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Ma L, Guo L, Yang Y, Guo K, Yan Y, Ma X, Huo YX. Protein-based biorefining driven by nitrogen-responsive transcriptional machinery. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:29. [PMID: 32127916 PMCID: PMC7045595 DOI: 10.1186/s13068-020-1667-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/25/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Protein-based bioconversion has been demonstrated as a sustainable approach to produce higher alcohols and ammonia fertilizers. However, owing to the switchover from transcription mediated by the bacterial RNA polymerase σ70 to that mediated by alternative σ factors, the biofuel production driven by σ70-dependent promoters declines rapidly once cells enter the stationary phase or encounter stresses. To enhance biofuel production, in this study the growth phase-independent and nitrogen-responsive transcriptional machinery mediated by the σ54 is exploited to drive robust protein-to-fuel conversion. RESULTS We demonstrated that disrupting the Escherichia coli ammonia assimilation pathways driven by glutamate dehydrogenase and glutamine synthetase could sustain the activity of σ54-mediated transcription under ammonia-accumulating conditions. In addition, two σ54-dependent promoters, argTp and glnAp2, were identified as suitable candidates for driving pathway expression. Using these promoters, biofuel production from proteins was shown to persist to the stationary phase, with the net production in the stationary phase being 1.7-fold higher than that derived from the optimal reported σ70-dependent promoter P LlacO1. Biofuel production reaching levels 1.3- to 3.4-fold higher than those of the σ70-dependent promoters was also achieved by argTp and glnAp2 under stressed conditions. Moreover, the σ54-dependent promoters realized more rapid and stable production than that of σ70-dependent promoters during fed-batch fermentation, producing up to 4.78 g L - 1 of total biofuels. CONCLUSIONS These results suggested that the nitrogen-responsive transcriptional machinery offers the potential to decouple production from growth, highlighting this system as a novel candidate to realize growth phase-independent and stress-resistant biofuel production.
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Affiliation(s)
- Lianjie Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081 People’s Republic of China
| | - Liwei Guo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081 People’s Republic of China
| | - Yunpeng Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081 People’s Republic of China
| | - Kai Guo
- Biology Institute, Shandong Province Key Laboratory for Biosensors, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103 China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, University of Georgia, Athens, GA 30602 USA
| | - Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081 People’s Republic of China
- Biology Institute, Shandong Province Key Laboratory for Biosensors, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103 China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing, 100081 People’s Republic of China
- Biology Institute, Shandong Province Key Laboratory for Biosensors, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250103 China
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2
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Yu H, Chen Z, Wang N, Yu S, Yan Y, Huo YX. Engineering transcription factor BmoR for screening butanol overproducers. Metab Eng 2019; 56:28-38. [PMID: 31449878 DOI: 10.1016/j.ymben.2019.08.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/09/2019] [Accepted: 08/22/2019] [Indexed: 01/15/2023]
Abstract
The wild-type transcription factors are sensitive to their corresponding signal molecules. Using wild-type transcription factors as biosensors to screen industrial overproducers are generally impractical because of their narrow detection ranges. This study took transcription factor BmoR as an example and aimed to expand the detection range of BmoR for screening alcohols overproducers. Firstly, a BmoR mutation library was established, and the mutations distributed randomly in all predicted functional domains of BmoR. Structure of BmoR-isobutanol complex were modelled, and isobutanol binding sites were confirmed by site-directed mutagenesis. Subsequently, the effects of the mutations on the detection range or output were confirmed in the BmoR mutants. Four combinatorial mutants containing one increased-detection-range mutation and one enhanced-output mutation were constructed. Compared with wild-type BmoR, F276A/E627N BmoR and D333N/E627N BmoR have wider detection ranges (0-100 mM) and relatively high outputs to the isobutanol added quantitatively or produced intracellularly, demonstrating they have potential for screening isobutanol overproduction strains. This work presented an example of engineering the wild-type transcription factors with physiological significance for industrial utilization.
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Affiliation(s)
- Huan Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Ning Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China; UCLA Institute for Technology Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, 215123, Suzhou, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, 30602, GA, USA
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China; UCLA Institute for Technology Advancement (Suzhou), 10 Yueliangwan Road, Suzhou Industrial Park, 215123, Suzhou, China.
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3
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Noise in bacterial gene expression. Biochem Soc Trans 2018; 47:209-217. [PMID: 30578346 DOI: 10.1042/bst20180500] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/22/2018] [Accepted: 11/26/2018] [Indexed: 12/25/2022]
Abstract
The expression level of a gene can fluctuate significantly between individuals within a population of genetically identical cells. The resultant phenotypic heterogeneity could be exploited by bacteria to adapt to changing environmental conditions. Noise is hence a genome-wide phenomenon that arises from the stochastic nature of the biochemical reactions that take place during gene expression and the relatively low abundance of the molecules involved. The production of mRNA and proteins therefore occurs in bursts, with alternating episodes of high and low activity during transcription and translation. Single-cell and single-molecule studies demonstrated that noise within gene expression is influenced by a combination of both intrinsic and extrinsic factors. However, our mechanistic understanding of this process at the molecular level is still rather limited. Further investigation is necessary that takes into account the detailed knowledge of gene regulation gained from biochemical studies.
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4
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McLaughlin PT, Bhardwaj V, Feeley BE, Higgs PI. MrpC, a CRP/Fnr homolog, functions as a negative autoregulator during the
Myxococcus xanthus
multicellular developmental program. Mol Microbiol 2018; 109:245-261. [DOI: 10.1111/mmi.13982] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/05/2018] [Accepted: 05/05/2018] [Indexed: 02/06/2023]
Affiliation(s)
| | - Vidhi Bhardwaj
- Department of EcophysiologyMax Planck Institute for Terrestrial MicrobiologyMarburg Hesse Germany
| | - Brooke E. Feeley
- Department of Biological SciencesWayne State UniversityDetroit MI USA
| | - Penelope I. Higgs
- Department of Biological SciencesWayne State UniversityDetroit MI USA
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5
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Cai W, Cai X, Yang Y, Yan S, Zhang H. Transcriptional Control of Dual Transporters Involved in α-Ketoglutarate Utilization Reveals Their Distinct Roles in Uropathogenic Escherichia coli. Front Microbiol 2017; 8:275. [PMID: 28270808 PMCID: PMC5318444 DOI: 10.3389/fmicb.2017.00275] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/09/2017] [Indexed: 12/14/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) are the primary causative agents of urinary tract infections. Some UPEC isolates are able to infect renal proximal tubule cells, and can potentially cause pyelonephritis. We have previously shown that to fulfill their physiological roles renal proximal tubule cells accumulate high concentrations of α-ketoglutarate (KG) and that gene cluster c5032–c5039 contribute to anaerobic utilization of KG by UPEC str. CFT073, thereby promoting its in vivo fitness. Given the importance of utilizing KG for UPEC, this study is designed to investigate the roles of two transporters KgtP and C5038 in KG utilization, their transcriptional regulation, and their contributions to UPEC fitness in vivo. Our phylogenetic analyses support that kgtP is a widely conserved locus in commensal and pathogenic E. coli, while UPEC-associated c5038 was acquired through horizontal gene transfer. Global anaerobic transcriptional regulators Fumarate and nitrate reduction (FNR) and ArcA induced c5038 expression in anaerobiosis, and C5038 played a major role in anaerobic growth on KG. KgtP was required for aerobic growth on KG, and its expression was repressed by FNR and ArcA under anaerobic conditions. Analyses of FNR and ArcA binding sites and results of EMS assays suggest that FNR and ArcA likely inhibit kgtP expression through binding to the –35 region of kgtP promoter and occluding the occupancy of RNA polymerases. Gene c5038 can be specifically induced by KG, whereas the expression of kgtP does not respond to KG, yet can be stimulated during growth on glycerol. In addition, c5038 and kgtP expression were further shown to be controlled by different alternative sigma factors RpoN and RpoS, respectively. Furthermore, dual-strain competition assays in a murine model showed that c5038 mutant but not kgtP mutant was outcompeted by the wild-type strain during the colonization of murine bladders and kidneys, highlighting the importance of C5038 under in vivo conditions. Therefore, different transcriptional regulation led to distinct roles played by C5038 and KgtP in KG utilization and fitness in vivo. This study thus potentially expanded our understanding of UPEC pathobiology.
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Affiliation(s)
- Wentong Cai
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Xuwang Cai
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University Wuhan, China
| | - Yongwu Yang
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Shigan Yan
- School of Bioengineering, Shandong Provincial Key Laboratory of Microbial Engineering, Qilu University of Technology Jinan, China
| | - Haibin Zhang
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China; Department of Clinical Veterinary Science, College of Veterinary Medicine, Nanjing Agricultural UniversityNanjing, China
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6
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Wang Y, Liu F, Wang W. Kinetics of transcription initiation directed by multiple cis-regulatory elements on the glnAp2 promoter. Nucleic Acids Res 2016; 44:10530-10538. [PMID: 27899598 PMCID: PMC5159524 DOI: 10.1093/nar/gkw1150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/31/2016] [Accepted: 11/03/2016] [Indexed: 11/21/2022] Open
Abstract
Transcription initiation is orchestrated by dynamic molecular interactions, with kinetic steps difficult to detect. Utilizing a hybrid method, we aim to unravel essential kinetic steps of transcriptional regulation on the glnAp2 promoter, whose regulatory region includes two enhancers (sites I and II) and three low-affinity sequences (sites III-V), to which the transcriptional activator NtrC binds. By structure reconstruction, we analyze all possible organization architectures of the transcription apparatus (TA). The main regulatory mode involves two NtrC hexamers: one at enhancer II transiently associates with site V such that the other at enhancer I can rapidly approach and catalyze the σ54-RNA polymerase holoenzyme. We build a kinetic model characterizing essential steps of the TA operation; with the known kinetics of the holoenzyme interacting with DNA, this model enables the kinetics beyond technical detection to be determined by fitting the input-output function of the wild-type promoter. The model further quantitatively reproduces transcriptional activities of various mutated promoters. These results reveal different roles played by two enhancers and interpret why the low-affinity elements conditionally enhance or repress transcription. This work presents an integrated dynamic picture of regulated transcription initiation and suggests an evolutionarily conserved characteristic guaranteeing reliable transcriptional response to regulatory signals.
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Affiliation(s)
- Yaolai Wang
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
| | - Feng Liu
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China .,Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China .,Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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7
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Lee JH, Sundin GW, Zhao Y. Identification of the HrpS binding site in the hrpL promoter and effect of the RpoN binding site of HrpS on the regulation of the type III secretion system in Erwinia amylovora. MOLECULAR PLANT PATHOLOGY 2016; 17:691-702. [PMID: 26440313 PMCID: PMC6638409 DOI: 10.1111/mpp.12324] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The type III secretion system (T3SS) is a key pathogenicity factor in Erwinia amylovora. Previous studies have demonstrated that the T3SS in E. amylovora is transcriptionally regulated by an RpoN-HrpL sigma factor cascade, which is activated by the bacterial alarmone (p)ppGpp. In this study, the binding site of HrpS, an enhancer binding protein, was identified for the first time in plant-pathogenic bacteria. Complementation of the hrpL mutant with promoter deletion constructs of the hrpL gene and promoter activity analyses using various lengths of the hrpL promoter fused to a promoter-less green fluorescent protein (gfp) reporter gene delineated the upstream region for HrpS binding. Sequence analysis revealed a dyad symmetry sequence between -138 and -125 nucleotides (TGCAA-N4-TTGCA) as the potential HrpS binding site, which is conserved in the promoter of the hrpL gene among plant enterobacterial pathogens. Results of quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) and electrophoresis mobility shift assay coupled with site-directed mutagenesis (SDM) analysis showed that the intact dyad symmetry sequence was essential for HrpS binding, full activation of T3SS gene expression and virulence. In addition, the role of the GAYTGA motif (RpoN binding site) of HrpS in the regulation of T3SS gene expression in E. amylovora was characterized by complementation of the hrpS mutant using mutant variants generated by SDM. Results showed that a Y100F substitution of HrpS complemented the hrpS mutant, whereas Y100A and Y101A substitutions did not. These results suggest that tyrosine (Y) and phenylalanine (F) function interchangeably in the conserved GAYTGA motif of HrpS in E. amylovora.
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Affiliation(s)
- Jae Hoon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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8
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Lee JH, Zhao Y. Integration Host Factor Is Required for RpoN-Dependent hrpL Gene Expression and Controls Motility by Positively Regulating rsmB sRNA in Erwinia amylovora. PHYTOPATHOLOGY 2016; 106:29-36. [PMID: 26368515 DOI: 10.1094/phyto-07-15-0170-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Erwinia amylovora requires an hrp-type III secretion system (T3SS) to cause disease. It has been reported that HrpL, the master regulator of T3SS, is transcriptionally regulated by sigma factor 54 (RpoN), YhbH, and HrpS. In this study, the role of integration host factor (IHF) in regulating hrpL and T3SS gene expression was investigated. IHF is a nucleoid-associated protein that regulates gene expression by influencing nucleoid structure and DNA bending. Our results showed that both ihfA and ihfB mutants of E. amylovora did not induce necrotic lesions on pear fruits. Growth of both mutants was greatly reduced, and expression of the hrpL and T3SS genes was significantly down-regulated as compared with those of the wild type. In addition, expression of the ihfA, but not the ihfB gene, was under auto-suppression by IHF. Furthermore, both ihfA and ihfB mutants were hypermotile, due to significantly reduced expression of small RNA (sRNA) rsmB. Electrophoresis mobility shift assay further confirmed that IHF binds to the promoters of the hrpL and ihfA genes, as well as the rsmB sRNA gene. These results indicate that IHF is required for RpoN-dependent hrpL gene expression and virulence, and controls motility by positively regulating the rsmB sRNA in E. amylovora.
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Affiliation(s)
- Jae Hoon Lee
- First and second authors: Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Youfu Zhao
- First and second authors: Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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9
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Zhang YT, Jiang F, Tian ZX, Huo YX, Sun YC, Wang YP. CRP-cyclic AMP dependent inhibition of the xylene-responsive σ(54)-promoter Pu in Escherichia coli. PLoS One 2014; 9:e86727. [PMID: 24466213 PMCID: PMC3900584 DOI: 10.1371/journal.pone.0086727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2013] [Indexed: 11/18/2022] Open
Abstract
The expression of σ(54)-dependent Pseudomonas putida Pu promoter is activated by XylR activator when cells are exposed to a variety of aromatic inducers. In this study, the transcriptional activation of the P. putida Pu promoter was recreated in the heterologous host Escherichia coli. Here we show that the cAMP receptor protein (CRP), a well-known carbon utilization regulator, had an inhibitory effect on the expression of Pu promoter in a cAMP-dependent manner. The inhibitory effect was not activator specific. In vivo KMnO4 and DMS footprinting analysis indicated that CRP-cAMP poised the RNA polymerase at Pu promoter, inhibiting the isomerization step of the transcription initiation even in the presence of an activator. Therefore, the presence of PTS-sugar, which eliminates cAMP, could activate the poised RNA polymerase at Pu promoter to transcribe. Moreover, the activation region 1 (AR1) of CRP, which interacts directly with the αCTD (C-terminal domain of α-subunit) of RNA polymerase, was found essential for the CRP-mediated inhibition at Pu promoter. A model for the above observations is discussed.
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Affiliation(s)
- Yuan-Tao Zhang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Feng Jiang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhe-Xian Tian
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Yi-Xin Huo
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
| | - Yi-Cheng Sun
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
- * E-mail:
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10
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Mehta P, Jovanovic G, Lenn T, Bruckbauer A, Engl C, Ying L, Buck M. Dynamics and stoichiometry of a regulated enhancer-binding protein in live Escherichia coli cells. Nat Commun 2013; 4:1997. [PMID: 23764692 PMCID: PMC3709507 DOI: 10.1038/ncomms2997] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 05/09/2013] [Indexed: 12/02/2022] Open
Abstract
Bacterial enhancer-dependent transcription systems support major adaptive responses and offer a singular paradigm in gene control analogous to complex eukaryotic systems. Here we report new mechanistic insights into the control of one-membrane stress-responsive bacterial enhancer-dependent system. Using millisecond single-molecule fluorescence microscopy of live cells we determine the localizations, two-dimensional diffusion dynamics and stoichiometries of complexes of the bacterial enhancer-binding ATPase PspF during its action at promoters as regulated by inner membrane interacting negative controller PspA. We establish that a stable repressive PspF–PspA complex is located in the nucleoid, transiently communicating with the inner membrane via PspA. The PspF as a hexamer stably binds only one of the two psp promoters at a time, suggesting that psp promoters will fire asynchronously and cooperative interactions of PspF with the basal transcription complex influence dynamics of the PspF hexamer–DNA complex and regulation of the psp promoters. Cellular adaptive responses require temporal and spatial control of key regulatory protein complexes. Mehta et al. describe the dynamic interaction of a transcriptional activator mediating membrane stress response in E. coli with its negative regulator, the cell membrane and the transcription machinery.
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Affiliation(s)
- Parul Mehta
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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11
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The role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription. Microbiol Mol Biol Rev 2013; 76:497-529. [PMID: 22933558 DOI: 10.1128/mmbr.00006-12] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial enhancer binding proteins (bEBPs) are transcriptional activators that assemble as hexameric rings in their active forms and utilize ATP hydrolysis to remodel the conformation of RNA polymerase containing the alternative sigma factor σ(54). We present a comprehensive and detailed summary of recent advances in our understanding of how these specialized molecular machines function. The review is structured by introducing each of the three domains in turn: the central catalytic domain, the N-terminal regulatory domain, and the C-terminal DNA binding domain. The role of the central catalytic domain is presented with particular reference to (i) oligomerization, (ii) ATP hydrolysis, and (iii) the key GAFTGA motif that contacts σ(54) for remodeling. Each of these functions forms a potential target of the signal-sensing N-terminal regulatory domain, which can act either positively or negatively to control the activation of σ(54)-dependent transcription. Finally, we focus on the DNA binding function of the C-terminal domain and the enhancer sites to which it binds. Particular attention is paid to the importance of σ(54) to the bacterial cell and its unique role in regulating transcription.
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12
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Friedman LJ, Gelles J. Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation. Cell 2012; 148:679-89. [PMID: 22341441 DOI: 10.1016/j.cell.2012.01.018] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 09/26/2011] [Accepted: 01/05/2012] [Indexed: 11/17/2022]
Abstract
Understanding the pathway and kinetic mechanisms of transcription initiation is essential for quantitative understanding of gene regulation, but initiation is a multistep process, the features of which can be obscured in bulk analysis. We used a multiwavelength single-molecule fluorescence colocalization approach, CoSMoS, to define the initiation pathway at an activator-dependent bacterial σ(54) promoter that recapitulates characteristic features of eukaryotic promoters activated by enhancer binding proteins. The experiments kinetically characterize all major steps of the initiation process, revealing heretofore unknown features, including reversible formation of two closed complexes with greatly differing stabilities, multiple attempts for each successful formation of an open complex, and efficient release of σ(54) from the polymerase core at the start of transcript synthesis. Open complexes are committed to transcription, suggesting that regulation likely targets earlier steps in the mechanism. CoSMoS is a powerful, generally applicable method to elucidate the mechanisms of transcription and other multistep biochemical processes.
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Affiliation(s)
- Larry J Friedman
- Department of Biochemistry, Brandeis University, Waltham, MA 02454-9110, USA.
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13
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Abstract
One of the greatest challenges facing synthetic biology is to develop a technology that allows gene regulatory circuits in microbes to integrate multiple inputs or stimuli using a small DNA sequence "foot-print", and which will generate precise and reproducible outcomes. Achieving this goal is hindered by the routine utilization of the commonplace σ(70) promoters in gene-regulatory circuits. These promoters typically are not capable of integrating binding of more than two or three transcription factors in natural examples, which has limited the field to developing integrated circuits made of two-input biological "logic" gates. In natural examples the regulatory elements, which integrate multiple inputs are called enhancers. These regulatory elements are ubiquitous in all organisms in the tree of life, and interestingly metazoan and bacterial enhancers are significantly more similar in terms of both Transcription Factor binding site arrangement and biological function than previously thought. These similarities imply that there may be underlying enhancer design principles or grammar rules by which one can engineer novel gene regulatory circuits. However, at present our current understanding of enhancer structure-function relationship in all organisms is limited, thus preventing us from using these objects routinely in synthetic biology application. In order to alleviate this problem, in this book chapter, I will review our current view of bacterial enhancers, allowing us to first highlight the potential of enhancers to be a game-changing tool in synthetic biology application, and subsequently to draw a road-map for developing the necessary quantitative understanding to reach this goal.
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Affiliation(s)
- Roee Amit
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel,
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14
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Domenzain C, Camarena L, Osorio A, Dreyfus G, Poggio S. Evolutionary origin of the Rhodobacter sphaeroides specialized RpoN sigma factors. FEMS Microbiol Lett 2011; 327:93-102. [PMID: 22093079 DOI: 10.1111/j.1574-6968.2011.02459.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 11/01/2011] [Accepted: 11/02/2011] [Indexed: 11/29/2022] Open
Abstract
Gene duplication and horizontal gene transfer (HGT) are two events that enable the generation of new genes. Rhodobacter sphaeroides (WS8 and 2.4.1 strains) has four copies of the rpoN gene that are not functionally interchangeable. Until now, this is the only example of specialization of this sigma factor. In this work, we aimed to determine whether the multiple copies of this gene originated from HGT or through gene duplication. Our results suggest a multiplication origin of the different rpoN copies that occurred after the Rhodobacter clade separated. Functional tests indicate that the specialization of the rpoN genes is not restricted to R. sphaeroides. We propose that the rpoN copy involved in nitrogen fixation is the ancestral gene and that the other rpoN genes have acquired new specificities.
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Affiliation(s)
- Clelia Domenzain
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, México
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15
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Amit R, Garcia HG, Phillips R, Fraser SE. Building enhancers from the ground up: a synthetic biology approach. Cell 2011; 146:105-18. [PMID: 21729783 DOI: 10.1016/j.cell.2011.06.024] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 01/25/2011] [Accepted: 06/14/2011] [Indexed: 11/25/2022]
Abstract
A challenge of the synthetic biology approach is to use our understanding of a system to recreate a biological function with specific properties. We have applied this framework to bacterial enhancers, combining a driver, transcription factor binding sites, and a poised polymerase to create synthetic modular enhancers. Our findings suggest that enhancer-based transcriptional control depends critically and quantitatively on DNA looping, leading to complex regulatory effects when the enhancer cassettes contain additional transcription factor binding sites for TetR, a bacterial transcription factor. We show through a systematic interplay of experiment and thermodynamic modeling that the level of gene expression can be modulated to convert a variable inducer concentration input into discrete or step-like output expression levels. Finally, using a different DNA-binding protein (TraR), we show that the regulatory output is not a particular feature of the specific DNA-binding protein used for the enhancer but a general property of synthetic bacterial enhancers.
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Affiliation(s)
- Roee Amit
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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16
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Abstract
Alternative σ-factors of bacteria bind core RNA polymerase to program the specific promoter selectivity of the holoenzyme. Signal-responsive changes in the availability of different σ-factors redistribute the RNA polymerase among the distinct promoter classes in the genome for appropriate adaptive, developmental and survival responses. The σ(54) -factor is structurally and functionally distinct from all other σ-factors. Consequently, binding of σ(54) to RNA polymerase confers unique features on the cognate holoenzyme, which requires activation by an unusual class of mechano-transcriptional activators, whose activities are highly regulated in response to environmental cues. This review summarizes the current understanding of the mechanisms of transcriptional activation by σ(54) -RNA polymerase and highlights the impact of global regulatory factors on transcriptional efficiency from σ(54) -dependent promoters. These global factors include the DNA-bending proteins IHF and CRP, the nucleotide alarmone ppGpp, and the RNA polymerase-targeting protein DksA.
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17
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Beraud M, Kolb A, Monteil V, D'Alayer J, Norel F. A proteomic analysis reveals differential regulation of the σ(S)-dependent yciGFE(katN) locus by YncC and H-NS in Salmonella and Escherichia coli K-12. Mol Cell Proteomics 2010; 9:2601-16. [PMID: 20713450 DOI: 10.1074/mcp.m110.002493] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The stationary phase sigma factor σ(S) (RpoS) controls a regulon required for general stress resistance of the closely related enterobacteria Salmonella and Escherichia coli. The σ(S)-dependent yncC gene encodes a putative DNA binding regulatory protein. Application of the surface-enhanced laser desorption/ionization-time of flight (SELDI-TOF) ProteinChip technology for proteome profiling of wild-type and mutant strains of Salmonella enterica serovar Typhimurium revealed potential protein targets for YncC regulation, which were identified by mass spectrometry, and subsequently validated. These proteins are encoded by the σ(S)-dependent operon yciGFEkatN and regulation of their expression by YncC operates at the transcriptional level, as demonstrated by gene fusion analyses and by in vitro transcription and DNase I footprinting experiments with purified YncC. The yciGFE genes are present (without katN) in E. coli K-12 but are poorly expressed, compared with the situation in Salmonella. We report that the yciGFE(katN) locus is silenced by the histone-like protein H-NS in both species, but that σ(S) efficiently relieves silencing in Salmonella but not in E. coli K-12. In Salmonella, YncC acts in concert with σ(S) to activate transcription at the yciG promoter (pyciG). When overproduced, YncC also activated σ(S)-dependent transcription at pyciG in E. coli K-12, but solely by countering the negative effect of H-NS. Our results indicate that differences between Salmonella and E. coli K-12, in the architecture of cis-acting regulatory sequences upstream of pyciG, contribute to the differential regulation of the yciGFE(katN) genes by H-NS and YncC in these two enterobacteria. In E. coli, this locus is subject to gene rearrangements and also likely to horizontal gene transfer, consistent with its repression by the xenogeneic silencer H-NS.
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Affiliation(s)
- Mélanie Beraud
- Institut Pasteur, Unité de Génétique moléculaire, Département de Microbiologie F-75015 Paris, France
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18
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Abstract
Gene transcription is a fundamental cellular process carried out by RNA polymerase (RNAP) enzymes and is highly regulated through the action of gene regulatory complexes. Important mechanistic insights have been gained from structural studies on multisubunit RNAP from bacteria, yeast and archaea, although the initiation process that involves the conversion of the inactive transcription complex to an active one has yet to be fully understood. RNAPs are unambiguously closely related in structure and function across all kingdoms of life and have conserved mechanisms. In bacteria, sigma (sigma) factors direct RNAP to specific promoter sites and the RNAP/sigma holoenzyme can either form a stable closed complex that is incompetent for transcription (as in the case of sigma(54)) or can spontaneously proceed to an open complex that is competent for transcription (as in the case of sigma(70)). The conversion of the RNAP/sigma(54) closed complex to an open complex requires ATP hydrolysis by enhancer-binding proteins, hence providing an ideal model system for studying the initiation process biochemically and structurally. In this review, we present recent structural studies of the two major bacterial RNAP holoenzymes and focus on mechanistic advances in the transcription initiation process via enhancer-binding proteins.
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Affiliation(s)
- Tamaswati Ghosh
- Department of Life Sciences, Centre for Structural Biology, Division of Molecular Biosciences, Imperial College London, London, UK
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19
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Xiao Y, Wigneshweraraj SR, Weinzierl R, Wang YP, Buck M. Construction and functional analyses of a comprehensive sigma54 site-directed mutant library using alanine-cysteine mutagenesis. Nucleic Acids Res 2009; 37:4482-97. [PMID: 19474350 PMCID: PMC2715252 DOI: 10.1093/nar/gkp419] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The sigma(54) factor associates with core RNA polymerase (RNAP) to form a holoenzyme that is unable to initiate transcription unless acted on by an activator protein. sigma(54) is closely involved in many steps of activator-dependent transcription, such as core RNAP binding, promoter recognition, activator interaction and open complex formation. To systematically define sigma(54) residues that contribute to each of these functions and to generate a resource for site specific protein labeling, a complete mutant library of sigma(54) was constructed by alanine-cysteine scanning mutagenesis. Amino acid residues from 3 to 476 of Cys(-)sigma(54) were systematically mutated to alanine and cysteine in groups of two adjacent residues at a time. The influences of each substitution pair upon the functions of sigma(54) were analyzed in vivo and in vitro and the functions of many residues were revealed for the first time. Increased sigma(54) isomerization activity seldom corresponded with an increased transcription activity of the holoenzyme, suggesting the steps after sigma(54) isomerization, likely to be changes in core RNAP structure, are also strictly regulated or rate limiting to open complex formation. A linkage between core RNAP-binding activity and activator responsiveness indicates that the sigma(54)-core RNAP interface changes upon activation.
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Affiliation(s)
- Yan Xiao
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
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20
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Huo YX, Zhang YT, Xiao Y, Zhang X, Buck M, Kolb A, Wang YP. IHF-binding sites inhibit DNA loop formation and transcription initiation. Nucleic Acids Res 2009; 37:3878-86. [PMID: 19395594 PMCID: PMC2709558 DOI: 10.1093/nar/gkp258] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Transcriptional activation of enhancer and σ54-dependent promoters requires efficient interactions between enhancer-binding proteins (EBP) and promoter bound σ54-RNA polymerase (Eσ54) achieved by DNA looping, which is usually facilitated by the integration host factor (IHF). Since the lengths of the intervening region supporting DNA-loop formation are similar among IHF-dependent and IHF-independent promoters, the precise reason(s) why IHF is selectively important for the frequency of transcription initiation remain unclear. Here, using kinetic cyclization and in vitro transcription assays we show that, in the absence of IHF protein, the DNA fragments containing an IHF-binding site have much less looping-formation ability than those that lack an IHF-binding site. Furthermore, when an IHF consensus-binding site was introduced into the intervening region between promoter and enhancer of the target DNA fragments, loop formation and DNA-loop-dependent transcriptional activation are significantly reduced in a position-independent manner. DNA-looping-independent transcriptional activation was unaffected. The binding of IHF to its consensus site in the target promoters clearly restored efficient DNA looping formation and looping-dependent transcriptional activation. Our data provide evidence that one function for the IHF protein is to release a communication block set by intrinsic properties of the IHF DNA-binding site.
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Affiliation(s)
- Yi-Xin Huo
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China
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21
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Organization of an activator-bound RNA polymerase holoenzyme. Mol Cell 2008; 32:337-46. [PMID: 18995832 PMCID: PMC2680985 DOI: 10.1016/j.molcel.2008.09.015] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 05/30/2008] [Accepted: 09/05/2008] [Indexed: 12/31/2022]
Abstract
Transcription initiation involves the conversion from closed promoter complexes, comprising RNA polymerase (RNAP) and double-stranded promoter DNA, to open complexes, in which the enzyme is able to access the DNA template in a single-stranded form. The complex between bacterial RNAP and its major variant sigma factor σ54 remains as a closed complex until ATP hydrolysis-dependent remodeling by activator proteins occurs. This remodeling facilitates DNA melting and allows the transition to the open complex. Here we present cryoelectron microscopy reconstructions of bacterial RNAP in complex with σ54 alone, and of RNAP-σ54 with an AAA+ activator. Together with photo-crosslinking data that establish the location of promoter DNA within the complexes, we explain why the RNAP-σ54 closed complex is unable to access the DNA template and propose how the structural changes induced by activator binding can initiate conformational changes that ultimately result in formation of the open complex.
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22
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Wigneshweraraj S, Bose D, Burrows PC, Joly N, Schumacher J, Rappas M, Pape T, Zhang X, Stockley P, Severinov K, Buck M. Modus operandi of the bacterial RNA polymerase containing the sigma54 promoter-specificity factor. Mol Microbiol 2008; 68:538-46. [PMID: 18331472 DOI: 10.1111/j.1365-2958.2008.06181.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial sigma (sigma) factors confer gene specificity upon the RNA polymerase, the central enzyme that catalyses gene transcription. The binding of the alternative sigma factor sigma(54) confers upon the RNA polymerase special functional and regulatory properties, making it suited for control of several major adaptive responses. Here, we summarize our current understanding of the interactions the sigma(54) factor makes with the bacterial transcription machinery.
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Affiliation(s)
- Sivaramesh Wigneshweraraj
- Department of Microbiology, Division of Investigative Sciences, Faculty of Medicine and Centre for Molecular Microbiology and Infection, Imperial College London, SW7 2AZ, UK.
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23
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Abstract
bEBPs (bacterial enhancer-binding proteins) are AAA+ (ATPase associated with various cellular activities) transcription activators that activate gene transcription through a specific bacterial sigma factor, sigma(54). Sigma(54)-RNAP (RNA polymerase) binds to promoter DNA sites and forms a stable closed complex, unable to proceed to transcription. The closed complex must be remodelled using energy from ATP hydrolysis provided by bEBPs to melt DNA and initiate transcription. Recently, large amounts of structural and biochemical data have produced insights into how ATP hydrolysis within the active site of bEBPs is coupled to the re-modelling of the closed complex. In the present article, we review some of the key nucleotides, mutations and techniques used and how they have contributed towards our understanding of the function of bEBPs.
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24
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Buck M, Bose D, Burrows P, Cannon W, Joly N, Pape T, Rappas M, Schumacher J, Wigneshweraraj S, Zhang X. A second paradigm for gene activation in bacteria. Biochem Soc Trans 2007; 34:1067-71. [PMID: 17073752 DOI: 10.1042/bst0341067] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Control of gene expression is key to development and adaptation. Using purified transcription components from bacteria, we employ structural and functional studies in an integrative manner to elaborate a detailed description of an obligatory step, the accessing of the DNA template, in gene expression. Our work focuses on a specialized molecular machinery that utilizes ATP hydrolysis to initiate DNA opening and permits a description of how the events triggered by ATP hydrolysis within a transcriptional activator can lead to DNA opening and transcription. The bacterial EBPs (enhancer binding proteins) that belong to the AAA(+) (ATPases associated with various cellular activities) protein family remodel the RNAP (RNA polymerase) holoenzyme containing the sigma(54) factor and convert the initial, transcriptionally silent promoter complex into a transcriptionally proficient open complex using transactions that reflect the use of ATP hydrolysis to establish different functional states of the EBP. A molecular switch within the model EBP we study [called PspF (phage shock protein F)] is evident, and functions to control the exposure of a solvent-accessible flexible loop that engages directly with the initial RNAP promoter complex. The sigma(54) factor then controls the conformational changes in the RNAP required to form the open promoter complex.
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Affiliation(s)
- M Buck
- Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK.
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25
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Mao XJ, Huo YX, Buck M, Kolb A, Wang YP. Interplay between CRP-cAMP and PII-Ntr systems forms novel regulatory network between carbon metabolism and nitrogen assimilation in Escherichia coli. Nucleic Acids Res 2007; 35:1432-40. [PMID: 17284458 PMCID: PMC1865078 DOI: 10.1093/nar/gkl1142] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, utilization of carbon sources is regulated by the phosphoenolpyruvate-dependent phosphotransferase system (PTS), which modulates the intracellular levels of cAMP. The cAMP receptor protein (CRP) controls the transcription of many catabolic genes. The availability of nitrogen is sensed by the PII protein at the level of intracellular glutamine. Glutamine is transported mainly by GlnHPQ, and synthesized by glutamine synthetase (GS) encoded by glnA. Previous studies suggest that CRP affects nitrogen assimilation. Here we showed that at least two mechanisms are involved. First, CRP activates glnHp1 via synergistic binding with sigma 70 RNA polymerase (Eσ70) and represses glnHp2. As a consequence, in the presence of glutamine, the overall enhancement of glnHPQ expression alters GlnB signalling and de-activates glnAp2. Second, in vitro studies show that CRP can be recruited by sigma 54 holoenzyme (Eσ54) to a site centred at −51.5 upstream of glnAp2. CRP-induced DNA-bending prevents the nitrogen regulation protein C (NtrC) activator from approaching the activator-accessible face of the promoter-bound Eσ54 closed complex, and inhibits glnAp2. Therefore, as the major transcriptional effector of the ‘glucose effect’, CRP affects both the signal transduction pathway and the overall geometry of the transcriptional machinery of components of the nitrogen regulon.
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Affiliation(s)
- Xian-Jun Mao
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, P. R. China, Department of Biological Science, Imperial College of Science, Technology and Medicine, London SW72AZ, UK and Unité des Régulations Transcriptionnelles, URA-CNRS 2172, Institut Pasteur, 75724 Paris, France
| | - Yi-Xin Huo
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, P. R. China, Department of Biological Science, Imperial College of Science, Technology and Medicine, London SW72AZ, UK and Unité des Régulations Transcriptionnelles, URA-CNRS 2172, Institut Pasteur, 75724 Paris, France
| | - Martin Buck
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, P. R. China, Department of Biological Science, Imperial College of Science, Technology and Medicine, London SW72AZ, UK and Unité des Régulations Transcriptionnelles, URA-CNRS 2172, Institut Pasteur, 75724 Paris, France
| | - Annie Kolb
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, P. R. China, Department of Biological Science, Imperial College of Science, Technology and Medicine, London SW72AZ, UK and Unité des Régulations Transcriptionnelles, URA-CNRS 2172, Institut Pasteur, 75724 Paris, France
| | - Yi-Ping Wang
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, P. R. China, Department of Biological Science, Imperial College of Science, Technology and Medicine, London SW72AZ, UK and Unité des Régulations Transcriptionnelles, URA-CNRS 2172, Institut Pasteur, 75724 Paris, France
- *To whom correspondence should be addressed. +86 10 6275 8490+86 10 6275 6325
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26
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Schumacher J, Joly N, Rappas M, Bradley D, Wigneshweraraj SR, Zhang X, Buck M. Sensor I threonine of the AAA+ ATPase transcriptional activator PspF is involved in coupling nucleotide triphosphate hydrolysis to the restructuring of sigma 54-RNA polymerase. J Biol Chem 2007; 282:9825-9833. [PMID: 17242399 DOI: 10.1074/jbc.m611532200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcriptional initiation invariably involves the transition from a closed RNA polymerase (RNAP) promoter complex to a transcriptional competent open complex. Activators of the bacterial sigma(54)-RNAP are AAA+ proteins that couple ATP hydrolysis to restructure the sigma(54)-RNAP promoter complex. Structures of the sigma(54) activator PspF AAA+ domain (PspF(1-275)) bound to sigma(54) show two loop structures proximal to sigma(54) as follows: the sigma(54) contacting the GAFTGA loop 1 structure and loop 2 that classifies sigma(54) activators as pre-sensor 1 beta-hairpin AAA+ proteins. We report activities for PspF(1-275) mutated in the AAA+ conserved sensor I threonine/asparagine motif (PspF(1-275)(T148A), PspF(1-275)(N149A), and PspF(1-275)(N149S)) within the second region of homology. We show that sensor I asparagine plays a direct role in ATP hydrolysis. However, low hydrolysis rates are sufficient for functional output in vitro. In contrast, PspF(1-275)(T148A) has severe defects at the distinct step of sigma(54) promoter restructuring. This defect is not because of the failure of PspF(1-275)(T148A) to stably engage with the closed sigma(54) promoter, indicating (i) an important role in ATP hydrolysis-associated motions during energy coupling for remodeling and (ii) distinguishing PspF(1-275)(T148A) from PspF(1-275) variants involved in signaling to the GAFTGA loop 1, which fail to stably engage with the promoter. Activities of loop 2 PspF(1-275) variants are similar to those of PspF(1-275)(T148A) suggesting a functional signaling link between Thr(148) and loop 2. In PspF(1-275) this link relies on the conserved nucleotide state-dependent interaction between the Walker B residue Glu(108) and Thr(148). We propose that hydrolysis is relayed via Thr(148) to loop 2 creating motions that provide mechanical force to the GAFTGA loop 1 that contacts sigma(54).
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Affiliation(s)
- Jörg Schumacher
- Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom.
| | - Nicolas Joly
- Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Mathieu Rappas
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Dominic Bradley
- Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Xiaodong Zhang
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Martin Buck
- Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom.
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27
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Rappas M, Bose D, Zhang X. Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription. Curr Opin Struct Biol 2006; 17:110-6. [PMID: 17157497 DOI: 10.1016/j.sbi.2006.11.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Revised: 10/30/2006] [Accepted: 11/24/2006] [Indexed: 10/23/2022]
Abstract
Bacterial transcription relies on the binding of dissociable sigma (sigma) factors to RNA polymerase (RNAP) for promoter specificity. The major variant sigma factor (sigma54) forms a stable closed complex with RNAP bound to DNA that rarely spontaneously isomerises to an open complex. ATP hydrolysis by bacterial enhancer-binding proteins is used to remodel the RNAP-sigma54-DNA closed complex. Recently, a wealth of structural information on bacterial enhancer-binding proteins has enabled unprecedented insights into their mechanism. These data provide a structural basis for nucleotide binding and hydrolysis, oligomerisation and the conversion of ATPase activity into remodelling events within the RNAP-sigma54 closed complex, and represent advances towards a complete understanding of the sigma54-dependent transcription activation mechanism.
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Affiliation(s)
- Mathieu Rappas
- Centre for Structural Biology, Division of Molecular Biosciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
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28
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Leach RN, Gell C, Wigneshweraraj S, Buck M, Smith A, Stockley PG. Mapping ATP-dependent activation at a sigma54 promoter. J Biol Chem 2006; 281:33717-26. [PMID: 16926155 DOI: 10.1074/jbc.m605731200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sigma(54) promoter specificity factor is distinct from other bacterial RNA polymerase (RNAP) sigma factors in that it forms a transcriptionally silent closed complex upon promoter binding. Transcriptional activation occurs through a nucleotide-dependent isomerization of sigma(54), mediated via its interactions with an enhancer-binding activator protein that utilizes the energy released in ATP hydrolysis to effect structural changes in sigma(54) and core RNA polymerase. The organization of sigma(54)-promoter and sigma(54)-RNAP-promoter complexes was investigated by fluorescence resonance energy transfer assays using sigma(54) single cysteine-mutants labeled with an acceptor fluorophore and donor fluorophore-labeled DNA sequences containing mismatches that mimic nifH early- and late-melted promoters. The results show that sigma(54) undergoes spatial rearrangements of functionally important domains upon closed complex formation. sigma(54) and sigma(54)-RNAP promoter complexes reconstituted with the different mismatched DNA constructs were assayed by the addition of the activator phage shock protein F in the presence or absence of ATP and of non-hydrolysable analogues. Nucleotide-dependent alterations in fluorescence resonance energy transfer efficiencies identify different functional states of the activator-sigma(54)-RNAP-promoter complex that exist throughout the mechano-chemical transduction pathway of transcriptional activation, i.e. from closed to open promoter complexes. The results suggest that open complex formation only occurs efficiently on replacement of a repressive fork junction with down-stream melted DNA.
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Affiliation(s)
- Robert N Leach
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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29
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Tian Z, Mao X, Su W, Li J, Becker A, Wang Y. Exogenous cAMP upregulates the expression of glnII and glnK-amtB genes in Sinorhizobium meliloti 1021. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s11434-006-2079-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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30
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Chen Y, Yang E, Liu Z, Tian Z, Wang Y. The role of CopG mediated DNA bending on the regulation of the σ54-dependent promoters in E. coli. CHINESE SCIENCE BULLETIN-CHINESE 2006. [DOI: 10.1007/s11434-006-0934-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Schumacher J, Joly N, Rappas M, Zhang X, Buck M. Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation. J Struct Biol 2006; 156:190-9. [PMID: 16531068 DOI: 10.1016/j.jsb.2006.01.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 01/16/2006] [Accepted: 01/19/2006] [Indexed: 11/29/2022]
Abstract
Initiation of transcription is a major point of transcriptional regulation and invariably involves the transition from a closed to an open RNA polymerase (RNAP) promoter complex. In the case of the sigma(54)-RNAP, this multi step process requires energy, provided by ATP hydrolysis occurring within the AAA+ domain of enhancer binding proteins (EBPs). Typically, EBPs have an N-terminal regulatory domain, a central AAA+ domain that directly contacts sigma(54) and a C-terminal DNA binding domain. The following AAA+ EBP crystal structures have recently become available: heptameric AAA+ domains of NtrC1 and dimeric NtrC1 with its regulatory domain, hexameric AAA+ domains of ZraR with DNA binding domains, apo and nucleotide bound forms of the AAA+ domain of PspF as well as a cryo-EM structure of the AAA+ domain of PspF complexed with sigma(54). These AAA+ domains reveal the structural conservation between EBPs and other AAA+ domains. EBP specific structural features involved in substrate remodelling are located proximal to the pore of the hexameric ring. Parallels with the substrate binding elements near the central pore of other AAA+ members are drawn. We propose a structural model of EBPs in complex with a sigma(54)-RNAP-promoter complex.
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Affiliation(s)
- Jörg Schumacher
- Division of Biology, Imperial College London, London, SW7 2AZ, UK.
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