Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability.

Jäger, Dominik, Sharma, C.M., Thomsen, Jens, Ehlers, Claudia, Vogel, J. and Schmitz, Ruth A. (2009) Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability. PNAS Proceedings of the National Academy of Sciences of the United States of America, 106 (51). pp. 21878-21882. DOI 10.1073/pnas.0909051106.

Full text not available from this repository.

Supplementary data:

Abstract

Methanosarcina mazei and related mesophilic archaea are the only organisms fermenting acetate, methylamines, and methanol to methane and carbon dioxide, contributing significantly to greenhouse gas production. The biochemistry of these metabolic processes is well studied, and genome sequences are available, yet little is known about the overall transcriptional organization and the noncoding regions representing 25% of the 4.01-Mb genome of M. mazei. We present a genome-wide analysis of transcription start sites (TSS) in M. mazei grown under different nitrogen availabilities. Pyrosequencing-based differential analysis of primary vs. processed 5′ ends of transcripts discovered 876 TSS across the M. mazei genome. Unlike in other archaea, in which leaderless mRNAs are prevalent, the majority of the detected mRNAs in M. mazei carry long untranslated 5′ regions. Our experimental data predict a total of 208 small RNA (sRNA) candidates, mostly from intergenic regions but also antisense to 5′ and 3′ regions of mRNAs. In addition, 40 new small mRNAs with ORFs of ≤30 aa were identified, some of which might have dual functions as mRNA and regulatory sRNA. We confirmed differential expression of several sRNA genes in response to nitrogen availability. Inspection of their promoter regions revealed a unique conserved sequence motif associated with nitrogen-responsive regulation, which might serve as a regulator binding site upstream of the common IIB recognition element. Strikingly, several sRNAs antisense to mRNAs encoding transposases indicate nitrogen-dependent transposition events. This global TSS map in archaea will facilitate a better understanding of transcriptional and posttranscriptional control in the third domain of life.

Document Type: Article
Research affiliation: Kiel University
OceanRep > The Future Ocean - Cluster of Excellence
Refereed: Yes
Open Access Journal?: No
Publisher: National Academy of Sciences
Projects: Future Ocean
Date Deposited: 11 Feb 2011 12:15
Last Modified: 23 Sep 2019 22:08
URI: https://oceanrep.geomar.de/id/eprint/9473

Actions (login required)

View Item View Item