Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function

• Published in: Scientific reports 2016-10, Vol.6 (1), p.34639-34639, Article 34639
• Main Authors: Liao, Y., Williams, T. J., Walsh, J. C., Ji, M., Poljak, A., Curmi, P. M. G., Duggin, I. G., Cavicchioli, R.
• Format: Article
• Language: English
• Subjects: 14; 14/10; 14/34; 14/63; 42/44; 631/326/26/2525; 631/326/325/1996; Amidohydrolases - deficiency; Amidohydrolases - genetics; Antarctic Regions; Archaeal Proteins - genetics; Archaeal Proteins - metabolism; Biodegradation, Environmental; Culture Media - chemistry; Culture Media - pharmacology; Formamidase; Gene Deletion; Gene Expression Regulation, Archaeal; Genes; Genetic Engineering; Genetic Vectors - chemistry; Genetic Vectors - metabolism; Halorubrum - classification; Halorubrum - drug effects; Halorubrum - enzymology; Halorubrum - genetics; Humanities and Social Sciences; Humans; Methanogenic bacteria; Microorganisms; multidisciplinary; Parasites; Phylogeny; Plastic pollution; Plastics; Plastics - metabolism; Pollutants; Restriction Mapping; Science; Transformation, Genetic; Water Pollutants, Chemical - metabolism
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep34639

No systems have been reported for genetic manipulation of cold-adapted Archaea . Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea , the acetamidase gene, amd3 , was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria . Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya ) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria ) or parasites of animals and plants (e.g. Chlamydiae ). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria , we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.