Molecular evolution of methanogens based on their metabolic facets

doi:10.1007/s11515-011-1154-2

Front Biol

2011, Vol. 6

Issue (6) : 490-503 https://doi.org/10.1007/s11515-011-1154-2

REVIEW

Molecular evolution of methanogens based on their metabolic facets

P. CHELLAPANDI(

)

Department of Bioinformatics, Centre for Excellence in School of Life Sciences, Bharathidasan University, Tiruchirappalli-620024, Tamil Nadu, India

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Abstract

The information provided by completely sequenced genomes of methanogens can yield insights into a deeper molecular understanding of evolutionary mechanisms. This review describes the advantages of using metabolic pathways to clarify evolutionary correlation of methanogens with archaea and prokaryotes. Metabolic trees can be used to highlight similarities in metabolic networks related to the biology of methanogens. Metabolic genes are among the most modular in the cell and their genes are expected to travel laterally, even in recent evolution. Phylogenetic analysis of protein superfamilies provides a perspective on the evolutionary history of some key metabolic modules of methanogens. Phage-related genes from distantly related organisms typically invade methanogens by horizontal gene transfer. Metabolic modules in methanogenesis are phylogenetically aligned in closely related methanogens. Reverse order reactions of methanogenesis are achieved in methylotrophic methanogens using metabolic and structural modules of key enzymes. A significant evolutionary process is thought to couple the utilization of heavy metal ions with energetic metabolism in methanogens. Over 30 of methanogens genomes have been sequenced to date, and a variety of databases are being developed that will provide for genome annotation and phylogenomic analysis of methanogens. Into the context of the evolutionary hypothesis, the integration of metabolomic and proteomic data into large-scale mathematical models holds promise for fostering rational strategies for strain improvement.

Keywords methanogens genomics metabolic module phylogeny protein superfamily molecular evolution

Corresponding Author(s): CHELLAPANDI P.,Email:pchellapandi@gmail.com

Issue Date: 01 December 2011

Cite this article:

P. CHELLAPANDI. Molecular evolution of methanogens based on their metabolic facets[J]. Front Biol, 2011, 6(6): 490-503.

URL:

https://academic.hep.com.cn/fib/EN/10.1007/s11515-011-1154-2
https://academic.hep.com.cn/fib/EN/Y2011/V6/I6/490

Taxon ID	Genome name	GC count	GC %	Bases	Genes	CDS	RNA	Pseudo genes	CRISPR
456442	Candidatus Methanoregula boonei 6A8	1386250	0.55	2542943	2518	2464	54	18	0
634498	Methanobrevibacter ruminantium M1	958732	0.33	2937203	2283	2217	66	5	4
420247	Methanobrevibacter smithii PS, ATCC 35061	575114	0.31	1853160	1841	1795	46	0	1
573064	Methanocaldococcus fervens AG86	485612	0.32	1507251	1663	1620	43	39	7
573063	Methanocaldococcus infernus ME	446519	0.34	1328194	1513	1467	46	26	16
243232	Methanocaldococcus jannaschii DSM 2661	544484	0.31	1739916	1844	1789	55	29	15
644281	Methanocaldococcus sp. FS406-22	568097	0.32	1773136	1893	1849	44	33	19
579137	Methanocaldococcus vulcanius M7, DSM 12094	556282	0.32	1761737	1808	1765	43	23	17
304371	Methanocella paludicola SANAE	1624241	0.55	2957635	3062	3004	58	0	0
351160	Methanocella sp. RC-I	1736328	0.55	3179916	3149	3085	64	0	1
259564	Methanococcoides burtonii DSM 6242	1049534	0.41	2575032	2506	2431	75	158	2
419665	Methanococcus aeolicus Nankai-3	471438	0.3	1569500	1554	1503	51	16	1
402880	Methanococcus maripaludis C5	589955	0.33	1789046	1896	1845	51	23	1
444158	Methanococcus maripaludis C6	582965	0.33	1744193	1874	1826	48	3	0
426368	Methanococcus maripaludis C7	590031	0.33	1772694	1858	1807	51	22	0
267377	Methanococcus maripaludis S2	549842	0.33	1661137	1777	1728	49	7	0
406327	Methanococcus vannielii SB	538862	0.31	1720048	1755	1701	54	26	2
456320	Methanococcus voltae A3	553702	0.29	1936387	1768	1721	47	4	3
410358	Methanocorpusculum labreanum Z	902600	0.5	1804962	1830	1765	65	26	2
368407	Methanoculleus marisnigri JR1, DSM 1498	1537981	0.62	2478101	2560	2506	54	17	0
547558	Methanohalophilus mahii SLP, DSM 5219	857659	0.43	2012424	2095	2032	63	45	0
679926	Methanoplanus petrolearius SEBR 4847, DSM 11571	1347696	0.47	2843290	2881	2824	57	39	0
190192	Methanopyrus kandleri AV19	1036629	0.61	1694969	1767	1727	40	17	4
349307	Methanosaeta thermophila PT	1006368	0.54	1879471	1785	1730	55	34	4
188937	Methanosarcina acetivorans C2A	2454788	0.43	5751492	4807	4721	86	278	5
269797	Methanosarcina barkeri Fusaro, DSM 804	1912156	0.39	4873766	3834	3758	76	134	5
192952	Methanosarcina mazei Go1, DSM 3647	1699365	0.41	4096345	3469	3398	71	94	2
339860	Methanosphaera stadtmanae DSM 3091	488399	0.28	1767403	1592	1536	56	2	3
521011	Methanosphaerula palustris E1-9c, DSM 19958	1617942	0.55	2922917	2859	2792	67	137	1
323259	Methanospirillum hungatei JF-1	1600415	0.45	3544738	3307	3239	68	99	6
187420	Methanothermobacter thermoautotrophicus Delta H	867701	0.5	1751377	1893	1845	48	23	3

Tab.1 Genomics features of completely sequenced methanogens

Tab.2 Comparative genomic statistics of gene entries in public domain databases for methanogens

Fig.1 Geneome scale based phylogentic tree of methanogens.

Tab.3 Comparative genomic statistics of gene entries in KEGG database for metabolism of methanogens

Fig.2 Abundance of protein/functional families of some methanogens as a heat map over all families of a specific type (COG) with red corresponding to the most abundant families. Each column on the map corresponds to a genome, while each row corresponds to a family. (A) DSM 6242, (B) Fusaro DSM 804, (C) DSM 3091 1. DSM 6242, 2. Fusaro DSM 804, 3. DSM 3091, 4. JF-1, 5. DSM 2661, 6. S2, 7. AV19, 8. C2A, 9. Go1, DSM 3647, 10. Delta H, 11. PT, 12. C5, 13. Z, 14. JR1, DSM 1498, 15. PS, ATCC 35061, 16. sp. RC-I, 17. 6A8, 18. Nankai-3, 19. C7, 20. SB, 21. C6, 22. V24S, DSM 2088, 23. SEBR 4847, DSM 11571.

Fig.3

Fig.4

Tab.4 Comparative genomic statistics of gene entries in COG database for metabolism of methanogens

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