Diverse alkane hydroxylase genes in microorganisms and environments

Scientific Reports

Volumn 4, Issue , 2014, Pages

  Nie, Yong ^a   Chi, Chang Qiao ^a   Fang, Hui ^a   Liang, Jie Liang ^a   Lu, She Lian ^a   Lai, Guo Li ^a   Tang, Yue Qin ^a,b   Wu, Xiao Lei ^a  

^a PEKING UNIVERSITY   (China)

^b SICHUAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALKANE; ALKANE 1 MONOOXYGENASE; BACTERIAL DNA; CYTOCHROME P 450 CYP153 (ACINETOBACTER); CYTOCHROME P-450 CYP153 (ACINETOBACTER); CYTOCHROME P450; FRESH WATER;

ARTICLE; BACTERIAL GENOME; ENVIRONMENT; GENETICS; METABOLISM; METAGENOME; MICROBIOLOGY; PHYLOGENY;

ALKANE 1-MONOOXYGENASE; ALKANES; CYTOCHROME P-450 ENZYME SYSTEM; DNA, BACTERIAL; ENVIRONMENT; FRESH WATER; GENOME, BACTERIAL; METAGENOME; PHYLOGENY;

EID: 84901036143     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep04968     Document Type: Article

References (74)

1. Brown, L. R. Microbial enhanced oil recovery (MEOR). Curr. Opin. Microbiol. 13, 316-320 (2010).
2. Rojo, F. Degradation of alkanes by bacteria. Environ. Microbiol. 11, 2477-2490 (2009).
3. Smits, T. H. M., Balada, S. B., Witholt, B. & van Beilen, J. B. Functional analysis of alkane hydroxylases from Gram-negative and Gram-positive bacteria. J. Bacteriol. 184, 1733-1742 (2002). (Pubitemid 34188225)
4. Smits, T. H. M., Rothlisberger, M., Witholt, B. & van Beilen, J. B. Molecular screening for alkane hydroxylase genes in Gram-negative and Gram-positive strains. Environ. Microbiol. 1, 307-317 (1999).
5. van Beilen, J. B. et al. Rubredoxins involved in alkane oxidation. J. Bacteriol. 184, 1722-1732 (2002). (Pubitemid 34188224)
6. van Beilen, J. B. &Funhoff, E. G. Alkane hydroxylases involved in microbial alkane degradation. Appl. Microbiol. Biotechnol. 74, 13-21 (2007). (Pubitemid 46183463)
7. Bihari, Z. et al. Functional analysis of long-chain n-alkane degradation by Dietzia spp. FEMS Microbiol. Lett. 316, 100-107 (2011).
8. Nie, Y., Liang, J., Fang, H., Tang, Y. Q. &Wu, X. L. Two novel alkane hydroxylaserubredoxin fusion genes isolated from a Dietzia bacterium and the functions of fused rubredoxin domains in long-chain n-alkane degradation. Appl. Environ. Microbiol. 77, 7279-7288 (2011).
9. Lo Piccolo, L., De Pasquale, C., Fodale, R., Puglia, A. M. & Quatrini, P. Involvement of an alkane hydroxylase system of Gordonia sp. strain SoCg in degradation of solid n-alkanes. Appl. Environ. Microbiol. 77, 1204-1213 (2011).
10. van Beilen, J. B. et al. Cytochrome P450 alkane hydroxylases of the CYP153 family are common in alkane-degrading eubacteria lacking integral membrane alkane hydroxylases. Appl. Environ. Microbiol. 72, 59-65 (2006).
11. Wang, X. B. et al. Degradation of petroleumhydrocarbons (C6-C40) and crude oil by a novel Dietzia strain. Bioresour. Technol. 102, 7755-7761 (2011).
12. Nie, Y., Liang, J.-L., Fang, H., Tang, Y.-Q. & Wu, X.-L. Characterization of a CYP153 alkane hydroxylase gene in a Gram-positive Dietzia sp. DQ12-45-1b and its ''team role'' with alkW1 in alkane degradation. Appl. Microbiol. Biotechnol. 98, 163-173 (2014).
13. Nie, Y. et al. The genome of the moderate halophile Amycolicicoccus subflavus DQS3-9A1T reveals four alkane hydroxylation systems and provides some clues on the genetic basis for its adaptation to a petroleum environment. PloS one 8, e70986 (2013).
14. Whyte, L. G. et al. Gene cloning and characterization of multiple alkane hydroxylase systems in Rhodococcus strains Q15 and NRRL B-16531. Appl. Environ. Microbiol. 68, 5933-5942 (2002). (Pubitemid 36342425)
15. Amouric, A. et al. Identification of different alkane hydroxylase systems in Rhodococcus ruberstrain SP2B, an hexane-degrading actinomycete. J. Appl. Microbiol. 108, 1903-1916 (2009).
16. Prince, R. C. Petroleum Microbiology (ASM press, Washington, 2005).
17. Benson, S., Fennewald, M., Shapiro, J. & Huettner, C. Fractionation of inducible alkane hydroxylase activity in Pseudomonas putida and characterization of hydroxylase-negative plasmid mutations. J. Bacteriol. 132, 614-621 (1977). (Pubitemid 8217404)
18. Feng, L. et al. Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc. Natl Acad. Sci. USA 104, 5602-5607 (2007). (Pubitemid 47175727)
19. Li, P., Wang, L. & Feng, L. Characterization of a novel Rieske-type alkane monooxygenase system in Pusillimonas sp. T7-7. J. Bacteriol. 195, 1892-1901 (2013).
20. Röling, W. F. M., Ortega-Lucach, S., Larter, S. R. & Head, I. M. Acidophilic microbial communities associated with a natural, biodegraded hydrocarbon seepage. J. Appl. Microbiol. 101, 290-299 (2006). (Pubitemid 44060409)
21. Yergeau, E., Sanschagrin, S., Beaumier, D. &Greer, C. W. Metagenomic analysis of the bioremediation of diesel-contaminated Canadian high arctic soils. PloS one 7, e30058 (2012).
22. Wen, Z., Jizhou, D., Liye, C. & Hongbo, S. Isolation of a nitrate-reducing bacteria strain from oil field brine and the inhibition of sulfate-reducing bacteria. African Journal of Biotechnology 10, 10019-10029 (2011).
23. Brakstad, O. G., Nonstad, I., Faksness, L.-G. & Brandvik, P. J. Responses of microbial communities in Arctic sea ice after contamination by crude petroleum oil. Microb. Ecol. 55, 540-552 (2008). (Pubitemid 351421342)
24. Schirmer, A., Rude, M. A., Li, X., Popova, E. & Del Cardayre, S. B. Microbial biosynthesis of alkanes. Science 329, 559-562 (2010).
25. Samuels, L., Kunst, L. & Jetter, R. Sealing plant surfaces: cuticular wax formation by epidermal cells. Plant Biol. 59, 683 (2008).
26. Heredia, A. Biophysical and biochemical characteristics of cutin, a plant barrier biopolymer. BBA-Gen. Subjects 1620, 1-7 (2003). (Pubitemid 36197890)
27. Tillman, J. A., Seybold, S. J., Jurenka, R. A. &Blomquist, G. J. Insect pheromones- an overview of biosynthesis and endocrine regulation. Insect Biochem. Mol. Biol. 29, 481-514 (1999). (Pubitemid 29297127)
28. Winters, K., Parker, P. & Van Baalen, C. Hydrocarbons of blue-green algae: geochemical signfficance. Science 163, 467-468 (1969).
29. McInnes, A. G., Walter, J. A. &Wright, J. L. Biosynthesis of hydrocarbons by algae: Decarboxylation of stearic acid to N-heptadecane in Anacystis nidulans determined by 13C-and 2H-labeling and 13Cnuclear magnetic resonance. Lipids 15, 609-615 (1980).
30. Dembitsky, V. & Srebnik, M. Variability of hydrocarbon and fatty acid components in cultures of the filamentous cyanobacterium Scytonema sp. isolated from microbial community ''black cover'' of limestone walls in Jerusalem. Biochemistry (Moscow) 67, 1276-1282 (2002).
31. Shiea, J., Brassell, S. C. & Ward, D. M. Mid-chain branched mono-and dimethyl alkanes in hot spring cyanobacterial mats: A direct biogenic source for branched alkanes in ancient sediments? Org. Geochem. 15, 223-231 (1990).
32. Giovannoni, S. J. & Stingl, U. Molecular diversity and ecology of microbial plankton. Nature 437, 343-348 (2005). (Pubitemid 41613489)
33. Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. science 304, 66-74 (2004). (Pubitemid 38451457)
34. Schulz, S. et al. Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments. ISME J. 6, 1763-1774 (2012).
35. Powell, S., Bowman, J., Ferguson, S. & Snape, I. The importance of soil characteristics to the structure of alkane-degrading bacterial communities on sub-Antarctic Macquarie Island. Soil Biol. Biochem. 42, 2012-2021 (2010).
36. Shade, A. et al. Culturing captures members of the soil rare biosphere. Environ. Microbiol. 14, 2247-2252 (2012).
37. Yooseph, S. et al. Genomic and functional adaptation in surface ocean planktonic prokaryotes. Nature 468, 60-66 (2010).
38. Kato, T., Haruki, M., Imanaka, T., Morikawa, M. & Kanaya, S. Isolation and characterization of long-chain-alkane degrading Bacillus thermoleovorans from deep subterranean petroleum reservoirs. J. Biosci. Bioeng. 91, 64-70 (2001). (Pubitemid 32163410)
39. Wang, L. et al. Isolation and characterization of a novel thermophilic Bacillus strain degrading long-chain n-alkanes. Extremophiles 10, 347-356 (2006). (Pubitemid 44325665)
40. Tourova, T. et al. alkB homologs in thermophilic bacteria of the genus Geobacillus. Mol. Biol. 42, 217-226 (2008). (Pubitemid 351752550)
41. Moore, R. C. & Purugganan, M. D. The early stages of duplicate gene evolution. Proc. Natl Acad. Sci. USA 100, 15682-15687 (2003). (Pubitemid 38021050)
42. Kondrashov, F. A., Rogozin, I. B., Wolf, Y. I. & Koonin, E. V. Selection in the evolution of gene duplications. Genome Biol. 3, 8. 1-8. 9 (2002).
43. Zhang, J. Evolution by gene duplication: an update. Trends Ecol. Evol. 18, 292-298 (2003). (Pubitemid 36631749)
44. Jones, C. D. & Begun, D. J. Parallel evolution of chimeric fusion genes. Proc. Natl Acad. Sci. USA 102, 11373-11378 (2005). (Pubitemid 41153827)
45. Gogarten, J. P. & Townsend, J. P. Horizontal gene transfer, genome innovation and evolution. Nature Rev. Microbiol. 3, 679-687 (2005). (Pubitemid 41195085)
46. Pasek, S., Risler, J.-L. & Brézellec, P. Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins. Bioinformatics 22, 1418-1423 (2006). (Pubitemid 43985310)
47. Daubin, V., Gouy, M. & Perriere, G. A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res. 12, 1080-1090 (2002). (Pubitemid 34785201)
48. Gogarten, J. P. & Olendzenski, L. Orthologs, paralogs and genome comparisons. Curr. Opin. Genet. Dev. 9, 630-636 (1999).
49. Syvanen, M. Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet. 28, 237-261 (1994).
50. Garcia-Vallvé, S., Romeu, A. & Palau, J. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10, 1719-1725 (2000).
51. Tan, H.-M. Bacterial catabolic transposons. Appl. Microbiol. Biotechnol. 51, 1-12 (1999). (Pubitemid 29066640)
52. Kok, M. et al. The Pseudomonas oleovorans alkane hydroxylase gene. Sequence and expression. J. Biol. Chem. 264, 5435-5441 (1989). (Pubitemid 19097995)
53. van Beilen, J. B. et al. Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes. Microbiology 147, 1621-1630 (2001).
54. van Beilen, J. B. et al. Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis. Environ. Microbiol. 6, 264-273 (2004). (Pubitemid 38261025)
55. Giebler, J., Wick, L. Y., Schloter, M., Harms, H. & Chatzinotas, A. Evaluating the assignment of alkB aerminal restriction fragments and sequence types to distinct bacterial taxa. Appl. Environ. Microbiol. 79, 3129-3132 (2013).
56. Cai, M. et al. Complete genome sequence of Amycolicicoccus subflavus DQS3-9A1T, an actinomycete isolated from crude oil-polluted soil. J. Bacteriol. 193, 4538-4539 (2011).
57. Patthy, L. Origin and Evolution of New Gene Functions (Springer Netherlands, 2003).
58. Nodate, M., Kubota, M. & Misawa, N. Functional expression system for cytochrome P450 genes using the reductase domain of self-sufficient P450RhF from Rhodococcus sp. NCIMB 9784. Appl. Microbiol. Biotechnol. 71, 455-462 (2006). (Pubitemid 44060948)
59. De Mot, R. & Parret, A. A novel class of self-sufficient cytochrome P450 monooxygenases in prokaryotes. Trends Microbiol. 10, 502-508 (2002). (Pubitemid 35284796)
60. Munro, A. W., Girvan, H. M. & McLean, K. J. Cytochrome P450-redox partner fusion enzymes. BBA-Gen. Subjects 1770, 345-359 (2007). (Pubitemid 46136745)
61. Peterson, J. A., Basu, D. & Coon, M. J. Enzymatic v-oxidation. J. Biol. Chem. 241, 5162-5164 (1966).
62. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004). (Pubitemid 38832724)
63. Eddy, S. R. Profile hidden Markov models. Bioinformatics 14, 755-763 (1998). (Pubitemid 28552108)
64. Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
65. Shanklin, J., Whittle, E. & Fox, B. G. Eight histidine residues are catalytically essential in a membrane-associated iron enzyme, stearoyl-CoA desaturase, and are conserved in alkane hydroxylase and xylenemonooxygenase. Biochemistry 33, 12787-12794 (1994). (Pubitemid 24352868)
66. Nelson, D. R. et al. P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 6, 1-42 (1996). (Pubitemid 26096749)
67. Letunic, I., Doerks, T. & Bork, P. SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res. 40, D302-D305 (2012).
68. Cole, J. et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37, D141-D145 (2009).
69. Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-D596 (2013).
70. Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363-1371 (2004). (Pubitemid 38854737)
71. Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425 (1987).
72. Langille, M. G. I. & Brinkman, F. S. L. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25, 664-665 (2009).
73. Markowitz, V. M. et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 36, D534-D538 (2008). (Pubitemid 351149780)
74. Huson, D. H., Mitra, S., Ruscheweyh, H. J., Weber, N. & Schuster, S. C. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 21, 1552-1560 (2011).