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

Denis, Antonia; Martínez-Núñez, Mario Alberto; Tenorio-Salgado, Silvia; Pérez‐Rueda, Ernesto

doi:10.3390/life8040040

Cited by 6 publications

(7 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…These families include HTH_24, FFRP (PF13412), and TrmB (PF01978). For instance, the FFRP contains proteins described as global regulators, such as LysM of S. solfataricus that, in the absence or at low concentrations of lysine, activates the biosynthesis of this amino acid via the alpha-aminoadipate (AAA) pathway [22]; members of the Sugar-specific transcriptional regulator TrmB family of Pyrococcus furiosus, which inhibit transcription of the trehalose/maltose transport gene cluster (malE operon), and of the maltodextrin transport gene cluster (mdxE operon) [23] (Fig 2 ).…”

Section: Plos Onementioning

confidence: 99%

Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms

et al. 2021

Self Cite

View full text Add to dashboard Cite

Archaea represent a diverse phylogenetic group that includes free-living, extremophile, mesophile, symbiont, and opportunistic organisms. These prokaryotic organisms share a high significant similarity with the basal transcriptional machinery of Eukarya, and they share regulatory mechanisms with Bacteria, such as operonic organization and DNA-binding transcription factors (TFs). In this work, we identified the repertoire of TFs in 415 archaeal genomes and compared them with their counterparts in bacterial genomes. The comparisons of TFs, at a global level and per family, allowed us to identify similarities and differences between the repertoires of regulatory proteins of bacteria and archaea. For example, 11 of 62 families are more highly abundant in archaea than bacteria, and 13 families are abundant in bacteria but not in archaea and 38 families have similar abundances in the two groups. In addition, we found that archaeal TFs have a lower isoelectric point than bacterial proteins, i.e., they contain more acidic amino acids, and are smaller than bacterial TFs. Our findings suggest a divergence occurred for the regulatory proteins, even though they are common to archaea and bacteria. We consider that this analysis contributes to the comprehension of the structure and functionality of regulatory proteins of archaeal organisms.

show abstract

Section: Plos Onementioning

confidence: 99%

Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…Exceptions are observed on this theme: for example, a wHTH-containing MarR-type TF in Sulfolobus tokodaii interacts in the major groove by its wing rather than by its recognition helix [14]. As an illustration for the widespread occurrence of wHTH folds, 73% of all TFs in the Euryarchaeon Pyrococcus furiosus are predicted to harbor a wHTH motif [15]. Also in bacteria, it is observed that most TFs harbor a HTH or wHTH motif [10].…”

Section: General Characteristics Of Archaeal Transcription Factorsmentioning

confidence: 99%

Transcription Regulators in Archaea: Homologies and Differences with Bacterial Regulators

Lemmens

Maklad

Bervoets

et al. 2019

Journal of Molecular Biology

View full text Add to dashboard Cite

“…The genome of the hyperthermophilic euryarchaeon Pyrococcus furiosus contains a total number of 86 putative DNA-binding TFs. However, the exact function of most of these factors, which represent about 4 % of all open reading frames (ORFs), is unknown ( Denis et al, 2018 ). In an attempt to close that knowledge gap, functional and structural aspects of some of these TFs have been analyzed over the last two decades.…”

Section: Introductionmentioning

confidence: 99%

CopR, a Global Regulator of Transcription to Maintain Copper Homeostasis in Pyrococcus furiosus

et al. 2021

View full text Add to dashboard Cite

Although copper is in many cases an essential micronutrient for cellular life, higher concentrations are toxic. Therefore, all living cells have developed strategies to maintain copper homeostasis. In this manuscript, we have analyzed the transcriptome-wide response of Pyrococcus furiosus to increased copper concentrations and described the essential role of the putative copper-sensing metalloregulator CopR in the detoxification process. To this end, we employed biochemical and biophysical methods to characterize the role of CopR. Additionally, a copR knockout strain revealed an amplified sensitivity in comparison to the parental strain towards increased copper levels, which designates an essential role of CopR for copper homeostasis. To learn more about the CopR-regulated gene network, we performed differential gene expression and ChIP-seq analysis under normal and 20 μM copper-shock conditions. By integrating the transcriptome and genome-wide binding data, we found that CopR binds to the upstream regions of many copper-induced genes. Negative-stain transmission electron microscopy and 2D class averaging revealed an octameric assembly formed from a tetramer of dimers for CopR, similar to published crystal structures from the Lrp family. In conclusion, we propose a model for CopR-regulated transcription and highlight the regulatory network that enables Pyrococcus to respond to increased copper concentrations.

show abstract

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

Cited by 6 publications

References 63 publications

Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms

Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms

Transcription Regulators in Archaea: Homologies and Differences with Bacterial Regulators

CopR, a Global Regulator of Transcription to Maintain Copper Homeostasis in Pyrococcus furiosus

Contact Info

Product

Resources

About