Crystal structure of HlyU, the hemolysin gene transcription activator, from Vibrio cholerae N16961 and functional implications

Mukherjee, Debarati; Datta, Aritreyee; Chakrabarti, Pinak

doi:10.1016/j.bbapap.2014.09.020

Cited by 17 publications

(30 citation statements)

References 63 publications

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“…However, L98D showed a similar DNA binding profile as wild-type HlyU_Vc in the same high range of protein concentrations. Among the four self-contact residues, Leu98 is the only one that lies at the rim of the dimeric interface ( 15 ); the others lie in the core region and therefore influence the dimeric association more strongly ( 30 ). Moreover, Leu98 makes fewer contacts than the others (Supplementary Figure S2), lying close to the protein exterior (Supplementary Figure S3).…”

Section: Resultsmentioning

confidence: 99%

“…Based on the crystal structure of HlyU_Vc (PDB ID: 4OOI, ( 15 )), in silico model of HlyU_Vc -DNA complex ( 14 ) and DNA binding studies on HlyU from Vibrio vulnificus (HlyU_Vv) ( 31 ), we predicted some amino acids which may be essential for HlyU_Vc's biological function. The amino acids chosen were Lys26 from the α1 helix, Asn30 from the loop between α1 and α2 and Arg32, and Arg33 from the α2, Ser62, Gln63, His64, Leu65, Ala66, Trp67, Arg69 and Arg70 from α4, Lys78 from β2, Gln81 from the turn, and Tyr85 from β3.…”

Section: Resultsmentioning

confidence: 99%

“…To have a complete picture of a gene expression system, it is of primary importance to elucidate the regulatory sequences that include the promoter region together with enhancer elements to which activator proteins bind. HlyU is an important virulence activator, responsible for the activation of the rtxA1 operon in V. vulnificus , the plp-vah1 gene cluster and the rtxACHBDE gene cluster in Vibrio anguillarum , and hlyA gene and probably other virulence factors in V. cholerae ( 15 ). Recent investigations by several groups have thrown light on regulation of virulence in V. vulnificus and V. anguillarum by HlyU ( 27 , 32 ).…”

Section: Discussionmentioning

confidence: 99%

“…The DNA models were analyzed using Curves+ ( 20 ). The DNA and the crystal structure of HlyU_Vc (PDB ID: 4OOI, ( 15 )) docking was done using Haddock server: easy interface ( 21 ). The experimentally determined active residues for both the protein and the DNA were mentioned in the submitted job.…”

Section: Methodsmentioning

confidence: 99%

“…HlyU of V. cholerae , (HlyU_Vc) is known to belong to the SmtB/ArsR family of regulatory proteins including NolR of Rhizobium meliloti , SmtB of Synechococcus sp ., ArsR of Staphylococcus aureus ( 14 ). The homology model of the protein and the very recently solved crystal structure (Protein Data Bank (PDB) ID: 4OOI, ( 15 )) show that the protein is a homodimer with a winged helix-turn-helix (wHTH) motif (Supplementary Figure S1). Unlike the other metallorepressor members of its family, HlyU_Vc is a transcription activator ( 16 ) lacking any metal binding domain ( 15 ).…”

Section: Introductionmentioning

confidence: 99%

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Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies

Mukherjee

Pal

Chakravarty

et al. 2015

Nucleic Acids Research

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HlyU, a transcriptional regulator common in many Vibrio species, activates the hemolysin gene hlyA in Vibrio cholerae, the rtxA1 operon in Vibrio vulnificus and the genes of plp-vah1 and rtxACHBDE gene clusters in Vibrio anguillarum. The protein is also proposed to be a potential global virulence regulator for V. cholerae and V. vulnificus. Mechanisms of gene control by HlyU in V. vulnificus and V. anguillarum are reported. However, detailed elucidation of the interaction of HlyU in V. cholerae with its target DNA at the molecular level is not available. Here we report a 17-bp imperfect palindrome sequence, 5′-TAATTCAGACTAAATTA-3′, 173 bp upstream of hlyA promoter, as the binding site of HlyU. This winged helix-turn-helix protein binds necessarily as a dimer with the recognition helices contacting the major grooves and the β-sheet wings, the minor grooves. Such interactions enhance hlyA promoter activity in vivo. Mutations affecting dimerization as well as those in the DNA–protein interface hamper DNA binding and transcription regulation. Molecular dynamic simulations show hydrogen bonding patterns involving residues at the mutation sites and confirmed their importance in DNA binding. On binding to HlyU, DNA deviates by ∼68º from linearity. Dynamics also suggest a possible redox control in HlyU.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies

Mukherjee

Pal

Chakravarty

et al. 2015

Nucleic Acids Research

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Metal homeostasis in bacteria: the role of ArsR–SmtB family of transcriptional repressors in combating varying metal concentrations in the environment

et al. 2017

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Bacterial infections cause severe medical problems worldwide, resulting in considerable death and loss of capital. With the ever-increasing rise of antibiotic-resistant bacteria and the lack of development of new antibiotics, research on metal-based antimicrobial therapy has now gained pace. Metal ions are essential for survival, but can be highly toxic to organisms if their concentrations are not strictly controlled. Through evolution, bacteria have acquired complex metal-management systems that allow them to acquire metals that they need for survival in different challenging environments while evading metal toxicity. Metalloproteins that controls these elaborate systems in the cell, and linked to key virulence factors, are promising targets for the anti-bacterial drug development. Among several metal-sensory transcriptional regulators, the ArsR-SmtB family displays greatest diversity with several distinct metal-binding and nonmetal-binding motifs that have been characterized. These prokaryotic metolloregulatory transcriptional repressors represses the expression of operons linked to stress-inducing concentrations of metal ions by directly binding to the regulatory regions of DNA, while derepression results from direct binding of metal ions by these homodimeric proteins. Many bacteria, e.g., Mycobacterium tuberculosis, Bacillus anthracis, etc., have evolved to acquire multiple metal-sensory motifs which clearly demonstrate the importance of regulating concentrations of multiple metal ions. Here, we discussed the mechanisms of how ArsR-SmtB family regulates the intracellular bioavailability of metal ions both inside and outside of the host. Knowledge of the metal-challenges faced by bacterial pathogens and their survival strategies will enable us to develop the next generation drugs.

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Increased intracellular persulfide levels attenuate HlyU-mediated hemolysin transcriptional activation in Vibrio cholerae

Pis Diez,

Antelo,

Dalia

et al. 2023

Journal of Biological Chemistry

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Crystal structure of HlyU, the hemolysin gene transcription activator, from Vibrio cholerae N16961 and functional implications

Cited by 17 publications

References 63 publications

Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies

Identification of the target DNA sequence and characterization of DNA binding features of HlyU, and suggestion of a redox switch for hlyA expression in the human pathogen Vibrio cholerae from in silico studies

Metal homeostasis in bacteria: the role of ArsR–SmtB family of transcriptional repressors in combating varying metal concentrations in the environment

Increased intracellular persulfide levels attenuate HlyU-mediated hemolysin transcriptional activation in Vibrio cholerae

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