-λCII), which comprises λCII, E. coli RNAP-σ70 holoenzyme, and the phage promoter PRE. The structure reveals the interactions between λCII and the direct repeats responsible for promoter specificity and the interactions between λCII and RNAP α subunit C-terminal domain responsible for transcription activation. We also determined a 3.4-Å cryo-EM structure of an RNAP-promoter open complex (RPo-PRE) from the same dataset. Structural comparison between TAC-λCII and RPo-PRE provides new insights into λCII-dependent transcription activation.
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Affiliation(s)
- Minxing Zhao
- Department of Emergency Medicine of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Bo Gao
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Aijia Wen
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yu Feng
- Department of Biophysics, and Department of Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Immunity and Inflammatory Diseases, Hangzhou 310058, China.
| | - Yuan-Qiang Lu
- Department of Emergency Medicine of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China.
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21
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Rothman DL, Moore PB, Shulman RG. The impact of metabolism on the adaptation of organisms to environmental change. Front Cell Dev Biol 2023; 11:1197226. [PMID: 37377740 PMCID: PMC10291235 DOI: 10.3389/fcell.2023.1197226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Since Jacob and Monod's discovery of the lac operon ∼1960, the explanations offered for most metabolic adaptations have been genetic. The focus has been on the adaptive changes in gene expression that occur, which are often referred to as "metabolic reprogramming." The contributions metabolism makes to adaptation have been largely ignored. Here we point out that metabolic adaptations, including the associated changes in gene expression, are highly dependent on the metabolic state of an organism prior to the environmental change to which it is adapting, and on the plasticity of that state. In support of this hypothesis, we examine the paradigmatic example of a genetically driven adaptation, the adaptation of E. coli to growth on lactose, and the paradigmatic example of a metabolic driven adaptation, the Crabtree effect in yeast. Using a framework based on metabolic control analysis, we have reevaluated what is known about both adaptations, and conclude that knowledge of the metabolic properties of these organisms prior to environmental change is critical for understanding not only how they survive long enough to adapt, but also how the ensuing changes in gene expression occur, and their phenotypes post-adaptation. It would be useful if future explanations for metabolic adaptations acknowledged the contributions made to them by metabolism, and described the complex interplay between metabolic systems and genetic systems that make these adaptations possible.
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Affiliation(s)
- Douglas L. Rothman
- Departments of Radiology, Yale University, New Haven, CT, United States
- Biomedical Engineering, Yale University, New Haven, CT, United States
- Yale Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
| | - Peter B. Moore
- Department of Molecular Biology and Biophysics, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Robert G. Shulman
- Yale Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
- Department of Molecular Biology and Biophysics, Yale University, New Haven, CT, United States
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22
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Junkermeier EH, Hengge R. Local signaling enhances output specificity of bacterial c-di-GMP signaling networks. MICROLIFE 2023; 4:uqad026. [PMID: 37251514 PMCID: PMC10211494 DOI: 10.1093/femsml/uqad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
Abstract
For many years the surprising multiplicity, signal input diversity, and output specificity of c-di-GMP signaling proteins has intrigued researchers studying bacterial second messengers. How can several signaling pathways act in parallel to produce specific outputs despite relying on the same diffusible second messenger maintained at a certain global cellular concentration? Such high specificity and flexibility arise from combining modes of local and global c-di-GMP signaling in complex signaling networks. Local c-di-GMP signaling can be experimentally shown by three criteria being met: (i) highly specific knockout phenotypes for particular c-di-GMP-related enzymes, (ii) actual cellular c-di-GMP levels that remain unchanged by such mutations and/or below the Kd's of the relevant c-di-GMP-binding effectors, and (iii) direct interactions between the signaling proteins involved. Here, we discuss the rationale behind these criteria and present well-studied examples of local c-di-GMP signaling in Escherichia coli and Pseudomonas. Relatively simple systems just colocalize a local source and/or a local sink for c-di-GMP, i.e. a diguanylate cyclase (DGC) and/or a specific phosphodiesterase (PDE), respectively, with a c-di-GMP-binding effector/target system. More complex systems also make use of regulatory protein interactions, e.g. when a "trigger PDE" responds to locally provided c-di-GMP, and thereby serves as a c-di-GMP-sensing effector that directly controls a target's activity, or when a c-di-GMP-binding effector recruits and directly activates its own "private" DGC. Finally, we provide an outlook into how cells can combine local and global signaling modes of c-di-GMP and possibly integrate those into other signaling nucleotides networks.
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Affiliation(s)
- Eike H Junkermeier
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany
| | - Regine Hengge
- Corresponding author. Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany. Tel: +49-30-2093-49686; Fax: +49-30-2093-49682; E-mail:
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Krol E, Werel L, Essen LO, Becker A. Structural and functional diversity of bacterial cyclic nucleotide perception by CRP proteins. MICROLIFE 2023; 4:uqad024. [PMID: 37223727 PMCID: PMC10187061 DOI: 10.1093/femsml/uqad024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/07/2023] [Accepted: 04/28/2023] [Indexed: 05/25/2023]
Abstract
Cyclic AMP (cAMP) is a ubiquitous second messenger synthesized by most living organisms. In bacteria, it plays highly diverse roles in metabolism, host colonization, motility, and many other processes important for optimal fitness. The main route of cAMP perception is through transcription factors from the diverse and versatile CRP-FNR protein superfamily. Since the discovery of the very first CRP protein CAP in Escherichia coli more than four decades ago, its homologs have been characterized in both closely related and distant bacterial species. The cAMP-mediated gene activation for carbon catabolism by a CRP protein in the absence of glucose seems to be restricted to E. coli and its close relatives. In other phyla, the regulatory targets are more diverse. In addition to cAMP, cGMP has recently been identified as a ligand of certain CRP proteins. In a CRP dimer, each of the two cyclic nucleotide molecules makes contacts with both protein subunits and effectuates a conformational change that favors DNA binding. Here, we summarize the current knowledge on structural and physiological aspects of E. coli CAP compared with other cAMP- and cGMP-activated transcription factors, and point to emerging trends in metabolic regulation related to lysine modification and membrane association of CRP proteins.
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Affiliation(s)
- Elizaveta Krol
- Department of Biology, Philipps-Universität Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany
| | - Laura Werel
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Lars Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Anke Becker
- Corresponding author. Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg. E-mail:
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24
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Chen Y, Lin YCD, Luo Y, Cai X, Qiu P, Cui S, Wang Z, Huang HY, Huang HD. Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis. Brief Bioinform 2023; 24:7145906. [PMID: 37114659 DOI: 10.1093/bib/bbad138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/29/2023] Open
Abstract
Cyclic AMP receptor proteins (CRPs) are important transcription regulators in many species. The prediction of CRP-binding sites was mainly based on position-weighted matrixes (PWMs). Traditional prediction methods only considered known binding motifs, and their ability to discover inflexible binding patterns was limited. Thus, a novel CRP-binding site prediction model called CRPBSFinder was developed in this research, which combined the hidden Markov model, knowledge-based PWMs and structure-based binding affinity matrixes. We trained this model using validated CRP-binding data from Escherichia coli and evaluated it with computational and experimental methods. The result shows that the model not only can provide higher prediction performance than a classic method but also quantitatively indicates the binding affinity of transcription factor binding sites by prediction scores. The prediction result included not only the most knowns regulated genes but also 1089 novel CRP-regulated genes. The major regulatory roles of CRPs were divided into four classes: carbohydrate metabolism, organic acid metabolism, nitrogen compound metabolism and cellular transport. Several novel functions were also discovered, including heterocycle metabolic and response to stimulus. Based on the functional similarity of homologous CRPs, we applied the model to 35 other species. The prediction tool and the prediction results are online and are available at: https://awi.cuhk.edu.cn/∼CRPBSFinder.
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Affiliation(s)
- Yigang Chen
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yang-Chi-Dung Lin
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Yijun Luo
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Xiaoxuan Cai
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Peng Qiu
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Shidong Cui
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Zhe Wang
- School of Humanities and Social Science, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Hsi-Yuan Huang
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
| | - Hsien-Da Huang
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
- Warshel Institute for Computational Biology, School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Longgang District, Shenzhen, Guangdong Province 518172, China
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25
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He J, Kang X, Wu J, Shao Z, Zhang Z, Wu Y, Yuan H, Zhao G, Wang J. Transcriptional Self-Regulation of the Master Nitrogen Regulator GlnR in Mycobacteria. J Bacteriol 2023; 205:e0047922. [PMID: 36943048 PMCID: PMC10127674 DOI: 10.1128/jb.00479-22] [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: 12/16/2022] [Accepted: 02/27/2023] [Indexed: 03/23/2023] Open
Abstract
As a master nitrogen regulator in most actinomycetes, GlnR both governs central nitrogen metabolism and regulates many carbon, phosphate, and secondary metabolic pathways. To date, most studies have been focused on the GlnR regulon, while little is known about the transcriptional regulator for glnR itself. It has been observed that glnR transcription can be upregulated in Mycobacterium smegmatis under nitrogen-limited growth conditions; however, the detailed regulatory mechanism is still unclear. Here, we demonstrate that the glnR gene in M. smegmatis is transcriptionally activated by its product GlnR in response to nitrogen limitation. The precise GlnR binding site was successfully characterized in its promoter region using the electrophoretic mobility shift assay and the DNase I footprinting assay. Site mutagenesis and genetic analyses confirmed that the binding site was essential for in vivo self-activation of glnR transcription. Moreover, based on bioinformatic analyses, we discovered that most of the mycobacterial glnR promoter regions (144 out of 147) contain potential GlnR binding sites, and we subsequently proved that the purified M. smegmatis GlnR protein could specifically bind 16 promoter regions that represent 119 mycobacterial species, including Mycobacterium tuberculosis. Together, our findings not only elucidate the transcriptional self-regulation mechanism of glnR transcription in M. smegmatis but also indicate the ubiquity of the mechanism in other mycobacterial species. IMPORTANCE In actinomycetes, the nitrogen metabolism not only is essential for the construction of life macromolecules but also affects the biosynthesis of secondary metabolites and even virulence (e.g., Mycobacterium tuberculosis). The transcriptional regulation of genes involved in nitrogen metabolism has been thoroughly studied and involves the master nitrogen regulator GlnR. However, the transcriptional regulation of glnR itself remains elusive. Here, we demonstrated that GlnR functions as a transcriptional self-activator in response to nitrogen starvation in the fast-growing model Mycobacterium species Mycobacterium smegmatis. We further showed that this self-regulation mechanism could be widespread in other mycobacteria, which might be beneficial for those slow-growing mycobacteria to adapt to the nitrogen-starvation environments such as within human macrophages for M. tuberculosis.
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Affiliation(s)
- Juanmei He
- CAS Key Laboratory of Synthetic Biology, Centre of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoman Kang
- CAS Key Laboratory of Synthetic Biology, Centre of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiacheng Wu
- CAS Key Laboratory of Synthetic Biology, Centre of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhihui Shao
- CAS Key Laboratory of Synthetic Biology, Centre of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | - Yuqian Wu
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hua Yuan
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guoping Zhao
- CAS Key Laboratory of Synthetic Biology, Centre of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Second People’s Hospital & Institute of Translational Medicine/the First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
- Guangdong Provincial Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital (Shenzhen Institute of Translational Medicine), Shenzhen, China
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26
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Hengge R, Pruteanu M, Stülke J, Tschowri N, Turgay K. Recent advances and perspectives in nucleotide second messenger signaling in bacteria. MICROLIFE 2023; 4:uqad015. [PMID: 37223732 PMCID: PMC10118264 DOI: 10.1093/femsml/uqad015] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/28/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
Nucleotide second messengers act as intracellular 'secondary' signals that represent environmental or cellular cues, i.e. the 'primary' signals. As such, they are linking sensory input with regulatory output in all living cells. The amazing physiological versatility, the mechanistic diversity of second messenger synthesis, degradation, and action as well as the high level of integration of second messenger pathways and networks in prokaryotes has only recently become apparent. In these networks, specific second messengers play conserved general roles. Thus, (p)ppGpp coordinates growth and survival in response to nutrient availability and various stresses, while c-di-GMP is the nucleotide signaling molecule to orchestrate bacterial adhesion and multicellularity. c-di-AMP links osmotic balance and metabolism and that it does so even in Archaea may suggest a very early evolutionary origin of second messenger signaling. Many of the enzymes that make or break second messengers show complex sensory domain architectures, which allow multisignal integration. The multiplicity of c-di-GMP-related enzymes in many species has led to the discovery that bacterial cells are even able to use the same freely diffusible second messenger in local signaling pathways that can act in parallel without cross-talking. On the other hand, signaling pathways operating with different nucleotides can intersect in elaborate signaling networks. Apart from the small number of common signaling nucleotides that bacteria use for controlling their cellular "business," diverse nucleotides were recently found to play very specific roles in phage defense. Furthermore, these systems represent the phylogenetic ancestors of cyclic nucleotide-activated immune signaling in eukaryotes.
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Affiliation(s)
- Regine Hengge
- Corresponding author. Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany. Tel: +49-30-2093-49686; Fax: +49-30-2093-49682; E-mail:
| | | | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Natalia Tschowri
- Institute of Microbiology, Leibniz-Universität Hannover, 30419 Hannover, Germany
| | - Kürşad Turgay
- Institute of Microbiology, Leibniz-Universität Hannover, 30419 Hannover, Germany
- Max Planck Unit for the Science of Pathogens, 10115 Berlin, Germany
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27
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Lilic M, Holmes NA, Bush MJ, Marti AK, Widdick DA, Findlay KC, Choi YJ, Froom R, Koh S, Buttner MJ, Campbell EA. Structural basis of dual activation of cell division by the actinobacterial transcription factors WhiA and WhiB. Proc Natl Acad Sci U S A 2023; 120:e2220785120. [PMID: 36888660 PMCID: PMC10243135 DOI: 10.1073/pnas.2220785120] [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: 12/06/2022] [Accepted: 01/26/2023] [Indexed: 03/09/2023] Open
Abstract
Studies of transcriptional initiation in different bacterial clades reveal diverse molecular mechanisms regulating this first step in gene expression. The WhiA and WhiB factors are both required to express cell division genes in Actinobacteria and are essential in notable pathogens such as Mycobacterium tuberculosis. The WhiA/B regulons and binding sites have been elucidated in Streptomyces venezuelae (Sven), where they coordinate to activate sporulation septation. However, how these factors cooperate at the molecular level is not understood. Here we present cryoelectron microscopy structures of Sven transcriptional regulatory complexes comprising RNA polymerase (RNAP) σA-holoenzyme and WhiA and WhiB, in complex with the WhiA/B target promoter sepX. These structures reveal that WhiB binds to domain 4 of σA (σA4) of the σA-holoenzyme, bridging an interaction with WhiA while making non-specific contacts with the DNA upstream of the -35 core promoter element. The N-terminal homing endonuclease-like domain of WhiA interacts with WhiB, while the WhiA C-terminal domain (WhiA-CTD) makes base-specific contacts with the conserved WhiA GACAC motif. Notably, the structure of the WhiA-CTD and its interactions with the WhiA motif are strikingly similar to those observed between σA4 housekeeping σ-factors and the -35 promoter element, suggesting an evolutionary relationship. Structure-guided mutagenesis designed to disrupt these protein-DNA interactions reduces or abolishes developmental cell division in Sven, confirming their significance. Finally, we compare the architecture of the WhiA/B σA-holoenzyme promoter complex with the unrelated but model CAP Class I and Class II complexes, showing that WhiA/WhiB represent a new mechanism in bacterial transcriptional activation.
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Affiliation(s)
- Mirjana Lilic
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Neil A. Holmes
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Matthew J. Bush
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Alexandra K. Marti
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - David A. Widdick
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
| | - Kim C. Findlay
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, UK
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Steven Koh
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
| | - Mark J. Buttner
- Department of Molecular Microbiology, John Innes Centre, NorwichNR4 7UH, UK
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28
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cAMP Activation of the cAMP Receptor Protein, a Model Bacterial Transcription Factor. J Microbiol 2023; 61:277-287. [PMID: 36892777 DOI: 10.1007/s12275-023-00028-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 03/10/2023]
Abstract
The active and inactive structures of the Escherichia coli cAMP receptor protein (CRP), a model bacterial transcription factor, are compared to generate a paradigm in the cAMP-induced activation of CRP. The resulting paradigm is shown to be consistent with numerous biochemical studies of CRP and CRP*, a group of CRP mutants displaying cAMP-free activity. The cAMP affinity of CRP is dictated by two factors: (i) the effectiveness of the cAMP pocket and (ii) the protein equilibrium of apo-CRP. How these two factors interplay in determining the cAMP affinity and cAMP specificity of CRP and CRP* mutants are discussed. Both the current understanding and knowledge gaps of CRP-DNA interactions are also described. This review ends with a list of several important CRP issues that need to be addressed in the future.
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29
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Zou M, Wang K, Zhao J, Lu H, Yang H, Huang M, Wang L, Wang G, Huang J, Min X. DegS protease regulates the motility, chemotaxis, and colonization of Vibrio cholerae. Front Microbiol 2023; 14:1159986. [PMID: 37089576 PMCID: PMC10113495 DOI: 10.3389/fmicb.2023.1159986] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023] Open
Abstract
In bacteria, DegS protease functions as an activating factor of the σE envelope stress response system, which ultimately activates the transcription of stress response genes in the cytoplasm. On the basis of high-throughput RNA sequencing, we have previously found that degS knockout inhibits the expression of flagellum synthesis- and chemotaxis-related genes, thereby indicating that DegS may be involved in the regulation of V. cholerae motility. In this study, we examined the relationships between DegS and motility in V. cholerae. Swimming motility and chemotaxis assays revealed that degS or rpoE deletion promotes a substantial reduction in the motility and chemotaxis of V. cholerae, whereas these activities were restored in ΔdegS::degS and ΔdegSΔrseA strains, indicating that DegS is partially dependent on σE to positively regulate V. cholerae activity. Gene-act network analysis revealed that the cAMP-CRP-RpoS signaling pathway, which plays an important role in flagellar synthesis, is significantly inhibited in ΔdegS mutants, whereas in response to the overexpression of cyaA/crp and rpoS in the ΔdegS strain, the motility and chemotaxis of the ΔdegS + cyaA/crp and ΔdegS + rpoS strains were partially restored compared with the ΔdegS strain. We further demonstrated that transcription levels of the flagellar regulatory gene flhF are regulated by DegS via the cAMP-CRP-RpoS signaling pathway. Overexpression of the flhF gene in the ΔdegS strain partially restored motility and chemotaxis. In addition, suckling mouse intestinal colonization experiments indicated that the ΔdegS and ΔrpoE strains were characterized by the poor colonization of mouse intestines, whereas colonization efficacy was restored in the ΔdegSΔrseA, ΔdegS + cyaA/crp, ΔdegS + rpoS, and ΔdegS + flhF strains. Collectively, our findings indicate that DegS regulates the motility and chemotaxis of V. cholerae via the cAMP-CRP-RpoS-FlhF pathway, thereby influencing the colonization of suckling mouse intestines.
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Affiliation(s)
- Mei Zou
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Kaiying Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jiajun Zhao
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Huifang Lu
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hui Yang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Meirong Huang
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
- Department of Blood Transfusion, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Lu Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Guangli Wang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jian Huang
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xun Min
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, Guizhou, China
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30
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Pearce VH, Groisman EA, Townsend GE. Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species. Gut Microbes 2023; 15:2221484. [PMID: 37358144 PMCID: PMC10294740 DOI: 10.1080/19490976.2023.2221484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/08/2023] [Indexed: 06/27/2023] Open
Abstract
The mammalian gut microbiota is a critical human health determinant with therapeutic potential for remediation of many diseases. The host diet is a key factor governing the gut microbiota composition by altering nutrient availability and supporting the expansion of distinct microbial populations. Diets rich in simple sugars modify the abundance of microbial subsets, enriching for microbiotas that elicit pathogenic outcomes. We previously demonstrated that diets rich in fructose and glucose can reduce the fitness and abundance of a human gut symbiont, Bacteroides thetaiotaomicron, by silencing the production of a critical intestinal colonization protein, called Roc, via its mRNA leader through an unknown mechanism. We have now determined that dietary sugars silence Roc by reducing the activity of BT4338, a master regulator of carbohydrate utilization. Here, we demonstrate that BT4338 is required for Roc synthesis, and that BT4338 activity is silenced by glucose or fructose. We show that the consequences of glucose and fructose on orthologous transcription factors are conserved across human intestinal Bacteroides species. This work identifies a molecular pathway by which a common dietary additive alters microbial gene expression in the gut that could be harnessed to modulate targeted microbial populations for future therapeutic interventions.
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Affiliation(s)
- Victoria H. Pearce
- Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
- Penn State Microbiome Center, Pennsylvania State University, State College, PA, USA
- Center for Molecular Carcinogenesis and Toxicology, Pennsylvania State University, State College, PA, USA
| | - Eduardo A. Groisman
- Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Guy E. Townsend
- Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
- Penn State Microbiome Center, Pennsylvania State University, State College, PA, USA
- Center for Molecular Carcinogenesis and Toxicology, Pennsylvania State University, State College, PA, USA
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31
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Parakkunnel R, Naik K B, Vanishree G, C S, Purru S, Bhaskar K U, Bhat KV, Kumar S. Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome. FRONTIERS IN PLANT SCIENCE 2022; 13:1076229. [PMID: 36618639 PMCID: PMC9817154 DOI: 10.3389/fpls.2022.1076229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Susmita C
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
| | - Supriya Purru
- ICAR- National Academy of Agricultural Research Management, Hyderabad, Telengana, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - KV. Bhat
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
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32
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Balakrishnan R, Mori M, Segota I, Zhang Z, Aebersold R, Ludwig C, Hwa T. Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria. Science 2022; 378:eabk2066. [PMID: 36480614 PMCID: PMC9804519 DOI: 10.1126/science.abk2066] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein concentrations are set by a complex interplay between gene-specific regulatory processes and systemic factors, including cell volume and shared gene expression machineries. Elucidating this interplay is crucial for discerning and designing gene regulatory systems. We quantitatively characterized gene-specific and systemic factors that affect transcription and translation genome-wide for Escherichia coli across many conditions. The results revealed two design principles that make regulation of gene expression insulated from concentrations of shared machineries: RNA polymerase activity is fine-tuned to match translational output, and translational characteristics are similar across most messenger RNAs (mRNAs). Consequently, in bacteria, protein concentration is set primarily at the promoter level. A simple mathematical formula relates promoter activities and protein concentrations across growth conditions, enabling quantitative inference of gene regulation from omics data.
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Affiliation(s)
- Rohan Balakrishnan
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
| | - Matteo Mori
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
| | - Igor Segota
- Departments of Medicine and Pharmacology, University of California at San Diego, La Jolla, California 92093
| | - Zhongge Zhang
- Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093
| | - Ruedi Aebersold
- Faculty of Science, University of Zurich, Zurich, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, California 92093-0374
- Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093
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33
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Alhammadi MM, Godfrey RE, Ingram JO, Singh G, Bathurst CL, Busby SJW, Browning DF. Novel organisation and regulation of the pic promoter from enteroaggregative and uropathogenic Escherichia coli. Virulence 2022; 13:1393-1406. [PMID: 35971774 PMCID: PMC9387333 DOI: 10.1080/21505594.2022.2111754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The serine protease autotransporters of the Enterobacteriaceae (SPATEs) are a large family of virulence factors commonly found in enteric bacteria. These secreted virulence factors have diverse functions during bacterial infection, including adhesion, aggregation and cell toxicity. One such SPATE, the Pic mucinase (protein involved in colonisation) cleaves mucin, allowing enteric bacterial cells to utilise mucin as a carbon source and to penetrate the gut mucus lining, thereby increasing mucosal colonisation. The pic gene is widely distributed within the Enterobacteriaceae, being found in human pathogens, such as enteroaggregative Escherichia coli (EAEC), uropathogenic E. coli (UPEC) and Shigella flexneri 2a. As the pic promoter regions from EAEC strain 042 and UPEC strain CFT073 differ, we have investigated the regulation of each promoter. Here, using in vivo and in vitro techniques, we show that both promoters are activated by the global transcription factor, CRP (cyclic AMP receptor protein), but the architectures of the EAEC and the UPEC pic promoter differ. Expression from both pic promoters is repressed by the nucleoid-associated factor, Fis, and maximal promoter activity occurs when cells are grown in minimal medium. As CRP activates transcription in conditions of nutrient depletion, whilst Fis levels are maximal in nutrient-rich environments, the regulation of the EAEC and UPEC pic promoters is consistent with Pic’s nutritional role in scavenging mucin as a suitable carbon source during colonisation and infection.
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Affiliation(s)
- Munirah M Alhammadi
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK.,Biology Department, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Rita E Godfrey
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Joseph O Ingram
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Gurdamanjit Singh
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Camilla L Bathurst
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Stephen J W Busby
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Douglas F Browning
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, UK.,College of Health & Life Sciences, Aston University, Birmingham, UK
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34
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Khan H, Paul P, Sevalkar RR, Kachhap S, Singh B, Sarkar D. Convergence of two global regulators to coordinate expression of essential virulence determinants of Mycobacterium tuberculosis. eLife 2022; 11:80965. [PMID: 36350294 PMCID: PMC9645806 DOI: 10.7554/elife.80965] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Cyclic AMP (cAMP) is known to function as a global regulator of Mycobacterium tuberculosis gene expression. Sequence-based transcriptomic profiling identified the mycobacterial regulon controlled by the cAMP receptor protein, CRP. In this study, we identified a new subset of CRP-associated genes including virulence determinants which are also under the control of a major regulator, PhoP. Our results suggest that PhoP as a DNA binding transcription factor, impacts expression of these genes, and phosphorylated PhoP promotes CRP recruitment at the target promoters. Further, we uncover a distinct regulatory mechanism showing that activation of these genes requires direct recruitment of both PhoP and CRP at their target promoters. The most fundamental biological insight is derived from the inhibition of CRP binding at the regulatory regions in a PhoP-deleted strain owing to CRP-PhoP protein-protein interactions. Based on these results, a model is proposed suggesting how CRP and PhoP function as co-activators of the essential pathogenic determinants. Taken together, these results uncover a novel mode of regulation where a complex of two interacting virulence factors impact expression of virulence determinants. These results have significant implications on TB pathogenesis.
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Affiliation(s)
- Hina Khan
- CSIR-Institute of Microbial Technology
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35
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Shi J, Wang L, Wen A, Wang F, Zhang Y, Yu L, Li F, Jin Y, Feng Z, Li J, Yang Y, Gao F, Zhang Y, Feng Y, Wang S, Zhao W, Lin W. Structural basis of three different transcription activation strategies adopted by a single regulator SoxS. Nucleic Acids Res 2022; 50:11359-11373. [PMID: 36243985 PMCID: PMC9638938 DOI: 10.1093/nar/gkac898] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/24/2022] Open
Abstract
Transcription activation is established through extensive protein–protein and protein–DNA interactions that allow an activator to engage and remodel RNA polymerase. SoxS, a global transcription activator, diversely regulates subsets of stress response genes with different promoters, but the detailed SoxS-dependent transcription initiation mechanisms remain obscure. Here, we report cryo-EM structures of three SoxS-dependent transcription activation complexes (SoxS-TACI, SoxS-TACII and SoxS-TACIII) comprising of Escherichia coli RNA polymerase (RNAP), SoxS protein and three representative classes of SoxS-regulated promoters. The structures reveal that SoxS monomer orchestrates transcription initiation through specific interactions with the promoter DNA and different conserved domains of RNAP. In particular, SoxS is positioned in the opposite orientation in SoxS-TACIII to that in SoxS-TACI and SoxS-TACII, unveiling a novel mode of transcription activation. Strikingly, two universally conserved C-terminal domains of alpha subunit (αCTD) of RNAP associate with each other, bridging SoxS and region 4 of σ70. We show that SoxS interacts with RNAP directly and independently from DNA, remodeling the enzyme to activate transcription from cognate SoxS promoters while repressing transcription from UP-element containing promoters. Our data provide a comprehensive summary of SoxS-dependent promoter architectures and offer new insights into the αCTD contribution to transcription control in bacteria.
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Affiliation(s)
- Jing Shi
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lu Wang
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Aijia Wen
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fulin Wang
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yuqiong Zhang
- MOE Key Laboratory of Laser Life Science and Institute of Laser Life Science, College of Biophotonics, South China Normal University, 510631 Guangzhou, Guangdong, China.,Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, 510631 Guangzhou, Guangdong, China.,Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong, China
| | - Libing Yu
- Institute of Materials, China Academy of Engineering Physics, Mianyang 621900, China
| | - Fangfang Li
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yuanling Jin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhenzhen Feng
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jiacong Li
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yujiao Yang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fei Gao
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yu Zhang
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yu Feng
- Department of Biophysics, Zhejiang University School of Medicine, Hangzhou 310058, China.,Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shuang Wang
- Songshan Lake Materials Laboratory, Dongguan 523808, Guangdong, China.,Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Wei Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing 210023, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210023, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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36
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Mathew SS, Ahamed AAS, Abraham I, Prabhu DD, John F, George J. Self‐Assemblies of DNA ‐ Amphiphiles Nanostructures for New Design Strategies of Varied Morphologies. ChemistrySelect 2022. [DOI: 10.1002/slct.202202146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - A A Subuhan Ahamed
- School of Chemistry University of Hyderabad Hyderabad 500046 Telangana India
| | - Ignatious Abraham
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Deepak D Prabhu
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Franklin John
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
| | - Jinu George
- Department of Chemistry Sacred Heart College (Autonomous) Thevara Kochi Kerala India 682013
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37
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Amin MR, Korchinski L, Yoneda JK, Thakkar R, Sanson CLA, Fitzgerald SF, Kelln RA, Cameron ADS. A mutation in the putative CRP binding site of the dctA promoter of Salmonella enterica serovar Typhimurium enables growth with low orotate concentrations. Can J Microbiol 2022; 68:615-621. [PMID: 35921682 DOI: 10.1139/cjm-2022-0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Salmonella enterica and Escherichia coli use the inner membrane transporter DctA to import the pyrimidine biosynthetic pathway intermediate orotate from the environment. To study the regulation of dctA expression, we used a S. enterica serovar Typhimurium pyrimidine auxotroph to select a mutant that could grow in an otherwise non-permissive culture medium containing glucose and a low concentration of orotate. Whole genome sequencing revealed a point mutation upstream of dctA in the putative cyclic AMP receptor protein (CRP) binding site. The C->T transition converted the least-favourable base to the most-favourable base for CRP-DNA affinity. A dctA::lux transcriptional fusion confirmed that the mutant dctA promoter gained responsiveness to CRP even in the presence of glucose. Moreover, dctA expression was higher in the mutant than the wild type in the presence of alternative carbon sources that activate CRP.
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Affiliation(s)
- Mohammad R Amin
- University of Regina, 6846, Department of Biology, Regina, Saskatchewan, Canada.,University of Regina, 6846, Institute for Microbial Systems and Society, Regina, Saskatchewan, Canada;
| | - Lisa Korchinski
- University of Regina, 6846, Department of Chemistry and Biochemistry, Regina, Saskatchewan, Canada;
| | - Joshua K Yoneda
- University of Regina, 6846, Department of Biology, Regina, Saskatchewan, Canada.,University of Regina, 6846, Institute for Microbial Systems and Society, Regina, Saskatchewan, Canada;
| | - Rishi Thakkar
- University of Regina, 6846, Department of Biology, Regina, Saskatchewan, Canada.,University of Regina, 6846, Institute for Microbial Systems and Society, Regina, Saskatchewan, Canada;
| | - Carla L A Sanson
- University of Regina, 6846, Department of Chemistry and Biochemistry, Regina, Saskatchewan, Canada.,Government of Saskatchewan Ministry of Labour Relations and Workplace Safety, 359189, Occupational Health and Safety Branch, Regina, Saskatchewan, Canada;
| | - Stephen F Fitzgerald
- University of Regina, 6846, Department of Biology, Regina, Saskatchewan, Canada.,Moredun Research Institute, 6485, Penicuik, United Kingdom of Great Britain and Northern Ireland;
| | - Rod A Kelln
- University of Regina, 6846, Department of Chemistry and Biochemistry, Regina, Saskatchewan, Canada;
| | - Andrew D S Cameron
- University of Regina, 6846, Department of Biology, Regina, Saskatchewan, Canada.,University of Regina, 6846, Institute for Microbial Systems and Society, Regina, Saskatchewan, Canada;
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38
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Dubanevics I, McLeish TCB. Optimising Elastic Network Models for Protein Dynamics and Allostery: Spatial and Modal Cut-offs and Backbone Stiffness. J Mol Biol 2022; 434:167696. [PMID: 35810792 DOI: 10.1016/j.jmb.2022.167696] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 01/15/2023]
Abstract
The family of coarse-grained models for protein dynamics known as Elastic Network Models (ENMs) require careful choice of parameters to represent well experimental measurements or fully-atomistic simulations. The most basic ENM that represents each protein residue by a node at the position of its C-alpha atom, all connected by springs of equal stiffness, up to a cut-off in distance. Even at this level a choice is required of the optimum cut-off distance and the upper limit of elastic normal modes taken in any sum for physical properties, such as dynamic correlation or allosteric effects on binding. Additionally, backbone-enhanced ENM (BENM) may improve the model by allocating a higher stiffness to springs that connect along the protein backbone. This work reports on the effect of varying these three parameters (distance and mode cutoffs, backbone stiffness) on the dynamical structure of three proteins, Catabolite Activator Protein (CAP), Glutathione S-transferase (GST), and the SARS-CoV-2 Main Protease (M pro ). Our main results are: (1) balancing B-factor and dispersion-relation predictions, a near-universal optimal value of 8.5 Å is advisable for ENMs; (2) inhomogeneity in elasticity brings the first mode containing spatial structure not well-resolved by the ENM typically within the first 20; (3) the BENM only affects modes in the upper third of the distribution, and, additionally to the ENM, is only able to model the dispersion curve better in this vicinity; (4) BENM does not typically affect fluctuation-allostery, which also requires careful treatment of the effector binding to the host protein to capture.
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39
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Gao J, Du M, Zhao J, Yue zhang, Xu N, Du H, Ju J, Wei L, Liu J. Design of a genetically encoded biosensor to establish a high-throughput screening platform for L-cysteine overproduction. Metab Eng 2022; 73:144-157. [DOI: 10.1016/j.ymben.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/03/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
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40
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The Escherichia coli Amino Acid Uptake Protein CycA: Regulation of Its Synthesis and Practical Application in l-Isoleucine Production. Microorganisms 2022; 10:microorganisms10030647. [PMID: 35336222 PMCID: PMC8948829 DOI: 10.3390/microorganisms10030647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
Amino acid transport systems perform important physiological functions; their role should certainly be considered in microbial production of amino acids. Typically, in the context of metabolic engineering, efforts are focused on the search for and application of specific amino acid efflux pumps. However, in addition, importers can also be used to improve the industrial process as a whole. In this study, the protein CycA, which is known for uptake of nonpolar amino acids, was characterized from the viewpoint of regulating its expression and range of substrates. We prepared a cycA-overexpressing strain and found that it exhibited high sensitivity to branched-chain amino acids and their structural analogues, with relatively increased consumption of these amino acids, suggesting that they are imported by CycA. The expression of cycA was found to be dependent on the extracellular concentrations of substrate amino acids. The role of some transcription factors in cycA expression, including of Lrp and Crp, was studied using a reporter gene construct. Evidence for the direct binding of Crp to the cycA regulatory region was obtained using a gel-retardation assay. The enhanced import of named amino acids due to cycA overexpression in the l-isoleucine-producing strain resulted in a significant reduction in the generation of undesirable impurities. This work demonstrates the importance of uptake systems with respect to their application in metabolic engineering.
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41
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Dual-function Spot 42 RNA encodes a 15-amino acid protein that regulates the CRP transcription factor. Proc Natl Acad Sci U S A 2022; 119:e2119866119. [PMID: 35239441 PMCID: PMC8916003 DOI: 10.1073/pnas.2119866119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceDual-function RNAs base pair with target messenger RNAs as small regulatory RNAs and encode small protein regulators. However, only a limited number of these dual-function regulators have been identified. In this study, we show that a well-characterized base-pairing small RNA surprisingly also encodes a 15-amino acid protein. The very small protein binds the cyclic adenosine monophosphate receptor protein transcription factor to block activation of some promoters, raising the question of how many other transcription factors are modulated by unidentified small proteins.
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42
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Ladant D. A Bacterial Two-Hybrid System for In Vivo Assays of Protein-Protein Interactions and Drug Discovery. Methods Mol Biol 2022; 2548:145-167. [PMID: 36151497 DOI: 10.1007/978-1-0716-2581-1_10] [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: 06/16/2023]
Abstract
The bacterial adenylate cyclase-based two-hybrid (BACTH) system is a robust and simple genetic assay used to monitor protein-protein interactions in vivo. This system is based on functional complementation between two fragments from the catalytic domain of Bordetella pertussis adenylate cyclase (AC) to reconstitute a cyclic AMP (cAMP)-signaling cascade in Escherichia coli. Interactions between two chimeric proteins result in the synthesis of cAMP, which activates the transcription of various catabolite operons, leading to selectable phenotypes. One advantageous feature of this signaling cascade is that the physical association between the two interacting hybrid proteins is spatially separated from the transcriptional activation readout. Consequently, the BACTH system can detect protein-protein interactions occurring at various subcellular localizations. The system has been used to characterize interactions between soluble or membrane proteins of prokaryotic, eukaryotic, or viral origin. The BACTH assay can be used to uncover the region(s), domain(s), or amino acid residue(s) of a protein involved in an interaction with a specific partner. The BACTH system can also be adapted for the high-throughput screening of small molecules able to interfere with protein-protein interactions.
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Affiliation(s)
- Daniel Ladant
- Unité de Biochimie des Interactions Macromoléculaires, Département de Biologie Structurale et Chimie, CNRS UMR 3528, Institut Pasteur, Paris Cedex 15, France.
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43
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Minor Alterations in Core Promoter Element Positioning Reveal Functional Plasticity of a Bacterial Transcription Factor. mBio 2021; 12:e0275321. [PMID: 34724814 PMCID: PMC8561392 DOI: 10.1128/mbio.02753-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
IscR is a global transcription factor that regulates Fe-S cluster homeostasis and other functions in Escherichia coli by either activating or repressing transcription. While the interaction of IscR with its DNA sites has been studied, less is known about the mechanism of IscR regulation of transcription. Here, we show that IscR recruits RNA polymerase to an activated promoter and that IscR binding compensates for the lack of an optimal RNA polymerase σ70 −35 promoter element. We also find that the position of the −35 promoter element within the IscR DNA site impacts whether IscR activates or represses transcription. RNA polymerase binding at a distally positioned −35 element within the IscR site results in IscR activation. Molecular modeling suggests that this position of the −35 element allows IscR and RNA polymerase to bind to the promoter from opposite faces of the helix. Shifting the −35 element 1 nucleotide upstream within the IscR binding site results in IscR repression and a steric clash of IscR and RNA polymerase binding in the models. We propose that the sequence similarity of the IscR binding site with the −35 element is an important feature in allowing plasticity in the mechanism of IscR regulation.
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44
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Distinct Interaction Mechanism of RNAP and ResD and Distal Subsites for Transcription Activation of Nitrite Reductase in Bacillus subtilisψ. J Bacteriol 2021; 204:e0043221. [PMID: 34898263 DOI: 10.1128/jb.00432-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ResD-ResE signal transduction system plays a pivotal role in anaerobic nitrate respiration in Bacillus subtilis. The nasD operon encoding nitrite reductase is essential for nitrate respiration and is tightly controlled by the ResD response regulator. To understand the mechanism of ResD-dependent transcription activation of the nasD operon, we explored ResD-RNA polymerase (RNAP), ResD-DNA, and RNAP-DNA interactions required for nasD transcription. Full transcriptional activation requires the upstream promoter region where five molecules of ResD bind. The distal ResD-binding subsite at -87 to -84 partially overlaps a sequence similar to the consensus distal subsite of the upstream (UP) element with which the Escherichia coli C-terminal domain of the α subunit (αCTD) of RNAP interacts to stimulate transcription. We propose that interaction between αCTD and ResD at the promoter-distal site is essential for stimulating nasD transcription. Although nasD has an extended -10 promoter, it lacks a reasonable -35 element. Genetic analysis and structural simulations predicted that the absence of the -35 element might be compensated by interactions between σA and αCTD, and between αCTD and ResD at the promoter-proximal ResD-binding subsite. Thus, our work suggested that ResD likely participates in nasD transcription activation by binding to two αCTD subunits at the proximal and distal promoter sites, representing a unique configuration for transcription activation. IMPORTANCE A significant number of ResD-controlled genes have been identified and transcription regulatory pathways in which ResD participates have emerged. Nevertheless, the mechanism of how ResD activates transcription of different genes in a nucleotide sequence-specific manner has been less explored. This study suggested that among the five ResD-binding subsites in the promoter of the nasD operon, the promoter-proximal and -distal ResD-binding subsites play important roles in nasD activation by adapting different modes of protein-protein and protein-DNA interactions. The finding of a new-type of protein-promoter architecture provides insight into the understanding of transcription activation mechanisms controlled by transcription factors including the ubiquitous response regulators of two-component regulatory systems particularly in Gram-positive bacteria.
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45
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Fang C, Zhang Y. Bacterial MerR family transcription regulators: activationby distortion. Acta Biochim Biophys Sin (Shanghai) 2021; 54:25-36. [PMID: 35130613 PMCID: PMC9909328 DOI: 10.3724/abbs.2021003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Transcription factors (TFs) modulate gene expression by regulating the accessibility of promoter DNA to RNA polymerases (RNAPs) in bacteria. The MerR family TFs are a large class of bacterial proteins unique in their physiological functions and molecular action: they function as transcription repressors under normal circumstances, but rapidly transform to transcription activators under various cellular triggers, including oxidative stress, imbalance of cellular metal ions, and antibiotic challenge. The promoters regulated by MerR TFs typically contain an abnormal long spacer between the -35 and -10 elements, where MerR TFs bind and regulate transcription activity through unique mechanisms. In this review, we summarize the function, ligand reception, DNA recognition, and molecular mechanism of transcription regulation of MerR-family TFs.
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Affiliation(s)
- Chengli Fang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Yu Zhang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
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46
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Gruscheski L, Brand T. The Role of POPDC Proteins in Cardiac Pacemaking and Conduction. J Cardiovasc Dev Dis 2021; 8:160. [PMID: 34940515 PMCID: PMC8706714 DOI: 10.3390/jcdd8120160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 11/17/2022] Open
Abstract
The Popeye domain-containing (POPDC) gene family, consisting of Popdc1 (also known as Bves), Popdc2, and Popdc3, encodes transmembrane proteins abundantly expressed in striated muscle. POPDC proteins have recently been identified as cAMP effector proteins and have been proposed to be part of the protein network involved in cAMP signaling. However, their exact biochemical activity is presently poorly understood. Loss-of-function mutations in animal models causes abnormalities in skeletal muscle regeneration, conduction, and heart rate adaptation after stress. Likewise, patients carrying missense or nonsense mutations in POPDC genes have been associated with cardiac arrhythmias and limb-girdle muscular dystrophy. In this review, we introduce the POPDC protein family, and describe their structure function, and role in cAMP signaling. Furthermore, the pathological phenotypes observed in zebrafish and mouse models and the clinical and molecular pathologies in patients carrying POPDC mutations are described.
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Affiliation(s)
| | - Thomas Brand
- National Heart and Lung Institute, Imperial College London, London W12 0NN, UK;
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47
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Ro C, Cashel M, Fernández-Coll L. The secondary messenger ppGpp interferes with cAMP-CRP regulon by promoting CRP acetylation in Escherichia coli. PLoS One 2021; 16:e0259067. [PMID: 34705884 PMCID: PMC8550359 DOI: 10.1371/journal.pone.0259067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
The cAMP-CRP regulon coordinates transcription regulation of several energy-related genes, the lac operon among them. Lactose, or IPTG, induces the lac operon expression by binding to the LacI repressor, and releasing it from the promoter sequence. At the same time, the expression of the lac operon requires the presence of the CRP-cAMP complex, which promotes the binding of the RNA polymerase to the promoter region. The modified nucleotide cAMP accumulates in the absence of glucose and binds to the CRP protein, but its ability to bind to DNA can be impaired by lysine-acetylation of CRP. Here we add another layer of control, as acetylation of CRP seems to be modified by ppGpp. In cells grown in glycerol minimal media, ppGpp seems to repress the expression of lacZ, where ΔrelA mutants show higher expression of lacZ than in WT. These differences between the WT and ΔrelA strains seem to depend on the levels of acetylated CRP. During the growth in minimal media supplemented with glycerol, ppGpp promotes the acetylation of CRP by the Nε-lysine acetyltransferases YfiQ. Moreover, the expression of the different genes involved in the production and degradation of Acetyl-phosphate (ackA-pta) and the enzymatic acetylation of proteins (yfiQ) are stimulated by the presence of ppGpp, depending on the growth conditions.
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Affiliation(s)
- Chunghwan Ro
- Eunice Kennedy Shriver National Institute of Child Health and Development, NIH, Bethesda, Maryland, United States of America
| | - Michael Cashel
- Eunice Kennedy Shriver National Institute of Child Health and Development, NIH, Bethesda, Maryland, United States of America
| | - Llorenç Fernández-Coll
- Eunice Kennedy Shriver National Institute of Child Health and Development, NIH, Bethesda, Maryland, United States of America
- * E-mail:
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Camakaris H, Yang J, Fujii T, Pittard J. Activation by TyrR in Escherichia coli K-12 by Interaction between TyrR and the α-Subunit of RNA Polymerase. J Bacteriol 2021; 203:e0025221. [PMID: 34309399 PMCID: PMC8425403 DOI: 10.1128/jb.00252-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/13/2021] [Indexed: 11/20/2022] Open
Abstract
A novel selection was developed for mutants of the C-terminal domain of RpoA (α-CTD) altered in activation by the TyrR regulatory protein of Escherichia coli K-12. This allowed the identification of an aspartate to asparagine substitution at residue 250 (DN250) as an activation-defective (Act-) mutation. Amino acid residues known to be close to D250 were altered by in vitro mutagenesis, and the substitutions DR250, RE310, and RD310 were all shown to be defective in activation. None of these mutations caused defects in regulation of the upstream promoter (UP) element. The rpoA mutation DN250 was transferred onto the chromosome to facilitate the isolation of suppressor mutations. The TyrR mutations EK139 and RG119 caused partial suppression of rpoA DN250, and TyrR RC119, RL119, RP119, RA77, and SG100 caused partial suppression of rpoA RE310. Additional activation-defective rpoA mutants (DT250, RS310, and EG288) were also isolated, using the chromosomal rpoA DN250 strain. Several new Act-tyrR mutants were isolated in an rpoA+ strain, adding positions R77, D97, K101, D118, R119, R121, and E141 to known residues S95 and D103 and defining the activation patch on the amino-terminal domain (NTD) of TyrR. These results support a model for activation of TyrR-regulated genes where the activation patch on the TyrR NTD interacts with the TyrR-specific patch on the α-CTD of RNA polymerase. Given known structures, both these sites appear to be surface exposed and suggest a model for activation by TyrR. They also help resolve confusing results in the literature that implicated residues within the 261 and 265 determinants as activator contact sites. IMPORTANCE Regulation of transcription by RNA polymerases is fundamental for adaptation to a changing environment and for cellular differentiation, across all kingdoms of life. The gene tyrR in Escherichia coli is a particularly useful model because it is involved in both activation and repression of a large number of operons by a range of mechanisms, and it interacts with all three aromatic amino acids and probably other effectors. Furthermore, TyrR has homologues in many other genera, regulating many different genes, utilizing different effector molecules, and in some cases affecting virulence and important plant interactions.
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Affiliation(s)
- Helen Camakaris
- School of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ji Yang
- School of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | | | - James Pittard
- School of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
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Seok JY, Han YH, Yang JS, Yang J, Lim HG, Kim SG, Seo SW, Jung GY. Synthetic biosensor accelerates evolution by rewiring carbon metabolism toward a specific metabolite. Cell Rep 2021; 36:109589. [PMID: 34433019 DOI: 10.1016/j.celrep.2021.109589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/01/2021] [Accepted: 08/02/2021] [Indexed: 12/29/2022] Open
Abstract
Proper carbon flux distribution between cell growth and production of a target compound is important for biochemical production because improper flux reallocation inhibits cell growth, thus adversely affecting production yield. Here, using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolve cells under the selective condition toward the acquisition of genotypes that optimally reallocate cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determine that mutations in the conserved regions of proteins involved in global transcriptional regulation alter the expression of several genes associated with central carbon metabolism. These changes rewire central carbon flux toward the 3-HP production pathway, increasing 3-HP yield and reducing acetate accumulation by alleviating overflow metabolism. Our study provides a perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization.
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Affiliation(s)
- Joo Yeon Seok
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Jae-Seong Yang
- Centre de Recerca en Agrigenòmica, Consortium CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Seong Gyeong Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Sang Woo Seo
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea.
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Sibley M, Ward JM. A cell engineering approach to enzyme-based fed-batch fermentation. Microb Cell Fact 2021; 20:146. [PMID: 34303374 PMCID: PMC8310608 DOI: 10.1186/s12934-021-01634-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/16/2021] [Indexed: 11/21/2022] Open
Abstract
Background A fundamental problem associated with E. coli fermentations is the difficulty in achieving high cell densities in batch cultures, attributed in large part to the production and accumulation of acetate through a phenomenon known as overflow metabolism when supplying enough glucose for the cell density desired. Although a fed-batch configuration is the standard method for reducing such issues, traditional fed-batch systems require components which become problematic when applying them at smaller scale. One alternative has been the development of a system whereby the enzymatic degradation of starch is used to release glucose at a controlled rate. However, to date, amylolytic enzymes have only been applied to the culture exogenously, whereas our goal is to design and construct a self-secreting amylolytic chassis capable of self-regulated enzyme-based fed-batch fermentation. Results A putative glucoamylase from C. violaceum has been cloned and expressed in E. coli BL21(DE3) and W3110, which exhibits significant glucose releasing amylolytic activity. Extracellular amylolytic activity was enhanced following a replacement of the enzymes native signal peptide with the DsbA signal sequence, contributing to a glucoamylase secreting strain capable of utilising starch as a sole carbon source in defined media. Introduction of PcstA, a glucose sensitive K12 compatible promoter, and the incorporation of this alongside C. violaceum glucoamylase in E. coli W3110, gave rise to increased cell densities in cultures grown on starch (OD600 ∼ 30) compared to those grown on an equivalent amount of glucose (OD600 ∼ 15). Lastly, a novel self-secreting enzyme-based fed-batch fermentation system was demonstrated via the simultaneous expression of the C. violaceum glucoamylase and a recombinant protein of interest (eGFP), resulting in a fourfold increase in yield when grown in media containing starch compared with the glucose equivalent. Conclusions This study has developed, through the secretion of a previously uncharacterised bacterial glucoamylase, a novel amylolytic E. coli strain capable of direct starch to glucose conversion. The ability of this strain to achieve increased cell densities as well as an associated increase in recombinant protein yield when grown on starch compared with an equivalent amount of glucose, demonstrates for the first time a cell engineering approach to enzyme-based fed-batch fermentation. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01634-y.
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Affiliation(s)
- Michael Sibley
- Department of Biochemical Engineering, UCL, Gower Street, London, WC1E 6BT, UK
| | - John M Ward
- Department of Biochemical Engineering, UCL, Gower Street, London, WC1E 6BT, UK.
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