ArticleProceedings of the National Academy of Sciences of the United States of America2009
Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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Who cites it
112 citing papers in PubMed, 201 citations in OpenAlex.
- CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.microLife · 2026Article
- 18S and 25S Exonuclease Resistant Ribosomal RNA Molecules Are Produced by 5'-End Modification During TOR Inhibition.Yeast (Chichester, England) · 2025Article
- Non-conserved microRNAs and their roles in plants: the case for legumes.Plant biology (Stuttgart, Germany) · 2025Review
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- Guided tour through the small protein landscape ofmicroLife · 2025Article
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
- A promoter-RBS library for fine-tuning gene expression inApplied and environmental microbiology · 2024Article
- Compiling a versatile toolbox for inducible gene expression inmicroLife · 2024Article
- Newly Established Genetic System for Functional Analysis of MetSV.International journal of molecular sciences · 2023Article
- Understanding and application of Bacillus nitrogen regulation: A synthetic biology perspective.Journal of advanced research · 2023Review
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- RNAP II produces capped 18S and 25S ribosomal RNAs resistant to 5'-monophosphate dependent processive 5' to 3' exonuclease in polymerase switched Saccharomyces cerevisiae.BMC molecular and cell biology · 2022Article
- Small Proteins in Archaea, a Mainly Unexplored World.Journal of bacteriology · 2022Review
- Small RNA-Sequencing Library Preparation for the Halophilic Archaeon Haloferax volcanii.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea.RNA biology · 2021Article
- Understanding small ORF diversity through a comprehensive transcription feature classification.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Review
- Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World.Frontiers in microbiology · 2021Article
- Whole-genome Identification of Transcriptional Start Sites by Differential RNA-seq in Bacteria.Bio-protocol · 2020Article
- The CARF Protein MM_0565 Affects Transcription of the Casposon-EncodedBiomolecules · 2020Article
52 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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 < or = 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.