Assimilation of aromatic compounds by Comamonas testosteroni: Characterization and spreadability of protocatechuate 4,5-cleavage pathway in bacteria

Applied Microbiology and Biotechnology

Volumn 97, Issue 13, 2013, Pages 6031-6041

  Ni, Bin ^a   Zhang, Yun ^a   Chen, Dong Wei ^a   Wang, Bao Jun ^a   Liu, Shuang Jiang ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

3 4 Hydroxybenzoate; 4 Oxalomesaconate tautomerase; Comamonas testosteroni; Protocatechuate 4,5 cleavage; Vanillate

Indexed keywords

3-/4-HYDROXYBENZOATE; COMAMONAS TESTOSTERONI; PROTOCATECHUATE; TAUTOMERASE; VANILLATES;

GENES;

CATALYSIS;

1 CHLORO 4 NITROBENZENE; 3 HYDROXYBENZOIC ACID; 4 CARBOXY 4 HYDROXY 2 OXOADIPATE ALDOLASE; 4 HYDROXYBENZOIC ACID; 4 OXALOMESACONATE TAUTOMERASE; AROMATIC COMPOUND; FRUCTOSE BISPHOSPHATE ALDOLASE; GAMMA OXALOMESACONATE HYDRATASE; GENTISIC ACID; HYDROLYASE; ISOMERASE; PHENOL; PROTOCATECHUATE 3,4 DIOXYGENASE; SUCCINIC ACID; UNCLASSIFIED DRUG; VANILLIC ACID;

ACTIVATED SLUDGE; AROMATIC HYDROCARBON; BACTERIUM; BIODEGRADATION; CARBON; ENZYME ACTIVITY; PROTEOMICS; SUBSTRATE;

ACTIVATED SLUDGE; AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATE; BIODEGRADATION; CATALYSIS; COMAMONAS TESTOSTERONI; ENZYME ACTIVITY; ENZYME SUBSTRATE; GENE EXPRESSION; GENETIC IDENTIFICATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PMDE GENE; PMDF GENE; PMDU GENE; PROTEIN EXPRESSION; PROTEOMICS; SEQUENCE ANALYSIS;

BIOTRANSFORMATION; COMAMONAS TESTOSTERONI; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; HYDROCARBONS, AROMATIC; HYDROXYBENZOATES; METABOLIC NETWORKS AND PATHWAYS;

BETAPROTEOBACTERIA; COMAMONAS TESTOSTERONI;

EID: 84879422674     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-012-4402-8     Document Type: Article

References (50)

1. Akagawamatsushita M, Matsuo M, Koga Y, Yamasato K (1992) Alteromonas atlantica sp. nov. and Alteromonas carrageenovora sp. nov., bacteria that decompose algal polysaccharides. Int J Syst Bacteriol 42:621-627
2. Cerdan P, Wasserfallen A, Rekik M, Timmis KN, Harayama S (1994) Substrate specificity of catechol 2,3-dioxygenase encoded by TOL plasmid pWW0 of Pseudomonas putida and its relationship to cell growth. J Bacteriol 176:6074-6081
3. Chou JH, Sheu SY, Lin KY, Chen WM, Arun AB, Young CC (2007) Comamonas odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus. Int J Syst Evol Microbiol 57:887-891
4. Crawford RL (1975) Novel pathway for degradation of protocatechuic acid in Bacillus species. J Bacteriol 121:531-536
5. Franklin FCH, Bagdasarian M, Bagdasarian MM, Timmis KN (1981) Molecular and functional analysis of the TOL plasmid pWWO from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta-cleavage pathway. Proc Natl Acad Sci USA 78:7458-7462
6. Giraud E, Moulin L, Vallenet D, Barbe V, Cytryn E, Avarre JC, Jaubert M, Simon D, Cartieaux F, Prin Y, Bena G, Hannibal L, Fardoux J, Kojadinovic M, Vuillet L, Lajus A, Cruveiller S, Rouy Z, Mangenot S, Segurens B, Dossat C, Franck WL, Chang WS, Saunders E, Bruce D, Richardson P, Normand P, Dreyfus B, Pignol D, Stacey G, Emerich D, Vermeglio A, Medigue C, Sadowsky M (2007) Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science 316:1307-1312
7. Gul M, Ciragil P, Bulbuloglu E, Aral M, Alkis S, Ezberci F (2007) Comamonas testosteroni bacteremia in a patient with perforated acute appendicitis. Acta Microbiol Immunol Hung 54:317-321
8. Gumaelius L, Magnusson G, Pettersson B, Dalhammar G (2001) Comamonas denitrificans sp. nov., an efficient denitrifying bacterium isolated from activated sludge. Int J Syst Evol Microbiol 51:999-1006
9. Hara H, Masai E, Katayama Y, Fukuda M (2000) The 4-oxalomesaconate hydratase gene, involved in the protocatechuate 4,5-cleavage pathway, is essential to vanillate and syringate degradation in Sphingomonas paucimobilis SYK-6. J Bacteriol 182:6950-6957
10. Hara H, Masai E, Miyauchi K, Katayama Y, Fukuda M (2003) Characterization of the 4-carboxy-4-hydroxy-2-oxoadipate aldolase gene and operon structure of the protocatechuate 4,5-cleavage pathway genes in Sphingomonas paucimobilis SYK-6. J Bacteriol 185:41-50
11. Harwood CS, Nichols NN, Kim MK, Ditty JL, Parales RE (1994) Identification of the pcaRKF gene cluster from Pseudomonas putida: involvement in chemotaxis, biodegradation, and transport of 4-hydroxybenzoate. J Bacteriol 176:6479-6488
12. Harwood CS, Parales RE (1996) The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 50:553-590
13. Kamimura N, Aoyama T, Yoshida R, Takahashi K, Kasai D, Abe T, Mase K, Katayama Y, Fukuda M, Masai E (2010a) Characterization of the protocatechuate 4,5-cleavage pathway operon in Comamonas sp. strain E6 and discovery of a novel pathway gene. Appl Environ Microb 76:8093-8101
14. Kamimura N, Kasai D, Senda T, Katayama Y, Fukuda M, Masai E (2010b) LigR, a LysR-type transcriptional regulator, controls expression of the protocatechuate 4,5-cleavage pathway genes in Sphingobium sp. strain SYK-6. J Biotechnol 150:236-237 (supplement)
15. Kasai D, Fujinami T, Abe T, Mase K, Katayama Y, Fukuda M, Masai E (2009) Uncovering the protocatechuate 2,3-cleavage pathway genes. J Bacteriol 191:6758-6768
16. Katsivela E, Wray V, Pieper DH, Wittich RM (1999) Initial reactions in the biodegradation of 1-chloro-4-nitrobenzene by a newly isolated bacterium, strain LW1. Appl Environ Microbiol 65:1405-1412
17. Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, Roop RM, Peterson KM (1995) 4 new derivatives of the broad-Host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175-176
18. 2-fixing grass endophyte Azoarcus sp. strain BH72. Nat Biotechnol 24:1385-1391
19. Liu L, Jiang CY, Liu XY, Wu JF, Han JG, Liu SJ (2007a) Plant-microbe association for rhizoremediation of chloronitroaromatic pollutants with Comamonas sp. strain CNB-1. Environ Microbiol 9:465-473
20. Liu L, Wu JF, Ma YF, Wang SY, Zhao GP, Liu SJ (2007b) A novel deaminase involved in chloronitrobenzene and nitrobenzene degradation with Comamonas sp. strain CNB-1. J Bacteriol 189:2677-2682
21. Lucas-Elio P, Marco-Noales E, Espinosa E, Ordax M, Lopez MM, Garcias-Bonet N, Marba N, Duarte CM, Sanchez-Amat A (2011) Marinomonas alcarazii sp. nov., M. rhizomae sp. nov., M. foliarum sp. nov., M. posidonica sp. nov. and M. aquiplantarum sp. nov., isolated from the microbiota of the seagrass Posidonia oceanica. Int J Syst Evol Microbiol 61:2191-2196
22. Ma YF, Wu JF, Wang SY, Jang CY, Zhang Y, Qi SW, Liu L, Zhao GP, Liu SJ (2007) Nucleotide sequence of plasmid pCNB1 from Comamonas strain CNB-1 reveals novel genetic organization and evolution for 4-chloronitrobenzene degradation. Appl Environ Microbiol 73:4477-4483
23. Ma YF, Zhang Y, Zhang JY, Chen DW, Zhu YQ, Zheng HJ, Wang SY, Jiang CY, Zhao GP, Liu SJ (2009) The complete genome of Comamonas testosteroni reveals its genetic adaptations to changing environments. Appl Environ Microbiol 75:6812-6819
24. Mampel J, Providenti MA, Cook AM (2005) Protocatechuate 4,5-dioxygenase from Comamonas testosteroni T-2: biochemical and molecular properties of a new subgroup within class III of extradiol dioxygenases. Arch Microbiol 183:130-139
25. Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor
26. Maruyama K, Miwa M, Tsujii N, Nagai T, Tomita N, Harada T, Sobajima H, Sugisaki H (2001) Cloning, sequencing, and expression of the gene encoding 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae NGJ1. Biosci Biotech Bioch 65:2701-2709
27. Maruyama K, Shibayama T, Ichikawa A, Sakou Y, Yamada S, Sugisaki H (2004) Cloning and characterization of the genes encoding enzymes for the protocatechuate meta-degradation pathway of Pseudomonas ochraceae NGJ1. Biosci Biotechnol Biochem 68:1434-1441
28. Masai E, Katayama Y, Fukuda M (2007) Genetic and biochemical investigations on bacterial catabolic pathways for lignin-derived aromatic compounds. Biosci Biotechnol Biochem 71:1-15
29. Masai E, Momose K, Hara H, Nishikawa S, Katayama Y, Fukuda M (2000) Genetic and biochemical characterization of 4-carboxy-2-hydroxymuconate-6- semialdehyde dehydrogenase and its role in the protocatechuate 4,5-cleavage pathway in Sphingomonas paucimobilis SYK-6. J Bacteriol 182:6651-6658
30. Masai E, Shinohara S, Hara H, Nishikawa S, Katayama Y, Fukuda M (1999) Genetic and biochemical characterization of a 2-pyrone-4,6-dicarboxylic acid hydrolase involved in the protocatechuate 4,5-cleavage pathway of Sphingomonas paucimobilis SYK-6. J Bacteriol 181:55-62
31. Noda Y, Nishikawa S, Shiozuka K, Kadokura H, Nakajima H, Yoda K, Katayama Y, Morohoshi N, Haraguchi T, Yamasaki M (1990) Molecular cloning of the protocatechuate 4,5-dioxygenase genes of Pseudomonas paucimobilis. J Bacteriol 172:2704-2709
32. Nogales J, Canales A, Jimenez-Barbero J, Serra B, Pingarron JM, Garcia JL, Diaz E (2011) Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol Microbiol 79:359-374
33. Ornston MK, Ornston LN (1972) Regulation of beta-ketoadipate pathway in Pseudomonas acidovorans and Pseudomonas testosteroni. J Gen Microbiol 73:455-464
34. Parke D, D'Argenio DA, Ornston LN (2000) Bacteria are not what they eat: that is why they are so diverse. J Bacteriol 182:257-263
35. Patil NK, Kundapur R, Shouche YS, Karegoudar TB (2006) Degradation of plasticizer di-n-butylphthalate by Delftia sp. TBKNP-05. Curr Microbiol 52:369-374
36. Pinel N, Davidson SK, Stahl DA (2008) Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny). Int J Syst Evol Microbiol 58:2147-2157
37. Providenti MA, Mampel J, MacSween S, Cook AM, Wyndham RC (2001) Comamonas testosteroni BR6020 possesses a single genetic locus for extradiol cleavage of protocatechuate. Microbiology 147:2157-2167
38. Providenti MA, O'Brien JM, Ruff J, Cook AM, Lambert IB (2006) Metabolism of isovanillate, vanillate, and veratrate by Comamonas testosteroni strain BR6020. J Bacteriol 188:3862-3869
39. Rawlings ND, Bateman A (2009) Pepsin homologues in bacteria. BMC Genomics 10:437
40. Roh H, Yun EJ, Lee S, Ko HJ, Kim S, Kim BY, Song H, Lim KI, Kim KH, Choi IG (2012) Genome sequence of Vibrio sp. strain EJY3, an agarolytic marine bacterium metabolizing 3,6-anhydro-L-galactose as a sole carbon source. J Bacteriol 194:2773-2774
41. Schäfer A, Tauch A, Jäger W, Kalinowski J, Thierbach G, Pühler A (1994) Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145:69-73
42. Shen XH, Jiang CY, Huang Y, Liu ZP, Liu SJ (2005) Functional identification of novel genes involved in the glutathione-independent gentisate pathway in Corynebacterium glutamicum. Appl Environ Microbiol 71:3442-3452
43. Shinomiya M, Iwata T, Kasuya K, Doi Y (1997) Cloning of the gene for poly(3-hydroxybutyric acid) depolymerase of Comamonas testosteroni and functional analysis of its substrate-binding domain. FEMS Microbiol Lett 154:89-94
44. Vandamme P, Goris J, Chen WM, de Vos P, Willems A (2002) Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes. Syst Appl Microbiol 25:507-512
45. Wang W, Mazurkewich S, Kimber MS, Seah SY (2010) Structural and kinetic characterization of 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2- oxoadipate aldolase, a protocatechuate degradation enzyme evolutionarily convergent with the HpaI and DmpG pyruvate aldolases. J Biol Chem 285:36608-36615
46. Wattiau P, Bastiaens L, van Herwijnen R, Daal L, Parsons JR, Renard ME, Springael D, Cornelis GR (2001) Fluorene degradation by Sphingomonas sp. LB126 proceeds through protocatechuic acid: a genetic analysis. Res Microbiol 152:861-872
47. Wu JF, Jiang CY, Wang BJ, Ma YF, Liu ZP, Liu SJ (2006) Novel partial reductive pathway for 4-chloronitrobenzene and nitrobenzene degradation in Comamonas sp. strain CNB-1. Appl Environ Microbiol 72:1759-1765
48. Wu JF, Sun CW, Jiang CY, Liu ZP, Liu SJ (2005) A novel 2-aminophenol 1,6-dioxygenase involved in the degradation of p-chloronitrobenzene by Comamonas strain CNB-1: purification, properties, genetic cloning and expression in Escherichia coli. Arch Microbiol 183:1-8
49. Yu XY, Li YF, Zheng JW, Li Y, Li LA, He JA, Li SP (2011) Comamonas zonglianii sp. nov., isolated from phenol-contaminated soil. Int J Syst Evol Microbiol 61:255-258
50. Zhang Y, Wu JF, Zeyer J, Meng B, Liu L, Jiang CY, Liu SQ, Liu SJ (2009) Proteomic and molecular investigation on the physiological adaptation of Comamonas sp. strain CNB-1 growing on 4-chloronitrobenzene. Biodegradation 20:55-66