Properties of DNA-Binding of HU Heterotypic and Homotypic Dimers from Escherichia coli

Tanaka, Hiromistu; Goshima, Naoki; Kohno, Keizo; Kano, Yasunobu; Imamoto, Fumio

doi:10.1093/oxfordjournals.jbchem.a124084

Cited by 35 publications

(30 citation statements)

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“…Five proteins, CbpA, H-NS, HU, IciA, and StpA, have been proposed to be curved DNAbinding proteins. The binding preference for curved DNA has been demonstrated for CbpA, H-NS, and HU (11,12,23), but no experimental evidence has been published for the specificity of curved DNA binding for IciA and StpA. The present study indicates that CbpA, H-NS, and IciA are indeed the curved DNA-binding proteins.…”

Section: A-e)mentioning

confidence: 44%

Twelve Species of the Nucleoid-associated Protein from Escherichia coli

Azam¹,

Ishihama²

1999

Journal of Biological Chemistry

426

314

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Section: A-e)mentioning

confidence: 44%

Twelve Species of the Nucleoid-associated Protein from Escherichia coli

Azam¹,

Ishihama²

1999

Journal of Biological Chemistry

426

314

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show abstract

“…The third NAP, HU, seems to interact with DNA in a nonspecific manner, but it has a preference for binding to distorted regions of the DNA (60). In E. coli HU functions as a heterodimer (HU␣ and HU␤) or a homodimer (61), and it was shown to control the expression of genes involved in Salmonella virulence (62). L. pneumophila harbors only one HU subunit, HupB (Lpg1858), and it probably functions as a homodimer.…”

Section: Discussionmentioning

confidence: 99%

Two Fis Regulators Directly Repress the Expression of Numerous Effector-Encoding Genes in Legionella pneumophila

2014

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Legionella pneumophila is an intracellular human pathogen that utilizes the Icm/Dot type IVB secretion system to translocate a large repertoire of effectors into host cells. For most of these effectors, there is no information regarding their regulation. Therefore, the aim of this study was to examine the involvement of the three L. pneumophila Fis homologs in the regulation of effector-encoding genes. Deletion mutants constructed in the genes encoding the three Fis regulators revealed that Fis1 (lpg0542 gene) and Fis3 (lpg1743) but not Fis2 (lpg1370) are partially required for intracellular growth of L. pneumophila in Acanthamoeba castellanii. To identify pathogenesis-related genes directly regulated by Fis, we established a novel in vivo system which resulted in the discovery of numerous effector-encoding genes directly regulated by Fis. Further examination of these genes revealed that Fis1 and Fis3 repress the level of expression of effector-encoding genes during exponential phase. Three groups of effector-encoding genes were identified: (i) effectors regulated mainly by Fis1, (ii) effectors regulated mainly by Fis3, and (iii) effectors regulated by both Fis1 and Fis3. Examination of the upstream regulatory region of all of these effector-encoding genes revealed multiple putative Fis regulatory elements, and site-directed mutagenesis confirmed that a few of these sites constitute part of a repressor binding element. Furthermore, gel mobility shift assays demonstrated the direct relation between the Fis1 and Fis3 regulators and these regulatory elements. Collectively, our results demonstrate for the first time that two of the three L. pneumophila Fis regulators directly repress the expression of Icm/Dot effector-encoding genes.

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“…The HU protein belongs to a class of DNAbending proteins associated with the folding of the bacterial nucleoid (White et al, 1989;Swinger & Rice, 2004). Known to exist in a monodimeric form, this protein in most bacteria is usually encoded by a single gene, whereas in others, such as the enterobacteria, it exists in a heterodimeric form encoded by two different genes (HU-b and HU-a) (Rouvière-Yaniv & Kjeldgaard, 1979) with different preferential binding affinities, and thus interacts differently with DNA, with effects on DNA replication and thermostability (Shindo et al, 1992;Tanaka et al, 1993;Bahloul et al, 2001).…”

Section: Discussionmentioning

confidence: 99%

Making heads or tails of the HU proteins in the planctomycete Gemmata obscuriglobus

2011

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Gemmata obscuriglobus has a highly condensed nucleoid which is implicated in its resistance to radiation. However, the mechanisms by which such compaction is achieved, and the proteins responsible, are still unknown. Here we have examined the genome of G. obscuriglobus for the presence of proteins homologous to those that have been associated with nucleoid condensation. We found two different proteins homologous to the bacterial nucleoid-associated protein HU, one with an N-terminal and one with a C-terminal extension relative to the amino acid sequence of the HU found in Escherichia coli. Sequence analysis revealed that one of these HU homologues represents a novel type with a high number of prolines in its C-terminal extension, whereas the other one has motifs similar to the N terminus of the HU homologue from the radio-resistant bacterium Deinococcus radiodurans. The occurrence of two such HU homologue proteins with these two different terminal extensions in one organism appears to be unique among the Bacteria. INTRODUCTIONArchitectural chromosomal proteins are best known for their role in the compaction of DNA in a cell. The compaction of the nucleoid is an important cellular process in all living cells, and is achieved via a combination or the single mode of action of bending, wrapping and bridging DNA. The architectural proteins are apparently functionally conserved but share neither sequence nor structural similarity (Luijsterburg et al., 2008). In eukaryotes, a massive reduction in volume of the genome is achieved predominantly via the action of having the DNA wrapped around histone complexes at specific regions called histone-fold domains (Luger et al., 1997). In bacteria, several proteins work in tandem to condense the bacterial nucleoid (Azam & Ishihama, 1999;Luijsterburg et al., 2006;Dillon & Dorman, 2010). Some of these proteins, such as the HU protein and histone-like nucleoid structuring protein (HN-S), have histone-like characteristics such as a similar amino acid composition and the ability to condense DNA into a densely packed nucleoid structure upon overexpression of the protein (Rouvière-Yaniv & Gros, 1975; Rouvière-Yaniv et al., 1979; Spurio et al., 1992).Members of the phylum Planctomycetes within the domain Bacteria have many uncommon features, both structural and molecular. All planctomycetes examined display a compartmentalized cell plan as well as a much more condensed nucleoid compared with most other bacteria, and in the case of Gemmata obscuriglobus, the nucleoid is further bounded within a double-membrane envelope (Fuerst & Webb, 1991;Lindsay et al., 2001;Fuerst, 2005). A recent study of G. obscuriglobus has revealed resistance to UV radiation 40 times greater than that of Escherichia coli, and this increased tolerance is proposed to be associated with a highly effective DNA repair mechanism at least partly due to the condensed chromatin structure in this species (Lieber et al., 2009). However, the identity and mechanism of the proteins responsible for the condensation of the nucle...

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Properties of DNA-Binding of HU Heterotypic and Homotypic Dimers from Escherichia coli

Cited by 35 publications

References 0 publications

Twelve Species of the Nucleoid-associated Protein from Escherichia coli

Twelve Species of the Nucleoid-associated Protein from Escherichia coli

Two Fis Regulators Directly Repress the Expression of Numerous Effector-Encoding Genes in Legionella pneumophila

Making heads or tails of the HU proteins in the planctomycete Gemmata obscuriglobus

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