ArticlePloS one2017
Comparison of histone-like HU protein DNA-binding properties and HU/IHF protein sequence alignment.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 45 citations in OpenAlex.
- The role of two major nucleoid-associated proteins in Streptomyces, HupA and HupS, in stress survival and gene expression regulation.Microbial cell factories · 2024Article
- Single-stranded DNA recruitment mechanism in replication origin unwinding by DnaA initiator protein and HU, an evolutionary ubiquitous nucleoid protein.Nucleic acids research · 2023Article
- Toward an understanding of the DNA replication initiation in bacteria.Frontiers in microbiology · 2023Review
- Pangenome-level analysis of nucleoid-associated proteins in theFrontiers in microbiology · 2023Article
- Preclinical stage abundance and nuclear antigen reactivity of faecal Immunoglobulin A vary among males and females of lupus-prone mouse models.Immunology · 2022Article
- Bacteriophage protein Gp46 is a cross-species inhibitor of nucleoid-associated HU proteins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- A HU-like protein is required for full virulence in Xanthomonas campestris pv. campestris.Molecular plant pathology · 2021Article
- Distribution and phasing of sequence motifs that facilitate CRISPR adaptation.Current biology : CB · 2021Article
- Epigallocatechin Gallate with Potent Anti-ACS omega · 2021Article
- Specialization of the Reiterated Copies of the Heterodimeric Integration Host Factor Genes inFrontiers in microbiology · 2021Article
- Acetylation at Lysine 86 ofFrontiers in microbiology · 2021Article
- NontypeableBiofilm · 2020Article
- Structure-based inhibitors targeting the alpha-helical domain of the Spiroplasma melliferum histone-like HU protein.Scientific reports · 2020Article
- Abundance and nuclear antigen reactivity of intestinal and fecal Immunoglobulin A in lupus-prone mice at younger ages correlate with the onset of eventual systemic autoimmunity.Scientific reports · 2020Article
- The structural basis of African swine fever virus pA104R binding to DNA and its inhibition by stilbene derivatives.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Urease Expression in PathogenicFrontiers in microbiology · 2020Article
- Transcription of Bacterial Chromatin.Journal of molecular biology · 2019Review
- Nucleoid-Associated Protein HU: A Lilliputian in Gene Regulation of Bacterial Virulence.Frontiers in cellular and infection microbiology · 2019Review
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe structure and function of bacterial nucleoid are controlled by histone-like proteins of HU/IHF family, omnipresent in bacteria and also founding archaea and some eukaryotes.HU protein binds dsDNA without sequence specificity and avidly binds DNA structures with propensity to be inclined such as forks, three/four-way junctions, nicks, overhangs and DNA bulges. Sequence comparison of thousands of known histone-like proteins from diverse bacteria phyla reveals relation between HU/IHF sequence, DNA-binding properties and other protein features. METHODOLOGY AND PRINCIPAL
findingsPerformed alignment and clusterization of the protein sequences show that HU/IHF family proteins can be unambiguously divided into three groups, HU proteins, IHF_A and IHF_B proteins. HU proteins, IHF_A and IHF_B proteins are further partitioned into several clades for IHF and HU; such a subdivision is in good agreement with bacterial taxonomy. We also analyzed a hundred of 3D fold comparative models built for HU sequences from all revealed HU clades. It appears that HU fold remains similar in spite of the HU sequence variations. We studied DNA-binding properties of HU from N. gonorrhoeae, which sequence is similar to one of E.coli HU, and HU from M. gallisepticum and S. melliferum which sequences are distant from E.coli protein. We found that in respect to dsDNA binding, only S. melliferum HU essentially differs from E.coli HU. In respect to binding of distorted DNA structures, S. melliferum HU and E.coli HU have similar properties but essentially different from M. gallisepticum HU and N. gonorrhea HU. We found that in respect to dsDNA binding, only S. melliferum HU binds DNA in non-cooperative manner and both mycoplasma HU bend dsDNA stronger than E.coli and N. gonorrhoeae. In respect to binding to distorted DNA structures, each HU protein has its individual profile of affinities to various DNA-structures with the increased specificity to DNA junction. CONCLUSIONS AND SIGNIFICANCE: HU/IHF family proteins sequence alignment and classification are updated. Comparative modeling demonstrates that HU protein 3D folding's even more conservative than HU sequence. For the first time, DNA binding characteristics of HU from N. gonorrhoeae, M. gallisepticum and S. melliferum are studied. Here we provide detailed analysis of the similarity and variability of DNA-recognizing and bending of four HU proteins from closely and distantly related HU clades.
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