630 results on '"Helix-turn-helix"'
Search Results
2. Unexpected Requirement of Small Amino Acids at Position 183 for DNA Binding in the Escherichia coli cAMP Receptor Protein
- Author
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Carranza, Marcus, Rea, Amanda, Pacheco, Daisy, Montiel, Christian, Park, Jin, and Youn, Hwan
- Published
- 2024
- Full Text
- View/download PDF
3. Transcription Factors and Signal Transduction
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Carlberg, Carsten, Velleuer, Eunike, Molnár, Ferdinand, Carlberg, Carsten, Velleuer, Eunike, and Molnár, Ferdinand
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- 2023
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4. Identification and Characterization of Mobile Genetic Elements in Gut Bacteroidota
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Ortañez, Jericho
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Microbiology ,Evolution & development ,Genetics ,Bacteroidota ,Conjugative Transposon ,CTnDOT ,Helix-turn-Helix ,Horizontal Gene Transfer ,Mobile Genetic Elements - Abstract
Mobile genetic elements (MGEs) are important drivers of bacterial evolution, facilitating the exchange of fitness determinant genes such as antibiotic resistance and virulence factors. Although various computational methods exist for identifying potential MGEs, confirming their ability to transfer requires additional experimental approaches. Here, we introduce the transposon (Tn) mutagenesis mobilization method (TMMM) as a means to confirm mobilization without the need for targeted mutations. Using this method, we identified two MGEs, one being a novel CTn labeled PvCTn, present in Phocaeicola vulgatus. Through Tn mutagenesis and subsequent gene deletion, we discovered that a helix-turn-helix motif gene, BVU3433, negatively regulated the conjugation efficiency of PvCTn in vitro. Furthermore, our transcriptomics data revealed that BVU3433 plays a crucial role in the repression concouof PvCTn genes, including genes involved in forming complete conjugation machinery (Type IV Secretion System (T4SS)). Finally, analysis of individual strain genomes and community metagenomes identified the widespread prevalence of PvCTn-like elements with putative BVU3433 homologs among human gut-associated bacteria. Tn mutagenesis detection of MGEs enables in vitro observation of transfer events. Further this method has potential for in vivo identification of additional functional MGEs and characterization of the fitness determinants they encode. For example, there is an increasing threat of antibiotic resistance in clinically relevant bacteria, often exacerbated by MGEs. We specifically investigated CTnDOT, a key contributor to tetracycline resistance in 80% of clinical and community isolates of Bacteroides. In this study, we observed the in vitro mobilization of a novel CTnDOT-like element (PmDOT), from Parabacteroides merdae into Bacteroides thetaiotaomicron. Subsequent genome screens revealed the presence of intact CTnDOT- like elements in ~50% of the 134 human-gut associated Bacteroidota genomes examined. Moreover, through the analysis of human fecal metagenomes, we determined the widespread prevalence of CTnDOT-like elements across diverse global human populations. Our findings confirm CTnDOT-like elements are a diverse and significant group of MGEs within the human gut microbiome.
- Published
- 2024
5. The structure of Vibrio cholerae FeoC reveals conservation of the helix-turn-helix motif but not the cluster-binding domain.
- Author
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Brown, Janae B., Lee, Mark A., and Smith, Aaron T.
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HELIX-loop-helix motifs , *VIBRIO cholerae , *BACTERIAL operons , *MEMBRANE proteins , *CARRIER proteins , *CHOLERA - Abstract
Most pathogenic bacteria require ferrous iron (Fe2+) in order to sustain infection within hosts. The ferrous iron transport (Feo) system is the most highly conserved prokaryotic transporter of Fe2+, but its mechanism remains to be fully characterized. Most Feo systems are composed of two proteins: FeoA, a soluble SH3-like accessory protein, and FeoB, a membrane protein that translocates Fe2+ across a lipid bilayer. Some bacterial feo operons encode FeoC, a third soluble, winged-helix protein that remains enigmatic in function. We previously demonstrated that selected FeoC proteins bind O2-sensitive [4Fe-4S] clusters via Cys residues, leading to the proposal that some FeoCs could sense O2 to regulate Fe2+ transport. However, not all FeoCs conserve these Cys residues, and FeoC from the causative agent of cholera (Vibrio cholerae) notably lacks any Cys residues, precluding cluster binding. In this work, we determined the NMR structure of VcFeoC, which is monomeric and conserves the helix-turn-helix domain seen in other FeoCs. In contrast, however, the structure of VcFeoC reveals a truncated winged β-sheet in which the cluster-binding domain is notably absent. Using homology modeling, we predicted the structure of VcNFeoB and used docking to identify an interaction site with VcFeoC, which is confirmed by NMR spectroscopy. These findings provide the first atomic-level structure of VcFeoC and contribute to a better understanding of its role vis-à-vis FeoB. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
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6. Transcription Factors and Signal Transduction
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Carlberg, Carsten, Molnár, Ferdinand, Carlberg, Carsten, and Molnár, Ferdinand
- Published
- 2020
- Full Text
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7. An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system
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Xia, Xide [Harvard Medical School, Boston, MA (United States)]
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- 2015
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8. X-ray crystal structure of putative transcription regulator lmo2088 from Listeria monocytogenes.
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Samad, Abdus, Li, Yuelong, Zhang, Caiying, Chen, Feng, Zeng, Weihong, Fan, Xiaojiao, and Jin, Tengchuan
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LISTERIA monocytogenes , *CRYSTAL structure , *ISOTHERMAL titration calorimetry , *NUCLEOTIDE sequence , *MULTIDRUG resistance , *CRYSTALLOIDS (Botany) - Abstract
Listeria monocytogenes is a gram-positive food borne pathogen. The lmo2088 belongs to the TetR family of transcriptional regulators from L. monocytogenes. These transcriptional factors regulate multidrug resistance transporters in L. monocytogenes. Here, we report native protein crystal structure of lmo2088 at a resolution of 1.7 Å. Lmo2088 comprises of an N-terminal DNA binding domain and a variable C-terminal effector binding domain. Furthermore, we identified specific consensus sequences selected by systematic evolution of ligands by exponential enrichment in vitro. The specific binding of lmo2088 with DNA consensus sequence was validated by electrophoretic mobility shift assay, fluorescence polarization and isothermal titration calorimetry. We speculate that the structure of lmo2088 might provide an insight into the regulatory function of lmo2088 of L. monocytogenes. • The lmo2088 belongs to putative TetR family of transcriptional regulator from L. monocytogenes. • The crystal structure is a homodimeric. • Lmo2088 exist in a α-helical form. • Lmo2088 recognizes specific consensus DNA sequence motif and shows binding complexes as a transcriptional regulator. [ABSTRACT FROM AUTHOR]
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- 2019
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9. Transcription Factors
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Carlberg, Carsten, Molnár, Ferdinand, Carlberg, Carsten, and Molnár, Ferdinand
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- 2016
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10. Transcription Factors
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Carlberg, Carsten, Molnár, Ferdinand, Carlberg, Carsten, and Molnár, Ferdinand
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- 2014
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11. Structural features of methionine aminopeptidase2-active core peptide essential for binding with S100A4.
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Katagiri, Naohiro, Nagatoishi, Satoru, Tsumoto, Kouhei, and Endo, Hideya
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SURFACE plasmon resonance , *MOLECULAR dynamics , *PROTEIN-protein interactions , *AMINO acids , *CIRCULAR dichroism - Abstract
Methionine aminopeptidase 2 (MetAP2) is one of the effector proteins of S100A4, a metastasis-associated calcium-binding protein. This interaction is involved in angiogenesis. The region of MetAP2 that interacts with S100A4 includes amino acids 170 to 208. A peptide corresponding to this region, named as NBD, has potent anti-angiogenic activity and suppresses tumor growth in a xenograft cancer model. However, the binding mode of NBD to S100A4 was totally unknown. Here we describe our analysis of the relationship between the inhibitory activity and the structure of NBD, which adopts a characteristic helix-turn-helix structure as shown by X-ray crystallographic analysis, and peptide fragments of NBD. We conducted physicochemical analyses of the interaction between S100A4 and the peptides, including surface plasmon resonance, microscale thermophoresis, and circular dichroism, and performed docking/molecular dynamics simulations. Active peptides had stable secondary structures, whereas inactive peptides had a little secondary structure. A computational analysis of the interaction mechanism led to the design of a peptide smaller than NBD, NBD-ΔN10, that possessed inhibitory activity. Our study provides a strategy for design for a specific peptide inhibitor against S100A4 that can be applied to the discovery of inhibitors of other protein-protein interactions. • Peptide inhibitors of the interaction between S100A4 and MetAP2 were investigated. • Helix-turn-helix structure of the peptide is necessary for its inhibitory activity. • Computational analysis revealed the mode of interaction of peptides with S100A4. • Combined physicochemical and computational analysis led to the design of a smaller peptide than NBD, NBD-ΔN10. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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12. Sequence specific integration by the family 1 casposase from CandidatusNitrosopumilus koreensis AR1
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Qinling Yuan, Yang Lv, Kejing Ren, Suyu Ji, Yibei Xiao, Xiaoke Wang, Wenxuan Zhang, and Meiling Lu
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Integrases ,biology ,AcademicSubjects/SCI00010 ,Nucleic Acid Enzymes ,Inverted repeat ,CRISPR-Associated Proteins ,Oligonucleotides ,Terminal Repeat Sequences ,High-Throughput Nucleotide Sequencing ,Helix-turn-helix ,Interspersed Repetitive Sequences ,Computational biology ,Archaea ,Integrase ,DNA Transposable Elements ,Genetics ,biology.protein ,CRISPR ,CRISPR-Cas Systems ,Mobile genetic elements ,Function (biology) ,Helix-Turn-Helix Motifs ,Sequence (medicine) - Abstract
Casposase, a homolog of Cas1 integrase, is encoded by a superfamily of mobile genetic elements known as casposons. While family 2 casposase has been well documented in both function and structure, little is known about the other three casposase families. Here, we studied the family 1 casposase lacking the helix-turn-helix (HTH) domain from Candidatus Nitrosopumilus koreensis AR1 (Ca. N. koreensis). The determinants for integration by Ca. N. koreensis casposase were extensively investigated, and it was found that a 13-bp target site duplication (TSD) sequence, a minimal 3-bp leader and three different nucleotides of the TSD sequences are indispensable for target specific integration. Significantly, the casposase can site-specifically integrate a broad range of terminal inverted repeat (TIR)-derived oligonucleotides ranging from 7-nt to ∼4000-bp, and various oligonucleotides lacking the 5′-TTCTA-3′ motif at the 3′ end of TIR sequence can be integrated efficiently. Furthermore, similar to some Cas1 homologs, the casposase utilizes a 5′-ATAA-3′ motif in the TSD as a molecular ruler to dictate nucleophilic attack at 9-bp downstream of the end of the ruler during the spacer-side integration. By characterizing the family 1 Ca. N. koreensis casposase, we have extended our understanding on mechanistic similarities and evolutionary connections between casposons and the adaptation elements of CRISPR-Cas immunity.
- Published
- 2021
13. MULTIPLE ANTIBIOTIC RESISTANCE ACTIVATOR (MarA) OF THE FAMILY ENTEROBACTERIACEAE: STRUCTURE AND CONSERVATION IN Salmonella enterica SUBSP. enterica SEROVAR TYPHIMURIUM.
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Chaudhry, Muhammad Tausif and Chaudhry, Raheela
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DRUG resistance in bacteria , *SALMONELLA enterica , *SALMONELLA enterica serovar typhimurium , *MULTIDRUG resistance in bacteria , *DNA synthesis - Abstract
MarA (the multiple antibiotic resistance activator) is a regulatory protein that plays a significant role in multidrug resistance in bacteria and archaea where cellular mechanisms such as DNA and protein synthesis are inhibited during dormancy and subsequently cells evade a sudden antibiotic stress. MarAs (125-127 residues) of species selected from ten genera of the family Enterobacteriaceae were selected for analyses. MarA consists of seven a-helices where about 81% of the residues in helices are conserved. The helices and folds in MarA of Salmonella enterica serovar typhimurium can be further divided into two structurally similar and interconnected subdomains, each containing a HTH DNA-binding motif. The recognition helices, H3 and H6 of the motifs are fully conserved, which are inserted into the adjacent major groove segments of DNA. The sequences show high similarity (83.4-100%) with MarA of E. coli K-12 with fully resolved three-dimensional structure at 2.3 Å. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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14. Characterization of the DNA binding domain of StbA, A key protein of a new type of DNA segregation system
- Author
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Valentin Quèbre, Irene del Campo, Ana Cuevas, Patricia Siguier, Jérôme Rech, Phan Thai Nguyen Le, Bao Ton-Hoang, François Cornet, Jean-Yves Bouet, Gabriel Moncalian, Fernando de la Cruz, Catherine Guynet, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), and Université Toulouse III Paul Sabatier
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History ,Polymers and Plastics ,DNA ,DNA segregation ,Nucleoside-Triphosphatase ,Plasmid ,Industrial and Manufacturing Engineering ,Helix-turn-helix ,Bacterial conjugation ,Bacterial Proteins ,Protein Domains ,Structural Biology ,Chromosome Segregation ,Operon ,Business and International Management ,Transcription factor ,Molecular Biology ,Plasmids - Abstract
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 domain, 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., This work was supported by the Spanish Ministry of Economy, Industry and Competitiveness grant BFU2017-86378-P to F.dlC., by the Spanish Ministry of Science (MCI/AEI/FEDER,UE) grant PGC2018-093885-B-I00 to G.M., by French National Research Agency, grant numberANR-18- CE35-0008 to J.-Y.B. and by University P. Sabatier grant to C.G.
- Published
- 2022
15. Synthesis of new 1,2-dideoxy C-linked carbo-β-amino acids and α/β-peptides with 11/9-helix, helix-turn and helix-turn-helix structures.
- Author
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Adepu, Ramesh, Kanakaraju, Marumudi, Chandramouli, Nagula, Reddy, Purushotham P., Sharma, Gangavaram V.M., Sarma, Akella V.S., and Kunwar, Ajit C.
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AMINO acids , *CHEMICAL synthesis , *PROTEINS , *CATALYSIS synthesis , *PEPTIDES , *CHEMICAL reactions - Abstract
Abstract The present study describes the synthesis of new C-linked carbo-β-amino acids [β-Caa (1,2-ddx) ], with a 1,2-dideoxy D- xylo furanoside side chain (a tetrahydro furan derivative). The stereochemistry at the newly created amine centers was determined by modified Mosher method. The (S)-β-Caa (1,2-ddx) prepared from d -mannose diacetonide were utilized for the synthesis of 1:1 α/β-peptides with L-Ala. The conformational analysis (NMR, MD and CD) revealed the presence of 11/9-helix, helix induced helix-turn (HT) and helix-turn-helix (HTH) in these peptides. These side chains with tetrahydrofuran ring facilitated the formation of robust helix, unlike some other side chains from earlier studies. Graphical abstract Image 1 [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
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16. Characterization of the DNA binding domain of StbA, A key protein of a new type of DNA segregation system
- Author
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Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Université Toulouse III Paul Sabatier, Quèbre, Valentin, Campo, Irene del, Cuevas, Ana, Siguier, Patricia, Rech, Jérôme, Nguyen, Phan Thai Le, Ton-Hoang, Bao, Cornet, François, Bouet, Jean-Yves, Moncalián, Gabriel, Cruz, Fernando de la, Guynet, Catherine, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Université Toulouse III Paul Sabatier, Quèbre, Valentin, Campo, Irene del, Cuevas, Ana, Siguier, Patricia, Rech, Jérôme, Nguyen, Phan Thai Le, Ton-Hoang, Bao, Cornet, François, Bouet, Jean-Yves, Moncalián, Gabriel, Cruz, Fernando de la, and Guynet, Catherine
- Abstract
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 domain, 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.
- Published
- 2022
17. Biophysical analysis ofPseudomonas-phage PaP3 small terminase suggests a mechanism for sequence-specific DNA-binding by lateral interdigitation
- Author
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Tyler J. Florio, Richard E. Gillilan, Marzia Niazi, Gino Cingolani, Ravi K. Lokareddy, Nicholas A. Swanson, and Ruoyu Yang
- Subjects
Models, Molecular ,AcademicSubjects/SCI00010 ,Protein subunit ,Helix-turn-helix ,medicine.disease_cause ,Genome ,Viral Proteins ,Podoviridae ,chemistry.chemical_compound ,Structural Biology ,Sequence-specific DNA binding ,Genetics ,medicine ,Escherichia coli ,Helix-Turn-Helix Motifs ,Endodeoxyribonucleases ,Base Sequence ,biology ,DNA ,biology.organism_classification ,Capsid ,chemistry ,Pseudomonas aeruginosa ,Biophysics ,Pseudomonas Phages ,Protein Binding - Abstract
The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a β-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA.
- Published
- 2020
18. The protein–protein interactions required for assembly of the Tn 3 resolution synapse
- Author
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Martin R. Boocock, Mary E. Burke, Sally-J. Rowland, W. Marshall Stark, and Phoebe A. Rice
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Tn3 transposon ,Multiprotein complex ,Recombinant Fusion Proteins ,Helix-turn-helix ,Biology ,Microbiology ,Genetic recombination ,Protein–protein interaction ,Bartonella bacilliformis ,03 medical and health sciences ,Bacterial Proteins ,Recombinase ,Protein Interaction Domains and Motifs ,Protein Structure, Quaternary ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Binding Sites ,Synapse assembly ,030306 microbiology ,Synapsis ,biochemical phenomena, metabolism, and nutrition ,Cell biology ,DNA-Binding Proteins ,DNA Nucleotidyltransferases ,DNA Transposable Elements ,Transposon Resolvases ,Dimerization - Abstract
The site-specific recombinase Tn3 resolvase initiates DNA strand exchange when two res recombination sites and six resolvase dimers interact to form a synapse. The detailed architecture of this intricate recombination machine remains unclear. We have clarified which of the potential dimer-dimer interactions are required for synapsis and recombination, using a novel complementation strategy that exploits a previously uncharacterized resolvase from Bartonella bacilliformis ("Bart"). Tn3 and Bart resolvases recognize different DNA motifs, via diverged C-terminal domains (CTDs). They also differ substantially at N-terminal domain (NTD) surfaces involved in dimerization and synapse assembly. We designed NTD-CTD hybrid proteins, and hybrid res sites containing both Tn3 and Bart dimer binding sites. Using these components in in vivo assays, we demonstrate that productive synapsis requires a specific "R" interface involving resolvase NTDs at all three dimer-binding sites in res. Synapses containing mixtures of wild-type Tn3 and Bart resolvase NTD dimers are recombination-defective, but activity can be restored by replacing patches of Tn3 resolvase R interface residues with Bart residues, or vice versa. We conclude that the Tn3/Bart family synapse is assembled exclusively by R interactions between resolvase dimers, except for the one special dimer-dimer interaction required for catalysis.
- Published
- 2020
19. A thermophilic phage uses a small terminase protein with a fixed helix–turn–helix geometry
- Author
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Christl Gaubitz, Brendan J. Hilbert, Brian A. Kelch, Nicholas P. Stone, and Janelle A. Hayes
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Protein Conformation, alpha-Helical ,0301 basic medicine ,Viral protein ,Static Electricity ,Helix-turn-helix ,Molecular Dynamics Simulation ,medicine.disease_cause ,Biochemistry ,DNA-binding protein ,Bacteriophage ,03 medical and health sciences ,chemistry.chemical_compound ,medicine ,Molecular motor ,Bacteriophages ,Protein Structure, Quaternary ,Molecular Biology ,Adenosine Triphosphatases ,Nuclease ,Endodeoxyribonucleases ,030102 biochemistry & molecular biology ,biology ,Chemistry ,Virus Assembly ,Cryoelectron Microscopy ,food and beverages ,Cell Biology ,biology.organism_classification ,Recombinant Proteins ,Protein Subunits ,030104 developmental biology ,Mutagenesis ,Protein Structure and Folding ,DNA, Viral ,Helix ,biology.protein ,Biophysics ,human activities ,DNA ,Protein Binding - Abstract
Tailed bacteriophages use a DNA-packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component of this DNA-packaging machinery acts as a molecular matchmaker that recognizes both the viral genome and the main motor component, the large terminase (TerL). However, how TerS binds DNA and the TerL protein remains unclear. Here we identified gp83 of the thermophilic bacteriophage P74-26 as the TerS protein. We found that TerS(P76-26) oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. A cryo-EM structure of TerS(P76-26) revealed that it forms a ring with a wide central pore and radially arrayed helix–turn–helix domains. The structure further showed that these helix–turn–helix domains, which are thought to bind DNA by wrapping the double helix around the ring, are rigidly held in an orientation distinct from that seen in other TerS proteins. This rigid arrangement of the putative DNA-binding domain imposed strong constraints on how TerS(P76-26) can bind DNA. Finally, the TerS(P76-26) structure lacked the conserved C-terminal β-barrel domain used by other TerS proteins for binding TerL. This suggests that a well-ordered C-terminal β-barrel domain is not required for TerS(P76-26) to carry out its matchmaking function. Our work highlights a thermophilic system for studying the role of small terminase proteins in viral maturation and presents the structure of TerS(P76-26), revealing key differences between this thermophilic phage and its mesophilic counterparts.
- Published
- 2020
20. Coevolution of the bacterial pheromone ComS and sensor ComR fine-tunes natural transformation in streptococci
- Author
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Denis Dereinne, Patrice Soumillion, Sylvie Nessler, Johann Mignolet, Felipe Viela, Laura Ledesma-Garcia, Pascal Hols, Yves F. Dufrêne, and Imke Ensinck
- Subjects
Models, Molecular ,Cell signaling ,Genome evolution ,DNA transformation ,competence ,Mutagenesis (molecular biology technique) ,Helix-turn-helix ,Computational biology ,PcomS, comS promoter ,Biochemistry ,CAP helix, capping helix α16 ,Pheromones ,(R)RNPP, (Rgg,) Rap, NprR, PlcR, and PrgX ,Evolution, Molecular ,pheromone ,XIP, SigX-inducing peptide ,Bacterial Proteins ,Protein Domains ,cell signaling ,Streptococcus thermophilus ,ComRSth, Streptococcus thermophilus ComR ,XIPSve, Streptococcus vestibularis XIP ,Molecular Biology ,TPR, tetratricopeptide repeat ,Mechanism (biology) ,Chemistry ,ComRSve, Streptococcus vestibularis ComR ,cell-to-cell communication ,Quorum Sensing ,streptococcus ,RLU, relative light unit ,Cell Biology ,HTH, helix-turn-helix ,XIPSth, Streptococcus thermophilus XIP ,Gene Expression Regulation, Bacterial ,CSP, competence-stimulating peptide ,AFM, atomic force microscopy ,Transformation (genetics) ,Quorum sensing ,Tetratricopeptide ,(R)RNPP ,XIP ,FP, fluorescence polarization ,Transformation, Bacterial ,Research Article - Abstract
Competence for natural transformation extensively contributes to genome evolution and the rapid adaptability of bacteria dwelling in challenging environments. In most streptococci, this process is tightly controlled by the ComRS signaling system, which is activated through the direct interaction between the (R)RNPP-type ComR sensor and XIP pheromone (mature ComS). The overall mechanism of activation and the basis of pheromone selectivity have been previously reported in Gram-positive salivarius streptococci; however, detailed 3D-remodeling of ComR leading up to its activation remains only partially understood. Here, we identified using a semi-rational mutagenesis approach two residues in the pheromone XIP that bolster ComR sensor activation by interacting with two aromatic residues of its XIP-binding pocket. Random and targeted mutagenesis of ComR revealed that the interplay between these four residues remodel a network of aromatic-aromatic interactions involved in relaxing the sequestration of the DNA-binding domain. Based on these data, we propose a comprehensive model for ComR activation based on two major conformational changes of the XIP-binding domain. Notably, the stimulation of this newly identified trigger point by a single XIP substitution resulted in higher competence and enhanced transformability, suggesting that pheromone-sensor co-evolution counter-selects for hyperactive systems in order to maintain a trade-off between competence and bacterial fitness. Overall, this study sheds new light on the ComRS activation mechanism and how it could be exploited for biotechnological and biomedical purposes.
- Published
- 2021
21. Mining of structural motifs in proteins using artificial bee colony optimization framework for druggability
- Author
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L S Suma and S. S. Vinod Chandra
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Matching (graph theory) ,business.industry ,Computer science ,Druggability ,Helix-turn-helix ,Pattern recognition ,Biochemistry ,Computer Science Applications ,Artificial bee colony algorithm ,Artificial Intelligence ,Benchmark (computing) ,Artificial intelligence ,Sensitivity (control systems) ,business ,Structural motif ,Molecular Biology ,Protein secondary structure ,Algorithms - Abstract
In this work, we have developed an optimization framework for digging out common structural patterns inherent in DNA binding proteins. A novel variant of the artificial bee colony optimization algorithm is proposed to improve the exploitation process. Experiments on four benchmark objective functions for different dimensions proved the speedier convergence of the algorithm. Also, it has generated optimum features of Helix Turn Helix structural pattern based on the objective function defined with occurrence count on secondary structure. The proposed algorithm outperformed the compared methods in convergence speed and the quality of generated motif features. The motif locations obtained using the derived common pattern are compared with the results of two other motif detection tools. 92% of tested proteins have produced matching locations with the results of the compared methods. The performance of the approach was analyzed with various measures and observed higher sensitivity, specificity and area under the curve values. A novel strategy for druggability finding by docking studies, targeting the motif locations is also discussed.
- Published
- 2021
22. Structural basis for DNA recognition by the transcription regulator MetR.
- Author
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Punekar, Avinash S., Porter, Jonathan, Carr, Stephen B., and Phillips, Simon E. V.
- Subjects
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DNA analysis , *METHIONINE , *CRYSTAL structure - Abstract
MetR, a LysR-type transcriptional regulator (LTTR), has been extensively studied owing to its role in the control of methionine biosynthesis in proteobacteria. A MetR homodimer binds to a 24-base-pair operator region of the met genes and specifically recognizes the interrupted palindromic sequence 5′-TGAA-N5-TTCA-3′. Mechanistic details underlying the interaction of MetR with its target DNA at the molecular level remain unknown. In this work, the crystal structure of the DNA-binding domain (DBD) of MetR was determined at 2.16 Å resolution. MetR-DBD adopts a winged-helix-turn-helix (wHTH) motif and shares significant fold similarity with the DBD of the LTTR protein BenM. Furthermore, a data-driven macromolecular-docking strategy was used to model the structure of MetR-DBD bound to DNA, which revealed that a bent conformation of DNA is required for the recognition helix α3 and the wing loop of the wHTH motif to interact with the major and minor grooves, respectively. Comparison of the MetR-DBD-DNA complex with the crystal structures of other LTTR-DBD-DNA complexes revealed residues that may confer operator-sequence binding specificity for MetR. Taken together, the results show that MetR-DBD uses a combination of direct base-specific interactions and indirect shape recognition of the promoter to regulate the transcription of met genes. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
23. An affinity-structure database of helix-turn- helix: DNA complexes with a universal coordinate system.
- Author
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AlQuraishi, Mohammed, Shengdong Tang, and Xide Xia
- Subjects
- *
DNA , *MOLECULAR interactions , *PROTEINS , *CHROMOSOME replication , *CHROMATIN , *BIOCHEMISTRY databases - Abstract
Background: Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. Description: We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Conclusions: This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
24. Structure and DNA damage-dependent derepression mechanism for the XRE family member DG-DdrO
- Author
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Kaiying Cheng, Yuejin Hua, Huizhi Lu, Hong Xu, Chaoming Pan, Ye Zhao, Yuxia Luo, Li Shengjie, Liangyan Wang, and Bing Tian
- Subjects
DNA damage ,Helix-turn-helix ,Biology ,DNA-binding protein ,Protein Structure, Secondary ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,Bacterial Proteins ,Structural Biology ,Genetics ,Deinococcus ,Amino Acid Sequence ,Promoter Regions, Genetic ,Helix-Turn-Helix Motifs ,030304 developmental biology ,0303 health sciences ,030306 microbiology ,Promoter ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,Cell biology ,chemistry ,Metalloproteases ,Deinococcus geothermalis ,DNA ,DNA Damage ,Protein Binding ,Transcription Factors - Abstract
DdrO is an XRE family transcription repressor that, in coordination with the metalloprotease PprI, is critical in the DNA damage response of Deinococcus species. Here, we report the crystal structure of Deinococcus geothermalis DdrO. Biochemical and structural studies revealed the conserved recognizing α-helix and extended dimeric interaction of the DdrO protein, which are essential for promoter DNA binding. Two conserved oppositely charged residues in the HTH motif of XRE family proteins form salt bridge interactions that are essential for promoter DNA binding. Notably, the C-terminal domain is stabilized by hydrophobic interactions of leucine/isoleucine-rich helices, which is critical for DdrO dimerization. Our findings suggest that DdrO is a novel XRE family transcriptional regulator that forms a distinctive dimer. The structure also provides insight into the mechanism of DdrO-PprI-mediated DNA damage response in Deinococcus.
- Published
- 2019
25. Characterization of the DNA Binding Domain of StbA, A Key Protein of A New Type of DNA Segregation System.
- Author
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Quèbre, Valentin, del Campo, Irene, Cuevas, Ana, Siguier, Patricia, Rech, Jérôme, Le, Phan Thai Nguyen, Ton-Hoang, Bao, Cornet, François, Bouet, Jean-Yves, Moncalian, Gabriel, de la Cruz, Fernando, and Guynet, Catherine
- Subjects
- *
OPERONS , *DNA , *CELL division , *PROTEINS , *CRYSTAL structure - Abstract
[Display omitted] • The N-ter DNA binding domain of StbA is structurally related to the PadR regulators. • The C-terminal domain of StbA is required for both segregation and conjugation. • Plasmid R388 conjugation depends on its subcellular positioning. 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 domain, 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. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
26. The N-terminal domain of MuB protein has striking structural similarity to DNA-binding domains and mediates MuB filament–filament interactions.
- Author
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Dramićanin, Marija, López-Méndez, Blanca, Boskovic, Jasminka, Campos-Olivas, Ramón, and Ramón-Maiques, Santiago
- Subjects
- *
N-terminal residues , *DNA-binding proteins , *PROTEIN structure , *PROTEIN-protein interactions , *TRANSPOSASES , *NUCLEAR magnetic resonance spectroscopy - Abstract
MuB is an ATP-dependent DNA-binding protein that regulates the activity of MuA transposase and delivers the target DNA for transposition of phage Mu. Mechanistic insight into MuB function is limited to its AAA+ ATPase module, which upon ATP binding assembles into helical filaments around the DNA. However, the structure and function of the flexible N-terminal domain (NTD) appended to the AAA+ module remains uncharacterized. Here we report the solution structure of MuB NTD determined by NMR spectroscopy. The structure reveals a compact domain formed by four α-helices connected by short loops, and confirms the presence of a helix-turn-helix motif. High structural similarity and sequence homology with λ repressor-like DNA-binding domains suggest a possible role of MuB NTD in DNA binding. We also demonstrate that the NTD directly mediates the ability of MuB to establish filament–filament interactions. These findings lead us to a model in which the NTD interacts with the AAA+ spirals and perhaps also with the DNA bound within the filament, favoring MuB polymerization and filament clustering. We propose that the MuB NTD-dependent filament interactions might be an effective mechanism to bridge distant DNA regions during Mu transposition. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
27. Structure of the response regulator ChrA in the haem-sensing two-component system of Corynebacterium diphtheriae.
- Author
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Doi, Akihiro, Nakamura, Hiro, Shiro, Yoshitsugu, and Sugimoto, Hiroshi
- Subjects
- *
CORYNEBACTERIUM diphtheriae , *CELLULAR signal transduction , *IRON porphyrins , *TRANSCRIPTION factors , *CRYSTAL structure , *DNA-binding proteins , *BACTERIA , *CRYSTALLOGRAPHY - Abstract
ChrA is a response regulator (RR) in the two-component system involved in regulating the degradation and transport of haem (Fe-porphyrin) in the pathogen Corynebacterium diphtheriae. Here, the crystal structure of full-length ChrA is described at a resolution of 1.8 Å. ChrA consists of an N-terminal regulatory domain, a long linker region and a C-terminal DNA-binding domain. A structural comparison of ChrA with other RRs revealed substantial differences in the relative orientation of the two domains and the conformation of the linker region. The structural flexibility of the linker could be an important feature in rearrangement of the domain orientation to create a dimerization interface to bind DNA during haem-sensing signal transduction. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
28. H, C and N resonance assignment of WHEP domains of human glutamyl-prolyl tRNA synthetase.
- Author
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Shin, ChinHo, Hwang, Geum-Sook, Ahn, Hee-Chul, Kim, Sunghoon, and Kim, Key-Sun
- Abstract
Human bifunctional glutamyl-prolyl tRNA synthetase (EPRS) contains three WHEP domains (R123) linking two catalytic domains. These three WHEP domains have been shown to be involved in protein-protein and protein-nucleic acid interactions. In translational control of gene expression, R12 repeats is known to interact with 3′UTR element in mRNAs of inflammatory gene for translational control mechanisms. While, R23 repeats interacts with NSAP1, which inhibits mRNA binding. Here we present the NMR chemical shift assignments for R12 (128 amino acids) as a 14 kDa recombinant protein and whole WHEP domains R123 (208 amino acids) as a 21 kDa recombinant protein. 97 % of backbone and 98 % of side-chain assignments have been completed in R12 analysis and 93 and 92 % of backbone and side-chain, respectively, assignments have been completed in R123 analysis based upon triple-resonance experiments. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
29. Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression.
- Author
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Shevtsov, M. B., Streeter, S. D., Thresh, S.-J., Swiderska, A., McGeehan, J. E., and Kneale, G. G.
- Subjects
- *
STRUCTURAL analysis (Science) , *DNA-binding proteins , *GENE expression , *ENDONUCLEASES , *GENETIC transcription , *PALINDROMIC DNA , *X-ray crystallography - Abstract
In a wide variety of bacterial restriction-modification systems, a regulatory `controller' protein (or C-protein) is required for effective transcription of its own gene and for transcription of the endonuclease gene found on the same operon. We have recently turned our attention to a new class of controller proteins (exemplified by C.Csp231I) that have quite novel features, including a much larger DNA-binding site with an 18 bp (∼60 Å) spacer between the two palindromic DNA-binding sequences and a very different recognition sequence from the canonical GACT/AGTC. Using X-ray crystallography, the structure of the protein in complex with its 21 bp DNA-recognition sequence was solved to 1.8 Å resolution, and the molecular basis of sequence recognition in this class of proteins was elucidated. An unusual aspect of the promoter sequence is the extended spacer between the dimer binding sites, suggesting a novel interaction between the two C-protein dimers when bound to both recognition sites correctly spaced on the DNA. A U-bend model is proposed for this tetrameric complex, based on the results of gel-mobility assays, hydrodynamic analysis and the observation of key contacts at the interface between dimers in the crystal. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
30. Structural and genomic DNA analysis of the putative TetR transcriptional repressor SCO7518 from Streptomyces coelicolor A3(2).
- Author
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Hayashi, Takeshi, Tanaka, Yoshikazu, Sakai, Naoki, Okada, Ui, Yao, Min, Watanabe, Nobuhisa, Tamura, Tomohiro, and Tanaka, Isao
- Subjects
- *
DNA analysis , *GENOMICS , *TRANSCRIPTION factors , *STREPTOMYCES coelicolor , *LIGANDS (Biochemistry) - Abstract
SCO7518 is a protein of unknown function from Streptomyces coelicolor A3(2) that has been classified into the TetR transcriptional regulator family. In this study, a crystal structure of SCO7518 was determined at 2.29 Å resolution. The structure is a homodimer of protomers that comprise an N-terminal DNA-binding domain and a C-terminal dimerization and regulatory domain, and possess a putative ligand-binding cavity. Genomic systematic evolution of ligands by exponential enrichment and electrophoretic mobility shift assays revealed that SCO7518 specifically binds to an operator sequence located upstream of the sco7519 gene, which encodes a maltose O-acetyltransferase. These results suggest that SCO7518 is a transcriptional repressor of sco7519 expression. [ABSTRACT FROM AUTHOR]
- Published
- 2014
- Full Text
- View/download PDF
31. The N-terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition
- Author
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Marina Corbella, Qinghua Liao, Cátia Moreira, Antonietta Parracino, Peter M. Kasson, and Shina Caroline Lynn Kamerlin
- Subjects
Helix-turn-helix ,010402 general chemistry ,01 natural sciences ,DNA sequencing ,Article ,Turn (biochemistry) ,chemistry.chemical_compound ,Bacterial Proteins ,0103 physical sciences ,Materials Chemistry ,Escherichia coli ,Physical and Theoretical Chemistry ,Transcription factor ,Helix-Turn-Helix Motifs ,Regulation of gene expression ,Binding Sites ,010304 chemical physics ,Effector ,Escherichia coli Proteins ,Biochemistry and Molecular Biology ,DNA ,0104 chemical sciences ,Surfaces, Coatings and Films ,Cell biology ,DNA-Binding Proteins ,chemistry ,Trans-Activators ,Function (biology) ,Biokemi och molekylärbiologi ,Transcription Factors - Abstract
DNA-binding proteins play an important role in gene regulation and cellular function. The transcription factors MarA and Rob are two homologous members of the AraC/XylS family that regulate multidrug resistance. They share a common DNA-binding domain, and Rob possesses an additional C-terminal domain that permits binding of low-molecular weight effectors. Both proteins possess two helix-turn-helix (HTH) motifs capable of binding DNA; however, while MarA interacts with its promoter through both HTH-motifs, prior studies indicate that Rob binding to DNA via a single HTH-motif is sufficient for tight binding. In the present work, we perform microsecond time scale all-atom simulations of the binding of both transcription factors to different DNA sequences to understand the determinants of DNA recognition and binding. Our simulations characterize sequence-dependent changes in dynamical behavior upon DNA binding, showcasing the role of Arg40 of the N-terminal HTH-motif in allowing for specific tight binding. Finally, our simulations demonstrate that an acidic C-terminal loop of Rob can control the DNA binding mode, facilitating interconversion between the distinct DNA binding modes observed in MarA and Rob. In doing so, we provide detailed molecular insight into DNA binding and recognition by these proteins, which in turn is an important step toward the efficient design of antivirulence agents that target these proteins.
- Published
- 2021
32. The ChiS-family DNA-binding domain contains a cryptic helix-turn-helix variant
- Author
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Catherine A. Klancher, Ram Podicheti, Ankur B. Dalia, Matthew B. Neiditch, Triana N. Dalia, George Minasov, Douglas B. Rusch, and Karla J. F. Satchell
- Subjects
Protein domain ,Repressor ,Helix-turn-helix ,Computational biology ,Lac repressor ,Microbiology ,DNA-binding protein ,chemistry.chemical_compound ,Bacterial Proteins ,Protein Domains ,Virology ,Transcriptional regulation ,structural biology ,Vibrio cholerae ,Helix-Turn-Helix Motifs ,Genetics ,Chemistry ,C-terminus ,QR1-502 ,DNA-Binding Proteins ,Structural biology ,Mutagenesis ,molecular genetics ,DNA ,Research Article ,Protein Binding ,Binding domain - Abstract
Regulating gene expression is essential in all domains of life. This process is commonly facilitated by the activity of DNA-binding transcription factors., Sequence-specific DNA-binding domains (DBDs) are conserved in all domains of life. These proteins carry out a variety of cellular functions, and there are a number of distinct structural domains already described that allow for sequence-specific DNA binding, including the ubiquitous helix-turn-helix (HTH) domain. In the facultative pathogen Vibrio cholerae, the chitin sensor ChiS is a transcriptional regulator that is critical for the survival of this organism in its marine reservoir. We recently showed that ChiS contains a cryptic DBD in its C terminus. This domain is not homologous to any known DBD, but it is a conserved domain present in other bacterial proteins. Here, we present the crystal structure of the ChiS DBD at a resolution of 1.28 Å. We find that the ChiS DBD contains an HTH domain that is structurally similar to those found in other DNA-binding proteins, like the LacI repressor. However, one striking difference observed in the ChiS DBD is that the canonical tight turn of the HTH is replaced with an insertion containing a β-sheet, a variant which we term the helix-sheet-helix. Through systematic mutagenesis of all positively charged residues within the ChiS DBD, we show that residues within and proximal to the ChiS helix-sheet-helix are critical for DNA binding. Finally, through phylogenetic analyses we show that the ChiS DBD is found in diverse proteobacterial proteins that exhibit distinct domain architectures. Together, these results suggest that the structure described here represents the prototypical member of the ChiS-family of DBDs.
- Published
- 2020
33. Transcription Factors and Signal Transduction
- Author
-
Ferdinand Molnár and Carsten Carlberg
- Subjects
Nuclear receptor ,Chemistry ,Cellular differentiation ,Gene expression ,Extracellular ,Helix-turn-helix ,DNA-binding domain ,Signal transduction ,Transcription factor ,Cell biology - Abstract
Transcription factors are key controllers of gene expression. The activities of these proteins determine how a cell functions and responds to environmental perturbations. The most characteristic domain of a transcription factor is its DBD, but the proteins also contain domains for homo- and heterodimerization and for contacts with co-factors and other nuclear proteins. The structural and functional understanding of site-specific transcription factors provides insight how they link to signal transduction and the sensing of intra- and extracellular lipophilic molecules via nuclear receptors (Chap. 4). Thus, a central characteristic of life, the response to molecules of the extracellular environment, is mediated by signal transduction cascades that mostly start with an extracellular signaling molecule and end with an activated transcription factor, i.e., with a change in gene expression. These principles will be explained at the example cellular differentiation, inflammatory responses and the sensing of cellular damage.
- Published
- 2020
34. Synthesis of new 1,2-dideoxy C-linked carbo-β-amino acids and α/β-peptides with 11/9-helix, helix-turn and helix-turn-helix structures
- Author
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Nagula Chandramouli, Purushotham P. Reddy, A. V. S. Sarma, Ajit C. Kunwar, Marumudi Kanakaraju, Ramesh Adepu, and Gangavaram V. M. Sharma
- Subjects
chemistry.chemical_classification ,010405 organic chemistry ,Stereochemistry ,Organic Chemistry ,Mannose ,Helix-turn-helix ,010402 general chemistry ,01 natural sciences ,Biochemistry ,0104 chemical sciences ,Amino acid ,Turn (biochemistry) ,chemistry.chemical_compound ,chemistry ,Furan ,Drug Discovery ,Helix ,Side chain ,Amine gas treating - Abstract
The present study describes the synthesis of new C-linked carbo-β-amino acids [β-Caa(1,2-ddx)], with a 1,2-dideoxy D-xylo furanoside side chain (a tetrahydro furan derivative). The stereochemistry at the newly created amine centers was determined by modified Mosher method. The (S)-β-Caa(1,2-ddx) prepared from d -mannose diacetonide were utilized for the synthesis of 1:1 α/β-peptides with L-Ala. The conformational analysis (NMR, MD and CD) revealed the presence of 11/9-helix, helix induced helix-turn (HT) and helix-turn-helix (HTH) in these peptides. These side chains with tetrahydrofuran ring facilitated the formation of robust helix, unlike some other side chains from earlier studies.
- Published
- 2018
35. A thermophilic phage uses a small terminase protein with a fixed helix-turn-helix geometry
- Author
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Hayes, Janelle A., Hilbert, Brendan J., Gaubitz, Christl, Stone, Nicholas P., and Kelch, Brian A.
- Subjects
0303 health sciences ,Nuclease ,biology ,030302 biochemistry & molecular biology ,food and beverages ,Helix-turn-helix ,DNA-binding domain ,biology.organism_classification ,Genome ,Bacteriophage ,03 medical and health sciences ,chemistry.chemical_compound ,chemistry ,Helix ,biology.protein ,Biophysics ,A-DNA ,human activities ,DNA ,030304 developmental biology - Abstract
SUMMARYTailed bacteriophage use a DNA packaging motor to encapsulate their genome during viral particle assembly. The small terminase (TerS) component acts as a molecular matchmaker by recognizing the viral genome as well as the main motor component, the large terminase (TerL). How TerS binds DNA and the TerL protein remains unclear. Here, we identify the TerS protein of the thermophilic bacteriophage P74-26. TerSP76-26 oligomerizes into a nonamer that binds DNA, stimulates TerL ATPase activity, and inhibits TerL nuclease activity. Our cryo-EM structure shows that TerSP76-26 forms a ring with a wide central pore and radially arrayed helix-turn-helix (HTH) domains. These HTH domains, which are thought to bind DNA by wrapping the helix around the ring, are rigidly held in an orientation distinct from that seen in other TerS proteins. This rigid arrangement of the putative DNA binding domain imposes strong constraints on how TerSP76-26 can bind DNA. Finally, the TerSP76-26 structure lacks the conserved C-terminal β-barrel domain used by other TerS proteins for binding TerL, suggesting that a well-ordered C-terminal β-barrel domain is not necessary for TerS to carry out its function as a matchmaker.
- Published
- 2019
36. Sequential DNA Binding and Dimerization Processes of the Photosensory Protein EL222
- Author
-
Yusuke Nakasone, Masahide Terazima, and Akira Takakado
- Subjects
0301 basic medicine ,Light ,Helix-turn-helix ,DNA ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Affinities ,Dissociation (chemistry) ,DNA sequencing ,0104 chemical sciences ,DNA-Binding Proteins ,Sphingomonadaceae ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Monomer ,Reaction rate constant ,Bacterial Proteins ,chemistry ,Reaction dynamics ,Biophysics ,Protein Multimerization ,Helix-Turn-Helix Motifs - Abstract
EL222 is a blue light sensor protein, which consists of a light-oxygen-voltage domain as a light sensor and a LuxR-type helix-turn-helix DNA-binding domain. The reaction dynamics of the protein-DNA binding were observed for the first time using the time-resolved transient grating method. The reaction scheme was determined, showing that photoexcited EL222 first binds DNA and the ground state EL222 monomer is subsequently associated with the complex. Rate constants on the millisecond scale were determined for these processes. In addition, binding rates for EL222 with three DNA sequences, with different binding affinities, were measured. Although EL222 binds nonspecific DNA sequences with affinities at least 5-fold lower than the target sequence affinity, the binding rates were almost the same as that for the target DNA. This observation indicates that the specific and nonspecific binding affinities are mainly controlled by differences in the dissociation of DNA binding.
- Published
- 2018
37. Designer proteins that competitively inhibit Gαq by targeting its effector site
- Author
-
John Sondek, Mahmud Hussain, Matthew Cummins, Stuart Endo-Streeter, and Brian Kuhlman
- Subjects
Phospholipase C ,biology ,GTPase-activating protein ,Chemistry ,G protein ,Protein design ,Helix-turn-helix ,Cell Biology ,Biochemistry ,Cell biology ,Gq alpha subunit ,Heterotrimeric G protein ,biology.protein ,Molecular Biology ,G protein-coupled receptor - Abstract
During signal transduction, the G protein, Gαq, binds and activates phospholipase C-β isozymes. Several diseases have been shown to manifest upon constitutively activating mutation of Gαq, such as uveal melanoma. Therefore, methods are needed to directly inhibit Gαq. Previously, we demonstrated that a peptide derived from a helix-turn-helix (HTH) region of PLC-β3 (residues 852-878) binds Gαq with low micromolar affinity and inhibits Gαq by competing with full-length PLC-β isozymes for binding. Since the HTH peptide is unstructured in the absence of Gαq, we hypothesized that embedding the HTH in a folded protein might stabilize the binding-competent conformation and further improve the potency of inhibition. Using the molecular modeling software Rosetta, we searched the Protein Data Bank for proteins with similar HTH structures near their surface. The candidate proteins were computationally docked against Gαq and their surfaces were redesigned to stabilize this interaction. We then used yeast surface display to affinity mature the designs. The most potent design bound Gαq/i with high affinity in vitro (KD = 18 nM) and inhibited activation of PLC-β isozymes in HEK293 cells. We anticipate that our genetically encoded inhibitor will help interrogate the role of Gαq in healthy and disease model systems. Our work demonstrates that grafting interaction motifs into folded proteins is a powerful approach for generating inhibitors of protein-protein interactions.
- Published
- 2021
38. Novel structural features drive DNA binding properties of Cmr, a CRP family protein in TB complex mycobacteria
- Author
-
M. Cassidy, Christopher S. Ginter, Sridevi Ranganathan, Janice D. Pata, Kathleen A. McDonough, and Jonah Cheung
- Subjects
0301 basic medicine ,Models, Molecular ,Protein Conformation ,Helix-turn-helix ,Cooperativity ,Computational biology ,Biology ,Crystallography, X-Ray ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,Structural Biology ,Sequence Homology, Nucleic Acid ,Genetics ,Amino Acid Sequence ,Binding site ,Nucleotide Motifs ,Gene ,Transcription factor ,Binding selectivity ,Helix-Turn-Helix Motifs ,Binding Sites ,030102 biochemistry & molecular biology ,Base Sequence ,Sequence Homology, Amino Acid ,DNA ,Mycobacterium tuberculosis ,3. Good health ,030104 developmental biology ,chemistry ,CAMP binding ,Nucleic Acid Conformation ,Protein Binding - Abstract
Mycobacterium tuberculosis (Mtb) encodes two CRP/FNR family transcription factors (TF) that contribute to virulence, Cmr (Rv1675c) and CRPMt (Rv3676). Prior studies identified distinct chromosomal binding profiles for each TF despite their recognizing overlapping DNA motifs. The present study shows that Cmr binding specificity is determined by discriminator nucleotides at motif positions 4 and 13. X-ray crystallography and targeted mutational analyses identified an arginine-rich loop that expands Cmr’s DNA interactions beyond the classical helix-turn-helix contacts common to all CRP/FNR family members and facilitates binding to imperfect DNA sequences. Cmr binding to DNA results in a pronounced asymmetric bending of the DNA and its high level of cooperativity is consistent with DNA-facilitated dimerization. A unique N-terminal extension inserts between the DNA binding and dimerization domains, partially occluding the site where the canonical cAMP binding pocket is found. However, an unstructured region of this N-terminus may help modulate Cmr activity in response to cellular signals. Cmr’s multiple levels of DNA interaction likely enhance its ability to integrate diverse gene regulatory signals, while its novel structural features establish Cmr as an atypical CRP/FNR family member.
- Published
- 2017
39. Crystal structure of an anti-CRISPR protein, AcrIIA1
- Author
-
So Young An, Jeong-Yong Suh, Donghyun Ka, and Euiyoung Bae
- Subjects
0301 basic medicine ,Models, Molecular ,Prophages ,Protein domain ,Helix-turn-helix ,Plasma protein binding ,Biology ,Crystallography, X-Ray ,03 medical and health sciences ,Viral Proteins ,Protein structure ,Protein Domains ,Structural Biology ,Genetics ,Escherichia coli ,CRISPR ,Amino Acid Sequence ,Peptide sequence ,Helix-Turn-Helix Motifs ,RNA ,Listeria monocytogenes ,030104 developmental biology ,Mutation ,Nucleic acid ,CRISPR-Cas Systems ,Protein Multimerization ,Protein Binding - Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide bacteria with RNA-based adaptive immunity against phage infection. To counteract this defense mechanism, phages evolved anti-CRISPR (Acr) proteins that inactivate the CRISPR-Cas systems. AcrIIA1, encoded by Listeria monocytogenes prophages, is the most prevalent among the Acr proteins targeting type II-A CRISPR-Cas systems and has been used as a marker to identify other Acr proteins. Here, we report the crystal structure of AcrIIA1 and its RNA-binding affinity. AcrIIA1 forms a dimer with a novel two helical-domain architecture. The N-terminal domain of AcrIIA1 exhibits a helix-turn-helix motif similar to transcriptional factors. When overexpressed in Escherichia coli, AcrIIA1 associates with RNAs, suggesting that AcrIIA1 functions via nucleic acid recognition. Taken together, the unique structural and functional features of AcrIIA1 suggest its distinct mode of Acr activity, expanding the diversity of the inhibitory mechanisms employed by Acr proteins.
- Published
- 2017
40. Characterization of the specific DNA-binding properties of Tnp26, the transposase of insertion sequence IS26
- Author
-
Ruth M. Hall, Sandro F. Ataide, Christopher J. Harmer, Janine K. Flores, and Carol H. Pong
- Subjects
TIRL, left terminal inverted repeat ,MST, microscale thermophoresis ,Transposases ,Helix-turn-helix ,Biochemistry ,Cm, chloramphenicol ,Tnpase, transposase ,Tc, tetracycline ,Insertion sequence ,Transposase ,chemistry.chemical_classification ,terminal inverted repeat ,Escherichia coli Proteins ,protein domain ,transposable element ,Amino acid ,Sm, streptomycin ,protein–DNA interaction ,Research Article ,insertion sequence ,DNA, Bacterial ,IS26 ,Stereochemistry ,HTH, helix–turn–helix ,MBP, maltose-binding protein ,Protein domain ,Mutation, Missense ,DNA-binding protein ,Protein Domains ,PDB, Protein Data Bank ,Escherichia coli ,Protein–DNA interaction ,Ap, ampicillin ,Binding site ,Molecular Biology ,TIRR, right terminal inverted repeat ,Terminal Repeat Sequences ,ApR, ampicillin resistant ,TCEP, Tris(2-carboxyethyl)phosphine ,Cell Biology ,DNA-binding domain ,Amino Acid Substitution ,chemistry ,DBD, DNA-binding domain ,IS, insertion sequence ,DNA Transposable Elements ,DDE, aspartate–aspartate–glutamate ,transposase Tnp26 ,helix–turn–helix DNA-binding domain ,bacterial genetics ,TIR, terminal inverted repeat - Abstract
The bacterial insertion sequence (IS) IS26 mobilizes and disseminates antibiotic resistance genes. It differs from bacterial IS that have been studied to date as it exclusively forms cointegrates via either a copy-in (replicative) or a recently discovered targeted conservative mode. To investigate how the Tnp26 transposase recognizes the 14-bp terminal inverted repeats (TIRs) that bound the IS, amino acids in two domains in the N-terminal (amino acids M1-P56) region were replaced. These changes substantially reduced cointegration in both modes. Tnp26 was purified as a maltose-binding fusion protein and shown to bind specifically to dsDNA fragments that included an IS26 TIR. However, Tnp26 with an R49A or a W50A substitution in helix 3 of a predicted trihelical helix-turn-helix domain (amino acids I13-R53) or an F4A or F9A substitution replacing the conserved amino acids in a unique disordered N-terminal domain (amino acids M1-D12) did not bind. The N-terminal M1-P56 fragment also bound to the TIR but only at substantially higher concentrations, indicating that other parts of Tnp26 enhance the binding affinity. The binding site was confined to the internal part of the TIR, and a G to T nucleotide substitution in the TGT at positions 6 to 8 of the TIR that is conserved in most IS26 family members abolished binding of both Tnp26 (M1-M234) and Tnp26 M1-P56 fragment. These findings indicate that the helix-turn-helix and disordered domains of Tnp26 play a role in Tnp26-TIR complex formation. Both domains are conserved in all members of the IS26 family.
- Published
- 2021
41. Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs
- Author
-
Zumft, Walter [Universitat Karlsruhe]
- Published
- 2003
- Full Text
- View/download PDF
42. SCO4008, a Putative TetR Transcriptional Repressor from Streptomyces coelicolor A3(2), Regulates Transcription of sco4007 by Multidrug Recognition.
- Author
-
Hayashi, Takeshi, Tanaka, Yoshikazu, Sakai, Naoki, Okada, Ui, Yao, Min, Watanabe, Nobuhisa, Tamura, Tomohiro, and Tanaka, Isao
- Subjects
- *
STREPTOMYCES coelicolor , *TRANSCRIPTION factors , *MULTIDRUG resistance , *N-terminal residues , *C-terminal binding proteins , *DNA-binding proteins , *ELECTROPHORESIS - Abstract
Abstract: SCO4008 from Streptomyces coelicolor A3(2) is a member of the TetR family. However, its precise function is not yet clear. In this study, the crystal structure of SCO4008 was determined at a resolution of 2.3Å, and its DNA-binding properties were analyzed. Crystal structure analysis showed that SCO4008 forms an Ω-shaped homodimer in which the monomer is composed of an N-terminal DNA-binding domain containing a helix–turn–helix and a C-terminal dimerization and regulatory domain possessing a ligand-binding cavity. The genomic systematic evolution of ligands by exponential enrichment and electrophoretic mobility shift assay revealed that four SCO4008 dimers bind to the two operator regions located between sco4008 and sco4007, a secondary transporter belonging to the major facilitator superfamily. Ligand screening analysis showed that SCO4008 recognizes a wide range of structurally dissimilar cationic and hydrophobic compounds. These results suggested that SCO4008 is a transcriptional repressor of sco4007 responsible for the multidrug resistance system in S. coelicolor A3(2). [Copyright &y& Elsevier]
- Published
- 2013
- Full Text
- View/download PDF
43. From keys to bulldozers: expanding roles for winged helix domains in nucleic-acid-binding proteins.
- Author
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Harami, Gábor M., Gyimesi, Máté, and Kovács, Mihály
- Subjects
- *
NUCLEIC acids , *HELIX (Mollusks) , *CARRIER proteins , *RECOMBINANT DNA , *HELICASES , *TRANSCRIPTION factors - Abstract
Highlights: [•] The winged helix domain is a versatile nucleic-acid-binding structural element. [•] This domain can exploit various nucleic acid structural features for recognition. [•] Transcription factors use this domain for sequence-specific DNA recognition. [•] DNA recombination and repair helicases use this domain as a strand-separating wedge. [•] Winged helix domains also mediate protein–protein interactions. [Copyright &y& Elsevier]
- Published
- 2013
- Full Text
- View/download PDF
44. The role of loop closure propensity in the refolding of Rop protein probed by molecular dynamics simulations
- Author
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Shukla, Rashmi Tambe, Baliga, Chetana, and Sasidhar, Yellamraju U.
- Subjects
- *
MOLECULAR dynamics , *HELIX-loop-helix motifs , *DIMERS , *PROTEIN folding , *DENATURATION of proteins , *FLUORESCENCE , *GENETIC mutation , *GLYCINE - Abstract
Abstract: Rop protein is a homo-dimer of helix-turn-helix and has relatively slow folding and unfolding rates compared to other dimeric proteins of similar size. Fluorescence studies cited in literature suggest that mutation of turn residues D30-A31 to G30-G31 (Gly2) increases its folding and unfolding rates considerably. A further increase in number of glycines in the turn region results in decrease of folding rates compared to Gly2 mutant. To understand the effect of glycine mutation on folding/unfolding rates of Rop and the conformational nature of turn region involved in formation of early folding species, we performed molecular dynamics simulations of turn peptides, 25KLNELDADEQ34 (DA peptide), 25KLNELGGDEQ34 (G 2 peptide), 25KLNELGGGDEQ35 (G 3 peptide) and 25KLNELGGGEQ34 (G 3′ peptide) from Rop at 300K. Further Wt-Rop and mutant G 2 -Rop monomers and dimers were also studied separately by molecular dynamics simulations. Our results show that glycine based peptides (G n peptides) have a higher loop closure propensity compared to DA. Comparison of monomeric and dimeric Rop simulations suggests that dimeric Rop necessarily requires αL conformation to be sampled at D30/G30 position in the turn region. Since glycine (at position 30) can readily adopt αL conformation, G n loop plays a dual role in both facilitating loop closure as well as facilitating reorganization/packing of helices required for structural adjustment during dimer formation in the folding of Rop. Based on our simulation results and available literature, we suggest a tentative kinetic model for Rop folding which allows us to estimate the contribution of loop closure propensity to the overall folding rates. [Copyright &y& Elsevier]
- Published
- 2013
- Full Text
- View/download PDF
45. The E. coli HicB Antitoxin Contains a Structurally Stable Helix-Turn-Helix DNA Binding Domain
- Author
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Manav, Melek Cemre, Turnbull, Kathryn Jane, Jurėnas, Dukas, Garcia-Pino, Abel, Gerdes, Kenn, Brodersen, Ditlev Egeskov, Manav, Melek Cemre, Turnbull, Kathryn Jane, Jurėnas, Dukas, Garcia-Pino, Abel, Gerdes, Kenn, and Brodersen, Ditlev Egeskov
- Abstract
The E. coli hicAB type II toxin-antitoxin locus is unusual by being controlled by two promoters and by having the toxin encoded upstream of the antitoxin. HicA toxins contain a double-stranded RNA-binding fold and cleaves both mRNA and tmRNA in vivo, while HicB antitoxins contain a partial RNase H fold and either a helix-turn-helix (HTH) or ribbon-helix-helix domain. It is not known how an HTH DNA-binding domain affects higher-order structure for the HicAB modules. Here, we present crystal structures of the isolated E. coli HicB antitoxin and full-length HicAB complex showing that HicB forms a stable DNA-binding module and interacts in a canonical way with HicA despite the presence of an HTH-type DNA-binding domain. No major structural rearrangements take place upon binding of the toxin. Both structures expose well-ordered DNA-binding motifs allowing a model for DNA binding by the antitoxin to be generated.
- Published
- 2019
46. Reengineering Cro Protein Functional Specificity with an Evolutionary Code
- Author
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Hall, Branwen M., Vaughn, Erin E., Begaye, Adrian R., and Cordes, Matthew H.J.
- Subjects
- *
VIRAL proteins , *NUCLEOTIDE sequence , *ETHYLENEDIAMINETETRAACETIC acid , *TRIAZOLES , *FLUORESCEIN , *SERUM albumin , *SNAKE venom , *PHOSPHODIESTERASES - Abstract
Abstract: Cro proteins from different lambdoid bacteriophages are extremely variable in their target consensus DNA sequences and constitute an excellent model for evolution of transcription factor specificity. We experimentally tested a bioinformatically derived evolutionary code relating switches between pairs of amino acids at three recognition helix sites in Cro proteins to switches between pairs of nucleotide bases in the cognate consensus DNA half-sites. We generated all eight possible code variants of bacteriophage λ Cro and used electrophoretic mobility shift assays to compare binding of each variant to its own putative cognate site and to the wild-type cognate site; we also tested the wild-type protein against all eight DNA sites. Each code variant showed stronger binding to its putative cognate site than to the wild-type site, except some variants containing proline at position 27; each also bound its cognate site better than wild-type Cro bound the same site. Most code variants, however, displayed poorer affinity and specificity than wild-type λ Cro. Fluorescence anisotropy assays on λ Cro and the triple code variant (PSQ) against the two cognate sites confirmed the switch in specificity and showed larger apparent effects on binding affinity and specificity. Bacterial one-hybrid assays of λ Cro and PSQ against libraries of sequences with a single randomized half-site showed the expected switches in specificity at two of three coded positions and no clear switches in specificity at noncoded positions. With a few caveats, these results confirm that the proposed Cro evolutionary code can be used to reengineer Cro specificity. [Copyright &y& Elsevier]
- Published
- 2011
- Full Text
- View/download PDF
47. Structural Analysis of a Novel Class of R–M Controller Proteins: C.Csp231I from Citrobacter sp. RFL231
- Author
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McGeehan, J.E., Streeter, S.D., Thresh, S.-J., Taylor, J.E.N., Shevtsov, M.B., and Kneale, G.G.
- Subjects
- *
PROTEIN structure , *CITROBACTER , *DIMERS , *BINDING sites , *ELECTROPHORESIS , *X-ray crystallography , *ULTRACENTRIFUGATION , *SMALL-angle X-ray scattering - Abstract
Abstract: Controller proteins play a key role in the temporal regulation of gene expression in bacterial restriction–modification (R–M) systems and are important mediators of horizontal gene transfer. They form the basis of a highly cooperative, concentration-dependent genetic switch involved in both activation and repression of R–M genes. Here we present biophysical, biochemical, and high-resolution structural analysis of a novel class of controller proteins, exemplified by C.Csp231I. In contrast to all previously solved C-protein structures, each protein subunit has two extra helices at the C-terminus, which play a large part in maintaining the dimer interface. The DNA binding site of the protein is also novel, having largely AAAA tracts between the palindromic recognition half-sites, suggesting tight bending of the DNA. The protein structure shows an unusual positively charged surface that could form the basis for wrapping the DNA completely around the C-protein dimer. [Copyright &y& Elsevier]
- Published
- 2011
- Full Text
- View/download PDF
48. Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding.
- Author
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Sharma, Hitesh, Shaoning Yu, Jilie Kong, Jimin Wang, and Steitz, Thomas A.
- Subjects
- *
ADENOSINE monophosphate , *ESCHERICHIA coli , *PROTEINS , *NUCLEOTIDE sequence , *GENETIC transcription , *BIOCHEMISTRY - Abstract
The binding of cAMP to the Escherichia coli catabolite gene activator protein (CAP) produces a conformational change that enables it to bind specific DNA sequences and regulate transcription, which it cannot do in the absence of the nucleotide. The crystal structures of the unliganded CAP containing a D138L mutation and the unliganded WT CAP were determined at 2.3 and 3.6 Å resolution, respectively, and reveal that the two DNA binding domains have dimerized into one rigid body and their two DNA recognition helices become buried. The WT structure shows multiple orientations of this rigid body relative to the nucleotide binding domain supporting earlier biochemical data suggesting that the inactive form exists in an equilibrium among different conformations. Comparison of the structures of the liganded and unliganded CAP suggests that cAMP stabilizes the active DNA binding conformation of CAP through the interactions that the N6 of the adenosine makes with the C-helices. These interactions are associated with the reorientation and elongation of the C-helices that precludes the formation of the inactive structure. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
49. A phylogenomic analysis of bacterial helix–turn–helix transcription factors.
- Author
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Santos, Catarina L., Tavares, Fernando, Thioulouse, Jean, and Normand, Philippe
- Subjects
- *
TRANSCRIPTION factors , *PHYLOGENY , *GENOMES , *CELL physiology , *DEVELOPMENTAL cytology , *BIOLOGY - Abstract
Perception by each individual organism of its environment's parameters is a key factor for survival. In a constantly changing environment, the ability to assess nutrient sources and potentially stressful situations constitutes the main basis for ecological adaptability. Transcription regulators are key decision-making proteins that mediate the communication between environmental conditions and DNA transcription through a multifaceted network. The parallel study of these regulators across microbial organisms adapted to contrasting biotopes constitutes an unexplored approach to understand the evolution of genome plasticity and cell function. We present here a reassessment of bacterial helix–turn–helix regulator diversity in different organisms from a multidisciplinary perspective, on the interface that links metabolism, ecology and phylogeny, further sustained by a statistically based approach. The present revision brought to light evidence of patterns among families of regulators, suggesting that multiple selective forces modulate the number and kind of regulators present in a given genome. Besides being an important step towards understanding the adaptive traits that influence the microbial responses to the varying environment on the very first and most prevalent line of reaction, the transcription of DNA, this approach is a promising tool to extract biological trends from genomic databases. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
50. RodZ, a component of the bacterial core morphogenic apparatus.
- Author
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AIyahya, S. Anisah, Alexander, Roger, Costa, Teresa, Henriques, Adriano O., Emonet, Thierry, and Jacobs-Wagner, Christine
- Subjects
- *
BACTERIA , *MORPHOGENESIS , *MORPHOLOGY , *CELLS , *DYNAMICS - Abstract
The molecular basis of bacterial cell morphogenesis remains largely an open question. Here we discover a morphogenic protein, RodZ, which is widely conserved across the bacterial kingdom. In Caulobacter crescentus, RodZ is essential for viability and is involved in all aspects of this organism's complex morphology. Depletion or over-production of RodZ results in grossly misshapen cells with stalk defects. RodZ exhibits a localization pattern during the cell cycle corresponding to sites of active peptidoglycan synthesis. The temporal transition of RodZ between patchy/helical and mid-cell localization mimics and depends on the actin-like MreB cytoskeleton. In Escherichia coli, an organism with a distinct mode of growth and MreB localization dynamics, RodZ follows MreB and retains its crucial role in cell morphogenesis, demonstrating conservation of function. Genomic analysis shows that RodZ represents an ancient function unique to bacteria. Multiple sequence alignment of 143 RodZ sequences from species across bacterial phyla identifies an N-terminal cytoplasmic domain with a helix-turn-helix motif, a transmembrane sequence, and a previously unidentified, conserved periplasmic or extracellular C-terminal domain. Both the N- and C-terminal domains are important for function, with the N-terminal domain containing localization determinants. This study uncovers a key missing player in the cytoskeleton-based growth machinery enabling heritable and defined cellular forms in bacteria. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
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