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Yella VR, Vanaja A. Computational analysis on the dissemination of non-B DNA structural motifs in promoter regions of 1180 cellular genomes. Biochimie 2023; 214:101-111. [PMID: 37311475 DOI: 10.1016/j.biochi.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/05/2023] [Accepted: 06/05/2023] [Indexed: 06/15/2023]
Abstract
The promoter regions of gene regulation are under evolutionary constraints and earlier studies uncovered that they are characterized by enrichment of functional non-B DNA structural signatures like curved DNA, cruciform DNA, G-quadruplex, triple-helical DNA, slipped DNA structures, and Z-DNA. However, these studies are restricted to a few model organisms, single non-B DNA motif types, or whole genomic sequences, and their comparative accumulation in promoter regions of different domains of life has not been reported comprehensively. In this study, for the first time, we investigated the preponderance of non-B DNA-prone motifs in promoter regions in 1180 genomes belonging to 28 taxonomic groups using the non-B DNA Motif Search Tool (nBMST). The trends suggest that they are predominant in promoters compared to the upstream and downstream regions of all three domains of life and variably linked to taxonomic groups. Cruciform DNA motif is the most abundant form of non-B DNA, spanning from archaea to lower eukaryotes. Curved DNA motifs are prominent in host-associated bacteria, and suppressed in mammals. Triplex-DNA and slipped DNA structure repeats are discretely dispersed in all lineages. G-quadruplex motifs are significantly enriched in mammals. We also observed that the unique enrichment of non-B DNA in promoters is strongly linked to genome GC, size, evolutionary time divergence, and ecological adaptations. Overall, our work systematically reports the unique non-B DNA structural landscape of cellular organisms from the perspective of the cis-regulatory code of genomes.
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Affiliation(s)
- Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India.
| | - Akkinepally Vanaja
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India; KL College of Pharmacy, Koneru Lakshmaiah Education Foundation, Guntur, 522302, Andhra Pradesh, India
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2
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Amodeo S, Bregy I, Ochsenreiter T. Mitochondrial genome maintenance-the kinetoplast story. FEMS Microbiol Rev 2023; 47:fuac047. [PMID: 36449697 PMCID: PMC10719067 DOI: 10.1093/femsre/fuac047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/13/2022] [Accepted: 11/24/2022] [Indexed: 12/17/2023] Open
Abstract
Mitochondrial DNA replication is an essential process in most eukaryotes. Similar to the diversity in mitochondrial genome size and organization in the different eukaryotic supergroups, there is considerable diversity in the replication process of the mitochondrial DNA. In this review, we summarize the current knowledge of mitochondrial DNA replication and the associated factors in trypanosomes with a focus on Trypanosoma brucei, and provide a new model of minicircle replication for this protozoan parasite. The model assumes the mitochondrial DNA (kinetoplast DNA, kDNA) of T. brucei to be loosely diploid in nature and the replication of the genome to occur at two replication centers at the opposing ends of the kDNA disc (also known as antipodal sites, APS). The new model is consistent with the localization of most replication factors and in contrast to the current model, it does not require the assumption of an unknown sorting and transport complex moving freshly replicated DNA to the APS. In combination with the previously proposed sexual stages of the parasite in the insect vector, the new model provides a mechanism for maintenance of the mitochondrial genetic diversity.
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Affiliation(s)
- Simona Amodeo
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland
| | - Irina Bregy
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland
| | - Torsten Ochsenreiter
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland
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3
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Yilmaz IC, Dunuroglu E, Ayanoglu IC, Ipekoglu EM, Yildirim M, Girginkardesler N, Ozbel Y, Toz S, Ozbilgin A, Aykut G, Gursel I, Gursel M. Leishmania kinetoplast DNA contributes to parasite burden in infected macrophages: Critical role of the cGAS-STING-TBK1 signaling pathway in macrophage parasitemia. Front Immunol 2022; 13:1007070. [PMID: 36405710 PMCID: PMC9667060 DOI: 10.3389/fimmu.2022.1007070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Leishmania parasites harbor a unique network of circular DNA known as kinetoplast DNA (kDNA). The role of kDNA in leishmania infections is poorly understood. Herein, we show that kDNA delivery to the cytosol of Leishmania major infected THP-1 macrophages provoked increased parasite loads when compared to untreated cells, hinting at the involvement of cytosolic DNA sensors in facilitating parasite evasion from the immune system. Parasite proliferation was significantly hindered in cGAS- STING- and TBK-1 knockout THP-1 macrophages when compared to wild type cells. Nanostring nCounter gene expression analysis on L. major infected wild type versus knockout cells revealed that some of the most upregulated genes including, Granulysin (GNLY), Chitotriosidase-1 (CHIT1), Sialomucin core protein 24 (CD164), SLAM Family Member 7 (SLAMF7), insulin-like growth factor receptor 2 (IGF2R) and apolipoprotein E (APOE) were identical in infected cGAS and TBK1 knockout cells, implying their involvement in parasite control. Amlexanox treatment (a TBK1 inhibitor) of L. major infected wild type cells inhibited both the percentage and the parasite load of infected THP-1 cells and delayed footpad swelling in parasite infected mice. Collectively, these results suggest that leishmania parasites might hijack the cGAS-STING-TBK1 signaling pathway to their own advantage and the TBK1 inhibitor amlexanox could be of interest as a candidate drug in treatment of cutaneous leishmaniasis.
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Affiliation(s)
- Ismail Cem Yilmaz
- Basic and Translational Research Program, Izmir Biomedicine and Genome Center, Izmir, Turkey
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Emre Dunuroglu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ihsan Cihan Ayanoglu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Emre Mert Ipekoglu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Muzaffer Yildirim
- Molecular Biology and Genetics Department, Bilkent University, Ankara, Turkey
| | - Nogay Girginkardesler
- Department of Parasitology, School of Medicine, Celal Bayar University, Manisa, Turkey
| | - Yusuf Ozbel
- Department of Parasitology, Ege University, Izmir, Turkey
| | - Seray Toz
- Department of Parasitology, Ege University, Izmir, Turkey
| | - Ahmet Ozbilgin
- Department of Parasitology, School of Medicine, Celal Bayar University, Manisa, Turkey
| | - Gamze Aykut
- Molecular Biology and Genetics Department, Bilkent University, Ankara, Turkey
| | - Ihsan Gursel
- Basic and Translational Research Program, Izmir Biomedicine and Genome Center, Izmir, Turkey
- Molecular Biology and Genetics Department, Bilkent University, Ankara, Turkey
| | - Mayda Gursel
- Basic and Translational Research Program, Izmir Biomedicine and Genome Center, Izmir, Turkey
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- *Correspondence: Mayda Gursel,
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4
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Cooper S, Wadsworth ES, Schnaufer A, Savill NJ. Organization of minicircle cassettes and guide RNA genes in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2022; 28:972-992. [PMID: 35414587 PMCID: PMC9202587 DOI: 10.1261/rna.079022.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Mitochondrial DNA of protists of order Kinetoplastida comprises thousands of interlinked circular molecules arranged in a network. There are two types of molecules called minicircles and maxicircles. Minicircles encode guide RNA (gRNA) genes whose transcripts mediate post-transcriptional editing of maxicircle encoded genes. Minicircles are diverse. The human sleeping sickness parasite Trypanosoma brucei has one of the most diverse sets of minicircle classes of all studied trypanosomatids with hundreds of different classes, each encoding one to four genes mainly within cassettes framed by 18 bp inverted repeats. A third of cassettes have no identifiable gRNA genes even though their sequence structures are similar to cassettes with identifiable genes. Only recently have almost all minicircle classes for some subspecies and isolates of T. brucei been sequenced and annotated with corresponding verification of gRNA expression by small-RNA transcriptome data. These data sets provide a rich resource for understanding the structure of minicircle classes, cassettes and gRNA genes and their transcription. Here, we provide a statistical description of the functionality, expression status, structure and sequence of gRNA genes in a differentiation-competent, laboratory-adapted strain of T. brucei We obtain a clearer definition of what is a gRNA gene. Our analysis supports the idea that many, if not all, cassettes without an identifiable gRNA gene contain decaying remnants of once functional gRNA genes. Finally, we report several new, unexplained discoveries such as the association between cassette position on the minicircle and gene expression and functionality, and the association between gene initiation sequence and anchor position.
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Affiliation(s)
- Sinclair Cooper
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, Scotland EH9 3FL, United Kingdom
| | - Elizabeth S Wadsworth
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, Scotland EH9 3FL, United Kingdom
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, Scotland EH9 3FL, United Kingdom
| | - Nicholas J Savill
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, Scotland EH9 3FL, United Kingdom
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Young RT, Czapla L, Wefers ZO, Cohen BM, Olson WK. Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration. LIFE (BASEL, SWITZERLAND) 2022; 12:life12050759. [PMID: 35629425 PMCID: PMC9146901 DOI: 10.3390/life12050759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/13/2022] [Accepted: 05/15/2022] [Indexed: 11/24/2022]
Abstract
DNA carries more than the list of biochemical ingredients that drive the basic functions of living systems. The sequence of base pairs includes a multitude of structural and energetic signals, which determine the degree to which the long, threadlike molecule moves and how it responds to proteins and other molecules that control its processing and govern its packaging. The chemical composition of base pairs directs the spatial disposition and fluctuations of successive residues. The observed arrangements of these moieties in high-resolution protein–DNA crystal structures provide one of the best available estimates of the natural, sequence-dependent structure and deformability of the double-helical molecule. Here, we update the set of knowledge-based elastic potentials designed to describe the observed equilibrium structures and configurational fluctuations of the ten unique base-pair steps. The large number of currently available structures makes it possible to characterize the configurational preferences of the DNA base-pair steps within the context of their immediate neighbors, i.e., tetrameric context. Use of these knowledge-based potentials shows promise in accounting for known effects of sequence in long chain molecules, e.g., the degree of curvature reported in classic gel mobility studies and the recently reported sequence-dependent responses of supercoiled minicircles to nuclease cleavage.
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Affiliation(s)
- Robert T. Young
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.T.Y.); (L.C.); (Z.O.W.); (B.M.C.)
| | - Luke Czapla
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.T.Y.); (L.C.); (Z.O.W.); (B.M.C.)
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zoe O. Wefers
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.T.Y.); (L.C.); (Z.O.W.); (B.M.C.)
| | - Benjamin M. Cohen
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.T.Y.); (L.C.); (Z.O.W.); (B.M.C.)
| | - Wilma K. Olson
- Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.T.Y.); (L.C.); (Z.O.W.); (B.M.C.)
- Correspondence:
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6
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Salina E, Muterko A, Kiseleva A, Liu Z, Korol A. Dissection of Structural Reorganization of Wheat 5B Chromosome Associated With Interspecies Recombination Suppression. FRONTIERS IN PLANT SCIENCE 2022; 13:884632. [PMID: 36340334 PMCID: PMC9629394 DOI: 10.3389/fpls.2022.884632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/08/2022] [Indexed: 06/16/2023]
Abstract
Chromosomal rearrangements that lead to recombination suppression can have a significant impact on speciation, and they are also important for breeding. The regions of recombination suppression in wheat chromosome 5B were identified based on comparisons of the 5B map of a cross between the Chinese Spring (CS) variety of hexaploid wheat and CS-5Bdic (genotype CS with 5B substituted with its homologue from tetraploid Triticum dicoccoides) with several 5B maps of tetraploid and hexaploid wheat. In total, two regions were selected in which recombination suppression occurred in cross CS × CS-5Bdic when compared with other maps: one on the short arm, 5BS_RS, limited by markers BS00009810/BS00022336, and the second on the long arm, 5BL_RS, between markers Ra_c10633_2155 and BS00087043. The regions marked as 5BS_RS and 5BL_RS, with lengths of 5 Mb and 3.6 Mb, respectively, were mined from the 5B pseudomolecule of CS and compared to the homoeologous regions (7.6 and 3.8 Mb, respectively) of the 5B pseudomolecule of Zavitan (T. dicoccoides). It was shown that, in the case of 5BS_RS, the local heterochromatin islands determined by the satellite DNA (119.2) and transposable element arrays, as well as the dissimilarity caused by large insertions/deletions (chromosome rearrangements) between 5BSs aestivum/dicoccoides, are likely the key determinants of recombination suppression in the region. Two major and two minor segments with significant loss of similarity were recognized within the 5BL_RS region. It was shown that the loss of similarity, which can lead to suppression of recombination in the 5BL_RS region, is caused by chromosomal rearrangements, driven by the activity of mobile genetic elements (both DNA transposons and long terminal repeat retrotransposons) and their divergence during evolution. It was noted that the regions marked as 5BS_RS and 5BL_RS are associated with chromosomal rearrangements identified earlier by С-banding analysis of intraspecific polymorphism of tetraploid emmer wheat. The revealed divergence in 5BS_RS and 5BL_RS may be a consequence of interspecific hybridization, plant genetic adaptation, or both.
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Affiliation(s)
- Elena Salina
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - Alexander Muterko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Antonina Kiseleva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel
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7
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Yin L, Li C, Wu X, Xu G, Li Z, Shen Y. Synthesis of (E)-N-(4-Styrene) Acrylamides for DNA Topoisomerase IIα Inhibitors and Antitumor Agents. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202105008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Examining the Effects of Netropsin on the Curvature of DNA A-Tracts Using Electrophoresis. Molecules 2021; 26:molecules26195871. [PMID: 34641414 PMCID: PMC8510488 DOI: 10.3390/molecules26195871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 11/17/2022] Open
Abstract
A-tracts are sequences of repeated adenine bases that, under the proper conditions, are capable of mediating DNA curvature. A-tracts occur naturally in the regulatory regions of many organisms, yet their biological functions are not fully understood. Orienting multiple A-tracts together constructively or destructively in a phase has the potential to create different shapes in the DNA helix axis. One means of detecting these molecular shape differences is from altered DNA mobilities measured using electrophoresis. The small molecule netropsin binds the minor groove of DNA, particularly at AT-rich sequences including A-tracts. Here, we systematically test the hypothesis that netropsin binding eliminates the curvature of A-tracts by measuring the electrophoretic mobilities of seven 98-base pair DNA samples containing different numbers and arrangements of centrally located A-tracts under varying conditions with netropsin. We find that netropsin binding eliminates the mobility difference between the DNA fragments with different A-tract arrangements in a concentration-dependent manner. This work provides evidence for the straightening of A-tracts upon netropsin binding and illustrates an artificial approach to re-sculpt DNA shape.
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Stellwagen NC. Using capillary electrophoresis to characterize the hydrodynamic and electrostatic properties of DNA in solutions containing various monovalent cations. Electrophoresis 2021; 43:309-326. [PMID: 34510492 DOI: 10.1002/elps.202100176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 11/08/2022]
Abstract
This review describes the results obtained by using free-solution capillary electrophoresis to probe the electrostatic and hydrodynamic properties of DNA in solutions containing various monovalent cations. In brief, we found that the mobilities of double-stranded DNAs (dsDNAs) increase with increasing molecular weight before leveling off and becoming constant at molecular weights ≥400 bp. The mobilities of single-stranded DNAs (ssDNAs) go through a maximum at ∼10-20 nucleotides before decreasing and becoming constant for oligomers larger than ∼30-50 bases. The mobilities of both ss- and dsDNAs increase linearly with the logarithm of increasing charge per unit length and decrease linearly with the logarithm of increasing ionic strength. Surprisingly, ss- and dsDNA mobilities level off and become nearly constant at ionic strengths ≥0.6 M. The thermal stabilities of dsDNAs decrease linearly with increasing solution viscosity. The diffusion coefficients of dsDNA are modulated by the diffusion coefficients of their counterions because of electrostatic DNA-cation coupling interactions. Finally, the anomalously slow mobilities observed for A-tract-containing DNAs can be attributed both to differences in shape and to the preferential localization of small cations in the A-tract minor groove. Since many of these results are mirrored in other polyion-counterion systems, free-solution electrophoresis can be viewed as a reporter of the electrostatics and hydrodynamics of highly charged polyions. New results describing the mobilities of dsDNA analogues of a microRNA-messenger RNA complex are also presented.
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10
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Wan T, Horová M, Beltran DG, Li S, Wong HX, Zhang LM. Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis. Mol Cell 2021; 81:2887-2900.e5. [PMID: 34171298 DOI: 10.1016/j.molcel.2021.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
WhiB7 represents a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, a unique group of iron-sulfur (4Fe-4S] cluster-containing proteins exclusive to the phylum of Actinobacteria. In Mycobacterium tuberculosis (Mtb), WhiB7 interacts with domain 4 of the primary sigma factor (σA4) in the RNA polymerase holoenzyme and activates genes involved in multiple drug resistance and redox homeostasis. Here, we report crystal structures of the WhiB7:σA4 complex alone and bound to its target promoter DNA at 1.55-Å and 2.6-Å resolution, respectively. These structures show how WhiB7 regulates gene expression by interacting with both σA4 and the AT-rich sequence upstream of the -35 promoter DNA via its C-terminal DNA-binding motif, the AT-hook. By combining comparative structural analysis of the two high-resolution σA4-bound Wbl structures with molecular and biochemical approaches, we identify the structural basis of the functional divergence between the two distinct subclasses of Wbl proteins in Mtb.
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Affiliation(s)
- Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Magdaléna Horová
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Shanren Li
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Huey-Xian Wong
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Li-Mei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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11
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Cai X, Arias DS, Velazquez LR, Vexler S, Bevier AL, Fygenson DK. DNA Nunchucks: Nanoinstrumentation for Single-Molecule Measurement of Stiffness and Bending. NANO LETTERS 2020; 20:1388-1395. [PMID: 31872766 DOI: 10.1021/acs.nanolett.9b04980] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bending of double-stranded DNA (dsDNA) has important applications in biology and engineering, but measurement of DNA bend angles is notoriously difficult and rarely dynamic. Here we introduce a nanoscale instrument that makes dynamic measurement of the bend in short dsDNAs easy enough to be routine. The instrument works by embedding the ends of a dsDNA in stiff, fluorescently labeled DNA nanotubes, thereby mechanically magnifying their orientations. The DNA nanotubes are readily confined to a plane and imaged while freely diffusing. Single-molecule bend angles are rapidly and reliably extracted from the images by a neural network. We find that angular variance across a population increases with dsDNA length, as predicted by the worm-like chain model, although individual distributions can differ significantly from one another. For dsDNAs with phased A6-tracts, we measure an intrinsic bend of 17 ± 1° per A6-tract, consistent with other methods, and a length-dependent angular variance that indicates A6-tracts are (80 ± 30)% stiffer than generic dsDNA.
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Affiliation(s)
- Xinyue Cai
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
| | - D Sebastian Arias
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
| | - Lourdes R Velazquez
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
- Biomolecular Science & Engineering Program , University of California, Santa Barbara , Santa Barbara , California , United States
| | - Shelby Vexler
- Biomolecular Science & Engineering Program , University of California, Santa Barbara , Santa Barbara , California , United States
| | - Alexander L Bevier
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
| | - D Kuchnir Fygenson
- Department of Physics , University of California, Santa Barbara , Santa Barbara , California , United States
- Biomolecular Science & Engineering Program , University of California, Santa Barbara , Santa Barbara , California , United States
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12
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Atomistic insight into sequence-directed DNA bending and minicircle formation propensity in the absence and presence of phased A-tracts. J Comput Aided Mol Des 2020; 34:253-265. [PMID: 31950463 DOI: 10.1007/s10822-020-00288-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/09/2020] [Indexed: 12/21/2022]
Abstract
Bending of double-stranded (ds) DNA plays a crucial role in many important biological processes and is relevant for nanotechnological applications. Among all the elements that have been studied in relation to dsDNA bending, A-tracts stand out as one of the most controversial. The "ApA wedge" theory was disproved when a series of linear polynucleotides containing phased 5'-A4T4-3' or 5'-T4A4-3' runs were shown to be bent or straight, respectively, and crystallographic evidence revealed that A-tracts are unbent. Furthermore, some of the smallest dsDNA minicircles described to date (~ 100 bp in size) lack A-tracts and are subjected to varying levels of torsional stress. Representative DNA sequences from this experimental background were modeled in atomic detail and their dynamic behavior was simulated over hundreds of nanoseconds using the AMBER force field ParmBSC1. Subsequent analysis of the resulting trajectories allowed us to (i) unambiguously establish the location of the bends in all cases; (ii) identify the structural elements that are directly responsible for the macroscopically detected curvature; and (iii) reveal the importance not only of coherently summing the effects of the bending elements when they are in synchrony with the natural repeat of the helix (i.e. separated by an integral number of helical turns) but also when alternated with a half-integral separation of opposite effects. We conclude that the major determinant of the macroscopically observed bending is the proper grouping and phasing of the positive roll imposed by pyrimidine-purine (YR) steps and the negative or null roll characteristic of RY steps and A-tracts, respectively. This conclusion is in very good agreement with the structural parameters experimentally derived for much smaller DNA molecules either alone or as found in DNA-protein complexes. We expect that this work will pave the way for future studies on drug-induced DNA bending, DNA shape readout by transcription factors, structure of circular extrachromosomal DNA, and custom design of curved DNA origami scaffolds.
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Nwokeoji AO, Kumar S, Kilby PM, Portwood DE, Hobbs JK, Dickman MJ. Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC. Analyst 2019; 144:4985-4994. [PMID: 31328735 DOI: 10.1039/c9an00954j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Long double-stranded (ds) RNA is emerging as a novel alternative to chemical and genetically-modified insect and fungal management strategies. The ability to produce large quantities of dsRNA in either bacterial systems, by in vitro transcription, in cell-free systems or in planta for RNA interference applications has generated significant demand for the development and application of analytical tools for analysis of dsRNA. We have utilised atomic force microscopy (AFM) in conjunction with ion-pair reverse-phase high performance liquid chromatography (IP-RP-HPLC) to provide novel insight into dsRNA for RNAi applications. The AFM analysis enabled direct structural characterisation of the A-form duplex dsRNA and accurate determination of the dsRNA duplex length. Moreover, further analysis under non-denaturing conditions revealed the presence of heterogeneous dsRNA species. IP-RP-HPLC fractionation and AFM analysis revealed that these alternative RNA species do not arise from different lengths of individual dsRNA molecules in the product, but represent misannealed RNA species that present as larger assemblies or multimeric forms of the RNA. These results for the first time provide direct structural insight into dsRNA produced both in vivo in bacterial systems and in vitro, highlighting the structural heterogeneity of RNA produced. These results are the first example of detailed characterisation of the different forms of dsRNA from two production systems and establish atomic force microscopy as an important tool for the characterisation of long dsRNA.
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Affiliation(s)
- Alison O Nwokeoji
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, S1 3JD, UK.
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14
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Cooper S, Wadsworth ES, Ochsenreiter T, Ivens A, Savill NJ, Schnaufer A. Assembly and annotation of the mitochondrial minicircle genome of a differentiation-competent strain of Trypanosoma brucei. Nucleic Acids Res 2019; 47:11304-11325. [PMID: 31665448 PMCID: PMC6868439 DOI: 10.1093/nar/gkz928] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 01/10/2023] Open
Abstract
Kinetoplastids are protists defined by one of the most complex mitochondrial genomes in nature, the kinetoplast. In the sleeping sickness parasite Trypanosoma brucei, the kinetoplast is a chain mail-like network of two types of interlocked DNA molecules: a few dozen ∼23-kb maxicircles (homologs of the mitochondrial genome of other eukaryotes) and thousands of ∼1-kb minicircles. Maxicircles encode components of respiratory chain complexes and the mitoribosome. Several maxicircle-encoded mRNAs undergo extensive post-transcriptional RNA editing via addition and deletion of uridines. The process is mediated by hundreds of species of minicircle-encoded guide RNAs (gRNAs), but the precise number of minicircle classes and gRNA genes was unknown. Here we present the first essentially complete assembly and annotation of the kinetoplast genome of T. brucei. We have identified 391 minicircles, encoding not only ∼930 predicted 'canonical' gRNA genes that cover nearly all known editing events (accessible via the web at http://hank.bio.ed.ac.uk), but also ∼370 'non-canonical' gRNA genes of unknown function. Small RNA transcriptome data confirmed expression of the majority of both categories of gRNAs. Finally, we have used our data set to refine definitions for minicircle structure and to explore dynamics of minicircle copy numbers.
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Affiliation(s)
- Sinclair Cooper
- Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, Scotland EH9 3FL, UK
| | - Elizabeth S Wadsworth
- Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, Scotland EH9 3FL, UK
| | | | - Alasdair Ivens
- Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, Scotland EH9 3FL, UK
| | - Nicholas J Savill
- Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, Scotland EH9 3FL, UK
| | - Achim Schnaufer
- Institute of Immunology & Infection Research, University of Edinburgh, Edinburgh, Scotland EH9 3FL, UK
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15
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Parallelized DNA tethered bead measurements to scrutinize DNA mechanical structure. Methods 2019; 169:46-56. [PMID: 31351926 DOI: 10.1016/j.ymeth.2019.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/01/2019] [Accepted: 07/22/2019] [Indexed: 01/05/2023] Open
Abstract
Tethering beads to DNA offers a panel of single molecule techniques for the refined analysis of the conformational dynamics of DNA and the elucidation of the mechanisms of enzyme activity. Recent developments include the massive parallelization of these techniques achieved by the fabrication of dedicated nanoarrays by soft nanolithography. We focus here on two of these techniques: the Tethered Particle motion and Magnetic Tweezers allowing analysis of the behavior of individual DNA molecules in the absence of force and under the application of a force and/or a torque, respectively. We introduce the experimental protocols for the parallelization and discuss the benefits already gained, and to come, for these single molecule investigations.
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16
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Paul A, Kumar A, Nanjunda R, Farahat AA, Boykin DW, Wilson WD. Systematic synthetic and biophysical development of mixed sequence DNA binding agents. Org Biomol Chem 2018; 15:827-835. [PMID: 27995240 DOI: 10.1039/c6ob02390h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is now well established that, although only about 5% of the human genome codes for protein, most of the DNA has some function, such as synthesis of specific, functional RNAs and/or control of gene expression. These functional sequences open immense possibilities in both biotechnology and therapeutics for the use of cell-permeable, small molecules that can bind mixed-base pair sequences of DNA for regulation of genomic functions. Unfortunately very few types of modules have been designed to recognize mixed DNA sequences and for progress in targeting specific genes, it is essential to have additional classes of compounds. Compounds that can be rationally designed from established modules and which can bind strongly to mixed base pair DNA sequences are especially attractive. Based on extensive experience in design of minor-groove agents for AT recognition, a small library of compounds with two AT specific binding modules, connected through linkers which can recognize the G·C base pairs, were prepared. The compound-DNA interactions were evaluated with a powerful array of biophysical methods and the results show that some pyridyl-linked compounds bind with the target sequence with sub-nanomolar KD, with very slow dissociation kinetics and 200 times selectivity over the related sequence without a G·C base pair. Interestingly, a set of compounds with AT module connected by different linkers shows cooperative dimer recognition of related sequences. This type of design approach can be expanded to additional modules for recognition of a wide variety of sequences.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - Rupesh Nanjunda
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA. and Janssen Research and Development, 1400 McKean Rd, Spring House, PA 19477, USA
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA. and Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
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17
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Smircich P, El-Sayed NM, Garat B. Intrinsic DNA curvature in trypanosomes. BMC Res Notes 2017; 10:585. [PMID: 29121981 PMCID: PMC5679330 DOI: 10.1186/s13104-017-2908-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 11/01/2017] [Indexed: 12/21/2022] Open
Abstract
Background Trypanosoma cruzi and Trypanosoma brucei are protozoan parasites
causing Chagas disease and African sleeping sickness, displaying unique features of cellular and molecular biology. Remarkably, no canonical signals for RNA polymerase II promoters, which drive protein coding genes transcription, have been identified so far. The secondary structure of DNA has long been recognized as a signal in biological processes and more recently, its involvement in transcription initiation in Leishmania was proposed. In order to study whether this feature is conserved in trypanosomatids, we undertook a genome wide search for intrinsic DNA curvature in T. cruzi and T. brucei. Results Using a region integrated intrinsic curvature (RIIC) scoring that we previously developed, a non-random distribution of sequence-dependent curvature was observed. High RIIC scores were found to be significantly correlated with transcription start sites in T. cruzi, which have been mapped in divergent switch regions, whereas in T. brucei, the high RIIC scores correlated with sites that have been involved not only in RNA polymerase II initiation but also in termination. In addition, we observed regions with high RIIC score presenting in-phase tracts of Adenines, in the subtelomeric regions of the T. brucei chromosomes that harbor the variable surface glycoproteins genes. Conclusions In both T. cruzi and T. brucei genomes, a link between DNA conformational signals and gene expression was found. High sequence dependent curvature is associated with transcriptional regulation regions. High intrinsic curvature also occurs at the T. brucei chromosome subtelomeric regions where the recombination processes involved in the evasion of the immune host system take place. These findings underscore the relevance of indirect DNA readout in these ancient eukaryotes. Electronic supplementary material The online version of this article (10.1186/s13104-017-2908-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pablo Smircich
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la Republica, 11400, Montevideo, Uruguay.,Departamento de Genética, Facultad de Medicina, Universidad de la Republica, 11800, Montevideo, Uruguay
| | - Najib M El-Sayed
- Department of Cell Biology and Molecular Genetics and Center for Bioinformatics and Computational Biology, University of Maryland College Park, College Park, MD, 20742, USA
| | - Beatriz Garat
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la Republica, 11400, Montevideo, Uruguay.
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18
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Yella VR, Bansal M. DNA structural features of eukaryotic TATA-containing and TATA-less promoters. FEBS Open Bio 2017; 7:324-334. [PMID: 28286728 PMCID: PMC5337902 DOI: 10.1002/2211-5463.12166] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 11/16/2016] [Indexed: 01/26/2023] Open
Abstract
Eukaryotic genes can be broadly classified as TATA‐containing and TATA‐less based on the presence of TATA box in their promoters. Experiments on both classes of genes have revealed a disparity in the regulation of gene expression and cellular functions between the two classes. In this study, we report characteristic differences in promoter sequences and associated structural properties of the two categories of genes in six different eukaryotes. We have analyzed three structural features, DNA duplex stability, bendability, and curvature along with the distribution of A‐tracts, G‐quadruplex motifs, and CpG islands. The structural feature analyses reveal that while the two classes of gene promoters are distinctly different from each other, the properties are also distinguishable across the six organisms.
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Affiliation(s)
- Venkata Rajesh Yella
- Molecular Biophysics Unit Indian Institute of Science Bangalore India; Present address: Department of Biotechnology K L University, Vaddeswaram Guntur 522502 India
| | - Manju Bansal
- Molecular Biophysics Unit Indian Institute of Science Bangalore India
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19
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Abstract
DNA bending is critical for DNA packaging, recognition, and repair, and occurs toward either the major or the minor groove. The anisotropy of B-DNA groove bending was quantified for eight DNA sequences by free energy simulations employing a novel reaction coordinate. The simulations show that bending toward the major groove is preferred for non-A-tracts while the A-tract has a high tendency of bending toward the minor groove. Persistence lengths were generally larger for bending toward the minor groove, which is thought to originate from differences in groove hydration. While this difference in stiffness is one of the factors determining the overall preference of bending direction, the dominant contribution is shown to be a free energy offset between major and minor groove bending. The data suggests that, for the A-tract, this offset is largely determined by inherent structural properties, while differences in groove hydration play a large role for non-A-tracts. By quantifying the energetics of DNA groove bending and rationalizing the origins of the anisotropy, the calculations provide important new insights into a key biological process.
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Affiliation(s)
- Ning Ma
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States
| | - Arjan van der Vaart
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, CHE 205, Tampa, Florida 33620, United States
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20
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Kim YJ, Kim DN. Structural Basis for Elastic Mechanical Properties of the DNA Double Helix. PLoS One 2016; 11:e0153228. [PMID: 27055239 PMCID: PMC4824394 DOI: 10.1371/journal.pone.0153228] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/25/2016] [Indexed: 01/20/2023] Open
Abstract
In this article, we investigate the principal structural features of the DNA double helix and their effects on its elastic mechanical properties. We develop, in the pursuit of this purpose, a helical continuum model consisting of a soft helical core and two stiff ribbons wrapping around it. The proposed model can reproduce the negative twist-stretch coupling of the helix successfully as well as its global stretching, bending, and torsional rigidities measured experimentally. Our parametric study of the model using the finite element method further reveals that the stiffness of phosphate backbones is a crucial factor for the counterintuitive overwinding behavior of the duplex and its extraordinarily high torsional rigidity, the major-minor grooves augment the twist-stretch coupling, and the change of the helicity might be responsible for the transition from a negative to a positive twist-stretching coupling when a tensile force is applied to the duplex.
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Affiliation(s)
- Young-Joo Kim
- Department of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Do-Nyun Kim
- Department of Mechanical and Aerospace Engineering, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea.,Institute of Advanced Machines and Design, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul, 08826, Republic of Korea
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21
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Alexandrov OS, Karlov GI. Molecular cytogenetic analysis and genomic organization of major DNA repeats in castor bean (Ricinus communis L.). Mol Genet Genomics 2016; 291:775-87. [PMID: 26589420 DOI: 10.1007/s00438-015-1145-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 11/07/2015] [Indexed: 12/11/2022]
Abstract
This article addresses the bioinformatic, molecular genetic, and cytogenetic study of castor bean (Ricinus communis, 2n = 20), which belongs to the monotypic Ricinus genus within the Euphorbiaceae family. Because castor bean chromosomes are small, karyotypic studies are difficult. However, the use of DNA repeats has yielded new prospects for karyotypic research and genome characterization. In the present study, major DNA repeat sequences were identified, characterized and localized on mitotic metaphase and meiotic pachytene chromosomes. Analyses of the nucleotide composition, curvature models, and FISH localization of the rcsat39 repeat suggest that this repeat plays a key role in building heterochromatic arrays in castor bean. Additionally, the rcsat390 sequences were determined to be chromosome-specific repeats located in the pericentromeric region of mitotic chromosome A (pachytene chromosome 1). The localization of rcsat39, rcsat390, 45S and 5S rDNA genes allowed for the development of cytogenetic landmarks for chromosome identification. General questions linked to heterochromatin formation, DNA repeat distribution, and the evolutionary emergence of the genome are discussed. The article may be of interest to biologists studying small genome organization and short monomer DNA repeats.
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Affiliation(s)
- O S Alexandrov
- Center for Molecular Biotechnology, Russian State Agrarian University, Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Street, Moscow, 127550, Russia
| | - G I Karlov
- Center for Molecular Biotechnology, Russian State Agrarian University, Moscow Timiryazev Agricultural Academy, 49 Timiryazevskaya Street, Moscow, 127550, Russia.
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22
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Kaushik M, Kaushik S, Roy K, Singh A, Mahendru S, Kumar M, Chaudhary S, Ahmed S, Kukreti S. A bouquet of DNA structures: Emerging diversity. Biochem Biophys Rep 2016; 5:388-395. [PMID: 28955846 PMCID: PMC5600441 DOI: 10.1016/j.bbrep.2016.01.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/28/2015] [Accepted: 01/22/2016] [Indexed: 11/29/2022] Open
Abstract
Structural polymorphism of DNA has constantly been evolving from the time of illustration of the double helical model of DNA by Watson and Crick. A variety of non-canonical DNA structures have constantly been documented across the globe. DNA attracted worldwide attention as a carrier of genetic information. In addition to the classical Watson–Crick duplex, DNA can actually adopt diverse structures during its active participation in cellular processes like replication, transcription, recombination and repair. Structures like hairpin, cruciform, triplex, G-triplex, quadruplex, i-motif and other alternative non-canonical DNA structures have been studied at length and have also shown their in vivo occurrence. This review mainly focuses on non-canonical structures adopted by DNA oligonucleotides which have certain prerequisites for their formation in terms of sequence, its length, number and orientation of strands along with varied solution conditions. This conformational polymorphism of DNA might be the basis of different functional properties of a specific set of DNA sequences, further giving some insights for various extremely complicated biological phenomena. Many of these structures have already shown their linkages with diseases like cancer and genetic disorders, hence making them an extremely striking target for structure-specific drug designing and therapeutic applications. DNA can adopt diverse range of structures other than classical Watson–Crick duplex. Discussion of alternate structures like hairpin, cruciform, triplex, quadruplex etc. This review gives some insights for the biological relevance of DNA structures.
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Affiliation(s)
- Mahima Kaushik
- Cluster Innovation Centre, University of Delhi, Delhi, India.,Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Kapil Roy
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Anju Singh
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Swati Mahendru
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Mohan Kumar
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Swati Chaudhary
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Saami Ahmed
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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23
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Muterko A, Kalendar R, Salina E. Novel alleles of the VERNALIZATION1 genes in wheat are associated with modulation of DNA curvature and flexibility in the promoter region. BMC PLANT BIOLOGY 2016; 16 Suppl 1:9. [PMID: 26822192 PMCID: PMC4895274 DOI: 10.1186/s12870-015-0691-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
BACKGROUND In wheat, the vernalization requirement is mainly controlled by the VRN genes. Different species of hexaploid and tetraploid wheat are widely used as genetic source for new mutant variants and alleles for fundamental investigations and practical breeding programs. In this study, VRN-A1 and VRN-B1 were analysed for 178 accessions representing six tetraploid wheat species (Triticum dicoccoides, T. dicoccum, T. turgidum, T. polonicum, T. carthlicum, T. durum) and five hexaploid species (T. compactum, T. sphaerococcum, T. spelta, T. macha, T. vavilovii). RESULTS Novel allelic variants in the promoter region of VRN-A1 and VRN-B1 were identified based on the change in curvature and flexibility of the DNA molecules. The new variants of VRN-A1 (designated as Vrn-A1a.2, Vrn-A1b.2 - Vrn-A1b.6 and Vrn-A1i) were found to be widely distributed in hexaploid and tetraploid wheat, and in fact were predominant over the known VRN-A1 alleles. The greatest diversity of the new variants of VRN-B1 (designated as VRN-B1.f, VRN-B1.s and VRN-B1.m) was found in the tetraploid and some hexaploid wheat species. For the first time, minor differences within the sequence motif known as the VRN-box of VRN1 were correlated with wheat growth habit. Thus, vrn-A1b.3 and vrn-A1b.4 were revealed in winter wheat in contrast to Vrn-A1b.2, Vrn-A1b.5, Vrn-A1b.6 and Vrn-A1i. It was found that single nucleotide mutation in the VRN-box can influence the vernalization requirement and growth habit of wheat. Our data suggest that both the A-tract and C-rich segment within the VRN-box contribute to its functionality, and provide a new view of the hypothesised role of the VRN-box in regulating transcription of the VRN1 genes. Specifically, it is proposed that combination of mutations in this region can modulate vernalization sensitivity and flowering time of wheat. CONCLUSIONS New allelic variants of the VRN-A1 and VRN-B1 genes were identified in hexaploid and tetraploid wheat. Mutations in A-tract and C-rich segments within the VRN-box of VRN-A1 are associated with modulation of the vernalization requirement and flowering time. New allelic variants will be useful in fundamental investigations into the regulation of VRN1 expression, and provide a valuable genetic resource for practical breeding of wheat.
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Affiliation(s)
- Alexandr Muterko
- Laboratory of Plant Molecular Genetics and Cytogenetics, The Federal Research Center Institute of Cytology and Genetics, Lavrentyeva Avenue 10, Novosibirsk, 630090, Russian Federation.
- Department of Common and Molecular Genetics, Plant Breeding and Genetics Institute - National Center of Seed and Cultivar Investigation, Ovidiopolskaya Road 3, Odessa, 65036, Ukraine.
| | - Ruslan Kalendar
- Laboratory of Plant Genomics and Bioinformatics, RSE "National Center for Biotechnology", Sh. Valikhanov 13/1, Astana, 010000, Kazakhstan
- University of Helsinki, Institute of Biotechnology, MTT Plant Genomics Laboratory, Biocentre 3, P.O. Box 65, Viikinkaari 1, Helsinki, 00014, Finland
| | - Elena Salina
- Laboratory of Plant Molecular Genetics and Cytogenetics, The Federal Research Center Institute of Cytology and Genetics, Lavrentyeva Avenue 10, Novosibirsk, 630090, Russian Federation
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24
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Fogen D, Wu SC, Ng KKS, Wong SL. Engineering Streptavidin and a Streptavidin-Binding Peptide with Infinite Binding Affinity and Reversible Binding Capability: Purification of a Tagged Recombinant Protein to High Purity via Affinity-Driven Thiol Coupling. PLoS One 2015; 10:e0139137. [PMID: 26406477 PMCID: PMC4583386 DOI: 10.1371/journal.pone.0139137] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/08/2015] [Indexed: 12/02/2022] Open
Abstract
To extend and improve the utility of the streptavidin-binding peptide tag (SBP-tag) in applications ranging from affinity purification to the reversible immobilization of recombinant proteins, a cysteine residue was introduced to the streptavidin mutein SAVSBPM18 and the SBP-tag to generate SAVSBPM32 and SBP(A18C), respectively. This pair of derivatives is capable of forming a disulfide bond through the newly introduced cysteine residues. SAVSBPM32 binds SBP-tag and biotin with binding affinities (Kd ~ 10-8M) that are similar to SAVSBPM18. Although SBP(A18C) binds to SAVSBPM32 more weakly than SBP-tag, the binding affinity is sufficient to bring the two binding partners together efficiently before they are locked together via disulfide bond formation–a phenomenon we have named affinity-driven thiol coupling. Under the condition with SBP(A18C) tags in excess, two SBP(A18C) tags can be captured by a tetrameric SAVSBPM32. The stoichiometry of the disulfide-bonded SAVSBPM32-SBP(A18C) complex was determined using a novel two-dimensional electrophoresis method which has general applications for analyzing the composition of disulfide-bonded protein complexes. To illustrate the application of this reversible immobilization technology, optimized conditions were established to use the SAVSBPM32-affinity matrix for the purification of a SBP(A18C)-tagged reporter protein to high purity. Furthermore, we show that the SAVSBPM32-affinity matrix can also be applied to purify a biotinylated protein and a reporter protein tagged with the unmodified SBP-tag. The dual (covalent and non-covalent) binding modes possible in this system offer great flexibility to many different applications which need reversible immobilization capability.
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Affiliation(s)
- Dawson Fogen
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sau-Ching Wu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Kenneth Kai-Sing Ng
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sui-Lam Wong
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
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25
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Weeks KM. Review toward all RNA structures, concisely. Biopolymers 2015; 103:438-48. [PMID: 25546503 PMCID: PMC4446244 DOI: 10.1002/bip.22601] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/10/2014] [Accepted: 12/11/2014] [Indexed: 01/05/2023]
Abstract
Profound insights regarding nucleic acid structure and function can be gleaned from very simple, direct, and chemistry-based strategies. Our approach strives to incorporate the elegant physical insights that Don Crothers instilled in those who trained in his laboratory. Don emphasized the advantages of focusing on direct and concise experiments even when the final objective was to understand something complex-potentially including the large-scale architectures of the genomes of RNA viruses and the transcriptomes of cells. Here, the author reviews the intellectual path, and a few detours, that led to the development of the SHAPE-MaP and RING-MaP technologies for interrogating RNA structure and function at large scales. The author also argues that greater attention to creating direct, less inferential experiments will convert "omics" investigations into lasting and definitive contributions to our understanding of biological function.
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Affiliation(s)
- Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599-3290,
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26
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Simpson L, Douglass SM, Lake JA, Pellegrini M, Li F. Comparison of the Mitochondrial Genomes and Steady State Transcriptomes of Two Strains of the Trypanosomatid Parasite, Leishmania tarentolae. PLoS Negl Trop Dis 2015. [PMID: 26204118 PMCID: PMC4512693 DOI: 10.1371/journal.pntd.0003841] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
U-insertion/deletion RNA editing is a post-transcriptional mitochondrial RNA modification phenomenon required for viability of trypanosomatid parasites. Small guide RNAs encoded mainly by the thousands of catenated minicircles contain the information for this editing. We analyzed by NGS technology the mitochondrial genomes and transcriptomes of two strains, the old lab UC strain and the recently isolated LEM125 strain. PacBio sequencing provided complete minicircle sequences which avoided the assembly problem of short reads caused by the conserved regions. Minicircles were identified by a characteristic size, the presence of three short conserved sequences, a region of inherently bent DNA and the presence of single gRNA genes at a fairly defined location. The LEM125 strain contained over 114 minicircles encoding different gRNAs and the UC strain only ~24 minicircles. Some LEM125 minicircles contained no identifiable gRNAs. Approximate copy numbers of the different minicircle classes in the network were determined by the number of PacBio CCS reads that assembled to each class. Mitochondrial RNA libraries from both strains were mapped against the minicircle and maxicircle sequences. Small RNA reads mapped to the putative gRNA genes but also to multiple regions outside the genes on both strands and large RNA reads mapped in many cases over almost the entire minicircle on both strands. These data suggest that minicircle transcription is complete and bidirectional, with 3’ processing yielding the mature gRNAs. Steady state RNAs in varying abundances are derived from all maxicircle genes, including portions of the repetitive divergent region. The relative extents of editing in both strains correlated with the presence of a cascade of cognate gRNAs. These data should provide the foundation for a deeper understanding of this dynamic genetic system as well as the evolutionary variation of editing in different strains. U-insertion/deletion RNA editing is a unique post-transcriptional mRNA modification process that occurs in trypanosomatid parasites and is required for viability. The participation of guide RNAs which are transcribed from the thousands of catenated minicircles in determining the precise sites and number of U’s inserted and deleted to create translatable mRNAs is novel and significant in terms of the recently realized importance of small RNAs in biology. This study contributes the necessary bioinformatics foundation for a deeper understanding of this important genetic system in molecular detail using a model trypanosomatid, Leishmania tarentolae. We used Next Generation Sequencing methods to determine the complete maxicircle and minicircle genomes and to map maxicircle pre-edited and edited transcripts and minicircle transcripts. The transcription of minicircle-encoded guide RNAs was confirmed and novel information about minicircle gene expression was obtained. The biological context involved a comparison of two strains of the parasites, one recently isolated and having an intact mitochondrial genetic system and the other an old lab strain that has developed a partially defective mitochondrial genome. The data are important for an understanding of the mitochondrial genomic complexity and expression of this dynamic genetic system.
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Affiliation(s)
- Larry Simpson
- Department of Microbiology, Immunology and Molecular Genetics, Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| | - Stephen M. Douglass
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, California, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - James A. Lake
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Matteo Pellegrini
- Department of Molecular, Cellular and Developmental Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Feng Li
- Dental Research Institute, School of Dentistry, University of California, Los Angeles, Los Angeles, California, United States of America
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27
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Giovan SM, Hanke A, Levene SD. DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation. Biopolymers 2015; 103:528-38. [PMID: 26014845 DOI: 10.1002/bip.22683] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/15/2015] [Accepted: 05/15/2015] [Indexed: 01/11/2023]
Abstract
For much of the last three decades, Monte Carlo-simulation methods have been the standard approach for accurately calculating the cyclization probability, J, or J factor, for DNA models having sequence-dependent bends or inhomogeneous bending flexibility. Within the last 10 years approaches based on harmonic analysis of semi-flexible polymer models have been introduced, which offer much greater computational efficiency than Monte Carlo techniques. These methods consider the ensemble of molecular conformations in terms of harmonic fluctuations about a well-defined elastic-energy minimum. However, the harmonic approximation is only applicable for small systems, because the accessible conformation space of larger systems is increasingly dominated by anharmonic contributions. In the case of computed values of the J factor, deviations of the harmonic approximation from the exact value of J as a function of DNA length have not been characterized. Using a recent, numerically exact method that accounts for both anharmonic and harmonic contributions to J for wormlike chains of arbitrary size, we report here the apparent error that results from neglecting anharmonic behavior. For wormlike chains having contour lengths less than four times the persistence length, the error in J arising from the harmonic approximation is generally small, amounting to free energies less than the thermal energy, kB T. For larger systems, however, the deviations between harmonic and exact J values increase approximately linearly with size.
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Affiliation(s)
- Stefan M Giovan
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX, 75083
| | - Andreas Hanke
- Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, TX, 78520
| | - Stephen D Levene
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX, 75083.,Department of Physics, University of Texas at Dallas, Richardson, TX, 75083.,Department of Bioengineering, University of Texas at Dallas, Richardson, TX, 75083
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28
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Paul A, Nanjunda R, Kumar A, Laughlin S, Nhili R, Depauw S, Deuser SS, Chai Y, Chaudhary AS, David-Cordonnier MH, Boykin DW, Wilson WD. Mixed up minor groove binders: Convincing A·T specific compounds to recognize a G·C base pair. Bioorg Med Chem Lett 2015; 25:4927-4932. [PMID: 26051649 DOI: 10.1016/j.bmcl.2015.05.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 05/06/2015] [Indexed: 01/08/2023]
Abstract
DNA minor-groove-binding compounds have limited biological applications, in part due to problems with sequence specificity that cause off-target effects. A model to enhance specificity has been developed with the goal of preparing compounds that bind to two AT sites separated by G·C base pairs. Compounds of interest were probed using thermal melting, circular dichroism, mass spectrometry, biosensor-SPR, and molecular modeling methods. A new minor groove binder that can strongly and specifically recognize a single G·C base pair with flanking AT sequences has been prepared. This multi-site DNA recognition mode offers novel design principles to recognize entirely new DNA motifs.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Rupesh Nanjunda
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Sarah Laughlin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Raja Nhili
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM-University of Lille and Centre Hospitalier of Lille, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | - Sabine Depauw
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM-University of Lille and Centre Hospitalier of Lille, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | - Shelby Sheldon Deuser
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Yun Chai
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Arpana S Chaudhary
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Marie-Hélène David-Cordonnier
- UMR-S1172-Jean-Pierre Aubert Research Centre (JPARC), INSERM-University of Lille and Centre Hospitalier of Lille, Institut pour la Recherche sur le Cancer de Lille, Place de Verdun, F-59045 Lille Cedex, France
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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29
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Muterko A, Kalendar R, Cockram J, Balashova I. Discovery, evaluation and distribution of haplotypes and new alleles of the Photoperiod-A1 gene in wheat. PLANT MOLECULAR BIOLOGY 2015; 88:149-164. [PMID: 25851614 DOI: 10.1007/s11103-015-0313-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 03/29/2015] [Indexed: 06/04/2023]
Abstract
Photoperiod response in wheat is determined to a large extent by the homoeologous series of Photoperiod 1 (Ppd1) genes. In this study, Ppd-A1 genomic sequences from the 5' UTR and promoter region were analysed in 104 accessions of six tetraploid wheat species (Triticum dicoccoides, T. dicoccum, T. turgidum, T. polonicum, T. carthlicum, T. durum) and 102 accessions of six hexaploid wheat species (T. aestivum, T. compactum, T. sphaerococcum, T. spelta, T. macha, T. vavilovii). This data was supplemented with in silico analysis of publicly available sequences from 46 to 193 accessions of diploid and tetraploid wheat, respectively. Analysis of a region of the Ppd-A1 promoter identified thirteen haplotypes, which were divided in two haplogroups. Distribution of the Ppd-A1 haplogroups and haplotypes in wheat species, and their geographical distributions were analysed. Polymerase chain reaction combined with a heteroduplex mobility assay was subsequently used to efficiently discriminate between Ppd-A1 alleles, allowing identification of the Ppd-A1b haplotypes and haplogroups. The causes of anomalous migration of Ppd-A1 heteroduplexes in gels were found to be the localization of mismatches relative to the center of fragment, the cumulative effect of neighbouring polymorphic sites, and the location of mismatches within A/T-tracts. Analysis of the Ppd-A1 5' UTR in hexaploid wheat revealed a novel mutation within the "photoperiod critical" region in a subset of T. compactum accessions. This putative photoperiod insensitive allele (designated Ppd-A1a.4) includes a 684 bp deletion which spans region in common with deletions previously identified in other photoperiod insensitive Ppd1 alleles.
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Affiliation(s)
- Alexandr Muterko
- Department of Genomics and Biotechnology, Plant Breeding and Genetics Institute - National Center of Seed and Cultivar Investigation, Ovidiopolskaya Road 3, Odessa, 65036, Ukraine,
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Brunet A, Chevalier S, Destainville N, Manghi M, Rousseau P, Salhi M, Salomé L, Tardin C. Probing a label-free local bend in DNA by single molecule tethered particle motion. Nucleic Acids Res 2015; 43:e72. [PMID: 25765645 PMCID: PMC4477641 DOI: 10.1093/nar/gkv201] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 03/01/2015] [Indexed: 02/07/2023] Open
Abstract
Being capable of characterizing DNA local bending is essential to understand thoroughly many biological processes because they involve a local bending of the double helix axis, either intrinsic to the sequence or induced by the binding of proteins. Developing a method to measure DNA bend angles that does not perturb the conformation of the DNA itself or the DNA-protein complex is a challenging task. Here, we propose a joint theory-experiment high-throughput approach to rigorously measure such bend angles using the Tethered Particle Motion (TPM) technique. By carefully modeling the TPM geometry, we propose a simple formula based on a kinked Worm-Like Chain model to extract the bend angle from TPM measurements. Using constructs made of 575 base-pair DNAs with in-phase assemblies of one to seven 6A-tracts, we find that the sequence CA6CGG induces a bend angle of 19° ± 4°. Our method is successfully compared to more theoretically complex or experimentally invasive ones such as cyclization, NMR, FRET or AFM. We further apply our procedure to TPM measurements from the literature and demonstrate that the angles of bends induced by proteins, such as Integration Host Factor (IHF) can be reliably evaluated as well.
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Affiliation(s)
- Annaël Brunet
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Sébastien Chevalier
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Nicolas Destainville
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France
| | - Manoel Manghi
- CNRS; LPT (Laboratoire de Physique Théorique); UMR UPS-CNRS 5152; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LPT; F-31062 Toulouse, France
| | - Philippe Rousseau
- CNRS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); UMR CNRS-UPS 5100; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LMGM; F-31062 Toulouse, France
| | - Maya Salhi
- CNRS; LMGM (Laboratoire de Microbiologie et Génétique Moléculaires); UMR CNRS-UPS 5100; 118 route de Narbonne, F-31062 Toulouse, France Université de Toulouse; UPS; LMGM; F-31062 Toulouse, France
| | - Laurence Salomé
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
| | - Catherine Tardin
- CNRS; IPBS (Institut de Pharmacologie et de Biologie Structurale); UMR UPS-CNRS 5089; 205 route de Narbonne, F-31077 Toulouse, France Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
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31
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Verner Z, Basu S, Benz C, Dixit S, Dobáková E, Faktorová D, Hashimi H, Horáková E, Huang Z, Paris Z, Peña-Diaz P, Ridlon L, Týč J, Wildridge D, Zíková A, Lukeš J. Malleable mitochondrion of Trypanosoma brucei. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:73-151. [PMID: 25708462 DOI: 10.1016/bs.ircmb.2014.11.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The importance of mitochondria for a typical aerobic eukaryotic cell is undeniable, as the list of necessary mitochondrial processes is steadily growing. Here, we summarize the current knowledge of mitochondrial biology of an early-branching parasitic protist, Trypanosoma brucei, a causative agent of serious human and cattle diseases. We present a comprehensive survey of its mitochondrial pathways including kinetoplast DNA replication and maintenance, gene expression, protein and metabolite import, major metabolic pathways, Fe-S cluster synthesis, ion homeostasis, organellar dynamics, and other processes. As we describe in this chapter, the single mitochondrion of T. brucei is everything but simple and as such rivals mitochondria of multicellular organisms.
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Affiliation(s)
- Zdeněk Verner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Present address: Faculty of Sciences, Charles University, Prague, Czech Republic
| | - Somsuvro Basu
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Germany
| | - Corinna Benz
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Sameer Dixit
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Present address: Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Zhenqiu Huang
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Priscila Peña-Diaz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Lucie Ridlon
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic; Present address: Salk Institute, La Jolla, San Diego, USA
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - David Wildridge
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
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32
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Zubatiuk T, Shishkin O, Gorb L, Hovorun D, Leszczynski J. Structural waters in the minor and major grooves of DNA--a major factor governing structural adjustments of the A-T mini-helix. J Phys Chem B 2014; 119:381-91. [PMID: 25495126 DOI: 10.1021/jp5075225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of microhydration in structural adjustments of the AT-tract in B-DNA was studied at the B97-D/def2-SV(P) level. The (dA:dT)5 complexes with 10 water molecules in minor and 15 water molecules in major grooves were studied. The obtained network of hydrogen bonds revealed the dependence between the groove width and the types of water patterns. In the minor groove, the following patterns were observed: interstrand one-water bridges similar to that of the Dickerson "water spine" and interstrand two-water bridges. The network of structural waters in the major groove is more diverse than that in the minor groove, which agrees with crystallographic data. As the major groove is wider, it is enriched by water molecules forming two- and three-water bridges. Results suggest the nucleobase-water interactions in both grooves prevent AT-tract twisting and its "collapse" along the minor groove. Whereby, a helix structure with narrow minor and wide major grooves is formed. The structural waters affect the polynucleotide conformation so that it becomes similar to poly(dA)·poly(dT) in fibers and acquires features of the A-tracts in DNA in solution. We suggest that formation of specific water patterns in both grooves is the factor responsible for stabilization of A-tracts with a narrowed minor groove, leading in turn to their strong intrinsic bending in DNA.
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Affiliation(s)
- Tetiana Zubatiuk
- Division of Functional Materials Chemistry, SSI "Institute for Single Crystals" National Academy of Science of Ukraine , Kharkiv, 61001, Ukraine
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Abstract
I knew nothing and had thought nothing about parasites until 1971. In fact, if you had asked me before then, I might have commented that parasites were rather disgusting. I had been at the Johns Hopkins School of Medicine for three years, and I was on the lookout for a new project. In 1971, I came across a paper in the Journal of Molecular Biology by Larry Simpson, a classmate of mine in graduate school. Larry's paper described a remarkable DNA structure known as kinetoplast DNA (kDNA), isolated from a parasite. kDNA, the mitochondrial genome of trypanosomatids, is a DNA network composed of several thousand interlocked DNA rings. Almost nothing was known about it. I was looking for a project on DNA replication, and I wanted it to be both challenging and important. I had no doubt that working with kDNA would be a challenge, as I would be exploring uncharted territory. I was also sure that the project would be important when I learned that parasites with kDNA threaten huge populations in underdeveloped tropical countries. Looking again at Larry's paper, I found the electron micrographs of the kDNA networks to be rather beautiful. I decided to take a chance on kDNA. Little did I know then that I would devote the next forty years of my life to studying kDNA replication.
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Affiliation(s)
- Paul T Englund
- From the Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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34
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Ferrándiz MJ, Arnanz C, Martín-Galiano AJ, Rodríguez-Martín C, de la Campa AG. Role of global and local topology in the regulation of gene expression in Streptococcus pneumoniae. PLoS One 2014; 9:e101574. [PMID: 25019515 PMCID: PMC4096756 DOI: 10.1371/journal.pone.0101574] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/09/2014] [Indexed: 11/19/2022] Open
Abstract
The most basic level of transcription regulation in Streptococcus pneumoniae is the organization of its chromosome in topological domains. In response to drugs that caused DNA-relaxation, a global transcriptional response was observed. Several chromosomal domains were identified based on the transcriptional response of their genes: up-regulated (U), down-regulated (D), non-regulated (N), and flanking (F). We show that these distinct domains have different expression and conservation characteristics. Microarray fluorescence units under non-relaxation conditions were used as a measure of gene transcriptional level. Fluorescence units were significantly lower in F genes than in the other domains with a similar AT content. The transcriptional level of the domains categorized them was D>U>F. In addition, a comparison of 12 S. pneumoniae genome sequences showed a conservation of gene composition within U and D domains, and an extensive gene interchange in F domains. We tested the organization of chromosomal domains by measuring the relaxation-mediated transcription of eight insertions of a heterologous Ptccat cassette, two in each type of domain, showing that transcription depended on their chromosomal location. Moreover, transcription from the four promoters directing the five genes involved in supercoiling homeostasis, located either in U (gyrB), D (topA), or N (gyrA and parEC) domains was analyzed both in their chromosomal locations and in a replicating plasmid. Although expression from the chromosomal PgyrB and PtopA showed the expected domain regulation, their expression was down-regulated in the plasmid, which behaved as a D domain. However, both PparE and PgyrA carried their own regulatory signals, their topology-dependent expression being equivalent in the plasmid or in the chromosome. In PgyrA a DNA bend acted as a DNA supercoiling sensor. These results revealed that DNA topology functions as a general transcriptional regulator, superimposed upon other more specific regulatory mechanisms.
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Affiliation(s)
- María-José Ferrándiz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Cristina Arnanz
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Antonio J. Martín-Galiano
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Carlos Rodríguez-Martín
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, Madrid, Spain
| | - Adela G. de la Campa
- Unidad de Genética Bacteriana, Centro Nacional de Microbiología, Instituto de Salud Carlos III and CIBER Enfermedades Respiratorias, Madrid, Spain
- Consejo Superior de Investigaciones Científicas, Madrid, Spain
- * E-mail:
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35
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Abstract
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with ∼100 base pairs, is addressed. Three minicircles with different radii and almost equal contents of AT and GC pairs are investigated. The DNA sequences are modeled by a mesoscopic Hamiltonian which describes the essential interactions in the helix at the level of the base pair and incorporates twisting and bending degrees of freedom. Helix unwinding and bubble formation patterns are consistently computed by a path integral method that sums over a large number of molecule configurations compatible with the model potential. The path ensembles are determined, as a function of temperature, by minimizing the free energy of the system. Fluctuational openings appear along the helix to release the stress due to the bending of the molecule backbone. In agreement with the experimental findings, base pair disruptions are found with larger probability in the smallest minicircle of 66 bps whose bending angle is ∼6°. For this minicircle, a sizeable untwisting is obtained with the helical repeat showing a step-like increase at T = 315 K. The method can be generalized to determine the bubble probability profiles of open ends linear sequences.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology - CNISM, Università di Camerino, I-62032 Camerino, Italy.
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36
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Role of promoter DNA sequence variations on the binding of EGR1 transcription factor. Arch Biochem Biophys 2014; 549:1-11. [PMID: 24657079 DOI: 10.1016/j.abb.2014.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 03/02/2014] [Accepted: 03/10/2014] [Indexed: 12/20/2022]
Abstract
In response to a wide variety of stimuli such as growth factors and hormones, EGR1 transcription factor is rapidly induced and immediately exerts downstream effects central to the maintenance of cellular homeostasis. Herein, our biophysical analysis reveals that DNA sequence variations within the target gene promoters tightly modulate the energetics of binding of EGR1 and that nucleotide substitutions at certain positions are much more detrimental to EGR1-DNA interaction than others. Importantly, the reduction in binding affinity poorly correlates with the loss of enthalpy and gain of entropy-a trend indicative of a complex interplay between underlying thermodynamic factors due to the differential role of water solvent upon nucleotide substitution. We also provide a rationale for the physical basis of the effect of nucleotide substitutions on the EGR1-DNA interaction at atomic level. Taken together, our study bears important implications on understanding the molecular determinants of a key protein-DNA interaction at the cross-roads of human health and disease.
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Abstract
In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered.
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Affiliation(s)
- Jack D Griffith
- From the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295
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38
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Matyášek R, Fulneček J, Kovařík A. Evaluation of DNA bending models in their capacity to predict electrophoretic migration anomalies of satellite DNA sequences. Electrophoresis 2013; 34:2511-21. [PMID: 23784748 DOI: 10.1002/elps.201300227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 06/06/2013] [Accepted: 06/06/2013] [Indexed: 01/05/2023]
Abstract
DNA containing a sequence that generates a local curvature exhibits a pronounced retardation in electrophoretic mobility. Various theoretical models have been proposed to explain relationship between DNA structural features and migration anomaly. Here, we studied the capacity of 15 static wedge-bending models to predict electrophoretic behavior of 69 satellite monomers derived from four divergent families. All monomers exhibited retarded mobility in PAGE corresponding to retardation factors ranging 1.02-1.54. The curvature varied both within and across the groups and correlated with the number, position, and lengths of A-tracts. Two dinucleotide models provided strong correlation between gel mobility and curvature prediction; two trinucleotide models were satisfactory while remaining dinucleotide models provided intermediate results with reliable prediction for subsets of sequences only. In some cases, similarly shaped molecules exhibited relatively large differences in mobility and vice versa. Generally less accurate predictions were obtained in groups containing less homogeneous sequences possessing distinct structural features. In conclusion, relatively universal theoretical models were identified suitable for the analysis of natural sequences known to harbor relatively moderate curvature. These models could be potentially applied to genome wide studies. However, in silico predictions should be viewed in context of experimental measurement of intrinsic DNA curvature.
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Affiliation(s)
- Roman Matyášek
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i, Brno, Czech Republic.
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39
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Grant BN, Dourlain EM, Araneda JN, Throneberry ML, McFail-Isom LA. DNA phosphate crowding correlates with protein cationic side chain density and helical curvature in protein/DNA crystal structures. Nucleic Acids Res 2013; 41:7547-55. [PMID: 23748560 PMCID: PMC3753625 DOI: 10.1093/nar/gkt492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Sequence-specific binding of proteins to their DNA targets involves a complex spectrum of processes that often induce DNA conformational variation in the bound complex. The forces imposed by protein binding that cause the helical deformations are intimately interrelated and difficult to parse or rank in importance. To investigate the role of electrostatics in helical deformation, we quantified the relationship between protein cationic residue density (Cpc) and DNA phosphate crowding (Cpp). The correlation between Cpc and Cpp was then calculated for a subset of 58 high resolution protein-DNA crystal structures. Those structures containing strong Cpc/Cpp correlation (>±0.25) were likely to contain DNA helical curvature. Further, the correlation factor sign predicted the direction of helical curvature with positive (16 structures) and negative (seven structures) correlation containing concave (DNA curved toward protein) and convex (DNA curved away from protein) curvature, respectively. Protein-DNA complexes without significant Cpc/Cpp (36 structures) correlation (-0.25<0<0.25) tended to contain DNA without significant curvature. Interestingly, concave and convex complexes also include more arginine and lysine phosphate contacts, respectively, whereas linear complexes included essentially equivalent numbers of Lys/Arg phosphate contacts. Together, these findings suggest an important role for electrostatic interactions in protein-DNA complexes involving helical curvature.
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Affiliation(s)
- Bryce N Grant
- Department of Chemistry, University of Central Arkansas, Conway, AR 72035, USA
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40
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Trifonov EN. Towards clarity in a very complex matter: comment on "Sequence-dependent collective properties of DNAs and their role in biological systems" by De Santis and Scipioni. Phys Life Rev 2013; 10:80-1; discussion 82-4. [PMID: 23499298 DOI: 10.1016/j.plrev.2013.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Edward N Trifonov
- Genome Diversity Center, Institute of Evolution, University of Haifa, Haifa 31905, Israel.
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41
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Sequence-dependent collective properties of DNAs and their role in biological systems. Phys Life Rev 2013; 10:41-67. [DOI: 10.1016/j.plrev.2013.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 01/22/2013] [Indexed: 12/19/2022]
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42
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Shimooka Y, Nishikawa JI, Ohyama T. Most methylation-susceptible DNA sequences in human embryonic stem cells undergo a change in conformation or flexibility upon methylation. Biochemistry 2013; 52:1344-53. [PMID: 23356538 DOI: 10.1021/bi301319y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA methylation in eukaryotes occurs on the cytosine bases in CG, CHG, and CHH (where H indicates non-G nucleotides) contexts and provides an important epigenetic mark in various biological processes. However, the structural and physical properties of methylated DNA are poorly understood. Using nondenaturing polyacrylamide gel electrophoresis, we performed a systematic study of the influence of DNA methylation on the conformation and physical properties of DNA for all CG, CHG, and CHH contexts. In the CG context, methylated multimers of the CG/CG-containing unit fragment migrated in gels slightly faster than their unmethylated counterparts. In the CHG context, both homo- and hemimethylation caused retarded migration of multimers of the CAG/CTG-containing fragment. In the CHH context, methylation caused or enhanced retarded migration of the multimers of CAA/TTG-, CAT/ATG-, CAC/GTG-, CTA/TAG-, or CTT/AAG-containing fragments. These results suggest that methylation increases DNA rigidity in the CG context and introduces distortions into several CHG and CHH sequences. More interestingly, we found that nearly all of the methylation repertoires in the CHG context and 98% of those in the CHH context in human embryonic stem cells were species that undergo conformational changes upon methylation. Similarly, most of the methylation repertoires in the Arabidopsis CHG and CHH contexts were sequences with methylation-induced distortion. We hypothesize that the methylation-induced properties or conformational changes in DNA may facilitate nucleosome formation, which provides the essential mechanism for alterations of chromatin density.
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Affiliation(s)
- Yasutoshi Shimooka
- Major in Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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43
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Nikolova EN, Bascom GD, Andricioaei I, Al-Hashimi HM. Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations. Biochemistry 2012; 51:8654-64. [PMID: 23035755 DOI: 10.1021/bi3009517] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Sequence-specific DNA flexibility plays a key role in a variety of cellular interactions that are critical for gene packaging, expression, and regulation, yet few studies have experimentally explored the sequence dependence of DNA dynamics that occur on biologically relevant time scales. Here, we use nuclear magnetic resonance (NMR) carbon spin relaxation combined with molecular dynamics (MD) simulations to examine the picosecond to nanosecond dynamics in a variety of dinucleotide steps as well as in varying length homopolymeric A(n)·T(n) repeats (A(n)-tracts, where n = 2, 4, or 6) that exhibit unusual structural and mechanical properties. We extend the NMR spin relaxation time scale sensitivity deeper into the nanosecond regime by using glycerol and a longer DNA duplex to slow overall tumbling. Our studies reveal a structurally unique A-tract core (for n > 3) that is uniformly rigid, flanked by junction steps that show increasing sugar flexibility with A-tract length. High sugar mobility is observed at pyrimidine residues at the A-tract junctions, which is encoded at the dinucleotide level (CA, TG, and CG steps) and increases with A-tract length. The MD simulations reproduce many of these trends, particularly the overall rigidity of A-tract base and sugar sites, and suggest that the sugar-backbone dynamics could involve transitions in sugar pucker and phosphate backbone BI ↔ BII equilibria. Our results reinforce an emerging view that sequence-specific DNA flexibility can be imprinted in dynamics occurring deep within the nanosecond time regime that is difficult to characterize experimentally at the atomic level. Such large-amplitude sequence-dependent backbone fluctuations might flag the genome for specific DNA recognition.
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Affiliation(s)
- Evgenia N Nikolova
- Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48109, USA
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44
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The Ashikaga case of Japan--Y-STR testing used as the exculpatory evidence to free a convicted felon after 17.5 years in prison. Forensic Sci Int Genet 2012; 7:e1-2. [PMID: 22884708 DOI: 10.1016/j.fsigen.2012.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 11/22/2022]
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45
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Lezov AV, Polushina GE. Electro-optics of solutions of biopolymers and their complexes. POLYMER SCIENCE SERIES A 2012. [DOI: 10.1134/s0965545x1205015x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Travers AA, Muskhelishvili G, Thompson JMT. DNA information: from digital code to analogue structure. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2012; 370:2960-2986. [PMID: 22615471 DOI: 10.1098/rsta.2011.0231] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The digital linear coding carried by the base pairs in the DNA double helix is now known to have an important component that acts by altering, along its length, the natural shape and stiffness of the molecule. In this way, one region of DNA is structurally distinguished from another, constituting an additional form of encoded information manifest in three-dimensional space. These shape and stiffness variations help in guiding and facilitating the DNA during its three-dimensional spatial interactions. Such interactions with itself allow communication between genes and enhanced wrapping and histone-octamer binding within the nucleosome core particle. Meanwhile, interactions with proteins can have a reduced entropic binding penalty owing to advantageous sequence-dependent bending anisotropy. Sequence periodicity within the DNA, giving a corresponding structural periodicity of shape and stiffness, also influences the supercoiling of the molecule, which, in turn, plays an important facilitating role. In effect, the super-helical density acts as an analogue regulatory mode in contrast to the more commonly acknowledged purely digital mode. Many of these ideas are still poorly understood, and represent a fundamental and outstanding biological question. This review gives an overview of very recent developments, and hopefully identifies promising future lines of enquiry.
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Affiliation(s)
- A A Travers
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.
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47
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Bullwinkle TJ, Samorodnitsky D, Rosati RC, Koudelka GB. Determinants of bacteriophage 933W repressor DNA binding specificity. PLoS One 2012; 7:e34563. [PMID: 22509323 PMCID: PMC3317979 DOI: 10.1371/journal.pone.0034563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 03/06/2012] [Indexed: 11/22/2022] Open
Abstract
We reported previously that 933W repressor apparently does not cooperatively bind to adjacent sites on DNA and that the relative affinities of 933W repressor for its operators differ significantly from that of any other lambdoid bacteriophage. These findings indicate that the operational details of the lysis-lysogeny switch of bacteriophage 933W are unique among lambdoid bacteriophages. Since the functioning of the lysis-lysogeny switch in 933W bacteriophage uniquely and solely depends on the order of preference of 933W repressor for its operators, we examined the details of how 933W repressor recognizes its DNA sites. To identify the specificity determinants, we first created a molecular model of the 933W repressor-DNA complex and tested the predicted protein-DNA interactions. These results of these studies provide a picture of how 933W repressor recognizes its DNA sites. We also show that, opposite of what is normally observed for lambdoid phages, 933W operator sequences have evolved in such a way that the presence of the most commonly found base sequences at particular operator positions serves to decrease, rather than increase, the affinity of the protein for the site. This finding cautions against assuming that a consensus sequence derived from sequence analysis defines the optimal, highest affinity DNA binding site for a protein.
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Affiliation(s)
- Tammy J. Bullwinkle
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Daniel Samorodnitsky
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Rayna C. Rosati
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
| | - Gerald B. Koudelka
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, United States of America
- * E-mail:
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48
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Tan HK, Li D, Gray RK, Yang Z, Ng MTT, Zhang H, Tan JMR, Hiew SH, Lee JY, Li T. Interference of intrinsic curvature of DNA by DNA-intercalating agents. Org Biomol Chem 2012; 10:2227-30. [PMID: 22331171 DOI: 10.1039/c2ob06811g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
It has been demonstrated in our studies that the intrinsic curvature of DNA can be easily interrupted by low concentrations of chloroquine and ethidium bromide. In addition, the changes of DNA curvature caused by varying the concentration of these two DNA intercalators can be readily verified through using an atomic force microscope.
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Affiliation(s)
- Hong Kee Tan
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371
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Matyasek R, Fulnecek J, Leitch AR, Kovarik A. Analysis of two abundant, highly related satellites in the allotetraploid Nicotiana arentsii using double-strand conformation polymorphism analysis and sequencing. THE NEW PHYTOLOGIST 2011; 192:747-59. [PMID: 21777247 DOI: 10.1111/j.1469-8137.2011.03827.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
• Allopolyploidy, a driving force in plant evolution, can induce rapid structural changes in parental subgenomes. Here, we examined the fate of homologous subtelomeric satellites in intrasection allotetraploid Nicotiana arentsii formed from N. undulata and N. wigandioides progenitors < 200,000 yr ago. • We cloned and sequenced a number of monomers from progenitors and the allotetraploid. Structural features of both cloned and genomic monomers were studied using double-strand conformation polymorphism analysis. • Two homologous satellites were isolated from N. undulata (called NUNSSP) and N. wigandioides (NWISSP). While the NUNSSP monomers were highly homogeneous in nucleotide sequences, the NWISSP monomers formed two separate clades. Likewise, the genomic NUNSSP monomers showed less DNA conformation heterogeneity than NWISSP monomers, with distinct conformations. While both satellites predominantly occupy subtelomeric positions, a fraction of the NWISSP repeats was found in an intercalary location, supporting the hypothesis that dispersion prevents the repeats becoming homogeneous. Sequence, structural and chromosomal features of the parental satellites were faithfully inherited by N. arentsii. • Our study revealed that intergenomic homogenization of subtelomeric satellite repeats does not occur in N. arentsii allotetraploid. We propose that the sequence and structural divergence of subtelomeric satellites may render allopolyploid chromosomes less vulnerable to intergenomic exchanges.
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Affiliation(s)
- Roman Matyasek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, vvi, Brno, Czech Republic.
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50
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Rawal K, Ramaswamy R. Genome-wide analysis of mobile genetic element insertion sites. Nucleic Acids Res 2011; 39:6864-78. [PMID: 21609951 PMCID: PMC3167599 DOI: 10.1093/nar/gkr337] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Mobile genetic elements (MGEs) account for a significant fraction of eukaryotic genomes and are implicated in altered gene expression and disease. We present an efficient computational protocol for MGE insertion site analysis. ELAN, the suite of tools described here uses standard techniques to identify different MGEs and their distribution on the genome. One component, DNASCANNER analyses known insertion sites of MGEs for the presence of signals that are based on a combination of local physical and chemical properties. ISF (insertion site finder) is a machine-learning tool that incorporates information derived from DNASCANNER. ISF permits classification of a given DNA sequence as a potential insertion site or not, using a support vector machine. We have studied the genomes of Homo sapiens, Mus musculus, Drosophila melanogaster and Entamoeba histolytica via a protocol whereby DNASCANNER is used to identify a common set of statistically important signals flanking the insertion sites in the various genomes. These are used in ISF for insertion site prediction, and the current accuracy of the tool is over 65%. We find similar signals at gene boundaries and splice sites. Together, these data are suggestive of a common insertion mechanism that operates in a variety of eukaryotes.
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Affiliation(s)
- Kamal Rawal
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110 067, India
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