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Diverse alkane hydroxylase genes in microorganisms and environments

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Nie, Yong, Chi, Chang-Qiao, Fang, Hui, Liang, Jie-Liang, Lu, She-Lian, Lai, Guo-Li, Tang, Yue-Qin, Wu, Xiao-Lei·2014·Scientific Reports

DOI 10.1038/srep04968

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Abstract

AlkB and CYP153 are important alkane hydroxylases responsible for aerobic alkane degradation in bioremediation of oil-polluted environments and microbial enhanced oil recovery. Since their distribution in nature is not clear, we made the investigation among thus-far sequenced 3,979 microbial genomes and 137 metagenomes from terrestrial, freshwater, and marine environments. Hundreds of diverse alkB and CYP153 genes including many novel ones were found in bacterial genomes, whereas none were found in archaeal genomes. Moreover, these genes were detected with different distributional patterns in the terrestrial, freshwater, and marine metagenomes. Hints for horizontal gene transfer, gene duplication, and gene fusion were found, which together are likely responsible for diversifying the alkB and CYP153 genes adapt to the ubiquitous distribution of different alkanes in nature. In addition, different distributions of these genes between bacterial genomes and metagenomes suggested the potentially important roles of unknown or less common alkane degraders in nature.

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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
(1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,715
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
ARB: a software environment for sequence data
Ludwig, W. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh293 · Cited by 6,702
Profile hidden Markov models
Eddy, S. R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.755 · Cited by 5,515
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T., Garrity, G. M., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn879 · Cited by 4,762
Environmental genome shotgun sequencing of the sargasso sea
Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W., et al. (2004) · Science · doi:10.1126/science.1093857 · Cited by 4,376
P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature
Nelson, D. R., Koymans, L., Kamataki, T., Stegeman, J. J., Feyereisen, R., Waxman, D. J., Waterman, M. R., Gotoh, O., Coon, M. J., Estabrook, R. W., et al. (1996) · Pharmacogenetics · doi:10.1097/00008571-199602000-00002 · Cited by 2,945
Evolution by gene duplication: An update
Zhang, J. (2003) · Trends in Ecology & Evolution · doi:10.1016/s0169-5347(03)00033-8 · Cited by 2,201
SMART 7: recent updates to the protein domain annotation resource
Letunic, I., Doerks, T., & Bork, P. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr931 · Cited by 1,721
Integrative analysis of environmental sequences using MEGAN4
Huson, D. H., Mitra, S., Ruscheweyh, H.-J., Weber, N., & Schuster, S. C. (2011) · Genome Research · doi:10.1101/gr.120618.111 · Cited by 1,541
Sealing Plant Surfaces: Cuticular Wax Formation by Epidermal Cells
Samuels, L., Kunst, L., & Jetter, R. (2008) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.59.103006.093219 · Cited by 1,089
ARB: A Software Environment for Sequence Data
Westram, R., Bader, K., Prüsse, E., Kumar, Y., Meier, H., Glöckner, F. O., & Ludwig, W. (2011) · Handbook of Molecular Microbial Ecology I · doi:10.1002/9781118010518.ch46 · Cited by 1,043
Microbial Biosynthesis of Alkanes
Schirmer, A., Rude, M. A., Li, X., Popova, E., & del Cardayre, S. B. (2010) · Science · doi:10.1126/science.1187936 · Cited by 1,040
Horizontal gene transfer, genome innovation and evolution
Gogarten, J. P., & Townsend, J. P. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1204 · Cited by 1,020
Degradation of alkanes by bacteria
Rojo, F. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.01948.x · Cited by 822
Selection in the evolution of gene duplications
Kondrashov, F. A., Rogozin, I. B., Wolf, Y. I., & Koonin, E. V. (2002) · Genome Biology · doi:10.1186/gb-2002-3-2-research0008 · Cited by 782
Eight Histidine Residues Are Catalytically Essential in a Membrane-Associated Iron Enzyme, Stearoyl-CoA Desaturase, and Are Conserved in Alkane Hydroxylase and Xylene Monooxygenase
Shanklin, J., Whittle, E., & Fox, B. G. (1994) · Biochemistry · doi:10.1021/bi00209a009 · Cited by 763
The early stages of duplicate gene evolution
Moore, R. C., & Purugganan, M. D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2535513100 · Cited by 647
Alkane hydroxylases involved in microbial alkane degradation
van Beilen, J. B., & Funhoff, E. G. (2007) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-006-0748-0 · Cited by 640
Molecular diversity and ecology of microbial plankton
Giovannoni, S. J., & Stingl, U. (2005) · Nature · doi:10.1038/nature04158 · Cited by 575
Insect pheromones—an overview of biosynthesis and endocrine regulation
Tillman, J. A., Seybold, S. J., Jurenka, R. A., & Blomquist, G. J. (1999) · Insect Biochemistry and Molecular Biology · doi:10.1016/s0965-1748(99)00016-8 · Cited by 552
Biophysical and biochemical characteristics of cutin, a plant barrier biopolymer
Heredia, A. (2003) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/s0304-4165(02)00510-x · Cited by 471
Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir
Feng, L., Wang, W., Cheng, J., Ren, Y., Zhao, G., Gao, C., Tang, Y., Liu, X., Han, W., Peng, X., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0609650104 · Cited by 396
Self-citation
IslandViewer: an integrated interface for computational identification and visualization of genomic islands
Langille, M. G. I., & Brinkman, F. S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp030 · Cited by 388
IMG/M: a data management and analysis system for metagenomes
Markowitz, V. M., Ivanova, N. N., Szeto, E., Palaniappan, K., Chu, K., Dalevi, D., Chen, I.-M. A., Grechkin, Y., Dubchak, I., Anderson, I., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm869 · Cited by 381
Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes
Garcia-Vallve, S. (2000) · Genome Research · doi:10.1101/gr.130000 · Cited by 368
Genomic and functional adaptation in surface ocean planktonic prokaryotes
Yooseph, S., Nealson, K. H., Rusch, D. B., McCrow, J. P., Dupont, C. L., Kim, M., Johnson, J., Montgomery, R., Ferriera, S., Beeson, K., et al. (2010) · Nature · doi:10.1038/nature09530 · Cited by 335
Cytochrome P450 Alkane Hydroxylases of the CYP153 Family Are Common in Alkane-Degrading Eubacteria Lacking Integral Membrane Alkane Hydroxylases
van Beilen, J. B., Funhoff, E. G., van Loon, A., Just, A., Kaysser, L., Bouza, M., Holtackers, R., Röthlisberger, M., Li, Z., & Witholt, B. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.1.59-65.2006 · Cited by 333
Analysis of Pseudomonas putida alkane-degradation gene clusters and flanking insertion sequences: evolution and regulation of the alk genes The EMBL accession numbers for the sequences reported in this paper are AJ245436 [P. putida (oleovorans) GPo1 alk gene clusters and flanking DNA], AJ233397 (P. putida P1 alk gene clusters and flanking DNA), AJ249793 (P. putida P1 nahKJ genes), AJ249825 [P. putida (oleovorans) GPo1 16S RNA gene] and AJ271219 (P. putida P1 16S RNA gene).
van Beilen, J. B., Panke, S., Lucchini, S., Franchini, A. G., Röthlisberger, M., & Witholt, B. (2001) · Microbiology · doi:10.1099/00221287-147-6-1621 · Cited by 326
HORIZONTAL GENE TRANSFER: Evidence and Possible Consequences
Syvanen, M. (1994) · Annual Review of Genetics · doi:10.1146/annurev.ge.28.120194.001321 · Cited by 318
A Phylogenomic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History
Daubin, V., Gouy, M., & Perrière, G. (2002) · Genome Research · doi:10.1101/gr.187002 · Cited by 313
Functional Analysis of Alkane Hydroxylases from Gram-Negative and Gram-Positive Bacteria
Smits, T. H. M., Balada, S. B., Witholt, B., & van Beilen, J. B. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.6.1733-1742.2002 · Cited by 293
Degradation of petroleum hydrocarbons (C6–C40) and crude oil by a novel Dietzia strain
Wang, X.-B., Chi, C.-Q., Nie, Y., Tang, Y.-Q., Tan, Y., Wu, G., & Wu, X.-L. (2011) · Bioresource Technology · doi:10.1016/j.biortech.2011.06.009 · Cited by 260
Self-citation
Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils
Yergeau, E., Sanschagrin, S., Beaumier, D., & Greer, C. W. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030058 · Cited by 250
Enzymatic ω-Oxidation
Peterson, J. A., Basu, D., & Coon, M. J. (1966) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)99684-5 · Cited by 247
Mid-chain branched mono- and dimethyl alkanes in hot spring cyanobacterial mats: A direct biogenic source for branched alkanes in ancient sediments?
Shiea, J., Brassell, S. C., & Ward, D. M. (1990) · Organic Geochemistry · doi:10.1016/0146-6380(90)90001-g · Cited by 242
Gene Cloning and Characterization of Multiple Alkane Hydroxylase Systems in Rhodococcus Strains Q15 and NRRL B-16531
Whyte, L. G., Smits, T. H. M., Labbé, D., Witholt, B., Greer, C. W., & van Beilen, J. B. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.12.5933-5942.2002 · Cited by 240
Molecular screening for alkane hydroxylase genes in Gram‐negative and Gram‐positive strains
Smits, T. H. M., Röthlisberger, M., Witholt, B., & Van Beilen, J. B. (1999) · Environmental Microbiology · doi:10.1046/j.1462-2920.1999.00037.x · Cited by 222
Culturing captures members of the soil rare biosphere
Shade, A., Hogan, C. S., Klimowicz, A. K., Linske, M., McManus, P. S., & Handelsman, J. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2012.02817.x · Cited by 210
Hydrocarbons of Blue-Green Algae: Geochemical Significance
Winters, K., Parker, P. L., & Van Baalen, C. (1969) · Science · doi:10.1126/science.163.3866.467 · Cited by 208
Cytochrome P450–redox partner fusion enzymes
Munro, A. W., Girvan, H. M., & McLean, K. J. (2007) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2006.08.018 · Cited by 205
The Pseudomonas oleovorans alkane hydroxylase gene
Kok, M., Oldenhuis, R., van der Linden, M. P. G., Raatjes, P., Kingma, J., van Lelyveld, P. H., & Witholt, B. (1989) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)83564-5 · Cited by 195
Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins
Pasek, S., Risler, J.-L., & Brézellec, P. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl135 · Cited by 172
Enzymatic ω-Oxidation
Lode, E. T., & Coon, M. J. (1971) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)62479-2 · Cited by 144
Isolation and characterization of a novel thermophilic Bacillus strain degrading long-chain n-alkanes
Wang, L., Tang, Y., Wang, S., et al. (2006) · Extremophiles · doi:10.1007/s00792-006-0505-4 · Cited by 137
Self-citation
Orthologs, paralogs and genome comparisons
Gogarten, J. P., & Olendzenski, L. (1999) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(99)00029-5 · Cited by 135
A novel class of self-sufficient cytochrome P450 monooxygenases in prokaryotes
Mot, R. D., & Parret, A. H. A. (2002) · Trends in Microbiology · doi:10.1016/s0966-842x(02)02458-7 · Cited by 122
Responses of Microbial Communities in Arctic Sea Ice After Contamination by Crude Petroleum Oil
Brakstad, O. G., Nonstad, I., Faksness, L.-G., et al. (2007) · Microbial Ecology · doi:10.1007/s00248-007-9299-x · Cited by 121
Characterization of two alkane hydroxylase genes from the marine hydrocarbonoclastic bacterium Alcanivorax borkumensis
van Beilen, J. B., Marin, M., Smits, T. H. M., Röthlisberger, M., Franchini, A. G., Witholt, B., & Rojo, F. (2004) · Environmental Microbiology · doi:10.1111/j.1462-2920.2004.00567.x · Cited by 119
Isolation and Characterization of Long-Chain-Alkane Degrading Bacillus thermoleovorans from Deep Subterranean Petroleum Reservoirs.
Kato, T., Haruki, M., Imanaka, T., Morikawa, M., & Kanaya, S. (2001) · Journal of Bioscience and Bioengineering · doi:10.1016/s1389-1723(01)80113-4 · Cited by 101
Involvement of an Alkane Hydroxylase System of Gordonia sp. Strain SoCg in Degradation of Solid n -Alkanes
Piccolo, L. L., PASQUALE, C. D., Fodale, R., Puglia, A. M., & Quatrini, P. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.02180-10 · Cited by 89
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
Nie, Y., Liang, J., Fang, H., Tang, Y., & Wu, X. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.00203-11 · Cited by 81
Self-citation
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
Nie, Y., Liang, J., Fang, H., Tang, Y., & Wu, X. (2013) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-013-4821-1 · Cited by 79
Self-citation
Parallel evolution of chimeric fusion genes
Jones, C. D., & Begun, D. J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0503528102 · Cited by 73
Identification of different alkane hydroxylase systems inRhodococcus ruberstrain SP2B, an hexane-degrading actinomycete
Amouric, A., Quéméneur, M., Grossi, V., Liebgott, P.-P., Auria, R., & Casalot, L. (2009) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2009.04592.x · Cited by 58
The importance of soil characteristics to the structure of alkane-degrading bacterial communities on sub-Antarctic Macquarie Island
Powell, S. M., Bowman, J. P., Ferguson, S. H., & Snape, I. (2010) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2010.07.027 · Cited by 54
Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments
Schulz, S., Giebler, J., Chatzinotas, A., Wick, L. Y., Fetzer, I., Welzl, G., Harms, H., & Schloter, M. (2012) · The ISME Journal · doi:10.1038/ismej.2012.17 · Cited by 53
Fractionation of inducible alkane hydroxylase activity in Pseudomonas putida and characterization of hydroxylase-negative plasmid mutations
Benson, S. A., Fennewald, M., Shapiro, J. A., et al. (1977) · Journal of Bacteriology · doi:10.1128/jb.132.2.614-621.1977 · Cited by 47
Characterization of a Novel Rieske-Type Alkane Monooxygenase System in Pusillimonas sp. Strain T7-7
Li, P., Wang, L., & Feng, L. (2013) · Journal of Bacteriology · doi:10.1128/jb.02107-12 · Cited by 44
Biosynthesis of hydrocarbons by algae: Decarboxylation of stearic acid to N‐heptadecane inAnacystis nidulans determined by13C‐ and2H‐labeling and13C nuclear magnetic resonance
MCINNES, A. G., Walter, J. A., & Wright, J. L. C. (1980) · Lipids · doi:10.1007/bf02534009 · Cited by 41
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
Dembitsky, V. M., & Srebnik, M. (2002) · Biochemistry (Moscow) · doi:10.1023/a:1021309623541 · Cited by 33
Isolation of a nitrate-reducing bacteria strain from oil field brine and the inhibition of sulfate-reducing bacteria
Zhuang, W., Duan, J., Chu, L.-Y., & Shao, H. (2011) · AFRICAN JOURNAL OF BIOTECHNOLOGY · doi:10.5897/ajb10.1814 · Cited by 14
Isolation of a nitrate-reducing bacteria strain from oil field brine and the inhibition of sulfate-reducing bacteria
Wen, Z., Jizhou, D., Chu, L.-Y., & Shao, H. (2011) · Knowledge Repository of Yantai Institute of Coastal Zone Research, CAS (Yantai Institute of Coastal Zone Research) · doi:10.4314/ajb.v10i49 · Cited by 13

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Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon‐degrading bacterium Alcanivorax borkumensis SK2 T
Gregson, B. H., Metodieva, G., Metodiev, M. V., & McKew, B. A. (2019) · Environmental Microbiology · doi:10.1111/1462-2920.14620 · Cited by 46
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Authors: Nie, Y., Chi, C.-Q., Fang, H., Liang, J.-L., Lu, S.-L., Lai, G.-L., Tang, Y.-Q., & Wu, X.-L.
Venue: Scientific Reports
Publisher: Springer Science and Business Media LLC
Published: 2014-05-15
Volume: 4
Issue: 1
Pages: 4968-4968
ISSN: 2045-2322 (ISSN-L)
DOI: 10.1038/srep04968
OpenAlex: W2069283211
Cited by: 261
References: 65
FWCI: 10.01
Type: journal article
Language: en
Open access: gold

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Diverse alkane hydroxylase genes in microorganisms and environments

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