New insights on gene regulation in archaea

Tenorio-Salgado, Silvia; Huerta-Saquero, Alejandro; Pérez‐Rueda, Ernesto

doi:10.1016/j.compbiolchem.2011.10.006

Cited by 9 publications

(13 citation statements)

References 55 publications

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“…This analysis allowed us to deduce the distribution of its TFs and their evolutionary families. Using this repertoire of TFs, we show that (1) 4% of the total genes encode TFs, reinforcing the notion that the genome of archaeal genomes encodes a low proportion of TFs as it was previously described [21] and being similar to bacteria described as intracellular pathogens, opportunistic pathogens and extremophiles (2) a considerable proportion of TFs entail one or two structural domains, contrasting to the observed in archaeal genomes, where most of TFs are monodomain, (3) seven regulons are present and were identified based on sequence inference and the published literature, being the first description in a global scale in this archaeaon, and (4) an overrepresentation of Sulfur and maltose metabolisms are associated with each regulon, among others.…”

Section: Introductionsupporting

confidence: 86%

Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638

Denis

Martínez-Núñez

Tenorio-Salgado

et al. 2018

Life

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In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains. The most abundant DNA-binding domain corresponds to the winged helix-turn-helix domain; with few alternative DNA-binding domains. We also identified seven regulons, which represent 13.5% (279 genes) of the total genes in this archaeon. These analyses increase our knowledge about gene regulation in P. furiosus DSM 3638 and provide additional clues for comprehensive modeling of transcriptional regulatory networks in the Archaea cellular domain.

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Section: Introductionsupporting

confidence: 86%

Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638

Denis

Martínez-Núñez

Tenorio-Salgado

et al. 2018

Life

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“…The HTH domain in EarA indicated by the protein fold recognition server Phyre2 seems to be the only structural domain predicted in this protein. This domain is the most abundant DNA-binding structure in archaeal transcriptional regulators (Tenorio-Salgado et al, 2011). The lack of a sensory domain in EarA suggests that this archaeal transcriptional regulator might require other proteins located upstream in a signal transduction pathway in order to respond to environmental stimuli to activate the transcription of the fla operon and production of archaella.…”

Section: Discussionmentioning

confidence: 99%

Identification of the first transcriptional activator of an archaellum operon in a euryarchaeon

Ding

Nash

Berezuk

et al. 2016

Molecular Microbiology

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The archaellum is the swimming organelle of the third domain, the Archaea. In the euryarchaeon Methanococcus maripaludis, genes involved in archaella formation, including the three archaellins flaB1, flaB2 and flaB3, are mainly located in the fla operon. Previous studies have shown that transcription of fla genes and expression of Fla proteins are regulated under different growth conditions. In this study, we identify MMP1718 as the first transcriptional activator that directly regulates the fla operon in M. maripaludis. Mutants carrying an in-frame deletion in mmp1718 did not express FlaB2 detected by western blotting. Quantitative reverse transcription PCR analysis of purified RNA from the Δmmp1718 mutant showed that transcription of flaB2 was negligible compared to wildtype cells. In addition, no archaella were observed on the cell surface of the Δmmp1718 mutant. FlaB2 expression and archaellation were restored when the Δmmp1718 mutant was complemented with mmp1718 in trans. Electrophoretic motility shift assay and isothermal titration calorimetry results demonstrated the specific binding of purified MMP1718 to DNA fragments upstream of the fla promoter. Four 6 bp consensus sequences were found immediately upstream of the fla promoter and are considered the putative MMP1718-binding sites. Herein, we designate MMP1718 as EarA, the first euryarchaeal archaellum regulator.

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“…For instance, bacteria that have free-living lifestyles, such as Pseudomonas aeruginosa or Escherichia coli, bear a much larger number and variety of genes encoding transcriptional proteins than do intracellular pathogens that thrive in more stable biotopes [7,8]. In contrast, archaea organisms seem to have a lower proportion of TFs than bacteria, suggesting the existence in archaea of alternative mechanisms to compensate for the apparent deficit of protein regulators, including conformations of diverse protein complexes as a function of metabolic status [6,9].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes

Sánchez

Hernandez-Guerrero

Méndez-Monroy

et al. 2020

Genes

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The ability of bacteria and archaea to modulate metabolic process, defensive response, and pathogenic capabilities depend on their repertoire of genes and capacity to regulate the expression of them. Transcription factors (TFs) have fundamental roles in controlling these processes. TFs are proteins dedicated to favor and/or impede the activity of the RNA polymerase. In prokaryotes these proteins have been grouped into families that can be found in most of the different taxonomic divisions. In this work, the association between the expansion patterns of 111 protein regulatory families was systematically evaluated in 1351 non-redundant prokaryotic genomes. This analysis provides insights into the functional and evolutionary constraints imposed on different classes of regulatory factors in bacterial and archaeal organisms. Based on their distribution, we found a relationship between the contents of some TF families and genome size. For example, nine TF families that represent 43.7% of the complete collection of TFs are closely associated with genome size; i.e., in large genomes, members of these families are also abundant, but when a genome is small, such TF family sizes are decreased. In contrast, almost 102 families (56.3% of the collection) do not exhibit or show only a low correlation with the genome size, suggesting that a large proportion of duplication or gene loss events occur independently of the genome size and that various yet-unexplored questions about the evolution of these TF families remain. In addition, we identified a group of families that have a similar distribution pattern across Bacteria and Archaea, suggesting common functional and probable coevolution processes, and a group of families universally distributed among all the genomes. Finally, a specific association between the TF families and their additional domains was identified, suggesting that the families sense specific signals or make specific protein-protein contacts to achieve the regulatory roles.

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New insights on gene regulation in archaea

Cited by 9 publications

References 55 publications

Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638

Dissecting the Repertoire of DNA-Binding Transcription Factors of the Archaeon Pyrococcus furiosus DSM 3638

Identification of the first transcriptional activator of an archaellum operon in a euryarchaeon

Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes

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