Analysis of Zobellella denitrificans ZD1 draft genome: Genes and gene clusters responsible for high polyhydroxybutyrate (PHB) production from glycerol under saline conditions and its CRISPR-Cas system
Autoři:
Yu-Wei Wu aff001; Shih-Hung Yang aff003; Myung Hwangbo aff003; Kung-Hui Chu aff003
Působiště autorů:
Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
aff001; Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
aff002; Zachry Department of Civil and Environmental Engineering, Texas A&M University, College Station, TX, United States of America
aff003
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0222143
Souhrn
Polyhydroxybutyrate (PHB) is biodegradable and renewable and thus considered as a promising alternative to petroleum-based plastics. However, PHB production is costly due to expensive carbon sources for culturing PHB-accumulating microorganisms under sterile conditions. We discovered a hyper PHB-accumulating denitrifying bacterium, Zobellella denitrificans ZD1 (referred as strain ZD1 hereafter) capable of using non-sterile crude glycerol (a waste from biodiesel production) and nitrate to produce high PHB yield under saline conditions. Nevertheless, the underlying genetic mechanisms of PHB production in strain ZD1 have not been elucidated. In this study, we discovered a complete pathway of glycerol conversion to PHB, a novel PHB synthesis gene cluster, a salt-tolerant gene cluster, denitrifying genes, and an assimilatory nitrate reduction gene cluster in the ZD1 genome. Interestingly, the novel PHB synthesis gene cluster was found to be conserved among marine Gammaproteobacteria. Higher levels of PHB accumulation were linked to higher expression levels of the PHB synthesis gene cluster in ZD1 grown with glycerol and nitrate under saline conditions. Additionally, a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas type-I-E antiviral system was found in the ZD1 genome along with a long spacer list, in which most of the spacers belong to either double-stranded DNA viruses or unknown phages. The results of the genome analysis revealed strain ZD1 used the novel PHB gene cluster to produce PHB from non-sterile crude glycerol under saline conditions.
Klíčová slova:
Physical sciences – Chemistry – Chemical compounds – Nitrates – Nitrites – Ammonia – Polymer chemistry – Monomers – Glycerol – Environmental chemistry – Biology and life sciences – Evolutionary biology – Evolutionary systematics – Phylogenetics – Phylogenetic analysis – Taxonomy – Bioengineering – CRISPR – Synthetic biology – Synthetic bioengineering – Genome engineering – Synthetic genome editing – Synthetic genomics – Organisms – Viruses – Bacteriophages – Computer and information sciences – Data management – Engineering and technology – Ecology and environmental sciences – Denitrification
Zdroje
1. Jendrossek D, Handrick R. Microbial degradation of polyhydroxyalkanoates. Annu Rev Microbiol. 2002;56:403–32. doi: 10.1146/annurev.micro.56.012302.160838 12213937
2. van der Walle GA, de Koning GJ, Weusthuis RA, Eggink G. Properties, modifications and applications of biopolyesters. Adv Biochem Eng Biotechnol. 2001;71:263–91. 11217415
3. Anderson AJ, Dawes EA. Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. Microbiol Rev. 1990;54(4):450–72. 2087222
4. Rodriguezvalera F, Lillo JAG. Halobacteria as producers of polyhydroxyalkanoates. FEMS Microbiol Lett. 1992;103(2–4):181–6.
5. Steinbuchel A, Fuchtenbusch B. Bacterial and other biological systems for polyester production. Trends Biotechnol. 1998;16(10):419–27. 9807839
6. Posada JA, Naranjo JM, Lopez JA, Higuita JC, Cardona CA. Design and analysis of poly-3-hydroxybutyrate production processes from crude glycerol. Process Biochem. 2011;46(1):310–7.
7. Wu YW, Shao Y, Khanipov K, Golovko G, Pimenova M, Fofanov Y, et al. Draft genome sequence of Zobellella denitrificans ZD1 (JCM 13380), a salt-tolerant denitrifying bacterium capable of producing poly(3-Hydroxybutyrate). Genome Announc. 2017;5(36).
8. Lin YT, Shieh WY. Zobellella denitrificans gen. nov., sp. nov. and Zobellella taiwanensis sp. nov., denitrifying bacteria capable of fermentative metabolism. Int J Syst Evol Microbiol. 2006;56(Pt 6):1209–15. doi: 10.1099/ijs.0.64121-0 16738093
9. Ayub ND, Pettinari MJ, Mendez BS, Lopez NI. Impaired polyhydroxybutyrate biosynthesis from glucose in Pseudomonas sp 14–3 is due to a defective beta-ketothiolase gene. FEMS Microbiol Lett. 2006;264(1):125–31. doi: 10.1111/j.1574-6968.2006.00446.x 17020558
10. Pettinari MJ, Vazquez GJ, Silberschmidt D, Rehm B, Steinbuchel A, Mendez BS. Poly(3-hydroxybutyrate) synthesis genes in Azotobacter sp. strain FA8. Appl Environ Microbiol. 2001;67(11):5331–4. doi: 10.1128/AEM.67.11.5331-5334.2001 11679365
11. Zhang W, Wei H, Gao H, Huang G. Cloning and characterization of ectABC cluster from Bacillus alcalophilus DTY1. Chin J Biotechnol. 2008;24(3):395–400.
12. Asiri F, Chen CH, Hwangbo M, Shao Y, Chu KH. From organic wastes to bioplastics: Feasibility of non-sterile polyhydroxybutyrate (PHB) production by Zobellella denitrificans ZD1. New Biotechnol. 2019. In review.
13. Hand S, Gill J, Chu K-H. Phage-based extraction of polyhydroxybutyrate (PHB) produced from synthetic crude glycerol. Sci Total Environ. 2016;557–558:317–21. doi: 10.1016/j.scitotenv.2016.03.089 27016679
14. Monteil-Rivera F, Betancourt A, Van Tra H, Yezza A, Hawari J. Use of headspace solid-phase microextraction for the quantification of poly(3-hydroxybutyrate) in microbial cells. J Chromatogr A. 2007;1154(1):34–41.
15. Yilmaz M, Soran H, Beyatli Y. Determination of poly-β-hydroxybutyrate (PHB) production by some Bacillus spp. World J Microbiol Biotechnol. 2005;21(4):565–6.
16. Winer J, Jung CKS, Shackel I, Williams PM. Development and validation of real-time quantitative reverse transcriptase–polymerase chain reaction for monitoring gene expression in Cardiac Myocytes in vitro. Anal Biochem. 1999;270(1):41–9. doi: 10.1006/abio.1999.4085 10328763
17. Wu YW. ezTree: an automated pipeline for identifying phylogenetic marker genes and inferring evolutionary relationships among uncultivated prokaryotic draft genomes. BMC Genomics. 2018;19(Suppl 1):921. doi: 10.1186/s12864-017-4327-9 29363425
18. 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(10):2731–9. doi: 10.1093/molbev/msr121 21546353
19. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS. 2008;12(2):137–41. doi: 10.1089/omi.2008.0017 18416670
20. Braker G, Tiedje JM. Nitric oxide reductase (norB) genes from pure cultures and environmental samples. Appl Environ Microbiol. 2003;69(6):3476–83. doi: 10.1128/AEM.69.6.3476-3483.2003 12788753
21. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7. doi: 10.1093/nar/gkh340 15034147
22. Price MN, Dehal PS, Arkin AP. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490. doi: 10.1371/journal.pone.0009490 20224823
23. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119. doi: 10.1186/1471-2105-11-119 20211023
24. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10:421. doi: 10.1186/1471-2105-10-421 20003500
25. He Z, Zhang H, Gao S, Lercher MJ, Chen WH, Hu S. Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees. Nucleic Acids Res. 2016;44(W1):W236–41. doi: 10.1093/nar/gkw370 27131786
26. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, et al. CDD: NCBI's conserved domain database. Nucleic Acids Res. 2015;43(Database issue):D222–6. doi: 10.1093/nar/gku1221 25414356
27. Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004;32(Web Server issue):W327–31. doi: 10.1093/nar/gkh454 15215404
28. Zhang Q, Ye Y. Not all predicted CRISPR-Cas systems are equal: Isolated cas genes and classes of CRISPR like elements. BMC Bioinformatics. 2017;18(1):92. doi: 10.1186/s12859-017-1512-4 28166719
29. Shmakov SA, Sitnik V, Makarova KS, Wolf YI, Severinov KV, Koonin EV. The CRISPR spacer space is dominated by sequences from species-specific Mobilomes. Mbio. 2017;8(5).
30. Kim E-J, Kim K-J. Crystal structure and biochemical characterization of PhaA from Ralstonia eutropha, a polyhydroxyalkanoate-producing bacterium. Biochem Biophys Res Commun. 2014;452(1):124–9. doi: 10.1016/j.bbrc.2014.08.074 25152395
31. Potter M, Muller H, Steinbuchel A. Influence of homologous phasins (PhaP) on PHA accumulation and regulation of their expression by the transcriptional repressor PhaR in Ralstonia eutropha H16. Microbiology. 2005;151(Pt 3):825–33. doi: 10.1099/mic.0.27613-0 15758228
32. Galan B, Dinjaski N, Maestro B, de Eugenio LI, Escapa IF, Sanz JM, et al. Nucleoid-associated PhaF phasin drives intracellular location and segregation of polyhydroxyalkanoate granules in Pseudomonas putida KT2442. Mol Microbiol. 2011;79(2):402–18. doi: 10.1111/j.1365-2958.2010.07450.x 21219460
33. York GM, Stubbe J, Sinskey AJ. The Ralstonia eutropha PhaR protein couples synthesis of the PhaP phasin to the presence of polyhydroxybutyrate in cells and promotes polyhydroxybutyrate production. J Bacteriol. 2002;184(1):59–66. doi: 10.1128/JB.184.1.59-66.2002 11741844
34. Martinez-Gomez K, Flores N, Castaneda HM, Martinez-Batallar G, Hernandez-Chavez G, Ramirez OT, et al. New insights into Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol. Microbial Cell Fact. 2012;11.
35. Pettinari MJ, Vazquez GJ, Silberschmidt D, Rehm B, Steinbuchel A, Mendez BS. Poly(3-hydroxybutyrate) synthesis genes in Azotobacter sp strain FA8. Appl Environ Microbiol. 2001;67(11):5331–4. doi: 10.1128/AEM.67.11.5331-5334.2001 11679365
36. Zhu D, Liu J, Han R, Shen G, Long Q, Wei X, et al. Identification and characterization of ectoine biosynthesis genes and heterologous expression of the ectABC gene cluster from Halomonas sp. QHL1, a moderately halophilic bacterium isolated from Qinghai Lake. J Microbiol. 2014;52(2):139–47. doi: 10.1007/s12275-014-3389-5 24500478
37. Louis P, Galinski EA. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology. 1997;143 (Pt 4):1141–9.
38. Gonzalez PJ, Correia C, Moura I, Brondino CD, Moura JJ. Bacterial nitrate reductases: Molecular and biological aspects of nitrate reduction. J Inorg Biochem. 2006;100(5–6):1015–23. doi: 10.1016/j.jinorgbio.2005.11.024 16412515
39. Kraft B, Strous M, Tegetmeyer HE. Microbial nitrate respiration—genes, enzymes and environmental distribution. J Biotechnol. 2011;155(1):104–17. doi: 10.1016/j.jbiotec.2010.12.025 21219945
40. Li Y, Katzmann E, Borg S, Schuler D. The periplasmic nitrate reductase Nap is required for anaerobic growth and involved in redox control of magnetite biomineralization in Magnetospirillum gryphiswaldense. J Bacteriol. 2012;194(18):4847–56. doi: 10.1128/JB.00903-12 22730130
41. Jepson BJ, Marietou A, Mohan S, Cole JA, Butler CS, Richardson DJ. Evolution of the soluble nitrate reductase: Defining the monomeric periplasmic nitrate reductase subgroup. Biochem Soc Trans. 2006;34(Pt 1):122–6. doi: 10.1042/BST0340122 16417499
42. Hartsock A, Shapleigh JP. Physiological roles for two periplasmic nitrate reductases in Rhodobacter sphaeroides 2.4.3 (ATCC 17025). J Bacteriol. 2011;193(23):6483–9. doi: 10.1128/JB.05324-11 21949073
43. Sparacino-Watkins C, Stolz JF, Basu P. Nitrate and periplasmic nitrate reductases. Chem Soc Rev. 2014;43(2):676–706. doi: 10.1039/c3cs60249d 24141308
44. Helen D, Kim H, Tytgat B, Anne W. Highly diverse nirK genes comprise two major clades that harbour ammonium-producing denitrifiers. BMC Genomics. 2016;17:155. doi: 10.1186/s12864-016-2465-0 26923558
45. Cramm R, Pohlmann A, Friedrich B. Purification and characterization of the single-component nitric oxide reductase from Ralstonia eutropha H16. FEBS Lett. 1999;460(1):6–10. doi: 10.1016/s0014-5793(99)01315-0 10571051
46. Moreno-Vivian C, Cabello P, Martinez-Luque M, Blasco R, Castillo F. Prokaryotic nitrate reduction: Molecular properties and functional distinction among bacterial nitrate reductases. J Bacteriol. 1999;181(21):6573–84. 10542156
47. Wu Q, Stewart V. NasFED proteins mediate assimilatory nitrate and nitrite transport in Klebsiella oxytoca (pneumoniae) M5al. J Bacteriol. 1998;180(5):1311–22. 9495773
48. Cole J. Nitrate reduction to ammonia by enteric bacteria: Redundancy, or a strategy for survival during oxygen starvation? FEMS Microbiol Lett. 1996;136(1):1–11. doi: 10.1111/j.1574-6968.1996.tb08017.x 8919448
49. Neubauer H, Pantel I, Gotz F. Molecular characterization of the nitrite-reducing system of Staphylococcus carnosus. J Bacteriol. 1999;181(5):1481–8. 10049379
50. Malm S, Tiffert Y, Micklinghoff J, Schultze S, Joost I, Weber I, et al. The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis. Microbiology. 2009;155(Pt 4):1332–9. doi: 10.1099/mic.0.023275-0 19332834
51. Akhtar S, Khan A, Sohaskey CD, Jagannath C, Sarkar D. Nitrite Reductase NirBD Is Induced and Plays an Important Role during In Vitro Dormancy of Mycobacterium tuberculosis. J Bacteriol. 2013;195(20):4592–9. doi: 10.1128/JB.00698-13 23935045
52. Kumar V, Park S. Potential and limitations of Klebsiella pneumoniae as a microbial cell factory utilizing glycerol as the carbon source. Biotechnol Adv. 2018;36(1):150–67. doi: 10.1016/j.biotechadv.2017.10.004 29056473
53. Bhattacharyya A, Saha J, Haldar S, Bhowmic A, Mukhopadhyay UK, Mukherjee J. Production of poly-3-(hydroxybutyrate-co-hydroxyvalerate) by Haloferax mediterranei using rice-based ethanol stillage with simultaneous recovery and re-use of medium salts. Extremophiles. 2014;18(2):463–70. doi: 10.1007/s00792-013-0622-9 24442255
54. Weissgram M, Gstottner J, Lorantfy B, Tenhaken R, Herwig C, Weber HK. Generation of PHB from spent sulfite liquor using halophilic microorganisms. Microorganisms. 2015;3(2):268–89. doi: 10.3390/microorganisms3020268 27682089
55. Simon J, Sanger M, Schuster SC, Gross R. Electron transport to periplasmic nitrate reductase (NapA) of Wolinella succinogenes is independent of a NapC protein. Mol Microbiol. 2003;49(1):69–79. doi: 10.1046/j.1365-2958.2003.03544.x 12823811
56. Rotthauwe JH, Witzel KP, Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl Environ Microb. 1997;63(12):4704–12.
57. MacDonnell JE, Lunn FA, Bearne SL. Inhibition of E. coli CTP synthase by the "positive" allosteric effector GTP. Biochim Biophys Acta. 2004;1699(1–2):213–20. doi: 10.1016/j.bbapap.2004.03.002 15158730
58. Hatse S, De Clercq E, Balzarini J. Role of antimetabolites of purine and pyrimidine nucleotide metabolism in tumor cell differentiation. Biochem Pharmacol. 1999;58(4):539–55. doi: 10.1016/s0006-2952(99)00035-0 10413291
59. Kilstrup M, Hammer K, Jensen PR, Martinussen J. Nucleotide metabolism and its control in lactic acid bacteria. FEMS Microbiol Rev. 2005;29(3):555–90. doi: 10.1016/j.femsre.2005.04.006 15935511
60. Buckling A, Brockhurst M. Bacteria-Virus Coevolution. Adv Exp Med Biol. 2012;751:347–70. doi: 10.1007/978-1-4614-3567-9_16 22821466
61. Westra ER, van Houte S, Gandon S, Whitaker R. The ecology and evolution of microbial CRISPR-Cas adaptive immune systems. Philos Trans R Soc Lond B Biol Sci. 2019;374(1772):20190101. doi: 10.1098/rstb.2019.0101 30905294
Článek vyšel v časopise
PLOS One
2019 Číslo 9
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