Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships

Microbial Cell Factories

Volumn 10, Issue , 2011, Pages

  Cai, Lei ^a   Tan, Dan ^a   Aibaidula, Gulsimay ^b   Dong, Xin Ran ^c   Chen, Jin Chun ^a   Tian, Wei Dong ^c   Chen, Guo Qiang ^a  

^a PEKING UNIVERSITY   (China)

^b XINJIANG UNIVERSITY   (China)

^c FUDAN UNIVERSITY   (China)

Author keywords

Genome; Halomonas spp.; Osmolytes; Phac; Phb; Polyhydroxyalkanoates

Indexed keywords

BINDING PROTEIN; ECTOINE; POLYHYDROXYALKANOATE SYNTHASE; POLYHYDROXYALKANOIC ACID; PROTEOME; BACTERIAL PROTEIN; DIAMINO ACID;

ACIDITY; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL METABOLISM; BACTERIAL STRAIN; COEVOLUTION; COMPUTER MODEL; ENZYME SYNTHESIS; ESCHERICHIA COLI; GAMMAPROTEOBACTERIA; GENETIC ENGINEERING; GENOMICS; HALOBACTERIALES; HALOMONAS; HALOPHILIC BACTERIUM; HORIZONTAL GENE TRANSFER; NONHUMAN; NUCLEOTIDE SEQUENCE; OSMOREGULATION; OSMOTIC PRESSURE; PHYLOGENY; SIGNAL TRANSDUCTION; AMINO ACID SEQUENCE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SEQUENCE ALIGNMENT;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; GAMMAPROTEOBACTERIA; HALOBACTERIA; HALOMONAS;

AMINO ACID SEQUENCE; AMINO ACIDS, DIAMINO; BACTERIAL PROTEINS; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; GENOMICS; HALOMONAS; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYHYDROXYALKANOATES; SEQUENCE ALIGNMENT;

EID: 80055030247     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-10-88     Document Type: Article

References (53)

1. Rehm BHA. Polyester synthases: natural catalysts for plastics. Biochem J 2003, 376:15-33. 10.1042/BJ20031254, 1223765, 12954080.
2. Potter M, Steinbüchel A. Poly(3-hydroxybutyrate) granule-associated proteins: Impacts on poly(3-hydroxybutyrate) synthesis and degradation. Biomacromolecules 2005, 6:552-560. 10.1021/bm049401n, 15762612.
3. Chen GQ. A microbial polyhydroxyalkanoates (PHA) based bio- and materials industry. Chem Soc Rev 2009, 38:2434-2446. 10.1039/b812677c, 19623359.
4. Joshi AA, Kanekar PP, Kelkar AS, Sarnaik SS, Shouche Y, Wani A. Moderately halophilic, alkalitolerant Halomonas campisalis MCM B-365 from Lonar Lake, India. J Basic Microbiol 2007, 47:213-221. 10.1002/jobm.200610223, 17518414.
5. Budde CF, Riedel SL, Willis LB, Rha C, Sinskey AJ. Production of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) from plant oil by engineered Ralstonia eutropha strains. Appl Environ Microbiol 2011, 77:2847-2854. 10.1128/AEM.02429-10, 3126409, 21398488.
6. Park SJ, Choi JI, Lee SY. Short-chain-length polyhydroxyalkanoates: Synthesis in metabolically engineered Escherichia coli and medical applications. J Microbiol Biotechnol 2005, 15:206-215.
7. Quillaguamán JH, Guzmán H, Van-Thuoc D, Hatti-Kaul R. Synthesis and production of polyhydroxyalkanoates by halophiles: current potential and future prospects. Appl Microbiol Biotechnol 2010, 85:1687-1696. 10.1007/s00253-009-2397-6, 20024541.
8. Oren A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Systems 2008, 4:2. 2329653, 18412960.
9. DasSarma P, DasSarma S. On the origin of prokaryotic "species": the taxonomy of halophilic Archaea. Saline Systems 2008, 4:5. 10.1186/1746-1448-4-5, 2397426, 18485204.
10. Kulkarni SO, Kanekar PP, Nilegaonkar SS, Sarnaik SS, Jog JP. Production and characterization of a biodegradable poly (hydroxybutyrate-co-hydroxyvalerate) (PHB-co-PHV) copolymer by moderately haloalkalitolerant Halomonas campisalis MCM B-1027 isolated from Lonar Lake, India. Bioresour Technol 2010, 101:9765-9771. 10.1016/j.biortech.2010.07.089, 20713308.
11. Kulkarni SO, Kanekar PP, Jog JP, Patil PA, Nilegaonkar SS, Sarnaik SS, Kshirsagar PR. Characterisation of copolymer, poly (hydroxybutyrate-co-hydroxyvalerate) (PHB-co-PHV) produced by Halomonas campisalis (MCM B-1027), its biodegradability and potential application. Bioresour Technol 2011, 102:6625-6628. 10.1016/j.biortech.2011.03.054, 21481588.
12. Choi J, Lee SY. Factors affecting the economics of polyhydroxyalkanoate production by bacterial fermentation. Appl Microbiol Biotechnol 1999, 51:13-21.
13. Tan D, Xue YS, Aibaidula G, Chen GQ. Unsterile and continuous production of polyhydroxybutyrate by Halomonas TD01. Biorescour Technol 2011, 102:8130-8136.
14. Hezayen FF, Steinbüchel A, Rehm BHA. Biochemical and enzymological properties of the polyhydroxybutyrate synthase from the extremely halophilic archaeon strain 56. Arch Biochem Biophys 2002, 403:284-291. 10.1016/S0003-9861(02)00234-5, 12139978.
15. Han J, Hou J, Liu HL, Cai SF, Feng B, Zhou JA, Xiang H. Wide distribution among halophilic archaea of a novel polyhydroxyalkanoate synthase subtype with homology to bacterial type III synthases. Appl Environ Microbiol 2010, 76:7811-7819. 10.1128/AEM.01117-10, 2988587, 20889776.
16. Lu QH, Han J, Zhou LG, Zhou J, Xiang H. Genetic and biochemical characterization of the poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthase in Haloferax mediterranei. J Bacteriol 2008, 190:4173-4180. 10.1128/JB.00134-08, 2446746, 18408025.
17. Roberts MF. Organic compatible solutes of halotolerant and halophilic microorganisms. Saline Systems 2005, 1:5. 10.1186/1746-1448-1-5, 1224877, 16176595.
18. Kolp S, Pietsch M, Galinski EA, Gütschow M. Compatible solutes as protectants for zymogens against proteolysis. Biochim Biophys Acta 2006, 1764:1234-1242.
19. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23:673-679. 10.1093/bioinformatics/btm009, 2387122, 17237039.
20. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 1999, 27:29-34. 10.1093/nar/27.1.29, 148090, 9847135.
21. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4:41. 10.1186/1471-2105-4-41, 222959, 12969510.
22. Schneider M, Lane L, Boutet E, Lieberherr D, Tognolli M, Bougueleret L, Bairoch A. The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. J Proteomics 2009, 72:567-573. 10.1016/j.jprot.2008.11.010, 2689360, 19084081.
23. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31:365-370. 10.1093/nar/gkg095, 165542, 12520024.
24. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
25. Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 2005, 33:W686-W689. 10.1093/nar/gki366, 1160127, 15980563.
26. Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007, 35:3100-3108. 10.1093/nar/gkm160, 1888812, 17452365.
27. Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A. Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res 2011, 39:D141-D145. 10.1093/nar/gkq1129, 3013711, 21062808.
28. Tarailo-Graovac M, Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics 2009, 4:10.
29. Reese MG. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem 2001, 26:51-56. 10.1016/S0097-8485(01)00099-7, 11765852.
30. Gordon JJ, Towsey MW, Hogan JM, Mathews SA, Timms P. Improved prediction of bacterial transcription start sites. Bioinformatics 2006, 22:142-148. 10.1093/bioinformatics/bti771, 16287942.
31. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340:783-795. 10.1016/j.jmb.2004.05.028, 15223320.
32. Papadopoulos JS, Agarwala R. COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 2007, 23:1073-1079. 10.1093/bioinformatics/btm076, 17332019.
33. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003, 31:3497-3500. 10.1093/nar/gkg500, 168907, 12824352.
34. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739. 10.1093/molbev/msr121, 21546353.
35. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Slotta D, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Wang Y, Wilbur WJ, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2010, 38:D5-D16. 10.1093/nar/gkp967, 2808881, 19910364.
36. Rehm BHA, Antonio RV, Spiekermann P, Amara AA, Steinbüchel A. Molecular characterization of the poly(3-hydroxybutyrate) (PHB) synthase from Ralstonia eutropha: in vitro evolution, site-specific mutagenesis and development of a PHB synthase protein model. Biochim Biophys Acta 2002, 1594:178-190. 10.1016/S0167-4838(01)00299-0, 11825620.
37. Schubert P, Krüger N, Steinbüchel A. Molecular analysis of the Alcaligenes Eutrophus poly(3-Hydroxybutyrate) biosynthetic operon: Identification of the N-terminus of poly(3-Hydroxybutyrate) synthase and identification of the promoter. J Bacteriol 1991, 173:168-175. 207171, 1987116.
38. Han J, Lu Q, Zhou L, Zhou J, Xiang H. Molecular characterization of the phaECHm genes, required for biosynthesis of poly(3-hydroxybutyrate) in the extremely halophilic archaeon Haloarcula marismortui. Appl Environ Microbiol 2007, 73:6058-6065. 10.1128/AEM.00953-07, 2075026, 17675423.
39. Hanley SZ, Pappin DJC, Rahman D, White AJ, Elborough KM, Slabas AR. Re-evaluation of the primary structure of Ralstonia eutropha phasin and implications for polyhydroxyalkanoic acid granule binding. FEBS Lett 1999, 447:99-105. 10.1016/S0014-5793(99)00235-5, 10218591.
40. Wieczorek R, Pries A, Steinbüchel A, Mayer F. Analysis of a 24-kilodalton protein associated with the polyhydroxyalkanoic acid granules in Alcaligenes Eutrophus. J Bacteriol 1995, 177:2425-2435. 176901, 7730274.
41. Schwibbert K, Marin-Sanguino A, Bagyan I, Heidrich G, Lentzen G, Seitz H, Rampp M, Schuster SC, Klenk HP, Pfeiffer F, Oesterhelt D, Kunte HJ. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T. Environ Microbiol
42. Peter H, Weil B, Burkovski A, Krämer R, Morbach S. Corynebacterium glutamicum is equipped with four secondary carriers for compatible solutes: Identification, sequencing, and characterization of the proline/ectoine uptake system, ProP, and the ectoine/proline/glycine betaine carrier, EctP. J Bacteriol 1998, 180:6005-6012. 107677, 9811661.
43. Chen CL, Beattie GA. Characterization of the osmoprotectant transporter OpuC from Pseudomonas syringae and demonstration that cystathionine-β-synthase domains are required for its osmoregulatory function. J Bacteriol 2007, 189:6901-6912. 10.1128/JB.00763-07, 2045199, 17660277.
44. Rabus R, Jack DL, Kelly DJ, Saier MH. TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters. Microbiology 1999, 145:3431-3445.
45. Jia Y, Yuan W, Wodzinska J, Park C, Sinskey AJ, Stubbe J. Mechanistic studies on class I polyhydroxybutyrate (PHB) synthase from Ralstonia eutropha: Class I and III synthases share a similar catalytic mechanism. Biochemistry 2001, 40:1011-1019. 10.1021/bi002219w, 11170423.
46. Sohn SB, Kim TY, Park JM, Lee SY. In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival. Biotechnol J 2010, 5:739-50. 10.1002/biot.201000124, 20540110.
47. Cai L, Yuan MQ, Liu F, Jian J, Chen GQ. Enhanced production of medium-chain-length polyhydroxyalkanoates (PHA) by PHA depolymerase knockout mutant of Pseudomonas putida KT2442. Bioresour Technol 2009, 100:2265-2270. 10.1016/j.biortech.2008.11.020, 19103481.
48. York GM, Lupberger J, Tian J, Lawrence AG, Stubbe J, Sinskey AJ. Ralstonia eutropha H16 encodes two and possibly three intracellular poly[D-(-)-3-hydroxybutyrate] depolymerase genes. J Bacteriol 2003, 185:3788-3794. 10.1128/JB.185.13.3788-3794.2003, 161563, 12813072.
49. Goo YA, Roach J, Glusman G, Baliga NS, Deutsch K, Pan M, Kennedy S, DasSarma S, Ng WV, Hood L. Low-pass sequencing for microbial comparative genomics. BMC Genomics 2004, 5:3. 10.1186/1471-2164-5-3, 331400, 14718067.
50. Bonneté F, Madern D, Zaccai G. Stability against denaturation mechanisms in halophilic malate-dehydrogenase "adapt" to solvent conditions. J Mol Biol 1994, 244:436-447. 10.1006/jmbi.1994.1741, 7990132.
51. Kennedy SP, Ng WV, Salzberg SL, Hood L, DasSarma S. Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence. Genome Res 2001, 11:1641-1650. 10.1101/gr.190201, 311145, 11591641.
52. Maskow T, Babel W. Calorimetrically obtained information about the efficiency of ectoine synthesis from glucose in Halomonas elongata. Biochim Biophys Acta 2001, 1527:4-10. 10.1016/S0304-4165(01)00115-5, 11420137.
53. Naughton LM, Blumerman SL, Carlberg M, Boyd EF. Osmoadaptation among Vibrio species and unique genomic features and physiological responses of Vibrio parahaemolyticus. Appl Environ Microbiol 2009, 75:2802-2810. 10.1128/AEM.01698-08, 2681680, 19286794.