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Journal of Bacteriology, April 2009, p. 2315-2329, Vol. 191, No. 7
0021-9193/09/$08.00+0     doi:10.1128/JB.01534-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

The Sac10b Homolog in Methanococcus maripaludis Binds DNA at Specific Sites{triangledown} ,{dagger}

Yuchen Liu,1,{ddagger} Li Guo,2,{ddagger} Rong Guo,2 Richard L. Wong,3 Hilda Hernandez,3 Jinchuan Hu,2 Yindi Chu,2 I. Jonathan Amster,3 William B. Whitman,1* and Li Huang2*

Departments of Microbiology,1 Chemistry, University of Georgia, Athens, Georgia 30602,3 State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China2

Received 29 October 2008/ Accepted 10 January 2009

The Sac10b protein family, also known as Alba, is widely distributed in Archaea. Sac10b homologs in thermophilic Sulfolobus species are very abundant. They bind both DNA and RNA with high affinity and without sequence specificity, and their physiological functions are still not fully understood. Mma10b from the euryarchaeote Methanococcus maripaludis is a mesophilic member of the Sac10b family. Mma10b is not abundant and constitutes only ~0.01% of the total cellular protein. Disruption of mma10b resulted in poor growth of the mutant in minimal medium at near the optimal growth temperature but had no detectable effect on growth in rich medium. Quantitative proteomics, real time reverse transcription-PCR, and enzyme assays revealed that the expression levels of some genes involved in CO2 assimilation and other activities were changed in the {Delta}mma10b mutant. Chromatin immunoprecipitation suggested a direct association of Mma10b with an 18-bp DNA binding motif in vivo. Electrophoretic mobility shift assays and DNase I footprinting confirmed that Mma10b preferentially binds specific sequences of DNA with an apparent Kd in the 100 nM range. These results suggested that the physiological role of Mma10b in the mesophilic methanococci is greatly diverged from that of homologs in thermophiles.

* Corresponding author. Mailing address for Li Huang: State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China. Phone: 86-10-64807430. Fax: 86-10-64807429. E-mail: huangl{at}sun.im.ac.cn. Mailing address for William B. Whitman: Department of Microbiology, University of Georgia, Athens, GA 30602. Phone: (706) 542-4219. Fax: (706) 542-2674. E-mail: whitman{at}uga.edu

{triangledown} Published ahead of print on 23 January 2009.

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

{ddagger} These authors contributed equally to this work.

Journal of Bacteriology, April 2009, p. 2315-2329, Vol. 191, No. 7
0021-9193/09/$08.00+0     doi:10.1128/JB.01534-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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