Molecular evolution of methanogens based on their metabolic facets

Balachandramohan

2012

Biopolym. Cell

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The conserved domain of sequences revealed in methanogens is considered for designing enzymes among which the attention has been focused on the metalloenzymes showing evolutionary significances. Methods. Molecular evolution, molecular modelling and molecular docking methods. Results. Molecular evolutionary hypothesis has been applied for designing cobalt-containing sirohydrocholine cobalt chelatase and nickel-containing coenzyme F 420 non-reducing hydrogenase from conserved domains encompassing metal-and substrate-binding sites. It was hypothesized that if any enzyme has similar or identical conserved domain in its catalytic region, the construct can bring similar catalytic activity. Using this approach, the region which covers such functional module has to be modeled for yielding enzyme constructs. The present approach has provided a high likelihood to design stable metalloenzyme constructs from the sequences of methanogens due to their low functional divergence. The resulted enzyme constructs have shown diverse reaction specificity and binding affinity with respective substrates. Conclusions. It seems to provide a new knowledge on understanding the catalytic competence as well as substrate-specificity of enzyme constructs. The resulted enzyme constructs could be experimentally reliable as the sequences originally driven from methanogenic archaea.

Section: Molecular Docking For Binding Energy Of Shccc and Cfnrh Consmentioning

confidence: 74%

Cobaltand nickel-containing enzyme constructs from the sequences of methanogens

Balachandramohan

2012

Biopolym. Cell

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“…CRISPR-CAS systems are actively involved in evolving adaptive immune systems of thermophiles against invading mobiloms (Chellapandi and Ranjani 2011;Chellapandi 2011;Shah et al 2013). Many viruses of crenarchaeota coexist in stable relationships with their hosts, suggested that CRISPR systems adopt a regulatory role by exhibiting limited levels of interference (Lillestøl et al 2006).…”

Section: Discussionmentioning

confidence: 99%

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

Ranjani

2015

Syst Synth Biol

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Clustered regularly interspaced short palindromic repeats (CRISPRs) are direct features of the prokaryotic genomes involved in resistance to their bacterial viruses and phages. Herein, we have identified CRISPR loci together with CRISPR-associated sequences (CAS) genes to reveal their immunity against genome invaders in the thermophilic archaea and bacteria. Genomic survey of this study implied that genomic distribution of CRISPR-CAS systems was varied from strain to strain, which was determined by the degree of invading mobiloms. Direct repeats found to be equal in some extent in many thermopiles, but their spacers were differed in each strain. Phylogenetic analyses of CAS superfamily revealed that genes cmr, csh, csx11, HD domain, devR were belonged to the subtypes of cas gene family. The members in cas gene family of thermophiles were functionally diverged within closely related genomes and may contribute to develop several defense strategies. Nevertheless, genome dynamics, geological variation and host defense mechanism were contributed to share their molecular functions across the thermophiles. A thermophilic archaean, Thermococcus gammotolerans and thermophilic bacteria, Petrotoga mobilis and Thermotoga lettingae have shown superoperons-like appearance to cluster cas genes, which were typically evolved for their defense pathways. A cmr operon was identified with a specific promoter in a thermophilic archaean, Caldivirga maquilingensis. Overall, we concluded that knowledge-based genomic survey and phylogeny-based functional assignment have suggested for designing a reliable genetic regulatory circuit naturally from CRISPR-CAS systems, acquired defense pathways, to thermophiles in future synthetic biology.

“…Most metal ions enter cells by an energy dependent saturable process via specific or generic metal ion carriers or channels (Bubb and Lester 1991). Metal chelate complexes may also be transported across the plasma membrane via specialized carriers (Cunningham and Berti 1993;Chellapandi 2011).…”

Section: Introductionmentioning

confidence: 99%

In silico description of cobalt and nickel assimilation systems in the genomes of methanogens

2011

Syst Synth Biol

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Methanogens are a diverse group of organisms that can live in a wide range of environments. Herein, cobalt and tungsten assimilation pathways have proposed to be established in the genomes of Methanococcus maripaludies C5 and Methanosarcina mazei Go1, respectively. All of the proteins involved in the proposed pathways were identified from public domain databases and then complied manually to reconstruct the pathways. The function of proteins with unknown function was assigned by a combined prediction approach. Totally, 17 proteins were identified to cobalt transport and assimilation processes whereas 7 proteins reported to tungsten assimilation system. Phylogenetic analysis of this study revealed that heavy metal transporter of methanogens could be evolved from closely related members in the different genera of methanogens. Nevertheless, genes encoding for metal resistance proteins could be originated from thermophilic and sulfur reducing bacteria. Many metalloenzymes in methanogens were very unique to the species of methanogens. It implied that these metal ions were utilized to produce the precursors for energy driven processes of methanogens. This study suggested that in combination of systems models and evolutionary inference can only correlate metabolic fluxes and physiological changes in methanogens. In silico models of this study will provide insights to design experiments for heavy metal assimilation processes of methanogens growing under heavy metal-rich environments and or in a laboratory condition.