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Choi U, Park SH, Lee HB, Son JE, Lee CR. Coordinated and Distinct Roles of Peptidoglycan Carboxypeptidases DacC and DacA in Cell Growth and Shape Maintenance under Stress Conditions. Microbiol Spectr 2023; 11:e0001423. [PMID: 37098975 PMCID: PMC10269652 DOI: 10.1128/spectrum.00014-23] [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: 01/08/2023] [Accepted: 04/09/2023] [Indexed: 04/27/2023] Open
Abstract
Peptidoglycan (PG) is an essential bacterial architecture pivotal for shape maintenance and adaptation to osmotic stress. Although PG synthesis and modification are tightly regulated under harsh environmental stresses, few related mechanisms have been investigated. In this study, we aimed to investigate the coordinated and distinct roles of the PG dd-carboxypeptidases (DD-CPases) DacC and DacA in cell growth under alkaline and salt stresses and shape maintenance in Escherichia coli. We found that DacC is an alkaline DD-CPase, the enzyme activity and protein stability of which are significantly enhanced under alkaline stress. Both DacC and DacA were required for bacterial growth under alkaline stress, whereas only DacA was required for growth under salt stress. Under normal growth conditions, only DacA was necessary for cell shape maintenance, while under alkaline stress conditions, both DacA and DacC were necessary for cell shape maintenance, but their roles were distinct. Notably, all of these roles of DacC and DacA were independent of ld-transpeptidases, which are necessary for the formation of PG 3-3 cross-links and covalent bonds between PG and the outer membrane lipoprotein Lpp. Instead, DacC and DacA interacted with penicillin-binding proteins (PBPs)-dd-transpeptidases-mostly in a C-terminal domain-dependent manner, and these interactions were necessary for most of their roles. Collectively, our results demonstrate the coordinated and distinct novel roles of DD-CPases in bacterial growth and shape maintenance under stress conditions and provide novel insights into the cellular functions of DD-CPases associated with PBPs. IMPORTANCE Most bacteria have a peptidoglycan architecture for cell shape maintenance and protection against osmotic challenges. Peptidoglycan dd-carboxypeptidases control the amount of pentapeptide substrates, which are used in the formation of 4-3 cross-links by the peptidoglycan synthetic dd-transpeptidases, penicillin-binding proteins (PBPs). Seven dd-carboxypeptidases exist in Escherichia coli, but the physiological significance of their redundancy and their roles in peptidoglycan synthesis are poorly understood. Here, we showed that DacC is an alkaline dd-carboxypeptidase for which both protein stability and enzyme activity are significantly enhanced at high pH. Strikingly, dd-carboxypeptidases DacC and DacA physically interacted with PBPs, and these interactions were necessary for cell shape maintenance as well as growth under alkaline and salt stresses. Thus, cooperation between dd-carboxypeptidases and PBPs may allow E. coli to overcome various stresses and to maintain cell shape.
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Affiliation(s)
- Umji Choi
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Si Hyoung Park
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Han Byeol Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Ji Eun Son
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido, Republic of Korea
- The Natural Science Research Institute, Myongji University, Yongin, Gyeonggido, Republic of Korea
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Divergent Effects of Peptidoglycan Carboxypeptidase DacA on Intrinsic β-Lactam and Vancomycin Resistance. Microbiol Spectr 2022; 10:e0173422. [PMID: 35758683 PMCID: PMC9430164 DOI: 10.1128/spectrum.01734-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Vancomycin and β-lactams are clinically important antibiotics that inhibit the formation of peptidoglycan cross-links, but their binding targets are different. The binding target of vancomycin is d-alanine-d-alanine (d-Ala-d-Ala), whereas that of β-lactam is penicillin-binding proteins (PBPs). In this study, we revealed the divergent effects of peptidoglycan (PG) carboxypeptidase DacA on vancomycin and β-lactam resistance in Escherichia coli and Bacillus subtilis. The deletion of DacA induced sensitivity to most β-lactams, whereas it induced strong resistance toward vancomycin. Notably, both phenotypes did not have a strong association with ld-transpeptidases, which are necessary for the formation of PG 3-3 cross-links and covalent bonds between PG and an Lpp outer membrane (OM) lipoprotein. Vancomycin resistance was induced by an increased amount of decoy d-Ala-d-Ala residues within PG, whereas β-lactam sensitivity was associated with physical interactions between DacA and PBPs. The presence of an OM permeability barrier strongly strengthened vancomycin resistance, but it significantly weakened β-lactam sensitivity. Collectively, our results revealed two distinct functions of DacA, which involved inverse modulation of bacterial resistance to clinically important antibiotics, β-lactams and vancomycin, and presented evidence for a link between DacA and PBPs. IMPORTANCE Bacterial PG hydrolases play important roles in various aspects of bacterial physiology, including cytokinesis, PG synthesis, quality control of PG, PG recycling, and stress adaptation. Of all the PG hydrolases, the role of PG carboxypeptidases is poorly understood, especially regarding their impacts on antibiotic resistance. We have revealed two distinct functions of PG carboxypeptidase DacA with respect to antibiotic resistance. The deletion of DacA led to sensitivity to most β-lactams, while it caused strong resistance to vancomycin. Our study provides novel insights into the roles of PG carboxypeptidases in the regulation of antibiotic resistance and a potential clue for the development of a drug to improve the clinical efficacy of β-lactam antibiotics.
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Reddy PT, O'Dell WB. Fusing an insoluble protein to GroEL apical domain enhances soluble expression in Escherichia coli. Methods Enzymol 2021; 659:171-188. [PMID: 34752284 DOI: 10.1016/bs.mie.2021.09.002] [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: 01/03/2023]
Abstract
A protocol for increasing soluble protein expression by fusing the chaperone GroEL apical domain with a gene of interest is described herein. GroEL apical domain, the minichaperone that functions independently of GroES and ATP in protein folding, is cloned downstream of the lambda CII ribosome binding site in the parent pRE vector. The pRE vector has tightly controlled transcription suitable for expressing toxic proteins. The GroEL minichaperone is fused to a glycine-serine rich linker followed by the enterokinase protease recognition sequence. A number of genes that are recalcitrant to protein production in the parent pRE vector 5were cloned into the pRE:GroEL fusion vector and successfully expressed as fusion proteins in Escherichia coli.
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Affiliation(s)
- Prasad T Reddy
- Biomolecular Measurement Division, National institute of Standards and Technology, Gaithersburg, MD, United States; Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD, United States.
| | - William B O'Dell
- Biomolecular Measurement Division, National institute of Standards and Technology, Gaithersburg, MD, United States; Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, Rockville, MD, United States
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Lee HB, Park SH, Lee CR. The inner membrane protein LapB is required for adaptation to cold stress in an LpxC-independent manner. J Microbiol 2021; 59:666-674. [PMID: 33990910 DOI: 10.1007/s12275-021-1130-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 11/29/2022]
Abstract
The inner membrane protein lipopolysaccharide assembly protein B (LapB) is an adaptor protein that activates the proteolysis of LpxC by an essential inner membrane metalloprotease, FtsH, leading to a decrease in the level of lipopolysaccharide in the membrane. In this study, we revealed the mechanism by which the essential inner membrane protein YejM regulates LapB and analyzed the role of the transmembrane domain of LapB in Escherichia coli. The transmembrane domain of YejM genetically and physically interacted with LapB and inhibited its function, which led to the accumulation of LpxC. The transmembrane domain of LapB was indispensable for both its physical interaction with YejM and its regulation of LpxC proteolysis. Notably, we found that the lapB mutant exhibited strong cold sensitivity and this phenotype was not associated with increased accumulation of LpxC. The transmembrane domain of LapB was also required for its role in adaptation to cold stress. Taken together, these results showed that LapB plays an important role in both the regulation of LpxC level, which is controlled by its interaction with the transmembrane domain of YejM, and adaptation to cold stress, which is independent of LpxC.
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Affiliation(s)
- Han Byeol Lee
- Department of Biological Sciences, Myongji University, Yongin, 17058, Republic of Korea
| | - Si Hyoung Park
- Department of Biological Sciences, Myongji University, Yongin, 17058, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, 17058, Republic of Korea.
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Mycobacterium tuberculosis chorismate mutase: A potential target for TB. Bioorg Med Chem 2017; 25:1725-1736. [PMID: 28202315 DOI: 10.1016/j.bmc.2017.02.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/01/2017] [Indexed: 12/27/2022]
Abstract
Mycobacterium tuberculosis chorismate mutase (MtbCM) catalyzes the rearrangement of chorismate to prephenate in the shikimate biosynthetic pathway to form the essential amino acids, phenylalanine and tyrosine. Two genes encoding chorismate mutase have been identified in Mtb. The secretory form,∗MtbCM (encoded by Rv1885c) is assumed to play a key role in pathogenesis of tuberculosis. Also, the inhibition of MtbCM may hinder the supply of nutrients to the organism. Indeed, the existence of chorismate mutase (CM) in bacteria, fungi and higher plants but not in human and low sequence homology among known CM makes it an interesting target for the discovery of anti-tubercular agents. The present article mainly focuses on the recent developments in the structure, function and inhibition of MtbCM. The understanding of various aspects of MtbCM as presented in the current article may facilitate the design and subsequent chemical synthesis of new inhibitors against ∗MtbCM, that could lead to the discovery and development of novel and potent anti-tubercular agents in future.
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Choi U, Park YH, Kim YR, Seok YJ, Lee CR. Increased expression of genes involved in uptake and degradation of murein tripeptide under nitrogen starvation in Escherichia coli. FEMS Microbiol Lett 2016; 363:fnw136. [PMID: 27231238 DOI: 10.1093/femsle/fnw136] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2016] [Indexed: 11/13/2022] Open
Abstract
Peptidoglycan (also known as murein) is an important envelope component of bacteria, and its turnover usually takes place at considerable levels during normal growth. Amino sugars and murein tripeptide resulting from murein degradation are used for resynthesis of peptidoglycan or as self-generated nutrients or energy sources for cell growth. PgrR (regulator of peptide glycan recycling; formerly YcjZ) was recently identified as a repressor of several genes participating in uptake and degradation of murein tripeptide. In this study, we identified the ycjG gene involved in murein tripeptide degradation as a new direct target of PgrR. The expression of PgrR-regulated genes including ycjY, mppA, mpaA and ycjG was repressed in the presence of a good nitrogen source, but their expression increased under poor nitrogen conditions. Under nitrogen starvation, the pgrR mutant cells exhibited faster growth than wild-type cells, implying that derepression of genes under the control of PgrR may help cells overcome nitrogen limitation. Therefore, these results suggest that nitrogen starvation induces derepression of PgrR-controlled genes involved in uptake and degradation of murein tripeptide, and this may stimulate the utilization of murein tripeptide as a nitrogen source.
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Affiliation(s)
- Umji Choi
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido 449-728, Republic of Korea
| | - Young-Ha Park
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yeon-Ran Kim
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yeong-Jae Seok
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido 449-728, Republic of Korea
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Park YH, Um SH, Song S, Seok YJ, Ha NC. Structural basis for the sequestration of the anti-σ(70) factor Rsd from σ(70) by the histidine-containing phosphocarrier protein HPr. ACTA ACUST UNITED AC 2015; 71:1998-2008. [PMID: 26457424 DOI: 10.1107/s1399004715013759] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/20/2015] [Indexed: 11/10/2022]
Abstract
Histidine-containing phosphocarrier protein (HPr) is a general component of the bacterial phosphoenolpyruvate:sugar phosphotransferase system (PTS) involved in the phosphorylation-coupled transport of numerous sugars called PTS sugars. HPr mainly exists in a dephosphorylated form in the presence of PTS sugars in the medium, while its phosphorylation increases in the absence of PTS sugars. A recent study revealed that the dephosphorylated form of HPr binds and antagonizes the function of the antisigma factor Rsd. This anti-sigma factor sequesters the housekeeping sigma factor σ(70) to facilitate switching of the sigma subunit on RNA polymerase from σ(70) to the stress-responsive sigma factor σ(S) in stationary-phase cells. In this study, the structure of the complex of Rsd and HPr was determined at 2.1 Å resolution and revealed that the binding site for HPr on the surface of Rsd partly overlaps with that for σ(70). The localization of the phosphorylation site on HPr at the binding interface for Rsd explains why phosphorylation of HPr abolishes its binding to Rsd. The mutation of crucial residues involved in the HPr-Rsd interaction significantly influenced the competition between HPr and σ(70) for binding to Rsd both in vitro and in vivo. The results provide a structural basis for the linkage of global gene regulation to nutrient availability in the external environment.
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Affiliation(s)
- Young Ha Park
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Si Hyeon Um
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Saemee Song
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Yeong Jae Seok
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Nam Chul Ha
- Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Research Institute for Agricultural and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
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Kim JA, Park JH, Lee MA, Lee HJ, Park SJ, Kim KS, Choi SH, Lee KH. Stationary-phase induction of vvpS expression by three transcription factors: repression by LeuO and activation by SmcR and CRP. Mol Microbiol 2015; 97:330-46. [PMID: 25869813 DOI: 10.1111/mmi.13028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2015] [Indexed: 11/27/2022]
Abstract
An exoprotease of Vibrio vulnificus, VvpS, exhibits an autolytic function during the stationary phase. To understand how vvpS expression is controlled, the regulators involved in vvpS transcription and their regulatory mechanisms were investigated. LeuO was isolated in a ligand-fishing experiment, and experiments using a leuO-deletion mutant revealed that LeuO represses vvpS transcription. LeuO bound the extended region including LeuO-binding site (LBS)-I and LBS-II. Further screening of additional regulators revealed that SmcR and cyclic adenosine monophosphate-receptor protein (CRP) play activating roles in vvpS transcription. SmcR and CRP bound the regions overlapping LBS-I and -II, respectively. In addition, the LeuO occupancy of LBS-I and LBS-II was competitively exchanged by SmcR and CRP, respectively. To examine the mechanism of stationary-phase induction of vvpS expression, in vivo levels of three transcription factors were monitored. Cellular level of LeuO was maximal at exponential phase, while those of SmcR and CRP were maximal at stationary phase and relatively constant after the early-exponential phase, respectively. Thus, vvpS transcription was not induced during the exponential phase by high cellular content of LeuO. When entering the stationary phase, however, LeuO content was significantly reduced and repression by LeuO was relieved through simultaneous binding of SmcR and CRP to LBS-I and -II, respectively.
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Affiliation(s)
- Jeong-A Kim
- Department of Life Science, Sogang University, Seoul, 121-742, South Korea
| | - Jin Hwan Park
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, South Korea
| | - Mi-Ae Lee
- Department of Life Science, Sogang University, Seoul, 121-742, South Korea
| | - Hyun-Jung Lee
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 120-752, South Korea
| | - Soon-Jung Park
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 120-752, South Korea
| | - Kun-Soo Kim
- Department of Life Science, Sogang University, Seoul, 121-742, South Korea
| | - Sang-Ho Choi
- National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Seoul National University, Seoul, 151-921, South Korea
| | - Kyu-Ho Lee
- Department of Life Science, Sogang University, Seoul, 121-742, South Korea
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Lee J, Park YH, Kim YR, Seok YJ, Lee CR. Dephosphorylated NPr is involved in an envelope stress response of Escherichia coli. MICROBIOLOGY-SGM 2015; 161:1113-1123. [PMID: 25701731 PMCID: PMC4635465 DOI: 10.1099/mic.0.000056] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/10/2015] [Indexed: 01/20/2023]
Abstract
Besides the canonical phosphoenolpyruvate-dependent phosphotransferase system (PTS) for carbohydrate transport, most Proteobacteria possess the so-called nitrogen PTS (PTSNtr) that transfers a phosphate group from phosphoenolpyruvate (PEP) over enzyme INtr (EINtr) and NPr to enzyme IIANtr (EIIANtr). The PTSNtr lacks membrane-bound components and functions exclusively in a regulatory capacity. While EIIANtr has been implicated in a variety of cellular processes such as potassium homeostasis, phosphate starvation, nitrogen metabolism, carbon metabolism, regulation of ABC transporters and poly-β-hydroxybutyrate accumulation in many Proteobacteria, the only identified role of NPr is the regulation of biosynthesis of the lipopolysaccharide (LPS) layer by direct interaction with LpxD in Escherichia coli. In this study, we provide another phenotype related to NPr. Several lines of evidence demonstrate that E. coli strains with increased levels of dephosphorylated NPr are sensitive to envelope stresses, such as osmotic, ethanol and SDS stresses, and these phenotypes are independent of LpxD. The C-terminal region of NPr plays an important role in sensitivity to envelope stresses. Thus, our data suggest that the dephospho-form of NPr affects adaptation to envelope stresses through a C-terminus-dependent mechanism.
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Affiliation(s)
- Jaeseop Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido 449-728, Republic of Korea
| | - Young-Ha Park
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yeon-Ran Kim
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yeong-Jae Seok
- Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151-742, Republic of Korea.,Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
| | - Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido 449-728, Republic of Korea
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Lee CR, Kim M, Park YH, Kim YR, Seok YJ. RppH-dependent pyrophosphohydrolysis of mRNAs is regulated by direct interaction with DapF in Escherichia coli. Nucleic Acids Res 2014; 42:12746-57. [PMID: 25313159 PMCID: PMC4227774 DOI: 10.1093/nar/gku926] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Similar to decapping of eukaryotic mRNAs, the RppH-catalyzed conversion of 5′-terminal triphosphate to monophosphate has recently been identified as the rate-limiting step for the degradation of a subset of mRNAs in Escherichia coli. However, the regulation of RppH pyrophosphohydrolase activity is not well understood. Because the overexpression of RppH alone does not affect the decay rate of most target mRNAs, the existence of a mechanism regulating its activity has been suggested. In this study, we identified DapF, a diaminopimelate (DAP) epimerase catalyzing the stereoinversion of L,L-DAP to meso-DAP, as a regulator of RppH. DapF showed a high affinity interaction with RppH and increased its RNA pyrophosphohydrolase activity. The simultaneous overexpression of both DapF and RppH increased the decay rates of RppH target RNAs by about a factor of two. Together, our data suggest that the cellular level of DapF is a critical factor regulating the RppH-catalyzed pyrophosphate removal and the subsequent degradation of target mRNAs.
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Affiliation(s)
- Chang-Ro Lee
- Department of Biological Sciences, Myongji University, Yongin, Gyeonggido 449-728, Republic of Korea
| | - Miri Kim
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| | - Young-Ha Park
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| | - Yeon-Ran Kim
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
| | - Yeong-Jae Seok
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea Department of Biophysics and Chemical Biology, Seoul National University, Seoul 151-742, Korea
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Lee CR, Park YH, Kim YR, Peterkofsky A, Seok YJ. Phosphorylation-Dependent Mobility Shift of Proteins on SDS-PAGE is Due to Decreased Binding of SDS. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.7.2063] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Lee CR, Park YH, Kim M, Kim YR, Park S, Peterkofsky A, Seok YJ. Reciprocal regulation of the autophosphorylation of enzyme INtr by glutamine and α-ketoglutarate in Escherichia coli. Mol Microbiol 2013; 88:473-85. [PMID: 23517463 DOI: 10.1111/mmi.12196] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2013] [Indexed: 11/28/2022]
Abstract
In addition to the phosphoenolpyruvate:sugar phosphotransferase system (sugar PTS), most proteobacteria possess a paralogous system (nitrogen phosphotransferase system, PTS(Ntr)). The first proteins in both pathways are enzymes (enzyme I(sugar) and enzyme I(Ntr)) that can be autophosphorylated by phosphoenolpyruvate. The most striking difference between enzyme I(sugar) and enzyme I(Ntr) is the presence of a GAF domain at the N-terminus of enzyme I(Ntr). Since the PTS(Ntr) was identified in 1995, it has been implicated in a variety of cellular processes in many proteobacteria and many of these regulations have been shown to be dependent on the phosphorylation state of PTS(Ntr) components. However, there has been little evidence that any component of this so-called PTS(Ntr) is directly involved in nitrogen metabolism. Moreover, a signal regulating the phosphorylation state of the PTS(Ntr) had not been uncovered. Here, we demonstrate that glutamine and α-ketoglutarate, the canonical signals of nitrogen availability, reciprocally regulate the phosphorylation state of the PTS(Ntr) by direct effects on enzyme I(Ntr) autophosphorylation and the GAF signal transduction domain is necessary for the regulation of enzyme I(Ntr) activity by the two signal molecules. Taken together, our results suggest that the PTS(Ntr) senses nitrogen availability.
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Affiliation(s)
- Chang-Ro Lee
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 151-742, Korea
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Adenylyl cyclase inMycobacterium tuberculosis H37Rv-A possible virulence factor. Indian J Clin Biochem 2012; 12:63-5. [PMID: 23100903 DOI: 10.1007/bf02873063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Eukaryotic-like adenylyl cyclase has been identified inMycobacterium tuberculosis H37Rv. TheM. tuberculosis adenylyl cyclase gene (cya) was cloned by complementation of a cAMP dependent expression of maltose operon in acya deletionE. coli strain. The nucleotide sequence analysis of thecya gene revealed an open reading frame that coded for 443 amino acids. A comparison ofM. tuberculosis adenylyl cyclase with the protein sequences in the data bank revealed its homology to the eukaryotic Type I and the calmodulin responsive adenylyl cyclases with an average of about 40% identical and 60% similar amino acids in the catalytic domain. The occurrence of eukaryotic-like adenylyl cyclase inM. tuberculosis suggests a role for this important enzyme in cell signaling and perhaps in the pathogenesis ofM. tuberculosis. We suggest that the human pathogenM. tuberculosis might have acquired the eukaryoticcya by a recombination event.
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Stable isotope-labeling of DNA repair proteins, and their purification and characterization. Protein Expr Purif 2011; 78:94-101. [DOI: 10.1016/j.pep.2011.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/18/2011] [Accepted: 02/23/2011] [Indexed: 02/06/2023]
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Ropers D, Baldazzi V, de Jong H. Model reduction using piecewise-linear approximations preserves dynamic properties of the carbon starvation response in Escherichia coli. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2011; 8:166-181. [PMID: 21071805 DOI: 10.1109/tcbb.2009.49] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The adaptation of the bacterium Escherichia coli to carbon starvation is controlled by a large network of biochemical reactions involving genes, mRNAs, proteins, and signalling molecules. The dynamics of these networks is difficult to analyze, notably due to a lack of quantitative information on parameter values. To overcome these limitations, model reduction approaches based on quasi-steady-state (QSS) and piecewise-linear (PL) approximations have been proposed, resulting in models that are easier to handle mathematically and computationally. These approximations are not supposed to affect the capability of the model to account for essential dynamical properties of the system, but the validity of this assumption has not been systematically tested. In this paper, we carry out such a study by evaluating a large and complex PL model of the carbon starvation response in E. coli using an ensemble approach. The results show that, in comparison with conventional nonlinear models, the PL approximations generally preserve the dynamics of the carbon starvation response network, although with some deviations concerning notably the quantitative precision of the model predictions. This encourages the application of PL models to the qualitative analysis of bacterial regulatory networks, in situations where the reference time scale is that of protein synthesis and degradation.
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Kim YJ, Ryu Y, Koo BM, Lee NY, Chun SJ, Park SJ, Lee KH, Seok YJ. A mammalian insulysin homolog is regulated by enzyme IIA(Glc) of the glucose transport system in Vibrio vulnificus. FEBS Lett 2010; 584:4537-44. [PMID: 20971110 DOI: 10.1016/j.febslet.2010.10.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 10/11/2010] [Accepted: 10/12/2010] [Indexed: 11/19/2022]
Abstract
Vibrio vulnificus is an opportunistic human pathogen that causes severe infections in susceptible individuals. While the components of the Escherichia coli phosphoenolpyruvate: sugar phosphotransferase system (PTS) have been shown to regulate numerous targets, little such information is available for the V. vulnificus PTS. Here we show that enzyme IIA(Glc) of the PTS regulates the peptidase activity of a mammalian insulysin homolog in V. vulnificus. While interaction of IIA(Glc) with the insulysin homolog is independent of the phosphorylation state of IIA(Glc), only unphosphorylated IIA(Glc) activates the insulysin homolog. Taken together, our results suggest that the V. vulnificus insulysin-IIA(Glc) complex plays a role in survival in the host by sensing glucose.
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Affiliation(s)
- You-Jin Kim
- Department of Biophysics and Chemical Biology and Institute of Microbiology, Seoul National University, Seoul 151-742, Republic of Korea
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18
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Lee CR, Cho SH, Kim HJ, Kim M, Peterkofsky A, Seok YJ. Potassium mediates Escherichia coli enzyme IIANtr-dependent regulation of sigma factor selectivity. Mol Microbiol 2010; 78:1468-83. [DOI: 10.1111/j.1365-2958.2010.07419.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Kim SK, Sims CL, Wozniak SE, Drude SH, Whitson D, Shaw RW. Antibiotic resistance in bacteria: novel metalloenzyme inhibitors. Chem Biol Drug Des 2009; 74:343-8. [PMID: 19751419 DOI: 10.1111/j.1747-0285.2009.00879.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Beta-lactam antibiotics are among the most important drugs used to fight bacterial infection. Overuse and misuse of beta-lactam antibiotics has caused the evolution of resistance mechanisms, allowing pathogenic bacteria to survive antibiotic treatment. The major source of resistance to beta-lactam antibiotics occurs through production of enzymes called beta-lactamases capable of catalyzing hydrolysis of the beta-lactam rings in these drug compounds. The metallo-beta-lactamases have become a major threat due to their broad substrate specificities; there are no clinically useful inhibitors for these metalloenzymes. We have obtained single-stranded DNA's that are potent inhibitors of the Bacillus cereus 5/B/6 metallo-beta-lactamase. These are rapid, reversible, non-competitive inhibitors of the metalloenzyme, with K(i) and K(i)' values in the nanomolar range. The inhibition patterns and metal ion dependence of their inhibition suggest that the oligonucleotides alter the coordination of the active site metal ion(s); inhibition is efficient and highly specific. Microbiological growth experiments, using combinations of ssDNA with the beta-lactam antibiotic cephalexin, reveal that the inhibitor is capable of causing cell death in liquid cultures of both Gram-positive and Gram-negative metallo-beta-lactamase producing bacteria in the micromolar concentration range.
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Affiliation(s)
- Sung-Kun Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
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20
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Kawe M, Horn U, Plückthun A. Facile promoter deletion in Escherichia coli in response to leaky expression of very robust and benign proteins from common expression vectors. Microb Cell Fact 2009; 8:8. [PMID: 19171063 PMCID: PMC2655282 DOI: 10.1186/1475-2859-8-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2008] [Accepted: 01/26/2009] [Indexed: 11/17/2022] Open
Abstract
Background Overexpression of proteins in Escherichia coli is considered routine today, at least when the protein is soluble and not otherwise toxic for the host. We report here that the massive overproduction of even such "benign" proteins can cause surprisingly efficient promoter deletions in the expression plasmid, leading to the growth of only non-producers, when expression is not well repressed in the newly transformed bacterial cell. Because deletion is so facile, it might impact on high-throughput protein production, e.g. for structural genomics, where not every expression parameter will be monitored. Results We studied the high-level expression of several robust non-toxic proteins using a T5 promoter under lac operator control. Full induction leads to no significant growth retardation. We compared expression from almost identical plasmids with or without the lacI gene together in strains expressing different levels of LacI. Any combination without net overexpression of LacI led to an efficient promoter deletion in the plasmid, although the number of growing colonies and even the plasmid size – all antibiotic-resistant non-producers – was almost normal, and thus the problem not immediately recognizable. However, by assuring sufficient repression during the initial establishment phase of the plasmid, deletion was completely prevented. Conclusion The deletions in the insufficiently repressed system are caused entirely by the burden of high-level translation. Since the E. coli Dps protein, known to protect DNA against stress in the stationary phase, is accumulated in the deletion mutants, the mutation may have taken place during a transient stationary phase. The cause of the deletion is thus distinct from the well known interference of high-level transcription with plasmid replication. The deletion can be entirely prevented by overexpressing LacI, a useful precaution even without any signs of stress caused by the protein.
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Affiliation(s)
- Martin Kawe
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
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21
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Pina K, Navarro C, Mcwalter L, Boxer DH, Price NC, Kelly SM, Mandrand-Berthelot MA, Wu LF. Purification and Characterization of the Periplasmic Nickel-Binding Protein NikA of Escherichia coli K12. ACTA ACUST UNITED AC 2008. [DOI: 10.1111/j.1432-1033.1995.0857p.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Solution structure of NPr, a bacterial signal-transducing protein that controls the phosphorylation state of the potassium transporter-regulating protein IIANtr. Amino Acids 2008; 35:531-9. [DOI: 10.1007/s00726-008-0079-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Accepted: 03/05/2008] [Indexed: 10/22/2022]
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23
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Kim SK, Reddy SK, Nelson BC, Vasquez GB, Davis A, Howard AJ, Patterson S, Gilliland GL, Ladner JE, Reddy PT. Biochemical and structural characterization of the secreted chorismate mutase (Rv1885c) from Mycobacterium tuberculosis H37Rv: an *AroQ enzyme not regulated by the aromatic amino acids. J Bacteriol 2007; 188:8638-48. [PMID: 17146044 PMCID: PMC1698256 DOI: 10.1128/jb.00441-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene Rv1885c from the genome of Mycobacterium tuberculosis H37Rv encodes a monofunctional and secreted chorismate mutase (*MtCM) with a 33-amino-acid cleavable signal sequence; hence, it belongs to the *AroQ class of chorismate mutases. Consistent with the heterologously expressed *MtCM having periplasmic destination in Escherichia coli and the absence of a discrete periplasmic compartment in M. tuberculosis, we show here that *MtCM secretes into the culture filtrate of M. tuberculosis. *MtCM functions as a homodimer and exhibits a dimeric state of the protein at a concentration as low as 5 nM. *MtCM exhibits simple Michaelis-Menten kinetics with a Km of 0.5 +/- 0.05 mM and a k(cat) of 60 s(-1) per active site (at 37 degrees C and pH 7.5). The crystal structure of *MtCM has been determined at 1.7 A resolution (Protein Data Bank identifier 2F6L). The protein has an all alpha-helical structure, and the active site is formed within a single chain without any contribution from the second chain in the dimer. Analysis of the structure shows a novel fold topology for the protein with a topologically rearranged helix containing Arg134. We provide evidence by site-directed mutagenesis that the residues Arg49, Lys60, Arg72, Thr105, Glu109, and Arg134 constitute the catalytic site; the numbering of the residues includes the signal sequence. Our investigation on the effect of phenylalanine, tyrosine, and tryptophan on *MtCM shows that *MtCM is not regulated by the aromatic amino acids. Consistent with this observation, the X-ray structure of *MtCM does not have an allosteric regulatory site.
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Affiliation(s)
- Sook-Kyung Kim
- Biochemical Science Division, National Institute of Standards and Technology, Mail stop 831.2, Bldg. 227, Room B244, Gaithersburg, MD 20899, USA
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24
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Kaur J, Rajamohan G, Dikshit KL. Cloning and characterization of promoter-active DNA sequences from Streptococcus equisimilis. Curr Microbiol 2006; 54:48-53. [PMID: 17171467 DOI: 10.1007/s00284-006-0249-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2006] [Accepted: 09/20/2006] [Indexed: 11/28/2022]
Abstract
Genomic fragments of Streptococcus equisimilis exhibiting potent promoter activity in Escherichia coli were isolated by transcriptional fusion to chloramphenicol acetyl transferase (CAT) structural gene. Random S. equanimities DNA, cloned in E. coli, exhibited a higher frequency of strong promoter activity than did similarly cloned E. coli fragments. The determination of the relative promoter strength of randomly selected clones with CAT assay demonstrated the dominance of sequences acting as a strong promoter in E. coli. Removal of downstream terminator from the strong promoter containing plasmid resulted in a twofold to threefold increase in CAT expression in some cases. Structural characteristics of promoter sequences of some representative streptococcal genes clearly indicate that the streptococcal promoter regions are rich in secondary structures and might be one of the factors of their instability in E. coli.
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Affiliation(s)
- Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India.
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25
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Park YH, Lee BR, Seok YJ, Peterkofsky A. In vitro reconstitution of catabolite repression in Escherichia coli. J Biol Chem 2006; 281:6448-54. [PMID: 16407219 DOI: 10.1074/jbc.m512672200] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A widely accepted model for catabolite repression posits that phospho-IIAGlc of the bacterial phosphotransferase system activates adenylyl cyclase (AC) activity. For many years, attempts to observe such regulatory properties of AC in vitro have been unsuccessful. To further study the regulation, AC was produced fused to the transmembrane segments of the serine chemoreceptor Tsr. Cells harboring Tsr-AC and normal AC, expressed from the cya promoter on a low copy number vector, exhibit similar behavior with respect to elevation of cAMP levels resulting from deletion of crp, expressing the catabolite regulatory protein. Membrane-bound Tsr-AC exhibits activity comparable with the native form of AC. Tsr-AC binds IIAGlc specifically, regardless of its phosphorylation state, but not the two general phosphotransferase system proteins, enzyme I and HPr; IIAGlc binding is localized to the C-terminal region of AC. Binding to membranes of either dephospho- or phospho-IIAGlc has no effect on AC activity. However, in the presence of an Escherichia coli extract, P-IIAGlc, but not IIAGlc, stimulates AC activity. Based on these findings of a direct interaction of IIAGlc with AC, but activity regulation only in the presence of E. coli extract, a revised model for AC activity regulation is proposed.
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Affiliation(s)
- Young-Ha Park
- Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
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26
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Nam TW, Park YH, Jeong HJ, Ryu S, Seok YJ. Glucose repression of the Escherichia coli sdhCDAB operon, revisited: regulation by the CRP*cAMP complex. Nucleic Acids Res 2005; 33:6712-22. [PMID: 16314304 PMCID: PMC1297706 DOI: 10.1093/nar/gki978] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Expression of the Escherichia coli sdhCDAB operon encoding the succinate dehydrogenase complex is regulated in response to growth conditions, such as anaerobiosis and carbon sources. An anaerobic repression of sdhCDAB is known to be mediated by the ArcB/A two-component system and the global Fnr anaerobic regulator. While the cAMP receptor protein (CRP) and Cra (formerly FruR) are known as key mediators of catabolite repression, they have been excluded from the glucose repression of the sdhCDAB operon. Although the glucose repression of sdhCDAB was reported to involve a mechanism dependent on the ptsG expression, the molecular mechanism underlying the glucose repression has never been clarified. In this study, we re-examined the mechanism of the sdhCDAB repression by glucose and found that CRP directly regulates expression of the sdhCDAB operon and that the glucose repression of this operon occurs in a cAMP-dependent manner. The levels of phosphorylated enzyme IIA(Glc) and intracellular cAMP on various carbon sources were proportional to the expression levels of sdhC-lacZ. Disruption of crp or cya completely abolished the glucose repression of sdhC-lacZ expression. Together with data showing correlation between the intracellular cAMP concentrations and the sdhC-lacZ expression levels in several mutants and wild type, in vitro transcription assays suggest that the decrease in the CRP.cAMP level in the presence of glucose is the major determinant of the glucose repression of the sdhCDAB operon.
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Affiliation(s)
| | | | | | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, School of Agricultural Biotechnology and Center for Agricultural Biomaterials, Seoul National UniversitySeoul 151-742, Korea
| | - Yeong-Jae Seok
- To whom correspondence should be addressed. Tel: +82 2 880 8827; Fax: +82 2 888 4911;
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27
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Lee CR, Koo BM, Cho SH, Kim YJ, Yoon MJ, Peterkofsky A, Seok YJ. Requirement of the dephospho-form of enzyme IIANtr for derepression of Escherichia coli K-12 ilvBN expression. Mol Microbiol 2005; 58:334-44. [PMID: 16164569 DOI: 10.1111/j.1365-2958.2005.04834.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While the proteins of the phosphoenolpyruvate:carbohydrate phosphotransferase system (carbohydrate PTS) have been shown to regulate numerous targets, little such information is available for the nitrogen-metabolic phosphotransferase system (nitrogen-metabolic PTS). To elucidate the physiological role of the nitrogen-metabolic PTS, we carried out phenotype microarray (PM) analysis with Escherichia coli K-12 strain MG1655 deleted for the ptsP gene encoding the first enzyme of the nitrogen-metabolic PTS. Together with the PM data, growth studies revealed that a ptsN (encoding enzyme IIA(Ntr)) mutant became extremely sensitive to leucine-containing peptides (LCPs), while both ptsP (encoding enzyme I(Ntr)) and ptsO (encoding NPr) mutants were more resistant than wild type. The toxicity of LCPs was found to be due to leucine and the dephospho-form of enzyme IIA(Ntr) was found to be necessary to neutralize leucine toxicity. Further studies showed that the dephospho-form of enzyme IIA(Ntr) is required for derepression of the ilvBN operon encoding acetohydroxy acid synthase I catalysing the first step common to the biosynthesis of the branched-chain amino acids.
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Affiliation(s)
- Chang-Ro Lee
- Laboratory of Macromolecular Interactions, Department of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
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28
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Wang G, Peterkofsky A, Keifer PA, Li X. NMR characterization of the Escherichia coli nitrogen regulatory protein IIANtr in solution and interaction with its partner protein, NPr. Protein Sci 2005; 14:1082-90. [PMID: 15741344 PMCID: PMC2253429 DOI: 10.1110/ps.041232805] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The solution form of IIA(Ntr) from Escherichia coli and its interaction with its partner protein, NPr, were characterized by nuclear magnetic resonance (NMR) spectroscopy. The diffusion coefficient of the protein (1.13 x 10(-6) cm/sec) falls between that of HPr (approximately 9 kDa) and the N-terminal domain of E. coli enzyme I (approximately 30 kDa), indicating that the functional form of IIA(Ntr) is a monomer (approximately 18 kDa) in solution. Thus, the dimeric structure of the protein found in the crystal is an artifact of crystal packing. The residual dipolar coupling data of IIA(Ntr) (covering residues 11-155) measured in the absence and presence of a 4% polyethyleneglycol-hexanol liquid crystal alignment medium fit well to the coordinates of both molecule A and molecule B of the dimeric crystal structure, indicating that the 3D structures in solution and in the crystal are indeed similar for that protein region. However, only molecule A possesses an N-terminal helix identical to that derived from chemical shifts of IIA(Ntr) in solution. Further, the (15)N heteronuclear nuclear Overhauser effect (NOE) data also support molecule A as the representative structure in solution, with the terminal residues 1-8 and 158-163 more mobile. Chemical shift mapping identified the surface on IIA(Ntr) for NPr binding. Residues Gly61, Asp115, Ser125, Thr156, and nearby regions of IIA(Ntr) are more perturbed and participate in interaction with NPr. The active-site His73 of IIA(Ntr) for phosphoryl transfer was found in the Ndelta1-H tautomeric state. This work lays the foundation for future structure and function studies of the signal transducing proteins from this nitrogen pathway.
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Affiliation(s)
- Guangshun Wang
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.
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29
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Reddy P, Jaruga P, O'Connor T, Rodriguez H, Dizdaroglu M. Overexpression and rapid purification of Escherichia coli formamidopyrimidine-DNA glycosylase. Protein Expr Purif 2004; 34:126-33. [PMID: 14766308 DOI: 10.1016/j.pep.2003.11.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2003] [Revised: 11/25/2003] [Indexed: 11/27/2022]
Abstract
Formamidopyrimidine DNA glycosylase (Fpg) is a DNA glycosylase with an associated AP lyase activity. As a DNA repair enzyme, Fpg excises several modified bases from DNA associated with exposure to oxidizing agents such as free radicals. Experiments in many laboratories have been limited by the availability of the enzyme, and its production required at least a week of work to complete its purification. We have devised a new method that decreases the time and expense of purification of Fpg that should render this protein accessible to any laboratory. Fpg was subcloned into a gamma P(L) promoter-containing vector (pRE) and overproduced in the appropriate Escherichia coli host cells to about 25% of the total cellular protein. Fpg was purified to homogeneity in a simple two-step procedure with a 50% saving in time when compared to the previously known procedure. Comparative studies showed that the excision of 8-hydroxyguanine, 2,6-diamino-4-hydroxy-5-formamidopyrimidine, and 4,6-diamino-5-formamidopyrimidine, and to a lesser extent, 8-hydroxyadenine was virtually identical for the Fpg purified using this method and for the Fpg purified by the original method. Therefore, this method should prove useful for a large number of laboratories and further research on oxidative DNA damage.
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Affiliation(s)
- Prasad Reddy
- Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
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30
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Jeong JY, Kim YJ, Cho N, Shin D, Nam TW, Ryu S, Seok YJ. Expression of ptsG encoding the major glucose transporter is regulated by ArcA in Escherichia coli. J Biol Chem 2004; 279:38513-8. [PMID: 15252051 DOI: 10.1074/jbc.m406667200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Because the phosphoenolpyruvate:sugar phosphotransferase system plays multiple regulatory roles in addition to the phosphorylation-coupled transport of many sugars in bacteria, synthesis of its protein components is regulated in a highly sophisticated way. Thus far, the cAMP receptor protein (CRP) complex and Mlc are known to be the major regulators of ptsHIcrr and ptsG expression in response to the availability of carbon sources. In this report, we performed ligand fishing experiments by using the promoters of ptsHIcrr and ptsG as bait to find out new factors involved in the transcriptional regulation of the phosphoenolpyruvate:sugar phosphotransferase system in Escherichia coli, and we found that the anaerobic regulator ArcA specifically binds to the promoters. Deletion of the arcA gene caused about a 2-fold increase in the ptsG expression, and overexpression of ArcA significantly decreased glucose consumption. In vitro transcription assays showed that phospho-ArcA (ArcA-P) represses ptsG P1 transcription. DNase I footprinting experiments revealed that ArcA-P binds to three sites upstream of the ptsG P1 promoter, two of which overlap the CRP-binding sites, and the ArcA-P binding decreases the CRP binding that is essential for the ptsG P1 transcription. These results suggest that the response regulator ArcA regulates expression of enzyme IICB(Glc) mediating the first step of glucose metabolism in response to the redox conditions of growth in E. coli.
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Affiliation(s)
- Jin-Young Jeong
- Laboratory of Macromolecular Interactions, School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
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31
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Koo BM, Yoon MJ, Lee CR, Nam TW, Choe YJ, Jaffe H, Peterkofsky A, Seok YJ. A novel fermentation/respiration switch protein regulated by enzyme IIAGlc in Escherichia coli. J Biol Chem 2004; 279:31613-21. [PMID: 15169777 DOI: 10.1074/jbc.m405048200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial phosphoenolpyruvate:sugar phosphotransferase system regulates a variety of physiological processes as well as effecting sugar transport. The crr gene product (enzyme IIA(Glc) (IIA(Glc))) mediates some of these regulatory phenomena. In this report, we characterize a novel IIA(Glc)-binding protein from Escherichia coli extracts, discovered using ligand-fishing with surface plasmon resonance spectroscopy. This protein, which we named FrsA (fermentation/respiration switch protein), is the 47-kDa product of the yafA gene, previously denoted as "function unknown." FrsA forms a 1:1 complex specifically with the unphosphorylated form of IIA(Glc), with the highest affinity of any protein thus far shown to interact with IIA(Glc). Orthologs of FrsA have been found to exist only in facultative anaerobes belonging to the gamma-proteobacterial group. Disruption of frsA increased cellular respiration on several sugars including glucose, while increased FrsA expression resulted in an increased fermentation rate on these sugars with the concomitant accumulation of mixed-acid fermentation products. These results suggest that IIA(Glc) regulates the flux between respiration and fermentation pathways by sensing the available sugar species via a phosphorylation state-dependent interaction with FrsA.
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Affiliation(s)
- Byoung-Mo Koo
- Laboratory of Macromolecular Interactions, School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742, Korea
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32
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Teplyakov A, Obmolova G, Bir N, Reddy P, Howard AJ, Gilliland GL. Crystal structure of the YajQ protein from Haemophilus influenzae reveals a tandem of RNP-like domains. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2004; 4:1-9. [PMID: 12943362 DOI: 10.1023/a:1024620416876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A hypothetical protein encoded by the gene YajQ of Haemophilus influenzae was selected, as part of a structural genomics project, for X-ray crystallographic structure determination and analysis to assist with the functional assignment. The protein is present in most bacteria, but not in archaea or eukaryotes. The amino acid sequence has no homology to that of other proteins. The YajQ protein was cloned, expressed, and the crystal structure determined at 2.1-A resolution by applying the multiwavelength anomalous dispersion method to a mercury derivative. The polypeptide chain is folded into two domains with identical folding topology. Each domain has a four-stranded antiparallel beta-sheet flanked on one side by two alpha-helices. This structural motif is a characteristic feature of many RNA-binding proteins. The tetrameric structure observed in the crystal suggests a possibility of binding two stretches of double-stranded nucleic acid.
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Affiliation(s)
- Alexey Teplyakov
- Center for Advanced Research in Biotechnology of the University of Maryland Biotechnology Institute and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
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33
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Reddy PT, Prasad CR, Reddy PH, Reeder D, McKenney K, Jaffe H, Dimitrova MN, Ginsburg A, Peterkofsky A, Murthy PS. Cloning and expression of the gene for a novel protein from Mycobacterium smegmatis with functional similarity to eukaryotic calmodulin. J Bacteriol 2003; 185:5263-8. [PMID: 12923099 PMCID: PMC180971 DOI: 10.1128/jb.185.17.5263-5268.2003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A calmodulin-like protein (CAMLP) from Mycobacterium smegmatis was purified to homogeneity and partially sequenced; these data were used to produce a full-length clone, whose DNA sequence contained a 55-amino-acid open reading frame. M. smegmatis CAMLP, expressed in Escherichia coli, exhibited properties characteristic of eukaryotic calmodulin: calcium-dependent stimulation of eukaryotic phosphodiesterase, which was inhibited by the calmodulin antagonist trifluoperazine, and reaction with anti-bovine brain calmodulin antibodies. Consistent with the presence of nine acidic amino acids (16%) in M. smegmatis CAMLP, there is one putative calcium-binding domain in this CAMLP, compared to four such domains for eukaryotic calmodulin, reflecting the smaller molecular size (approximately 6 kDa) of M. smegmatis CAMLP. Ultracentrifugation and mass spectral studies excluded the possibility that calcium promotes oligomerization of purified M. smegmatis CAMLP.
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Affiliation(s)
- Prasad T Reddy
- Bioprocess Engineering Group, Biotechnology Division, Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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34
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Lehmann C, Lim K, Chalamasetty VR, Krajewski W, Melamud E, Galkin A, Howard A, Kelman Z, Reddy PT, Murzin AG, Herzberg O. The HI0073/HI0074 protein pair from Haemophilus influenzae is a member of a new nucleotidyltransferase family: structure, sequence analyses, and solution studies. Proteins 2003; 50:249-60. [PMID: 12486719 DOI: 10.1002/prot.10260] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The crystal structure of HI0074 from Haemophilus influenzae, a protein of unknown function, has been determined at a resolution of 2.4 A. The molecules form an up-down, four-helix bundle, and associate into homodimers. The fold is most closely related to the substrate-binding domain of KNTase, yet the amino acid sequences of the two proteins exhibit no significant homology. Sequence analyses of completely and incompletely sequenced genomes reveal that the two adjacent genes, HI0074 and HI0073, and their close relatives comprise a new family of nucleotidyltransferases, with 15 members at the time of writing. The analyses also indicate that this is one of eight families of a large nucleotidyltransferase superfamily, whose members were identified based on the proximity of the nucleotide- and substrate-binding domains on the respective genomes. Both HI0073 and HI0074 were annotated "hypothetical" in the original genome sequencing publication. HI0073 was cloned, expressed, and purified, and was shown to form a complex with HI0074 by polyacrylamide gel electrophoresis under nondenaturing conditions, analytic size exclusion chromatography, and dynamic light scattering. Double- and single-stranded DNA binding assays showed no evidence of DNA binding to HI0074 or to HI0073/HI0074 complex despite the suggestive shape of the putative binding cleft formed by the HI0074 dimer.
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Affiliation(s)
- Christopher Lehmann
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
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35
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Willis MA, Krajewski W, Chalamasetty VR, Reddy P, Howard A, Herzberg O. Structure of HI1333 (YhbY), a putative RNA-binding protein from Haemophilus influenzae. Proteins 2002; 49:423-6. [PMID: 12360533 DOI: 10.1002/prot.10225] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mark A Willis
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
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36
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Cornilescu G, Lee BR, Cornilescu CC, Wang G, Peterkofsky A, Clore GM. Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system. J Biol Chem 2002; 277:42289-98. [PMID: 12202490 DOI: 10.1074/jbc.m207314200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The solution structure of the complex between the cytoplasmic A domain (IIA(Mtl)) of the mannitol transporter II(Mannitol) and the histidine-containing phosphocarrier protein (HPr) of the Escherichia coli phosphotransferase system has been solved by NMR, including the use of conjoined rigid body/torsion angle dynamics, and residual dipolar couplings, coupled with cross-validation, to permit accurate orientation of the two proteins. A convex surface on HPr, formed by helices 1 and 2, interacts with a complementary concave depression on the surface of IIA(Mtl) formed by helix 3, portions of helices 2 and 4, and beta-strands 2 and 3. The majority of intermolecular contacts are hydrophobic, with a small number of electrostatic interactions at the periphery of the interface. The active site histidines, His-15 of HPr and His-65 of IIA(Mtl), are in close spatial proximity, and a pentacoordinate phosphoryl transition state can be readily accommodated with no change in protein-protein orientation and only minimal perturbations of the backbone immediately adjacent to the histidines. Comparison with two previously solved structures of complexes of HPr with partner proteins of the phosphotransferase system, the N-terminal domain of enzyme I (EIN) and enzyme IIA(Glucose) (IIA(Glc)), reveals a number of common features despite the fact that EIN, IIA(Glc), and IIA(Mtl) bear no structural resemblance to one another. Thus, entirely different underlying structural elements can form binding surfaces for HPr that are similar in terms of both shape and residue composition. These structural comparisons illustrate the roles of surface and residue complementarity, redundancy, incremental build-up of specificity and conformational side chain plasticity in the formation of transient specific protein-protein complexes in signal transduction pathways.
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Affiliation(s)
- Gabriel Cornilescu
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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37
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Reddy SK, Kamireddi M, Dhanireddy K, Young L, Davis A, Reddy PT. Eukaryotic-like adenylyl cyclases in Mycobacterium tuberculosis H37Rv: cloning and characterization. J Biol Chem 2001; 276:35141-9. [PMID: 11431477 DOI: 10.1074/jbc.m104108200] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Screening the Mycobacterium tuberculosis H37Rv genomic library for complementation of catabolic defect for cAMP-dependent expression of maltose operon produced the adenylyl cyclase gene (Mtb cya, (1997)) annotated later as Rv1625c (Cole, S. T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., III, et al. (1998) Nature 393, 537-544). The deduced amino acid (aa) sequence (443 aa) encoded by Mtb cya contains a single hydrophobic domain of six transmembrane helices (152 aa) in the amino-terminal half of the protein. Flanking this domain are an arginine-rich (17%) amino-terminal cytoplasmic tail (46 aa) and a carboxyl-terminal cytoplasmic domain (245 aa) with extensive homology to the catalytic core of eukaryotic adenylyl cyclases. Site-directed mutagenesis of Arg(43) and Arg(44) to alanine/glycine showed a loss of adenylyl cyclase activity, whereas mutagenesis to lysine restored the activity. Hence it is proposed that the formation of the catalytic site in Mtb adenylyl cyclase requires an interaction between Arg(43) and Arg(44) residues in the distal cytoplasmic tail and the carboxyl-terminal cytoplasmic domain. Mtb adenylyl cyclase activity at the physiological concentration of ATP (1 mm) was 475 nmol of cAMP/min/mg of membrane protein in the presence of Mn(2+) but only 10 nmol of cAMP/min/mg of membrane protein in the presence of Mg(2+). The physiological significance of the activation of Mtb adenylyl cyclase by Mn(2+) is discussed in view of the presence of manganese transporter protein in mycobacteria and macrophages wherein mycobacteria reside.
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Affiliation(s)
- S K Reddy
- DNA Technologies Group, Biotechnology Division, Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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38
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Nam TW, Cho SH, Shin D, Kim JH, Jeong JY, Lee JH, Roe JH, Peterkofsky A, Kang SO, Ryu S, Seok YJ. The Escherichia coli glucose transporter enzyme IICB(Glc) recruits the global repressor Mlc. EMBO J 2001; 20:491-8. [PMID: 11157755 PMCID: PMC133465 DOI: 10.1093/emboj/20.3.491] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In addition to effecting the catalysis of sugar uptake, the bacterial phosphoenolpyruvate:sugar phosphotransferase system regulates a variety of physiological processes. Exposure of cells to glucose can result in repression or induction of gene expression. While the mechanism for carbon catabolite repression by glucose was well documented, that for glucose induction was not clearly understood in Escherichia coli. Recently, glucose induction of several E.coli genes has been shown to be mediated by the global repressor Mlc. Here, we elucidate a general mechanism for glucose induction of gene expression in E.coli, revealing a novel type of regulatory circuit for gene expression mediated by the phosphorylation state-dependent interaction of a membrane-bound protein with a repressor. The dephospho-form of enzyme IICB(Glc), but not its phospho-form, interacts directly with Mlc and induces transcription of Mlc-regulated genes by displacing Mlc from its target sequences. Therefore, the glucose induction of Mlc-regulated genes is caused by dephosphorylation of the membrane-bound transporter enzyme IICB(Glc), which directly recruits Mlc to derepress its regulon.
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Affiliation(s)
| | | | - Dongwoo Shin
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742,
School of Agricultural Biotechnology, Seoul National University, Suwon 441-744, Korea and Laboratory of Biochemical Genetics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA Corresponding author e-mail: T.-W.Nam, S.-H.Cho and D.Shin contributed equally to this work
| | | | | | | | | | - Alan Peterkofsky
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742,
School of Agricultural Biotechnology, Seoul National University, Suwon 441-744, Korea and Laboratory of Biochemical Genetics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA Corresponding author e-mail: T.-W.Nam, S.-H.Cho and D.Shin contributed equally to this work
| | | | - Sangryeol Ryu
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742,
School of Agricultural Biotechnology, Seoul National University, Suwon 441-744, Korea and Laboratory of Biochemical Genetics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA Corresponding author e-mail: T.-W.Nam, S.-H.Cho and D.Shin contributed equally to this work
| | - Yeong-Jae Seok
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 151-742,
School of Agricultural Biotechnology, Seoul National University, Suwon 441-744, Korea and Laboratory of Biochemical Genetics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA Corresponding author e-mail: T.-W.Nam, S.-H.Cho and D.Shin contributed equally to this work
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39
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Drum CL, Yan SZ, Sarac R, Mabuchi Y, Beckingham K, Bohm A, Grabarek Z, Tang WJ. An extended conformation of calmodulin induces interactions between the structural domains of adenylyl cyclase from Bacillus anthracis to promote catalysis. J Biol Chem 2000; 275:36334-40. [PMID: 10926933 DOI: 10.1074/jbc.m004778200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The edema factor exotoxin produced by Bacillus anthracis is an adenylyl cyclase that is activated by calmodulin (CaM) at resting state calcium concentrations in infected cells. A C-terminal 60-kDa fragment corresponding to the catalytic domain of edema factor (EF3) was cloned, overexpressed in Escherichia coli, and purified. The N-terminal 43-kDa domain (EF3-N) of EF3, the sole domain of edema factor homologous to adenylyl cyclases from Bordetella pertussis and Pseudomonas aeruginosa, is highly resistant to protease digestion. The C-terminal 160-amino acid domain (EF3-C) of EF3 is sensitive to proteolysis in the absence of CaM. The addition of CaM protects EF3-C from being digested by proteases. EF3-N and EF3-C were expressed separately, and both fragments were required to reconstitute full CaM-sensitive enzyme activity. Fluorescence resonance energy transfer experiments using a double-labeled CaM molecule were performed and indicated that CaM adopts an extended conformation upon binding to EF3. This contrasts sharply with the compact conformation adopted by CaM upon binding myosin light chain kinase and CaM-dependent protein kinase type II. Mutations in each of the four calcium binding sites of CaM were examined for their effect on EF3 activation. Sites 3 and 4 were found critical for the activation, and neither the N- nor the C-terminal domain of CaM alone was capable of activating EF3. A genetic screen probing loss-of-function mutations of EF3 and site-directed mutations based on the homology of the edema factor family revealed a conserved pair of aspartate residues and an arginine that are important for catalysis. Similar residues are essential for di-metal-mediated catalysis in mammalian adenylyl cyclases and a family of DNA polymerases and nucleotidyltransferases. This suggests that edema factor may utilize a similar catalytic mechanism.
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Affiliation(s)
- C L Drum
- Department of Neurobiology, Pharmacology, and Physiology, University of Chicago, Chicago, Illinois 60637, USA
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40
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Hoskins JR, Kim SY, Wickner S. Substrate recognition by the ClpA chaperone component of ClpAP protease. J Biol Chem 2000; 275:35361-7. [PMID: 10952988 DOI: 10.1074/jbc.m006288200] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ClpA, a member of the Clp/Hsp100 ATPase family, is a molecular chaperone and regulatory component of ClpAP protease. We explored the mechanism of protein recognition by ClpA using a high affinity substrate, RepA, which is activated for DNA binding by ClpA and degraded by ClpAP. By characterizing RepA derivatives with N- or C-terminal deletions, we found that the N-terminal portion of RepA is required for recognition. More precisely, RepA derivatives lacking the N-terminal 5 or 10 amino acids are degraded by ClpAP at a rate similar to full-length RepA, whereas RepA derivatives lacking 15 or 20 amino acids are degraded much more slowly. Thus, ClpA recognizes an N-terminal signal in RepA beginning in the vicinity of amino acids 10-15. Moreover, peptides corresponding to RepA amino acids 4-13 and 1-15 inhibit interactions between ClpA and RepA. We constructed fusions of RepA and green fluorescent protein, a protein not recognized by ClpA, and found that the N-terminal 15 amino acids of RepA are sufficient to target the fusion protein for degradation by ClpAP. However, fusion proteins containing 46 or 70 N-terminal amino acids of RepA are degraded more efficiently in vitro and are noticeably stabilized in vivo in clpADelta and clpPDelta strains compared with wild type.
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Affiliation(s)
- J R Hoskins
- Laboratory of Molecular Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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41
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Rao CN, Reddy P, Reeder DJ, Liu Y, Stack SM, Kisiel W, Woodley DT. Prokaryotic expression, purification, and reconstitution of biological activities (Antiprotease, antitumor, and heparin-binding) for tissue factor pathway inhibitor-2. Biochem Biophys Res Commun 2000; 276:1286-94. [PMID: 11027624 DOI: 10.1006/bbrc.2000.3611] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report the expression of tissue factor pathway inhibitor-2 (TFPI-2) (also known as PP-5, placental protein-5; MSPI, matrix-associated serine protease inhibitor) in E. coli as a 25-kDa nonglycosylated protein with a glycine substituted for aspartic acid at the amino terminus. High-level expression of TFPI-2 was obtained with pRE1 expression vector under the transcriptional and translational controls of the lambdaP(L) promoter and lambdacII ribosome-binding site, respectively, with ATG initiation codon. TFPI-2 was produced as inclusion bodies and accounted for 25-30% of the total E. coli proteins. The inclusion bodies containing TFPI-2 were solubilized with urea, sulfitolyzed, purified, and refolded through a disulfide interchange reaction. The refolded E. coli TFPI-2 inhibited plasmin with an inhibition constant (K(i)) of 5 nM that is similar with the TFPI-2 expressed in a mammalian system. The refolded E. coli TFPI-2 bound heparin and also inhibited plasmin, regardless of whether the enzyme was in the fluid phase or was bound to the membranes of HT-1080 fibrosarcoma cells. In addition, refolded E. coli TFPI-2 inhibited radiolabeled matrix degradation and Matrigel matrix invasion by HT-1080 fibrosarcoma cells and B16-F10 melanoma cells. Together, our results suggest that glycosylation is not essential for antiprotease, antitumor, and matrix-binding activities of TFPI-2. Based on these collective data, we conclude that a biologically active nonglycosylated TFPI-2 can be produced in E. coli and that the protein can be produced in high-enough quantities to conduct in vivo studies for determination of the role of this inhibitor in tumor invasion and metastasis.
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Affiliation(s)
- C N Rao
- Department of Dermatology, Department of Obstetrics and Gynecology, Northwestern University Medical School, 303 East Chicago Avenue, Chicago, Illinois, 60611, USA
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42
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Daniels C, Morona R. Analysis of Shigella flexneri wzz (Rol) function by mutagenesis and cross-linking: wzz is able to oligomerize. Mol Microbiol 1999; 34:181-94. [PMID: 10540296 DOI: 10.1046/j.1365-2958.1999.01591.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The modal length or degree of polymerization (dp) of the Shigella flexneri O-antigen is determined in an unknown manner by the Wzz/Rol protein. The Wzz protein is anchored into the cytoplasmic membrane by two transmembrane domains (TM1 amino acids 32-52; TM2 amino acids 295-315) with the central loop of the protein located in the periplasm. Plasmids were constructed encoding hybrid Wzz proteins consisting of regions of S. flexneri Wzz (WzzSF) and Salmonella typhimurium Wzz (WzzST). These imparted O-antigen modal chain lengths that implied that the carboxy-terminal region of Wzz was involved in chain length determination. Site-directed mutagenesis was undertaken to investigate the functional significance of highly conserved residues in amino-/carboxy-terminal domains of WzzSF. Some of the WzzSF variants resulted in O-antigen modal chain lengths much shorter than those of wild-type WzzSF, whereas other mutants inactivated WzzSF function entirely and a third class had a longer O-antigen chain length distribution. The data indicate that amino acids throughout the length of the WzzSF protein are important in determination of O-antigen modal chain length. In vivo cross-linking experiments were performed to investigate the interactions between Wzz proteins. The experiments indicated that the WzzSF protein is able to form dimers and oligomers of at least six WzzSF proteins. A carboxy-terminal-truncated WzzSF protein having the amino terminal 194 amino acids was able to oligomerize, indicating that the amino-terminal region is sufficient for the Wzz-Wzz interaction observed. Shortened WzzSF proteins having internal deletions in the amino-terminal region were also able to oligomerize, suggesting that residues 59-194 are not essential for oligomerization. Cross-linking of WzzSF proteins with mutationally altered residues showed that loss of WzzSF function may be correlated to a reduced/altered ability to form oligomers, and that mutational alteration of glycine residues in the TM2 segment affects WzzSF-WzzSF dimer mobility in SDS polyacrylamide gels. These results provide the first evidence of protein-protein interactions for proteins involved in O-antigen polysaccharide biosynthesis.
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Affiliation(s)
- C Daniels
- Department of Microbiology and Immunology, The University of Adelaide, Adelaide, South Australia, Australia 5005
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43
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Reizer J, Hoischen C, Titgemeyer F, Rivolta C, Rabus R, Stülke J, Karamata D, Saier MH, Hillen W. A novel protein kinase that controls carbon catabolite repression in bacteria. Mol Microbiol 1998; 27:1157-69. [PMID: 9570401 DOI: 10.1046/j.1365-2958.1998.00747.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
HPr(Ser) kinase is the sensor in a multicomponent phosphorelay system that controls catabolite repression, sugar transport and carbon metabolism in gram-positive bacteria. Unlike most other protein kinases, it recognizes the tertiary structure in its target protein, HPr, a phosphocarrier protein of the bacterial phosphotransferase system and a transcriptional cofactor controlling the phenomenon of catabolite repression. We have identified the gene (ptsK) encoding this serine/threonine protein kinase and characterized the purified protein product. Orthologues of PtsK have been identified only in bacteria. These proteins constitute a novel family unrelated to other previously characterized protein phosphorylating enzymes. The Bacillus subtilis kinase is shown to be allosterically activated by metabolites such as fructose 1,6-bisphosphate and inhibited by inorganic phosphate. In contrast to wild-type B. subtilis, the ptsK mutant is insensitive to transcriptional regulation by catabolite repression. The reported results advance our understanding of phosphorylation-dependent carbon control mechanisms in Gram-positive bacteria.
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Affiliation(s)
- J Reizer
- Department of Biology, University of California at San Diego, La Jolla 92093-0116, USA
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44
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Reddy P, Kamireddi M. Modulation of Escherichia coli adenylyl cyclase activity by catalytic-site mutants of protein IIA(Glc) of the phosphoenolpyruvate:sugar phosphotransferase system. J Bacteriol 1998; 180:732-6. [PMID: 9457881 PMCID: PMC106945 DOI: 10.1128/jb.180.3.732-736.1998] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
It is demonstrated here that in Escherichia coli, the phosphorylated form of the glucose-specific phosphocarrier protein IIA(Glc) of the phosphoenolpyruvate:sugar phosphotransferase system is an activator of adenylyl cyclase and that unphosphorylated IIA(Glc) has no effect on the basal activity of adenylyl cyclase. To elucidate the specific role of IIA(Glc) phosphorylation in the regulation of adenylyl cyclase activity, both the phosphorylatable histidine (H90) and the interactive histidine (H75) of IIA(Glc) were mutated by site-directed mutagenesis to glutamine and glutamate. Wild-type IIA(Glc) and the H75Q mutant, in which the histidine in position 75 has been replaced by glutamine, were phosphorylated by the phosphohistidine-containing phosphocarrier protein (HPr-P) and were equally potent activators of adenylyl cyclase. Neither the H90Q nor the H90E mutant of IIA(Glc) was phosphorylated by HPr-P, and both failed to activate adenylyl cyclase. Furthermore, replacement of H75 by glutamate inhibited the appearance of a steady-state level of phosphorylation of H90 of this mutant protein by HPr-P, yet the H75E mutant of IIA(Glc) was a partial activator of adenylyl cyclase. The H75E H90A double mutant, which cannot be phosphorylated, did not activate adenylyl cyclase. This suggests that the H75E mutant was transiently phosphorylated by HPr-P but the steady-state level of the phosphorylated form of the mutant protein was decreased due to the repulsive forces of the negatively charged glutamate at position 75 in the catalytic pocket. These results are discussed in the context of the proximity of H75 and H90 in the IIA(Glc) structure and the disposition of the negative charge in the modeled glutamate mutants.
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Affiliation(s)
- P Reddy
- Biotechnology Division, Chemical Science and Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-0001, USA.
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45
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Seok YJ, Sondej M, Badawi P, Lewis MS, Briggs MC, Jaffe H, Peterkofsky A. High affinity binding and allosteric regulation of Escherichia coli glycogen phosphorylase by the histidine phosphocarrier protein, HPr. J Biol Chem 1997; 272:26511-21. [PMID: 9334229 DOI: 10.1074/jbc.272.42.26511] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The histidine phosphocarrier protein (HPr) is an essential element in sugar transport by the bacterial phosphoenolpyruvate:sugar phosphotransferase system. Ligand fishing, using surface plasmon resonance, was used to show the binding of HPr to a nonphosphotransferase protein in extracts of Escherichia coli; the protein was subsequently identified as glycogen phosphorylase (GP). The high affinity (association constant approximately 10(8) M-1), species-specific interaction was also demonstrated in electrophoretic mobility shift experiments by polyacrylamide gel electrophoresis. Equilibrium ultracentrifugation analysis indicates that HPr allosterically regulates the oligomeric state of glycogen phosphorylase. HPr binding increases GP activity to 250% of the level in control assays. Kinetic analysis of coupled enzyme assays shows that the binding of HPr to GP causes a decrease in the Km for glycogen and an increase in the Vmax for phosphate, indicating a mixed type activation. The stimulatory effect of E. coli HPr on E. coli GP activity is species-specific, and the unphosphorylated form of HPr activates GP more than does the phosphorylated form. Replacement of specific amino acids in HPr results in reduced GP activation; HPr residues Arg-17, Lys-24, Lys-27, Lys-40, Ser-46, Gln-51, and Lys-72 were established to be important. This novel mechanism for the regulation of GP provides the first evidence directly linking E. coli HPr to the regulation of carbohydrate metabolism.
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Affiliation(s)
- Y J Seok
- NHLBI, National Institutes of Health, Bethesda, Maryland 20892, USA
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46
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Kamireddi M, Eisenstein E, Reddy P. Stable expression and rapid purification of Escherichia coli GroEL and GroES chaperonins. Protein Expr Purif 1997; 11:47-52. [PMID: 9325138 DOI: 10.1006/prep.1997.0764] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
An Escherichia coli expression vector pRE (P. Reddy, A. Peterkofsky, and K. McKenney, 1989, Nucleic Acids Res. 17, 10473-10488), originally developed for the cloning and expression of lethal genes, was used for cloning and hyperexpression of GroEL and GroES genes. Regulated gene expression is achieved in the pRE vector under the tight control of the lambda PL promoter. Upon induction of the promoter, stable expression of GroEL to about 60% of the total cell protein was observed. Similarly, stable expression of GroES to about 40% of the total cell protein was achieved. GroES was found to be a heat-stable protein while GroEL was not. Both GroE chaperonins were purified in a single chromatographic step with a yield of about 100 mg GroEL and 25 mg GroES per liter of E. coli culture. GroE chaperonins purified by the protocols described here were active in the renaturation of urea-denatured rhodanese.
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Affiliation(s)
- M Kamireddi
- DNA Technologies Group, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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47
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Jha PK, Sarkar S. DNA sequencing and comparative sequence analysis reveal that the Escherichia coli genomic DNA may replace the target DNA during molecular cloning: evidence for the erroneous assembly of E. coli DNA into database sequences. Comp Biochem Physiol B Biochem Mol Biol 1997; 118:333-9. [PMID: 9440226 DOI: 10.1016/s0305-0491(97)00175-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA sequencing and similarity search of databases provide experimental evidence that portions of the host Escherichia coli genome may get ligated into the cloning vector, resulting in clones containing nontargeted inserts. Several lines of evidence suggest that this non-targeted ligation, as observed by us while subcloning troponin I cDNA, is presumably due to a recombination-mediated mechanism by which host DNA replaces the target DNA in the cloning vector. The E. coli genome mapping to 64-65 min and 92.8-00.1 min, the latter containing insertion sequences, appears to be the hotspot regions involved in this process. We examined the possibility that some sequences reported in the databases may also contain genomic sequences of E. coli. A search of current databases revealed that a rat hepatic glutathione transporter cDNA contains a 2.2-kb-long portion of the E. coli genome that has been wrongly assembled into its 5' untranslated and coding regions. In addition, about 30 sequences in databases, including a Yersinia pestis toxin gene, showed relatively high sequence identity with those portions of the E. coli genome that were present in the nonauthentic clones.
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Affiliation(s)
- P K Jha
- Department of Anatomy & Cellular Biology, Tufts University Health Science Campus, Boston, MA 02111, USA.
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48
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Cao GJ, Pogliano J, Sarkar N. Identification of the coding region for a second poly(A) polymerase in Escherichia coli. Proc Natl Acad Sci U S A 1996; 93:11580-5. [PMID: 8876178 PMCID: PMC38100 DOI: 10.1073/pnas.93.21.11580] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
We had earlier identified the pcnB locus as the gene for the major Escherichia coli poly(A) polymerase (PAP I). In this report, we describe the disruption and identification of a candidate gene for a second poly(A) polymerase (PAP II) by an experimental strategy which was based on the assumption that the viability of E. coli depends on the presence of either PAP I or PAP II. The coding region thus identified is the open reading frame f310, located at about 87 min on the E. coli chromosome. The following lines of evidence support f310 as the gene for PAP II: (i) the deduced peptide encoded by f310 has a molecular weight of 36,300, similar to the molecular weight of 35,000 estimated by gel filtration of PAP II; (ii) the deduced f310 product is a relatively hydrophobic polypeptide with a pI of 9.4, consistent with the properties of partially purified PAP II; (iii) overexpression of f310 leads to the formation of inclusion bodies whose solubilization and renaturation yields poly(A) polymerase activity that corresponds to a 35-kDa protein as shown by enzyme blotting; and (iv) expression of a f310 fusion construct with hexahistidine at the N-terminus of the coding region allowed purification of a poly(A) polymerase fraction whose major component is a 36-kDa protein. E. coli PAP II has no significant sequence homology either to PAP I or to the viral and eukaryotic poly(A) polymerases, suggesting that the bacterial poly(A) polymerases have evolved independently. An interesting feature of the PAP II sequence is the presence of sets of two paired cysteine and histidine residues that resemble the RNA binding motifs seen in some other proteins.
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Affiliation(s)
- G J Cao
- Boston Biomedical Research Institute, MA 02114, USA
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49
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Moore JL, Gorshkova II, Brown JW, McKenney KH, Schwarz FP. Effect of cAMP binding site mutations on the interaction of cAMP receptor protein with cyclic nucleoside monophosphate ligands and DNA. J Biol Chem 1996; 271:21273-8. [PMID: 8702903 DOI: 10.1074/jbc.271.35.21273] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Although cAMP binding to wild type cAMP receptor protein (CRP) induces specific DNA binding and activates transcription, cyclic nucleoside monophosphate (cNMP) binding to the CRP mutant Ser128 --> Ala does not, whereas the double CRP mutant Thr127 --> Leu/Ser128 --> Ala activates transcription even in the absence of cNMP. Isothermal titration calorimetry measurements on the cNMP binding reactions to the S128A and T127L/S128A mutants show that the reactions are mainly entropically driven as is cAMP binding to CRP. In contrast to cAMP binding to CRP, the binding reactions are noncooperative and exothermic with binding enthalpies (DeltaHb) ranging from -23.4 +/- 0.9 kJ mol-1 for cAMP binding to S128A at 39 degrees C to -4.1 +/- 0.6 kJ mol-1 for cAMP binding to T127L/S128A at 24 degrees C and exhibit enthalpy-entropy compensation. To account for the inactivity of the S128A mutant, in vitro and in vivo DNA binding experiments were performed on the cAMP-ligated S128A mutant. The cAMP-ligated S128A mutant binds to the consensus DNA binding site with approximately the same affinity as that of cAMP-ligated CRP but forms a different type of complex, which may account for loss of transcriptional activity by the mutant. Energy minimization computations on the cAMP-ligated S128A mutant show that amino acid conformational differences between S128A and CRP occur at Ser179, Glu181, and Thr182 in the center of the DNA binding site, implying that these conformational changes may account for the difference in DNA binding.
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Affiliation(s)
- J L Moore
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, Rockville, Maryland 20850, USA
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Arnaud M, Débarbouillé M, Rapoport G, Saier MH, Reizer J. In vitro reconstitution of transcriptional antitermination by the SacT and SacY proteins of Bacillus subtilis. J Biol Chem 1996; 271:18966-72. [PMID: 8702561 DOI: 10.1074/jbc.271.31.18966] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Expression of the sacPA and sacB genes of Bacillus subtilis is positively modulated by transcriptional regulatory proteins encoded by the sacT and sacY genes, respectively. Previous genetic studies led to the suggestion that SacT and SacY function as nascent mRNA binding proteins preventing early termination of transcription at terminators located in the leader regions of the corresponding genes. Here we report the overproduction, purification to near homogeneity, and characterization of the two antiterminators, SacT and SacY. Using mRNA band migration retardation assays and a reconstituted transcriptional antitermination system, the mRNA binding functions and antitermination activities of purified SacT and SacY are demonstrated under in vitro conditions. The results establish for the first time that members of the BglG family of antiterminators function in antitermination in the absence of other proteins in vitro. Purified SacT is shown to be phosphorylated by phosphoenolpyruvate in a phosphotransferase-catalyzed reaction dependent on Enzyme I and HPr. Unexpectedly, the purified SacT is shown to be functional in mRNA binding and in transcriptional antitermination independently of its phosphorylation state.
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Affiliation(s)
- M Arnaud
- Unité de Biochimie Microbienne, Institut Pasteur, URA 1300 Centre National de la Recherche Scientifique 25, rue du Docteur Roux-75724 Paris Cedex 15, France
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