Faculty Opinions recommendation of Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.

AbstractTranscription Factors (TFs) are proteins that control the flow of genetic information by regulating cellular gene expression. Here we describe PredicTF, a first platform supporting the prediction and classification of novel bacterial TF in complex microbial communities. We evaluated PredicTF using a two-step approach. First, we tested PredictTF’s ability to predict TFs for the genome of an environmental isolate. In the second evaluation step, PredicTF was used to predict TFs in a metagenome and 11 metatranscriptomes recovered from a community performing anaerobic ammonium oxidation (anammox) in a bioreactor. PredicTF is open source pipeline available at https://github.com/mdsufz/PredicTF.

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Structure and functional implications of WYL-domain-containing transcription factor PafBC involved in the mycobacterial DNA damage response

10.1101/612655 ◽

2019 ◽

Author(s):

Andreas U. Müller ◽

Marc Leibundgut ◽

Nenad Ban ◽

Eilika Weber-Ban

Keyword(s):

Dna Damage ◽

Transcription Factor ◽

Transcription Factors ◽

Rna Binding ◽

Rna Binding Proteins ◽

Structural Information ◽

Rna Molecules ◽

Bacterial Transcription ◽

Arthrobacter Aurescens

AbstractIn mycobacteria, transcriptional activator PafBC is responsible for upregulating the majority of genes induced by DNA damage. Understanding the mechanism of PafBC activation is impeded by a lack of structural information on this transcription factor that contains a widespread, but poorly understood WYL domain frequently encountered in bacterial transcription factors. Here, we determined the crystal structure ofArthrobacter aurescensPafBC. The protein consists of two modules, each harboring an N-terminal helix-turn-helix DNA binding domain followed by a central WYL and a C-terminal extension (WCX) domain. The WYL domains exhibit Sm-folds, while the WCX domains adopt ferredoxin-like folds, both characteristic for RNA binding proteins. Our results suggest a mechanism of regulation in which WYL domain-containing transcription factors may be activated by binding RNA molecules. Using anin vivomutational screen inMycobacterium smegmatis, we identify potential co-activator binding sites on PafBC.

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Sensing new chemicals with bacterial transcription factors

Current Opinion in Microbiology ◽

10.1016/j.mib.2016.07.006 ◽

2016 ◽

Vol 33 ◽

pp. 105-112 ◽

Cited By ~ 36

Author(s):

Vincent Libis ◽

Baudoin Delépine ◽

Jean-Loup Faulon

Keyword(s):

Transcription Factors ◽

Bacterial Transcription

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Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC

Nature Communications ◽

10.1038/s41467-019-12567-x ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 3

Author(s):

Andreas U. Müller ◽

Marc Leibundgut ◽

Nenad Ban ◽

Eilika Weber-Ban

Keyword(s):

Dna Damage ◽

Transcription Factors ◽

Rna Binding ◽

Rna Binding Proteins ◽

Structural Information ◽

Response Regulator ◽

Bacterial Dna ◽

Bacterial Transcription ◽

Arthrobacter Aurescens

Abstract In mycobacteria, transcriptional activator PafBC is responsible for upregulating the majority of genes induced by DNA damage. Understanding the mechanism of PafBC activation is impeded by a lack of structural information on this transcription factor that contains a widespread, but poorly understood WYL domain frequently encountered in bacterial transcription factors. Here, we determine the crystal structure of Arthrobacter aurescens PafBC. The protein consists of two modules, each harboring an N-terminal helix-turn-helix DNA-binding domain followed by a central WYL and a C-terminal extension (WCX) domain. The WYL domains exhibit Sm-folds, while the WCX domains adopt ferredoxin-like folds, both characteristic for RNA-binding proteins. Our results suggest a mechanism of regulation in which WYL domain-containing transcription factors may be activated by binding RNA or other nucleic acid molecules. Using an in vivo mutational screen in Mycobacterium smegmatis, we identify potential co-activator binding sites on PafBC.

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