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Talyzina AA, Agapova YK, Podshivalov DD, Timofeev VI, Sidorov-Biryukov DD, Rakitina TV. Application of virtual screening and molecular dynamics for the analysis of selectivity of inhibitors of HU proteins targeted to the DNA-recognition site. CRYSTALLOGR REP+ 2017. [DOI: 10.1134/s1063774517060244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kamashev D, Agapova Y, Rastorguev S, Talyzina AA, Boyko KM, Korzhenevskiy DA, Vlaskina A, Vasilov R, Timofeev VI, Rakitina TV. Comparison of histone-like HU protein DNA-binding properties and HU/IHF protein sequence alignment. PLoS One 2017; 12:e0188037. [PMID: 29131864 PMCID: PMC5683647 DOI: 10.1371/journal.pone.0188037] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/12/2017] [Indexed: 12/12/2022] Open
Abstract
Background The 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 findings Performed 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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Affiliation(s)
- Dmitri Kamashev
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
- * E-mail:
| | - Yulia Agapova
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
| | - Sergey Rastorguev
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
| | - Anna A. Talyzina
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Konstantin M. Boyko
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry A. Korzhenevskiy
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
| | - Anna Vlaskina
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
| | - Raif Vasilov
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
| | - Vladimir I. Timofeev
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
- Federal Scientific Research Center “Crystallography and Photonics”, RAS, Moscow, Russian Federation
| | - Tatiana V. Rakitina
- Kurchatov Complex of NBICS-Technologies, National Research Center «Kurchatov Institute», Moscow, Russian Federation
- Shemyakin&Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russian Federation
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DNA-RNA interactions are critical for chromosome condensation in Escherichia coli. Proc Natl Acad Sci U S A 2017; 114:12225-12230. [PMID: 29087325 DOI: 10.1073/pnas.1711285114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial chromosome (nucleoid) conformation dictates faithful regulation of gene transcription. The conformation is condition-dependent and is guided by several nucleoid-associated proteins (NAPs) and at least one nucleoid-associated noncoding RNA, naRNA4. Here we investigated the molecular mechanism of how naRNA4 and the major NAP, HU, acting together organize the chromosome structure by establishing multiple DNA-DNA contacts (DNA condensation). We demonstrate that naRNA4 uniquely acts by forming complexes that may not involve long stretches of DNA-RNA hybrid. Also, uncommonly, HU, a chromosome-associated protein that is essential in the DNA-RNA interactions, is not present in the final complex. Thus, HU plays a catalytic (chaperone) role in the naRNA4-mediated DNA condensation process.
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Structural basis of the high thermal stability of the histone-like HU protein from the mollicute Spiroplasma melliferum KC3. Sci Rep 2016; 6:36366. [PMID: 27808161 PMCID: PMC5093408 DOI: 10.1038/srep36366] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/13/2016] [Indexed: 02/07/2023] Open
Abstract
The three-dimensional structure of the histone-like HU protein from the mycoplasma Spiroplasma melliferum KC3 (HUSpm) was determined at 1.4 Å resolution, and the thermal stability of the protein was evaluated by differential scanning calorimetry. A detailed analysis revealed that the three-dimensional structure of the HUSpm dimer is similar to that of its bacterial homologues but is characterized by stronger hydrophobic interactions at the dimer interface. This HUSpm dimer interface lacks salt bridges but is stabilized by a larger number of hydrogen bonds. According to the DSC data, HUSpm has a high denaturation temperature, comparable to that of HU proteins from thermophilic bacteria. To elucidate the structural basis of HUSpm thermal stability, we identified amino acid residues potentially responsible for this property and modified them by site-directed mutagenesis. A comparative analysis of the melting curves of mutant and wild-type HUSpm revealed the motifs that play a key role in protein thermal stability: non-conserved phenylalanine residues in the hydrophobic core, an additional hydrophobic loop at the N-terminal region of the protein, the absence of the internal cavity present at the dimer interface of some HU proteins, and the presence of additional hydrogen bonds between the monomers that are missing in homologous proteins.
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Samoilova EO, Krasheninnikov IA, Vinogradova EN, Kamenski PA, Levitskii SA. Binding of DNA with Abf2p increases efficiency of DNA uptake by isolated mitochondria. BIOCHEMISTRY (MOSCOW) 2016; 81:723-30. [DOI: 10.1134/s0006297916070087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Nikolaeva AY, Timofeev VI, Boiko KM, Korzhenevskii DA, Rakitina TV, Dorovatovskii PV, Lipkin AV. Isolation, purification, crystallization, and preliminary X-ray diffraction study of the crystals of HU protein from M. gallisepticum. CRYSTALLOGR REP+ 2015. [DOI: 10.1134/s1063774515060231] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Vanyushkina AA, Fisunov GY, Gorbachev AY, Kamashev DE, Govorun VM. Metabolomic analysis of three Mollicute species. PLoS One 2014; 9:e89312. [PMID: 24595068 PMCID: PMC3942410 DOI: 10.1371/journal.pone.0089312] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 01/22/2014] [Indexed: 01/19/2023] Open
Abstract
We present a systematic study of three bacterial species that belong to the class Mollicutes, the smallest and simplest bacteria, Spiroplasma melliferum, Mycoplasma gallisepticum, and Acholeplasma laidlawii. To understand the difference in the basic principles of metabolism regulation and adaptation to environmental conditions in the three species, we analyzed the metabolome of these bacteria. Metabolic pathways were reconstructed using the proteogenomic annotation data provided by our lab. The results of metabolome, proteome and genome profiling suggest a fundamental difference in the adaptation of the three closely related Mollicute species to stress conditions. As the transaldolase is not annotated in Mollicutes, we propose variants of the pentose phosphate pathway catalyzed by annotated enzymes for three species. For metabolite detection we employed high performance liquid chromatography coupled with mass spectrometry. We used liquid chromatography method - hydrophilic interaction chromatography with silica column - as it effectively separates highly polar cellular metabolites prior to their detection by mass spectrometer.
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Affiliation(s)
| | - Gleb Y. Fisunov
- Russian Institute of Physico-Chemical Medicine, Moscow, Russian Federation
| | | | - Dmitri E. Kamashev
- Russian Institute of Physico-Chemical Medicine, Moscow, Russian Federation
- Russian Research Center Kurchatov Institute, Moscow, Russian Federation
- * E-mail:
| | - Vadim M. Govorun
- Russian Institute of Physico-Chemical Medicine, Moscow, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russian Federation
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Gorbachev AY, Fisunov GY, Izraelson M, Evsyutina DV, Mazin PV, Alexeev DG, Pobeguts OV, Gorshkova TN, Kovalchuk SI, Kamashev DE, Govorun VM. DNA repair in Mycoplasma gallisepticum. BMC Genomics 2013; 14:726. [PMID: 24148612 PMCID: PMC4007778 DOI: 10.1186/1471-2164-14-726] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 10/15/2013] [Indexed: 01/04/2023] Open
Abstract
Background DNA repair is essential for the maintenance of genome stability in all living beings. Genome size as well as the repertoire and abundance of DNA repair components may vary among prokaryotic species. The bacteria of the Mollicutes class feature a small genome size, absence of a cell wall, and a parasitic lifestyle. A small number of genes make Mollicutes a good model for a “minimal cell” concept. Results In this work we studied the DNA repair system of Mycoplasma gallisepticum on genomic, transcriptional, and proteomic levels. We detected 18 out of 22 members of the DNA repair system on a protein level. We found that abundance of the respective mRNAs is less than one per cell. We studied transcriptional response of DNA repair genes of M. gallisepticum at stress conditions including heat, osmotic, peroxide stresses, tetracycline and ciprofloxacin treatment, stationary phase and heat stress in stationary phase. Conclusions Based on comparative genomic study, we determined that the DNA repair system M. gallisepticum includes a sufficient set of proteins to provide a cell with functional nucleotide and base excision repair and mismatch repair. We identified SOS-response in M. gallisepticum on ciprofloxacin, which is a known SOS-inducer, tetracycline and heat stress in the absence of established regulators. Heat stress was found to be the strongest SOS-inducer. We found that upon transition to stationary phase of culture growth transcription of DNA repair genes decreases dramatically. Heat stress does not induce SOS-response in a stationary phase.
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Affiliation(s)
- Alexey Y Gorbachev
- Research Institute of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, Moscow 119992, Russian Federation.
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Vanyushkina AA, Kamashev DE, Altukhov IA, Govorun VM. Identification of intracellular Spiroplasma melliferum metabolites by the HPLC-MS method. BIOCHEMISTRY (MOSCOW) 2013; 77:864-77. [PMID: 22860908 DOI: 10.1134/s000629791208007x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In contrast to the abundance of systems-oriented approaches describing changes on the transcriptome or proteome level, relatively few studies have employed the metabolome. The goal of the presented research was to identify as many intracellular metabolites as possible in a Spiroplasma melliferum extract by flow injection time-of-flight mass spectrometry. The Mollicutes class bacterium S. melliferum is a member of a unique category of bacteria that have in common the absence of a cell wall, a reduced genome, and simplified metabolic pathways. Metabolite identification was confirmed by fragmentation of previously detected ions by target mass spectrometry. The selected liquid chromatography approach, hydrophilic interaction chromatography with amino and silica columns, effectively separates highly polar cellular metabolites prior to their detection on a high accuracy mass spectrometer in positive and negative acquisition mode for each column. Here we present reliable measurement of 76 metabolites, including components of sugar, amino acid, and nucleotide metabolism. We have identified about a third of the possible intracellular S. melliferum metabolites predicted by genome annotation.
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Affiliation(s)
- A A Vanyushkina
- Russian Research Center Kurchatov Institute, pl. Akademika Kurchatova 1, 123182 Moscow, Russia.
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Li F, Weber DK, Morgan JL, Collins JG, Keene FR. An approach to therapeutic agents through selective targeting of destabilised nucleic acid duplex sequences. Dalton Trans 2012; 41:6528-35. [PMID: 22311066 DOI: 10.1039/c2dt12146h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The binding of ΔΔ/ΛΛ-[{Ru(phen)(2)}(2)(μ-bb(n))](4+) {where phen = 1,10-phenanthroline, bb(n) = 1,n-bis[4(4'-methyl-2,2'-bipyridyl)]-alkane (ΔΔ/ΛΛ-Rubb(n))} to the non-self complementary oligonucleotide 5'-d(CGCGATAAGCCGC·5'-GCGGCATTACGCG) (3-DB) has been examined using a 4',6-diamidino-2-phenylindole dihydrochloride (DAPI) displacement assay. The 3-DB oligonucleotide contains two single adenine bulge nucleotides that are separated by three base pairs. (1)H NMR spectroscopy data demonstrated that the adenine bases are intra-helical and that the segment containing the two bulge nucleotides and the three A·T base pairs between the bulges forms a destabilised segment within the stable duplex oligonucleotide. The DAPI displacement assay demonstrated that ΔΔ-Rubb(7)-bound 3-DB with higher affinity than the other members of the ΔΔ/ΛΛ-Rubb(n) series. Molecular models suggested that the seven-carbon chain length in ΔΔ-Rubb(7) was ideal to span the distance between the two bulge sites. The binding of ΔΔ-Rubb(7) to 3-DB was also studied by (1)H NMR spectroscopy and molecular modelling. The selective changes in chemical shifts for the resonances from 3-DB upon addition of ΔΔ-Rubb(7) suggested that the metal complex specifically bound at the destabilised segment between A(5) and A(19). Observation in NOESY spectra of NOE cross peaks between 3-DB and ΔΔ-Rubb(7) confirmed that one of the ruthenium centres bound at the A(5) bulge site, with the other metal centre positioned at the A(19) bulge. In addition, ΔΔ-Rubb(7) was found to bind chromosomal DNA extracted from a suspension of Staphylococcus aureus that had been incubated with the ruthenium(ii) complex. As inert dinuclear ruthenium(ii) complexes are capable of being transported into a bacterial cell and bind chromosomal DNA, it is possible that they could be developed into anti-microbial agents that specifically target destabilised segments of DNA that are recognised by essential DNA-binding proteins.
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Affiliation(s)
- Fangfei Li
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales, Australian Defence Force Academy, Canberra, ACT 2600, Australia
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Kamashev D, Oberto J, Serebryakova M, Gorbachev A, Zhukova Y, Levitskii S, Mazur AK, Govorun V. Mycoplasma gallisepticum Produces a Histone-like Protein That Recognizes Base Mismatches in DNA. Biochemistry 2011; 50:8692-702. [DOI: 10.1021/bi2009097] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dmitri Kamashev
- Research Institute for Physico-Chemical Medicine, Moscow
119435, Russia
- National Research Centre Kurchatov Institute, Moscow, 123182, Russia
| | - Jacques Oberto
- Institut
de Génétique et Microbiologie, CNRS UMR 8621, Université Paris XI, Paris, France
| | | | - Alexey Gorbachev
- Research Institute for Physico-Chemical Medicine, Moscow
119435, Russia
| | - Yulia Zhukova
- Research Institute for Physico-Chemical Medicine, Moscow
119435, Russia
| | - Sergei Levitskii
- Research Institute for Physico-Chemical Medicine, Moscow
119435, Russia
- National Research Centre Kurchatov Institute, Moscow, 123182, Russia
| | - Alexey K. Mazur
- UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut
de Biologie Physico-Chimique, 13, rue Pierre et Marie Curie, Paris
75005, France
| | - Vadim Govorun
- Research Institute for Physico-Chemical Medicine, Moscow
119435, Russia
- National Research Centre Kurchatov Institute, Moscow, 123182, Russia
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Sharadamma N, Khan K, Kumar S, Patil KN, Hasnain SE, Muniyappa K. Synergy between the N-terminal and C-terminal domains of Mycobacterium tuberculosis HupB is essential for high-affinity binding, DNA supercoiling and inhibition of RecA-promoted strand exchange. FEBS J 2011; 278:3447-62. [PMID: 21787377 DOI: 10.1111/j.1742-4658.2011.08267.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The occurrence of DNA architectural proteins containing two functional domains derived from two different architectural proteins is an interesting emerging research theme in the field of nucleoid structure and function. Mycobacterium tuberculosis HupB, unlike Escherichia coli HU, is a two-domain protein that, in the N-terminal region, shows broad sequence homology with bacterial HU. The long C-terminal extension, on the other hand, contains seven PAKK/KAAK motifs, which are characteristic of the histone H1/H5 family of proteins. In this article, we describe several aspects of HupB function, in comparison with its truncated derivatives lacking either the C-terminus or N-terminus. We found that HupB binds a variety of DNA repair and replication intermediates with K(d) values in the nanomolar range. By contrast, the N-terminal fragment of M. tuberculosis HupB (HupB(MtbN)) showed diminished DNA-binding activity, with K(d) values in the micromolar range, and the C-terminal domain was completely devoid of DNA-binding activity. Unlike HupB(MtbN) , HupB was able to constrain DNA in negative supercoils and introduce negative superhelical turns into relaxed DNA. Similarly, HupB exerted a robust inhibitory effect on DNA strand exchange promoted by cognate and noncognate RecA proteins, whereas HupB(MtbN), even at a 50-fold molar excess, had no inhibitory effect. Considered together, these results suggest that synergy between the N-terminal and C-terminal domains of HupB is essential for its DNA-binding ability, and to modulate the topological features of DNA, which has implications for processes such as DNA compaction, gene regulation, homologous recombination, and DNA repair.
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Affiliation(s)
- N Sharadamma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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