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Complete genome sequence of Pantoea intestinalis SRCM103226, a microbial C40 carotenoid zeaxanthin producer

식용곤충 갈색거저리에서 분리한 카로테노이드 생성균주인 Pantoea intestinalis SRCM103226 균주의 유전체 해독

Kim, Jin Won;Ha, Gwangsu;Jeong, Seong-Yeop;Jeong, Do-Youn
김진원;하광수;정성엽;정도연

  • Received : 2019.03.25
  • Accepted : 2019.04.10
  • Published : 2019.06.30

Abstract

Pantoea intestinalis SRCM103226, isolated from edible insect mealworm overproduces zeaxanthin as a main carotenoid. The complete genome of P. intestinalis SRCM103226 was sequenced using the Pacific Biosciences (PacBio) RS II platform. The genome of P. intestinalis SRCM103226 comprises a 4,784,919 bp circular chromosome (53.41% G+C content), and is devoid of any extrachromosomal plasmids. Annotation using the RAST server reveals 4,332 coding sequences and 107 RNAs (22 rRNA genes, 85 tRNA genes). Genome annotation analysis revealed that it has five genes involved in the carotenoid pathway. The genome information provides fundamental knowledge for comparative genomics studies of the zeaxanthin pathway.

Keywords

Pantoea intestinalis;C40 carotenoid;complete genome sequence;mealworm

References

  1. Albermann C. 2011. High versus low level expression of the lycopene biosynthesis genes from Pantoea ananatis in Escherichia coli. Biotechnol. Lett. 33, 313-319.
  2. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, and Kubal M. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9, 75. https://doi.org/10.1186/1471-2164-9-75
  3. Delcher AL, Harmon D, Kasif S, White O, and Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 27, 4636-4641.
  4. Holt NE, Zigmantas D, Valkunas L, Li XP, Niyogi KK, and Fleming GR. 2005. Carotenoid cation formation and the regulation of photosynthetic light harvesting. Science 307, 433-436. https://doi.org/10.1126/science.1105833
  5. Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA, and Harris SR. 2015. Circlator: automated circularization of genome assemblies using long sequencing reads. Genome Biol. 16, 294. https://doi.org/10.1186/s13059-015-0849-0
  6. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119. https://doi.org/10.1186/1471-2105-11-119
  7. Johnson ET and Schmidt-Dannert C. 2008. Light-energy conversion in engineered microorganisms. Trends Biotechnol. 26, 682-689. https://doi.org/10.1016/j.tibtech.2008.09.002
  8. Kim SH, Kim JH, Lee BY, and Lee PC. 2014. The astaxanthin dideoxyglycoside biosynthesis pathway in Sphingomonas sp. PB304. Appl. Microbiol. Biotechnol. 98, 9993-10003.
  9. Kim SH, Kim MS, Lee BY, and Lee PC. 2016. Generation of structurally novel short carotenoids and study of their biological activity. Sci. Rep. 6, 21987.
  10. Kim SH and Lee PC. 2012. Functional expression and extension of staphylococcal staphyloxanthin biosynthetic pathway in Escherichia coli. J. Biol. Chem. 287, 21575-21583. https://doi.org/10.1074/jbc.M112.343020
  11. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, and Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722-736. https://doi.org/10.1101/gr.215087.116
  12. Krinsky NI, Landrum JT, and Bone RA. 2003. Biologic mechanisms of the protective role of lutein and zeaxanthin in the eye. Annu. Rev. Nutr. 23, 171-201. https://doi.org/10.1146/annurev.nutr.23.011702.073307
  13. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, and Marra MA. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645.
  14. Lagesen K, Hallin P, Rodland EA, Stærfeldt HH, Rognes T, and Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100-3108. https://doi.org/10.1093/nar/gkm160
  15. Lee P and Schmidt-Dannert C. 2002. Metabolic engineering towards biotechnological production of carotenoids in microorganisms. Appl. Microbiol. Biotechnol. 60, 1-11. https://doi.org/10.1007/s00253-002-1101-x
  16. Lowe TM and Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955-964. https://doi.org/10.1093/nar/25.5.0955
  17. Nishino H, Murakoshi M, Tokuda H, and Satomi Y. 2009. Cancer prevention by carotenoids. Arch. Biochem. Biophys. 483, 165-168. https://doi.org/10.1016/j.abb.2008.09.011
  18. Sedkova N, Tao L, Rouviere PE, and Cheng Q. 2005. Diversity of carotenoid synthesis gene clusters from environmental Enterobacteriaceae strains. Appl. Environ. Microbiol. 71, 8141-8146. https://doi.org/10.1128/AEM.71.12.8141-8146.2005
  19. Song GH, Kim SH, Choi BH, Han SJ, and Lee PC. 2013. Heterologous carotenoid-biosynthetic enzymes: functional complementation and effects on carotenoid profiles in Escherichia coli. Appl. Environ. Microbiol. 79, 610-618. https://doi.org/10.1128/AEM.02556-12
  20. Tatusov RL, Galperin MY, Natale DA, and Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33-36. https://doi.org/10.1093/nar/28.1.33
  21. Walter MH and Strack D. 2011. Carotenoids and their cleavage products: biosynthesis and functions. Nat. Prod. Rep. 28, 663-692. https://doi.org/10.1039/c0np00036a

Acknowledgement

Supported by : Korea Institute for Advancement of Technology (KIAT)