Summary
A combination of cosmid genome walking and pulse field gel electrophoresis was used to construct a high resolution physical and genetic map of the 3.8 Mb genome of Rhodobacter capsulatus SB1003. The mapping was done by grouping and further mapping of cosmids and bacteriophages from genomic libraries using PFGE-generated DNA fragments and SP6 and T7 specific transcripts corresponding to the ends of the cosmid inserts. Cosmid and phage clones formed two uninterrupted and ordered groups, one corresponding to the chromosome of Rb. capsulatus, the other to its 134 kb plasmid. Cos site end-labeling and partial EcoRV digestion of cosmids were used to construct a high resolution restriction map of the genome. Overlapping of the cosmids was confirmed by the resemblance of the cosmid restriction maps and by direct end-to-end hybridization. 34 genes or gene clusters were located in the ordered gene library and mapped with an accuracy of 1–10 kb. Three Rb. capsulatus strains; KB-1, St. Louis and 2.3.1., were chosen out of 14 others for a detailed comparison of their physical maps, which were partially constructed using the minimal cosmid set of Rb. capsulatus SB1003 as a source of ordering probes. Blots of the minimal set of 192 cosmids, covering the chromosome and the plasmid, with known map position of each cosmid, gives to Rb. capsulatus the same advantages that the Kohara phage panel gives to E. coli. Blots of this minimal cosmid set digested with EcoRV represent the entire genome split into gene-size pieces, and provide an opportunity for direct high resolution mapping of genes and transcripts.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Armstrong GA, Alberti M, Leach F and Hearst JE (1989) Nucleotide sequence, organization, and nature of the protein products of the carotenoid biosynthesis gene cluster of Rhodobacter capsulatus. Mol Gen Genet 216:254–268
Armstrong GA, Schmidt A, Sandmann G and Hearst JE (1990) Genetic and biochemical characterization of carotenoid biosynthesis mutants of Rhodobacter capsulatus. J Biol Chem 265:8329–8338
Bauer C, Buggy J and Mosley C (1993) Control of photosystem genes in Rhodobacter capsulatus. Trends Genet 9:56–60
Becker RM, Young DA and Marrs BL (1992) Sequence of the indoleglycerol phosphate synthase (trpC) gene from Rhodobacter capsulatus. J Bacteriol 174:5482–5484
Beckman DL and Kranz RG (1991a) A bacterial homolog to HPRT. Biochim Biophys Acta 1129:112–114
Beckman DL and Kranz RG (1991b) A bacterial homolog to the mitochondrial enoyl-CoA hydratase. Gene 107:171–172
Beckman DL and Kranz RG (1993) Cytochromes c biogenesis in a photosynthetic bacterium requires a periplasmic thioredoxin-like protein. Proc Natl Acad Sci U S A 90:2179–2183
Beckman DL, Trawick DR and Kranz RG (1992) Bacterial cytochromes c biogenesis. Genes Dev 6:268–283
Biel AJ (1992) Oxygen-regulated steps in the Rhodobacter capsulatus tetrapyrrole biosynthetic pathway. J Bacteriol 174:5272–5274
Buggy JJ, Sganga MW and Bauer CE (1994a) Nucleotide sequence and characterization of the Rhodobacter capsulatus hvrB gene: HvrB is an activator of S-adenosyl-L-homocysteine hydrolase expression and is a member of the LysR family. J Bacteriol 176:61–69
Buggy JJ, Sganga MW and Bauer CE (1994b) Characterization of a light responding trans-activator responsible for differentially controlling reaction center and light harvesting-I gene expression in R. capsulatus. J Bacteriol 176:6936–6943
Chuang EC and Blattner FR (1993) Characterization of twenty six new heat shock genes of Escherichia coli. J Bacteriol 175:5242–5252
Chuang SE, Daniels DL and Blattner FR (1993) Global regulation of gene expression in Escherichia coli. J Bacteriol 175:2026–2036
Colbeau A, Richaud P, Toussaint B, Caballero J, Elster C, Delphin C, Smith RL, Chabert J and Vignais PM (1993) Organization of the genes necessary for hydrogenase expression in Rhodobacter capsulatus. Sequence analysis and identification of two hyp regulatory mutants. Mol Microbiol 8: 15–29
Daldal F, Cheng S, Applebaum J, Davidson E and Prince RC (1986) Cytochrome c2 is not essential for photosynthetic growth of Rhodopseudomonas capsulata. Proc Natl Acad Sci USA 83:2012–2016
Daniels GA, Drews G and Saier MJ (1988) Properties of a Tn5 insertion mutant defective in the structural gene (fruA) of the fructose-specific phosphotransferase system of Rhodobacter capsulatus and cloning of the fru regulon. J Bacteriol 170:1698–1703
Davidson E and Daldal F (1987a) fbc operon, encoding the Rieske Fe-S protein cytochrome b, and cytochrome c1 apoproteins previously described from Rhodopseudomonas sphaeroides, is from Rhodopseudomonas capsulata. J Mol Biol 195:25–29
Davidson E and Daldal F (1987b) Primary structure of the bc1 complex of Rhodopseudomonas capsulata. Nucleotide sequence of the pet operon encoding the Rieske cytochrome b, and cytochrome c1 apoproteins. J Mol Biol 19:513–524
Donohue TJ and Kaplan S (1991) Genetic techniques in Rhodospirillaceae. Methods Enzymol 204:459–485
Fonstein M and Haselkorn R (1993) Chromosomal structure of Rhodobacter capsulatus strain SB 1003: cosmid encyclopedia and high-resolution physical and genetic map. Proc Natl Acad Sci USA 90:2522–2526
Fonstein M, Zheng S and Haselkorn R (1992) Physical map of the genomeof Rhodobacter capsulatus SB 1003. J Bacteriol 174:4070–4077
Fonstein M, Koshy EG, Nikolskaya T, Mourachov P and Haselkorn R (1995a) Refinement of the high-resolution physical and genetic map of Rhodobacter capsulatus and genome surveys using blots of the cosmid encyclopedia. EMBO J 14: 1827–1841
Fonstein M, Nikolskaya T and Haselkorn R (1995b) High-resolution alignment of a 1-megabase-long genome region of three strains of Rhodobacter capsulatus. J Bacteriol 177: 2368–2372
Gibson JL, Falcone DL and Tabita FR (1991) Nucleotide sequence, transcriptional analysis, and expression of genes encoded within the form I fixation operon of Rhodobacter sphaeroides. J Biol Chem 266:14646–4653
Hamblin MJ, Shaw JG and Kelly DJ (1993) Sequence analysis and interposon mutagenesis of a sensor-kinase (DctS) and response-regulator (DctR) controlling synthesis of the high-affinity C4-dicarboxylate transport system in Rhodobacter capsulatus. Mol Gen Genet 237:215–224
Johnson JA, Wong WK and Beatty JT (1986) Expression of cellulase genes in Rhodobacter capsulatus by use of plasmid expression vectors. J Bacteriol 167:604–610
Jones R and Haselkorn R (1989) The DNA sequence of the Rhodobacter capsulatus ntrA, ntrB and ntrC gene analogues required for nitrogen fixation. Mol Gen Genet 215:507–516
Klipp W, Masepohl B and Puhler A (1988) Identification and mapping of nitrogen fixation genes of Rhodobacter capsulatus: duplication of a nifA-nifB region. J Bacteriol 170:693–699
Kranz RG, Pace VM and Caldicott IM (1990) Inactivation, sequence, and lacZ fusion analysis of a regulatory locus required for repression of nitrogen fixation genes in Rhodobacter capsulatus. J Bacteriol 172:53–62
Kranz RG, Beckman DL and Foster HD (1992) DNA gyrase activities from Rhodobacter capsulatus: analysis of target(s) of coumarins and cloning of the gyrB locus. FEMS Microbiol Lett 72:25–32
Marrs B (1981) Mobilization of the genes for photosynthesis from Rhodopseudomonas capsulata by a promiscuous plasmid. J Bacteriol 146:1003–1012
Mosely CS, Suzuki JY and Bauer CE (1994) Identification and molecular genetic characterization of a sensor kinase responsible for coordinately regulating light harvesting and reaction center gene expression in response to anaerobiosis. J Bacteriol 176: 7566–7573
Preker P, Hubner P, Schmehl M, Klipp W and Bickle TA (1992) Mapping and characterization of the promoter elements of the regulatory nif genes rpoN, nifA1 and nifA2 in Rhodobacter capsulatus. Mol Microbiol 6:1035–1047
Regensburger A, Ludwig W, Frank R, Blocker H and Schleifer KH (1988) Complete nucleotide sequence of a 23S ribosomal RNA gene from Micrococcus luteus. Nucleic Acids Res 16:2344
Saeki K, Miyatake Y, Young DA, Marrs BL and Matsubara H (1990) A plant-ferredoxin-like gene is located upstream of ferredoxin I gene (fdxN) of Rhodobacter capsulatus. Nucleic Acids Res 18:1060
Sganga MW and Bauer CE (1992) Regulatory factors controlling photosynthetic reaction center and light-harvesting gene expression in Rhodobacter capsulatus. Cell 68:945–954
Sganga MW, Aksamit RR, Cantoni GL and Bauer CE (1992) Mutational and nucleotide sequence analysis of S-adenosyl-L-homocysteine hydrolase from Rhodobacter capsulatus. Proc Natl Acad Sci USA 89:6328–6332
Shaw JG, Hamblin MJ and Kelly DJ (1991) Purification, characterization and nucleotide sequence of the periplasmic C4-dicarboxylate-binding protein (DctP) from Rhodobacter capsulatus. Mol Microbiol 5:3055–3062
Tichy HV, Oberle B, Stiehle H, Schiltz E and Drews G (1989) Genes downstream from pucB and pucA are essential for formation of the B800-850 complex of Rhodobacter capsulatus. J Bacteriol 171:4914–4922
Tichy HV, Albien KU, Gad’on N and Drews G (1991) Analysis of the Rhodobacter capsulatus puc operon: the pucC gene plays a central role in the regulation of LHII (B800-850 complex) expression. EMBO J 10:2949–2955
Tokito MK and Daldal F (1992) petR, located upstream of the fbc FBC operon encoding the cytochrome bc1 complex, is homologous to bacterial response regulators and necessary for photosynthetic and respiratory growth of Rhodobacter capsulatus. Mol Microbiol 6:1645–1654
Wellington CL and Beatty JT (1989) Promoter mapping and nucleotide sequence of the bchC bacteriochlorophyll biosynthesis gene from Rhodobacter capsulatus. Gene 83:251–261
Willison JC (1992) An essential gene (efg) located at 38.1 minutes on the Escherichia coli chromosome. J Bacteriol 174:5765–5766
Willison JC (1993) Biochemical genetics revisited: the use of mutants to study carbon and nitrogen metabolism in the photosynthetic bacteria. FEMS Microbiol Rev 10:1–38
Willison JC, Ahombo G, Chabert J, Magnin JP and Vignais PM (1985) Genetic mapping of Rhodopseudomonas capsulata chromosome shows non-clustering of genes involved in nitrogen fixation. J Gen Microbiol 131:3001–3015
Wright MS, Eckert JJ, Biel SW and Biel AJ (1991) Use of a lacZ fusion to study transcriptional regulation of the Rhodobacter capsulatus hemA gene. FEMS Microbiol Lett 62:339–342
Wu LF and Saier MJ (1990) Nucleotide sequence of the fruA gene, encoding the fructose permease of the Rhodobacter capsulatus phosphotransferase system, and analyses of the deduced protein sequence. J Bacteriol 172:7167–7178
Wu LF, Tomich JM and Saier MJ (1990) Structure and evolution ofa multidomain multiphosphoryl transfer protein. Nucleotide sequence of the fruB(HI) gene in Rhodobacter capsulatus and comparisons with homologous genes from other organisms. J Mol Biol 213:687–703
Yen HC and Marrs B (1976) Map of genes for carotenoid and bacteriochlorophyll biosynthesis in Rhodopseudomonas capsulata. J Bacteriol 126:619–629
Yen HC, Hu NT and Marrs BL (1979) Characterization of the gene transfer agent made by an overproducer mutant of Rhodopseudomonas capsulata. J Mol Biol 131:157–168
Youvan DC, Bylina EJ, Alberti M, Begusch H and Hearst JE (1984) Nucleotide and deduced polypetide sequences of the photosynthetic reacton-center, B870 antenna, and flanking polypeptides from R. capsulata. Cell 37:949–957
Zhu YS and Hearst JE (1986) Regulation of expression of genes for light-harvesting antenna proteins LH-I and LH-II; reaction center polypeptides RC-L, RC-M, and RC-H; and enzymes of bacteriochlorophyll and carotenoid biosynthesis in Rhodobacter capsulatus by light and oxygen. Proc Natl Acad Sci USA 83: 7613–7617
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1995 Kluwer Academic Publishers
About this chapter
Cite this chapter
Fonstein, M., Haselkorn, R. (1995). Physical Mapping of Rhodobacter capsulatus: Cosmid Encyclopedia and High Resolution Genetic Map. In: Blankenship, R.E., Madigan, M.T., Bauer, C.E. (eds) Anoxygenic Photosynthetic Bacteria. Advances in Photosynthesis and Respiration, vol 2. Springer, Dordrecht. https://doi.org/10.1007/0-306-47954-0_49
Download citation
DOI: https://doi.org/10.1007/0-306-47954-0_49
Publisher Name: Springer, Dordrecht
Print ISBN: 978-0-7923-3681-5
Online ISBN: 978-0-306-47954-0
eBook Packages: Springer Book Archive