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Schwab S, Hu Y, van Erp B, Cajili MKM, Hartmann MD, Hernandez Alvarez B, Alva V, Boyle AL, Dame RT. Histones and histone variant families in prokaryotes. Nat Commun 2024; 15:7950. [PMID: 39261503 PMCID: PMC11390915 DOI: 10.1038/s41467-024-52337-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/30/2024] [Indexed: 09/13/2024] Open
Abstract
Histones are important chromatin-organizing proteins in eukaryotes and archaea. They form superhelical structures around which DNA is wrapped. Recent studies have shown that some archaea and bacteria contain alternative histones that exhibit different DNA binding properties, in addition to highly divergent sequences. However, the vast majority of these histones are identified in metagenomes and thus are difficult to study in vivo. The recent revolutionary breakthroughs in computational protein structure prediction by AlphaFold2 and RoseTTAfold allow for unprecedented insights into the potential function and structure of previously uncharacterized proteins. Here, we categorize the prokaryotic histone space into 17 distinct groups based on AlphaFold2 predictions. We identify a superfamily of histones, termed α3 histones, which are common in archaea and present in several bacteria. Importantly, we establish the existence of a large family of histones throughout archaea and in some bacteriophages that, instead of wrapping DNA, bridge DNA, thereby diverging from conventional nucleosomal histones.
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Affiliation(s)
- Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Yimin Hu
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Bert van Erp
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Marc K M Cajili
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Birte Hernandez Alvarez
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Aimee L Boyle
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
- School of Chemistry, University of Bristol, Bristol, UK
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands.
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands.
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Mukherjee A, Bhattacharyya G, Grove A. The C-Terminal Domain of HU-Related Histone-like Protein Hlp from Mycobacterium smegmatis Mediates DNA End-Joining. Biochemistry 2008; 47:8744-53. [DOI: 10.1021/bi800010s] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Anirban Mukherjee
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Gargi Bhattacharyya
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803
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Vitko J, Rujan I, Androga L, Mukerji I, Bolton PH. Molecular beacon-equilibrium cyclization detection of DNA-protein complexes. Biophys J 2007; 93:3210-7. [PMID: 17631534 PMCID: PMC2025667 DOI: 10.1529/biophysj.106.097642] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular beacon detection of equilibrium cyclization (MBEC) is a novel, high sensitivity technique that can allow DNA-protein complex formation to be studied under diverse conditions in a cost effective and rapid manner that can be adapted to high throughput screening. To demonstrate the ease and utility of applying MBEC to the investigation of the K(D) values of protein-DNA complexes, the sequence-specific Escherichia coli integration host factor (IHF) protein has been used as a test system. Competition between a labeled MBEC DNA construct and unlabeled duplex DNA for IHF binding allows the determination of K(D) values as a function of the DNA duplex sequence. This allows sequence specificity to be monitored while using only a single molecular beacon-labeled DNA. The robustness of MBEC for monitoring protein-DNA complex formation has been further demonstrated by determining the K(D) values as a function of salt concentration to investigate the net number of salt bridges formed in sequence-specific and -nonspecific IHF-DNA complexes. These MBEC results have been compared with those from other approaches.
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Affiliation(s)
- Jason Vitko
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459, USA
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4
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Wojtuszewski K, Mukerji I. The HU-DNA binding interaction probed with UV resonance Raman spectroscopy: structural elements of specificity. Protein Sci 2005; 13:2416-28. [PMID: 15322284 PMCID: PMC2280020 DOI: 10.1110/ps.04730204] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The Escherichia coli protein HU functions as an architectural DNA-binding protein by facilitating DNA looping or bending to form multiprotein complexes. Although HU does not recognize a specific DNA sequence, site-specific binding to a number of discontinuous, looped, or bent DNA substrates has been observed. In this study UV resonance Raman (UVRR) spectroscopy is used to identify structural elements associated with low- and high-affinity binding by examining three different HU-DNA complexes. UVRR spectra obtained with an excitation wavelength of 210 nm, which preferentially enhances protein backbone amide vibrations, indicate that HU secondary structure content increases and the protein structure becomes more rigid upon binding to DNA. The increase in alpha-helical content is attributed to the C-terminal helix, which interacts with the DNA and may play a role in binding affinity and specificity. UVRR spectra obtained with a 215 nm excitation wavelength demonstrate that Pro mode intensity at 1455 cm(-1) decreases upon complex formation. This intensity decrease is attributed to the intercalation of Pro residues between DNA base pairs to induce a bend in the DNA, as has been observed previously in the IHF-DNA and HU-DNA cocrystal structures. DNA vibrational modes are also indicative of significant base unstacking and opening of the minor groove upon protein binding, consistent with bending and distortion of the DNA. In all three complexes, A-DNA conformational features are indicated by deoxyribose-phosphate backbone modes. These and other results suggest that protein-induced bending plays an important role in HU site-specific binding and supports a model of a mutually induced fit.
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Affiliation(s)
- Kristi Wojtuszewski
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT 06459-0175, USA
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Read EK, Gumport RI, Gardner JF. Specific recognition of DNA by integration host factor. Glutamic acid 44 of the beta-subunit specifies the discrimination of a T:A from an A:T base pair without directly contacting the DNA. J Biol Chem 2000; 275:33759-64. [PMID: 10930420 DOI: 10.1074/jbc.m910381199] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Integration host factor (IHF) is a protein that binds to the H' site of bacteriophage lambda with sequence specificity. Genetic experiments implicated amino acid residue Glu(44) of the beta-subunit of IHF in discrimination against substitution of A for T at position 44 of the TTR submotif of the binding site (Lee, E. C., Hales, L. M., Gumport, R. I., Gardner, J. F. (1992) EMBO J., 11, 305-313). We have extended this observation by generating all possible single-base substitutions at positions 43, 44, and 45 of the H' site. IHF failed to bind these H' site substitution mutants in vivo. The K(d)(app) value for each H' site substitution, except for H'45A mutant, was reduced >2000-fold relative to the wild-type site. Substitution of amino acid beta-Glu(44) with alanine prevented IHF from discriminating against the H'44A variant but not the other H' site substitution mutants. Further analysis with other substitutions at position beta44 demonstrated that both oxygens of the wild-type glutamic acid are necessary for discrimination of AT at position 44. Because the beta-Glu(44) residue does not contact the DNA, this residue probably enforces binding specificity indirectly through interaction with amino acids that themselves contact the DNA.
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Affiliation(s)
- E K Read
- Departments of Microbiology and Biochemistry and College of Medicine, University of Illinois, Urbana, Illinois 61801, USA
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Sojda J, Gu B, Lee J, Hoover TR, Nixon BT. A rhizobial homolog of IHF stimulates transcription of dctA in Rhizobium leguminosarum but not in Sinorhizobium meliloti. Gene 1999; 238:489-500. [PMID: 10570977 DOI: 10.1016/s0378-1119(99)00366-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Sequence inspection identified several potential IHF binding sites adjacent to the Rhizobium leguminosarum dctA promoter. IHF protected the -30 to -76 region from DNase I digestion, but systematic error in quantitative assays suggested that this protein DNA interaction is complex. IHF stimulated DctD-mediated transcriptional activation from the R. leguminosarum dctA promoter both in vivo and in vitro. In contrast to R. leguminosarum dctA, the Sinorhizobium meliloti dctA promoter region was found to have a much weaker match to the consensus IHF binding site and a low affinity for IHF. Moreover, IHF had no effect on transcriptional activation from the S. meliloti dctA promoter in vitro. A base substitution was introduced into the IHF binding site of R. leguminosarum dtA that reduced the affinity of the promoter regulatory region for IHF by approximately 30-fold and resulted in an eight-fold decrease in transcriptional activation in both R. leguminosarum and S. meliloti. These data suggest that both rhizobial species have an IHF homolog that stimulates DctD-mediated transcriptional activation from the R. leguminosarum dctA promoter. Consistent with this hypothesis, a 12.5 kDa protein was identified from R. leguminosarum as a putative homolog of IHF subunit beta by immunoblotting and N-terminal sequence analysis.
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Affiliation(s)
- J Sojda
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802, USA
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van Ulsen P, Hillebrand M, Zulianello L, van de Putte P, Goosen N. The integration host factor-DNA complex upstream of the early promoter of bacteriophage Mu is functionally symmetric. J Bacteriol 1997; 179:3073-5. [PMID: 9139933 PMCID: PMC179079 DOI: 10.1128/jb.179.9.3073-3075.1997] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Inversion of the ihf site in the promoter region of the early promoter of bacteriophage Mu did not influence the integration host factor (IHF)-mediated functions. IHF bound to this inverted site could counteract H-NS-mediated repression, directly activate transcription, and support lytic growth of bacteriophage Mu. This implies that the IHF heterodimer and its asymmetrical binding site form a functionally symmetrical complex.
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Affiliation(s)
- P van Ulsen
- Laboratory of Molecular Genetics, Leiden University, The Netherlands
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Abstract
IHF and HU belong to a family of proteins that introduce sharp bends into DNA and act as accessory factors in a variety of cellular processes in prokaryotes. In addition to the crystal structure of IHF bound to DNA, the past year has seen a number of advances in the understanding of the interactions of these proteins with DNA in solution.
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Affiliation(s)
- P A Rice
- Laboratory of Molecular Biology, National Institute of Digestive, Diabetes and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892-0540, USA.
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Abstract
Integration host factor (IHF) is a small heterodimeric protein that specifically binds to DNA and functions as an architectural factor in many cellular processes in prokaryotes. Here, we report the crystal structure of IHF complexed with 35 bp of DNA. The DNA is wrapped around the protein and bent by >160 degrees, thus reversing the direction of the helix axis within a very short distance. Much of the bending occurs at two large kinks where the base stacking is interrupted by intercalation of a proline residue. IHF contacts the DNA exclusively via the phosphodiester backbone and the minor groove and relies heavily on indirect readout to recognize its binding sequence. One such readout involves a six-base A tract, providing evidence for the importance of a narrow minor groove.
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Affiliation(s)
- P A Rice
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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van Ulsen P, Hillebrand M, Zulianello L, van de Putte P, Goosen N. Integration host factor alleviates the H-NS-mediated repression of the early promoter of bacteriophage Mu. Mol Microbiol 1996; 21:567-78. [PMID: 9082117 DOI: 10.1111/j.1365-2958.1996.tb02565.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Integration host factor (IHF), which is a histone-like protein, has been shown to positively regulate transcription in two different ways. It can either help the formation of a complex between a transcription factor and RNA polymerase or it can itself activate RNA polymerase without the involvement of other transcription factors. In this study, we present a third mechanism for IHF-stimulated gene expression, by counteracting the repression by another histone-like protein, H-NS. The early (Pe) promoter of bacteriophage Mu is specifically inhibited by H-NS, both in vivo and in vitro. For this inhibition, H-NS binds to a large DNA region overlapping the Pe promoter. Binding of IHF to a binding site just upstream of Pe alleviates the H-NS-mediated repression of transcription. This same ihf site is also involved in the direct activation of Pe by IHF. In contrast to the direct activation by IHF, however, the alleviating effect of IHF appears not to be dependent on the relevant position of the ihf site on the DNA helix, and it also does not require the presence of the C-terminal domain of the alpha subunit of RNA polymerase. Footprint analysis shows that binding of IHF to the ihf site destabilizes the interaction of H-NS with the DNA, not only in the IHF-binding region but also in the DNA regions flanking the ihf site. These results suggest that IHF disrupts a higher-order nucleoprotein complex that is formed by H-NS and the DNA.
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Affiliation(s)
- P van Ulsen
- Laboratory of Molecular Genetics, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, The Netherlands
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Goosen N, van Ulsen P, Zulianello L, van de Putte P. Transcription activation by histone-like protein integration host factor. Methods Enzymol 1996; 274:32-43. [PMID: 8902794 DOI: 10.1016/s0076-6879(96)74006-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- N Goosen
- Laboratory of Molecular Genetics, Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, The Netherlands
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