scholarly journals Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2)

2014 ◽  
Vol 42 (15) ◽  
pp. 10122-10133 ◽  
Author(s):  
Hussain Bhukya ◽  
Ruchika Bhujbalrao ◽  
Aruna Bitra ◽  
Ruchi Anand
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Dna Sequences ◽  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
Antibiotic Resistant ◽  
Transporter Protein ◽  
Dimeric Interface ◽  
Transcriptional Regulatory ◽  
Family Protein

AbstractAntibiotic production and resistance pathways in Streptomyces are dictated by the interplay of transcriptional regulatory proteins that trigger downstream responses via binding to small diffusible molecules. To decipher the mode of DNA binding and the associated allosteric mechanism in the sub-class of transcription factors that are induced by γ-butyrolactones, we present the crystal structure of CprB in complex with the consensus DNA element to a resolution of 3.25 Å. Binding of the DNA results in the restructuring of the dimeric interface of CprB, inducing a pendulum-like motion of the helix-turn-helix motif that inserts into the major groove. The crystal structure revealed that, CprB is bound to DNA as a dimer of dimers with the mode of binding being analogous to the broad spectrum multidrug transporter protein QacR from the antibiotic resistant strain Staphylococcus aureus. It was demonstrated that the CprB displays a cooperative mode of DNA binding, following a clamp and click model. Experiments performed on a subset of DNA sequences from Streptomyces coelicolor A3(2) suggest that CprB is most likely a pleiotropic regulator. Apart from serving as an autoregulator, it is potentially a part of a network of proteins that modulates the γ-butyrolactone synthesis and antibiotic regulation pathways in S. coelicolor A3(2).

Crystal structure of the DNA-binding domain of BldD, a central regulator of aerial mycelium formation in Streptomyces coelicolor A3(2)

2006 ◽  
Vol 60 (5) ◽  
pp. 1179-1193 ◽  
Author(s):  
In-Kwon Kim ◽  
Chang-Jin Lee ◽  
Min-Kyu Kim ◽  
Jeong-Mok Kim ◽  
Ji-Hye Kim ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Streptomyces Coelicolor ◽  
Aerial Mycelium ◽  
Binding Domain ◽  
Dna Binding Domain

scholarly journals The bldC Developmental Locus of Streptomyces coelicolor Encodes a Member of a Family of Small DNA-Binding Proteins Related to the DNA-Binding Domains of the MerR Family

2005 ◽  
Vol 187 (2) ◽  
pp. 716-728 ◽  
Author(s):  
Alison C. Hunt ◽  
Luis Servín-González ◽  
Gabriella H. Kelemen ◽  
Mark J. Buttner
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
Aerial Mycelium ◽  
Dna Binding Proteins ◽  
S1 Nuclease ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Wide Range

ABSTRACT The bldC locus, required for formation of aerial hyphae in Streptomyces coelicolor, was localized by map-based cloning to the overlap between cosmids D17 and D25 of a minimal ordered library. Subcloning and sequencing showed that bldC encodes a member of a previously unrecognized family of small (58- to 78-residue) DNA-binding proteins, related to the DNA-binding domains of the MerR family of transcriptional activators. BldC family members are found in a wide range of gram-positive and gram-negative bacteria. Constructed ΔbldC mutants were defective in differentiation and antibiotic production. They failed to form an aerial mycelium on minimal medium and showed severe delays in aerial mycelium formation on rich medium. In addition, they failed to produce the polyketide antibiotic actinorhodin, and bldC was shown to be required for normal and sustained transcription of the pathway-specific activator gene actII-orf4. Although ΔbldC mutants produced the tripyrrole antibiotic undecylprodigiosin, transcripts of the pathway-specific activator gene (redD) were reduced to almost undetectable levels after 48 h in the bldC mutant, in contrast to the bldC + parent strain in which redD transcription continued during aerial mycelium formation and sporulation. This suggests that bldC may be required for maintenance of redD transcription during differentiation. bldC is expressed from a single promoter. S1 nuclease protection assays and immunoblotting showed that bldC is constitutively expressed and that transcription of bldC does not depend on any of the other known bld genes. The bldC18 mutation that originally defined the locus causes a Y49C substitution that results in instability of the protein.

scholarly journals Reconstruction of a global gene regulatory network for Streptomyces coelicolor: Curation, inference, and assessment

2021 ◽  
Author(s):  
Andrea Zorro-Aranda ◽  
Juan Miguel Escorcia-Rodriguez ◽  
Jose Kenyi Gonzalez-Kise ◽  
Julio Augusto Freyre-Gonzalez
Keyword(s):  
Gene Regulatory Network ◽  
Dna Sequences ◽  
Regulatory Network ◽  
Sequence Data ◽  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
System Level ◽  
Upstream Region ◽  
Regulatory Interactions ◽  
Gene Regulatory

Streptomyces coelicolor A3(2) is a model microorganism for the study of Streptomycetes, antibiotic production, and secondary metabolism in general. However, little effort to globally study its transcription has been made even though S. coelicolor has an outstanding variety of regulators among bacteria. We manually curated 29 years of literature and databases to assemble a meta-curated experimentally-validated gene regulatory network (GRN) with 5386 genes and 9707 regulatory interactions (~41% of the total expected interactions). This provides the most extensive and up-to-date reconstruction available for the regulatory circuitry of this organism. We found a low level of direct experimental validation for the regulatory interactions reported in the literature and curated in this work. Only ~6% (533/9687) are supported by experiments confirming the binding of the transcription factor to the upstream region of the target gene, the so-called "strong" evidence. To tackle network incompleteness, we performed network inference using several methods (including two proposed here) for motif detection in DNA sequences and GRN inference from transcriptomics. Further, we contrasted the structural properties and functional architecture of the networks to assess the predictions' reliability, finding the inference from DNA sequence data to be the most trustworthy. Finally, we show two possible applications of the inferred and the curated network. The inferred one allowed us to identify putative novel transcription factors for the key Streptomyces antibiotic regulatory proteins (SARPs). The curated one allows us to study the conservation of the system-level components between S. coelicolor and Corynebacterium glutamicum. There we identified the basal machinery as the common signature between the two organisms. The curated networks were deposited in Abasy Atlas (https://abasy.ccg.unam.mx/) while the inferences are available as Supplementary Material.

scholarly journals Crystal Structure of a Conserved Hypothetical Protein MJ0927 fromMethanocaldococcus jannaschiiReveals a Novel Quaternary Assembly in the Nif3 Family

2014 ◽  
Vol 2014 ◽  
pp. 1-8
Author(s):  
Sheng-Chia Chen ◽  
Chi-Hung Huang ◽  
Chia Shin Yang ◽  
Shu-Min Kuan ◽  
Ching-Ting Lin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Hypothetical Protein ◽  
Mobility Shift ◽  
Methanocaldococcus Jannaschii ◽  
Double Stranded Dna ◽  
Family Protein ◽  
Electrophoretic Mobility Shift Assays ◽  
Quaternary Assembly ◽  
Positively Charged

A Nif3 family protein ofMethanocaldococcus jannaschii, MJ0927, is highly conserved from bacteria to humans. Although several structures of bacterial Nif3 proteins are known, no structure representing archaeal Nif3 has yet been reported. The crystal structure ofMethanocaldococcus jannaschiiMJ0927 was determined at 2.47 Å resolution to understand the structural differences between the bacterial and archaeal Nif3 proteins. Intriguingly, MJ0927 is found to adopt an unusual assembly comprising a trimer of dimers that forms a cage-like architecture. Electrophoretic mobility-shift assays indicate that MJ0927 binds to both single-stranded and double-stranded DNA. Structural analysis of MJ0927 reveals a positively charged region that can potentially explain its DNA-binding capability. Taken together, these data suggest that MJ0927 adopts a novel quartenary architecture that could play various DNA-binding roles inMethanocaldococcus jannaschii.

scholarly journals Reconstruction of a Global Gene Regulatory Network for Streptomyces Coelicolor: Curation, Inference, and Assessment

2021 ◽  
Author(s):  
Andrea Zorro-Aranda ◽  
Juan Miguel Escorcia-Rodríguez ◽  
José Kenyi González-Kise ◽  
Julio Augusto Freyre-González
Keyword(s):  
Gene Regulatory Network ◽  
Dna Sequences ◽  
Regulatory Network ◽  
Network Inference ◽  
Sequence Data ◽  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
Community Integration ◽  
System Level ◽  
Gene Regulatory

Abstract Streptomyces coelicolor A3(2) is a model microorganism for the study of Streptomycetes, antibiotic production, and secondary metabolism in general. However, little effort to globally study its transcription has been made even though S. coelicolor has an outstanding variety of regulators among bacteria. We manually curated 29 years of literature and databases to assemble a meta-curated experimentally-validated gene regulatory network (GRN) with 5386 genes and 9707 regulatory interactions (~41% of the total expected interactions). We performed network inference using several methods (including two proposed here) for motif detection in DNA sequences and GRN inference from transcriptomics to tackle network incompleteness, using a community integration approach to reduce false positives. Further, we contrasted the structural properties and functional architecture of the networks to assess the predictions’ reliability, finding the inference from DNA sequence data to be the most trustworthy. The inferences allowed us to identify putative novel transcription factors for key Streptomyces antibiotic regulatory proteins (SARPs). Finally, we studied the conservation of the system-level components between S. coelicolor and Corynebacterium glutamicum and identified the basal machinery as the common signature between the two organisms. The curated networks were deposited in Abasy Atlas (https://abasy.ccg.unam.mx/) while the inferences are available as supplementary material.

scholarly journals Distinct DNA-binding feature of the peroxide response regulator from group A streptococcus

2014 ◽  
Vol 70 (a1) ◽  
pp. C426-C426
Author(s):  
Shu-Ying Wang ◽  
Chang Sheng-Huei Lin ◽  
Shi-Yu Chao ◽  
Michal Hammel ◽  
Jay Nix ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Dna Binding ◽  
Dna Sequences ◽  
Structural Information ◽  
Group A Streptococcus ◽  
Response Regulator ◽  
Interaction Model ◽  
Molecular Architecture ◽  
Winged Helix ◽  
Group A

Group A streptococcus (GAS) is a significant human pathogen, renowned for its rapidly and highly desctructive ability to infect a wide variety of tissues. Clinical manifestation of GAS infection ranges from mild pharyngitis to severe life-threating disease such as necrotizing fasciitis. Unlike other gram-positive bacteria, GAS does not produce catalase, but has an ability to resist killing by reactive oxygen species through unknown novel mechanisms. Our previous studies have discovered that the peroxide response regulator (PerR) is crucial for GAS to cope with oxidative stress and it directly regulates the expression of an iron-binding protein Dpr [1,2]. PerR is a member of Fur (ferric uptake regulator) family which is known to be dimeric, metal-binding regulators. Currently, no structural information is available to understand how the similar structures of the Fur family regulators recognize divergent DNA sequences. To study how PerR interacts with dpr promoter DNA, we have conducted a series of mutagenesis, biochemical and structural studies by combining protein crystallography and small-angle X-ray scattering (SAXS). We have determined the PerR crystal structure to 1.6 Å resolution and identified the DNA-binding residues, which suggest PerR binds to the dpr promoter through a winged-helix motif. By performing SAXS studies, we confirmed that the PerR crystal structure reflects its conformation in solution. Furthermore, SAXS analysis allowed us to resolve the molecular architecture of PerR-DNA complex, in which two 30 bp DNA fragments wrap around two PerR homodimers by interacting with the adjacent positively-charged winged-helix motifs. Our results have revealed the PerR-DNA interaction model and illustrated the DNA-binding mode of PerR that is distinct from all other regulators in Fur family [3].

scholarly journals Putative TetR Family Transcriptional Regulator SCO1712 Encodes an Antibiotic Downregulator in Streptomyces coelicolor

2010 ◽  
Vol 76 (9) ◽  
pp. 3039-3043 ◽  
Author(s):  
Han-Na Lee ◽  
Jianqiang Huang ◽  
Jong-Hyuk Im ◽  
Seon-Hye Kim ◽  
Jun-Hee Noh ◽  
...  
Keyword(s):  
Microarray Analysis ◽  
Dna Microarray ◽  
Deletion Mutant ◽  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
Regulatory Gene ◽  
Transcriptional Regulator ◽  
Antibiotic Biosynthesis ◽  
Dna Microarray Analysis ◽  
Transcriptional Regulatory

ABSTRACT A tetR family transcriptional regulatory gene (SCO1712) was identified as a global antibiotic regulatory gene from a Streptomyces interspecies DNA microarray analysis. SCO1712 disruption in S treptomyces coelicolor not only upregulated antibiotic biosynthesis through pathway-specific regulators when a previously identified pleiotropic downregulatory wblA was expressed but also further stimulated antibiotic production in a wblA deletion mutant, implying that SCO1712 might encode a novel antibiotic downregulator.

scholarly journals Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal

PLoS ONE ◽  
2016 ◽  
Vol 11 (12) ◽  
pp. e0167763 ◽  
Author(s):  
Michele D. Kattke ◽  
Albert H. Chan ◽  
Andrew Duong ◽  
Danielle L. Sexton ◽  
Michael R. Sawaya ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Streptomyces Coelicolor ◽  
Binding Mode ◽  
The Novel ◽  
Sorting Signal ◽  
Insight Into ◽  
Class E
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