RubisCO gene clusters found in a metagenome microarray from acid mine drainage

Applied and Environmental Microbiology

Volumn 79, Issue 6, 2013, Pages 2019-2026

  Guo, Xue ^a   Yin, Huaqun ^a   Cong, Jing ^a   Dai, Zhimin ^a   Dai, Yili ^a   Liu, Xueduan ^a  

^a CENTRAL SOUTH UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOTROPHIC BACTERIA; CARBON DIOXIDE FIXATION; EVOLUTIONARY HISTORY; GENOMIC ORGANIZATION; HORIZONTAL TRANSFER; MICROBIAL COMMUNITIES; MOLECULAR PHYLOGENETICS; PHYLOGENETIC ANALYSIS;

BIOLOGY; RNA;

GENES;

BACTERIAL DNA; RIBOSOME DNA; RIBULOSEBISPHOSPHATE CARBOXYLASE; RNA 16S;

ACID MINE DRAINAGE; AUTOTROPHY; BACTERIUM; CARBON DIOXIDE; CARBON FIXATION; GENE EXPRESSION; GENE TRANSFER; GENETIC MARKER; GENOME; MICROBIAL COMMUNITY; PHYLOGENETICS; PHYLOGENY; PLASMID;

ARTICLE; BACTERIUM; CHEMISTRY; CLUSTER ANALYSIS; DNA SEQUENCE; ENZYMOLOGY; GENETIC VARIABILITY; GENETICS; METAGENOME; MICROBIOLOGY; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY;

BACTERIA; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; ENVIRONMENTAL MICROBIOLOGY; GENETIC VARIATION; METAGENOME; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; RIBULOSE-BISPHOSPHATE CARBOXYLASE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84874823502     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03400-12     Document Type: Article

References (41)

1. Shively J, Devore W, Stratford L, Porter L, Medlin L, Stevens S, Jr. 1986. Molecular evolution of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). FEMS Microbiol. Lett. 37:251-257.
2. Ellis RJ. 1979. The most abundant protein in the world. Trends Biochem. Sci. 4:241-244.
3. Tabita F. 1988. Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms. Microbiol. Rev. 52:155-189.
4. Bainbridge G, Madgwick P, Parmar S, Mitchell R, Paul M, Pitts J, Keys AJ, Parry MAJ. 1995. Engineering Rubisco to change its catalytic properties. J. Exp. Bot. 46:1269.
5. Kellogg EA, Juliano ND. 1997. The structure and function of RuBisCO and their implications for systematic studies. Am. J. Bot. 84:413. doi:10 .2307/2446015.
6. Selesi D, Schmid M, Hartmann A. 2005. Diversity of green-like and red-like ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes (cbbL) in differently managed agricultural soils. Appl. Environ. Microbiol. 71:175-184.
7. Tabita FR, Hanson TE, Li H, Satagopan S, Singh J, Chan S. 2007. Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol. Mol. Biol. Rev. 71:576 -599.
8. Jordan DB, Ogren WL. 1983. Species variation in kinetic properties of ribulose 1,5-bisphosphate carboxylase/oxygenase. Arch. Biochem. Biophys. 227:425- 433.
9. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD. 1996. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058. doi:10.1126/science.273.5278.1058.
10. Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390: 364 -370
11. Kunst F, Ogasawara N, Moszer I, Albertini A, Alloni G, Azevedo V, Bertero M, Bessieres P, Bolotin A, Borchert S. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249 -256.
12. Hanson TE, Tabita FR. 2001. A ribulose-1,5-bisphosphate carboxylase/ oxygenase (RubisCO)-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. Proc. Natl. Acad. Sci. U. S. A. 98:4397. doi:10.1073/pnas.081610398.
13. Delwiche CF, Palmer JD. 1996. Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol. Biol. Evol. 13:873- 882.
14. Uchino Y, Yokota A. 2003. "Green-like" and "red-like" RubisCO cbbL genes in Rhodobacter azotoformans. Mol. Biol. Evol. 20:821- 830.
15. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. 2004. Commu- RubisCO Gene Clusters in Acid Mine Drainagenity structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37- 43.
16. Bond PL, Smriga SP, Banfield JF. 2000. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol. 66:3842-3849.
17. Zhou J, Bruns MA, Tiedje JM. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316 -322.
18. Park SJ, Kang CH, Chae JC, Rhee SK. 2008. Metagenome microarray for screening of fosmid clones containing specific genes. FEMS Microbiol. Lett. 284:28 -34.
19. Bae JW, Rhee SK, Park JR, Chung WH, Nam YD, Lee I, Kim H, Park YH. 2005. Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. Appl. Environ. Microbiol. 71:8825- 8835.
20. Rhee SK, Liu X, Wu L, Chong SC, Wan X, Zhou J. 2004. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70:4303- 4317.
21. Chaisson MJ, Pevzner PA. 2008. Short read fragment assembly of bacterial genomes. Genome Res. 18:324 -330.
22. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27: 4636-4641.
23. Aziz R, Bartels D, Best A, DeJongh M, Disz T, Edwards R, Formsma K, Gerdes S, Glass E, Kubal M. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75. doi:10.1186/1471 -2164-9-75.
24. Eddy SR. 2008. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput. Biol. 4:e1000069. doi:10.1371/journal.pcbi.1000069.
25. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. 2005. ACT: the Artemis comparison tool. Bioinformatics 21: 3422-3423.
26. Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H, Valentin F, Wallace I, Wilm A, Lopez R. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
27. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596 -1599.
28. Imker HJ, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA. 2007. Mechanistic diversity in the RuBisCO superfamily: the "enolase" in the methionine salvage pathway in Geobacillus kaustophilus. Biochemistry 46: 4077-4089.
29. Hayashi NR, Arai H, Kodama T, Igarashi Y. 1997. The novel genes, cbbQ and cbbO, located downstream from the RubisCO genes of Pseudomonas hydrogenothermophila, affect the conformational states and activity of RubisCO. Biochem. Biophys. Res. Commun. 241 565-569
30. Kusian B, Bowien B. 1997. Organization and regulation of cbb CO2 assimilation genes in autotrophic bacteria. FEMS Microbiol. Rev. 21:135- 155.
31. Valdés J, Pedroso I, Quatrini R, Dodson RJ, Tettelin H, Blake R, II, Eisen JA, Holmes DS. 2008. Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications. BMC Genomics 9:597. doi:10.1186/1471-2164-9-597.
32. Iancu CV, Ding HJ, Morris DM, Dias DP, Gonzales AD, Martino A, Jensen GJ. 2007. The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography. J. Mol. Biol. 372: 764-773.
33. Xu Y, Feng L, Jeffrey PD, Shi Y, Morel FMM. 2008. Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms. Nature 452:56-61.
34. Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively JM. 2008. Protein-based organelles in bacteria: carboxysomes and related microcompartments. Nat. Rev. Microbiol. 6,681- 691
35. Elsaied H, Kimura H, Naganuma T. 2002. Molecular characterization and endosymbiotic localization of the gene encoding D-ribulose 1,5- bisphosphate carboxylase-oxygenase (RuBisCO) form II in the deep-sea vestimentiferan trophosome. Microbiology 148(Pt 6):1947-1957.
36. Badger MR, Bek EJ. 2008. Multiple Rubisco forms in proteobacteria: their functional significance in relation to CO2 acquisition by the CBB cycle. J. Exp. Bot. 59:1525. doi:10.1093/jxb/erm297.
37. Badger MR, Hanson D, Price GD. 2002. Evolution and diversity of CO2 concentrating mechanisms in cyanobacteria. Funct. Plant Biol. 29:161- 173.
38. Paoli GC, Soyer F, Shively J, Tabita FR. 1998. Rhodobacter capsulatus genes encoding form I ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbLS) and neighbouring genes were acquired by a horizontal gene transfer. Microbiology 144:219. doi:10.1099/00221287-144-1-219.
39. Valdes J, Quatrini R, Hallberg K, Dopson M, Valenzuela PDT, Holmes DS. 2009. Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus. J. Bacteriol. 191:5877-5878.
40. Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, Benotmane MA, Leys N, Vallaeys T, Lapidus A. 2010. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One 5:e10433. doi:10.1371/journal.pone.0010433.
41. Kusano T, Takeshima T, Inoue C, Sugawara K. 1991. Evidence for two sets of structural genes coding for ribulose bisphosphate carboxylase in Thiobacillus ferrooxidans. J. Bacteriol. 173:7313-7323.