생명과학회지 (Journal of Life Science)

  • 제29권1호
  • /
  • Pages.123-128
  • /
  • 2019
  • /
  • 1225-9918(pISSN)
  • /
  • 2287-3406(eISSN)
한국생명과학회 (Korean Society of Life Science)
권호 표지
DOI QR코드

DOI QR Code

동일한 속 원핵생물들의 보존 유전자와 대사경로

Conserved Genes and Metabolic Pathways in Prokaryotes of the Same Genus

  • 이동근 (신라대학교 바이오산업학부 제약공학전공) ;
  • 이상현 (신라대학교 바이오산업학부 제약공학전공)
  • Lee, Dong-Geun (Major in Pharmaceutical Engineering, Division of Bio-industry, College of Medical and Life Sciences, Silla University) ;
  • Lee, Sang-Hyeon (Major in Pharmaceutical Engineering, Division of Bio-industry, College of Medical and Life Sciences, Silla University)
  • 투고 : 2018.08.14
  • 심사 : 2018.09.28
  • 발행 : 2019.01.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

원핵생물 분류의 기본단위인 종(species)의 동정에 16S rDNA가 사용되지만 한계가 있고 원핵생물의 속(genus)에 대한 연구가 많지 않다. 본 연구에서는 보존 유전자를 확보한 COG database와 대사경로를 확보한 MetaCyc database에 공통적인 원핵생물 중 속이 같고 종이 다른 13개 속 28개의 원핵생물을 대상으로 속 수준에서 연구하였다. 전체 유전자에서 core-genome인 속 보존 유전자의 비율은 최저 27.62%(Nostoc 속)에서 71.76%(Spiribacter 속)의 범위로 평균 46.72%였다. 각 원핵생물에서 core-genome의 비율이 낮으면 특이한 생명현상을 보이거나 서식지가 다양할 수 있을 것이다. 속 수준의 공통 대사경로의 비율은 최저 58.79%(Clostridium 속)에서 최대 96.31%(Mycoplasma 속), 평균 75.86%로 core-genome의 비율보다 높았다. 비교대상을 확장하면 속 특이 보존 유전자와 대사경로는 확인할 수 없었다. 보존 유전자와 대사경로 보유 계통수에서는 대체로 같은 속의 구성원들이 가장 인접하였으며, Bacillus속과 Clostridium 속이 그룹을 형성하였고, 고세균끼리 그룹을 형성하였다. 보존 유전자 보유계통수에서는 Acidobacteria, Cyanobacteria, Proteobacteria 문(phylum)의 Granulicella, Nostoc, Bradyrhizobium의 3개 속이 하나의 그룹을 형성하였다. 본 연구 결과는 (i) 각 계통 단계에서 보존유전자와 대사경로의 확인, (ii) 수평적 유전자 전달 또는 부위 지정 돌연변이를 통한 균주의 개선 등의 분야에 기초자료로 활용될 수 있을 것이다.

The use of 16S rDNA is commonplace in the determination of prokaryotic species. However, it has limitations, and there are few studies at the genus level. We investigated conserved genes and metabolic pathways at the genus level in 28 strains of 13 genera of prokaryotes using the COG database (conserved genes) and MetaCyc database (metabolic pathways). Conserved genes compared to total genes (core genome) at the genus level ranged from 27.62%(Nostoc genus) to 71.76%(Spiribacter genus), with an average of 46.72%. The lower ratio of core genome meant the higher ratio of peculiar genes of a prokaryote, namely specific biological activities or the habitat may be varied. The ratio of common metabolic pathways at the genus level was higher than the ratio of core genomes, from 58.79% (Clostridium genus) to 96.31%(Mycoplasma genus), with an average of 75.86%. When compared among other genera, members of the same genus were positioned in the closest nodes to each other. Interestingly, Bacillus and Clostridium genera were positioned in closer nodes than those of the other genera. Archaebacterial genera were grouped together in the ortholog and metabolic pathway nodes in a phylogenetic tree. The genera Granulicella, Nostoc, and Bradyrhizobium of the Acidobacteria, Cyanobacteria, and Proteobacteria phyla, respectively, were grouped in an ortholog content tree. The results of this study can be used for (i) the identification of common genes and metabolic pathways at each phylogenetic level and (ii) the improvement of strains through horizontal gene transfer or site-directed mutagenesis.

키워드

SMGHBM_2019_v29n1_123_f0001.png 이미지

Fig. 1. ML(Maximum Likelihood) phylogenetic tree of 28 procaryotes in the point of presence or absence of the union of 4,631 COGs. Bootstrap values at each node are expressed as a percentage of 1,000 trials. See table 1 for abbreviations of prokaryotes

SMGHBM_2019_v29n1_123_f0002.png 이미지

Fig. 2. ML (Maximum Likelihood) phylogenetic tree of 28 procaryotes in the point of presence or absence of the union of 2,526 metabolic pathways. Bootstrap values at each node are expressed as a percentage of 1,000 trials. See Table 1 for abbreviations of prokaryotes.

SMGHBM_2019_v29n1_123_f0003.png 이미지

Fig. 3. ML (Maximum Likelihood) phylogenetic tree of 28 procaryotes in the point of 16S rRNA genes. Bootstrap values at each node are expressed as a percentage of 1,000 trials. See Table 1 for abbreviations of prokaryotes.

Table 1. Studied prokaryotes and their numbers (#) and percentage (%) of total genes, conservative genes (orthologs) and metabolic pathways at each prokaryote and genus

SMGHBM_2019_v29n1_123_t0001.png 이미지

참고문헌

  1. Asai, T., Zaporojets, D., Squires, C. and Squires, C. L. 1999. An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc. Natl. Acad. Sci. USA. 96, 1971-1976. https://doi.org/10.1073/pnas.96.5.1971
  2. Bassil, N. M. and Lloyd, J. R. 2017. Draft genome sequences of four alkaliphilic bacteria belonging to the Anaerobacillus genus. Genome Announc. 5, e01493-16.
  3. Caspi, R., Altman, T., Dreher, K., Fulcher, C. A., Subhraveti, P., Keseler, I., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L. A., Ong, Q., Paley, S., Pujar, A., Shearer, A. G., Travers, M., Weerasinghe, D., Zhang, P. and Karp, P. D. 2012. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nuc. Acids Res. 40, D742-D753. https://doi.org/10.1093/nar/gkr1014
  4. Galperin, M. Y., Makarova, K. S., Wolf, Y. I. and Koonin, E. V. 2015. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43, D261-D269. https://doi.org/10.1093/nar/gku1223
  5. Gan, H. M., Hudson, A. O., Rahman, A. Y., Chan, K. G. and Savka, M. A. 2013. Comparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation. BMC Genomics 28, 431.
  6. Gupta, R. S. 2016. Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification. FEMS Microbiol. Rev. 40, 520-553. https://doi.org/10.1093/femsre/fuw011
  7. Han, K., Li, Z. F., Peng, R., Zhu, L. P., Zhou, T., Wang, L. G., Li, S. G., Zhang, X. B., Hu, W., Wu, Z. H., Qin, N. and Li, Y. Z. 2013. Extraordinary expansion of a Sorangium cellulosum genome from an alkaline milieu. Sci. Rep. 3, 2101. https://doi.org/10.1038/srep02101
  8. Johnson, K. N. 2015. Bacteria and antiviral immunity in insects. Curr. Opin. Insect Sci. 8, 97-103. https://doi.org/10.1016/j.cois.2015.01.008
  9. Klein-Marcuschamer, D., Santos, C. N., Yu, H. and Stephanopoulos, G. 2009. Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes. Appl. Environ. Microbiol. 75, 2705-2711. https://doi.org/10.1128/AEM.01888-08
  10. Lee, D. G. and Lee, S. H. 2015. Investigation of conservative genes in 711 prokaryotes. J. Life Sci. 25, 1007-1013. https://doi.org/10.5352/JLS.2015.25.9.1007
  11. Lee, D. G. 2018. Comparison of metabolic pathways of less orthologous prokaryotes than Mycoplasma genitalium. J. Life Sci. 28, 369-375. https://doi.org/10.5352/JLS.2018.28.3.369
  12. Qin, Q. L., Xie, B. B., Zhang, X. Y., Chen, X. L., Zhou, B. C., Zhou, J., Oren, A. and Zhang, Y. Z. 2014. A proposed genus boundary for the prokaryotes based on genomic insights. J. Bacteriol. 196, 2210-2215. https://doi.org/10.1128/JB.01688-14
  13. Rajendhran, J. and Gunasekaran, P. 2011. Microbial phylogeny and diversity : Small subunit ribosomal RNA sequence analysis and beyond. Microbiol. Res. 166, 99-110. https://doi.org/10.1016/j.micres.2010.02.003
  14. Wang,Y., Zhang, Z. and Ramanan, N. 1997. Theactinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes. J. Bacteriol. 179, 3270-3276. https://doi.org/10.1128/jb.179.10.3270-3276.1997
  15. Zhong, Z., Zhang, W., Song, Y., Liu, W., Xu, H., Xi, X., Menghe, B., Zhang, H. and Sun, Z. 2017. Comparative genomic analysis of the genus Enterococcus. Microbiol. Res. 196, 95-105. https://doi.org/10.1016/j.micres.2016.12.009