Component identification of electron transport chains in curdlan-producing Agrobacterium sp. ATCC 31749 and its genome-specific prediction using comparative genome and phylogenetic trees analysis

Journal of Industrial Microbiology and Biotechnology

Volumn 38, Issue 6, 2011, Pages 667-677

  Zhang, Hongtao ^a,d   Setubal, Joao Carlos ^b,c   Zhan, Xiaobei ^a   Zheng, Zhiyong ^a   Yu, Lijun ^a   Wu, Jianrong ^a   Chen, Dingqiang ^a  

^a JIANGNAN UNIVERSITY   (China)

^b State University   (United States)

^c VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^d IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Agrobacterium sp.; Comparative genomic analysis; Curdlan; Electron transport chains; Genomic specificity analysis

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; CURDLAN; CYTOCHROME BO TERMINAL OXIDASE; CYTOCHROME C; CYTOCHROME CAA3 TYPE TERMINAL OXIDASE; CYTOCHROME CBB3; CYTOCHROME D TERMINAL OXIDASE; MALATE DEHYDROGENASE; PROTEIN UBIB; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE (UBIQUINONE); SUCCINATE DEHYDROGENASE; UBIQUINOL CYTOCHROME C REDUCTASE; UBIQUINONE; UNCLASSIFIED DRUG;

ARTICLE; DNA SEQUENCE; ELECTRON TRANSPORT; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; PROTEIN SYNTHESIS; RHIZOBIUM;

BETA-GLUCANS; CYTOCHROME D GROUP; ELECTRON TRANSPORT; ELECTRON TRANSPORT COMPLEX IV; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; OXIDOREDUCTASES; PHYLOGENY; RHIZOBIUM; SUCCINATE DEHYDROGENASE;

AGROBACTERIUM; AGROBACTERIUM SP.; AGROBACTERIUM SP. ATCC 31749; AGROBACTERIUM TUMEFACIENS; ALCALIGENES FAECALIS; BACTERIA (MICROORGANISMS);

EID: 80051670372     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-010-0810-x     Document Type: Article

References (51)

1. Alpes I, Scherer S, Boger P (1989) The respiratory NADH dehydrogenase of the Cyanobacterium anabaena variabilis: purification and characterization. Biochim Biophys Acta 973:41-46
2. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402 (Pubitemid 27359211)
3. Anraku Y, Gennis RB (1987) The aerobic respiratory-chain of Escherichia coli. Trends Biochem Sci 12:262-266
4. 3-type oxidase of Bradyrhizobium japonicum is a proton pump. FEBS Lett 470:7-10. doi:S0014-5793 (00) 01277-1 (Pubitemid 30155613)
5. Awai K, Kakimoto T, Awai C, Kaneko T, Nakamura Y, Takamiya K et al (2006) Comparative genomic analysis revealed a gene for monoglucosyldiacylglycerol synthase, an enzyme for photosynthetic membrane lipid synthesis in cyanobacteria. Plant Physiol 141:1120-1127. doi:10.1104/pp.106.082859 (Pubitemid 44061617)
6. Bott M, Niebisch A (2003) The respiratory chain of Corynebacterium glutamicum. J Biotechnol 104:129-153. doi:10.1016/S0168-1656 (03) 00144-5 (Pubitemid 37011354)
7. 3 branch of the Bradyrhizobium japonicum respiratory-chain. Mol Microbiol 4:2147-2157 (Pubitemid 120005275)
8. Cecchini G, Schroder I, Gunsalus RP, Maklashina E (2002) Succinate dehydrogenase and fumarate reductase from Escherichia coli. Biochim Biophys Acta 1553:140-157 (Pubitemid 34137066)
9. 3-type family of cytochrome c Oxidases. J Biol Chem 265:11185-11192
10. Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR et al (2001) Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res 11:1175-1186. doi:10.1101/gr.182901 (Pubitemid 32677291)
11. Cotter PA, Chepuri V, Gennis RB, Gunsalus RP (1990) Cytochrome-o (Cyoabcde) and d (Cydab) oxidase gene-expression in Escherichia-coli is regulated by oxygen, pH, and the Fnr geneproduct. J Bacteriol 172:6333-6338 (Pubitemid 20372773)
12. de Gier JW, Lubben M, Reijnders WN, Tipker CA, Slotboom DJ, van Spanning RJ et al (1994) The terminal oxidases of Paracoccus denitrificans. Mol Microbiol 13:183-196
13. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F et al (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36:W465-W469
14. Futatsuyama H, Yui T, Ogawa K (1999) Viscometry of curdlan, a linear (1 → 3)-beta-D-glucan, in DMSO or alkaline solutions. Biosci Biote Bioch 63:1481-1483 (Pubitemid 129549165)
15. Hida TH, Ishibashi K, Miura NN, Adachi Y, Shirasu Y, Ohno N (2009) Cytokine induction by a linear 1, 3-glucan, curdlan-oligo, in mouse leukocytes in vitro. Inflamm Res 58:9-14
16. Hill BC, Greenwood C (1984) The reaction of fully reduced cytochrome c oxidase with oxygen studied by flow flash spectrophotometry at room-temperature: evidence for new pathways of electron-transfer. Biochem J 218:913-921
17. Jin LH, Um HJ, Yin CJ, Kim YH, Lee JH (2008) Proteomic analysis of curdlan-producing Agrobacterium sp in response to pH downshift. J Biotechnol 138:80-87. doi:10.1016/j.jbiotec.2008. 08.010
18. Kana BD, Weinstein EA, Avarbock D, Dawes SS, Rubin H, Mizrahi V (2001) Characterization of the cydAB encoded cytochrome bd oxidase from Mycobacterium smegmatis. J Bacteriol 183:7076-7086. doi:10.1128/JB.183.24.7076-7086.2001 (Pubitemid 33121840)
19. Karnezis T, Epa VC, Stone BA, Stanisich VA (2003) Topological characterization of an inner membrane (1 → 3)-beta-D-glucan (curdlan) synthase from Agrobacterium sp strain ATCC31749. Glycobiology 13:693-706. doi:10.1093/glycob/cwg093 (Pubitemid 37337050)
20. Kim MK, Lee IY, Ko JH, Rhee YH, Park YH (1999) Higher intracellular levels of uridinemonophosphate under nitrogen-limited conditions enhance metabolic flux of curdlan synthesis in Agrobacterium species. Biotechnol Bioeng 62:317-323
21. Kim MJ, Hong SY, Kim SK, Cheong C, Park HJ, Chun HK et al (2009) beta-Glucan enhanced apoptosis in human colon cancer cells SNU-C4. Nutr Res Pract 3:180-184
22. Lee JH, Lee IY (2001) Optimization of uracil addition for curdlan (beta-1 → 3-glucan) production by Agrobacterium sp. Biotechnol Lett 23:1131-1134 (Pubitemid 32786345)
23. Lee IY, Seo WT, Kim GJ, Kim MK, Park CS, Park YH (1997) Production of curdlan using sucrose or sugar cane molasses by two-step fed-batch cultivation of Agrobacterium species. J Ind Microbiol Biotechnol 18:255-259 (Pubitemid 27467108)
24. Lee JH, Lee IY, Kim MK, Park YH (1999) Optimal pH control of batch processes for production of curdlan by Agrobacterium species. J Ind Microbiol Biotechnol 23:143-148
25. Matsushita M (1990) Curdlan, a (1 → 3)-beta-D-glucan from Alcaligenes-faecalis var myxogenes IFO13140, activates the alternative complement pathway by heat-treatment. Immunol Lett 26:95-97
26. Matsushita K, Ohnishi T, Kaback HR (1987) NADH-ubiquinone oxidoreductases of the Escherichia coli aerobic respiratory chain. Biochemistry 26:7732-7737
27. Meganathan R (2001) Ubiquinone biosynthesis in microorganisms. FEMS Microbiol Lett 203:131-139 (Pubitemid 32913605)
28. Mogi T, Saiki K, Anraku Y (1994) Biosynthesis and functional: role of heme O and heme A. Mol Microbiol 14:391-398
29. Na K, Park KH, Kim SW, Bae YH (2000) Self-assembled hydrogel nanoparticles from curdlan derivatives: characterization, anticancer drug release and interaction with a hepatoma cell line (HepG2). J Control Release 69:225-236
30. Poon WW, Davis DE, Ha HT, Jonassen T, Rather PN, Clarke CF (2000) Identification of Escherichia coli ubiB, a gene required for the first monooxygenase step in ubiquinone biosynthesis. J Bacteriol 182:5139-5146
31. 3-type cytochrome oxidase terminates the symbiosis-specific respiratory chain of Bradyrhizobium japonicum. J Bacteriol 178:1532-1538
32. Richter OM, Ludwig B (2009) Electron transfer and energy transduction in the terminal part of the respiratory chain: lessons from bacterial model systems. Biochim Biophys Acta 1787:626-634. doi:10.1016/j.bbabio.2009.02.020
33. Rinner O, Morgenstern B (2002) AGenDA: gene prediction by comparative sequence analysis. In Silico Biol 2:195-205 (Pubitemid 35469196)
34. Ruffing A, Mao Z, Chen RRZ (2006) Metabolic engineering of Agrobacterium sp for UDP-galactose regeneration and oligosaccharide synthesis. Metab Eng 8:465-473. doi:10.1016/j.ymben. 2006.05.004 (Pubitemid 44278728)
35. Saraste M, Metso T, Nakari T, Jalli T, Lauraeus M, Van der Oost J (1991) The Bacillus subtilis cytochrome-c oxidase: variations on a conserved protein theme. Eur J Biochem 195:517-525
36. Schneider D, Pohl T, Walter J, Dorner K, Kohlstadt M, Berger A et al (2008) Assembly of the Escherichia coli NADH: ubiquinone oxidoreductase (complex I). Biochim Biophys Acta 1777:735-739. doi:10.1016/j.bbabio.2008.03.003
37. Setubal JC, Wood D, Burr T, Farrand S, Goldman B, Goodner B, Otten L, Slater S (2009) The Genomics of Agrobacterium: insights into pathogenicity, biocontrol, and evolution. In: Jackson R (ed) Plant pathogenic bacteria: genomics and molecular biology. Caister academic press, UK, pp 91-112
38. Slater SC, Goldman BS, Goodner B, Setubal JC, Farrand SK, Nester EW et al (2009) Genome sequences of three Agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. J Bacteriol 191:2501-2511. doi:10.1128/JB.01779-08
39. Smith A, Hill S, Anthony C (1990) The purification, characterization and role of the d-type cytochrome oxidase of Klebsiella pneumoniae during nitrogen fixation. J Gen Microbiol 136:171-180 (Pubitemid 20045984)
40. Trubitsin BV, Ptushenko VV, Koksharova OA, Mamedov MD, Vitukhnovskaya LA, Grigor'ev IA et al (2005) EPR study of electron transport in the Cyanobacterium Synechocystis sp PCC 6803: oxygen-dependent interrelations between photosynthetic and respiratory electron transport chains. Biochim Biophys Acta 1708:238-249. doi:10.1016/j.bbabio.2005.03.004 (Pubitemid 40824954)
41. Vera J, Fenutria R, Canadas O, Figueras M, Mota R, Sarrias MR et al (2009) The CD5 ectodomain interacts with conserved fungal cell wall components and protects from zymosan-induced septic shock-like syndrome. PNAS 106:1506-1511
42. Wang TQ, Deng L, Li SK, Tan TW (2007) Structural characterization of a water-insoluble (1 → 3)-α-D-glucan isolated from the Penicillium chrysogenum. Carbohydr Polym 67:133-137. doi:10.1016/j.carbpol.2006.05.001 (Pubitemid 44755322)
43. West TP (2006) Pyrimidine base supplementation effects curdlan production in Agrobacterium sp ATCC 31749. J Basic Microbiol 46:153-157. doi:10.1002/jobm.200510067
44. West TP, Nemmers B (2008) Curdlan production by Agrobacterium sp ATCC 31749 on an ethanol fermentation coproduct. J Basic Microbiol 48:65-68
45. Westenberg DJ, Guerinot ML (1999) Succinate dehydrogenase (Sdh) from Bradyrhizobium japonicum is closely related to mitochondrial Sdh. J Bacteriol 181:4676-4679 (Pubitemid 29357954)
46. Wheatcroft R, Watson RJ (1988) A positive strain identification method for Rhizobium meliloti. Appl Environ Microbiol 54:574-576
47. Williams HD, Hubbard JAM, Nugent JHA, Poole RK (1991) Functional size measurements of the ubiquinol oxidase activity of the cytochrome-O terminal oxidase complex of Escherichia coli. Biochem J 276:555-557
48. Wood DW, Setubal JC, Kaul R, Monks DE, Kitajima JP, Okura VK et al (2001) The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:2317-2323. doi:10.1126/science.1066804294/5550/2317 (Pubitemid 33140549)
49. Wu M, Eisen JA (2008) A simple, fast, and accurate method of phylogenomic inference. Genome Biol 9:R51
50. Yumoto I (2002) Bioenergetics of alkaliphilic Bacillus spp. J Biosci Bioeng 93:342-353
51. Zheng ZY, Lee JW, Zhan XB, Shi Z, Wang L, Zhu L et al (2007) Effect of metabolic structures and energy requirements on curdlan production by Alcaligenes faecalis. Biotechnol Bioproc Eng 12:359-365. doi:10.1007/BF02931057 (Pubitemid 47408268)