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The Korean Society for Biotechnology and Bioengineering (한국생물공학회)
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Prediction of Genes Lacking in an Ammonia Oxidizing Archaeon for Independent Growth

암모니아 산화 고세균의 독립성장에 필요한 결손 유전자 예측

  • Han, Sang-Soo (Department of Biological Sciences, College of Natural Sciences, Chonnam National University) ;
  • Lee, Jin-Young (Department of Biological Sciences, College of Natural Sciences, Chonnam National University) ;
  • Rhee, Sung-Keun (Department of Microbiology, Chungbuk National University) ;
  • Kim, Geun-Joong (Department of Biological Sciences, College of Natural Sciences, Chonnam National University)
  • Received : 2011.05.04
  • Accepted : 2011.05.30
  • Published : 2011.06.30
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Abstract

As a number of archaea are ubiquitously found in non-extreme habitats, elucidation of their functional roles becomes currently an emerging issue. However, most of them are unable to grow in pure culture and so it remains to be established. In order to find genes lacking in the genome of an ammonia-oxidizing archaeon (AOA), we here report on the comparative analyses of an AOA genome with those of experimentally or theoretically established minimal genomes for independent growth. We assessed the genes lacking in AOA using logic of clusters of orthologous groups (COG), remote homology, consensus sequence weight matrix, function-based motif or domain, and then further excluded genes encoding hypothetical orarchaea-specific proteins. The results of these combination analyses revealed 19 candidate genes lacking in the genome of an AOA. Thus, our results provide a possibility of inducing independent growth of AOA when supplemented with product (s) of the lacking gene (s), and also give a chance for finding new proteins with novel sequence or structure space even if the predicted lacking-genes will be found using another algorithms or biochemical studies.

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References

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