Journal of Life Science (생명과학회지)

Korean Society of Life Science (한국생명과학회)
권호 표지
DOI QR코드

DOI QR Code

Comparison of Metabolic Pathways of Less Orthologous Prokaryotes than Mycoplasma genitalium

Mycoplasma genitalium 보다 보존적 유전자 수가 작은 원핵생물들의 대사경로 비교

  • Lee, Dong-Geun (Major in Pharmaceutical Engineering, Division of Bio-industry, College of Medical and Life Science, Silla University)
  • 이동근 (신라대학교 의생명과학대학 바이오산업학부 제약공학전공)
  • Received : 2017.12.27
  • Accepted : 2018.02.23
  • Published : 2018.03.30
Download PDF
⟨ Previous Next ⟩

Abstract

Mycoplasma genitalium has 367 conserved genes and the smallest genome among mono-culturable prokaryotes. Conservative metabolic pathways were examined among M. genitalium and 14 prokaryotes, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans and 13 intracellular eubacteria of plants or insects, with fewer conserved genes than M. genitalium. They have 11 to 71 metabolic pathways, however complete metabolic pathways ranged from 1 to 24. Totally, metabolic pathway hole is very high due to the lack of 45.8% of the enzymes required for the whole metabolic pathways and it could be suggested that the shared metabolic pathway with the host's enzyme would work or the essential substances are host dependent. The number of genes necessary for mass transfer through the cell membrane is also very low, and it may be considered that the simple diffusion or the protein of the host will function in the cell membrane of these prokaryotes. Although the tRNA charging pathway was distributed in all 15 prokaryotes, each has 5-20 tRNA charging genes. This study would give clues to the understanding of the metabolic pathways of intracellular parasitic bacteria of plant and endosymbiotic bacteria of insects, and could provide basic data for prevention of crop damage, development of insect pests and human medicines.

Mycoplasma genitalium은 367개의 보존적 유전자를 가지고 있으며 단독배양이 가능한 원핵생물 중 게놈크기가 최소이다. 본 연구에서는 M. genitalium과 M. genitalium보다 보존적 유전자 수가 적은 14개 원핵생물 즉 세포외 공생을 하는 초고온성 고세균 Nanoarchaeum equitans, 식물 세포 내부 기생성 진정세균 혹은 곤충 세포 내부 공생성 진정세균 13종 등의 원핵생물에 보존적인 대사경로를 검토하였다. 이들은 11~71개의 대사경로를 가졌지만 완전한 대사경로는 1~24개였다. 전체 대사경로에 필요한 효소의 45.8%가 결핍되어 대사경로 구멍(metabolic pathway hole)이 매우 많아, 숙주의 효소와 함께 공유대사경로(shared metabolic pathway)를 나타내거나 필수물질의 상당 부분이 숙주에 의존적일 것으로 사료되었다. 세포막을 통한 물질이동에 필요한 유전자의 개수도 아주 적어 단순확산 내지 숙주의 단백질이 이들의 세포막에서 물질이동의 기능을 할 것으로 사료되었다. tRNA charging 경로만이 15개의 분석 대상 원핵생물 모두에 분포하였지만, 분석 대상 원핵생물들은 각각 5~20개의 tRNA charging 유전자를 보유하였다. 본 연구 결과는 배양 불가능한 식물 세포 내 기생성 그리고 곤충 세포 내 공생성 원핵생물들의 대사경로 이해에 대한 단서와 함께 농작물 피해 방지와 해충구제, 의약품 개발 등에 사용할 기초자료를 제공할 수 있을 것이다.

Keywords

References

  1. Berasategui, A., Shukla, S., Salem, H. and Kaltenpoth, M. 2016. Potential applications of insect symbionts in biotechnology. Appl. Microbiol. Biotechnol. 100, 1567-1577. https://doi.org/10.1007/s00253-015-7186-9
  2. Burger, G., Gray, M. W., Forget, L. and Lang, B. F. 2013. Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists. Genome Biol. Evol. 5, 418-438. https://doi.org/10.1093/gbe/evt008
  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.
  4. Firrao, G., Gibb, K. and Streten, C. 2005. Short taxonomic guide to the genus 'Candidatus Phytoplasma'. J. Plant Pathol. 87, 249-263.
  5. 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
  6. Ghai, R., Mizuno, C. M., Picazo, A., Camacho, A. and Rodriguez- Valera, F. 2013. Metagenomics uncovers a new group of low GC and ultra-small marine actinobacteria. Sci. Rep. 3, 2471. https://doi.org/10.1038/srep02471
  7. Glockner, G., Rosenthal, A. and Valentin, K. 2000. The structure and gene repertoire of an ancient red algal plastid genome. J. Mol. Evol. 51, 382-390.
  8. 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
  9. https://ko.wikipedia.org/wiki/%EC%83%9D%EB%AC% BC%EC%A0%95%EB%B3%B4%ED%95%99.
  10. https://www.ncbi.nlm.nih.gov/books/NBK6033/?report= reader.
  11. Jimenez, E., Langa, S., Martin, V., Arroyo, R., Martin, R., Fernandez, L. and Rodriguez, J. M. 2010. Complete genome sequence of Lactobacillus fermentum CECT 5716, a probiotic strain isolated from human milk. J. Bacteriol. 192, 4800. https://doi.org/10.1128/JB.00702-10
  12. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. and Hirakawa, M. 2010. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360. https://doi.org/10.1093/nar/gkp896
  13. Kelkar, Y. D. and Ochman, H. 2013. Genome reduction promotes increase in protein functional complexity in bacteria. Genetics 193, 303-307. https://doi.org/10.1534/genetics.112.145656
  14. Lee, D. G. 2014. Comparison of mitochondria-related conserved genes in eukaryotes and prokaryotes. J. Life Sci. 24, 791-797. https://doi.org/10.5352/JLS.2014.24.7.791
  15. Lee, D. G. 2017. Conservative genes of less orthologous prokaryotes. J. Life Sci. 27, 694-701.
  16. Martinez-Cano, D. J., Reyes-Prieto, M., Martinez-Romero, E., Partida-Martinez, L. P., Latorre, A., Moya, A. and Delaye, L. 2015. Evolution of small prokaryotic genomes. Front Microbiol. 5, 742.
  17. McCutcheon, J. P. and Moran, N. A. 2010. Functional convergence in reduced genomes of bacterial symbionts spanning 200 million years of evolution. Genome Biol. Evol. 2, 708-718.
  18. Nilsson, A. I., Koskiniemi, S., Eriksson, S., Kugelberg, E., Hinton, J. C. and Andersson, D. I. 2005. Bacterial genome size reduction by experimental evolution. Proc. Natl. Acad. Sci. USA. 102, 12112-12116.
  19. Oakeson, K. F., Gil, R., Clayton, A. L., Dunn, D. M., von Niederhausern, A. C., Hamil, C., Aoyagi, A., Duval, B., Baca, A., Silva, F. J., Vallier, A., Jackson, D. G., Latorre, A., Weiss, R. B., Heddi, A., Moya, A. and Dale, C. 2014. Genome degeneration and adaptation in a nascent stage of symbiosis. Genome Biol. Evol. 6, 76-93. https://doi.org/10.1093/gbe/evt210
  20. Russell, C. W., Bouvaine, S., Newell, P. D. and Douglas, A. E. 2013. Shared metabolic pathways in a coevolved insect- bacterial symbiosis. Appl. Environ. Microbiol. 79, 6117-6123. https://doi.org/10.1128/AEM.01543-13
  21. Williams, K. P., Sobral, B. W. and Dickerman, A. W. 2007. A robust species tree for the alphaproteobacteria. J. Bacteriol. 189, 4578-4586. https://doi.org/10.1128/JB.00269-07
  22. Zimorski, V., Ku, C., Martin, W. F. and Gould, S. B. 2014. Endosymbiotic theory for organelle origins. Curr. Opin. Microbiol. 22, 38-48. https://doi.org/10.1016/j.mib.2014.09.008