Diverse Organization of Genes of the β-Ketoadipate Pathway in Members of the Marine Roseobacter Lineage

Applied and Environmental Microbiology

Volumn 70, Issue 3, 2004, Pages 1658-1668

  Buchan, Alison ^a,b   Neidle, Ellen L ^a   Moran, Mary Ann ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AROMATIC COMPOUNDS; ECOLOGY; ECOSYSTEMS; GENES; LIGNIN; MICROBIOLOGY; REACTION KINETICS;

GENE ORGANIZATION; GENE SEQUENCES;

BACTERIA;

3 OXOADIPIC ACID; 3,4 DIOXYGENASE; ADIPIC ACID DERIVATIVE; AROMATIC COMPOUND; LIGNIN; OXYGENASE; PROTOCATECHUIC ACID; RIBOSOME RNA; UNCLASSIFIED DRUG;

MICROBIOLOGY;

ARTICLE; BACTERIAL GENE; GENE CLUSTER; GENE SEQUENCE; GENETIC ORGANIZATION; GENOMIC FRAGMENT; GRAM NEGATIVE BACTERIUM; OPEN READING FRAME; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; ROSEOBACTER; SEQUENCE ANALYSIS; SILICIBACTER POMEROYI;

ADIPIC ACIDS; BASE SEQUENCE; DNA, BACTERIAL; ECOSYSTEM; ESCHERICHIA COLI; GENE EXPRESSION; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RESTRICTION MAPPING; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; ROSEOBACTER; SPECIES SPECIFICITY;

ALPHAPROTEOBACTERIA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROKARYOTA; ROSEOBACTER; SILICIBACTER; SILICIBACTER POMEROYI DSS-3;

EID: 1642359998     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.70.3.1658-1668.2004     Document Type: Article

References (49)

1. Ampe, F., and N. D. Lindley. 1995. Acetate utilization is inhibited by benzoate in Alcaligenes eutrophus: evidence for transcriptional control of the expression of acoE coding for acetyl coenzyme A synthetase. J. Bacteriol. 177:5826-5833.
2. Bradford, M. M. 1976, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
3. Brzostowicz, P. C., A. B. Reams, T. J. Clark, and E. L. Neidle. 2003. Transcriptional cross-regulation of the catechol and protocatechuate branches of the β-ketoadipate pathway contributes to carbon source-dependent expression of the Acinetobacter sp. strain ADP1 pobA gene. Appl. Environ. Microbiol. 69:1598-1606.
4. Buchan, A., L. S. Collier, E. L. Neidle, and M. A. Moran. 2000. Key aromaticring-cleaving enzyme, protocatechuate 3,4-dioxygenase, in the ecologically important marine Roseobacter lineage. Appl. Environ. Microbiol. 66:4662-4672.
5. Buchan, A., E. L. Neidle, and M. A. Moran. 2001. Diversity of the ring-cleaving dioxygenase gene pcaH in a salt marsh bacterial community. Appl. Environ. Microbiol. 67:5801-5809.
6. Coco, W. M., R. K. Rothmel, S. Henikoff, and A. M. Chakrabarty. 1993. Nucleotide sequence and initial functional characterization of the clcR gene encoding a LysR family activator of the clcABD chlorocatechol operon in Pseudomonas putida. J. Bacteriol. 175:417-427.
7. Collier, L. S., G. L. Gaines, and E. L. Neidle. 1998. Regulation of benzoate degradation in Acinetobacter sp. strain ADP1 by BenM, a LysR-type transcriptional activator. J. Bacteriol. 180:2493-2501.
8. Dal, S., I. Steiner, and U. Gerischer. 2002. Multiple operons connected with catabolism of aromatic compounds in Acinetobacter sp. strain ADP1 are under carbon catabolite repression. J. Mol. Microbiol. Biotechnol. 4:389-404.
9. Dang, H. Y., and C. R. Lovell. 2000. Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl. Environ. Microbiol. 66:467-475.
10. D'Argenio, D. A., M. W. Vetting, D. H. Ohlendorf, and L. N. Ornston. 1999. Substitution, insertion, deletion, suppression, and altered substrate specificity in functional protocatechuate 3,4-dioxygenases. J. Bacteriol. 181:6478-6487.
11. Dykhuizen, D. E., and L. Green. 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173:7257-7268.
12. Eulberg, D., S. Lakner, L. A. Golovieva, and M. Schlömann. 1998. Characterization of a protocatechuate catabolic gene cluster from Rhodococcus opacus ICP: evidence for a merged enzyme with. 4-carboxymuconolactone-decarboxylating and 3-oxoadipate enol-lactone-hydrolyzing activity. J. Bacteriol. 180:1072-1081.
13. Felsenstein, J. 1989. PHYLIP-Phylogeny Inference Package (version 3.2). Cladistics 5:164-166.
14. Fuhrman, J. A., S. H. Lee, Y. Masuchi, A. A. Davis, and R. M. Wilcox. 1994. Characterization of marine prokaryotic communities via DNA and RNA. Microb. Ecol. 28:133-145.
15. Gaines, G. L., L. Smith, and E. L. Neidle. 1996. Novel nuclear magnetic resonance spectroscopy methods demonstrate preferential carbon utilization by Acinetobacter calcoaceticus. J. Bacteriol. 178:6833-6841.
16. González, J. M., J. S. Covert, W. B. Whitman, J. Henriksen, F. Mayer, B. Scharf, R. Schmitt. A. Buchan, J. A. Fuhrman, R. P. Kiene, and M. A. Moran. 2003. Silicibacter pomeroyi sp. nov. and Roseovarius nubinhibens sp. nov., two dimethylsulfoniopropionate-demethylating bacteria from marine environments. Int. J. Syst. Evol. Microbiol. 53:1261-1269.
17. González, J. M., R. P. Kiene, and M. A. Moran. 1999. Transformations of sulfur compounds by an abundant lineage of marine bacteria in the α-subclass of the class Proteobacteria. Appl. Environ. Microbiol. 65:3810-3819.
18. González, J. M., F. Mayer, M. A. Moran, R. E. Hodson, and W. B. Whitman. 1997. Sagittula stellata gen. nov., sp. nov., a lignin-transforming bacterium from a coastal environment. Int. J. Syst. Bacteriol. 47:773-780.
19. González, J. M., and M. A. Moran. 1997. Numerical dominance of a group of marine bacteria in the α-subclass of the class Proteobacteria in coastal seawater. Appl. Environ. Microbiol. 63:4237-4242.
20. González, J. M., W. B. Whitman, R. E. Hodson, and M. A. Moran. 1996. Identifying numerically abundant culturable bacteria from complex communities: an example from a lignin enrichment culture. Appl. Environ. Microbiol. 62:4433-4440.
21. Grassly, N. C., and E. C. Holmes. 1997. A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol. Biol. Evol. 14:239-247.
22. Hartnett, G. B., B. Averhoff, and L. N. Ornston. 1990. Selection of Acinetobacter calcoaceticus mutants deficient in the p-hydroxybenzoate hydroxylase gene (pobA), a member of a supraoperonic cluster. J. Bacteriol. 172:6160-6161.
23. Hartnett, G. B., and L. N. Ornston. 1994. Acquisition of apparent DNA slippage structures during extensive evolutionary divergence of pcaD and catD genes encoding identical catalytic activities in Acinetobacter calcoaceticus. Gene 142:23-29.
24. Harwood, C. S., and R. E. Parales. 1996. The β-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol. 50:553-590.
25. Itoh, T., K. Takemoto, H. Mori, and T. Gojobori. 1999. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol. 16:332-346.
26. Lawrence, J. G., and J. R. Roth. 1996. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843-1860.
27. Matrubutham, U., and A. R. Harker. 1994. Analysis of duplicated gene sequences associated with tfdR and tfdS in Alicaligenes eutrophus JMP34. J. Bacteriol. 176:2348-2353.
28. Mullins, T. D., T. B. Britschgi, R. L. Krest, and S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankon communities. Limnol. Oceanogr. 40:148-158.
29. Nichols, N. N., and C. S. Harwood. 1995. Repression of 4-hydroxybenzoate transport and degradation by benzoate: a new layer of regulatory control in the Pseudomonasputida β-ketoadipate pathway. J. Bacteriol. 177:7033-7040.
30. 3+ ligand displacement in response to substrate binding. Biochemistry 36:10052-10066.
31. Pao, S. S., I. T. Paulsen, and M. H. Saier. 1998. Major facilitator superfamily. Microbiol. Mol. Biol. Rev. 62:1-34.
32. Parales, R. E., and C. S. Harwood. 1993. Regulation of the pcaIJ genes for aromatic acid degradation in Pseudomonas putida. J. Bacteriol. 175:5829-5838.
33. Parke, D. 1996. Characterization of PcaQ, a LysR-type transcriptional activator required for catabolism of phenolic compounds in Agrobacterium tumefaciens. J. Bacteriol. 178:266-272.
34. Parke, D. 1997. Acquisition, reorganization, and merger of genes: novel management of the β-ketoadipate pathway in Agrobacterium tumefaciens. FEMS Microbiol. Lett. 146:3-12.
35. Parke, D., D. A. D'Argenio, and L. N. Ornston. 2000. Bacteria are not what they eat: that is why they are so diverse. J. Bacteriol. 182:257-263.
36. Parke, D., and L. N. Ornston. 2003. Hydroxycinnamate (hca) catabolic genes from Acinetobacter sp. strain ADP1 are repressed by HcaR and are induced by hydroxycinnamoyl-coenzyme A thioesters. Appl. Environ. Microbiol. 69: 5398-5409.
37. Pathak, D., G. Ashley, and D. Ollis. 1991. Thiol protease-like active site found in the enzyme dienelactone hydrolase - localization using biochemical, genetic and structural tools. Proteins 9:267-279.
38. Petersen, E. I., J. Zuegg, D. W. Ribbons, and H. Schwab. 1996. Molecular cloning and homology modeling of protocatechuate 3,4-dioxygenase from Pseudomonas marginata. Microbiol. Res. 151:359-370.
39. Reams, A. B., and E. L. Neidle. 2003. Genome plasticity in Acinetobacter: new degradative capabilities acquired by spontaneous amplification of large chromosomal segments. Mol. Microbiol. 47:1291-1304.
40. Rothmel, R. K., T. L. Aldrich, J. E. Houghton, W. M. Coco, L. N. Ornston, and A. M. Chakrabarty. 1990. Nucleotide sequencing and characterization of Pseudomonas putida catR: a postive regulator of the catBC operon is a member of the LysR family. J. Bacteriol. 172:922-931.
41. Schell, M. A. 1993. Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol. 47:597-626.
42. Shanley, M. S., E. L. Neidle, R. E. Parales, and L. N. Ornston. 1986. Cloning and expression of Acinetobacter calcoaceticus catBCDE genes in Pseudomonas putida and Escherichia coli. J. Bacteriol. 165:557-563.
43. Sorokin, D. Y., and A. M. Lysenko. 1993. Heterotrophic bacteria from the Black Sea oxidizing reduced sulfur compounds to sulfate. Mikrobiologiya 62:1018-1031.
44. Stanier, R. Y., and J. L. Ingraham. 1954. Protocatechuic acid oxidase. J. Biol. Chem. 210:799-808.
45. Suzuki, M. T., M. S. Rappé, Z. W. Haimberger, H. Winfield, N. Adair, J. Ströbel, and S. J. Giovannoni. 1997. Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample. Appl. Environ. Microbiol. 63:983-989.
46. Van Berkel, W., A. Westphal, K. Eschrich, M. Eppink, and A. Dekok. 1992. Substitution of Arg214 at the substrate-binding site of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens. Eur. J. Biochem. 210:411-419.
47. van der Meer, J. R., A. C. Frijters, J. H. Leveau, R. I. Eggen, A. J. Zehnder, and W. M. de Vos. 1991. Characterization of the Pseudomonas sp. strain P51 gene tcbR, a LysR-type transcriptional activator of the tcbCDEF chlorocatechol oxidative operon, and analysis of the regulatory region. J. Bacteriol. 173:3700-3708.
48. Vetting, M. W., D. A. D'Argenio, L. N. Ornston, and D. H. Ohlendorf. 2000. Structure of Acinetobacter strain ADP1 protocatechuate 3,4-dioxygenase at 2.2 Å resolution: implications for the mechanism of an intradiol dioxygenase. Biochemistry 39:7943-7955.
49. Young, D. A., D. Parke, D. A. D'Argenio, M. A. Smith, and L. N. Ornston. 2001. Evolution of a catabolic pathway. ASM News 67:362-369.