Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Assessment of Erythrobacter Species Diversity through Pan-Genome Analysis with Newly Isolated Erythrobacter sp. 3-20A1M

  • Cho, Sang-Hyeok (Department of Biological Sciences, Korea Advanced Institute of Science and Technology) ;
  • Jeong, Yujin (Department of Biological Sciences, Korea Advanced Institute of Science and Technology) ;
  • Lee, Eunju (Department of Biological Sciences, Korea Advanced Institute of Science and Technology) ;
  • Ko, So-Ra (Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Ahn, Chi-Yong (Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Oh, Hee-Mock (Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Cho, Byung-Kwan (Department of Biological Sciences, Korea Advanced Institute of Science and Technology) ;
  • Cho, Suhyung (Department of Biological Sciences, Korea Advanced Institute of Science and Technology)
  • Received : 2020.12.31
  • Accepted : 2021.02.02
  • Published : 2021.04.28
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Abstract

Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pan-genome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.

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References

  1. Worden AZ, Follows MJ, Giovannoni SJ, Wilken S, Zimmerman AE, Keeling PJ. 2015. Rethinking the marine carbon cycle: factoring in the multifarious lifestyles of microbes. Science 347: 1257594. https://doi.org/10.1126/science.1257594
  2. Faust K, Raes J. 2012. Microbial interactions: from networks to models. Nat. Rev. Microbiol. 10: 538. https://doi.org/10.1038/nrmicro2832
  3. Lidicker Jr WZ. 1979. A clarification of interactions in ecological systems. Bioscience 29: 475-477. https://doi.org/10.2307/1307540
  4. Kolber ZS, Gerald F, Lang AS, Beatty JT, Blankenship RE, VanDover CL, et al. 2001. Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292: 2492-2495. https://doi.org/10.1126/science.1059707
  5. Zheng Q, Lin W, Liu Y, Chen C, Jiao N. 2016. A comparison of 14 Erythrobacter genomes provides insights into the genomic divergence and scattered distribution of phototrophs. Front. Microbiol. 7: 984. https://doi.org/10.3389/fmicb.2016.00984
  6. SHIBA T, SIMIDU U. 1982. Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll a. Int. J. Syst. Evol. Microbiol. 32: 211-217.
  7. Takaichi S. 2009. Distribution and biosynthesis of carotenoids, pp. 97-117. The Purple Phototrophic Bacteria, Ed. Springer, New York, USA.
  8. Takaichi S, Shimada K, Ishidsu J-i. 1990. Carotenoids from the aerobic photosynthetic bacterium, Erythrobacter longus: β-carotene and its hydroxyl derivatives. Arch. Microbiol. 153: 118-122. https://doi.org/10.1007/BF00247807
  9. Galasso C, Corinaldesi C, Sansone C. 2017. Carotenoids from marine organisms: Biological functions and industrial applications. Antioxidants 6: 96. https://doi.org/10.3390/antiox6040096
  10. Yurkov VV, Beatty JT. 1998. Aerobic anoxygenic phototrophic bacteria. Microbiol. Mol. Biol. Rev. 62: 695-724. https://doi.org/10.1128/mmbr.62.3.695-724.1998
  11. Breed MF, Harrison PA, Blyth C, Byrne M, Gaget V, Gellie NJ, et al. 2019. The potential of genomics for restoring ecosystems and biodiversity. Nat. Rev. Genet. 20: 615-628. https://doi.org/10.1038/s41576-019-0152-0
  12. Cho S-H, Lee E, Ko S-R, Jin S, Song Y, Ahn C-Y, et al. 2020. Elucidation of the biosynthetic pathway of Vitamin B groups and potential secondary metabolite gene clusters via genome analysis of a marine bacterium Pseudoruegeria sp. M32A2M. J. Microbiol. Biotechnol. 30: 505-514. https://doi.org/10.4014/jmb.1911.11006
  13. Roosaare M, Puustusmaa M, Mols M, Vaher M, Remm M. 2018. PlasmidSeeker: identification of known plasmids from bacterial whole genome sequencing reads. PeerJ. 6: e4588. https://doi.org/10.7717/peerj.4588
  14. Na S-I, Kim YO, Yoon S-H, Ha S-m, Baek I, Chun J. 2018. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J. Microbiol. 56: 280-285. https://doi.org/10.1007/s12275-018-8014-6
  15. Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312-1313. https://doi.org/10.1093/bioinformatics/btu033
  16. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35: 1547-1549. https://doi.org/10.1093/molbev/msy096
  17. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, et al. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44: 6614-6624. https://doi.org/10.1093/nar/gkw569
  18. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2015. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 44: D457-D462. https://doi.org/10.1093/nar/gkv1070
  19. Tatusov RL, Galperin MY, Natale DA, 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
  20. Consortium TGO. 2014. Gene Ontology Consortium: going forward. Nucleic Acids Res. 43: D1049-D1056. https://doi.org/10.1093/nar/gku1179
  21. Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, et al. 2010. eggNOG v2. 0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res. 38: D190-D195. https://doi.org/10.1093/nar/gkp951
  22. Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. 2012. PGAP: pan-genomes analysis pipeline. Bioinformatics 28: 416-418. https://doi.org/10.1093/bioinformatics/btr655
  23. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, et al. 2019. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47: W81-W87. https://doi.org/10.1093/nar/gkz310
  24. Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31: 3210-3212. https://doi.org/10.1093/bioinformatics/btv351
  25. Li X, Koblizek M, Feng F, Li Y, Jian J, Zeng Y. 2013. Whole-genome sequence of a freshwater aerobic anoxygenic phototroph, Porphyrobacter sp. strain AAP82, isolated from the Huguangyan Maar Lake in Southern China. Genome Announc. 1: e0007213. https://doi.org/10.1128/genomeA.00072-13
  26. Xu X-W, Wu Y-H, Wang C-S, Wang X-G, Oren A, Wu M. 2009. Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae. Int. J. Syst. Evol. Microbiol. 59: 2247-2253. https://doi.org/10.1099/ijs.0.004267-0
  27. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. 2005. The microbial pan-genome. Curr. Opin. Genet. Dev. 15: 589-594. https://doi.org/10.1016/j.gde.2005.09.006
  28. Dertli E, Mayer MJ, Colquhoun IJ, Narbad A. 2016. EpsA is an essential gene in exopolysaccharide production in Lactobacillus johnsonii FI9785. Microb. Biotechnol. 9: 496-501. https://doi.org/10.1111/1751-7915.12314
  29. Domozych DS, Sorensen I, Popper ZA, Ochs J, Andreas A, Fangel JU, et al. 2014. Pectin metabolism and assembly in the cell wall of the charophyte green alga Penium margaritaceum. Plant Physiol. 165: 105-118. https://doi.org/10.1104/pp.114.236257
  30. Coleman RJ, Patel YN, Harding NE. 2008. Identification and organization of genes for diutan polysaccharide synthesis from Sphingomonas sp. ATCC 53159. J. Ind. Microbiol. Biotechnol. 35: 263-274. https://doi.org/10.1007/s10295-008-0303-3
  31. Alvarez-Martinez CE, Christie PJ. 2009. Biological diversity of prokaryotic type IV secretion systems. Microbiol. Mol. Biol. Rev. 73: 775-808. https://doi.org/10.1128/MMBR.00023-09
  32. Minamino T. 2018. Hierarchical protein export mechanism of the bacterial flagellar type III protein export apparatus. FEMS Microbiol. Lett. 365: fny117. https://doi.org/10.1093/femsle/fny117
  33. Oldfield E, Lin FY. 2012. Terpene biosynthesis: modularity rules. Angew. Chem. Int. Ed. 51: 1124-1137. https://doi.org/10.1002/anie.201103110
  34. Moskvin OV, Gomelsky L, Gomelsky M. 2005. Transcriptome analysis of the Rhodobacter sphaeroides PpsR regulon: PpsR as a master regulator of photosystem development. J. Bacteriol. 187: 2148-2156. https://doi.org/10.1128/JB.187.6.2148-2156.2005
  35. Lee I, Kim YO, Park S-C, Chun J. 2016. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int. J. Syst. Evol. Microbiol. 66: 1100-1103. https://doi.org/10.1099/ijsem.0.000760