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Global Responses of Methanococcus maripaludis to Specific Nutrient Limitations and Growth Rate ^,

Department of Microbiology, University of Washington, Seattle, Washington,¹ Department of Microbiology, University of Georgia, Athens, Georgia,² Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut,³ Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, Pennsylvania⁴

Received 14 November 2007/ Accepted 7 January 2008

Continuous culture, transcriptome arrays, and measurements of cellular amino acid pools and tRNA charging levels were used to determine the response of Methanococcus maripaludis to leucine limitation. For comparison, the responses to phosphate and H₂ limitations were measured as well. In addition, the effect of growth rate was determined. Leucine limitation resulted in a broad response. tRNA^Leu charging decreased, but only small increases in mRNA were seen for amino acid biosynthesis genes. However, the cellular levels of free isoleucine and valine showed significant increases, indicating a coordinate regulation of branched-chain amino acids at a post-mRNA level. Leucine limitation also resulted in increased mRNA abundance for ribosomal protein genes, increased rRNA abundance, and decreased mRNA abundance for genes of methanogenesis. In contrast, phosphate limitation induced a specific response, a marked increase in mRNA levels for a phosphate transporter. Some mRNA levels responded to more than one factor; for example, transcripts for flagellum synthesis genes decreased under conditions of leucine limitation and increased under H₂ limitation. Increased growth rate resulted in increased mRNA levels for ribosomal protein genes, increased rRNA abundance, and increased mRNA for a gene encoding an S-layer protein.

Published ahead of print on 18 January 2008.

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