Structural and functional analysis of BF2549, a PadR-like transcription factor from Bacteroides fragilis

Lee, Choongdeok; Kim, Meong Il; Hong, Minsun

doi:10.1016/j.bbrc.2016.12.155

Cited by 18 publications

(5 citation statements)

References 23 publications

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“…The PadR subfamily-1 contains two domains and dimerizes using the C-terminal domain that is physically separated from the N-terminal wHTH motif ( 20 ). In contrast, the subfamily-2 that includes Lactococcus lactis LmrR and Synechococcus elongatus Pex adopts a single-domain structure with a molecular weight of 11–13 kDa and forms a dimer primarily through the C-terminal helix that is appended to the wHTH motif ( 19 , 23 , 24 , 26 , 27 ).…”

Section: Introductionmentioning

confidence: 99%

Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR

Park

Kwak

Song

et al. 2017

Nucleic Acids Research

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The PadR family is a large group of transcriptional regulators that function as environmental sensors. PadR negatively controls the expression of phenolic acid decarboxylase, which detoxifies harmful phenolic acids. To identify the mechanism by which PadR regulates phenolic acid-mediated gene expression, we performed structural and mutational studies of effector and operator recognition by Bacillus subtilis PadR. PadR contains an N-terminal winged helix-turn-helix (wHTH) domain (NTD) and a C-terminal homodimerization domain (CTD) and dimerizes into a dolmen shape. The PadR dimer interacts with the palindromic sequence of the operator DNA using the NTD. Two tyrosine residues and a positively charged residue in the NTD provide major DNA-binding energy and are highly conserved in the PadR family, suggesting that these three residues represent the canonical DNA-binding motif of the PadR family. PadR directly binds a phenolic acid effector molecule using a unique interdomain pocket created between the NTD and the CTD. Although the effector-binding site of PadR is positionally segregated from the DNA-binding site, effector binding to the interdomain pocket causes PadR to be rearranged into a DNA binding-incompatible conformer through an allosteric interdomain-reorganization mechanism.

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Section: Introductionmentioning

confidence: 99%

Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR

Park

Kwak

Song

et al. 2017

Nucleic Acids Research

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“…In the structure, a hydrogen bond formed by Asp 5 from monomer 1 and Lys 69 from monomer 3 may stabilize the interactions between dimers (Figure S4B). Oligomerization of StbA may also involve the C-terminal domain of the protein, as described for several PadR-like proteins ((38); (39); (36); (31); (40)).…”

Section: Resultsmentioning

confidence: 96%

Characterization of the DNA binding domain of StbA, a key protein of a new type of DNA segregation system

Quèbre

Campo

Cuevas

et al. 2022

Preprint

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Low-copy-number plasmids require sophisticated genetic devices to achieve efficient segregation of plasmid copies during cell division. Plasmid R388 uses a unique segregation mechanism, based on StbA, a small multifunctional protein. StbA is the key protein in a segregation system not involving a plasmid-encoded NTPase partner, it regulates the expression of several plasmid operons, and it is the main regulator of plasmid conjugation. The mechanisms by which StbA, together with the centromere-like sequence stbS, achieves segregation, is largely uncharacterized. To better understand the molecular basis of R388 segregation, we determined the crystal structure of the conserved N-terminal domain of StbA to 1.9 Å resolution. It folds into an HTH DNA-binding motif, structurally related to that of the PadR subfamily II of transcriptional regulators. StbA is organized in two domains. Its N-terminal domain carries the specific stbS DNA binding activity. A truncated version of StbA, deleted of its C-terminal domain, displays only partial activities in vivo, indicating that the non-conserved C-terminal domain is required for efficient segregation and subcellular plasmid positioning. The structure of StbA DNA-binding domain also provides some insight into how StbA monomers cooperate to repress transcription by binding to the stbDR and to form the segregation complex with stbS.

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“…Some Bacillus species have an unexpected potential to produce secondary metabolites and to activate stress responses. The protein polyketide synthase (spot 40) is involved in some intermediate steps for the synthesis of the antibiotic polyketide bacillaene 63,64 ; PadR (spot 123) functions as a transcriptional repressor that inhibits gene expression associated with stress responses 65 ; and MoxR family ATPase (spot 17) takes part in a chaperone system that is important for the folding/activation of proteins and protein complexes 66 . Hypothetical protein N399_09015 is very similar (93%) to type II toxin-antitoxin system PemK/MazF family toxin of Aneurinibacillus terranovensis .…”

Section: Resultsmentioning

confidence: 99%

Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica

Martínez‐Alonso

Pena-Perez

Serrano

et al. 2019

Sci Rep

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Glaciers are populated by a large number of microorganisms including bacteria, archaea and microeukaryotes. Several factors such as solar radiation, nutrient availability and water content greatly determine the diversity and abundance of these microbial populations, the type of metabolism and the biogeochemical cycles. Three ecosystems can be differentiated in glaciers: supraglacial, subglacial and englacial ecosystems. Firstly, the supraglacial ecosystem, sunlit and oxygenated, is predominantly populated by photoautotrophic microorganisms. Secondly, the subglacial ecosystem contains a majority of chemoautotrophs that are fed on the mineral salts of the rocks and basal soil. Lastly, the englacial ecosystem is the least studied and the one that contains the smallest number of microorganisms. However, these unknown englacial microorganisms establish a food web and appear to have an active metabolism. In order to study their metabolic potentials, samples of englacial ice were taken from an Antarctic glacier. Microorganisms were analyzed by a polyphasic approach that combines a set of -omic techniques: 16S rRNA sequencing, culturomics and metaproteomics. This combination provides key information about diversity and functions of microbial populations, especially in rare habitats. Several whole essential proteins and enzymes related to metabolism and energy production, recombination and translation were found that demonstrate the existence of cellular activity at subzero temperatures. In this way it is shown that the englacial microorganisms are not quiescent, but that they maintain an active metabolism and play an important role in the glacial microbial community.

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Structural and functional analysis of BF2549, a PadR-like transcription factor from Bacteroides fragilis

Cited by 18 publications

References 23 publications

Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR

Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR

Characterization of the DNA binding domain of StbA, a key protein of a new type of DNA segregation system

Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica

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