Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Coates, R Cameron ^a   Podell, Sheila ^a   Korobeynikov, Anton ^c,d   Lapidus, Alla ^c,d   Pevzner, Pavel ^c,e   Sherman, David H ^f   Allen, Eric E ^a   Gerwick, Lena ^a   Gerwick, William H ^a,b  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c ST PETERSBURG ACADEMIC UNIVERSITY   (Russian Federation)

^d ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALDEHYDE DEFORMYLATING OXYGENASE; FATTY ACID; FATTY ACYL ACP REDUCTASE; HYDROCARBON; OLEFIN SYNTHASE; OXIDOREDUCTASE; OXYGENASE; POLYKETIDE SYNTHASE; SYNTHETASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL METABOLISM; BACTERIAL STRAIN; BIOCHEMICAL COMPOSITION; BIOSYNTHESIS; CONTROLLED STUDY; CYANOBACTERIUM; DECARBOXYLATION; HORIZONTAL GENE TRANSFER; MOLECULAR PHYLOGENY; NONHUMAN; SIGNAL TRANSDUCTION; STRUCTURE ANALYSIS;

ALDEHYDE OXIDOREDUCTASES; BAYES THEOREM; BIOSYNTHETIC PATHWAYS; COMPUTATIONAL BIOLOGY; CYANOBACTERIA; FATTY ACIDS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; HYDROCARBONS; MODELS, GENETIC; PHYLOGENY; SPECIES SPECIFICITY;

EID: 84899714134     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0085140     Document Type: Article

References (48)

1. Sharma N, Tiwari S, Tripathi K, Rai A (2010) Sustainability and cyanobacteria (bluegreen algae): facts and challenges. J Appl Phycol 23:1-23.
2. Han J, McCarthy ED, Van Hoeven W, Calvin M, Bradley WH (1968) Organic geochemical studies, II. A preliminary report on the distribution of aliphatic hydrocarbons in algae, in bacteria, and in a recent lake sediment. PNAS 59: 29-33.
3. Han J, Chan HWS, Calvin M (1969) Biosynthesis of alkanes in Nostoc muscorum. J Am Chem Soc 91: 5156-5159.
4. Winters K, Parker PL, Van Baalen C (1969) Hydrocarbons of blue-green algae: geochemical significance. Science 163: 467-468.
5. Schirmer A, Rude MA, Li X, Popova E, del Cardayre S (2010) Microbial biosynthesis of alkanes. Science 329: 559-562.
6. Peralta-Yahya PP, Zhang F, del Cardayre SB, Keasling JD (2012) Microbial engineering for the production of advanced biofuels. Nature 488: 320-328.
7. Balaban AT (1983) Topological indices based on topological distances in molecular graphs. Pure Appl Chem 55: 199-206.
8. Creton B, Dartiguelongue C, de Bruin T, Toulhoat H (2010) Prediction of the cetane number of diesel compounds using the quantitative structure property relationship. Energy Fuels 24: 5396-5403.
9. Mendez-Perez D, Begemann MB, Pfleger BF (2011) Modular synthase-encoding gene involved in a-olefin biosynthesis in Synechococcus sp. strain PCC 7002. App Envir Micro 77: 4264-4267.
10. Rude MA, Baron TS, Brubaker S, Alibhai M, del Cardayre SB, et al. (2011) Terminal olefin (1-alkene) biosynthesis by a novel P450 fatty acid decarboxylase from Jeotgalicoccus sp. Appl Environ Microbiol 77: 1718-1727.
11. Beller HR, Goh EB, Keasling JD (2010) Genes involved in long-chain alkene biosynthesis in Micrococcus luteus. Appl Environ Microbiol 76: 1212-1223.
12. Dennis MW, Kolattukudy PE (1991) Alkane biosynthesis by decarbonylation of aldehyde catalyzed by a microsomal preparation from Botryococcus braunii . Arch Biochem Biophys 287: 268-275.
13. Metzger P, Largeau C (2005) Botryococcus braunii: a rich source for hydrocarbons and related ether lipids. Appl Microbiol Biotechnol 66: 486-496.
14. Pohnert G, Boland W (2002) The oxylipin chemistry of attraction and defense in brown algae and diatoms. Nat Prod Rep 19: 108-122. (Pubitemid 34140336)
15. Blomquist GJ, Bagneres AG, editors (2010) Insect hydrocarbons: biology, biochemistry, and chemical ecology. New York: Cambridge University Press.
16. Qiu Y, Tittige C, Wicker-Thomas C, Le Goff G, Young S, et al. (2012) An insect-specific P450 oxidative decarbonylase forcuticular hydrocarbon biosynthesis. PNAS 109:14858-14863.
17. Li M, Chang W, Warui DM, Booker SJ, Krebs C, et al. (2012) Evidence for only oxygenative cleavage of aldehydes to alk(a/e)nes and formate by cyanobacterial aldehyde decarbonylases. Biochemistry 51: 7908-7916.
18. Doan TTP, Carlsson AS, Hamberg M, Bülow L, Stymne S, et al. (2009) Functional expression of five Arabidopsis fatty acyl-CoA reductase genes in Escherichia coli. J Plant Physiol 166: 787-796.
19. Eser BE, Das D, Han J, Jones PR, Marsh EN (2011) Oxygen-independent alkane formation by non-heme iron-dependent cyanobacterial aldehyde decarbonylase: investigation of kinetics and requirement for an external electron donor. Biochemistry 50: 10743-10750.
20. Ridley CP, Reppas NP (2010) Biosynthesis of 1-alkenes in engineered microorganisms. US Patent Appl 12/821,107.
21. Donia MS, Fricke WF, Ravel J, Schmidt EW (2011) Variation in tropical reef symbiont metagenomes defined by secondary metabolism. PLoS ONE 6:e17897. doi:10.1371/journal.pone.0017897
22. Gehret-McCarthy J, Eisman EB, Kulkarni S, Gerwick L, Gerwick WH, et al. (2012) Structural basis of functional group activation by sulfotransferases in complex metabolic pathways. ACS Chem Biol 7: 1994-2003 doi: 10.1021/cb300385m
23. Gu L, Wang B, Kulkarni A, Gehret JJ, Lloyd KR, et al. (2009) Polyketide decarboxylative chain termination preceded by O-sulfonation in curacin A biosynthesis. J Am Chem Soc 131: 16033-16035.
24. Engene N, Rottacker EC, Kaštovský J, Byrum T, Choi H, et al. (2012). Moorea producens gen. nov., sp. nov. and Moorea bouillonii comb. nov., tropical marine cyanobacteria rich in bioactive secondary metabolites. Ins J Syst Evol Microbiol 62:1171-1178.
25. Chang Z, Sitachitta N, Rossi JV, Roberts MA, Flatt PM, et al. (2004) Biosynthetic pathway and gene cluster analysis of curacin A, an antitubulin natural product from the tropical marine cyanobacterium Lyngbya majuscula. JNat Prod 67: 1356-1367. (Pubitemid 39145643)
26. Castenholz RW (2001) Phylum BX. Cyanobacteria. Oxygenic Photosynthetic Bacteria. In: Garrity G, Boone DR, Castenholz RW editors. Bergey's Manual of Systematic Bacteriology. Volume 1: The Archaea and the Deeply Branching and Phototropic Bacteria. Second Edition. New York: Springer-Verlag. pp. 473-599.
27. Schirrmeister BE, Antonelli A, Bagheri HC (2011) The origin of multicellularity in cyanobacteria. BMC Evolutionary Biology 11:45-66. doi:10.1186/1471- 2148-11-45
28. Dembitsky VM, Srebnik M (2002) 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.
29. Tan XM, Yao L, Gao QQ, Wang WH, Qi FX, et al. (2011) Photosynthesis drive conversion of carbon dioxide to fatty alcohols and hydrocarbons in cyanobacteria. Metab Eng 13: 169-176.
30. Gelpi E, Schneider H, Mann J, Oró J (1970) Hydrocarbons of geochemical significance in microscopic algae. Phytochemistry 9: 603-612.
31. Paoletti C, Pushparaj B, Florenzano G, Capella P, Lerker G (1976) Unsaponifiable matter of green and blue-green algal lipids as a factor of biochemical differentiation of their biomasses: I. Total unsapononifiable and hydrocarbon fraction. Lipids 11: 258-265.
32. Dembitsky VM, Shkrobb I, Dor I (1999). Separation and identification of hydrocarbons and other volatile compounds from cultured blue-green alga Nostoc sp. by gas chromatography-mass spectrometry using serially coupled capillary columns with consecutive nonpolar and semipolar stationary phases. J Chromatogr A 682: 221-229. (Pubitemid 29497815)
33. Liu A, Zhu T, Lu X, Song L (2013) Hydrocarbon profiles and phylogenetic analyses of diversified cyanobacterial species. Appl Energy 111: 383-393.
34. Williamson RT, Boulanger A, Vulpanovici A, Roberts MA, Gerwick WH (2002) Structure and absolute stereochemistry of phormidolide, a new toxic metabolite from the marine cyanobacterium Phormidium sp. J Org Chem 67: 7927-7936. (Pubitemid 35331968)
35. Engene N, Paul VJ, Byrum T, Gerwick WH, Thor A, et al. (2013) Five chemically rich species of tropical marine cyanobacteria of the genus Okeania gen. nov. (Oscillatoriales, Cyanoprokaryota). J Phycol doi: 10.1111/jpy.12115
36. Vincent M, Guglielmetti G, Cassani G, Tonini C (1987) Determination of double-bond position in diunsaturated compounds by mass spectrometry of dimethyl disulfide derivatives. Anal Chem 59: 694-699.
37. Bennett S (2004) Solexa Ltd. Pharmacogenomics 5: 433-438.
38. Kelley DR, Schatz MC, Salzberg SL (2010) Quake: quality-aware detection and correction of sequencing errors. Genome Biol 11: R116. doi:10.1186/gb-2010- 11-11-r116
39. Bankevich AS, Nurk D, Antipov AA, Gurevich M, Dvorkin AS, et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455-477.
40. Benson DA, Cavanaugh M, Karsch-Mizrachi I, Lipman DJ, Ostell J, et al. (2013) GenBank. Nucleic Acids Res 41: D36-42. doi: 10.1093/nar/gks1195
41. Markowitz VM, Chen IA, Palaniappan K, Chu K, Szeto E, et al. (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucl Acids Res 40:D115-D122.
42. Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, et al. (2013) TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res 41: D387-95. doi: 10.1093/nar/gks1234
43. Zarzycki J, Axen SD, Kinney JN, Kerfeld CA (2012) Cyanobacterial-based approaches to improving photosynthesis in plants. J Exp Bot 64: 787-798. doi:10.1093/jxb/ers294
44. Allen ME, Neilan BA, Burnes BP, Jahnke LL, Summons RE (2010) Lipid biomarkers in Hamelin Pool microbial mats and stromatolites. Org Geochem 41: 1207-1218.
45. Sata N, Wada H (2010) Lipid biosynthesis and its regulation in cyanobacteria. In: Wada H, Murata N, editors. Lipids in photosynthesis. Advances in photosynthesis and respiration. Dordrect: Springer. 30: pp 157-177.
46. 3] methionine into 7- and 8-methylheptadecanes. Biochemistry 9: 418-422.
47. 14C] adenosylmethionine. Biochemistry 11: 2411-2416.
48. Shih PM, Wua D, Latifid A, Axena SD, Fewere DP, et al. (2013) Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. PNAS 110: 1053-1058.