Determining the DNA sequence elements required for binding integration host factor to two different target sites.

L M Hales; R I Gumport; J F Gardner

doi:10.1128/jb.176.10.2999-3006.1994

Home/Archive/PubMed

PubMed · 8188600

Determining the DNA sequence elements required for binding integration host factor to two different target sites.

L M Hales·R I Gumport·J F Gardner

View original source ↗Export metadata ↓

Abstract

Binding sites for the Escherichia coli protein integration host factor (IHF) include a set of conserved bases that can be summarized by the consensus sequence WATCAANNNNTTR (W is dA or dT, R is dA or dG, and N is any nucleotide). However, additional 5'-proximal bases, whose common feature is a high dA+dT content, are also thought to be required for binding at some sites. We examine the relative contribution of these two sequence elements to IHF binding to the H' and H1 sites in attP of bacteriophage lambda by using the bacteriophage P22-based challenge-phage system. IHF was unable to act as a repressor in the challenge-phage assay at H' sites containing the core consensus element but lacking the dA+dT-rich element. This indicates that both elements are required for IHF to bind to the H' site. In contrast, the core consensus determinant alone is sufficient for IHF binding to the H1 site, which lacks an upstream dA+dT-rich region. Fifty mutants that decreased or eliminated IHF binding to the H1 site were isolated. Sequence analysis showed changes in the bases in the core consensus element only, further indicating that this determinant is sufficient for IHF binding to the H1 site. We found that placement of a dA+dT-rich element upstream of the H1 core consensus element significantly increased the affinity, suggesting that the presence of a dA+dT-rich element enhances IHF binding.

Explore related subjects

Bacterial Proteins Bacteriophage lambda Base Sequence Consensus Sequence DNA, Bacterial Escherichia coli Integration Host Factors Molecular Sequence Data Mutation Protein Binding Regulatory Sequences, Nucleic Acid Sequence Analysis, DNA Structure-Activity Relationship Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S.

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

L M Hales, R I Gumport, J F Gardner. 1994. Determining the DNA sequence elements required for binding integration host factor to two different target sites.. https://doi.org/10.1128/jb.176.10.2999-3006.1994

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2026

Prediction of bacterial protein-compound interactions with only positive samples.

MOTIVATION: Prediction of Compound-Protein Interactions (CPI) in bacteria is crucial to advance various pharmaceutical and chemical engineering fields, including biocatalysis, drug discovery, and industrial processing. However, current CPI models cannot be applied for bacterial CPI prediction due to the lack of curated negative interaction samples. RESULTS: We propose a novel Positive-Unlabeled (PU) learning framework, named BIN-PU, to address this limitation. BIN-PU generates pseudo positive and negative labels from known positive interaction data, enabling effective training of deep learning models for CPI prediction. We also propose a weighted positive loss function that weights to truly positive samples. We have validated BIN-PU coupled with multiple CPI backbone models, comparing the performance with the existing PU models using bacterial cytochrome P450 (CYP) data. Extensive experiments demonstrate the superiority of BIN-PU over the benchmark models in predicting CPIs with only truly positive samples. Furthermore, we have validated BIN-PU on additional bacterial proteins obtained from literature review, human CYP datasets, and uncurated data for its reproducibility. We have also validated the CPI prediction for the uncurated CYP data with biological and biophysical experiments. BIN-PU represents a significant advancement in CPI prediction for bacterial proteins, opening new possibilities for improving predictive models in related biological interaction tasks. AVAILABILITY AND IMPLEMENTATION: The source code and data are available at https://github.com/datax-lab/CYP.

Bacterial Proteins↗

PubMed2025

ComFB, a widespread family of c-di-NMP receptor proteins.

Cyclic dimeric-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that regulates a variety of cellular processes, including motility, biofilm formation, secretion, cell cycle progression, and development, and also contributes to the virulence of many bacterial pathogens. While the genes encoding c-di-GMP cyclases and hydrolases are readily identifiable in microbial genomes, known c-di-GMP receptor domains are quite few, with only PilZ and MshEN broadly distributed across bacterial phyla. Recently, a new c-di-GMP receptor, named CdgR or ComFB, has been identified in cyanobacteria and shown to regulate cell size and natural competence. We demonstrated that CdgR proteins exhibit sequence and structural similarity to the Bacillus subtilis late competence development protein ComFB, a conserved protein of unknown function associated with bacterial competence. This prompted us to hypothesize that ComFB and ComFB-like proteins could also serve as c-di-GMP receptors. Here, we comprehensively investigated the ComFB protein family and demonstrated that ComFB proteins are evolutionarily widespread among bacteria and function as a novel family of c-di-GMP receptors. We showed that ComFB proteins from Gram-positive bacteria (B. subtilis, Thermoanaerobacter brockii) and Gram-negative pathogens (Vibrio cholerae, Treponema denticola) bind c-di-GMP with high affinity. Several ComFB proteins also bind cyclic di-adenosine monophosphate (c-di-AMP), suggesting that ComFB represents a widely distributed bacterial protein family with dual specificity for c-di-GMP and c-di-AMP. Our physiological studies further showed that ComFB plays vital roles in controlling motility in a c-di-GMP-dependent manner in two phylogenetically distant bacteria, B. subtilis and the gram-negative Shewanella oneidensis, attesting to the biological relevance of ComFB as a c-di-GMP binding protein.

Bacterial Proteins↗

PubMed2024

Dynamic structural determinants in bacterial microcompartment shells.

Bacterial microcompartments (BMCs) are polyhedral structures that segregate enzymatic cargo from the cytosol via encapsulation within a protein shell. Unlike other biological polyhedra, such as viral capsids and encapsulins, BMC shells can exhibit a highly advantageous structural and functional plasticity, conforming to a variety of anabolic (CO2 fixation in carboxysomes) and catabolic (nutrient assimilation in metabolosomes) roles. Consequently, understanding the subunit properties and associated protein-protein interaction processes that guide shell assembly and function is a necessary step to fully harness BMCs as modular, biotechnological nanomachines. Here, we describe the recent insights into the dynamics of structural features of the key BMC domain (Pfam00936)-containing proteins, which serve as a structural template for BMC-H and BMC-T shell building blocks.

Bacterial Proteins↗