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Paper 4 – Reference list

March 27, 2017

1 Leave a comment on paragraph 1 0 Here are the references for paper 4. I’ve included PubMed links for most of them so you should be able to look up any background information you need by simply clicking on the link.

2 Leave a comment on paragraph 2 0 1.

3 Leave a comment on paragraph 3 0 Kanaly, R. & Harayama, S. Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by bacteria. J. Bacteriol.182, 2059–2067 (2000).

4 Leave a comment on paragraph 4 0 PubMed

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6 Leave a comment on paragraph 6 0 Kweon, O. et al. Polycyclic Aromatic Hydrocarbon Metabolic Network in Mycobacterium vanbaalenii PYR-1. J. Bacteriol. 193, 4326–4337 (2011).

7 Leave a comment on paragraph 7 0 PubMed

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9 Leave a comment on paragraph 9 0 Fuchs, G., Boll, M. & Heider, J. Microbial degradation of aromatic compounds – from one strategy to four. Nat. Rev. Microbiol. 9, 803–816 (2011).

10 Leave a comment on paragraph 10 0 PubMed

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12 Leave a comment on paragraph 12 0 Kweon, O. et al. A polyomic approach to elucidate the fluoranthene-degradative pathway in Mycobacterium vanbaalenii PYR-1. J. Bacteriol. 189, 4635–4647 (2007).

13 Leave a comment on paragraph 13 0 PubMed

14 Leave a comment on paragraph 14 0 5.

15 Leave a comment on paragraph 15 0 Lee, S. E., Seo, J. S., Keum, Y. S., Lee, K. J. & Li, Q. X. Fluoranthene metabolism and associated proteins in Mycobacterium sp. JS14. Proteomics 7, 2059–2069 (2007).

16 Leave a comment on paragraph 16 0 PubMed

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18 Leave a comment on paragraph 18 0 Keum, Y. S., Seo, J. S., Hu, Y. & Li, Q. X. Degradation pathways of phenanthrene by Sinorhizobium sp. C4. Appl. Microbiol. Biotechnol. 71, 935–941 (2006).

19 Leave a comment on paragraph 19 0 PubMed

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21 Leave a comment on paragraph 21 0 van Herwijnen, R. et al. Elucidation of the metabolic pathway of fluorene and cometabolic pathways of phenanthrene, fluoranthene, anthracene and dibenzothiophene by Sphingomonas sp. LB126. Res. Microbiol. 154, 199–206 (2003).

22 Leave a comment on paragraph 22 0 PubMed

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24 Leave a comment on paragraph 24 0 Akhtar, N., Ghauri, M. A., Anwar, M. A. & Akhtar, K. Analysis of the dibenzothiophene metabolic pathway in a newly isolated Rhodococcus spp. FEMS Microbiol. Lett. 301, 95–102 (2009).

25 Leave a comment on paragraph 25 0 PubMed

26 Leave a comment on paragraph 26 0 9.

27 Leave a comment on paragraph 27 0 Šepič, E., Bricelj, M. & Leskovsek, H. Degradation of fluoranthene by Pasteurella sp. IFA and Mycobacterium sp. PYR-1:isolation and identification of metabolites. J. Appl. Microbiol. 85, 746–754 (1998).

28 Leave a comment on paragraph 28 0 PubMed

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30 Leave a comment on paragraph 30 0 Mallick, S., Chatterjee, S. & Dutta, T. K. A novel degradation pathway in the assimilation of phenanthrene by Staphylococcus sp strain PN/Y via meta-cleavage of 2-hydroxy-1-naphthoic acid: formation of trans-2,3-dioxo-5-(2′-hydroxyphenyl)pent-4-enoic acid. Microbiology 153, 2104–2115 (2007).

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33 Leave a comment on paragraph 33 0 Marx, C. J., Miller, J. A., Chistoserdova, L. & Lidstrom, M. E.Multiple formaldehyde oxidation/detoxification pathways in Burkholderia fungorum LB400. J. Bacteriol. 186, 2173–2178 (2004).

34 Leave a comment on paragraph 34 0 PubMed

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36 Leave a comment on paragraph 36 0 Prabhu, Y. & Phale, P. S. Biodegradation of phenanthrene by Pseudomonas sp. strain PP2: novel metabolic pathway, role of biosurfactant and cell surface hydrophobicity in hydrocarbon assimilation. Appl. Microbiol. Biotechnol. 61, 342–351 (2003).

37 Leave a comment on paragraph 37 0 PubMed

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39 Leave a comment on paragraph 39 0 Baboshin, M. et al. Conversion of polycyclic aromatic hydrocarbons by Sphingomonas sp. VKM B-2434. Biodegradation19, 567–576 (2008).

40 Leave a comment on paragraph 40 0 PubMed

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42 Leave a comment on paragraph 42 0 Weissenfels, W. D., Beyer, M. & Klein, J. Degradation of phenanthrene, fluorene and fluoranthene by pure bacterial cultures. Appl. Microbiol. Biotechnol. 32, 479–484 (1990).

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45 Leave a comment on paragraph 45 0 Juhasz, A. L., Britz, M. L. & Stanley, G. A. Degradation of fluoranthene, pyrene, benz[a]anthracene and dibenz[a,h]anthracene by Burkholderia cepacia. J. Appl. Microbiol.83, 189–198 (1997).

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47 Leave a comment on paragraph 47 0 Gordon, L. & Dobson, A. D. Fluoranthene degradation in Pseudomonas alcaligenes PA-10. Biodegradation 12, 393–400 (2001).

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50 Leave a comment on paragraph 50 0 Rehmann, K., Hertkorn, N. & Kettrup, A. A. Fluoranthene metabolism in Mycobacterium sp. strain KR20: identity of pathway intermediates during degradation and growth. Microbiology 147, 2783–2794 (2001).

51 Leave a comment on paragraph 51 0 PubMed

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53 Leave a comment on paragraph 53 0 López, Z., Vila, J., Minguillón, C. & Grifoll, M. Metabolism of fluoranthene by Mycobacterium sp. strain AP1. Appl. Microbiol. Biotechnol. 70, 747–756 (2006).

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56 Leave a comment on paragraph 56 0 Walter, U., Beyer, M., Klein, J. & Rehm, H.-J. Degradation of pyrene by Rhodococcus sp. UW1. Appl. Microbiol. Biotechnol. 34, 671–676 (1991).

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58 Leave a comment on paragraph 58 0 Wu, Y. R. et al. Isolation of marine benzo[a]pyrene-degrading Ochrobactrum sp. BAP5 and proteins characterization. J. Environ. Sci. (China) 21, 1446–1451 (2009).

59 Leave a comment on paragraph 59 0 PubMed

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61 Leave a comment on paragraph 61 0 Yuan, J., Lai, Q., Zheng, T. & Shao, Z. Novosphingobium indicum sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from a deep-sea environment. Int. J. Syst. Evol. Microbiol.59, 2084–2088 (2009).

62 Leave a comment on paragraph 62 0 PubMed

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64 Leave a comment on paragraph 64 0 Geiselbrecht, A. D., Hedlund, B. P., Tichi, M. A. & Staley, J. T.Isolation of marine polycyclic aromatic hydrocarbon (PAH)-degrading Cycloclasticus strains from the Gulf of Mexico and comparison of their PAH degradation ability with that of Puget Sound Cycloclasticus strains. Appl. Environ. Microbiol. 64, 4703–4710 (1998).

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67 Leave a comment on paragraph 67 0 Lai, Q., Cao, J., Yuan, J., Li, F. & Shao, Z. Celeribacter indicus sp. nov. a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov. Int. J. Syst. Evol. Microbiol. 64, 4160–4167 (2014).

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69 Leave a comment on paragraph 69 0 24.

70 Leave a comment on paragraph 70 0 Weissenfels, W., Beyer, M., Klein, J. & Rehm, H. Microbial metabolism of fluoranthene: isolation and identification of ring fission products. Appl. Microbiol. Biotechnol. 34, 528–535 (1991).

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72 Leave a comment on paragraph 72 0 Kim, S. J., Kweon, O., Jones, R. C., Edmondson, R. D. & Cerniglia, C. E. Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation19, 859–881 (2008).

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75 Leave a comment on paragraph 75 0 Hickey, W. J., Chen, S. & Zhao, J. The phn Island: A New Genomic Island Encoding Catabolism of Polynuclear Aromatic Hydrocarbons. Front. microbiol. 3, 125 (2012).

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78 Leave a comment on paragraph 78 0 Math, R. K. et al. Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions: cold tolerance and aromatic hydrocarbon metabolism. PLoS ONE 7, e35784 (2012).

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81 Leave a comment on paragraph 81 0 Yagi, J. M., Sims, D., Brettin, T., Bruce, D. & Madsen, E. L. The genome of Polaromonas naphthalenivorans strain CJ2, isolated from coal tar-contaminated sediment, reveals physiological and metabolic versatility and evolution through extensive horizontal gene transfer. Environ. Microbiol. 11, 2253–2270 (2009).

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84 Leave a comment on paragraph 84 0 Langille, M. G. & Brinkman, F. S. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 25, 664–665 (2009).

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87 Leave a comment on paragraph 87 0 Beales, N. Adaptation of microorganisms to cold temperatures, weak acid preservatives, low pH, and osmotic stress: a review. Compr. Rev. Food Sci. Food Saf. 3, 1–20 (2004).

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89 Leave a comment on paragraph 89 0 Saier, M. H., Jr, Yen, M. R., Noto, K., Tamang, D. G. & Elkan, C. The Transporter Classification Database: recent advances. Nucleic Acids Res. 37, D274–278 (2009).

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92 Leave a comment on paragraph 92 0 Davidson, A. L., Dassa, E., Orelle, C. & Chen, J. Structure, function, and evolution of bacterial ATP-binding sette systems. Microbiol. Mol. Biol. Rev. 72, 317–364 (2008).

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95 Leave a comment on paragraph 95 0 Chang, H. K., Dennis, J. J. & Zylstra, G. J. Involvement of two transport systems and a specific porin in the uptake of phthalate by Burkholderia spp. J. Bacteriol. 191, 4671–4673 (2009).

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98 Leave a comment on paragraph 98 0 Mulligan, C., Fischer, M. & Thomas, G. H. Tripartite ATP-independent periplasmic (TRAP) transporters in bacteria and archaea. FEMS Microbiol. Rev. 35, 68–86 (2011).

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101 Leave a comment on paragraph 101 0 Chaudhry, M. T. et al. Genome-wide investigation of aromatic acid transporters in Corynebacterium glutamicum. Microbiology 153, 857–865 (2007).

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104 Leave a comment on paragraph 104 0 Hosaka, M. et al. Novel tripartite aromatic acid transporter essential for terephthalate uptake in Comamonas sp. strain E6. Appl. Environ. Microbiol. 79, 6148–6155 (2013).

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107 Leave a comment on paragraph 107 0 Kahng, H. Y., Byrne, A. M., Olsen, R. H. & Kukor, J. J.Characterization and role of tbuX in utilization of toluene by Ralstonia pickettii PKO1. J. Bacteriol. 182, 1232–1242 (2000).

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110 Leave a comment on paragraph 110 0 Maddocks, S. E. & Oyston, P. C. Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154, 3609–3623 (2008).

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113 Leave a comment on paragraph 113 0 Tropel, D. & van der Meer, J. R. Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Microbiol. Mol. Biol. Rev. 68, 474–500 (2004).

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116 Leave a comment on paragraph 116 0 Molina-Henares, A. J., Krell, T., Eugenia Guazzaroni, M., Segura, A. & Ramos, J. L. Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors. FEMS Microbiol. Rev. 30, 157–186 (2006).

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119 Leave a comment on paragraph 119 0 Mazur, A., Majewska, B., Stasiak, G., Wielbo, J. & Skorupska, A.repABC-based replication systems of Rhizobium leguminosarum bv. trifolii TA1 plasmids: incompatibility and evolutionary analyses. Plasmid 66, 53–66 (2011).

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122 Leave a comment on paragraph 122 0 Markowitz, V. M. et al. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res.38, D382–390 (2010).

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125 Leave a comment on paragraph 125 0 Kuyukina, M. S. & Ivshina, I. B. in Biology of Rhodococcus Vol. 16 Microbiology Monographs (ed Héctor M. Alvarez) Ch. Rhodococcus Biosurfactants: Biosynthesis, Properties, and Potential Applications, 291–313 (Springer, 2010).

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127 Leave a comment on paragraph 127 0 Himmelreich, R. et al. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24, 4420–4449 (1996).

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133 Leave a comment on paragraph 133 0 Nie, Y. et al. 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 (2012).

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136 Leave a comment on paragraph 136 0 Kim, J. S., Chang, J. H., Chung, S. I. & Yum, J. S. Molecular cloning and characterization of the Helicobacter pylori fliD gene, an essential factor in flagellar structure and motility. J. Bacteriol. 181, 6969–6976 (1999).

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139 Leave a comment on paragraph 139 0 Mukherjee, S., Babitzke, P. & Kearns, D. B. FliW and FliS function independently to control cytoplasmic flagellin levels in Bacillus subtilis. J. Bacteriol. 195, 297–306 (2013).

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142 Leave a comment on paragraph 142 0 Wilkinson, D. A., Chacko, S. J., Venien-Bryan, C., Wadhams, G. H. & Armitage, J. P. Regulation of flagellum number by FliA and FlgM and role in biofilm formation by Rhodobacter sphaeroides. J. Bacteriol. 193, 4010–4014 (2011).

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145 Leave a comment on paragraph 145 0 Macnab, R. M. Type III flagellar protein export and flagellar assembly. Biochim. Biophys. Acta 1694, 207–217 (2004).

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148 Leave a comment on paragraph 148 0 Pilsl, H., Smajs, D. & Braun, V. Characterization of colicin S4 and its receptor, OmpW, a minor protein of the Escherichia coli outer membrane. J. Bacteriol. 181, 3578–3581 (1999).

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154 Leave a comment on paragraph 154 0 van den Berg, B., Black, P. N., Clemons, W. M., Jr & Rapoport, T. A.Crystal structure of the long-chain fatty acid transporter FadL. Science 304, 1506–1509 (2004).

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159 Leave a comment on paragraph 159 0 Pinyakong, O. et al. Isolation and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase from acenaphthene and acenaphthylene degrading Sphingomonas sp. strain A4. FEMS Microbiol. Lett. 238, 297–305 (2004).

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162 Leave a comment on paragraph 162 0 Jouanneau, Y., Meyer, C., Jakoncic, J., Stojanoff, V. & Gaillard, J.Characterization of a naphthalene dioxygenase endowed with an exceptionally broad substrate specificity toward polycyclic aromatic hydrocarbons. Biochemistry 45, 12380–12391 (2006).

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