Transcription Factor-Mediated Gene Regulation in Archaea

Karr, Elizabeth A.; Isom, Catherine E.; Trinh, Vy; Peeters, Eveline

doi:10.1007/978-3-319-65795-0_2

Cited by 5 publications

(3 citation statements)

References 204 publications

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“…One-component regulators are characterized by two domains: an N-terminal DNA-binding domain, with a wHTH or an HTH motif, and a C-terminal ligand-binding domain. The structural resemblance between TFs and wHTH-containing NAPs sometimes complicates their distinction, and dual-function DNAbinding proteins can be found within the entire spectrum between a specifically acting regulatory TF and a globally acting chromatin protein (Karr et al 2017;Dorman et al 2020). This is illustrated by the archaea-specific Lrs14 family of DNAbinding proteins, which is widespread in Sulfolobales and shown to bind DNA non-specifically and to regulate biofilm formation and motility in S. acidocaldarius (Orell et al 2013a) (see the section 'Regulation of biofilm processes').…”

Section: Regulatory Transcription Factors In the Sulfolobalesmentioning

confidence: 99%

The biology of thermoacidophilic archaea from the order Sulfolobales

Lewis

Recalde

Bräsen

et al. 2021

FEMS Microbiology Reviews

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Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered more than 50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further the probe novel features of these microbes, but have also paved the way for potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes, and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.

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Section: Regulatory Transcription Factors In the Sulfolobalesmentioning

confidence: 99%

The biology of thermoacidophilic archaea from the order Sulfolobales

Lewis

Recalde

Bräsen

et al. 2021

FEMS Microbiology Reviews

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“…Based on the observations that Lrs14 members have been retrieved from independently performed pulldown assays using Sulfolobus crude cell extracts and seem to be involved in a variety of cellular processes (Napoli et al, 2001;Fiorentino et al, 2003;Kessler et al, 2006;Abella et al, 2007), it was cautiously postulated that Lrs14 regulators might rather be chromatin-organizing proteins than transcriptional regulators and regulate transcription indirectly (Karr et al, 2017). Previously, it was demonstrated that heat and cold shock influences the overall topology of the DNA in hyperthermophilic archaea leading to respectively positively supercoiled and negative supercoiled DNA (López-García and Forterre, 2000).…”

Section: Transcriptional Expression Of Putative Transcription Factors (Tfs) Upon Hsmentioning

confidence: 99%

Defining heat shock response for the thermoacidophilic model crenarchaeon Sulfolobus acidocaldarius

et al. 2020

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“…To survive these challenges, cells must sense and respond to oxidant challenge, shifts in redox balance, and the damage encountered due to oxidative stress. Transcription factors (TFs) that sense and respond to reactive species are found to mediate global changes in gene expression to remedy the damage (2,3). These TFs often have metalloclusters, cofactors, or residues (cysteine, histidine or methionine) that are sensitive to oxidant and serve as "redox switches" (4,5).…”

Section: Introductionmentioning

confidence: 99%

TrmB family transcription factor as a thiol-based regulator of oxidative stress response

Mondragon

Hwang

Kasirajan

et al. 2022

Preprint

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Oxidative stress causes cellular damage including DNA mutations, protein dysfunction and loss of membrane integrity. Here we discovered TrmB (transcription regulator of mal operon) family proteins (Pfam PF01978) composed of a single winged-helix DNA binding domain (InterPro IPR002831) can function as thiol-based transcriptional regulators of oxidative stress responses. Using the archaeon Haloferax volcanii as a model system, we demonstrate that the TrmB-like OxsR is important for recovery of cells from hypochlorite stress. OxsR is shown to bind specific regions of genomic DNA, particularly during hypochlorite stress. OxsR-bound intergenic regions were found proximal to oxidative stress operons including genes associated with thiol relay and low molecular weight thiol biosynthesis. Further analysis of a subset of these sites, revealed OxsR to function during hypochlorite stress as a transcriptional activator and repressor. OxsR was shown to require a conserved cysteine (C24) for function and to use a CG-rich motif upstream of conserved BRE/TATA box promoter elements for transcriptional activation. Protein modeling suggested the C24 is located at a homodimer interface formed by antiparallel α helices, and that oxidation of this cysteine would result in the formation of an intersubunit disulfide bond. This covalent linkage may promote stabilization of an OxsR homodimer with the enhanced DNA binding properties observed in the presence of hypochlorite stress. The phylogenetic distribution TrmB family proteins, like OxsR, that have a single winged-helix DNA binding domain and conserved cysteine residue suggests this type of redox signaling mechanism is widespread in Archaea.ImportanceTrmB-like proteins, while not yet correlated with redox stress, are found in bacteria and widespread in archaea. Here we expand annotation of a large group of TrmB-like single winged-helix DNA binding domain proteins from diverse archaea to function as thiol-based transcriptional regulators of oxidative stress response. Using Haloferax volcanii as a model, we reveal the TrmB-like OxsR functions during hypochlorite stress as a transcriptional activator and repressor of an extensive gene co-expression network associated with thiol relay and other related activities. A conserved cysteine residue of OxxR serves as the thiol-based sensor for this function and likely forms an intersubunit disulfide bond during hypochlorite stress that stabilizes a homodimeric configuration with enhanced DNA binding properties. A CG-rich DNA motif in the promoter region of a subset of sites identified to be OxsR-bound is required for regulation; however, not all sites have this motif suggesting added complexity to the regulatory network.

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Transcription Factor-Mediated Gene Regulation in Archaea

Cited by 5 publications

References 204 publications

The biology of thermoacidophilic archaea from the order Sulfolobales

The biology of thermoacidophilic archaea from the order Sulfolobales

Defining heat shock response for the thermoacidophilic model crenarchaeon Sulfolobus acidocaldarius

TrmB family transcription factor as a thiol-based regulator of oxidative stress response

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