Integration Host Factor: Putting a Twist on Protein–DNA Recognition

Lynch, Thomas W.; Read, Erik K.; Mattis, Aras N.; Gardner, Jeffrey F.; Rice, Phoebe A.

doi:10.1016/s0022-2836(03)00529-1

Cited by 71 publications

(88 citation statements)

References 39 publications

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“…Encoded are replisome components, such as DNA polymerase (encoded by orf137 and orf138), helicase (encoded by orf111), primase (encoded by orf113 and orf117), and a putative sigma factor (encoded orf143). The integration host factor (gp136) is a member of the DNA binding protein family that binds and bends DNA, and is required in many cellular processes, including transcription, recombination, and higher-order nucleoprotein complex assembly (44). Again, significant similarities to products of K, P100, LP65, and others were observed in this cluster ( Fig.…”

Section: Resultsmentioning

confidence: 86%

The Terminally Redundant, Nonpermuted Genome ofListeriaBacteriophage A511: a Model for the SPO1-Like Myoviruses of Gram-Positive Bacteria

et al. 2008

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Only little information on a particular class of myoviruses, the SPO1-like bacteriophages infecting low-G؉C-content, gram-positive host bacteria (Firmicutes), is available. We present the genome analysis and molecular characterization of the large, virulent, broad-host-range Listeria phage A511. A511 contains a unit (informational) genome of 134,494 bp, encompassing 190 putative open reading frames (ORFs) and 16 tRNA genes, organized in a modular fashion common among the Caudovirales. Electron microscopy, enzymatic fragmentation analyses, and sequencing revealed that the A511 DNA molecule contains linear terminal repeats of a total of 3,125 bp, encompassing nine small putative ORFs. This particular genome structure explains why A511 is unable to perform general transduction. A511 features significant sequence homologies to Listeria phage P100 and other morphologically related phages infecting Firmicutes such as Staphylococcus phage K and Lactobacillus phage LP65. Equivalent but more-extensive terminal repeats also exist in phages P100 (ϳ6 kb) and K (ϳ20 kb). High-resolution electron microscopy revealed, for the first time, the presence of long tail fibers organized in a sixfold symmetry in these viruses. Mass spectrometry-based peptide fingerprinting permitted assignment of individual proteins to A511 structural components. On the basis of the data available for A511 and relatives, we propose that SPO1-like myoviruses are characterized by (i) their infection of gram-positive, low-G؉C-content bacteria; (ii) a wide host range within the host bacterial genus and a strictly virulent lifestyle; (iii) similar morphology, sequence relatedness, and collinearity of the phage genome organization; and (iv) large double-stranded DNA genomes featuring nonpermuted terminal repeats of various sizes.Listeria monocytogenes is a gram-positive, opportunistic pathogen that can cause a wide spectrum of diseases, such as meningitis, septicemia, abortion, and gastroenteritis, associated with mortality rates as high as 25 to 30% (17, 62). Listeria bacteria are ubiquitously found in nature and can enter the food chain at many points (26, 66). They are able to proliferate over a wide range of external conditions, including low temperatures and high salt concentrations, thus posing severe problems to the food industry (2,22,15,48).Almost all of the Listeria bacteriophages described to date are temperate (38); only very little is known about virulent phages infecting this host. Listeria phages are valuable sources of biological information and useful tools for the study, differentiation, manipulation, and control of these bacteria (6,33,41). Phage A511 and some of its components have been particularly useful in phage typing schemes (35, 61), as reporter phage (39), with respect to their endolysins (16), and also for the control of Listeria contamination of foods (7; S. Guenther, D. Huwyler, S. Richard, and M. J. Loessner, submitted for publication). In contrast to temperate Listeria phages A118 and PSA (36, 71), A511 is a virulent (i.e., s...

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Section: Resultsmentioning

confidence: 86%

The Terminally Redundant, Nonpermuted Genome ofListeriaBacteriophage A511: a Model for the SPO1-Like Myoviruses of Gram-Positive Bacteria

et al. 2008

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“…Expression and Purification of E. coli IHF␣␤-E. coli IHF␣␤ was purified as described previously (44). The plasmid pET21a IHF, harboring E. coli ihfA and ihfB, was purchased from Addgene (Cambridge, MA) and transformed into E. coli Rosetta2(DE3)pLysS strain.…”

Section: Construction Of M Tuberculosis Mutant Ihf Expressionmentioning

confidence: 99%

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Sharadamma

Harshavardhana

Ravishankar

et al. 2014

Journal of Biological Chemistry

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Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF␣␤. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts.

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“…The preference for ApA steps at both sites of proline intercalation might be explained as due to its energetic preference, relative to other base pair steps, to form the particular kinked conformation found in the complex (41). Recent structural and biochemical analysis of a reduced specificity IHF mutant indicates how the unique, sequence-dependent structure of the TTR element contributes to specificity (42). Thus, pre-formed, sequence-dependent structural characteristics constitute a strong component of recognition for each of the conserved elements (17,18).…”

Section: Discussionmentioning

confidence: 99%

Indirect Recognition in Sequence-specific DNA Binding by Escherichia coli Integration Host Factor

Aeling

Opel

Steffen

et al. 2006

Journal of Biological Chemistry

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Integration host factor (IHF) is a bacterial histone-like protein whose primary biological role is to condense the bacterial nucleoid and to constrain DNA supercoils. It does so by binding in a sequence-independent manner throughout the genome. However, unlike other structurally related bacterial histone-like proteins, IHF has evolved a sequence-dependent, high affinity DNA-binding motif. The high affinity binding sites are important for the regulation of a wide range of cellular processes. A remarkable feature of IHF is that it employs an indirect readout mechanism to bind and wrap DNA at both the nonspecific and high affinity (sequence-dependent) DNA sites. In this study we assessed the contributions of pre-formed and protein-induced DNA conformations to the energetics of IHF binding. Binding energies determined experimentally were compared with energies predicted for the IHF-induced deformation of the DNA helix (DNA deformation energy) in the IHF-DNA complex. Combinatorial sets of de novo DNA sequences were designed to systematically evaluate the influence of sequence-dependent structural characteristics of the conserved IHF recognition elements of the consensus DNA sequence. We show that IHF recognizes pre-formed conformational characteristics of the consensus DNA sequence at high affinity sites, whereas at all other sites relative affinity is determined by the deformational energy required for nearest-neighbor base pairs to adopt the DNA structure of the bound DNA-IHF complex.Site-specific DNA binding by regulatory proteins is a feature of the regulatory processes that maintain, expand, and express genetic information such as replication, recombination, transposition, and transcription. The chemical and physical mechanisms that underlie sequence-specific recognition of regulatory elements by cognate DNA-binding proteins are typically classified as direct versus indirect readout. The former refers primarily to hydrogen bonds between proteins and the unique extra-cyclic substituents at C-4 of pyrimidines, C-6 of purines, and N-7 of purines. These groups provide a base pair-specific pattern of hydrogen bond donors and acceptors in the major groove of DNA that can be directly read by a complementary pattern of amino acid side chain donors and acceptors. Indirect readout refers to recognition of aspects of DNA structure such as intrinsic curvature, topology of major and minor grooves, ordered water structures, local geometry of backbone phosphates, and flexibility or deformability. Because both the local DNA structure and energy to deform DNA are themselves intrinsic sequence-dependent properties, the conserved sequences that distinguish binding sites necessarily include contributions from both direct and indirect mechanisms. Consequently, although the contribution from indirect mechanisms is expected to be significant in protein-DNA complexes that feature substantial DNA deformation, it has proven difficult to evaluate these contributions quantitatively. A protein that relies exclusively, or primarily, on indir...

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Integration Host Factor: Putting a Twist on Protein–DNA Recognition

Cited by 71 publications

References 39 publications

The Terminally Redundant, Nonpermuted Genome ofListeriaBacteriophage A511: a Model for the SPO1-Like Myoviruses of Gram-Positive Bacteria

The Terminally Redundant, Nonpermuted Genome ofListeriaBacteriophage A511: a Model for the SPO1-Like Myoviruses of Gram-Positive Bacteria

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Indirect Recognition in Sequence-specific DNA Binding by Escherichia coli Integration Host Factor

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