1
|
Regulation of arginine biosynthesis, catabolism and transport in Escherichia coli. Amino Acids 2019; 51:1103-1127. [DOI: 10.1007/s00726-019-02757-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
|
2
|
Charlier D, Nguyen Le Minh P, Roovers M. Regulation of carbamoylphosphate synthesis in Escherichia coli: an amazing metabolite at the crossroad of arginine and pyrimidine biosynthesis. Amino Acids 2018; 50:1647-1661. [PMID: 30238253 PMCID: PMC6245113 DOI: 10.1007/s00726-018-2654-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/11/2018] [Indexed: 12/17/2022]
Abstract
In all organisms, carbamoylphosphate (CP) is a precursor common to the synthesis of arginine and pyrimidines. In Escherichia coli and most other Gram-negative bacteria, CP is produced by a single enzyme, carbamoylphosphate synthase (CPSase), encoded by the carAB operon. This particular situation poses a question of basic physiological interest: what are the metabolic controls coordinating the synthesis and distribution of this high-energy substance in view of the needs of both pathways? The study of the mechanisms has revealed unexpected moonlighting gene regulatory activities of enzymes and functional links between mechanisms as diverse as gene regulation and site-specific DNA recombination. At the level of enzyme production, various regulatory mechanisms were found to cooperate in a particularly intricate transcriptional control of a pair of tandem promoters. Transcription initiation is modulated by an interplay of several allosteric DNA-binding transcription factors using effector molecules from three different pathways (arginine, pyrimidines, purines), nucleoid-associated factors (NAPs), trigger enzymes (enzymes with a second unlinked gene regulatory function), DNA remodeling (bending and wrapping), UTP-dependent reiterative transcription initiation, and stringent control by the alarmone ppGpp. At the enzyme level, CPSase activity is tightly controlled by allosteric effectors originating from different pathways: an inhibitor (UMP) and two activators (ornithine and IMP) that antagonize the inhibitory effect of UMP. Furthermore, it is worth noticing that all reaction intermediates in the production of CP are extremely reactive and unstable, and protected by tunneling through a 96 Å long internal channel.
Collapse
Affiliation(s)
- Daniel Charlier
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Phu Nguyen Le Minh
- Research Group of Microbiology, Department of Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Martine Roovers
- LABIRIS Institut de Recherches, Av. Emile Gryson 1, 1070, Brussels, Belgium
| |
Collapse
|
3
|
Landeta C, Meehan BM, McPartland L, Ingendahl L, Hatahet F, Tran NQ, Boyd D, Beckwith J. Inhibition of virulence-promoting disulfide bond formation enzyme DsbB is blocked by mutating residues in two distinct regions. J Biol Chem 2017; 292:6529-6541. [PMID: 28232484 DOI: 10.1074/jbc.m116.770891] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/09/2017] [Indexed: 01/30/2023] Open
Abstract
Disulfide bonds contribute to protein stability, activity, and folding in a variety of proteins, including many involved in bacterial virulence such as toxins, adhesins, flagella, and pili, among others. Therefore, inhibitors of disulfide bond formation enzymes could have profound effects on pathogen virulence. In the Escherichia coli disulfide bond formation pathway, the periplasmic protein DsbA introduces disulfide bonds into substrates, and then the cytoplasmic membrane protein DsbB reoxidizes DsbA's cysteines regenerating its activity. Thus, DsbB generates a protein disulfide bond de novo by transferring electrons to the quinone pool. We previously identified an effective pyridazinone-related inhibitor of DsbB enzymes from several Gram-negative bacteria. To map the protein residues that are important for the interaction with this inhibitor, we randomly mutagenized by error-prone PCR the E. coli dsbB gene and selected dsbB mutants that confer resistance to this drug using two approaches. We characterized in vivo and in vitro some of these mutants that map to two areas in the structure of DsbB, one located between the two first transmembrane segments where the quinone ring binds and the other located in the second periplasmic loop of DsbB, which interacts with DsbA. In addition, we show that a mutant version of a protein involved in lipopolysaccharide assembly, lptD4213, is synthetically lethal with the deletion of dsbB as well as with DsbB inhibitors. This finding suggests that drugs decreasing LptD assembly may be synthetically lethal with inhibitors of the Dsb pathway, potentiating the antibiotic effects.
Collapse
Affiliation(s)
- Cristina Landeta
- From the Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Brian M Meehan
- From the Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Laura McPartland
- From the Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Linda Ingendahl
- From the Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Feras Hatahet
- From the Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Ngoc Q Tran
- From the Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Dana Boyd
- From the Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Jon Beckwith
- From the Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02115
| |
Collapse
|
4
|
Abstract
Early investigations on arginine biosynthesis brought to light basic features of metabolic regulation. The most significant advances of the last 10 to 15 years concern the arginine repressor, its structure and mode of action in both E. coli and Salmonella typhimurium, the sequence analysis of all arg structural genes in E. coli and Salmonella typhimurium, the resulting evolutionary inferences, and the dual regulation of the carAB operon. This review provides an overall picture of the pathways, their interconnections, the regulatory circuits involved, and the resulting interferences between arginine and polyamine biosynthesis. Carbamoylphosphate is a precursor common to arginine and the pyrimidines. In both Escherichia coli and Salmonella enterica serovar Typhimurium, it is produced by a single synthetase, carbamoylphosphate synthetase (CPSase), with glutamine as the physiological amino group donor. This situation contrasts with the existence of separate enzymes specific for arginine and pyrimidine biosynthesis in Bacillus subtilis and fungi. Polyamine biosynthesis has been particularly well studied in E. coli, and the cognate genes have been identified in the Salmonella genome as well, including those involved in transport functions. The review summarizes what is known about the enzymes involved in the arginine pathway of E. coli and S. enterica serovar Typhimurium; homologous genes were identified in both organisms, except argF (encoding a supplementary OTCase), which is lacking in Salmonella. Several examples of putative enzyme recruitment (homologous enzymes performing analogous functions) are also presented.
Collapse
|
5
|
Proteome response of an extraintestinal pathogenic Escherichia coli strain with zoonotic potential to human and chicken sera. J Proteomics 2012; 75:4853-62. [PMID: 22677113 DOI: 10.1016/j.jprot.2012.05.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 05/20/2012] [Accepted: 05/29/2012] [Indexed: 12/29/2022]
Abstract
A subset of extraintestinal pathogenic Escherichia coli is zoonotic and has developed strategies to adapt to different host-specific environments. However, the underlying mechanisms of these adaptive strategies have yet to be discerned. Here, the proteomic response of an avian pathogenic E. coli strain, which appears indistinguishable from neonatal meningitis E. coli, was compared following growth in human and avian sera to determine whether it uses the same mechanisms to overcome the antibacterial effects of sera from different host species. Proteins involved in biosynthesis of iron receptors were up-regulated under both sera, suggesting that serum, regardless of the host of origin, is an iron-limited environment. However, several proteins involved in synthesis of nucleic acids, sulfur-containing amino acids and fatty acids, were differentially expressed in response to the sera from different hosts. Mutational analysis showed that this APEC strain required nucleotide biosynthesis during incubation in human, but not avian serum, and deletion of genes involved in the biosynthesis of sulfur-containing amino acids increased its resistance to human serum. Continued investigation of the proteome of 'zoonotic' ExPEC strains, grown under other 'dual' host conditions, will contribute to our understanding of ExPEC pathogenesis and host specificity and development of effective therapies and control strategies.
Collapse
|
6
|
Mollá-Morales A, Sarmiento-Mañús R, Robles P, Quesada V, Pérez-Pérez JM, González-Bayón R, Hannah MA, Willmitzer L, Ponce MR, Micol JL. Analysis of ven3 and ven6 reticulate mutants reveals the importance of arginine biosynthesis in Arabidopsis leaf development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:335-45. [PMID: 21265888 DOI: 10.1111/j.1365-313x.2010.04425.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Arabidopsis thaliana reticulate mutants exhibit differential pigmentation of the veinal and interveinal leaf regions, a visible phenotype that often indicates impaired mesophyll development. We performed a metabolomic analysis of one ven6 (venosa6) and three ven3 reticulate mutants that revealed altered levels of arginine precursors, namely increased ornithine and reduced citrulline levels. In addition, the mutants were more sensitive than the wild-type to exogenous ornithine, and leaf reticulation and mesophyll defects of these mutants were completely rescued by exogenous citrulline. Taken together, these results indicate that ven3 and ven6 mutants experience a blockage of the conversion of ornithine into citrulline in the arginine pathway. Consistent with the participation of VEN3 and VEN6 in the same pathway, the morphological phenotype of ven3 ven6 double mutants was synergistic. Map-based cloning showed that the VEN3 and VEN6 genes encode subunits of Arabidopsis carbamoyl phosphate synthetase (CPS), which is assumed to be required for the conversion of ornithine into citrulline in arginine biosynthesis. Heterologous expression of the Arabidopsis VEN3 and VEN6 genes in a CPS-deficient Escherichia coli strain fully restored bacterial growth in minimal medium, demonstrating the enzymatic activity of the VEN3 and VEN6 proteins, and indicating a conserved role for CPS in these distinct and distant species. Detailed study of the reticulate leaf phenotype in the ven3 and ven6 mutants revealed that mesophyll development is highly sensitive to impaired arginine biosynthesis.
Collapse
Affiliation(s)
- Almudena Mollá-Morales
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, E-03202 Elche, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Mormann S, Lömker A, Rückert C, Gaigalat L, Tauch A, Pühler A, Kalinowski J. Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway. BMC Genomics 2006; 7:205. [PMID: 16901339 PMCID: PMC1590026 DOI: 10.1186/1471-2164-7-205] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Accepted: 08/10/2006] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Corynebacterium glutamicum, a Gram-positive bacterium of the class Actinobacteria, is an industrially relevant producer of amino acids. Several methods for the targeted genetic manipulation of this organism and rational strain improvement have been developed. An efficient transposon mutagenesis system for the completely sequenced type strain ATCC 13032 would significantly advance functional genome analysis in this bacterium. RESULTS A comprehensive transposon mutant library comprising 10,080 independent clones was constructed by electrotransformation of the restriction-deficient derivative of strain ATCC 13032, C. glutamicum RES167, with an IS6100-containing non-replicative plasmid. Transposon mutants had stable cointegrates between the transposon vector and the chromosome. Altogether 172 transposon integration sites have been determined by sequencing of the chromosomal inserts, revealing that each integration occurred at a different locus. Statistical target site analyses revealed an apparent absence of a target site preference. From the library, auxotrophic mutants were obtained with a frequency of 2.9%. By auxanography analyses nearly two thirds of the auxotrophs were further characterized, including mutants with single, double and alternative nutritional requirements. In most cases the nutritional requirement observed could be correlated to the annotation of the mutated gene involved in the biosynthesis of an amino acid, a nucleotide or a vitamin. One notable exception was a clone mutagenized by transposition into the gene cg0910, which exhibited an auxotrophy for histidine. The protein sequence deduced from cg0910 showed high sequence similarities to inositol-1(or 4)-monophosphatases (EC 3.1.3.25). Subsequent genetic deletion of cg0910 delivered the same histidine-auxotrophic phenotype. Genetic complementation of the mutants as well as supplementation by histidinol suggests that cg0910 encodes the hitherto unknown essential L-histidinol-phosphate phosphatase (EC 3.1.3.15) in C. glutamicum. The cg0910 gene, renamed hisN, and its encoded enzyme have putative orthologs in almost all Actinobacteria, including mycobacteria and streptomycetes. CONCLUSION The absence of regional and sequence preferences of IS6100-transposition demonstrate that the established system is suitable for efficient genome-scale random mutagenesis in the sequenced type strain C.glutamicum ATCC 13032. The identification of the hisN gene encoding histidinol-phosphate phosphatase in C. glutamicum closed the last gap in histidine synthesis in the Actinobacteria. The system might be a valuable genetic tool also in other bacteria due to the broad host-spectrum of IS6100.
Collapse
Affiliation(s)
- Sascha Mormann
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Alexander Lömker
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Christian Rückert
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Lars Gaigalat
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Andreas Tauch
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Universität Bielefeld, D-33594 Bielefeld, Germany
| | - Jörn Kalinowski
- Institut für Genomforschung, Universität Bielefeld, D-33594 Bielefeld, Germany
| |
Collapse
|
8
|
Ruiz N, Falcone B, Kahne D, Silhavy TJ. Chemical conditionality: a genetic strategy to probe organelle assembly. Cell 2005; 121:307-17. [PMID: 15851036 DOI: 10.1016/j.cell.2005.02.014] [Citation(s) in RCA: 240] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2004] [Revised: 02/03/2005] [Accepted: 02/10/2005] [Indexed: 11/16/2022]
Abstract
The assembly of the Escherichia coli outer membrane (OM) is poorly understood. Although insight into fundamental cellular processes is often obtained from studying mutants, OM-defective mutants have not been very informative because they generally have nonspecific permeability defects. Here we show that toxic small molecules can be used in selections employing strains with permeability defects to create particular chemical conditions that demand specific suppressor mutations. Suppressor phenotypes are correlated with the physical properties of the small molecules, but the mutations are not in their target genes. Instead, mutations allow survival by partially restoring membrane impermeability. Using "chemical conditionality," we identified mutations in yfgL, and, here and in the accompanying paper by Wu et al. published in this issue of Cell (Wu et al., 2005), we show that YfgL is part of a multiprotein complex involved in the assembly of OM beta barrel proteins. We posit that panels of toxic small molecules will be useful for generating chemical conditionalities that enable identification of genes required for organelle assembly in other organisms.
Collapse
Affiliation(s)
- Natividad Ruiz
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | | | | | | |
Collapse
|
9
|
Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
Collapse
Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
| |
Collapse
|
10
|
Abstract
A 22-kb segment of chromosomal DNA from Enterococcus faecalis OG1RF containing the pyrimidine biosynthesis genes pyrC and pyrD was previously detected as complementing Escherichia coli pyrC and pyrD mutations. In the present study, it was found that the E. faecalis pyrimidine biosynthetic genes in this clone (designated pKV48) are part of a larger cluster resembling that seen in Bacillus spp. Transposon insertions were isolated at a number of sites throughout the cluster and resulted in loss of the ability to complement E. coli auxotrophs. The DNA sequences of the entire pyrD gene of E. faecalis and selected parts of the rest of the cluster were determined, and computer analyses found these to be similar to genes from Bacillus subtilis and Bacillus caldolyticus pyrimidine biosynthesis operons. Five of the transposon insertions were introduced back into the E. faecalis chromosome, and all except insertions in pyrD resulted in pyrimidine auxotrophy. The prototrophy of pyrD knockouts was observed for two different insertions and suggests that E. faecalis is similar to Lactococcus lactis, which has been shown to possess two pyrD genes. A similar analysis was performed with the purL gene from E. faecalis, contained in another cosmid clone, and purine auxotrophs were isolated. In addition, a pool of random transposon insertions in pKV48, isolated in E. coli, was introduced into the E. faecalis chromosome en masse, and an auxotroph was obtained. These results demonstrate a new methodology for constructing defined knockout mutations in E. faecalis.
Collapse
Affiliation(s)
- X Li
- Department of Microbiology and Molecular Genetics, University of Texas Medical School, Houston 77030, USA
| | | | | |
Collapse
|
11
|
Reiser J, Glumoff V, Ochsner UA, Fiechter A. Molecular analysis of the Trichosporon cutaneum DSM 70698 argA gene and its use for DNA-mediated transformations. J Bacteriol 1994; 176:3021-32. [PMID: 8188603 PMCID: PMC205460 DOI: 10.1128/jb.176.10.3021-3032.1994] [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: 01/29/2023] Open
Abstract
Genomic clones capable of complementing a previously isolated arginine auxotrophic mutant strain of the filamentous yeast Trichosporon cutaneum DSM 70698 have been identified by DNA-mediated transformation, and a complementing 4,082-bp subfragment was sequenced. This analysis revealed an intact gene (arg4) showing a high degree of homology with the Saccharomyces cerevisiae CPA2 gene encoding the large subunit of carbamoyl-phosphate synthetase (CPS-A). The inferred amino acid sequence of the T. cutaneum argA-encoded protein contains 1,168 residues showing 62% identity with the sequence of the S. cerevisiae CPA2 protein, and the comparison of the two sequences uncovered a putative intron sequence of 81 nucleotides close to the 5' end of the coding region of the T. cutaneum argA gene. The presence of this intron was confirmed by nuclease protection studies and by direct DNA sequence analysis of a cDNA fragment which had been obtained by PCR amplification. The T. cutaneum intron shares the general characteristics of introns found in yeasts and filamentous fungi. A major transcript of around 4 kb was found in Northern (RNA) blots. The T. cutaneum argA coding region was expressed in Escherichia coli under the control of the regulatable tac promoter. A roughly 130-kDa protein which was found to cross-react with an anti-rat CPS antibody in Western blots (immunoblots) was observed. Two putative ATP-binding domains were identified, one in the amino-terminal half of the argA-encoded protein and the other in the carboxy-terminal half. These domains are highly conserved among the known CPS-A sequences from S. cerevisiae, E. coli, and the rat. From these results we conclude that the T. cutaneum argA gene encodes the large subunit of CPS. This is the first gene to be identified and analyzed in the T. cutaneum DSM 70698 strain.
Collapse
Affiliation(s)
- J Reiser
- Institut für Biotechnologie, ETH-Hönggerberg, Zürich, Switzerland
| | | | | | | |
Collapse
|
12
|
Sampson BA, Misra R, Benson SA. Identification and characterization of a new gene of Escherichia coli K-12 involved in outer membrane permeability. Genetics 1989; 122:491-501. [PMID: 2547691 PMCID: PMC1203724 DOI: 10.1093/genetics/122.3.491] [Citation(s) in RCA: 192] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Using a genetic selection for mutations which allow large maltodextrins to cross the outer membrane of Escherichia coli in the absence of the LamB maltoporin, we have obtained and characterized two mutations that define a new locus of E. coli. We have designated this locus imp for increased membrane permeability. Mapping studies show that the imp gene resides at approximately 1.2 min on the E. coli chromosome. The mutations alter the permeability of the outer membrane resulting in increased sensitivity to detergents, antibiotics and dyes. The mutations are nonreverting and codominant. Genetic analysis of the mutations suggest that the imp gene is an essential gene. We describe a general cloning strategy that can be used to clone both dominant and recessive alleles. Using this technique, we have cloned the wild-type and mutant imp alleles onto a low copy number plasmid.
Collapse
Affiliation(s)
- B A Sampson
- Department of Biology, Princeton University, New Jersey 08544-1014
| | | | | |
Collapse
|
13
|
Picard FJ, Dillon JR. Cloning and organization of seven arginine biosynthesis genes from Neisseria gonorrhoeae. J Bacteriol 1989; 171:1644-51. [PMID: 2493452 PMCID: PMC209793 DOI: 10.1128/jb.171.3.1644-1651.1989] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A genomic library for Neisseria gonorrhoeae, constructed in the lambda cloning vector EMBL4, was screened for clones carrying arginine biosynthesis genes by complementation of Escherichia coli mutants. Clones complementing defects in argA, argB, argE, argG, argIF, carA, and carB were isolated. An E. coli defective in the acetylornithine deacetylase gene (argE) was complemented by the ornithine acetyltransferase gene (argJ) from N. gonorrhoeae. This heterologous complementation is reported for the first time. The carAB operon from E. coli hybridized with the gonococcal clones that carried carA or carB genes under conditions of high stringency, detecting 80% or greater similarity and showing that the nucleotide sequence of the carbamoylphosphate synthetase genes is very similar in these two organisms. Under these conditions for hybridization, the gonococcal clones carrying argB or argF genes did not hybridize with plasmids containing the corresponding E. coli gene. Cocomplementation experiments established gene linkage between carA and carB. Clones complementing a gene defect in argE were also able to complement an argA mutation. This suggests that the enzyme ornithine acetyltransferase from N. gonorrhoeae (encoded by argJ) may be able to complement both argA and argE mutations in E. coli. The arginine biosynthesis genes in N. gonorrhoeae appear to be scattered as in members of the family Pseudomonadaceae.
Collapse
Affiliation(s)
- F J Picard
- Department of Biology, University of Ottawa, Ontario, Canada
| | | |
Collapse
|
14
|
In vivo synthesis of carbamyl phosphate from NH3 by the large subunit of Escherichia coli carbamyl phosphate synthetase. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61359-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
15
|
Rubino SD, Nyunoya H, Lusty CJ. Catalytic domains of carbamyl phosphate synthetase. Glutamine-hydrolyzing site of Escherichia coli carbamyl phosphate synthetase. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(18)67386-7] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
16
|
Blum P, Blaha L, Artz S. Reversion and immobilization of phage Mud1 cts (Apr lac) insertion mutations in Salmonella typhimurium. MOLECULAR & GENERAL GENETICS : MGG 1986; 202:327-30. [PMID: 3010054 DOI: 10.1007/bf00331659] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Phage Mud1 cts (Apr lac), or Mud1, insertion mutations may be accompanied by adjacent deletion formation which can complicate use of lac fusions generated with this phage for gene regulatory studies. As for phage Mu insertion mutations, phage Mud1 insertions fail to revert at significant frequency (whether or not accompanied by an adjacent deletion). We describe isolation of revertible (X mutant) derivatives of phage Mud1 in Salmonella typhimurium. The X mutant derivatives allow use of reversion as a simple test to determine whether a Mud1 insertion has occurred precisely without an adjacent deletion that may have fused the lac genes to a promoter outside of the gene of interest. In addition, a simple method for stabilizing Mud1 generated lac fusions against subsequent transposition is described.
Collapse
|
17
|
Weyens G, Rose K, Falmagne P, Glansdorff N, Piérard A. Synthesis of Escherichia coli carbamoylphosphate synthetase initiates at a UUG codon. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 150:111-5. [PMID: 3894020 DOI: 10.1111/j.1432-1033.1985.tb08995.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The ribosome binding region of the messenger RNA for the Escherichia coli carA gene contains two adjacent putative translational start codons, UUG and AUU, both of them unusual. By Edman degradation and mass spectrometry of purified carA protein, we show that only UUG is used in vivo. Translation initiation at UUG in carA appears about half as efficient as at AUG in lacZ.
Collapse
|
18
|
Piette J, Nyunoya H, Lusty CJ, Cunin R, Weyens G, Crabeel M, Charlier D, Glansdorff N, Piérard A. DNA sequence of the carA gene and the control region of carAB: tandem promoters, respectively controlled by arginine and the pyrimidines, regulate the synthesis of carbamoyl-phosphate synthetase in Escherichia coli K-12. Proc Natl Acad Sci U S A 1984; 81:4134-8. [PMID: 6330744 PMCID: PMC345383 DOI: 10.1073/pnas.81.13.4134] [Citation(s) in RCA: 127] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The carAB operon of Escherichia coli K-12, which encodes the two subunits of carbamoyl-phosphate synthetase (glutamine hydrolyzing) [carbon-dioxide: L-glutamine amido-ligase (ADP-forming, carbamate-phosphorylating); EC 6.3.5.5], is cumulatively repressed by arginine and the pyrimidines. We describe the structure of the control region of carAB and the sequence of the carA gene. Nuclease S1 mapping experiments show that two adjacent tandem promoters within the carAB control region serve as initiation sites. The upstream promoter P1 is controlled by pyrimidines; the downstream promoter P2 is regulated by arginine. Attenuation control does not appear to be involved in the expression of carAB. A possible mechanism by which control at these promoters concurs to produce a cumulative pattern of repression is discussed. The translational start of carA is atypical; it consists of a UUG or AUU codon.
Collapse
|
19
|
Bouvier J, Patte JC, Stragier P. Multiple regulatory signals in the control region of the Escherichia coli carAB operon. Proc Natl Acad Sci U S A 1984; 81:4139-43. [PMID: 6377309 PMCID: PMC345384 DOI: 10.1073/pnas.81.13.4139] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The first reaction in pyrimidine and arginine biosynthesis in Escherichia coli is catalyzed by a single enzyme, carbamoyl-phosphate synthetase (EC 6.3.5.5), the product of the carAB operon. Expression of this operon is cumulatively repressed by arginine and pyrimidines. The nucleotide sequence of the carAB control region was determined and transcriptional starts were localized. Two adjacent promoters, 70 base pairs apart, appear to be used in vivo, the downstream one overlapping a typical arginine operator. The absence of any attenuation-like sequence excludes such a mechanism for pyrimidine-mediated repression. Various fragments of the carA promoter-proximal region were fused in vitro with the lacZ gene. Results obtained with these fusions indicate that (i) translation of the carA gene can be initiated in vivo without an AUG codon but very likely with an UUG or an AUU codon; (ii) the carAB downstream promoter is repressed by arginine; and (iii) the carAB upstream promoter is repressed by pyrimidines and subject to stringent control. When carried by a multicopy plasmid the carAB control region escapes repression by arginine and pyrimidines. The existence of a pyrimidine repressor, present in limiting amounts in the cell, is therefore postulated.
Collapse
|
20
|
Jensen KF, Larsen JN, Schack L, Sivertsen A. Studies on the structure and expression of Escherichia coli pyrC, pyrD, and pyrF using the cloned genes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 140:343-52. [PMID: 6370696 DOI: 10.1111/j.1432-1033.1984.tb08107.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The Escherichia coli pyrC, pyrD and pyrF genes were cloned on multicopy plasmids derived from pBR322 and analysed by means of restriction endonucleases. It was found that the pyrC gene is destroyed by cutting with the restriction endonuclease BamHI, that the entire pyrD gene can be isolated on a 1300-base pairs DNA fragment generated by EcoRI cleavage and that cutting with EcoRI removes the promotor and probably also the translational start site from the pyrF gene. More details on the restriction maps are presented. Further, it was found that the presence of a pyr gene in multiple copies on a plasmid does not significantly interfere with the activity of the chromosomal pyr genes. Using the 'minicell' technique, the polypeptides encoded by the three cloned pyr genes were identified. The relative molecular masses for the pyrC-encoded and pyrD-encoded polypeptides are 38 000-40 000 and 36 000-38 000, respectively. Thus in their native form, dihydroorotase and dihydroorotate oxidase appear to be dimeric proteins. The 'minicell' experiments positively identified a protein chain of Mr 23 000-24 000 as being a subunit of OMP decarboxylase encoded by pyrF. Moreover, the coding frame for this polypeptide seems to be expressed as the first gene in the operon with the coding frame for another protein chain of Mr 13 000-14 000. Since, however, the native OMP decarboxylase during sedimentation and gel filtration behaves as a protein of Mr 45 000 +/- 4000, this latter polypeptide (Mr 13 000-14 000) is hardly a component of the enzyme. Pyr-lac+ operon fusions were constructed by the Mu d1 procedure. By integrating an F'lac episome into the lac part of the fusions and determining the direction of chromosomal transfer from the resultant Hfr strains, the direction of pyrC transcription was found to be counter-clockwise, while pyrD and pyrF were found to be transcribed in a clockwise direction.
Collapse
|
21
|
Nyunoya H, Lusty CJ. The carB gene of Escherichia coli: a duplicated gene coding for the large subunit of carbamoyl-phosphate synthetase. Proc Natl Acad Sci U S A 1983; 80:4629-33. [PMID: 6308632 PMCID: PMC384097 DOI: 10.1073/pnas.80.15.4629] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Previous genetic and biochemical studies indicate that the carB gene of Escherichia coli codes for the large subunit of carbamoyl-phosphate synthetase (EC 6.3.5.5). We have determined the nucleotide sequence of a 4-kilobase-pair cloned fragment of E. coli DNA with genetic determinants for carB. The DNA sequence is a 3,219-nucleotide-long reading frame. The polypeptide encoded by this reading frame has been verified to be the large subunit of carbamoyl-phosphate synthetase. The gene product is similar to the large subunit in its molecular weight, amino acid composition and amino-terminal residue, and carboxyl-terminal sequence. The amino acid sequence derived from the nucleotide sequence shows a highly significant homology between the amino- and carboxyl-terminal halves of the protein. We propose that the carB gene was formed by an internal duplication of a smaller ancestral gene.
Collapse
|
22
|
|
23
|
Crabeel M, Charlier D, Weyens G, Feller A, Piérard A, Glansdorff N. Use of gene cloning to determine polarity of an operon: genes carAB of Escherichia coli. J Bacteriol 1980; 143:921-5. [PMID: 6451616 PMCID: PMC294395 DOI: 10.1128/jb.143.2.921-925.1980] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A gene-cloning approach was used to determine the transcription polarity of the carbamoylphosphate operon (carAB) of Escherichia coli. In agreement with the accompanying paper (J. Bacteriol. 143:914-920, 1980), our results lead to the conclusion that carA is the proximal gene of the carAB operon.
Collapse
|