ArticleMolecular biology and evolution2010
Identification and genomic analysis of transcription factors in archaeal genomes exemplifies their functional architecture and evolutionary origin.
Article in Molecular biology and evolution, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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45 citing papers in PubMed, 78 citations in OpenAlex.
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Rapid rewiring of an archaeal transcription factor function via flexible cis-trans interactions.Molecular biology of the cell · 2025Article
- ENcyclopedia of TRAnscription Factors in Bacteria and Archaea genomes (ENTRAF) version 2.0.Database : the journal of biological databases and curation · 2025Article
- TbsP and TrmB jointly regulate gapII to influence cell development phenotypes in the archaeon Haloferax volcanii.Molecular microbiology · 2024Article
- TroR is the primary regulator of the iron homeostasis transcription network in the halophilic archaeon Haloferax volcanii.Nucleic acids research · 2024Article
- Diversity and Potential Multifunctionality of Archaeal CetZ Tubulin-like Cytoskeletal Proteins.Biomolecules · 2023Article
- Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes.Frontiers in microbiology · 2022Article
- The biology of thermoacidophilic archaea from the order Sulfolobales.FEMS microbiology reviews · 2021Article
- Analysis ofGenes · 2021Article
- Towards the Elucidation of AssimilativeGenes · 2021Article
- Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order.Scientific reports · 2020Article
- Article
- Evolution of Regulated Transcription.Cells · 2020Review
- Article
- Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms.PloS one · 2020Article
- Global Transcriptional Programs in Archaea Share Features with the Eukaryotic Environmental Stress Response.Journal of molecular biology · 2019Review
- Old cogs, new tricks: the evolution of gene expression in a chromatin context.Nature reviews. Genetics · 2019Review
- Double autoinhibition mechanism of signal transduction ATPases with numerous domains (STAND) with a tetratricopeptide repeat sensor.Nucleic acids research · 2019Article
- YtrAFrontiers in microbiology · 2019Article
- Conserved principles of transcriptional networks controlling metabolic flexibility in archaea.Emerging topics in life sciences · 2018Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Archaea, which represent a large fraction of the phylogenetic diversity of organisms, are prokaryotes with eukaryote-like basal transcriptional machinery. This organization makes the study of their DNA-binding transcription factors (TFs) and their transcriptional regulatory networks particularly interesting. In addition, there are limited experimental data regarding their TFs. In this work, 3,918 TFs were identified and exhaustively analyzed in 52 archaeal genomes. TFs represented less than 5% of the gene products in all the studied species comparable with the number of TFs identified in parasites or intracellular pathogenic bacteria, suggesting a deficit in this class of proteins. A total of 75 families were identified, of which HTH_3, AsnC, TrmB, and ArsR families were universally and abundantly identified in all the archaeal genomes. We found that archaeal TFs are significantly small compared with other protein-coding genes in archaea as well as bacterial TFs, suggesting that a large fraction of these small-sized TFs could supply the probable deficit of TFs in archaea, by possibly forming different combinations of monomers similar to that observed in eukaryotic transcriptional machinery. Our results show that although the DNA-binding domains of archaeal TFs are similar to bacteria, there is an underrepresentation of ligand-binding domains in smaller TFs, which suggests that protein-protein interactions may act as mediators of regulatory feedback, indicating a chimera of bacterial and eukaryotic TFs' functionality. The analysis presented here contributes to the understanding of the details of transcriptional apparatus in archaea and provides a framework for the analysis of regulatory networks in these organisms.
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