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Campbell RP, Whittington AC, Zorio DAR, Miller BG. Recruitment of a Middling Promiscuous Enzyme Drives Adaptive Metabolic Evolution in Escherichia coli. Mol Biol Evol 2023; 40:msad202. [PMID: 37708398 PMCID: PMC10519446 DOI: 10.1093/molbev/msad202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
A key step in metabolic pathway evolution is the recruitment of promiscuous enzymes to perform new functions. Despite the recognition that promiscuity is widespread in biology, factors dictating the preferential recruitment of one promiscuous enzyme over other candidates are unknown. Escherichia coli contains four sugar kinases that are candidates for recruitment when the native glucokinase machinery is deleted-allokinase (AlsK), manno(fructo)kinase (Mak), N-acetylmannosamine kinase (NanK), and N-acetylglucosamine kinase (NagK). The catalytic efficiencies of these enzymes are 103- to 105-fold lower than native glucokinases, ranging from 2,400 M-1 s-1 for the most active candidate, NagK, to 15 M-1 s-1 for the least active candidate, AlsK. To investigate the relationship between catalytic activities of promiscuous enzymes and their recruitment, we performed adaptive evolution of a glucokinase-deficient E. coli strain to restore glycolytic metabolism. We observed preferential recruitment of NanK via a trajectory involving early mutations that facilitate glucose uptake and amplify nanK transcription, followed by nonsynonymous substitutions in NanK that enhance the enzyme's promiscuous glucokinase activity. These substitutions reduced the native activity of NanK and reduced organismal fitness during growth on an N-acetylated carbon source, indicating that enzyme recruitment comes at a cost for growth on other substrates. Notably, the two most active candidates, NagK and Mak, were not recruited, suggesting that catalytic activity alone does not dictate evolutionary outcomes. The results highlight our lack of knowledge regarding biological drivers of enzyme recruitment and emphasize the need for a systems-wide approach to identify factors facilitating or constraining this important adaptive process.
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Affiliation(s)
- Ryan P Campbell
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - A Carl Whittington
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Diego A R Zorio
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
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A Class IV Adenylate Cyclase, CyaB, Is Required for Capsule Polysaccharide Production and Biofilm Formation in Vibrio parahaemolyticus. Appl Environ Microbiol 2023; 89:e0187422. [PMID: 36602323 PMCID: PMC9888186 DOI: 10.1128/aem.01874-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cyclic AMP (cAMP) receptor protein (CRP), encoded by crp, is a global regulator that is activated by cAMP, a second messenger synthesized by a class I adenylate cyclase (AC-I) encoded by cyaA in Escherichia coli. cAMP-CRP is required for growth on nonpreferred carbon sources and is a global regulator. We constructed in-frame nonpolar deletions of the crp and cyaA homologs in Vibrio parahaemolyticus and found that the Δcrp mutant did not grow in minimal media supplemented with nonpreferred carbon sources, but the ΔcyaA mutant grew similarly to the wild type. Bioinformatics analysis of the V. parahaemolyticus genome identified a 181-amino-acid protein annotated as a class IV adenylate cyclase (AC-IV) named CyaB, a member of the CYTH protein superfamily. AC-IV phylogeny showed that CyaB was present in Gammaproteobacteria and Alphaproteobacteria as well as Planctomycetes and Archaea. Only the bacterial CyaB proteins contained an N-terminal motif, HFxxxxExExK, indicative of adenylyl cyclase activity. Both V. parahaemolyticus cyaA and cyaB genes functionally complemented an E. coli ΔcyaA mutant. The Δcrp and ΔcyaB ΔcyaA mutants showed defects in growth on nonpreferred carbon sources and in swimming and swarming motility, indicating that cAMP-CRP is an activator. The ΔcyaA and ΔcyaB single mutants had no defects in these phenotypes, indicating that AC-IV complements AC-I. Capsule polysaccharide and biofilm production assays showed significant defects in the Δcrp, ΔcyaBΔcyaA, and ΔcyaB mutants, whereas the ΔcyaA strain behaved similarly to the wild type. This is consistent with a role of cAMP-CRP as an activator of these phenotypes and establishes a cellular role for AC-IV in capsule and biofilm formation, which to date has been unestablished. IMPORTANCE Here, we characterized the roles of CRP and CyaA in V. parahaemolyticus, showing that cAMP-CRP is an activator of metabolism, motility, capsule production, and biofilm formation. These results are in contrast to cAMP-CRP in V. cholerae, which represses capsule and biofilm formation. Previously, only an AC-I CyaA had been identified in Vibrio species. Our data showed that an AC-IV CyaB homolog is present in V. parahaemolyticus and is required for optimal growth. The data demonstrated that CyaB is essential for capsule production and biofilm formation, uncovering a physiological role of AC-IV in bacteria. The data showed that the cyaB gene was widespread among Vibrionaceae species and several other Gammaproteobacteria, but in general, its phylogenetic distribution was limited. Our phylogenetic analysis also demonstrated that in some species the cyaB gene was acquired by horizontal gene transfer.
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Seok JY, Han YH, Yang JS, Yang J, Lim HG, Kim SG, Seo SW, Jung GY. Synthetic biosensor accelerates evolution by rewiring carbon metabolism toward a specific metabolite. Cell Rep 2021; 36:109589. [PMID: 34433019 DOI: 10.1016/j.celrep.2021.109589] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 06/01/2021] [Accepted: 08/02/2021] [Indexed: 12/29/2022] Open
Abstract
Proper carbon flux distribution between cell growth and production of a target compound is important for biochemical production because improper flux reallocation inhibits cell growth, thus adversely affecting production yield. Here, using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolve cells under the selective condition toward the acquisition of genotypes that optimally reallocate cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determine that mutations in the conserved regions of proteins involved in global transcriptional regulation alter the expression of several genes associated with central carbon metabolism. These changes rewire central carbon flux toward the 3-HP production pathway, increasing 3-HP yield and reducing acetate accumulation by alleviating overflow metabolism. Our study provides a perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization.
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Affiliation(s)
- Joo Yeon Seok
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Yong Hee Han
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Jae-Seong Yang
- Centre de Recerca en Agrigenòmica, Consortium CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Seong Gyeong Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea
| | - Sang Woo Seo
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Engineering Research, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, Korea.
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Coward C, Dharmalingham G, Abdulle O, Avis T, Beisken S, Breidenstein E, Carli N, Figueiredo L, Jones D, Khan N, Malara S, Martins J, Nagalingam N, Turner K, Wain J, Williams D, Powell D, Mason C. High-density transposon libraries utilising outward-oriented promoters identify mechanisms of action and resistance to antimicrobials. FEMS Microbiol Lett 2020; 367:fnaa185. [PMID: 33186989 PMCID: PMC7735965 DOI: 10.1093/femsle/fnaa185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/11/2020] [Indexed: 01/07/2023] Open
Abstract
The use of bacterial transposon mutant libraries in phenotypic screens is a well-established technique for determining which genes are essential or advantageous for growth in conditions of interest. Standard, inactivating, transposon libraries cannot give direct information about genes whose over-expression gives a selective advantage. We report the development of a system wherein outward-oriented promoters are included in mini-transposons, generation of transposon mutant libraries in Escherichia coli and Pseudomonas aeruginosa and their use to probe genes important for growth under selection with the antimicrobial fosfomycin, and a recently-developed leucyl-tRNA synthase inhibitor. In addition to the identification of known mechanisms of action and resistance, we identify the carbon-phosphorous lyase complex as a potential resistance liability for fosfomycin in E. coli and P. aeruginosa. The use of this technology can facilitate the development of novel mechanism-of-action antimicrobials that are urgently required to combat the increasing threat worldwide from antimicrobial-resistant pathogenic bacteria.
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Affiliation(s)
- Chris Coward
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Gopujara Dharmalingham
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Omar Abdulle
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Tim Avis
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Stephan Beisken
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Elena Breidenstein
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Natasha Carli
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Luis Figueiredo
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - David Jones
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Nawaz Khan
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Sara Malara
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Joana Martins
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Nabeetha Nagalingam
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Keith Turner
- Quadram Institute, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - John Wain
- Quadram Institute, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - David Williams
- Nanna Therapeutics, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - David Powell
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
| | - Clive Mason
- Summit Therapeutics plc, The Merrifield Centre, 12 Rosemary Lane, Cambridge, CB1 3LQ, UK
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5
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Efficient production of cyclic adenosine monophosphate from adenosine triphosphate by the N-terminal half of adenylate cyclase from Escherichia coli. Chin J Chem Eng 2020. [DOI: 10.1016/j.cjche.2020.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Zhuang Q, Wang Q, Liang Q, Qi Q. Synthesis of polyhydroxyalkanoates from glucose that contain medium-chain-length monomers via the reversed fatty acid β-oxidation cycle in Escherichia coli. Metab Eng 2014; 24:78-86. [PMID: 24836703 DOI: 10.1016/j.ymben.2014.05.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 04/17/2014] [Accepted: 05/05/2014] [Indexed: 10/25/2022]
Abstract
Polyhydroxyalkanoates that contain the medium-chain-length monomers (mcl-PHAs) have a wide range of applications owing to their superior physical and mechanical properties. A challenge to synthesize such mcl-PHAs from unrelated and renewable sources is exploiting the efficient metabolic pathways that lead to the formation of precursor (R)-3-hydroxyacyl-CoA. Here, by engineering the reversed fatty acid β-oxidation cycle, we were able to synthesize mcl-PHAs in Escherichia coli directly from glucose. After deletion of the major thioesterases, the engineered E. coli produced 6.62wt% of cell dry weight mcl-PHA heteropolymers. Furthermore, when a low-substrate-specificity PHA synthase from Pseudomonas stutzeri 1317 was employed, recombinant E. coli synthesized 12.10wt% of cell dry weight scl-mcl PHA copolymers, of which 21.18mol% was 3-hydroxybutyrate and 78.82mol% was medium-chain-length monomers. The reversed fatty acid β-oxidation cycle offered an efficient metabolic pathway for mcl-PHA biosynthesis in E. coli and can be further optimized.
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Affiliation(s)
- Qianqian Zhuang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China.
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7
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Selective reduction of xylose to xylitol from a mixture of hemicellulosic sugars. Metab Eng 2010; 12:462-8. [DOI: 10.1016/j.ymben.2010.04.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 03/24/2010] [Accepted: 04/26/2010] [Indexed: 11/15/2022]
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8
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Abstract
Class I adenylate cyclases are found in gamma- and delta-proteobacteria. They play central roles in processes such as catabolite repression in Escherichia coli or development of full virulence in pathogens such as Yersinia enterocolitica and Vibrio vulnificus. The catalytic domain (residues 2-446) of the adenylate cyclase of E. coli was overexpressed and purified. It displayed a V(max) of 665 nmol of cAMP x mg(-1) x min(-1) and a K(m) of 270 microM. Titration of the metal cofactor Mg(2+) against the substrate ATP showed a requirement for free metal ions in addition to the MgATP complex, suggesting a two-metal-ion mechanism as is known for class II and class III adenylate cyclases. Twelve residues which are essential for catalysis were identified by mutagenesis of a total of 20 polar residues conserved in all class I adenylate cyclases. Five essential residues (Ser(103), Ser(113), Asp(114), Asp(116) and Trp(118)) were part of a region which is found in all members of the large DNA polymerase beta-like nucleotidyltransferase superfamily. Alignment of the E. coli adenylate cyclase with the crystal structure of a distant member of the superfamily, archaeal tRNA CCA-adding enzyme, suggested that Asp(114) and Asp(116) are the metal-cofactor-ion-binding residues. The S103A mutant had a 17-fold higher K(m) than wild-type, demonstrating its important role in substrate binding. In comparison with the tRNA CCA-adding enzyme, Ser(103) of the E. coli adenylate cyclase apparently binds the gamma-phosphate group of ATP. Consistent with this function, the S103A mutation caused a marked reduction of discrimination between ATP- and ADP- or AMP-derived inhibitors.
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9
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Deutscher J, Francke C, Postma PW. How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 2007; 70:939-1031. [PMID: 17158705 PMCID: PMC1698508 DOI: 10.1128/mmbr.00024-06] [Citation(s) in RCA: 989] [Impact Index Per Article: 58.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens.
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Affiliation(s)
- Josef Deutscher
- Microbiologie et Génétique Moléculaire, INRA-CNRS-INA PG UMR 2585, Thiverval-Grignon, France.
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10
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Roberts DP, McKenna LF, Hu X, Lohrke SM, Kong HS, de Souza JT, Baker CJ, Lydon J. Mutation in cyaA in Enterobacter cloacae decreases cucumber root colonization. Arch Microbiol 2006; 187:101-15. [PMID: 17024489 DOI: 10.1007/s00203-006-0177-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 08/29/2006] [Accepted: 09/01/2006] [Indexed: 10/24/2022]
Abstract
Strains of Enterobacter cloacae show promise as biological control agents for Pythium ultimum-induced damping-off on cucumber and other crops. Enterobacter cloacae M59 is a mini-Tn5 Km transposon mutant of strain 501R3. Populations of M59 were significantly lower on cucumber roots and decreased much more rapidly than those of strain 501R3 with increasing distance from the soil line. Strain M59 was decreased or deficient in growth and chemotaxis on most individual compounds detected in cucumber root exudate and on a synthetic cucumber root exudate medium. Strain M59 was also slightly less acid resistant than strain 501R3. Molecular characterization of strain M59 demonstrated that mini-Tn5 Km was inserted in cyaA, which encodes adenylate cyclase. Adenylate cyclase catalyzes the formation of cAMP and cAMP levels in cell lysates from strain M59 were approximately 2% those of strain 501R3. Addition of exogenous, nonphysiological concentrations of cAMP to strain M59 restored growth (1 mM) and chemotaxis (5 mM) on synthetic cucumber root exudate and increased cucumber seedling colonization (5 mM) by this strain without serving as a source of reduced carbon, nitrogen, or phosphorous. These results demonstrate a role for cyaA in colonization of cucumber roots by Enterobacter cloacae.
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Affiliation(s)
- Daniel P Roberts
- Sustainable Agricultural Systems Laboratory, USDA-Agricultural Research Service, Bldg. 001, Rm. 140, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA.
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Strozen TG, Langen GR, Howard SP. Adenylate cyclase mutations rescue the degP temperature-sensitive phenotype and induce the sigma E and Cpx extracytoplasmic stress regulons in Escherichia coli. J Bacteriol 2005; 187:6309-16. [PMID: 16159763 PMCID: PMC1236634 DOI: 10.1128/jb.187.18.6309-6316.2005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Inactivation of the gene encoding the periplasmic protease DegP confers a high-temperature-sensitive phenotype in Escherichia coli. We have previously demonstrated that a degP mutant of E. coli strain CBM (W3110 pldA1) is not temperature sensitive and showed that this was most likely due to constitutive activation of the sigma E and Cpx extracytoplasmic stress regulons in the parent strain. In this study, further characterization of this strain revealed a previously unknown cryptic mutation that rescued the degP temperature-sensitive phenotype by inducing the extracytoplasmic stress regulons. We identified the cryptic mutation as an 11-bp deletion of nucleotides 1884 to 1894 of the adenylate cyclase-encoding cyaA gene (cyaAdelta11). The mechanism in which cyaAdelta11 induces the sigma E and Cpx regulons involves decreased activity of the mutant adenylate cyclase. Addition of exogenous cyclic AMP (cAMP) to the growth medium of a cyaAdelta11 mutant strain that contains a Cpx- and sigma E-inducible degP-lacZ reporter fusion decreased beta-galactosidase expression to levels observed in a cyaA+ strain. We also found that a cyaA null mutant displayed even higher levels of extracytoplasmic stress regulon activation compared to a cyaAdelta11 mutant. Thus, we conclude that the lowered concentration of cAMP in cyaA mutants induces both sigma E and Cpx extracytoplasmic stress regulons and thereby rescues the degP temperature-sensitive phenotype.
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Affiliation(s)
- Timothy G Strozen
- Department of Microbiology and Immunology, 107 Wiggins Road, Room A224, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5E5, Canada
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Krin E, Sismeiro O, Danchin A, Bertin PN. The regulation of Enzyme IIA(Glc) expression controls adenylate cyclase activity in Escherichia coli. MICROBIOLOGY (READING, ENGLAND) 2002; 148:1553-1559. [PMID: 11988530 DOI: 10.1099/00221287-148-5-1553] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
During the last few years, several genes, such as pap, bgl and flhDC, have been shown to be coregulated by the histone-like nucleoid-structuring (H-NS) protein and the cyclic AMP-catabolite activator protein (cAMP/CAP) complex, suggesting an interaction between both systems in the control of some cellular functions. In this study, the possible effect of H-NS on the cAMP level was investigated. In a CAP-deficient strain, the presence of an hns mutation results in a strong reduction in the amount of cAMP, due to a decrease in adenylate cyclase activity. This is caused by the reduced expression of crr, which encodes the Enzyme IIA(Glc) of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS), from its specific P2 promoter. This leads to a twofold reduction in the global amount of Enzyme IIA(Glc), the adenylate cyclase activator, responsible for the decrease in adenylate cyclase activity observed in the hns crp strain.
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Affiliation(s)
- Evelyne Krin
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France1
| | - Odile Sismeiro
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France1
| | - Antoine Danchin
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France1
| | - Philippe N Bertin
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France1
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Naula C, Schaub R, Leech V, Melville S, Seebeck T. Spontaneous dimerization and leucine-zipper induced activation of the recombinant catalytic domain of a new adenylyl cyclase of Trypanosoma brucei, GRESAG4.4B. Mol Biochem Parasitol 2001; 112:19-28. [PMID: 11166383 DOI: 10.1016/s0166-6851(00)00338-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this study, we describe the isolation and characterization of a new adenylyl cyclase from Trypanosoma brucei and its activation by dimerization of the catalytic domain. In agreement with the current nomenclature of trypanosomal adenylyl cyclases, this new gene is termed GRESAG4.4B. The complete ORF of the GRESAG4.4B gene encodes a protein of 1291 amino acids. Its predicted protein structure is consistent with the structure of other trypanosomal cyclases, and with the cyclases of L. donovani. GRESAG 4.4B is constitutively expressed during the life cycle of trypanosomes. GRESAG4.4B is a member of a gene family, which contains at least six members, which are all clustered on chromosome IV. The catalytic domain of GRESAG4.4B is able to dimerize spontaneously. However, these spontaneously formed, stable dimers only show minimal enzymatic activity. The addition of a leucine zipper (LZ) derived from the S. cerevisiae GCN 4 gene to the N-terminus of the catalytic domain of GRESAG4.4B strongly activated its enzymatic activity. The LZ appears to enforce a distinct conformation of the dimer, which leads to an increased enzymatic activity, and thus may mimic the effect of ligand-induced dimerization of adenylyl cyclase in vivo.
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Affiliation(s)
- C Naula
- Institute for Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012 Bern, Switzerland
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14
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Kotrba P, Inui M, Yukawa H. Bacterial phosphotransferase system (PTS) in carbohydrate uptake and control of carbon metabolism. J Biosci Bioeng 2001. [DOI: 10.1016/s1389-1723(01)80308-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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15
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Crasnier-Mednansky M, Park MC, Studley WK, Saier MH. Cra-mediated regulation of Escherichia coli adenylate cyclase. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 3):785-792. [PMID: 9084162 DOI: 10.1099/00221287-143-3-785] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In Escherichia coli, expression of certain genes and operons, including the fructose operon, is controlled by Cra, the pleiotropic catabolite repressor/activator protein formerly known as FruR. In this study we have demonstrated that cra mutant strains synthesize 10-fold less cAMP than isogenic wild-type strains, specifically when grown in fructose-containing minimal media. The glucose-specific IIA protein (IIAglc) of the phosphotransferase system, which activates adenylate cyclase when phosphorylated, is largely dephosphorylated in cra but not wild-type strains growing under these conditions. Dephosphorylation of IIAglc in cra strains apparently results from enhanced fructose operon transcription and fructose uptake. These conclusions were supported by showing that fructose-grown cra strains possess 2.5-fold higher fructose-1-phosphate kinase activity than fructose-grown wild-type strains. Moreover, artificially increasing fructose operon expression in cells transporting fructose dramatically decreased the activity of adenylate cyclase. The results establish that Cra indirectly regulates the activity of adenylate cyclase by controlling the expression of the fructose operon in cells growing with fructose as the sole carbon source.
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Affiliation(s)
| | - Maxwell C Park
- University of California at San Diego, Department of Biology, La Jolla, CA 92093-0116, USA
| | - William K Studley
- University of California at San Diego, Department of Biology, La Jolla, CA 92093-0116, USA
| | - Milton H Saier
- University of California at San Diego, Department of Biology, La Jolla, CA 92093-0116, USA
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Affiliation(s)
- M Crasnier
- University of California San Diego, Department of Biology, La Jolla 92093-0116, USA
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17
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Dumay V, Danchin A, Crasnier M. Regulation of Escherichia coli adenylate cyclase activity during hexose phosphate transport. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 3):575-583. [PMID: 8868432 DOI: 10.1099/13500872-142-3-575] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In Escherichia coli, cAMP levels vary with the carbon source used in the culture medium. These levels are dependent on the cellular concentration of phosphorylated EnzymeIIAglc, a component of the glucose-phosphotransferase system, which activates adenylate cyclase (AC). When cells are grown on glucose 6-phosphate (Glc6P), the cAMP level is particularly low. In this study, we investigated the mechanism leading to the low cAMP level when Glc6P is used as the carbon source, i.e. the mechanism preventing the activation of AC by phosphorylated EnzymeIIAglc. Glc6P is transported via the Uhp system which is inducible by extracellular Glc6P. The Uhp system comprises a permease UhpT and three proteins UhpA, UhpB and UhpC which are necessary for uhpT gene transcription. Controlled expression of UhpT in the absence of the regulatory proteins (UhpA, UhpB and UhpC) allowed us to demonstrate that (i) the Uhp regulatory proteins do not prevent the activation of AC by direct interaction with EnzymeIIAglc and (ii) an increase in the amount of UhpT synthesized (corresponding to an increase in the amount of Glc6P transported) correlates with a decrease in the cAMP level. We present data indicating that Glc6P per se or its degradation is unlikely to be responsible for the low cAMP level. It is concluded that the level of cAMP in the cell is determined by the flux of Glc6P through UhpT.
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Affiliation(s)
- Valérie Dumay
- Unité de Régulation de l'Expression Génétique (Centre National de la Recherche Scientifique Unité Associée 1129), Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Antoine Danchin
- Unité de Régulation de l'Expression Génétique (Centre National de la Recherche Scientifique Unité Associée 1129), Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
| | - Martine Crasnier
- Unité de Régulation de l'Expression Génétique (Centre National de la Recherche Scientifique Unité Associée 1129), Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris cedex 15, France
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Trotot P, Sismeiro O, Vivarès C, Glaser P, Bresson-Roy A, Danchin A. Comparative analysis of the cya locus in enterobacteria and related gram-negative facultative anaerobes. Biochimie 1996; 78:277-87. [PMID: 8874804 DOI: 10.1016/0300-9084(96)82192-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Comparison of the cya loci (cya codes for adenylyl cyclase (AC)) from a variety of phylogenetically divergent facultative anaerobic Gram-negative bacteria reveals conserved sequence features. The entire locus structure in enterobacteria is preserved, including two major promoters (a conserved cya strong promoter, P2, and a divergent promoter for a heme biosynthetic operon, hemCD) present in the upstream region of the cya gene. The region between hemC and cya is much longer in Proteus mirabilis than in other enterobacteria, and lacks the P1 upstream cya promoter. In Aeromonas hydrophila the cya promoter (the strong P2 promoter in E coli) is preserved, including a putative GATC methylation site situated immediately downstream from the -10 box. Each cya frame analyzed uses TTG as the translation start codon and is preceded by an unusual ribosome binding site. This suggests that a lower translation efficiency of the cya transcript could be the result of some selection pressure. This has been substantiated by in vitro mutagenesis and by selection of up mutations which all map at the cya ribosome binding site. In enterobacteria the cyaY frame is the only conserved reading frame downstream of cya, with the orientation opposite to that of cya. This organization is not preserved in Aeromonas. Experiments involving fusions with the lacZ gene demonstrated that cyaY is expressed. Finally, comparison of the different polypeptide sequences of ACs permits discussion of important features of the catalytic and regulatory centers of the protein.
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Affiliation(s)
- P Trotot
- Institut Pasteur, Département de Biochimie et Génétique Moléculaire, Paris, France
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Archdeacon J, Talty J, Boesten B, Danchin A, O'Gara F. Cloning of the second adenylate cyclase gene (cya2) from Rhizobium meliloti F34: sequence similarity to eukaryotic cyclases. FEMS Microbiol Lett 1995; 128:177-84. [PMID: 7750735 DOI: 10.1111/j.1574-6968.1995.tb07519.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A second adenylate cyclase (cya2) gene was isolated from a Rhizobium meliloti F34 gene bank. Complemented E. coli delta cya mutants were capable of utilizing a number of, but not all, carbon sources known to be regulated by cAMP. DNA hybridization studies showed cya2 to be unique to R. meliloti strains. The cya2 nucleotide sequence was determined and found to encode a protein of 363 amino acids. Residues were identified within the C-terminal domain which are conserved in both eukaryotic adenylate and guanylate cyclases, including a putative ATP binding site. Similar residues were also found in the prokaryotic R. meliloti Cya1 protein. A R. meliloti cya1/cya2 double mutant was constructed and characterized; however, cAMP production was still observed in this strain indicating the presence of a third cya gene.
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Affiliation(s)
- J Archdeacon
- Microbiology Department, University College Cork, Ireland
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Ryu S, Ramseier TM, Michotey V, Saier MH, Garges S. Effect of the FruR regulator on transcription of the pts operon in Escherichia coli. J Biol Chem 1995; 270:2489-96. [PMID: 7852310 DOI: 10.1074/jbc.270.6.2489] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The promoters of the pts operon of Escherichia coli are controlled by the cyclic AMP receptor protein (CRP) complexed with cAMP (CRP.cAMP). In addition, glucose stimulates pts operon expression in vivo. The pts promoter region has a fructose repressor (FruR)-binding site (the FruR box) that partially overlaps with one of the CRP.cAMP-binding sites. The effects of the pleiotropic transcriptional regulator FruR on pts operon expression were studied to determine whether the in vivo glucose effect on pts operon expression is mediated by FruR. In vitro, FruR can repress P1b transcription, which is activated by CRP.cAMP, and restore P1a transcription, which is repressed by CRP.cAMP. FruR can displace CRP.cAMP from its binding site in the presence of RNA polymerase even though FruR and CRP.cAMP can bind simultaneously to their partially overlapping binding sites in the absence of RNA polymerase. FruR had very little effect on the transcription of the P0 promoter, which is most important for regulation by glucose. Consistent with the in vitro results, pts P0 transcription did not increase as much in cells grown in the presence of fructose or in fruR- mutant cells as in cells grown in the presence of glucose. These results suggest that FruR alone does not mediate the in vivo glucose effect on pts operon expression.
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Affiliation(s)
- S Ryu
- Laboratory of Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892-4255
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Bârzu O, Danchin A. Adenylyl cyclases: a heterogeneous class of ATP-utilizing enzymes. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1994; 49:241-83. [PMID: 7863008 DOI: 10.1016/s0079-6603(08)60052-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- O Bârzu
- Institut Pasteur, Paris, France
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