Abstract
The phylogenetic analysis based on molecular characteristics indicates that lithotrophic metabolism was followed by phototrophy. Hydrogen (H2) metabolism is a signature of such environments. This property is prominent among organisms found in geothermal conditions and in deep aquifers. H2 is generated readily by abiotic mechanisms where the terminal electron acceptor is likely to be the limiting factor. In the post-fossil fuel era, H2 has in fact emerged as a strong contender for future fuel. It is thus important to understand the molecular mechanisms which lead to H2 production and associated biological systems. These can help to comprehend issues such as sustainability, environmental emissions and energy security. Comparative genomic analysis reveals events of horizontal transfer of genes of H2 metabolism among taxonomically diverse organisms. This offers an opportunity to identify those genomes which can be tailored for transforming presently ‘non’-H2 producers into producers. This also suggests that naturally occurring events can be mimicked to provide future fuel H2.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Achtman M, Hakenbeck R (1992) Recent developments regarding the evolution of pathogenic bacteria. In: Hormaeche CE (ed) Molecular biology of bacterial infection: current status and future perspective. Cambridge University Press, New York, pp 13–31
Angenent LT, Karim K, Al-Dahhan MH, Wrenn BA, Domiguez-Espinosa R (2004) Production of bioenergy and biochemicals from industrial and agricultural wastewater. Trends Biotechnol 22:477–485. doi:10.1016/j.tibtech.2004.07.001
Aravind L, Tatusov RL, Wolf YI, Walker DR, Koonin EV (1998) Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet 14:442–444. doi:10.1016/S0168-9525(98)01553-4
Brown RJ (2003) Ancient horizontal gene transfer. Nat Rev Genet 4:121–132. doi:10.1038/nrg1000
Bui ET, Bradley PJ, Johnson PJ (1996) A possible mitochondrial gene in the early-branching amitochondriate protist Trichomonas vaginalis. Proc Natl Acad Sci U S A 93:9651–9656
Calteau A, Gouy M, Perriere G (2005) Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea. J Mol Evol 60:557–565. doi:10.1007/s00239-004-0094-8
Campbell A, Mrazek J, Karlin S (1999) Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc Natl Acad Sci U S A 96:9184–9189. doi:10.1073/pnas.96.16.9184
Carbone A, Zinovyev A, Kepes F (2003) Codon adaptation index as a measure of dominating codon bias. Bioinform 19:2005–2015. doi:10.1093/bioinformatics/btg272
Caro-Quintero A, Konstantinidis KT (2014) Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria. ISME J. doi:10.1038/ismej.2014.193
Cavalier-Smith T (1993) Kingdom protozoa and its 18 phyla. Microbiol Rev 57:953–994
Delmotte F, Rispe C, Schaber J, Silva FJ, Moya A (2006) Tempo and mode of early gene loss in endosymbiotic bacteria from insects. BMC Evol Biol 6:56. doi:10.1186/1471-2148-6-56
Di Gioia D, Peel M, Fava F, Wyndham RC (1998) Structures of homologous composite transposons carrying cbaABC genes from Europe and North America. Appl Environ Microbiol 64:1940–1946
Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284:2124–2128. doi:10.1126/science.284.5423.2124
Dubnau D (1999) DNA uptake in bacteria. Annu Rev Microbiol 53:217–244. doi:10.1146/annurev.micro.53.1.217
Embley TM, van der Giezen M, Horner DS, Dyal PL, Bell S, Foster PG (2003) Hydrogenosomes, mitochondria and early eukaryotic evolution. IUBMB Life 55:387–395. doi:10.1080/15216540310001592834
Ermolaeva O, Rastogi M, Pruitt KD, Schuler GD, Bittner ML, Chen Y, Simon R, Meltzer P, Trent JM, Boguski MS (1998) Data management and analysis for gene expression arrays. Nat Genet 20:19–23. doi:10.1038/1670
Felmlee T, Pellett S, Welch RA (1985) Nucleotide sequence of an Escherichia coli chromosomal hemolysin. J Bacteriol 163:94–105
Foflonker F, Price DC, Qiu H, Palenik B, Wang S, Bhattacharya D (2015) Genome of the halotolerant green alga Picochlorum sp. Reveals strategies for thriving under fluctuating environmental conditions. Environ Microbiol 17:412–426. doi:10.1111/1462-2920.12541
Fraser AA (2004) Hydrogenases: active site puzzles and progress. Curr Opin Chem Biol 8:133–140. doi:10.1016/j.cbpa.2004.02.004
Garcia-Vallve S, Guzman E, Montero MA, Romeu A (2003) Horizontal gene transfer in bacterial and archaeal complete genomes. Nucleic Acids Res 31:187–189. doi:10.1093/nar/gkg004
Ge F, Wang LS, Kim J (2005) The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol 3, e316. doi:10.1371/journal.pbio.0030316
Germot A, Philippe H, Guyader HL (1996) Presence of a mitochondrial-type 70 kDa heat shock protein in Trichomonas vaginalis suggests a very early mitochondrial endosymbiosis in eukaryotes. Proc Natl Acad Sci U S A 93:14614–14617
Ghiorse WC (1997) Subterranean life. Science 275:789–790
Hacker J, Blum-Oehler G, Mühldorfer I, Tschäpe H (1997) Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol 23:1089–1097. doi:10.1046/j.1365-2958.1997.3101672.x
Jackson CR, Dugas SL (2003) Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin arsenate reductase. BMC Evol Biol 3:18. doi:10.1186/1471-2148-3-18
Jain R, Rivera MC, Moore JE, Lake JA (2003) Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol 20:1598–1602. doi:10.1093/molbev/msg154
John ME, Keller G (1996) Metabolic pathway engineering in cotton: biosynthesis of polyhydroxybutyrate in fiber cells. Proc Natl Acad Sci U S A 93:12768–12773
Kalia VC, Chauhan A, Bhattacharyya G, Rashmi (2003a) Genomic databases yield novel bioplastic producers. Nature Biotechnol 21:845–846. doi:10.1038/nbt0803-845
Kalia VC, Lal S, Ghai R, Mandal M, Chauhan A (2003b) Mining genomic databases to identify novel hydrogen producers. Trends Biotechnol 21:152–156. doi:10.1016/S0167-7799(03)00028-3
Kalia VC, Lal S, Cheema S (2007) Insight in to the phylogeny of polyhydroxyalkanoate biosynthesis: horizontal gene transfer. Gene 389:19–26. doi:10.1016/j.gene.2006.09.010
Kandler O (1993) The early diversification of life. In: Bengtson S (ed) Early life on earth. Nobel symp 84. Columbia Univ Press, New York, pp 152–160
Karube I, Urano N, Yamada T, Hirochika H, Sakaguchi K (1983) Cloning and expression of the hydrogenase gene from Clostridium butyricum in Escherichia coli. FEBS Lett 158:119–122
Koonin EV, Makarova KS, Aravind L (2001) Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol 55:709–742. doi:10.1146/annurev.micro.55.1.709
Koumandou VL, Kossida S (2014) Evolution of the F0F1 ATP synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes. PLoS Comput Biol 10, e1003821. doi:10.1371/journal.pcbi.1003821
Lal S, Cheema S, Kalia VC (2008) Phylogeny vs genome reshuffling: horizontal gene transfer. Indian J Microbiol 48:228–242. doi:10.1007/s12088-008-0034-1
Lawrence JG, Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci U S A 95:9413–9417
Lerat E, Daubin V, Moran NA (2003) From gene trees to organismal phylogeny in prokaryotes: the case of the γ-proteobacteria. PLoS Biol 1, e19. doi:10.1371/journal.pbio.0000019
Liu S-J, Steinbüchel A (2000) A novel genetically engineered pathway for synthesis of poly (hydroxyalkanoic acids) in Escherichia coli. Appl Environ Microbiol 66:739–743. doi:10.1128/AEM.66.2.739-743.2000
Martin W, Embley TM (2004) Early evolution comes full circle. Nature 431:134–137. doi:10.1038/431134a
Mount DW (2001) Phylogenetic prediction. In: Argentine J (ed) Bioinformatics: sequence and genome analysis, 2nd edn. Cold Spring Harbour Laboratory Press, New York, pp 247–248
Norman RP (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740
Poirier Y, Dennis DE, Klomparens K, Somerville C (1992) Polyhydroxybutyrate, a biodegradable thermoplastic, produced in transgenic plants. Science 256:520–523
Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE (2002) Whole-genome analysis of photosynthetic prokaryotes. Science 298:1616–1620. doi:10.1126/science.1075558
Rivera MC, Lake JA (2004) The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152–155. doi:10.1038/nature02848
Rochette NC, Brochier-Armanet C, Gouy M (2014) Phylogenomic test of the hypotheses for the evolutionary origin of eukaryotes. Mol Biol Evol 31:832–845. doi:10.1093/molbev/mst272
Roger AJ, Clark CG, Doolittle WF (1996) A possible mitochondrial gene in the amitochondriate protist Trichomonas vaginalis. Proc Natl Acad Sci U S A 93:14618–14622
Sharp PM, Li WH (1987) The codon adaptation index- a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295
Soboh B, Linder D, Hedderich R (2004) A multisubunit membrane-bound (NiFe) hydrogenase and a NADH-dependent Fe-only hydrogenase in the fermenting bacterium Thermoanaerobacter tengcongensis. Microbiology 150:2451–2463. doi:10.1099/mic.0.27159-0
Stevens TO, McKinley JP (1995) Lithoautotrophic microbial ecosystems in deep basalt aquifers. Science 270:450–455
Turner JA (2004) Sustainable hydrogen production. Science 305:972–974. doi:10.1126/science.1103197
Veziroglu TN (1995) Twenty years of hydrogen movement 1974–1994. Int J Hydrog Energ 20:1–7
Vignais PM, Billoud B, Meyer J (2001) Classification and phylogeny of hydrogenases. FEMS Microbiol Rev 25:455–501. doi:10.1111/j.1574-6976.2001.tb00587.x
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
Wolf YI, Aravind L, Koonin EV (1998) Rickettsiae and Chlamydia: evidence of horizontal gene transfer and gene exchange. Trends Genet 14:442–444. doi:10.1016/S0168-9525(98)01553-4
Acknowledgments
We are thankful to Directors of CSIR-Institute of Genomics and Integrative Biology, CSIR- National Environmental Engineering Research Institute and CSIR and CSIR project WUM (ESC0108) for providing the necessary funds, facilities and moral support.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer India
About this chapter
Cite this chapter
Lal, S., Raje, D.V., Cheema, S., Kapley, A., Purohit, H.J., Kalia, V.C. (2015). Investigating the Phylogeny of Hydrogen Metabolism by Comparative Genomics: Horizontal Gene Transfer. In: Kalia, V. (eds) Microbial Factories. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2595-9_20
Download citation
DOI: https://doi.org/10.1007/978-81-322-2595-9_20
Publisher Name: Springer, New Delhi
Print ISBN: 978-81-322-2594-2
Online ISBN: 978-81-322-2595-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)