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Li M, Wu C, Yang Y, Zheng M, Yu S, Wang J, Chen L, Li H. 3-Phosphoglycerate dehydrogenase: a potential target for cancer treatment. Cell Oncol (Dordr) 2021; 44:541-556. [PMID: 33735398 DOI: 10.1007/s13402-021-00599-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 02/23/2021] [Accepted: 02/25/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Metabolic changes have been recognized as an important hallmark of cancer cells. Cancer cells can promote their own growth and proliferation through metabolic reprogramming. Particularly, serine metabolism has frequently been reported to be dysregulated in tumor cells. 3-Phosphoglycerate dehydrogenase (PHGDH) catalyzes the first step in the serine biosynthesis pathway and acts as a rate-limiting enzyme involved in metabolic reprogramming. PHGDH upregulation has been observed in many tumor types, and inhibition of PHGDH expression has been reported to inhibit the proliferation of PHGDH-overexpressing tumor cells, indicating that it may be utilized as a target for cancer treatment. Recently identified inhibitors targeting PHGDH have already shown effectiveness. A further in-depth analysis and concomitant development of PHGDH inhibitors will be of great value for the treatment of cancer. CONCLUSIONS In this review we describe in detail the role of PHGDH in various cancers and inhibitors that have recently been identified to highlight progression in cancer treatment. We also discuss the development of new drugs and treatment modalities based on PHGDH targets. Overexpression of PHGDH has been observed in melanoma, breast cancer, nasopharyngeal carcinoma, parathyroid adenoma, glioma, cervical cancer and others. PHGDH may serve as a molecular biomarker for the diagnosis, prognosis and treatment of these cancers. The design and development of novel PHGDH inhibitors may have broad implications for cancer treatment. Therapeutic strategies of PHGDH inhibitors in combination with traditional chemotherapeutic drugs may provide new perspectives for precision medicine and effective personalized treatment for cancer patients.
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Affiliation(s)
- Mingxue Li
- Wuya College of Innovation, School of Pharmacy, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Canrong Wu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Yueying Yang
- Wuya College of Innovation, School of Pharmacy, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Mengzhu Zheng
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Silin Yu
- Department of Medicinal Chemistry and Natural Medicine Chemistry (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, 150081, China
| | - Jinhui Wang
- Department of Medicinal Chemistry and Natural Medicine Chemistry (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), Harbin Medical University, Harbin, 150081, China.
| | - Lixia Chen
- Wuya College of Innovation, School of Pharmacy, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China.
| | - Hua Li
- Wuya College of Innovation, School of Pharmacy, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China.
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2
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Waditee R, Bhuiyan NH, Hirata E, Hibino T, Tanaka Y, Shikata M, Takabe T. Metabolic engineering for betaine accumulation in microbes and plants. J Biol Chem 2007; 282:34185-93. [PMID: 17884813 DOI: 10.1074/jbc.m704939200] [Citation(s) in RCA: 44] [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
Plants accumulate a variety of osmoprotectants that improve their ability to combat abiotic stresses. Among them, betaine appears to play an important role in conferring resistance to stresses. Betaine is synthesized via either choline oxidation or glycine methylation. An increased betaine level in transgenic plants is one of the potential strategies to generate stress-tolerant crop plants. Here, we showed that an exogenous supply of serine or glycine to a halotolerant cyanobacterium Aphanothece halophytica, which synthesizes betaine from glycine by a three-step methylation, elevated intracellular accumulation of betaine under salt stress. The gene encoding 3-phosphoglycerate dehydrogenase (PGDH), which catalyzes the first step of the phosphorylated pathway of serine biosynthesis, was isolated from A. halophytica. Expression of the Aphanothece PGDH gene in Escherichia coli caused an increase in levels of betaine as well as glycine and serine. Expression of the Aphanothece PGDH gene in Arabidopsis plants, in which the betaine synthetic pathway was introduced via glycine methylation, further increased betaine levels and improved the stress tolerance. These results demonstrate that PGDH enhances the levels of betaine by providing the precursor serine for both choline oxidation and glycine methylation pathways.
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Affiliation(s)
- Rungaroon Waditee
- Research Institute of Meijo University, Tenpaku-ku, Nagoya, Aichi, Japan
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3
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Larsen MH, Kallipolitis BH, Christiansen JK, Olsen JE, Ingmer H. The response regulator ResD modulates virulence gene expression in response to carbohydrates in Listeria monocytogenes. Mol Microbiol 2006; 61:1622-35. [PMID: 16968229 DOI: 10.1111/j.1365-2958.2006.05328.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Listeria monocytogenes is a versatile bacterial pathogen that is able to accommodate to diverse environmental and host conditions. Presently, we have identified a L. monocytogenes two-component response regulator, ResD that is required for the repression of virulence gene expression known to occur in the presence of easily fermentable carbohydrates not found inside host organisms. Structurally and functionally, ResD resembles the respiration regulator ResD in Bacillus subtilis as deletion of the L. monocytogenes resD reduces respiration and expression of cydA, encoding a subunit of cytochrome bd. The resD mutation also reduces expression of mptA encoding the EIIABman component of a mannose/glucose-specific PTS system, indicating that ResD controls sugar uptake. This notion was supported by the poor growth of resD mutant cells that was alleviated by excess of selected carbohydrates. Despite the growth deficient phenotype of the mutant in vitro the mutation did not affect intracellular multiplication in epithelial or macrophage cell lines. When examining virulence gene expression we observed traditional induction by charcoal in both mutant and wild-type cells whereas the repression observed in wild-type cells by fermentable carbohydrates did not occur in resD mutant cells. Thus, ResD is a central regulator of L. monocytogenes when present in the external environment.
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Affiliation(s)
- Marianne H Larsen
- Department of Veterinary Pathobiology, The Royal Veterinary and Agricultural University, Stigbøjlen 4, DK-1870 Frederiksberg C, Denmark
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4
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Glaser P, Kunst F, Arnaud M, Coudart MP, Gonzales W, Hullo MF, Ionescu M, Lubochinsicy B, Marcelino L, Moszer I, Presecan E, Santana M, Schneider E, Schwelzer J, Vertes A, Rapoport G, Danchin A. Bacillus subtilis genome project: cloning and sequencing of the 97 kb region from 325° to 333deg. Mol Microbiol 2006; 10:371-384. [PMID: 28776854 DOI: 10.1111/j.1365-2958.1993.tb01963.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the framework of the European project aimed at the sequencing of the Bacillus subtilis genome the DNA region located between gerB (314°) and sacXV (333°) was assigned to the Institut Pasteur. In this paper we describe the cloning and sequencing of a segment of 97 kb of contiguous DNA. Ninety-two open reading frames were predicted to encode putative proteins among which only forty-two were found to display significant similarities to known proteins present in databanks, e.g. amino acid permeases, proteins involved in cell wall or antibiotic biosynthesis, various regulatory proteins, proteins of several dehydrogenase families and enzymes II of the phosphotransferase system involved in sugar transport. Additional experiments led to the identification of the products of new B. subtilis genes, e.g. galactokinase and an operon involved in thiamine biosynthesis.
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Affiliation(s)
- P Glaser
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - F Kunst
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - M Arnaud
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - M-P Coudart
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - W Gonzales
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - M-F Hullo
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - M Ionescu
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - B Lubochinsicy
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - L Marcelino
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - I Moszer
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - E Presecan
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - M Santana
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - E Schneider
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - J Schwelzer
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - A Vertes
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - G Rapoport
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
| | - A Danchin
- Unité de Régulation de l'Expression GénétiqueUnité de Biochimie Microbienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.GDR 1029, Centre National de la Recherche Scientifique, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.Laboratoire de Biochimie Cellulaire et de Biologie Moléculaire, 40 avenue du Recteur Pineau, 86022 Poitiers Cedex, France
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5
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Yoshimura M, Asai K, Sadaie Y, Yoshikawa H. Interaction of Bacillus subtilis extracytoplasmic function (ECF) sigma factors with the N-terminal regions of their potential anti-sigma factors. MICROBIOLOGY-SGM 2004; 150:591-599. [PMID: 14993308 DOI: 10.1099/mic.0.26712-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Extracytoplasmic function (ECF) sigma factors constitute a diverse family of proteins, within the class of the sigma 70 subunit of RNA polymerase. Most members of the family studied to date are known to regulate gene expression in response to stress conditions. The Bacillus subtilis genome encodes at least 17 distinct sigma factors, seven of which are members of the ECF subfamily. Among these, five sigma factors, namely SigV, SigW, SigX, SigY and SigM, are encoded by the first genes of the cognate sigma operons. Disruption or repressed expression of the downstream gene(s) resulted in transcriptional activation of the cognate sigma operon. Moreover, in vivo protein-protein interaction analyses by yeast two-hybrid experiments indicated that these immediate downstream gene products bind the cognate ECF sigma factor, suggesting that they function as anti-sigma factors by capturing sigma factor on the inner surface of the cytoplasmic membrane. Interaction with other sigma factors was not observed. The results presented here also show that these anti-sigma factors interact with ECF sigma factors through their N-terminal region, implying that the N-terminal domain resides inside the cytoplasmic membrane.
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Affiliation(s)
- Mika Yoshimura
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kei Asai
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Saitama University, Saitama 338-7507, Japan
| | - Yoshito Sadaie
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Saitama University, Saitama 338-7507, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
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6
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Rasmussen AA, Søgaard-Andersen L. TodK, a putative histidine protein kinase, regulates timing of fruiting body morphogenesis in Myxococcus xanthus. J Bacteriol 2003; 185:5452-64. [PMID: 12949097 PMCID: PMC193762 DOI: 10.1128/jb.185.18.5452-5464.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In response to starvation, Myxococcus xanthus initiates a developmental program that results in the formation of spore-filled multicellular fruiting bodies. Fruiting body formation depends on the temporal and spatial coordination of aggregation and sporulation. These two processes are induced by the cell surface-associated C signal, with aggregation being induced after 6 h and sporulation being induced once cells have completed the aggregation process. We report the identification of TodK, a putative histidine protein kinase of two-component regulatory systems that is important for the correct timing of aggregation and sporulation. Loss of TodK function results in early aggregation and early, as well as increased levels of, sporulation. Transcription of todK decreases 10-fold in response to starvation independently of the stringent response. Loss of TodK function specifically results in increased expression of a subset of C-signal-dependent genes. Accelerated development in a todK mutant depends on the known components in the C-signal transduction pathway. TodK is not important for synthesis of the C signal. From these results we suggest that TodK is part of a signal transduction system which converges on the C-signal transduction pathway to negatively regulate aggregation, sporulation, and the expression of a subset of C-signal-dependent genes. TodK and the SdeK histidine protein kinase, which is part of a signal transduction system that converges on the C-signal transduction pathway to stimulate aggregation, sporulation, and C-signal-dependent gene expression, act in independent genetic pathways. We suggest that the signal transduction pathways defined by TodK and SdeK act in concert with the C-signal transduction pathway to control the timing of aggregation and sporulation.
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Affiliation(s)
- Anders A Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark Odense, 5230 Odense M, Denmark
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7
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Asai K, Yamaguchi H, Kang CM, Yoshida KI, Fujita Y, Sadaie Y. DNA microarray analysis of Bacillus subtilis sigma factors of extracytoplasmic function family. FEMS Microbiol Lett 2003; 220:155-60. [PMID: 12644242 DOI: 10.1016/s0378-1097(03)00093-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Target gene candidates of the seven extracytoplasmic function (ECF) sigma factors of Bacillus subtilis have been surveyed using DNA microarray analysis of mRNA extracted from cells grown in Luria-Bertani broth, in which an ECF sigma factor gene was placed under the control of the spac promoter on multicopy plasmid pDG148 and overexpressed. The number of target candidates for each of the sigma factors varied greatly, and a total of 278 genes were selected. Interestingly, the above target gene candidates shared only one gene out of 94 target genes of the general stress sigma B that have been reported in the literature thus far. Furthermore, lacZ-fusion experiments based on the results of DNA microarray analysis indicated that each ECF sigma factor directs transcription of its own operon, with the exception of sigZ. The DNA microarray data collected in this study are available at the KEGG Expression Database web site (http://www.genome.ad.jp/kegg/expression/).
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Affiliation(s)
- Kei Asai
- Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Saitama, 338-8570 Saitama, Japan
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8
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Kimura Y, Nakano H, Terasaka H, Takegawa K. Myxococcus xanthus mokA encodes a histidine kinase-response regulator hybrid sensor required for development and osmotic tolerance. J Bacteriol 2001; 183:1140-6. [PMID: 11157925 PMCID: PMC94986 DOI: 10.1128/jb.183.4.1140-1146.2001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A gene, mokA, encoding a protein with similarities to histidine kinase-response regulator hybrid sensor, was cloned from a Myxococcus xanthus genomic library. The predicted mokA gene product was found to contain three domains: an amino-terminal input domain, a central transmitter domain, and a carboxy-terminal receiver domain. mokA mutants placed under starvation conditions exhibited reduced sporulation. Mutation of mokA also caused marked growth retardation at high osmolarity. These results indicated that M. xanthus MokA is likely a transmembrane sensor that is required for development and osmotic tolerance. The putative function of MokA is similar to that of the hybrid histidine kinase, DokA, of the eukaryotic slime mold Dictyostelium discoideum.
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Affiliation(s)
- Y Kimura
- Department of Life Sciences, Faculty of Agriculture, Kagawa University, Miki-cho, Kagawa, Japan 761-0795.
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9
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Zhang X, Hulett FM. ResD signal transduction regulator of aerobic respiration in Bacillus subtilis: ctaA promoter regulation. Mol Microbiol 2000; 37:1208-19. [PMID: 10972837 DOI: 10.1046/j.1365-2958.2000.02076.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A two-component signal transduction system composed of a sensor kinase, ResE, and a response regulator, ResD, encoded by resD and resE genes of the res operon (resABCDE), has a regulatory role in both aerobic and anaerobic respiration. In terms of aerobic respiration, resD functions upstream of ctaA, a gene required for haem A biogenesis and hence for the synthesis of haem A-containing cytochrome terminal oxidases. Although ResD is probably a transcription factor, there was no direct evidence that ResD protein, either phosphorylated or unphosphorylated, interacts directly with regulatory regions of ResD-controlled genes. Here, we report the overexpression and purification of ResD and ResE and their role in gene activation. ResD can be phosphorylated by ResE in vitro and is a monomer in solution in either the phosphorylated or unphosphorylated state. The binding activity of ResD to the ctaA promoter was examined by gel shift assays and DNase I footprinting assays. DNase I footprinting showed both unphosphorylated and phosphorylated ResD binding to the ctaA promoter and showed that there are three binding sites (A1, A2 and A3), two (A1 and A2) upstream of the -35 promoter region and one (A3) downstream of the -10 of the promoter. The role of each site in ctaA promoter activity and ResD binding was characterized using deletion analysis, followed by the DNase I footprinting and in vivo transcription assays of promoter-lacZ fusions. Our results showed that the concentration of ResD required to bind at each site is different and that ResD binding at the A1 site is independent of the other two ResD binding sites, but that the concentration of ResD approximately P required to protect site A2 is reduced when site A3 is present. In vivo transcription assays from promoter-lacZ fusion constructs showed that DNA containing ResD-binding site A2 was essential for promoter activity and that promoter constructs containing both binding sites A2 and A3 were sufficient for full promoter activity.
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Affiliation(s)
- X Zhang
- Laboratory for Molecular Biology, Department of Biological Sciences University of Illinois at Chicago, 900 S. Ashland Avenue (M/C 567), Chicago, IL 60607, USA
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10
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Abstract
Cytochromes of c-type contain covalently bound haem and in bacteria are located on the periplasmic side of the cytoplasmic membrane. More than eight different gene products have been identified as being specifically required for the synthesis of cytochromes c in Gram-negative bacteria. Corresponding genes are not found in the genome sequences of Gram-positive bacteria. Using two random mutagenesis approaches, we have searched for cytochrome c biogenesis genes in the Gram-positive bacterium Bacillus subtilis. Three genes, resB, resC and ccdA, were identified. CcdA has been found previously and is required for a late step in cytochrome c synthesis and also plays a role in spore synthesis. No function has previously been assigned for ResB and ResC but these predicted membrane proteins show sequence similarity to proteins required for cytochrome c synthesis in chloroplasts. Attempts to inactivate resB and resC in B. subtilis have indicated that these genes are essential for growth. We demonstrate that various nonsense mutations in resB or resC can block synthesis of cytochromes c with no effect on other types of cytochromes and little effect on sporulation and growth. The results strongly support the recent proposal that Gram-positive bacteria, cyanobacteria, epsilon-proteobacteria, and chloroplasts have a similar type of machinery for cytochrome c synthesis (System II), which is very different from those of most Gram-negative bacteria (System I) and mitochondria (System III).
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Affiliation(s)
- N E Le Brun
- Department of Microbiology, Lund University, SE-223 62 Lund, Sweden
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11
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Ikura T, Hayano T, Takahashi N, Kuwajima K. Fast folding of Escherichia coli cyclophilin A: a hypothesis of a unique hydrophobic core with a phenylalanine cluster. J Mol Biol 2000; 297:791-802. [PMID: 10731429 DOI: 10.1006/jmbi.2000.3580] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Escherichia coli cyclophilin A, a 164 residue globular protein, shows fast and slow phases of refolding kinetics from the urea-induced unfolded state at pH 7.0. Given that the slow phases are independent of the denaturant concentration and may be rate-limited by cis/trans isomerizations of prolyl peptide bonds, the fast phase represents the true folding reaction. The extrapolation of the fast-phase rate constant to 0 M urea indicates that the folding reaction of cyclophilin A is extraordinarily fast and has about 700 s(-1) of the rate constant. Interrupted refolding experiments showed that the protein molecules formed in the fast phase had already been fully folded to the native state. This finding overthrows the accepted view that the fast folding is observed only in small proteins of fewer than 100 amino acid residues. Examination of the X-ray structure of cyclophilin A has shown that this protein has only one unique hydrophobic core (phenylalanine cluster) formed by evolutionarily conserved phenylalanine residues, and suggests that this architecture of the molecule may be responsible for the fast folding behavior.
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Affiliation(s)
- T Ikura
- Department of Physics, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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12
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Cho HM, Jun DY, Bae MA, Ahn JD, Kim YH. Nucleotide sequence and differential expression of the human 3-phosphoglycerate dehydrogenase gene. Gene 2000; 245:193-201. [PMID: 10713460 DOI: 10.1016/s0378-1119(00)00009-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The nucleotide sequence of Hs 3-PGDH gene, encoding human 3-phosphoglycerate dehydrogenase that catalyzes the initiating step in the phosphorylated pathway of serine biosynthesis, has been determined. The 3-PGDH gene has a predicted 533 amino acid open reading frame, encoding a 56.8kDa protein that shares 94.0% similarity with rat-liver 3-PGDH. Two different transcripts corresponding to 3-PGDH mRNA were detected in human normal tissues. A dominant 2.1kb transcript was expressed at high levels in prostate, testis, ovary, brain, liver, kidney, and pancreas, and weakly expressed in thymus, colon, and heart. A 710bp transcript also appeared as a weaker band where the 2.1kb mRNA was expressed, and it was more significant than the 2.1kb mRNA in heart and skeletal muscle. The TPA-induced monocytic differentiation of U937, which also resulted in growth arrest, abruptly downregulated the expression of 3-PGDH. Removal of TPA restored cell growth through the retrodifferentiation process and subsequent expression of 3-PGDH. The 3-PGDH mRNA was markedly expressed in human leukemias, lymphoma Sup-T1, colon adenocarcinoma COLO 320DM, epitheloid carcinoma HeLa S3, and murine lymphoma BW5147.G.1.4, but not in human leukemia K562. This report demonstrates that the human 3-PGDH gene is regulated at the transcriptional level depending on tissue specificty and cellular proliferative status, and its transcriptional regulation mechanism may be a useful target for diagnosis and therapy of cancer.
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MESH Headings
- 3T3 Cells
- Amino Acid Sequence
- Animals
- Base Sequence
- Blotting, Northern
- Carbohydrate Dehydrogenases/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Female
- Gene Expression Regulation, Enzymologic
- HL-60 Cells
- HeLa Cells
- Humans
- Jurkat Cells
- K562 Cells
- Male
- Mice
- Molecular Sequence Data
- Phosphoglycerate Dehydrogenase
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Tissue Distribution
- Tumor Cells, Cultured
- U937 Cells
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Affiliation(s)
- H M Cho
- Department of Microbiology, College of Natural Sciences, Kyungpook National University, Taegu, South Korea
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13
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Kawabata S, Terao Y, Hamada S. Molecular cloning, sequence and characterization of a novel streptococcal phosphoglycerate dehydrogenase gene. ORAL MICROBIOLOGY AND IMMUNOLOGY 2000; 15:58-62. [PMID: 11155166 DOI: 10.1034/j.1399-302x.2000.150110.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The nucleotide sequence of a Streptococcus mutans serA gene that encodes D-3-phosphoglycerate dehydrogenase has been determined. The gene consisted of 1308-bp nucleotides coding for a 436-amino-acid polypeptide (48,546 Da). The deduced amino acid sequence showed a 66% identity with SerA from Bacillus subtilis and possessed specific residues (G-R-P-N-V-G) in the coenzyme-binding domain, alpha B helix. Recombinant streptococcal SerA was expressed using pMAL-c2 expression vector and purified by amylose resin affinity chromatography and DEAE-Sephacel column chromatography. This SerA enzyme catalyzed detectable reduction of alpha-ketoglutarate to 2-hydroxyglutaric acid. These findings indicate that the novel streptococcal phosphoglycerate dehydrogenase, SerA, is a member of a D-isomer-specific family of 2-hydroxyacid dehydrogenases.
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Affiliation(s)
- S Kawabata
- Department of Oral Microbiology, Osaka University Faculty of Dentistry, Suita-Osaka, 565-0871 Japan
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14
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Nakano MM, Zhu Y, Haga K, Yoshikawa H, Sonenshein AL, Zuber P. A mutation in the 3-phosphoglycerate kinase gene allows anaerobic growth of Bacillus subtilis in the absence of ResE kinase. J Bacteriol 1999; 181:7087-97. [PMID: 10559176 PMCID: PMC94185 DOI: 10.1128/jb.181.22.7087-7097.1999] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bacillus subtilis ResD-ResE two-component signal transduction system is essential for aerobic and anaerobic respiration. A spontaneous suppressor mutant that expresses ResD-controlled genes and grows anaerobically in the absence of the ResE histidine kinase was isolated. In addition, aerobic expression of ResD-controlled genes in the suppressed strain was constitutive and occurred at a much higher level than that observed in the wild-type strain. The suppressing mutation, which mapped to pgk, the gene encoding 3-phosphoglycerate kinase, failed to suppress a resD mutation, suggesting that the suppressing mutation creates a pathway for phosphorylation of the response regulator, ResD, which is independent of the cognate sensor kinase, ResE. The pgk-1 mutant exhibited very low but measurable 3-phosphoglycerate kinase activity compared to the wild-type strain. The results suggest that accumulation of a glycolytic intermediate, probably 1, 3-diphosphoglycerate, is responsible for the observed effect of the pgk-1 mutation on anaerobiosis of resE mutant cells.
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Affiliation(s)
- M M Nakano
- Department of Biochemistry, Louisiana State University Medical Center, Shreveport, Louisiana 71130, USA.
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15
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Kusano K, Berres ME, Engels WR. Evolution of the RECQ family of helicases: A drosophila homolog, Dmblm, is similar to the human bloom syndrome gene. Genetics 1999; 151:1027-39. [PMID: 10049920 PMCID: PMC1460517 DOI: 10.1093/genetics/151.3.1027] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several eukaryotic homologs of the Escherichia coli RecQ DNA helicase have been found. These include the human BLM gene, whose mutation results in Bloom syndrome, and the human WRN gene, whose mutation leads to Werner syndrome resembling premature aging. We cloned a Drosophila melanogaster homolog of the RECQ helicase family, Dmblm (Drosophila melanogaster Bloom), which encodes a putative 1487-amino-acid protein. Phylogenetic and dot plot analyses for the RECQ family, including 10 eukaryotic and 3 prokaryotic genes, indicate Dmblm is most closely related to the Homo sapiens BLM gene, suggesting functional similarity. Also, we found that Dmblm cDNA partially rescued the sensitivity to methyl methanesulfonate of Saccharomyces cerevisiae sgs1 mutant, demonstrating the presence of a functional similarity between Dmblm and SGS1. Our analyses identify four possible subfamilies in the RECQ family: (1) the BLM subgroup (H. sapiens Bloom, D. melanogaster Dmblm, and Caenorhabditis elegans T04A11.6); (2) the yeast RECQ subgroup (S. cerevisiae SGS1 and Schizosaccharomyces pombe rqh1/rad12); (3) the RECQL/Q1 subgroup (H. sapiens RECQL/Q1 and C. elegans K02F3.1); and (4) the WRN subgroup (H. sapiens Werner and C. elegans F18C5.2). This result may indicate that metazoans hold at least three RECQ genes, each of which may have a different function, and that multiple RECQ genes diverged with the generation of multicellular organisms. We propose that invertebrates such as nematodes and insects are useful as model systems of human genetic diseases.
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Affiliation(s)
- K Kusano
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706, USA
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16
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Abstract
There was a long-held belief that the gram-positive soil bacterium Bacillus subtilis is a strict aerobe. But recent studies have shown that B. subtilis will grow anaerobically, either by using nitrate or nitrite as a terminal electron acceptor, or by fermentation. How B. subtilis alters its metabolic activity according to the availability of oxygen and alternative electron acceptors is but one focus of study. A two-component signal transduction system composed of a sensor kinase, ResE, and a response regulator, ResD, occupies an early stage in the regulatory pathway governing anaerobic respiration. One of the essential roles of ResD and ResE in anaerobic gene regulation is induction of fnr transcription upon oxygen limitation. FNR is a transcriptional activator for anaerobically induced genes, including those for respiratory nitrate reductase, narGHJI.B. subtilis has two distinct nitrate reductases, one for the assimilation of nitrate nitrogen and the other for nitrate respiration. In contrast, one nitrite reductase functions both in nitrite nitrogen assimilation and nitrite respiration. Unlike many anaerobes, which use pyruvate formate lyase, B. subtilis can carry out fermentation in the absence of external electron acceptors wherein pyruvate dehydrogenase is utilized to metabolize pyruvate.
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Affiliation(s)
- M M Nakano
- Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, Shreveport 71130-3932, USA.
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17
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Ho CL, Noji M, Saito M, Saito K. Regulation of serine biosynthesis in Arabidopsis. Crucial role of plastidic 3-phosphoglycerate dehydrogenase in non-photosynthetic tissues. J Biol Chem 1999; 274:397-402. [PMID: 9867856 DOI: 10.1074/jbc.274.1.397] [Citation(s) in RCA: 65] [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
In plants, Ser is synthesized through a couple of pathways. 3-Phosphoglycerate dehydrogenase (PGDH), the first enzyme that is involved in the phosphorylated pathway of Ser biosynthesis, is responsible for the oxidation of 3-phosphoglycerate to phosphohydroxypyruvate. Here we report the first molecular cloning and characterization of PGDH from Arabidopsis thaliana. Sequence analysis of cDNA and a genomic clone revealed that the PGDH gene is composed of three exons, encoding a 623-amino acid polypeptide (66, 453 Da). The deduced protein, containing three of the most conserved regions in the NAD-dependent 2-hydroxyacid dehydrogenase family, has 38-39% identity to its animal and bacterial counterparts. The presence of an N-terminal signal sequence for translocation into plastids was confirmed by particle-gun bombardment experiments using green fluorescence protein as a reporter protein for subcellular localization. Southern hybridization analysis and restriction fragment length polymorphism mapping indicated that PGDH is a single-copy gene that is mapped to the upper arm of chromosome 1. Northern hybridization analysis indicated preferential expression of PGDH mRNA in root tissues of light-grown plants, suggesting that the phosphorylated pathway of Ser biosynthesis plays an important role in supplying Ser to non-photosynthetic tissues. The recombinant enzyme overproduced in Escherichia coli displayed hyperbolic kinetics with respect to 3-phosphoglycerate and NAD+.
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Affiliation(s)
- C L Ho
- Laboratory of Molecular Biology and Biotechnology, Research Center of Medicinal Resources, Faculty of Pharmaceutical Sciences, Chiba University, Yayoi-cho 1-33, Inage-ku, Chiba 263-8522, Japan
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18
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Fabret C, Hoch JA. A two-component signal transduction system essential for growth of Bacillus subtilis: implications for anti-infective therapy. J Bacteriol 1998; 180:6375-83. [PMID: 9829949 PMCID: PMC107725 DOI: 10.1128/jb.180.23.6375-6383.1998] [Citation(s) in RCA: 218] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/1998] [Accepted: 09/25/1998] [Indexed: 11/20/2022] Open
Abstract
A two-component signal transduction system encoded by the yycF and yycG genes is part of an operon containing three genes, yycH, yycI, and yycJ, with no known function and a gene, yycK, coding for an HtrA-like protease. This operon was transcribed during growth, and its transcription shut down as the cells approached stationary phase. This decreased transcription was not Spo0A dependent. The HtrA protease gene was separately controlled during sporulation from a sigmaG promoter. Studies using insertional inactivation plasmids revealed that neither yycF nor yycG could be inactivated, whereas the other genes were inactivated without loss of viability. A temperature-sensitive YycF response regulator mutant was isolated and shown to have an H215P mutation in a putative DNA-binding domain which is closely related to the OmpR family of response regulators. At the nonpermissive temperature, cultures of the mutant strain stopped growth within 30 min, and this was followed by a decrease in optical density. Microscopically, many of the cells appeared to retain their structure while being empty of their contents. The essential processes regulated by this two-component system remain unknown. A search of the genome databases revealed YycF, YycG, and YycJ homologues encoded by three linked genes in Streptococcus pyogenes. The high level of identity of these proteins (71% for YycF) suggests that this system may play a similar role in gram-positive pathogens.
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Affiliation(s)
- C Fabret
- Division of Cellular Biology, Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
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19
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Vagner V, Dervyn E, Ehrlich SD. A vector for systematic gene inactivation in Bacillus subtilis. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 11):3097-3104. [PMID: 9846745 DOI: 10.1099/00221287-144-11-3097] [Citation(s) in RCA: 548] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To study the functions of the uncharacterized open reading frames identified in the Bacillus subtilis genome, several vectors were constructed to perform insertional mutagenesis in the chromosome. All the pMUTIN plasmids carry a lacZ reporter gene and an inducible Pspac promoter, which is tightly regulated and can be induced about 1000-fold. The integration of a pMUTIN vector into the target gene has three consequences: (1) the target gene is inactivated; (2) lacZ becomes transcriptionally fused to the gene, allowing its expression pattern to be monitored; (3) the Pspac promoter controls the transcription of downstream genes in an IPTG-dependent fashion. This last feature is important because B. subtilis genes are often organized in operons. The potential polar effects generated by the integration of the vectors can be alleviated by addition of IPTG. Also, conditional mutants of essential genes can be obtained by integrating pMUTIN vectors upstream of the target gene. The vectors are currently being used for systematic inactivation of genes without known function within the B. subtilis European consortium. pMUTIN characteristics and the inactivation of eight genes in the resA-serA region of the chromosome are presented.
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Affiliation(s)
- Valerie Vagner
- Genetique Microbienne, lnstitut National de la Recherche Ag ronom ique,Domaine de Vilvefl, 78352 Jouy-en-Josas cedex,France
| | - Etienne Dervyn
- Genetique Microbienne, lnstitut National de la Recherche Ag ronom ique,Domaine de Vilvefl, 78352 Jouy-en-Josas cedex,France
| | - S Dusko Ehrlich
- Genetique Microbienne, lnstitut National de la Recherche Ag ronom ique,Domaine de Vilvefl, 78352 Jouy-en-Josas cedex,France
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20
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21
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Wipat A, Brignell SC, Guy BJ, Rose M, Emmerson PT, Harwood CR. The yvsA-yvqA (293 degrees-289 degrees) region of the Bacillus subtilis chromosome containing genes involved in metal ion uptake and a putative sigma factor. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 6):1593-1600. [PMID: 9639930 DOI: 10.1099/00221287-144-6-1593] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The region between yvsA (293 degrees) and yvqA (289 degrees) of the Bacillus subtilis chromosome has been sequenced within the framework of the B. subtilis 168 international sequencing programme. A primary analysis of the 42 ORFs identified in this 43 kb region is presented. The region included a high proportion of genes that did not show homology with genes in other bacteria. The identified ORFs showed homology to proteins involved in the transport of metal ions, two-component signal transducers, ATP-binding-cassette-type transporters and a sigma factor.
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Affiliation(s)
- Anil Wipat
- School of Microbiological, Immunological and Virological Sciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - S Caroline Brignell
- School of Microbiological, Immunological and Virological Sciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - B Jane Guy
- School of Microbiological, Immunological and Virological Sciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Matthias Rose
- Johann Wolfgang Goethe-Universitaet Frankfurt, Institut für Mikrobiologie, Marie-Curie-Str., 9 Geb. N250, 60439 Frankfurt am Main, Germany
| | - Peter T Emmerson
- Department of Biochemistry & Genetics, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Colin R Harwood
- School of Microbiological, Immunological and Virological Sciences, University of Newcastle upon Tyne, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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22
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Mian IS, Moser MJ, Holley WR, Chatterjee A. Statistical modelling and phylogenetic analysis of a deaminase domain. J Comput Biol 1998; 5:57-72. [PMID: 9541871 DOI: 10.1089/cmb.1998.5.57] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Deamination reactions are catalyzed by a variety of enzymes including those involved in nucleoside/nucleotide metabolism and cytosine to uracil (C-->U) and adenosine to inosine (A-->I) mRNA editing. The active site of the deaminase (DM) domain in these enzymes contains a conserved histidine (or rarely cysteine), two cysteines and a glutamate proposed to act as a proton shuttle during deamination. Here, a statistical model, a hidden Markov model (HMM), of the DM domain has been created which identifies currently known DM domains and suggests new DM domains in viral, bacterial and eucaryotic proteins. However, no DM domains were identified in the currently predicted proteins from the archaeon Methanococcus jannaschii and possible causes for, and a potential means to ameliorate this situation are discussed. In some of the newly identified DM domains, the glutamate is changed to a residue that could not function as a proton shuttle and in one instance (Mus musculus spermatid protein TENR) the cysteines are also changed to lysine and serine. These may be non-competent DM domains able to bind but not act upon their substrate. Phylogenetic analysis using an HMM-generated alignment of DM domains reveals three branches with clear substructure in each branch. The results suggest DM domains that are candidates for yeast, platyhelminth, plant and mammalian C-->U and A-->I mRNA editing enzymes. Some bacterial and eucaryotic DM domains form distinct branches in the phylogenetic tree suggesting the existence of common, novel substrates.
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Affiliation(s)
- I S Mian
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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23
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Florova G, Denoya CD, Morgenstern MR, Skinner DD, Reynolds KA. Cloning, expression, and characterization of a type II 3-dehydroquinate dehydratase gene from Streptomyces hygroscopicus. Arch Biochem Biophys 1998; 350:298-306. [PMID: 9473305 DOI: 10.1006/abbi.1997.0536] [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: 02/06/2023]
Abstract
A gene encoding dehydroquinate dehydratase (DHQase) was cloned from Streptomyces hygroscopicus var. ascomyceticus. The 528-bp open reading frame specified a primary translation product of 175 amino acids with a calculated Mr of 18,789. The predicted amino acid sequence of the DHQase showed similarities to bacterial and fungal type II DHQases. Overexpression of the dhq gene was accomplished in Escherichia coli using a gene fusion technique in which a malE, the gene encoding the maltose binding protein (MBP), was fused via a short oligonucleotide region to the beginning of dhq. The recombinant MBP-DHQase fusion protein was purified by affinity chromatography and cleaved using thrombin. The resulting DHQase, separated from the MBP, demonstrated typical properties of a type II DHQase: a relatively high Km for the dehydroquinate substrate (650 microM) and extreme thermal stability. The subunit Mr estimated by SDS-PAGE was 19,000, and the native Mr estimated by gel-exclusion chromatography and sucrose-density centrifugation was 130,000, suggesting that the enzyme is a homoheptamer (type II DHQases are typically homododecamers). The MBP-DHQase complex also adopted a heptameric structure and was a thermostable, fully active DHQase, indicating that the N-terminus is not involved in formation of protomer-protomer complexes. Previous analyses have supported positioning the N-terminus of type II DHQases close to the active site and a conformational change in this region coincident with ligand binding. Nonetheless, the Km and relative kcat obtained for MBP-DHQase were indistinguishable from those observed for DHQase. Inactivation data of the DHQase from S. hygroscopicus with the arginine-specific reagent phenylglyoxal showed that a modified Arg residue(s) is likely close to the N-terminus and active site of DHQase, but does not play an essential role in catalysis.
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Affiliation(s)
- G Florova
- School of Pharmacy and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia 23219, USA
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24
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Inoue K, Dreyfuss BW, Kindle KL, Stern DB, Merchant S, Sodeinde OA. Ccs1, a nuclear gene required for the post-translational assembly of chloroplast c-type cytochromes. J Biol Chem 1997; 272:31747-54. [PMID: 9395519 DOI: 10.1074/jbc.272.50.31747] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Nuclear genes play important regulatory roles in the biogenesis of the photosynthetic apparatus of eukaryotic cells by encoding factors that control steps ranging from chloroplast gene transcription to post-translational processes. However, the identities of these genes and the mechanisms by which they govern these processes are largely unknown. By using glass bead-mediated transformation to generate insertional mutations in the nuclear genome of Chlamydomonas reinhardtii, we have generated four mutants that are defective in the accumulation of the cytochrome b6f complex. One of them, strain abf3, also fails to accumulate holocytochrome c6. We have isolated a gene, Ccs1, from a C. reinhardtii genomic library that complements both the cytochrome b6f and cytochrome c6 deficiencies in abf3. The predicted protein product displays significant identity with Ycf44 from the brown alga Odontella sinensis, the red alga Porphyra purpurea, and the cyanobacterium Synechocystis strain PCC 6803 (25-33% identity). In addition, we note limited sequence similarity with ResB of Bacillus subtilis and an open reading frame in a homologous operon in Mycobacterium leprae (11-12% identity). On the basis of the pleiotropic c-type cytochrome deficiency in the ccs1 mutant, the predicted plastid localization of the protein, and its relationship to candidate cytochrome biosynthesis proteins in Gram-positive bacteria, we conclude that Ccs1 encodes a protein that is required for chloroplast c-type holocytochrome formation.
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Affiliation(s)
- K Inoue
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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25
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Abstract
Bacillus subtilis grows anaerobically by at least two different pathways, respiration using nitrate as an electron acceptor and fermentation in the absence of electron acceptors. Regulatory mechanisms have evolved allowing cells to shift to these metabolic capabilities in response to changes in oxygen availability. These include transcriptional activation of fnr upon oxygen limitation, a process requiring the ResD-ResE two-component signal transduction system that also regulates aerobic respiration. FNR then activates transcription of other anaerobically induced genes including the narGHJI operon which encodes a respiratory nitrate reductase. Genes involved in fermentative growth are controlled by an unidentified FNR-independent regulatory pathway.
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Affiliation(s)
- M M Nakano
- Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, Shreveport 71130-3932, USA.
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26
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Lapidus A, Galleron N, Sorokin A, Ehrlich SD. Sequencing and functional annotation of the Bacillus subtilis genes in the 200 kb rrnB-dnaB region. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 11):3431-3441. [PMID: 9387221 DOI: 10.1099/00221287-143-11-3431] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The 200 kb region of the Bacillus subtilis chromosome spanning from 255 to 275 degrees on the genetic map was sequenced. The strategy applied, based on use of yeast artificial chromosomes and multiplex Long Accurate PCR, proved to be very efficient for sequencing a large bacterial chromosome area. A total of 193 genes of this part of the chromosome was classified by level of knowledge and biological category of their functions. Five levels of gene function understanding are defined. These are: (i) experimental evidence is available of gene product or biological function; (ii) strong homology exists for the putative gene product with proteins from other organisms; (iii) some indication of the function can be derived from homologies with known proteins; (iv) the gene product can be clustered with hypothetical proteins; (v) no indication on the gene function exists. The percentage of detected genes in each category was: 20, 28, 20, 15 and 17, respectively. In the sequenced region, a high percentage of genes are implicated in transport and metabolic linking of glycolysis and the citric acid cycle. A functional connection of several genes from this region and the genes close to 140 degrees in the chromosome was also observed.
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Affiliation(s)
- Alia Lapidus
- Laboratoire de Genetique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas cedex, France
| | - Nathalie Galleron
- Laboratoire de Genetique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas cedex, France
| | - Alexei Sorokin
- Laboratoire de Genetique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas cedex, France
| | - S Dusko Ehrlich
- Laboratoire de Genetique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas cedex, France
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27
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Jock CA, Pulakat L, Lee S, Gavini N. Nucleotide sequence and genetic complementation analysis of lep from Azotobacter vinelandii. Biochem Biophys Res Commun 1997; 239:393-400. [PMID: 9344840 DOI: 10.1006/bbrc.1997.7452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The lep of Azotobacter vinelandii is an 852-base-pair open reading frame (ORF) which encodes a protein of 284 amino acid residues. The translated protein shares 75% homology with leader peptidase I isolated from Pseudomonas fluorescens and 37% homology with leader peptidase I isolated from Escherichia coli. Five highly conserved regions found in the family of leader peptidase I proteins are conserved in A. vinelandii Lep. The putative membrane topology of the protein seems similar to that of E. coli leader peptidase I based on the hydrophobicity analysis of the predicted amino acid sequence. Southern blotting analysis of the A. vinelandii chromosome by probing with lep specific DNA revealed that lep is present as a single copy per the chromosome. A multicopy plasmid carrying A. vinelandii lep could complement a temperature sensitive lep mutant of E. coli strain IT41, suggesting that we have identified the functional copy of lep present on A. vinelandii genome.
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Affiliation(s)
- C A Jock
- Department of Biological Sciences, Bowling Green State University, Ohio 43403, USA
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28
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Tjalsma H, Noback MA, Bron S, Venema G, Yamane K, van Dijl JM. Bacillus subtilis contains four closely related type I signal peptidases with overlapping substrate specificities. Constitutive and temporally controlled expression of different sip genes. J Biol Chem 1997; 272:25983-92. [PMID: 9325333 DOI: 10.1074/jbc.272.41.25983] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Most biological membranes contain one or two type I signal peptidases for the removal of signal peptides from secretory precursor proteins. In this respect, the Gram-positive bacterium Bacillus subtilis seems to be exceptional, because it contains at least four chromosomally-encoded type I signal peptidases, denoted SipS, SipT, SipU, and SipV. Here, we report the identification of the sipT and sipV genes, and the functional characterization of SipT, SipU, and SipV. The four signal peptidases have similar substrate specificities, as they can all process the same beta-lactamase precursor. Nevertheless, they seem to prefer different pre-proteins, as indicated by studies on the processing of the pre-alpha-amylase of Bacillus amyloliquefaciens in strains lacking SipS, SipT, SipU, or SipV. The sipU and sipV genes are constitutively transcribed at a low level, suggesting that they are required for processing of (pre-)proteins secreted during all growth phases. In contrast, the transcription of sipS and sipT is temporally controlled, in concert with the expression of the genes for most secretory proteins, which suggests that SipS and SipT serve to increase the secretory capacity of B. subtilis. Taken together, our findings suggest that SipS, SipT, SipU, and SipV serve different functions during the exponential and post-exponential growth phase of B. subtilis.
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Affiliation(s)
- H Tjalsma
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Kerklaan 30, 9751 NN Haren, The Netherlands
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Sorokin A, Bolotin A, Purnelle H, Hilbert H, Lauber J, Düsterhöft A, Ehrlich SD. Sequence of the Bacillus subtilis genome region in the vicinity of the lev operon reveals two new extracytoplasmic function RNA polymerase sigma factors SigV and SigZ. MICROBIOLOGY (READING, ENGLAND) 1997; 143 ( Pt 9):2939-2943. [PMID: 9308178 DOI: 10.1099/00221287-143-9-2939] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Two regions with sizes 18,900 and 25,400 bp, which join previously known contigs containing levRDEFG, aadK and blt genes near 235 degrees of the Bacillus subtilis chromosome, were sequenced. Among others, two genes, which encode proteins homologous to RNA polymerase sigma-factors, were identified within this region. The gene products designated SigV and SigZ, show the highest homology with sigma-factors encoded by the gene carQ of Myxococcus xanthus and sigX (formerly orfX20) of B. subtilis, correspondingly. All sigma-factors which show statistically significant homology to SigV and SigZ, belong to the ECF (extracytoplasmic functions) subfamily. SigV and SigZ do not have N-terminal sequence which prevents such proteins from binding to DNA without RNA polymerase core enzyme.
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Affiliation(s)
| | | | | | | | | | | | - S Dusko Ehrlich
- Laboratoire de GéAnéAtique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy-en-Josas cedex, France
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Hubschmann T, Wilde A, Elanskaya I, Shestakov SV, Borner T. A putative cytochrome c biogenesis gene in Synechocystis sp. PCC 6803. FEBS Lett 1997; 408:201-5. [PMID: 9187367 DOI: 10.1016/s0014-5793(97)00421-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A gene (orf334) with homology to chloroplast ycf5 (ccsA) was isolated from the cyanobacterium Synechocystis PCC 6803. The mRNA level of orf334 decreases in the dark and increases rapidly upon illumination. Transcription is initiated 69 nucleotides upstream of the start site of translation. The deduced amino acid sequence of orf334 has limited identity with bacterial proteins involved in cytochrome c biogenesis. Sequence comparison indicates differing pathways of cytochrome c biogenesis in cyanobacteria/chloroplasts and Gram positive bacteria versus proteobacteria and mitochondria. Insertional inactivation of the orf334 gene gave rise to a heterozygous mutant, i.e. complete absence of the orf334 product seems to be lethal to the cell.
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Affiliation(s)
- T Hubschmann
- Department of Biology (Genetics), Humboldt-University Berlin, Germany. Thomas=
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31
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Huang X, Decatur A, Sorokin A, Helmann JD. The Bacillus subtilis sigma(X) protein is an extracytoplasmic function sigma factor contributing to survival at high temperature. J Bacteriol 1997; 179:2915-21. [PMID: 9139908 PMCID: PMC179054 DOI: 10.1128/jb.179.9.2915-2921.1997] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The sigX gene, identified as part of the international effort to sequence the Bacillus subtilis genome, has been proposed to encode an alternative sigma factor of the extracytoplasmic function (ECF) subfamily. The sigX gene is cotranscribed with a downstream gene, ypuN, during logarithmic and early stationary phases of growth. We now report that strains lacking sigma(X) are impaired in the ability to survive at high temperature whereas a ypuN mutant has increased thermotolerance. We overproduced and purified sigma(X) from Escherichia coli and demonstrate that in vitro, both sigma(A) and sigma(X) holoenzymes recognize promoter elements within the sigX-ypuN control region. However, they have distinct salt optima such that sigma(A)-dependent transcription predominates at low salt while sigma(X)-dependent transcription predominates at high salt. A 54-bp region upstream of sigX suffices as a sigma(X)-dependent promoter in vivo, demonstrating that sigX is at least partially under positive autoregulatory control. Mutation of ypuN increases expression from the sigma(X)-dependent promoter in vivo, suggesting that ypuN may encode a negative regulator of sigma(X) activity.
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Affiliation(s)
- X Huang
- Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853-8101, USA
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32
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Achouri Y, Rider MH, Schaftingen EV, Robbi M. Cloning, sequencing and expression of rat liver 3-phosphoglycerate dehydrogenase. Biochem J 1997; 323 ( Pt 2):365-70. [PMID: 9163325 PMCID: PMC1218328 DOI: 10.1042/bj3230365] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Rat liver d-3-phosphoglycerate dehydrogenase was purified to homogeneity and digested with trypsin, and the sequences of two peptides were determined. This sequence information was used to screen a rat hepatoma cDNA library. Among 11 positive clones, two covered the whole coding sequence. The deduced amino acid sequence (533 residues; Mr 56493) shared closer similarity with Bacillus subtilis 3-phosphoglycerate dehydrogenase than with the enzymes from Escherichia coli, Haemophilus influenzae and Saccharomyces cerevisiae. In all cases the similarity was most apparent in the substrate- and NAD+-binding domains, and low or insignificant in the C-terminal domain. A corresponding 2.1 kb mRNA was present in rat tissues including kidney, brain and testis, whatever the dietary status, and also in livers of animals fed a protein-free, carbohydrate-rich diet, but not in livers of control rats, suggesting transcriptional regulation. The full-length rat 3-phosphoglycerate dehydrogenase was expressed in E. coli and purified. The recombinant enzyme and the protein purified from liver displayed hyperbolic kinetics with respect to 3-phosphoglycerate, NAD+ and NADH, but substrate inhibition by 3-phosphohydroxypyruvate was observed; this inhibition was antagonized by salts. Similar properties were observed with a truncated form of 3-phosphoglycerate dehydrogenase lacking the C-terminal domain, indicating that the latter is not implicated in substrate inhibition or in salt effects. By contrast with the bacterial enzyme, rat 3-phosphoglycerate dehydrogenase did not catalyse the reduction of 2-oxoglutarate, indicating that this enzyme is not involved in human D- or L-hydroxyglutaric aciduria.
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Affiliation(s)
- Y Achouri
- Laboratory of Physiological Chemistry, International Institute of Cellular and Molecular Pathology and Université Catholique de Louvain, B-1200 Brussels, Belgium
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Bottomley JR, Clayton CL, Chalk PA, Kleanthous C. Cloning, sequencing, expression, purification and preliminary characterization of a type II dehydroquinase from Helicobacter pylori. Biochem J 1996; 319 ( Pt 2):559-65. [PMID: 8912695 PMCID: PMC1217804 DOI: 10.1042/bj3190559] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A heat-stable dehydroquinase was purified to near homogeneity from a plate-grown suspension of the Gram-negative stomach pathogen Helicobacter pylori, and shown from both its subunit and native molecular masses to be a member of the type II family of dehydroquinases. This was confirmed by N-terminal amino acid sequence data. The gene encoding this activity was isolated following initial identification, by random sequencing of the H. pylori genome, of a 96 bp fragment, the translated sequence of which showed strong identity to a C-terminal region of other type II enzymes. Southern blot analysis of a cosmid library identified several potential clones, one of which complemented an Escherichia coli aroD point mutant strain deficient in host dehydroquinase. The gene encoding the H. pylori type II dehydroquinase (designated aroQ) was sequenced. The translated sequence was identical to the N-terminal sequence obtained directly from the purified protein, and showed strong identity to other members of the type II family of dehydroquinases. The enzyme was readily expressed in E. coli from a plasmid construct from which several milligrams of protein could be isolated, and the molecular mass of the protein was confirmed by electrospray MS. The aroQ gene in H. pylori may function in the central biosynthetic shikimate pathway of this bacterium, thus opening the way for the construction of attenuated strains as potential vaccines as well as offering a new target for selective enzyme inhibition.
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Affiliation(s)
- J R Bottomley
- School of Biological Sciences, University of East Anglia, Norwhich, U.K
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Lee PJ, Stock AM. Characterization of the genes and proteins of a two-component system from the hyperthermophilic bacterium Thermotoga maritima. J Bacteriol 1996; 178:5579-85. [PMID: 8824600 PMCID: PMC178394 DOI: 10.1128/jb.178.19.5579-5585.1996] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
As a step towards studying representative members of the two-component family of signal transduction proteins, we have cloned genes encoding a histidine protein kinase and a response regulator from the hyperthermophilic bacterium Thermotoga maritima. The genes have been designated HpkA and drrA, respectively. The deduced HpkA sequence contains all five characteristic histidine protein kinase motifs with the same relative order and spacing found in the mesophilic bacterial proteins. A hydropathy profile indicates that HpkA possesses only one membrane-spanning segment located at the extreme N terminus. The N-terminal region of DrrA exhibits all of the characteristics of the conserved domains of mesophilic bacterial response regulators, and the C-terminal region shows high similarity to the OmpR-PhoB subfamily of DNA-binding proteins. Recombinant T. maritima proteins, truncated HpkA lacking the putative membrane-spanning N- terminal amino acids and DrrA, were expressed in Escherichia coli. Partial purification of T. maritima proteins was achieved by heat denaturation of E. coli host proteins. In an in vitro assay, truncated HpkA protein was autophosphorylated in the presence of ATP. Thus, the N-terminal hydrophobic region is not required for kinase activity. Phosphotransfer between truncated HpkA and DrrA was demonstrated in vitro with the partially purified proteins. The phosphorylation reactions were strongly temperature dependent. The results indicate that the recombinant T. maritima two-component proteins overexpressed in E. coli are stable as well as enzymatically active at elevated temperatures.
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Affiliation(s)
- P J Lee
- Center for Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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35
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Kappes RM, Kempf B, Bremer E. Three transport systems for the osmoprotectant glycine betaine operate in Bacillus subtilis: characterization of OpuD. J Bacteriol 1996; 178:5071-9. [PMID: 8752321 PMCID: PMC178300 DOI: 10.1128/jb.178.17.5071-5079.1996] [Citation(s) in RCA: 185] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The accumulation of the osmoprotectant glycine betaine from exogenous sources provides a high degree of osmotic tolerance to Bacillus subtilis. We have identified, through functional complementation of an Escherichia coli mutant defective in glycine betaine uptake, a new glycine betaine transport system from B. subtilis. The DNA sequence of a 2,310-bp segment of the cloned region revealed a single gene (opuD) whose product (OpuD) was essential for glycine betaine uptake and osmoprotection in E. coli. The opuD gene encodes a hydrophobic 56.13-kDa protein (512 amino acid residues). OpuD shows a significant degree of sequence identity to the choline transporter BetT and the carnitine transporter CaiT from E. coli and a BetT-like protein from Haemophilus influenzae. These membrane proteins form a family of transporters involved in the uptake of trimethylammonium compounds. The OpuD-mediated glycine betaine transport activity in B. subtilis is controlled by the environmental osmolarity. High osmolarity stimulates de novo synthesis of OpuD and activates preexisting OpuD proteins to achieve maximal glycine betaine uptake activity. An opuD mutant was constructed by marker replacement, and the OpuD-mediated glycine betaine uptake activity was compared with that of the previously identified multicomponent OpuA and OpuC (ProU) glycine betaine uptake systems. In addition, a set of mutants was constructed, each of which synthesized only one of the three glycine betaine uptake systems. These mutants were used to determine the kinetic parameters for glycine betaine transport through OpuA, OpuC, and OpuD. Each of these uptake systems shows high substrate affinity, with Km values in the low micromolar range, which should allow B. subtilis to efficiently acquire the osmoprotectant from the environment. The systems differed in their contribution to the overall glycine betaine accumulation and osmoprotection. A triple opuA, opuC, and opuD mutant strain was isolated, and it showed no glycine betaine uptake activity, demonstrating that three transport systems for this osmoprotectant operate in B. subtilis.
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Affiliation(s)
- R M Kappes
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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Nakano MM, Zuber P, Glaser P, Danchin A, Hulett FM. Two-component regulatory proteins ResD-ResE are required for transcriptional activation of fnr upon oxygen limitation in Bacillus subtilis. J Bacteriol 1996; 178:3796-802. [PMID: 8682783 PMCID: PMC232639 DOI: 10.1128/jb.178.13.3796-3802.1996] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Bacillus subtilis can grow anaerobically in the presence of nitrate as a terminal electron acceptor. The two component regulatory proteins, ResD and ResE, and an anaerobic gene regulator, FNR, were previously shown to be indispensable for nitrate respiration in B. subtilis. Unlike Escherichia coli fnr, B. subtilis fnr transcription was shown to be highly induced by oxygen limitation. fnr is transcribed from its own promoter as well as from a promoter located upstream of narK, the first gene in the narK-fnr dicistronic operon. DNA fragments containing the narK promoter, the fnr promoter, and both of the promoters were used to construct three lacZ fusions to examine the transcriptional regulation of the narK-fnr operon. ResDE was found to be required for transcriptional activation of fnr from the fnr-specific promoter, and FNR was required for activation of narK-fnr transcription from the FNR-dependent narK operon promoter under anaerobiosis. In order to determine if the requirement for ResDE in nitrate respiration is solely to activate fnr transcription, fnr was placed under control of the IPTG (isopropyl-beta-D-thiogalactopyranoside)-inducible promoter, Pspac. The observed defect in anaerobic growth of a Pspac-fnr delta resDE mutant in the presence of IPTG indicated that resDE has an additional role in B. subtilis anaerobic gene regulation.
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Affiliation(s)
- M M Nakano
- Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, Shreveport, Louisiana 71130-3932, USA
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37
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Abstract
The international programme to sequence the 4.2 Mb genome of Bacillus subtilis, a model Gram-positive bacterium, is a joint project involving European, Japanese and US research groups. To date ca. 3.0 Mb of the genome has been sequenced, with the remaining 1.2 Mb expected to be completed in 1997. The amenability of B.subtilis to genetic manipulation, combined with the availability of extensive expertise on its biochemistry and physiology, makes this bacterium a valuable organism in which to investigate the properties of genes for which functions cannot be readily ascribed by standard methods.
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Affiliation(s)
- C R Harwood
- Department of Microbiology, School of Microbiological, Immunological and Virological Sciences, Medical School, University of Newcastle upon Tyne, UK.
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Sun G, Sharkova E, Chesnut R, Birkey S, Duggan MF, Sorokin A, Pujic P, Ehrlich SD, Hulett FM. Regulators of aerobic and anaerobic respiration in Bacillus subtilis. J Bacteriol 1996; 178:1374-85. [PMID: 8631715 PMCID: PMC177812 DOI: 10.1128/jb.178.5.1374-1385.1996] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Two Bacillus subtilis genes, designated resD and resE, encode proteins that are similar to those of two-component signal transduction systems and play a regulatory role in respiration. The overlapping resD-resE genes are transcribed during vegetative growth from a very weak promoter directly upstream of resD. They are also part of a larger operon that includes three upstream genes, resABC (formerly orfX14, -15, and -16), the expression of which is strongly induced postexponentially. ResD is required for the expression of the following genes: resA, ctaA (required for heme A synthesis), and the petCBD operon (encoding subunits of the cytochrome bf complex). The resABC genes are essential genes which encode products with similarity to cytochrome c biogenesis proteins. resD null mutations are more deleterious to the cell than those of resE. resD mutant phenotypes, directly related to respiratory function, include streptomycin resistance, lack of production of aa3 or caa3 terminal oxidases, acid accumulation when grown with glucose as a carbon source, and loss of ability to grow anaerobically on a medium containing nitrate. A resD mutation also affected sporulation, carbon source utilization, and Pho regulon regulation. The data presented here support an activation role for ResD, and to a lesser extent ResE, in global regulation of aerobic and anaerobic respiration i B.subtilis.
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Affiliation(s)
- G Sun
- Laboratory for Molecular Biology, Department of Biological Sciences, University of Illinois at Chicago 60607, USA
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Brunskill EW, Bayles KW. Identification and molecular characterization of a putative regulatory locus that affects autolysis in Staphylococcus aureus. J Bacteriol 1996; 178:611-8. [PMID: 8550490 PMCID: PMC177702 DOI: 10.1128/jb.178.3.611-618.1996] [Citation(s) in RCA: 157] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Previously in our laboratory, a PCR-based strategy was used to isolate potential sensor gene fragments from the Staphyloccus aureus genome. One DNA fragment was isolated that shared strong sequence similarity to genes encoding bacterial sensor proteins, indicating that it originated from within a potential staphylococcal sensor protein gene. In this study, the DNA surrounding the PCR product origin was cloned and sequenced. This analysis revealed the presence of two genes, termed lytS and lytR, whose deduced amino acid sequences were similar to those of members of the two-component regulatory system family of proteins. S. aureus cells containing an insertional disruption of lytS exhibited a marked propensity to form aggregates in liquid culture, suggesting that alterations in cell surface components exist in this strain. Transmission electron microscopic examination of these cells revealed that the cell surface was rough and diffuse and that a large proportion of the cell population had lysed. The lytS mutant also exhibited increased autolysis and an altered level of murein hydrolase activity produced compared with the parental strain, NCTC 8325-4. These data suggest that the lytS and lytR gene products control the rate of autolysis in S. aureus by affecting the intrinsic murein hydrolase activity associated with the cell.
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Affiliation(s)
- E W Brunskill
- Program in Molecular and Cell Biology, University of Maryland, Baltimore County 21228, USA
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Wei ZM, Beer SV. hrpL activates Erwinia amylovora hrp gene transcription and is a member of the ECF subfamily of sigma factors. J Bacteriol 1995; 177:6201-10. [PMID: 7592386 PMCID: PMC177461 DOI: 10.1128/jb.177.21.6201-6210.1995] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
hrpL of Erwinia amylovora Ea321 encodes a 21.7-kDa regulatory protein, similar to members of the ECF (extra cytoplasmic functions) subfamily of eubacterial RNA polymerase sigma factors. hrpL is a single-gene operon in complementation group VI of the E. amylovora hrp gene cluster. Its product is required by Ea321 to elicit the hypersensitive response (HR) and to cause disease. HrpL controls the expression of five independent hrp loci, including hrpN, which encodes harpin, a proteinaceous elicitor of the HR. hrpL is environmentally regulated, and its expression is affected by hrpS, another regulatory gene of the hrp gene cluster of E. amylovora. pCPP1078, a multicopy plasmid carrying hrpL, is able to restore HR-eliciting ability to hrpS mutants. A conserved motif was identified upstream of the hrpI and hrpN operons, which are transcriptionally regulated by hrpL. This conserved motif shares a high degree of similarity with other biochemically defined or putative ECF-dependent promoter sequences, including sequences upstream of Streptomyces coelicolor dagA P2, Pseudomonas aeruginosa algD, Pseudomonas syringae pv. syringae 61 hrpZ, and P. syringae pv. tomato avrD. In spite of the similarity between the hrpL genes of E. amylovora and P. syringae 61, no functional cross-complementation was observed.
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Affiliation(s)
- Z M Wei
- Department of Plant Pathology, Cornell University, Ithaca, New York 14853, USA
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Popham DL, Sengupta S, Setlow P. Heat, hydrogen peroxide, and UV resistance of Bacillus subtilis spores with increased core water content and with or without major DNA-binding proteins. Appl Environ Microbiol 1995; 61:3633-8. [PMID: 7486999 PMCID: PMC167661 DOI: 10.1128/aem.61.10.3633-3638.1995] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Spores of a Bacillus subtilis strain with an insertion mutation in the dacB gene, which codes for an enzyme involved in spore cortex biosynthesis, have a higher core water content than wild-type spores. Spores lacking the two major alpha/beta-type small, acid-soluble proteins (SASP) (termed alpha-beta- spores) have the same core water content as do wild-type spores, but alpha-beta- dacB spores had more core water than did dacB spores. The resistance of alpha-beta-, alpha-beta- dacB, dacB, and wild-type spores to dry and moist heat, hydrogen peroxide, and UV radiation has been determined, as has the role of DNA damage in spore killing by moist heat and hydrogen peroxide. These data (i) suggest that core water content has little if any role in spore UV resistance and are consistent with binding of alpha/beta-type SASP to DNA being the major mechanism providing protection to spores from UV radiation; (ii) suggest that binding of alpha/beta-type SASP to DNA is the major mechanism unique to spores providing protection from dry heat; (iii) suggest that spore resistance to moist heat and hydrogen peroxide is affected to a large degree by the core water content, as increased core water resulted in large decreases in spore resistance to these agents; and (iv) indicate that since this decreased resistance (i.e., in dacB spores) is not associated with increased spore killing by DNA damage, spore DNA must normally be extremely well protected against such damage, presumably by the saturation of spore DNA by alpha/beta-type SASP.
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Affiliation(s)
- D L Popham
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06030, USA
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Wong SL. Advances in the use of Bacillus subtilis for the expression and secretion of heterologous proteins. Curr Opin Biotechnol 1995; 6:517-22. [PMID: 7579663 DOI: 10.1016/0958-1669(95)80085-9] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During the past year, significant progress has been made using Bacillus subtilis to produce a wide range of foreign proteins. Through strain improvement and co-expression of molecular chaperones, secretory proteins can be produced at a higher level. Through protein engineering, target proteins can be redesigned to have better stability and solubility. A combination of these two strategies would be a useful approach to produce heterologous proteins from B. subtilis at high quality and with a high yield.
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Affiliation(s)
- S L Wong
- Department of Biological Science, University of Calgary, Alberta, Canada
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Enz S, Braun V, Crosa JH. Transcription of the region encoding the ferric dicitrate-transport system in Escherichia coli: similarity between promoters for fecA and for extracytoplasmic function sigma factors. Gene 1995; 163:13-8. [PMID: 7557462 DOI: 10.1016/0378-1119(95)00380-o] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We have analyzed the molecular mechanism of regulation of the ferric dicitrate transport system in Escherichia coli (Ec), by studying the transcription of the regulatory and structural genes under various environmental conditions, and by determining the location of their transcriptional start points and promoter regions. We report here that the main species observed in Northern hybridization analyses were a 2.5-kb mRNA, encoded by the outer membrane protein receptor gene fecA, and a 1.5-kb mRNA encoded by a region including the fecIR genes. The synthesis of the 2.5-kb fecA mRNA is regulated by both citrate and iron. Furthermore, transcription of fecA is dependent on the presence of FecI. The promoter region for the fecA mRNA, a likely site of action for FecI, is not related to the consensus promoter region for sigma 70 RNA polymerase in Ec K-12. However, it shows greatest similarity with promoters of genes regulated by a new sub-family of sigma factors, i.e., the extracytoplasmic function (ECF) sigma factors, which are associated with the expression of genes involved in extracytoplasmic functions, suggesting that FecI may act as a specialized sigma factor. We also show that the fecB,C,D,E transport genes are linked in operon fashion to fecA. Since the levels of the fecB,C,D,E RNAs are extremely low, as compared to the level of fecA mRNA, it is likely that processing from the 3' end must occur and stop near the end of fecA where a hairpin structure is located.
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Affiliation(s)
- S Enz
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health Sciences University, Portland 97201-3098, USA
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Popham DL, Illades-Aguiar B, Setlow P. The Bacillus subtilis dacB gene, encoding penicillin-binding protein 5*, is part of a three-gene operon required for proper spore cortex synthesis and spore core dehydration. J Bacteriol 1995; 177:4721-9. [PMID: 7642500 PMCID: PMC177238 DOI: 10.1128/jb.177.16.4721-4729.1995] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Studies of gene expression using fusions to lacZ demonstrated that the Bacillus subtilis dacB gene, encoding penicillin-binding protein 5*, is in an operon with two downstream genes, spmA and spmB. Mutations affecting any one of these three genes resulted in the production of spores with reduced heat resistance. The cortex peptidoglycan in dacB mutant spores had more peptide side chains, a higher degree of peptide cross-linking, and possibly less muramic acid lactam than that of wild-type spores. These cortex structure parameters were normal in spmA and spmB mutant spores, but these spores did not attain normal spore core dehydration. This defect in spore core dehydration was exaggerated by the additional loss of dacB expression. However, loss of dacB alone did not alter the spore core water content. Spores produced by spmA and spmB mutants germinated faster than did those of the wild type. Spores produced by dacB mutants germinated normally but were delayed in spore outgrowth. Electron microscopy revealed a drastically altered appearance of the cortex in dacB mutants and a minor alteration in an spmA mutant. Measurements of electron micrographs indicate that the ratio of the spore protoplast volume to the sporoplast (protoplast-plus-cortex) volume was increased in dacB and spmA mutants. These results are consistent with spore core water content being the major determinant of spore heat resistance. The idea that loosely cross-linked, flexible cortex peptidoglycan has a mechanical activity involved in achieving spore core dehydration is not consistent with normal core dehydration in spores lacking only dacB.
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Affiliation(s)
- D L Popham
- Department of Biochemistry, University of Connecticut Health Center, Farmington 06030-3305, USA
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Helmann JD. Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res 1995; 23:2351-60. [PMID: 7630711 PMCID: PMC307037 DOI: 10.1093/nar/23.13.2351] [Citation(s) in RCA: 304] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Sequence analysis of 236 promoters recognized by the Bacillus subtilis sigma A-RNA polymerase reveals an extended promoter structure. The most highly conserved bases include the -35 and -10 hexanucleotide core elements and a TG dinucleotide at position -15, -14. In addition, several weakly conserved A and T residues are present upstream of the -35 region. Analysis of dinucleotide composition reveals A2- and T2-rich sequences in the upstream promoter region (-36 to -70) which are phased with the DNA helix: An tracts are common near -43, -54 and -65; Tn tracts predominate at the intervening positions. When compared with larger regions of the genome, upstream promoter regions have an excess of An and Tn sequences for n > 4. These data indicate that an RNA polymerase binding site affects DNA sequence as far upstream as -70. This sequence conservation is discussed in light of recent evidence that the alpha subunits of the polymerase core bind DNA and that the promoter may wrap around RNA polymerase.
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Affiliation(s)
- J D Helmann
- Section of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA
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Abstract
The members of the bacterial genus Bacillus are important organisms for both research and industrial purposes, and a major international effort is under way to sequence the complete genome of Bacillus subtilis, the type species for this genus. In this article the organization of the project is summarized; the strategies employed for cloning, sequencing and data handling; the progress to date, and the likely benefits which will accrue to basic research and to the biotechnology industry upon completion of the sequence.
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Affiliation(s)
- K M Devine
- Department of Genetics, Trinity College, Dublin 2, Ireland
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Affiliation(s)
- M Fonstein
- Department of Molecular Genetics and Cell Biology, University of Chicago, Illinois 60637, USA
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Abe A, Koide H, Kohno T, Watabe K. A Bacillus subtilis spore coat polypeptide gene, cotS. MICROBIOLOGY (READING, ENGLAND) 1995; 141 ( Pt 6):1433-1442. [PMID: 7545510 DOI: 10.1099/13500872-141-6-1433] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A gene, cotS, encoding a spore coat polypeptide of Bacillus subtilis, was isolated from an EcoRI fragment (5.4 kb) of the chromosome by using synthetic oligonucleotide probes corresponding to the NH2-terminal amino acid sequence of Cot40-2 previously purified from the spore coat of B. subtilis. The nucleotide sequence (2603 bp) was determined and sequence analysis suggested the presence of two contiguous ORFs, ORF X and cotS, followed by the 5'-region of an additional ORF, ORF Y, downstream of cotS. The cotS gene is 1053 nucleotides long and encodes a polypeptide of 351 amino acids with a predicted molecular mass of 41083 Da. The predicted amino acid sequence was in complete agreement with the NH2-terminal amino acid sequence of Cot40-2. The orfX gene is 1131 nucleotides long and encodes a polypeptide of 377 amino acids with a predicted molecular mass of 42911 Da. The gene product of cotS was confirmed to be identical to Cot40-2 by SDS-PAGE and immunoblotting from Escherichia coli transformed with a plasmid containing the cotS region. Northern hybridization analysis indicated that a transcript of cotS and orfX appeared at about 5 h after the onset of sporulation. The transcriptional start point determined by primer extension analysis suggested that -10 and -35 regions are present upstream of orfX and are very similar to the consensus sequence for the sigma k-dependent promoter. Terminator-like sequences were not found in the DNA fragment (2603 bp) sequenced in this paper, which suggested that the cotS locus may be part of a multicistronic operon. The cotS gene is located between dnaB and degQ at about 270-275 degrees on the genetic map. Insertional mutagenesis of the cotS gene by introducing an integrative plasmid resulted in no alteration of growth or sporulation, and had no effect on germination or resistance to chloroform.
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Affiliation(s)
- Akiko Abe
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka 573-01, Japan
| | - Hidekatsu Koide
- Meditopia Research Center, 43-6, Hongo 3-chome, Bunkyo-ku, Tokyo 113, Japan
| | - Takeyuki Kohno
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka 573-01, Japan
| | - Kazuhito Watabe
- Faculty of Pharmaceutical Sciences, Setsunan University, 45-1, Nagaotoge-cho, Hirakata, Osaka 573-01, Japan
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Bonner CA, Jensen RA. Cloning of cDNA encoding the bifunctional dehydroquinase.shikimate dehydrogenase of aromatic-amino-acid biosynthesis in Nicotiana tabacum. Biochem J 1994; 302 ( Pt 1):11-4. [PMID: 8067995 PMCID: PMC1137184 DOI: 10.1042/bj3020011] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Nicotiana tabacum cDNA encoding a bifunctional protein having catalytic domains for dehydroquinase and shikimate dehydrogenase was cloned and sequenced. Complementation of Escherichia coli aroD and aroE auxotrophs was successful. Amino acid sequencing located the N-terminus of the mature protein. The two catalytic domains exhibited greater amino acid identity with prokaryote homologues than with yeast and fungal homologues.
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Affiliation(s)
- C A Bonner
- Department of Microbiology and Cell Science, University of Florida, Gainesville 32611-0100
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Lonetto MA, Brown KL, Rudd KE, Buttner MJ. Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial RNA polymerase sigma factors involved in the regulation of extracytoplasmic functions. Proc Natl Acad Sci U S A 1994; 91:7573-7. [PMID: 8052622 PMCID: PMC44444 DOI: 10.1073/pnas.91.16.7573] [Citation(s) in RCA: 365] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
sigma E, an RNA polymerase sigma factor of apparent M(r) 28,000, was previously identified by its ability to direct transcription from the P2 promoter of the agarose gene (dagA) of Streptomyces coelicolor. A degenerate oligonucleotide probe, designed from the N-terminal sequence of purified sigma E, was used to isolate the sigma E gene (sigE). The predicted sequence of sigma E shows greatest similarity to sequences of seven other proteins: Myxococcus xanthus CarQ, Pseudomonas aeruginosa AlgU, Pseudomonas syringae HrpL, Escherichia coli sigma E, Alcaligenes eutrophus CnrH, E. coli FecI, and Bacillus subtilis SigX, a protein of unknown function. These eight proteins define a subfamily of eubacterial RNA polymerase factors sufficiently different from other sigma s that, in many cases, they are not identified by standard similarity searching methods. Available information suggests that all of them regulate extracytoplasmic functions and that they function as effector molecules responding to extracytoplasmic stimuli. A. eutrophus CnrH appears to be a plasmid-encoded factor.
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Affiliation(s)
- M A Lonetto
- Department of Stomatology, University of California at San Francisco 94143-0512
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