Chellapandi P
Department of Bioinformatics, Centre for Excellence in Life Sciences, Bharathidasan University, Tiruchirappalli, 620024 Tamil Nadu India.
Syst Synth Biol. 2011 Dec;5(3-4):105-14. doi: 10.1007/s11693-011-9087-2. Epub 2011 Oct 15.
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.
产甲烷菌是一类多样化的生物体，能够生活在广泛的环境中。在此，已提出钴和钨的同化途径分别在马氏甲烷球菌C5和马氏甲烷八叠球菌Go1的基因组中得以确立。参与所提出途径的所有蛋白质均从公共领域数据库中鉴定出来，然后手动整理以重建这些途径。功能未知的蛋白质的功能通过组合预测方法来确定。总共，有17种蛋白质被鉴定参与钴的转运和同化过程，而有7种蛋白质与钨同化系统相关。本研究的系统发育分析表明，产甲烷菌的重金属转运蛋白可能从产甲烷菌不同属的密切相关成员进化而来。然而，编码金属抗性蛋白的基因可能起源于嗜热菌和硫酸盐还原菌。产甲烷菌中的许多金属酶对产甲烷菌物种而言非常独特。这意味着这些金属离子被用于产生产甲烷菌能量驱动过程的前体。本研究表明，系统模型和进化推断相结合只能关联产甲烷菌中的代谢通量和生理变化。本研究的计算机模型将为设计实验提供见解，以研究在富含重金属的环境中或在实验室条件下生长的产甲烷菌的重金属同化过程。
