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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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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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Hicks MN, Gunasekara S, Serate J, Park J, Mosharaf P, Zhou Y, Lee JW, Youn H. Gly184 of the Escherichia coli cAMP receptor protein provides optimal context for both DNA binding and RNA polymerase interaction. J Microbiol 2017; 55:816-822. [DOI: 10.1007/s12275-017-7266-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/11/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022]
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4
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Murchland I, Ahlgren-Berg A, Priest DG, Dodd IB, Shearwin KE. Promoter activation by CII, a potent transcriptional activator from bacteriophage 186. J Biol Chem 2014; 289:32094-32108. [PMID: 25294872 DOI: 10.1074/jbc.m114.608026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The lysogeny promoting protein CII from bacteriophage 186 is a potent transcriptional activator, capable of mediating at least a 400-fold increase in transcription over basal activity. Despite being functionally similar to its counterpart in phage λ, it shows no homology at the level of protein sequence and does not belong to any known family of transcriptional activators. It also has the unusual property of binding DNA half-sites that are separated by 20 base pairs, center to center. Here we investigate the structural and functional properties of CII using a combination of genetics, in vitro assays, and mutational analysis. We find that 186 CII possesses two functional domains, with an independent activation epitope in each. 186 CII owes its potent activity to activation mechanisms that are dependent on both the σ(70) and α C-terminal domain (αCTD) components of RNA polymerase, contacting different functional domains. We also present evidence that like λ CII, 186 CII is proteolytically degraded in vivo, but unlike λ CII, 186 CII proteolysis results in a specific, transcriptionally inactive, degradation product with altered self-association properties.
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Affiliation(s)
- Iain Murchland
- Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Alexandra Ahlgren-Berg
- Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - David G Priest
- Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ian B Dodd
- Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Keith E Shearwin
- Department of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.
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5
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Cyclic AMP receptor protein regulates cspD, a bacterial toxin gene, in Escherichia coli. J Bacteriol 2014; 196:1569-77. [PMID: 24509317 DOI: 10.1128/jb.01476-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
cspD, a member of cspA family of cold shock genes in Escherichia coli, is not induced during cold shock. Its expression is induced during stationary phase. CspD inhibits DNA replication, and a high level of the protein is toxic to cells. Recently, CspD was proposed to be associated with persister cell formation in E. coli. Here, we show that cyclic AMP receptor protein (CRP) upregulates cspD transcription. Sequence analysis of the cspD upstream region revealed two tandem CRP target sites, CRP site-I (the proximal site centered at -83.5 with respect to the transcription start) and CRP site-II (the distal site centered at -112.5). The results from electrophoretic mobility shift assays showed that CRP indeed binds to these two target sites in PcspD. The promoter-proximal CRP target site was found to play a major role in PcspD activation by CRP, as studied by transcriptional fusions carrying mutations in the target sites. The results from in vitro transcription assays demonstrated that CRP activates PcspD transcription in the absence of additional factors other than RNA polymerase. The requirement for activating region 1 of CRP in PcspD activation, along with the involvement of the 287, 265, and 261 determinants of the α-CTD, suggest that CRP activates by a class I-type mechanism. However, only moderate activation in vitro was observed compared to high activation in vivo, suggesting there might be additional activators of PcspD. Overall, our findings show that CRP, a global metabolic regulator in E. coli, activates a gene potentially related to persistence.
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Cyclic AMP receptor protein regulates cspE, an early cold-inducible gene, in Escherichia coli. J Bacteriol 2011; 193:6142-51. [PMID: 21926233 DOI: 10.1128/jb.05728-11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
cspE, a member of the cspA family of cold shock proteins in Escherichia coli, is an early cold-inducible protein. The nucleic acid melting ability and transcription antiterminator activity of CspE have been reported to be critical for growth at low temperature. Here, we show that the cyclic AMP receptor protein (CRP), a global regulator involved in sugar metabolism, upregulates cspE in E. coli. Sequence analysis of the cspE upstream region revealed a putative CRP target site centered at -61.5 relative to the transcription start. The binding of CRP to this target site was demonstrated using electrophoretic mobility shift assays. The presence of this site was shown to be essential for P(cspE) activation by CRP. Mutational analysis of the binding site indicated that the presence of an intact second core motif is more important than the first core motif for CRP-P(cspE) interaction. Based on the promoter architecture, we classified P(cspE) as a class I CRP-dependent promoter. This was further substantiated by our data demonstrating the involvement of the AR1 domain of CRP in P(cspE) transcription. Furthermore, the substitutions in the key residues of the RNA polymerase α-subunit C-terminal domain (α-CTD), which are important for class I CRP-dependent transcription, showed the involvement of 265 and 287 determinants in P(cspE) transcription. In addition, the deletion of crp led to a growth defect at low temperature, suggesting that CRP plays an important role in cold adaptation.
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Passner JM, Steitz TA. The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer. Proc Natl Acad Sci U S A 1997; 94:2843-7. [PMID: 9096308 PMCID: PMC20284 DOI: 10.1073/pnas.94.7.2843] [Citation(s) in RCA: 134] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The 2.2 A resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with cAMP and a 46-bp DNA fragment reveals a second cAMP molecule bound to each protein monomer. The second cAMP is in the syn conformation and is located on the DNA binding domain interacting with the helix-turn-helix, a beta-hairpin from the regulatory domain and the DNA (via water molecules). The presence of this second cAMP site resolves the apparent discrepancy between the NMR and x-ray data on the conformation of cAMP, and explains the cAMP concentration-dependent behaviors of the protein. In addition, this site's close proximity to mutations affecting transcriptional activation and its water-mediated interactions with a DNA recognition residue (E181) and DNA raise the possibility that this site has biological relevance.
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Affiliation(s)
- J M Passner
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
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8
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Schneider TD. Reading of DNA sequence logos: prediction of major groove binding by information theory. Methods Enzymol 1996; 274:445-55. [PMID: 8902824 DOI: 10.1016/s0076-6879(96)74036-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
DNA sequences to which the OxyR protein binds under oxidizing conditions were analyzed by the sequence logo method, a quantitative graphic technique based on information theory. A sequence logo shows both the sequence conservation and the frequencies of bases at each position in a site. Unlike the consensus sequence, the sequence logo analysis revealed that OxyR should bind to four major grooves of DNA. This was later confirmed by experiments. Detailed interpretation of the sequence logo also allowed the prediction of likely major and minor groove OxyR-DNA base contacts, consistent with available experimental results. Because the sequence logo shows the original base frequencies in a clear, easily interpreted graphic that does not distort the data, highly refined analysis of binding site contacts becomes easy. Not only can these methods be applied to any DNA sequence binding site, they can also be applied to sites on RNA and proteins.
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Affiliation(s)
- T D Schneider
- Laboratory of Mathematical Biology, Frederick Cancer Research and Development Center, National Cancer Institute, Maryland 21702, USA
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9
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Giraud-Panis MJ, Toulmé F, Blazy B, Maurizot JC, Culard F. Fluorescence study on the non-specific binding of cyclic-AMP receptor protein to DNA: effect of pH. Biochimie 1994; 76:133-9. [PMID: 8043649 DOI: 10.1016/0300-9084(94)90005-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The binding of the cyclic-AMP receptor protein (CRP) of Escherichia coli to a non-specific DNA fragment of 46 base pairs has been studied using fluorescence spectroscopy. The equilibrium binding constant was found to be several orders of magnitude lower than in the specific binding to a DNA fragment of the same size. The salt dependence of the equilibrium binding constant indicates that the CRP makes an identical number (8) of ion pairs to this non-specific DNA fragment in the presence and absence of cAMP. This number is larger than that previously found in the specific binding process. The effect of pH on the non-specific binding was investigated. The number of ion pairs does not vary between pH 6 and 8. From the variation of the binding constant with pH it was deduced that two histidines are involved in the binding in the absence of cAMP. These are most probably the histidines 199 of each subunit. In the presence of cAMP, only one histidine participates in the binding process, indicating an asymmetric interaction between the two subunits of the CRP and the DNA.
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10
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The Guanidinium Group: Its Biological Role and Synthetic Analogs. BIOORGANIC CHEMISTRY FRONTIERS 1993. [DOI: 10.1007/978-3-642-78110-0_6] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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11
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Hinds MG, King RW, Feeney J. 19F n.m.r. studies of conformational changes accompanying cyclic AMP binding to 3-fluorophenylalanine-containing cyclic AMP receptor protein from Escherichia coli. Biochem J 1992; 287 ( Pt 2):627-32. [PMID: 1332679 PMCID: PMC1133211 DOI: 10.1042/bj2870627] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A fluorine-containing analogue of the cyclic AMP (cAMP) receptor protein (CRP) from Escherichia coli was prepared by biosynthetic incorporation of 3-fluorophenylalanine (3-F-Phe). 19F n.m.r. studies on this protein have provided direct evidence for cAMP-induced conformational changes not only within the cAMP-binding domain but also within the hinge region connecting the cAMP-binding domain to the DNA-binding headpiece. At 313 K, the 19F n.m.r. spectrum of [3-F-Phe]CRP showed five signals corresponding to the five phenylalanine residues as expected for a symmetrical dimer. Proteolysis of [3-F-Phe]CRP with subtilisin produced a fragment (the alpha-fragment) containing the cAMP-binding domain. The alpha-fragment contains all the phenylalanines except for Phe-136, a residue located in the hinge region. By comparing the 19F spectra of [3-F-Phe]CRP and its alpha-fragment, the signal for Phe-136 was assigned. The chemical shifts of the corresponding signals in the two spectra are similar, indicating that the alpha-fragment retains the structure it has in the intact protein. The largest cAMP-induced shift was observed for the signal from Phe-136 providing direct evidence for a conformational change in the hinge region. However, whereas binding of a single cAMP molecule to a CRP dimer is known to be sufficient to activate the DNA binding, the n.m.r. data indicate that the hinge region does not have the same conformation in both subunits when only one cAMP molecule is bound.
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Affiliation(s)
- M G Hinds
- Laboratory of Molecular Structure, National Institute for Medical Research, Mill Hill, London, U.K
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12
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Giraud-Panis MJ, Toulmé F, Maurizot JC, Culard F. Specific binding of cyclic-AMP receptor protein to DNA. Effect of the sequence and of the introduction of a nick in the binding site. J Biomol Struct Dyn 1992; 10:295-309. [PMID: 1334673 DOI: 10.1080/07391102.1992.10508648] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The binding of Escherichia coli Cyclic AMP Receptor Protein (CRP) to several DNA fragments of about 45 base pairs, bearing the natural lactose or galactose sites, as well as several synthetic related sites, was investigated using fluorescence spectroscopy and gel retardation experiments. The salt dependence of the equilibrium binding constant indicates that CRP makes an identical number of ion pairs with the lac, lacL8 and gal sites although the binding constants are drastically different. However increasing the symmetry of the gal site leads to an increase of the number of ion pairs between the protein and the DNA. A single strand nick was introduced at the centre of a symmetrized gal site and this reduces the binding energy of CRP by about 0.6 Kcal. These results are discussed with respect to the bending constraints imposed on the DNA by the binding of CRP. The results are in agreement with the recently published crystal structure of the CRP complexed with DNA [Schutz, S.C., Shields, G.C. and Steitz, T.A., Science 253, 1001-1007 (1991)] showing that the 90 degrees bending of the DNA in the complex results from two kinks.
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Schultz SC, Shields GC, Steitz TA. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 1991; 253:1001-7. [PMID: 1653449 DOI: 10.1126/science.1653449] [Citation(s) in RCA: 870] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 90 degrees. This bend results almost entirely from two 40 degrees kinks that occur between TG/CA base pairs at positions 5 and 6 on each side of the dyad axis of the complex. DNA sequence discrimination by CAP derives both from sequence-dependent distortion of the DNA helix and from direct hydrogen-bonding interactions between three protein side chains and the exposed edges of three base pairs in the major groove of the DNA. The structure of this transcription factor--DNA complex provides insights into possible mechanisms of transcription activation.
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Affiliation(s)
- S C Schultz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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Kawamukai M, Utsumi R, Takeda K, Higashi A, Matsuda H, Choi YL, Komano T. Nucleotide sequence and characterization of the sfs1 gene: sfs1 is involved in CRP*-dependent mal gene expression in Escherichia coli. J Bacteriol 1991; 173:2644-8. [PMID: 2013578 PMCID: PMC207832 DOI: 10.1128/jb.173.8.2644-2648.1991] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have cloned at least 12 different Escherichia coli genes which enable strain MK2001 to use maltose. The genes were designated sfs1 through sfs12 (sugar fermentation stimulation). Previously, one (sfs7) of them was mapped at 65 min on the E. coli chromosome and identified as nlp, which has high homology to repressor protein (Ner) of Mu phage, which contains a putative DNA binding region (Y.-L. Choi, T. Nishida, M. Kawamukai, R. Utsumi, H. Sakai, and T. Komano, J. Bacteriol. 171:5222-5225, 1989). In this study, another gene (sfs1) located at 3.5 min was newly found and analyzed. The nucleotide sequence of sfs1 encoded a protein of 234 amino acids (molecular mass, 26,227 Da) which also has a putative DNA binding domain. Overexpression of the sfs1 gene in MK2001 resulted in a 10-fold increase of amylomaltase, which was still dependent on MalT. These results suggest that Sfs1 could be a new regulatory factor involved in maltose metabolism.
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Affiliation(s)
- M Kawamukai
- Laboratory of Applied Microbiology, Faculty of Agriculture, Shimane University, Matsue, Japan
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Spiro S, Gaston KL, Bell AI, Roberts RE, Busby SJ, Guest JR. Interconversion of the DNA-binding specificities of two related transcription regulators, CRP and FNR. Mol Microbiol 1990; 4:1831-8. [PMID: 2136332 DOI: 10.1111/j.1365-2958.1990.tb02031.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In Escherichia coli, FNR and CRP are homologous transcriptional regulators which recognize similar nucleotide sequences via DNA-binding domains containing analogous helix-turn-helix motifs. The molecular basis for recognition and discrimination of their target sites has been investigated by directed amino acid substitutions in the corresponding DNA-recognition helices. In FNR, Glu-209 and Ser-212 are essential residues for the recognition of FNR sites. A V208R substitution confers CRP-site specificity without loss of FNR specificity, but this has adverse effects on anaerobic growth. In contrast, changes at two (V208R and E209D) or three (V208R, S212G and G216K) positions in FNR endow a single CRP-site binding specificity. In reciprocal experiments, two substitutions (R180V and G184S) were required to convert the binding specificity of CRP to that of FNR. Altering Asp-199 in FNR failed to produce a positive control phenotype, unlike substitutions at the comparable site in CRP. Implications for the mechanism of sequence discrimination by FNR and CRP are discussed.
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Affiliation(s)
- S Spiro
- Department of Molecular Biology and Biotechnology, University of Sheffield, UK
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Bell AI, Cole JA, Busby SJ. Molecular genetic analysis of an FNR-dependent anaerobically inducible Escherichia coli promoter. Mol Microbiol 1990; 4:1753-63. [PMID: 2077359 DOI: 10.1111/j.1365-2958.1990.tb00553.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
From the effects of 13 deletions and three linker-scanner mutations at the Escherichia coli nirB promoter we have located sequences necessary for FNR-dependent induction of activity by anaerobiosis and further nitrite-dependent stimulation of expression. We describe a nirB promoter derivative that allows the cloning of 'cassettes' carrying different FNR-binding sequences and experiments in which a number of point mutations were introduced into these sequences. FNR-dependent stimulation of expression from the nirB promoter is critically dependent on the location of the FNR-binding site, and deletion or insertion of one base pair is sufficient to disrupt promoter function. We have transferred a number of cassette FNR-binding sequences from the nirB promoter to the unrelated melR promoter. The insertion of FNR-binding sequences at the melR promoter is sufficient to confer fnr-dependency on expression. However expression from these hybrid promoters is not as efficiently repressed during aerobic growth, suggesting that the function of bound FNR is dependent on the sequence context of the FNR-binding sequence.
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Affiliation(s)
- A I Bell
- School of Biochemistry, University of Birmingham, UK
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17
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Abstract
Bacteria which can grow in different environments have developed regulatory systems which allow them to exploit specific habitats to their best advantage. In the facultative anaerobe Escherichia coli two transcriptional regulators controlling independent networks of oxygen-regulated gene expression have been identified. One is a two-component sensor-regulator system (ArcB-A), which represses a wide variety of aerobic enzymes under anaerobic conditions. The other is FNR, the transcriptional regulator which is essential for expressing anaerobic respiratory processes. The purpose of this review is to summarize what is known about FNR. The fnr gene was initially defined by the isolation of some pleiotropic mutants which characteristically lacked the ability to use fumarate and nitrate as reducible substrates for supporting anaerobic growth and several other anaerobic respiratory functions. Its role as a transcriptional regulator emerged from genetic and molecular studies in which its homology with CRP (the cyclic AMP receptor protein which mediates catabolite repression) was established and has since been particularly important in identifying the structural basis of its regulatory specificities. FNR is a member of a growing family of CRP-related regulatory proteins which have a DNA-binding domain based on the helix-turn-helix structural motif, and a characteristic beta-roll that is involved in nucleotide-binding in CRP. The FNR protein has been isolated in a monomeric form (Mr 30,000) which exhibits a high but as yet non-specific affinity for DNA. Nevertheless, the DNA-recognition site and important residues conferring the functional specificity of FNR have been defined by site-directed mutagenesis. A consensus for the sequences that are recognized by FNR in the promoter regions of FNR-regulated genes, has likewise been identified. The basic features of the genes and operons regulated by FNR are reviewed, and examples in which FNR functions negatively as an anaerobic repressor as well as positively as an anaerobic activator, are included. Less is known about the way in which FNR senses anoxia and is thereby transformed into its 'active' form, but it seems likely that cysteine residues and possibly a metal ion are involved. Four of the five cysteine residues of FNR are clustered in an essential N-terminal 'domain' which is conserved in FNR and the HlyX protein of Actinobacillus pleuropneumoniae, but not in CRP or the FixK protein of Rhizobium meliloti. The relationships between FNR and other oxygen-related systems in E. coli are discussed, as well as parallel systems in other organisms.(ABSTRACT TRUNCATED AT 400 WORDS)
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Affiliation(s)
- S Spiro
- Department of Molecular Biology and Biotechnology, University of Sheffield, U.K
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18
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Steitz TA. Structural studies of protein-nucleic acid interaction: the sources of sequence-specific binding. Q Rev Biophys 1990; 23:205-80. [PMID: 2204954 DOI: 10.1017/s0033583500005552] [Citation(s) in RCA: 460] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Structural studies of DNA-binding proteins and their complexes with DNA have proceeded at an accelerating pace in recent years due to important technical advances in molecular genetics, DNA synthesis, protein crystallography and nuclear magnetic resonance. The last major review on this subject by Pabo & Sauer (1984) summarized the structural and functional studies of the three sequence-specific DNA-binding proteins whose crystal structures were then known, theE. colicatabolite gene activator protein (CAP) (McKay & Steitz, 1981; McKayet al.1982; Weber & Steitz, 1987), acrorepressor from phage λ (Andersonet al.1981), and the DNA-binding proteolytic fragment ofλcIrepressor protein (Pabo & Lewis, 1982) Although crystallographic studies of theE. coli lacrepressor protein were initiated as early as 1971 when it was the only regulatory protein available in sufficient quantities for structural studies (Steitzet al.1974), little was established about the structural aspects of DNA-binding proteins until the structure of CAP was determined in 1980 followed shortly thereafter by the structure ofλcrorepressor and subsequently that of the λ repressor fragment. There are now determined at high resolution the crystal structures of seven prokaryotic gene regulatory proteins or fragments [CAP,λcro,λcIrepressor fragment, 434 repressor fragment (Andersonet al.1987), 434crorepressor (Wolbergeret al.1988),E. coli trprepressor (Schevitzet al.1985),E. coli metrepressor (Raffertyet al.1989)],EcoRI restriction endonuclease (McClarinet al.1986), DNAse I (Suck & Ofner, 1986), the catalytic domain of γδ resolvase (Hatfullet al.1989) and two sequence-independent double-stranded DNA-binding proteins [the Klenow fragment ofE. coliDNA polymerase I (Olliset al.1985) and theE. coliHu protein (Tanakaet al., 1984)].
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Affiliation(s)
- T A Steitz
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University
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Schultz SC, Shields GC, Steitz TA. Crystallization of Escherichia coli catabolite gene activator protein with its DNA binding site. The use of modular DNA. J Mol Biol 1990; 213:159-66. [PMID: 2160019 DOI: 10.1016/s0022-2836(05)80128-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To obtain crystals of the Escherichia coli catabolite gene activator protein (CAP) complexed with its DNA-binding site, we have searched for crystallization conditions with 26 different DNA segments greater than or equal to 28 base-pairs in length that explore a variety of nucleotide sequences, lengths, and extended 5' or 3' termini. In addition to utilizing uninterrupted asymmetric lac site sequences, we devised a novel approach of synthesizing half-sites that allowed us to efficiently generate symmetric DNA segments with a wide variety of extended termini and lengths in the large size range (greater than or equal to 28 bp) required by this protein. We report three crystal forms that are suitable for X-ray analysis, one of which (crystal form III) gives measurable diffraction amplitudes to 3 A resolution. Additives such as calcium, n-octyl-beta-D-glucopyranoside and spermine produce modest improvements in the quality of diffraction from crystal form III. Adequate stabilization of crystal form III is unexpectedly complex, requiring a greater than tenfold reduction in the salt concentration followed by addition of 2-methyl-2,4-pentanediol and then an increase in the concentration of polyethylene glycol.
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Affiliation(s)
- S C Schultz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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Ebright RH, Gunasekera A, Zhang XP, Kunkel TA, Krakow JS. Lysine 188 of the catabolite gene activator protein (CAP) plays no role in specificity at base pair 7 of the DNA half site. Nucleic Acids Res 1990; 18:1457-64. [PMID: 2158078 PMCID: PMC330512 DOI: 10.1093/nar/18.6.1457] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex ('model I,' Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973-3977, 1984; 'model II,' Ebright, et al., Proc. Natl. Acad. Sci. USA, 81, 7274-7278, 1984). The most important difference between the two models involves Lys188 of CAP. Model I predicts that Lys188 of CAP makes a specificity determining contact with base pair 7 of the DNA half site. In contrast, model II predicts that Lys188 makes no contact with base pair 7 of the DNA half site. In the present work, we have used site-directed mutagenesis to replace Lys188 of CAP by Asn, an amino acid unable to make the putative contact. We have assessed the specificities of the following proteins, both in vitro and in vivo: wild-type CAP, [Asn188]CAP, [Val181]CAP, and [Val181;Asn188]CAP. The results indicate that Lys188 makes no contribution to specificity at base pair 7 of the DNA half site. We propose, contrary to model I, that Lys188 makes no contact with base pair 7 of the DNA half site.
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Affiliation(s)
- R H Ebright
- Department of Chemistry, Rutgers University, New Brunswick, NJ 08855
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Cherfils J, Gibrat JF, Levin J, Batut J, Kahn D. Model-building of Fnr and FixK DNA-binding domains suggests a basis for specific DNA recognition. J Mol Recognit 1989; 2:114-21. [PMID: 2561529 DOI: 10.1002/jmr.300020303] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The DNA-binding C-terminal domains of the regulatory proteins Fnr from Escherichia coli and FixK from Rhizobium meliloti have been modelled on the basis of their homologies to the CAP protein from E. coli. Residues Glu181, Thr182 and Arg185 of CAP, which are exposed residues of the DNA-recognition helix alpha F, are conserved in Fnr and FixK. However, Arg180 and Gly184 are substituted by Val and Ser respectively in Fnr. We propose that this valine makes a Van der Waals' contact with the first thymine in the Fnr consensus TTGA-N6-TCAA, and that the serine contributes to the binding by displacing a thymine-bound water molecule. The corresponding residues in FixK, Ile and Ser allow the same interactions with a thymine. Therefore we predict that FixK may recognize the same sites as Fnr. This is supported experimentally by showing that Fnr can substitute for FixK in activating the fixN gene in E. coli.
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Affiliation(s)
- J Cherfils
- Laboratoire de Biologie Physicochimique, INRA, Université Paris-Sud, Orsay, France
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Gaston K, Kolb A, Busby S. Binding of the Escherichia coli cyclic AMP receptor protein to DNA fragments containing consensus nucleotide sequences. Biochem J 1989; 261:649-53. [PMID: 2673223 PMCID: PMC1138872 DOI: 10.1042/bj2610649] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Binding of the Escherichia coli CRP protein to DNA fragments carrying nucleotide sequences closely corresponding to the consensus is very tight with a dissociation time of over 2 h in our conditions. The concentration of cyclic AMP required for this binding is below the physiological range of intracellular cyclic AMP concentrations. Changes in nucleotide sequence at positions that are not well-conserved between different naturally-occurring CRP sites allow a more rapid dissociation of CRP-DNA complexes. There is an inverse correlation between the stability of CRP binding to sites in vitro and the repression by glucose of expression dependent on these sites in vivo: expression that is dependent on the tighter binding sites cannot be repressed by the inclusion of glucose in the growth medium.
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Affiliation(s)
- K Gaston
- School of Biochemistry, University of Birmingham, U.K
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23
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Bell AI, Gaston KL, Cole JA, Busby SJ. Cloning of binding sequences for the Escherichia coli transcription activators, FNR and CRP: location of bases involved in discrimination between FNR and CRP. Nucleic Acids Res 1989; 17:3865-74. [PMID: 2543955 PMCID: PMC317865 DOI: 10.1093/nar/17.10.3865] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Expression from the E.coli melR promoter (pmelR) is normally totally dependent on the transcription activator protein, CRP. We describe experiments with a genetically engineered DNA fragment carrying pmelR in which the wild type CRP binding site was replaced with synthetic oligonucleotides containing either FNR or CRP binding sequences. When the synthetic oligonucleotide contains the 22 bp consensus for FNR binding sites, expression from pmelR is dependent on FNR but not CRP. Single changes at either of two symmetrically-related positions create sites that are recognised by both FNR and CRP. Changes at both positions result in a site that is not recognised by FNR but which binds CRP tightly.
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Affiliation(s)
- A I Bell
- University of Birmingham, School of Biochemistry, UK
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Gronenborn AM, Sandulache R, Gärtner S, Clore GM. Mutations in the cyclic AMP binding site of the cyclic AMP receptor protein of Escherichia coli. Biochem J 1988; 253:801-7. [PMID: 2845936 PMCID: PMC1149374 DOI: 10.1042/bj2530801] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Mutants in the cyclic AMP binding site of the cyclic AMP receptor protein (CRP) of Escherichia coli have been constructed by oligonucleotide-directed mutagenesis. They have been phenotypically characterized and their ability to enhance the expression of catabolite-repressible operons has been tested. In addition, the binding of cyclic nucleotides to the mutants has been investigated. It is shown that the six mutants made fall into one of three classes: (i) those that bind cyclic AMP better than the wild type protein (Ser-62----Ala) and result in greater transcription enhancement; (ii) those that bind cyclic AMP similarly to wild type (Ser-83----Ala, Ser-83----Lys, Thr-127----Ala, Ser-129----Ala); and (iii) those that do not bind cyclic AMP at all (Arg-82----Leu). Implications of these findings with respect to present models of the cyclic nucleotide binding pocket of CRP are discussed.
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Affiliation(s)
- A M Gronenborn
- Max-Planck-Institut für Biochemie, Martinsried bei München, Federal Republic of Germany
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Gaston K, Chan B, Kolb A, Fox J, Busby S. Alterations in the binding site of the cyclic AMP receptor protein at the Escherichia coli galactose operon regulatory region. Biochem J 1988; 253:809-18. [PMID: 2845937 PMCID: PMC1149375 DOI: 10.1042/bj2530809] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Gene manipulation techniques have been used to alter the binding site for the cyclic AMP-cyclic AMP receptor protein complex (cAMP-CRP) at the regulatory region of the Escherichia coli galactose (gal) operon. The effects of these changes on CRP-dependent stimulation of expression from the galP1 promoter in vivo have been measured, and gel binding assays have been used to measure the affinity of cAMP-CRP for the modified sites. Firstly we have deleted progressively longer sequences from upstream of the gal CRP site in order to locate the functional limit of the site. A deletion to -49, removing the first base that corresponds to the consensus sequence for a CRP binding site, is sufficient to reduce CRP binding and block CRP-dependent stimulation of P1. Secondly, we used synthetic oligonucleotides to invert the asymmetric nucleotide sequence at the gal CRP binding site or to make the sequence symmetric. Inversion of the site has little effect on CRP binding, the architecture of open complexes at P1 revealed by DNAase I footprinting, or the stimulation of transcription from P1. Making the site symmetric increases the affinity for CRP by over 50-fold and leads to increased transcription from P1, whilst hardly altering the DNAase I footprint of open complexes. Our results confirm that the strength of binding of CRP depends on the nature of the site and show that it is this that principally accounts for differences in CRP-dependent stimulation of transcription.
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Affiliation(s)
- K Gaston
- Department of Biochemistry, University of Birmingham, U.K
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Jansen C, Gronenborn AM, Clore GM. The binding of the cyclic AMP receptor protein to synthetic DNA sites containing permutations in the consensus sequence TGTGA. Biochem J 1987; 246:227-32. [PMID: 3675557 PMCID: PMC1148262 DOI: 10.1042/bj2460227] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The binding of the cyclic AMP receptor protein (CRP) to symmetrical synthetic DNA-binding sites was investigated with a gel-retardation assay. A set of ten different sequences was employed, comprising all base permutations at positions 2, 4, and 5 of the consensus sequence 5'(TGTGA)3'. We show that: (i) CRP has a higher affinity for the completely symmetrical site than towards the lac wild-type site; (ii) base substitutions at position 2 lead to either a complete loss of specific CRP binding (G----C), a reduction in specific CRP binding (G----A) or only marginal effects on specific CRP binding (G----T); (iii) changes at position 4 abolish (G----C; G----A) or reduce (G----T) specific CRP binding; and (iv) base permutations at position 5 reduce specific CRP binding, but never completely abolish it. Thus position 4, and to a lesser extent position 2, in the DNA consensus sequence are the most crucial ones for specific binding by CRP.
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Affiliation(s)
- C Jansen
- Max-Planck Institut fur Biochemie, Martinsried bei München, Federal Republic of Germany
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