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

Volumn 8, Issue 8, 2013, Pages

  Nie, Yong ^a   Fang, Hui ^a   Li, Yan ^a   Chi, Chang Qiao ^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 HYDROXYLASE; CYTOCHROME P450; CYTOCHROME P450 CYP153; INTEGRAL MEMBRANE NON HEME IRON MONOOXYGENASE; OXYGENASE; PETROLEUM; PROPANE MONOOXYGENASE; SODIUM CHLORIDE; UNCLASSIFIED DRUG;

AMYCOLICICOCCUS SUBFLAVUS DQS3 9A1; ARTICLE; BACTERIAL GROWTH; BIOREMEDIATION; CARBON SOURCE; CONTROLLED STUDY; DEGRADATION; EVOLUTIONARY ADAPTATION; GENE SEQUENCE; GENOME ANALYSIS; HALOPHILE; HYDROXYLATION; NONHUMAN; NUCLEOTIDE SEQUENCE; NUTRIENT CONTENT; OIL FIELD; OSMOTIC PRESSURE; OSMOTIC STRESS; PRECIPITATION; SALINITY;

ACTINOMYCETALES; ADAPTATION, PHYSIOLOGICAL; ALKANES; ENVIRONMENT; GENOME, BACTERIAL; GENOMICS; HYDROLASES; HYDROXYLATION; PETROLEUM; SALINITY; TRANSCRIPTION, GENETIC;

EID: 84881490791     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0070986     Document Type: Article

References (52)

1. Brown LR, (2010) Microbial enhanced oil recovery (MEOR). Current Opinion in Microbiology 13: 316-320.
2. Leahy JG, Colwell RR, (1990) Microbial degradation of hydrocarbons in the environment. Microbiology and Molecular Biology Reviews 54: 305-315.
3. Kok M, Oldenhuis R, Van Der Linden M, Raatjes P, Kingma J, et al. (1989) The Pseudomonas oleovorans alkane hydroxylase gene. Journal of Biological Chemistry 264: 5435-5441.
4. Maier T, Forster HH, Asperger O, Hahn U, (2001) Molecular characterization of the 56-kDa CYP153 from Acinetobacter sp. EB104. Biochemical and Biophysical Research Communications 286: 652-658.
5. van Beilen JB, Funhoff EG, (2007) Alkane hydroxylases involved in microbial alkane degradation. Applied Microbiology and Biotechnology 74: 13-21.
6. Merkx M, Kopp DA, Sazinsky MH, Blazyk JL, Müller J, et al. (2001) Dioxygen Activation and Methane Hydroxylation by Soluble Methane Monooxygenase: A Tale of Two Irons and Three Proteins. Angewandte Chemie (International Edition) 40: 2782-2807.
7. Kopp DA, Lippard SJ, (2002) Soluble methane monooxygenase: activation of dioxygen and methane. Current Opinion in Chemical Biology 6: 568-576.
8. Feng L, Wang W, Cheng J, Ren Y, Zhao G, et al. (2007) Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir. Proc Natl Acad Sci U S A 104: 5602-5607.
9. Throne-Holst M, Wentzel A, Ellingsen TE, Kotlar HK, Zotchev SB, (2007) Identification of Novel Genes Involved in Long-Chain n-Alkane Degradation by Acinetobacter sp. Strain DSM 17874. Applied and Environmental Microbiology 73: 3327-3332.
10. Nie Y, Liang J, Fang H, Tang YQ, Wu XL, (2011) Two novel alkane hydroxylase-rubredoxin fusion genes isolated from a Dietzia bacterium and the functions of fused rubredoxin domains in long-chain n-alkane degradation. Applied and Environmental Microbiology 77: 7279-7288.
11. Wentzel A, Ellingsen TE, Kotlar HK, Zotchev SB, Throne-Holst M, (2007) Bacterial metabolism of long-chain n-alkanes. Appl Microbiol Biotechnol 76: 1209-1221.
12. Wang XB, Chi CQ, Nie Y, Tang YQ, Tan Y, et al. (2011) Degradation of petroleum hydrocarbons (C6-C40) and crude oil by a novel Dietzia strain. Bioresource Technology 102: 7755-7761.
13. Bihari Z, Szvetnik A, Szabó Z, Blastyák A, Zombori Z, et al. (2011) Functional analysis of long-chain n-alkane degradation by Dietzia spp. FEMS Microbiology Letters 316: 100-107.
14. Liu C, Wang W, Wu Y, Zhou Z, Lai Q, et al. (2011) Multiple alkane hydroxylase systems in a marine alkane degrader, Alcanivorax dieselolei B-5. Environmental Microbiology 13: 1168-1178.
15. Wang YN, Chi CQ, Cai M, Lou ZY, Tang YQ, et al. (2010) Amycolicicoccus subflavus gen. nov., sp. nov., an actinomycete isolated from a saline soil contaminated by crude oil. International Journal of Systematic and Evolutionary Microbiology 60: 638-643.
16. Cai M, Chen WM, Nie Y, Chi CQ, Wang YN, et al. (2011) Complete genome sequence of Amycolicicoccus subflavus DQS3-9A1T, an actinomycete isolated from crude oil-polluted soil. Journal of Bacteriology 193: 4538-4539.
17. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
18. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59.
19. Delcher AL, Bratke KA, Powers EC, Salzberg SL, (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
20. Langille MGI, Brinkman FSL, (2009) IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25: 664-665.
21. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, et al. (2010) The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Research 38: D382-390.
22. Sakia R (1992) The Box-Cox transformation technique: a review. The statistician: 169-178.
23. Yamada T, Letunic I, Okuda S, Kanehisa M, Bork P, (2011) iPath2.0: interactive pathway explorer. Nucleic Acids Research 39: W412-415.
24. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-DD CT method. Methods 25: 402-408.
25. Langille MG, Hsiao WW, Brinkman FS, (2008) Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 9: 329.
26. Whyte LG, Smits THM, Labbe D, Witholt B, Greer CW, et al. (2002) Gene Cloning and Characterization of Multiple Alkane Hydroxylase Systems in Rhodococcus Strains Q15 and NRRL B-16531. Applied and Environmental Microbiology 68: 5933-5942.
27. McLeod MP, Warren RL, Hsiao WWL, Araki N, Myhre M, et al. (2006) The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proceedings of the National Academy of Sciences 103: 15582-15587.
28. Rojo F, (2009) Degradation of alkanes by bacteria. Environmental Microbiology 11: 2477-2490.
29. Epstein W, (2003) The roles and regulation of potassium in bacteria. Progress in Nucleic Acid Research and Molecular Biology 75: 293-320.
30. Kramer R, Morbach S, (2004) BetP of Corynebacterium glutamicum, a transporter with three different functions: betaine transport, osmosensing, and osmoregulation. Biochimica et Biophysica Acta: Protein Structure and Molecular Enzymology 1658: 31-36.
31. Wood JM, (1999) Osmosensing by bacteria: signals and membrane-based sensors. Microbiology and Molecular Biology Reviews 63: 230-262.
32. Moker N, Brocker M, Schaffer S, Kramer R, Morbach S, et al. (2004) Deletion of the genes encoding the MtrA-MtrB two-component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Molecular Microbiology 54: 420-438.
33. Kramer R, (2009) Osmosensing and osmosignaling in Corynebacterium glutamicum. Amino Acids 37: 487-497.
34. Heermann R, Jung K, (2010) The complexity of the 'simple' two-component system KdpD/KdpE in Escherichia coli. FEMS Microbiology Letters 304: 97-106.
35. Hunte C, Screpanti E, Venturi M, Rimon A, Padan E, et al. (2005) Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH. Nature 435: 1197-1202.
36. Hiramatsu T, Kodama K, Kuroda T, Mizushima T, Tsuchiya T, (1998) A Putative Multisubunit Na+/H+ Antiporter fromStaphylococcus aureus. Journal of Bacteriology 180: 6642-6648.
37. Nie Y, Tang YQ, Li Y, Chi CQ, Cai M, et al. (2012) The Genome Sequence of Polymorphum gilvum SL003B-26A1T Reveals Its Genetic Basis for Crude Oil Degradation and Adaptation to the Saline Soil. PLoS one 7: e31261.
38. Cai M, Wang L, Cai H, Li Y, Tang YQ, et al. (2011) Rubrimonas shengliensis sp. nov. and Polymorphum gilvum gen. nov., sp. nov., novel members of Alphaproteobacteria from crude oil contaminated saline soil. Systematic and Applied Microbiology 34: 321-327.
39. Curcic R, Dhandayuthapani S, Oeretic V, (1994) Gene expression in mycobacteria: transcriptional fusions based on xylE and analysis of the promoter region of the response regulator mtrA from Mycobacterium tuberculosis. Molecular Microbiology 13: 1057-1064.
40. Heermann R, Jung K, (2004) Structural features and mechanisms for sensing high osmolarity in microorganisms. Current Opinion in Microbiology 7: 168-174.
41. Kryachko Y, Dong X, Sensen CW, Voordouw G, (2012) Compositions of microbial communities associated with oil and water in a mesothermic oil field. Antonie Van Leeuwenhoek 101: 493-506.
42. Li H, Yang SZ, Mu BZ, Rong ZF, Zhang J, (2007) Molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an offshore oilfield. FEMS Microbiology Ecology 60: 74-84.
43. Wang XB, Nie Y, Tang YQ, Wu G, Wu XL, (2013) n-Alkane Chain Length Alters Dietzia sp. Strain DQ12-45-1b Biosurfactant Production and Cell Surface Activity. Appl Environ Microbiol 79: 400-402.
44. Gallegos MT, Schleif R, Bairoch A, Hofmann K, Ramos JL, (1997) Arac/XylS family of transcriptional regulators. Microbiology and Molecular Biology Reviews 61: 393-410.
45. Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, et al. (2005) The TetR family of transcriptional repressors. Microbiology and Molecular Biology Reviews 69: 326-356.
46. Schneiker S, dos Santos VAPM, Bartels D, Bekel T, Brecht M, et al. (2006) Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nature Biotechnology 24: 997-1004.
47. Wang W, Shao Z, (2012) Genes involved in alkane degradation in the Alcanivorax hongdengensis strain A-11-3. Applied Microbiology and Biotechnology 94: 437-448.
48. Nie Y, Liang JL, Fang H, Tang YQ, Wu XL (2013) 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. Applied Microbiology and Biotechnology: DOI: 10.1007/s00253-00013-04821-00251 (In press).
49. Stothard P, Wishart DS, (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21: 537-539.
50. Bonnefoy V, Demoss JA, (1994) Nitrate reductases in Escherichia coli. Antonie Van Leeuwenhoek 66: 47-56.
51. Ogawa K-i, Akagawa E, Yamane K, Sun Z-W, LaCelle M, et al. (1995) The nasB operon and nasA gene are required for nitrate/nitrite assimilation in Bacillus subtilis. Journal of Bacteriology 177: 1409-1413.
52. Luque I, Flores E, Herrero A, (1993) Nitrite reductase gene from Synechococcus sp. PCC 7942: homology between cyanobacterial and higher-plant nitrite reductases. Plant Molecular Biology 21: 1201-1205.