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Genome Sequence of Thermofilum pendens Reveals an Exceptional Loss of Biosynthetic Pathways without Genome Reduction ^,

Iain Anderson,^1* Jason Rodriguez,^2,3 Dwi Susanti,^2,5 Iris Porat,^6, Claudia Reich,⁷ Luke E. Ulrich,⁸ James G. Elkins,⁹ Kostas Mavromatis,¹ Athanasios Lykidis,¹ Edwin Kim,¹ Linda S. Thompson,^1,10 Matt Nolan,¹ Miriam Land,⁹ Alex Copeland,¹ Alla Lapidus,¹ Susan Lucas,¹ Chris Detter,^1,10 Igor B. Zhulin,⁸ Gary J. Olsen,⁷ William Whitman,⁶ Biswarup Mukhopadhyay,^2,3,4,5 James Bristow,¹ and Nikos Kyrpides¹

Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598,¹ Virginia Bioinformatics Institute,² Departments of Biochemistry,³ Biological Sciences,⁴ Genetics, Bioinformatics and Computational Biology Graduate Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061,⁵ Department of Microbiology, University of Georgia, Athens, Georgia 30602,⁶ Department of Microbiology, University of Illinois, Urbana, Illinois 61801,⁷ Joint Institute for Computational Sciences, University of Tennessee-Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,⁸ Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,⁹ Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545,¹⁰

Received 14 December 2007/ Accepted 1 February 2008

We report the complete genome of Thermofilum pendens, a deeply branching, hyperthermophilic member of the order Thermoproteales in the archaeal kingdom Crenarchaeota. T. pendens is a sulfur-dependent, anaerobic heterotroph isolated from a solfatara in Iceland. It is an extracellular commensal, requiring an extract of Thermoproteus tenax for growth, and the genome sequence reveals that biosynthetic pathways for purines, most amino acids, and most cofactors are absent. In fact, T. pendens has fewer biosynthetic enzymes than obligate intracellular parasites, although it does not display other features that are common among obligate parasites and thus does not appear to be in the process of becoming a parasite. It appears that T. pendens has adapted to life in an environment rich in nutrients. T. pendens was known previously to utilize peptides as an energy source, but the genome revealed a substantial ability to grow on carbohydrates. T. pendens is the first crenarchaeote and only the second archaeon found to have a transporter of the phosphotransferase system. In addition to fermentation, T. pendens may obtain energy from sulfur reduction with hydrogen and formate as electron donors. It may also be capable of sulfur-independent growth on formate with formate hydrogen lyase. Additional novel features are the presence of a monomethylamine:corrinoid methyltransferase, the first time that this enzyme has been found outside the Methanosarcinales, and the presence of a presenilin-related protein. The predicted highly expressed proteins do not include proteins encoded by housekeeping genes and instead include ABC transporters for carbohydrates and peptides and clustered regularly interspaced short palindromic repeat-associated proteins.

Published ahead of print on 8 February 2008.

Supplemental material for this article may be found at http://jb.asm.org/.

Present address: Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802.

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