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Journal of Bacteriology, February 2009, p. 782-794, Vol. 191, No. 3
0021-9193/09/$08.00+0     doi:10.1128/JB.00965-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Transcriptional Map of Respiratory Versatility in the Hyperthermophilic Crenarchaeon Pyrobaculum aerophilum{triangledown} ,{dagger}

Aaron E. Cozen,1 Matthew T. Weirauch,2 Katherine S. Pollard,3,{ddagger} David L. Bernick,2 Joshua M. Stuart,2 and Todd M. Lowe2*

Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064,1 Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064,2 Department of Statistics, University of California Davis, One Shields Ave., Davis, California 956163

Received 14 July 2008/ Accepted 22 November 2008

Hyperthermophilic crenarchaea in the genus Pyrobaculum are notable for respiratory versatility, but relatively little is known about the genetics or regulation of crenarchaeal respiratory pathways. We measured global gene expression in Pyrobaculum aerophilum cultured with oxygen, nitrate, arsenate and ferric iron as terminal electron acceptors to identify transcriptional patterns that differentiate these pathways. We also compared genome sequences for four closely related species with diverse respiratory characteristics (Pyrobaculum arsenaticum, Pyrobaculum calidifontis, Pyrobaculum islandicum, and Thermoproteus neutrophilus) to identify genes associated with different respiratory capabilities. Specific patterns of gene expression in P. aerophilum were associated with aerobic respiration, nitrate respiration, arsenate respiration, and anoxia. Functional predictions based on these patterns include separate cytochrome oxidases for aerobic growth and oxygen scavenging, a nitric oxide-responsive transcriptional regulator, a multicopper oxidase involved in denitrification, and an archaeal arsenate respiratory reductase. We were unable to identify specific genes for iron respiration, but P. aerophilum exhibited repressive transcriptional responses to iron remarkably similar to those controlled by the ferric uptake regulator in bacteria. Together, these analyses present a genome-scale view of crenarchaeal respiratory flexibility and support a large number of functional and regulatory predictions for further investigation. The complete gene expression data set can be viewed in genomic context with the Archaeal Genome Browser at archaea.ucsc.edu.

* Corresponding author. Mailing address: Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, SOE-2, Santa Cruz, CA 95064. Phone: (831) 459-1511. Fax: (831) 459-4829. E-mail: lowe{at}soe.ucsc.edu

{triangledown} Published ahead of print on 1 December 2008.

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

{ddagger} Present address: Gladstone Institutes, 1650 Owens St., San Francisco, CA 94158.

Journal of Bacteriology, February 2009, p. 782-794, Vol. 191, No. 3
0021-9193/09/$08.00+0     doi:10.1128/JB.00965-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



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