Design of Peptide that Recognizes Double-Stranded DNA

Fukumori, Takashi; Morita, Yasutaka; Tamiya, Eiichi; Yokoyama, Kenji

doi:10.2116/analsci.19.181

Cited by 5 publications

(2 citation statements)

References 8 publications

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“…For example, two of the invariant residues, G4 and R11, are located within the predicted DNA-binding domain. While the role of glycine has not been well studied, structural analysis of other XRE-type helix-turn-helix domains has revealed that arginine in this position contributes to the stability of the DNA-protein complex through formation of a fold-stabilizing salt bridge with a conserved glutamic acid residue (22) or side chain contacts with phosphate groups in target DNA (11,(36)(37)(38). Invariant tryptophan residues are often involved in protein-protein interactions (19), and W142 may localize to the interface of a critical RopB-protein complex.…”

Section: Vol 189 2007 Notes 653mentioning

confidence: 99%

Contribution of Invariant Residues to the Function of Rgg Family Transcription Regulators

Loughman

Caparon

2007

J Bacteriol

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The Rgg family of transcription regulators is widely distributed among gram-positive bacteria, yet how these proteins control transcription is poorly understood. Using Streptococcus pyogenes RopB as a model, we demonstrated that residues invariant among Rgg-like regulators are critical for function and obtained evidence for a mechanism involving protein complex formation.The Rgg-like regulators constitute a conserved family of proteins that modulate transcription in gram-positive bacteria. This group is widely distributed, and the members occur in both pathogenic and commensal species and include Rgg of Streptococcus gordonii, which is required for extracellular glucosyltransferase expression (29, 30); GadR of Lactococcus lactis, which is required for glutamate-dependent acid tolerance (27); MutR, which is required for expression of the mutacin lantibiotic, MutA, of Streptococcus mutans (23); and the plasmid-encoded LasX protein of Lactobacillus sakei, which regulates the synthesis of and immunity to the lantibiotic lactocin S (25, 28). Additional uncharacterized Rgg-like proteins are encoded by the genomes of Streptococcus pneumoniae (31), Streptococcus agalactiae (13), Streptococcus oralis (10), Streptococcus sanguis (34), Streptococcus equi (http://www.sanger.ac.uk), and Listeria monocytogenes (12), and some genomes, like those of S. pyogenes (9), S. gordonii (15, 33), S. pneumoniae (31), and S. mutans (1), contain multiple rgg-like genes.How the members of this extensive family function to regulate gene expression is not well understood. Rgg-like proteins have a helix-turn-helix motif in the amino terminus of the polypeptide, which is a conserved DNA-binding domain found in other families of transcription regulators (17). Only recently has it been established that any Rgg-like proteins bind specifically to DNA to regulate transcription. For example, association with nucleic acid has been demonstrated for Rgg of S. gordonii (35), RopB (21), and LasX (24), but there is only a weak consensus binding site (24). The absence of a conserved regulatory motif in the promoter regions of genes regulated by Rgg-like proteins and the functional diversity of the regulated gene products suggest that Rgg-like proteins interact with additional regulatory networks to alter gene expression. Experimental data supporting this hypothesis were obtained in an analysis of the speB regulatory program in S. pyogenes, where RopB is necessary but not sufficient for activation of transcription (21) and may influence gene expression via its ability to influence the expression of other regulators (5). The integration of Rgg pathways with other regulatory pathways could also be established through protein-protein interactions. For example, RopB has been shown to associate with a negative regulator, LacD.1, which may be a mechanism for maintaining temporally controlled expression programs (16a).Although the members of the Rgg family have been adapted to individual regulatory programs, it is likely that these proteins have a common structure ...

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Section: Vol 189 2007 Notes 653mentioning

confidence: 99%

Contribution of Invariant Residues to the Function of Rgg Family Transcription Regulators

Loughman

Caparon

2007

J Bacteriol

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“…At present there are several reviews [20,21,22,23] and a book [24] summarizing antibody engineering, including the phage display method. Using the phage display method, double-stranded DNA (dsDNA) recognizing peptide was recently designed [25].…”

Section: Antibodies and Their Recognition Elementsmentioning

confidence: 99%

Current research activity in biosensors

Nakamura

Karube

2003

Analytical and Bioanalytical Chemistry

259

129

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Biosensors consist of a molecular recognition element and a transducer. Since the first biosensor was developed by Updike and Hicks many biosensors and their associated techniques have been studied and developed. In this review current research activity on the fundamentals and applications of biosensors is summarized. In discussion of the former, molecular recognition elements, techniques and tools for biosensor construction, and basic biosensor devices are introduced. Coverage of the latter includes description of biosensors for environmental, food, and clinical fields. Chemical sensors developed in our laboratory for environmental monitoring are also described. This review mainly summarizes work performed by our group and by our colleagues, and refers to the main review articles summarizing each field of biosensor research in recent years.

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Survey of the year 2003 commercial optical biosensor literature

2005

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In the year 2003 there was a 17% increase in the number of publications citing work performed using optical biosensor technology compared with the previous year. We collated the 962 total papers for 2003, identified the geographical regions where the work was performed, highlighted the instrument types on which it was carried out, and segregated the papers by biological system. In this overview, we spotlight 13 papers that should be on everyone's 'must read' list for 2003 and provide examples of how to identify and interpret high-quality biosensor data. Although we still find that the literature is replete with poorly performed experiments, over-interpreted results and a general lack of understanding of data analysis, we are optimistic that these shortcomings will be addressed as biosensor technology continues to mature.

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Design of Peptide that Recognizes Double-Stranded DNA

Cited by 5 publications

References 8 publications

Contribution of Invariant Residues to the Function of Rgg Family Transcription Regulators

Contribution of Invariant Residues to the Function of Rgg Family Transcription Regulators

Current research activity in biosensors

Survey of the year 2003 commercial optical biosensor literature

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