β-Arm flexibility of HU from<i>Staphylococcus aureus</i>dictates the DNA-binding and recognition mechanism

Kim, Do Hee; Im, Hyung‐Jun; Jee, Jun Goo; Jang, Sun-Bok; Yoon, Hye Jin; Kwon, Ae‐Ran; Kang, Sung Min; Lee, Bong Jin

doi:10.1107/s1399004714023931

Cited by 35 publications

(29 citation statements)

References 108 publications

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“…Thus, the conformational flexibility of the binding site greatly influences the protein's DNA-binding specificity ( 80 ). Based on our study, the flexible nature of HicB plays a crucial role in the protein's regulatory dynamics with respect to its target DNA ( 81 , 82 ). As a transcriptional regulator, the flexible form of HicB is essential for bacterial cell life and death.…”

Section: Discussionmentioning

confidence: 92%

Functional insights into the Streptococcus pneumoniae HicBA toxin–antitoxin system based on a structural study

Kim

Kang

Park

et al. 2018

Nucleic Acids Research

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Streptococcus pneumonia has attracted increasing attention due to its resistance to existing antibiotics. TA systems are essential for bacterial persistence under stressful conditions such as nutrient deprivation, antibiotic treatment, and immune system attacks. In particular, S. pneumoniae expresses the HicBA TA gene, which encodes the stable HicA toxin and the labile HicB antitoxin. These proteins interact to form a non-toxic TA complex under normal conditions, but the toxin is activated by release from the antitoxin in response to unfavorable growth conditions. Here, we present the first crystal structure showing the complete conformation of the HicBA complex from S. pneumonia. The structure reveals that the HicA toxin contains a double-stranded RNA-binding domain that is essential for RNA recognition and that the C-terminus of the HicB antitoxin folds into a ribbon-helix-helix DNA-binding motif. The active site of HicA is sterically blocked by the N-terminal region of HicB. RNase activity assays show that His36 is essential for the ribonuclease activity of HicA, and nuclear magnetic resonance (NMR) spectra show that several residues of HicB participate in binding to the promoter DNA of the HicBA operon. A toxin-mimicking peptide that inhibits TA complex formation and thereby increases toxin activity was designed, providing a novel approach to the development of new antibiotics.

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Section: Discussionmentioning

confidence: 92%

Functional insights into the Streptococcus pneumoniae HicBA toxin–antitoxin system based on a structural study

Kim

Kang

Park

et al. 2018

Nucleic Acids Research

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“…Upon interacting with DNA, the β-strands pack tightly to form a complete DNA-binding domain ( 40 ). Proteins, such as HU, have flexible β-arms and bend inward when binding to DNA ( 87 ). However, VapB26 naturally forms a homodimer in solution, as shown in our MALS data ( Supplementary Figure S1 ) and the RHH domain of VapB26 was confirmed by analyzing the crystal structure of the DNA-free protein.…”

Section: Discussionmentioning

confidence: 99%

Functional details of the Mycobacterium tuberculosis VapBC26 toxin-antitoxin system based on a structural study: insights into unique binding and antibiotic peptides

Kang

Kim

Lee

et al. 2017

Nucleic Acids Research

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Toxin-antitoxin (TA) systems are essential for bacterial persistence under stressful conditions. In particular, Mycobacterium tuberculosis express VapBC TA genes that encode the stable VapC toxin and the labile VapB antitoxin. Under normal conditions, these proteins interact to form a non-toxic TA complex, but the toxin is activated by release from the antitoxin in response to unfavorable conditions. Here, we present the crystal structure of the M. tuberculosis VapBC26 complex and show that the VapC26 toxin contains a pilus retraction protein (PilT) N-terminal (PIN) domain that is essential for ribonuclease activity and that, the VapB26 antitoxin folds into a ribbon-helix-helix DNA-binding motif at the N-terminus. The active site of VapC26 is sterically blocked by the flexible C-terminal region of VapB26. The C-terminal region of free VapB26 adopts an unfolded conformation but forms a helix upon binding to VapC26. The results of RNase activity assays show that Mg2+ and Mn2+ are essential for the ribonuclease activity of VapC26. As shown in the nuclear magnetic resonance spectra, several residues of VapB26 participate in the specific binding to the promoter region of the VapBC26 operon. In addition, toxin-mimicking peptides were designed that inhibit TA complex formation and thereby increase toxin activity, providing a novel approach to the development of new antibiotics.

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“…SasF would counteract such adverse effects. HU protein is one of the major nucleoid-associated proteins involved in DNA bending and thus the determination of prokaryotic chromosome structure (Kim et al, 2014a ). It also acts as a transcriptional regulator of genes, responding to anaerobiosis, acid stress, high osmolarity and SOS induction (Oberto et al, 2009 ).…”

Section: Resultsmentioning

confidence: 99%

Joint Genomic and Proteomic Analysis Identifies Meta-Trait Characteristics of Virulent and Non-virulent Staphylococcus aureus Strains

Bonar

Bukowski

Hydzik

et al. 2018

Front. Cell. Infect. Microbiol.

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Staphylococcus aureus is an opportunistic pathogen of humans and warm-blooded animals and presents a growing threat in terms of multi-drug resistance. Despite numerous studies, the basis of staphylococcal virulence and switching between commensal and pathogenic phenotypes is not fully understood. Using genomics, we show here that S. aureus strains exhibiting virulent (VIR) and non-virulent (NVIR) phenotypes in a chicken embryo infection model genetically fall into two separate groups, with the VIR group being much more cohesive than the NVIR group. Significantly, the genes encoding known staphylococcal virulence factors, such as clumping factors, are either found in different allelic variants in the genomes of NVIR strains (compared to VIR strains) or are inactive pseudogenes. Moreover, the pyruvate carboxylase and gamma-aminobutyrate permease genes, which were previously linked with virulence, are pseudogenized in NVIR strain ch22. Further, we use comprehensive proteomics tools to characterize strains that show opposing phenotypes in a chicken embryo virulence model. VIR strain CH21 had an elevated level of diapolycopene oxygenase involved in staphyloxanthin production (protection against free radicals) and expressed a higher level of immunoglobulin-binding protein Sbi on its surface compared to NVIR strain ch22. Furthermore, joint genomic and proteomic approaches linked the elevated production of superoxide dismutase and DNA-binding protein by NVIR strain ch22 with gene duplications.

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β-Arm flexibility of HU fromStaphylococcus aureusdictates the DNA-binding and recognition mechanism

Cited by 35 publications

References 108 publications

Functional insights into the Streptococcus pneumoniae HicBA toxin–antitoxin system based on a structural study

Functional insights into the Streptococcus pneumoniae HicBA toxin–antitoxin system based on a structural study

Functional details of the Mycobacterium tuberculosis VapBC26 toxin-antitoxin system based on a structural study: insights into unique binding and antibiotic peptides

Joint Genomic and Proteomic Analysis Identifies Meta-Trait Characteristics of Virulent and Non-virulent Staphylococcus aureus Strains

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