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Cook TW, Wilstermann AM, Mitchell JT, Arnold NE, Rajasekaran S, Bupp CP, Prokop JW. Understanding Insulin in the Age of Precision Medicine and Big Data: Under-Explored Nature of Genomics. Biomolecules 2023; 13:257. [PMID: 36830626 PMCID: PMC9953665 DOI: 10.3390/biom13020257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Insulin is amongst the human genome's most well-studied genes/proteins due to its connection to metabolic health. Within this article, we review literature and data to build a knowledge base of Insulin (INS) genetics that influence transcription, transcript processing, translation, hormone maturation, secretion, receptor binding, and metabolism while highlighting the future needs of insulin research. The INS gene region has 2076 unique variants from population genetics. Several variants are found near the transcriptional start site, enhancers, and following the INS transcripts that might influence the readthrough fusion transcript INS-IGF2. This INS-IGF2 transcript splice site was confirmed within hundreds of pancreatic RNAseq samples, lacks drift based on human genome sequencing, and has possible elevated expression due to viral regulation within the liver. Moreover, a rare, poorly characterized African population-enriched variant of INS-IGF2 results in a loss of the stop codon. INS transcript UTR variants rs689 and rs3842753, associated with type 1 diabetes, are found in many pancreatic RNAseq datasets with an elevation of the 3'UTR alternatively spliced INS transcript. Finally, by combining literature, evolutionary profiling, and structural biology, we map rare missense variants that influence preproinsulin translation, proinsulin processing, dimer/hexamer secretory storage, receptor activation, and C-peptide detection for quasi-insulin blood measurements.
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Affiliation(s)
- Taylor W. Cook
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Jackson T. Mitchell
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Nicholas E. Arnold
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Division of Medical Genetics, Corewell Health, Grand Rapids, MI 49503, USA
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Office of Research, Corewell Health, Grand Rapids, MI 49503, USA
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2
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Synthesis, spectral investigation, biological activities and docking stimulation of novel metal complexes of Trifluoro phenylthiazol derivative with computational studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Ghoshdastidar D, Bansal M. Flexibility of flanking DNA is a key determinant of transcription factor affinity for the core motif. Biophys J 2022; 121:3987-4000. [PMID: 35978548 PMCID: PMC9674967 DOI: 10.1016/j.bpj.2022.08.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 07/28/2022] [Accepted: 08/15/2022] [Indexed: 11/02/2022] Open
Abstract
Selective gene regulation is mediated by recognition of specific DNA sequences by transcription factors (TFs). The extremely challenging task of searching out specific cognate DNA binding sites among several million putative sites within the eukaryotic genome is achieved by complex molecular recognition mechanisms. Elements of this recognition code include the core binding sequence, the flanking sequence context, and the shape and conformational flexibility of the composite binding site. To unravel the extent to which DNA flexibility modulates TF binding, in this study, we employed experimentally guided molecular dynamics simulations of ternary complex of closely related Hox heterodimers Exd-Ubx and Exd-Scr with DNA. Results demonstrate that flexibility signatures embedded in the flanking sequences impact TF binding at the cognate binding site. A DNA sequence has intrinsic shape and flexibility features. While shape features are localized, our analyses reveal that flexibility features of the flanking sequences percolate several basepairs and allosterically modulate TF binding at the core. We also show that lack of flexibility in the motif context can render the cognate site resistant to protein-induced shape changes and subsequently lower TF binding affinity. Overall, this study suggests that flexibility-guided DNA shape, and not merely the static shape, is a key unexplored component of the complex DNA-TF recognition code.
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Affiliation(s)
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, Karnataka, India.
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4
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Synthesis of novel antipyrine-azole-S-alkyl derivatives antimicrobial activity, molecular docking, and computational studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132810] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Synthesis, X-ray crystal structure, Hirshfeld analysis and computational investigation of bis(methylthio)acrylonitrile with antimicrobial and docking evaluation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132793] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Fahim AM, Magar HS, Ayoub MA. Synthesis, characterization, thermal Studies, electrochemical behavior, antimicrobial, docking studies, and computational simulation of triazole‐thiol metal complexes. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Asmaa M. Fahim
- Department of Green chemistry National Research Center, Dokki Cairo Egypt
| | - Hend S. Magar
- App. Org. Chemistry Department, National Research Centre, Dokki Cairo Egypt
| | - Manara A. Ayoub
- Chemistry Department, Faculty of Women for Arts, Science and Education, Ain‐Shams University Cairo Egypt
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7
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Enhancement of Molecular imprinted polymer as organic fillers on bagasse cellulose fibers with biological evaluation and computational calculations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130660] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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8
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Duan B, Ding P, Navarre WW, Liu J, Xia B. Xenogeneic Silencing and Bacterial Genome Evolution: Mechanisms for DNA Recognition Imply Multifaceted Roles of Xenogeneic Silencers. Mol Biol Evol 2021; 38:4135-4148. [PMID: 34003286 PMCID: PMC8476142 DOI: 10.1093/molbev/msab136] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/08/2021] [Indexed: 12/14/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from nonself DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli, Lsr2 of Mycobacterium, MvaT of Pseudomonas, and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
| | - William Wiley Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5G 1M1, Canada
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing, 100871, China
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9
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Performance efficiency of MIPOH polymers as organic filler on cellulose pulp waste to form cellulosic paper sheets with biological evaluation and computational studies. Polym Bull (Berl) 2021. [DOI: 10.1007/s00289-021-03685-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Soror S, Fahim AM, Elabbady S, Nassar E, Aboelnaga A. Synthesis, antimicrobial activities, docking studies and computational calculations of new bis-1,4-phenylene -1 H-1,2,3-triazole derivatives utilized ultrasonic energy. J Biomol Struct Dyn 2021; 40:5409-5426. [PMID: 33522432 DOI: 10.1080/07391102.2021.1875051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
In this elucidation, we studied the utility of condensation reaction between 1,4-phenylenediamine (1) with acetyl acetone (2) with hydrazine hydrate utilized ultrasonic energy in one step reaction to afford the corresponding 1,1'-(1,4-phenylenebis (5-methyl-1H-1,2,3-triazole-1,4-diyl))bis(ethan-1-one) (4) in excellent yield. The ethanol solution of bis triazole (4) and different aldehyde derivatives were sonicated at 75 °C for 2 h to afford chalcone derivatives 5a-d which were confirmed via spectral data such as FTIR, 1HNMR, 13CNMR and mass spectra. Moreover, the intermolecular cyclization of chalcone (5a) with NH2NH2 in sodium hydroxide solution to give the corresponding 4,5-dihydro-1H-pyrazol-5-yl)-1H-indole (6) using ultrasonic energy for 4 h, while the Michael addition of chalcones (5a) and (5 b) with thiourea in basic condition to afford the corresponding pyrimidine-2-thiol derivatives (7) and (9). Treatment of compound (7) with NH2NH2 to afford 1,4-bis(4-(2-hydrazineyl-6-(1H-indol-3-yl)pyrimidin-4-yl) derivatives (8). The synthesized compounds were screened against various microbial strains and displayed excellent antimicrobial potential. Additionally, the docking studies of these nine compounds were carried out with (PDB ID:3t88), (PDB ID:2wje), (PDB ID:4ynt) and (PDB ID:1tgh) which were attached with different amino acids with shortage bond length, and it was noticed that PMTS1, PMTS2 and PMTS3 were the most stable compounds with the lowest energy affinity which is compatible with biological study. Furthermore, the theoretical investigation of bis-triazole compounds were optimized via DFT/B3LYP/6-31G(d) level which showed the hyperconjugation of nitrogen atoms and elucidated their physical parameters and NBO charges and confirmed their stability and biological activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sahar Soror
- Chemistry Department, Faculty of Women of Arts, Science and Education, Ain Shams University, Heliopolis, Egypt
| | - Asmaa M Fahim
- Green Chemistry Department, National Research Center, Cairo, Egypt
| | - Samia Elabbady
- Chemistry Department, Faculty of Women of Arts, Science and Education, Ain Shams University, Heliopolis, Egypt
| | - Ekhlass Nassar
- Chemistry Department, Faculty of Women of Arts, Science and Education, Ain Shams University, Heliopolis, Egypt
| | - Asmaa Aboelnaga
- Chemistry Department, Faculty of Women of Arts, Science and Education, Ain Shams University, Heliopolis, Egypt
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11
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Gutiérrez-Flores J, Hernández-Lemus E, Cortés-Guzmán F, Ramos E. Do weak interactions affect the biological behavior of DNA? A DFT study of CpG island-like chains. J Mol Model 2020; 26:266. [PMID: 32918237 DOI: 10.1007/s00894-020-04501-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/03/2020] [Indexed: 01/06/2023]
Abstract
The origin, stability, and contribution to the formation of noncovalent interactions, such as hydrogen bonds and π - π stacking, have been already widely discussed. However, there are few discussions about the relevance of these weak interactions in DNA performance. In this work, we seek to shed light on the effect of hydrogen bonds and π - π stacking interactions on the biological behavior of DNA through the description of these intermolecular forces in CpG island-like (GC-rich) chains. Furthermore, we made some comparisons with TATA box-like (TA-rich) chains in order to describe hydrogen bond and π - π stacking interactions as a function of the DNA sequence. For hydrogen bonds, we found that there is not a significant effect related to the number of base pairs. Whereas for π - π stacking interactions, the energy tended to decrease as the number of base pairs increased. We observed anticooperative effects for both hydrogen bonds and π - π stacking interactions. These results are in contrast with those of TATA box-like chains since cooperative and additive effects were found for both hydrogen bonds and π - π stacking, respectively. Based on the chemical hardness and density of states, we can conclude that proteins may interact easier with GC-rich chains. We conclude that regardless of the chain length, a protein could interact more easily with these genomics regions because the π - π stacking energies did not increase as a function of the number of base pairs, making, for the first time, a first approximation of the influence of noncovalent interaction on DNA behavior. We did all this work by means of DFT framework included in the DMol3 code (M06-L/DNP). Graphical Abstract Cartoon representation of how nocovalent interactions affect the interaction of DNA with a protein, i.e., how hydrogen bond and π - π stacking interactions influence the biological behavior of DNA.
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Affiliation(s)
- Jorge Gutiérrez-Flores
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, CDMX, México
| | | | - Fernando Cortés-Guzmán
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, CDMX, México
| | - Estrella Ramos
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, CDMX, México.
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12
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Parra-Marín O, López-Pacheco K, Hernández R, López-Villaseñor I. The highly diverse TATA box-binding proteins among protists: A review. Mol Biochem Parasitol 2020; 239:111312. [PMID: 32771681 DOI: 10.1016/j.molbiopara.2020.111312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/28/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Transcription is the first step of gene expression regulation and is a fundamental mechanism for establishing the viability and development of a cell. The TATA box-binding protein (TBP) interaction with a TATA box in a promoter is one of the best studied mechanisms in transcription initiation. TBP is a transcription factor that is highly conserved from archaea to humans and is essential for the transcription initiated by each of the three RNA polymerases. In addition, the discovery of TBP-related factor 1 (TRF1) and other factors related to TBP shed light on the variability among transcription initiation complexes, thus demonstrating that the compositions of these complexes are, in fact, more complicated than originally believed. Despite these facts, the majority of studies on transcription have been performed on animal, plant and fungal cells, which serve as canonical models, and information regarding protist cells is relatively scarce. The aim of this work is to review the diversity of the TBPs that have been documented in protists and describe some of the specific features that differentiate them from their counterparts in higher eukaryotes.
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Affiliation(s)
- Olivia Parra-Marín
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Karla López-Pacheco
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico.
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13
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Synthesis, antimicrobial evaluation, molecular docking and theoretical calculations of novel pyrazolo[1,5-a]pyrimidine derivatives. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127025] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Garcia-Gimenez G, Russell J, Aubert MK, Fincher GB, Burton RA, Waugh R, Tucker MR, Houston K. Barley grain (1,3;1,4)-β-glucan content: effects of transcript and sequence variation in genes encoding the corresponding synthase and endohydrolase enzymes. Sci Rep 2019. [PMID: 31754200 DOI: 10.1038/s41598-019-53798-53798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
The composition of plant cell walls is important in determining cereal end uses. Unlike other widely consumed cereal grains barley is comparatively rich in (1,3;1,4)-β-glucan, a source of dietary fibre. Previous work showed Cellulose synthase-like genes synthesise (1,3;1,4)-β-glucan in several tissues. HvCslF6 encodes a grain (1,3;1,4)-β-glucan synthase, whereas the function of HvCslF9 is unknown. Here, the relationship between mRNA levels of HvCslF6, HvCslF9, HvGlbI (1,3;1,4)-β-glucan endohydrolase, and (1,3;1,4)-β-glucan content was studied in developing grains of four barley cultivars. HvCslF6 was differentially expressed during mid (8-15 DPA) and late (38 DPA) grain development stages while HvCslF9 transcript was only clearly detected at 8-10 DPA. A peak of HvGlbI expression was detected at 15 DPA. Differences in transcript abundance across the three genes could partially explain variation in grain (1,3;1,4)-β-glucan content in these genotypes. Remarkably narrow sequence variation was found within the HvCslF6 promoter and coding sequence and does not explain variation in (1,3;1,4)-β-glucan content. Our data emphasise the genotype-dependent accumulation of (1,3;1,4)-β-glucan during barley grain development and a role for the balance between hydrolysis and synthesis in determining (1,3;1,4)-β-glucan content, and suggests that other regulatory sequences or proteins are likely to be involved in this trait in developing grain.
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Affiliation(s)
- Guillermo Garcia-Gimenez
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Guillermo Garcia-Gimenez, Agriculture & Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Canberra, ACT 2601, Australia
| | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Matthew K Aubert
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Geoffrey B Fincher
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Rachel A Burton
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Plant Sciences Division, College of Life Sciences, University of Dundee. Dundee, DD1 5EH, Scotland, UK
| | - Matthew R Tucker
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Kelly Houston
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK.
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15
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Garcia-Gimenez G, Russell J, Aubert MK, Fincher GB, Burton RA, Waugh R, Tucker MR, Houston K. Barley grain (1,3;1,4)-β-glucan content: effects of transcript and sequence variation in genes encoding the corresponding synthase and endohydrolase enzymes. Sci Rep 2019; 9:17250. [PMID: 31754200 PMCID: PMC6872655 DOI: 10.1038/s41598-019-53798-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/31/2019] [Indexed: 01/13/2023] Open
Abstract
The composition of plant cell walls is important in determining cereal end uses. Unlike other widely consumed cereal grains barley is comparatively rich in (1,3;1,4)-β-glucan, a source of dietary fibre. Previous work showed Cellulose synthase-like genes synthesise (1,3;1,4)-β-glucan in several tissues. HvCslF6 encodes a grain (1,3;1,4)-β-glucan synthase, whereas the function of HvCslF9 is unknown. Here, the relationship between mRNA levels of HvCslF6, HvCslF9, HvGlbI (1,3;1,4)-β-glucan endohydrolase, and (1,3;1,4)-β-glucan content was studied in developing grains of four barley cultivars. HvCslF6 was differentially expressed during mid (8-15 DPA) and late (38 DPA) grain development stages while HvCslF9 transcript was only clearly detected at 8-10 DPA. A peak of HvGlbI expression was detected at 15 DPA. Differences in transcript abundance across the three genes could partially explain variation in grain (1,3;1,4)-β-glucan content in these genotypes. Remarkably narrow sequence variation was found within the HvCslF6 promoter and coding sequence and does not explain variation in (1,3;1,4)-β-glucan content. Our data emphasise the genotype-dependent accumulation of (1,3;1,4)-β-glucan during barley grain development and a role for the balance between hydrolysis and synthesis in determining (1,3;1,4)-β-glucan content, and suggests that other regulatory sequences or proteins are likely to be involved in this trait in developing grain.
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Affiliation(s)
- Guillermo Garcia-Gimenez
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Guillermo Garcia-Gimenez, Agriculture & Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Canberra, ACT 2601, Australia
| | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Matthew K Aubert
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Geoffrey B Fincher
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Rachel A Burton
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Plant Sciences Division, College of Life Sciences, University of Dundee. Dundee, DD1 5EH, Scotland, UK
| | - Matthew R Tucker
- ARC Centre of Excellence in Plant Cell Walls, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Kelly Houston
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK.
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16
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An in vitro characterisation of the Trichomonas vaginalis TATA box-binding proteins (TBPs). Parasitol Res 2019; 118:3019-3031. [DOI: 10.1007/s00436-019-06438-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/22/2019] [Indexed: 10/26/2022]
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17
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Ding K, Celma CC, Zhang X, Chang T, Shen W, Atanasov I, Roy P, Zhou ZH. In situ structures of rotavirus polymerase in action and mechanism of mRNA transcription and release. Nat Commun 2019; 10:2216. [PMID: 31101900 PMCID: PMC6525196 DOI: 10.1038/s41467-019-10236-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/25/2019] [Indexed: 01/11/2023] Open
Abstract
Transcribing and replicating a double-stranded genome require protein modules to unwind, transcribe/replicate nucleic acid substrates, and release products. Here we present in situ cryo-electron microscopy structures of rotavirus dsRNA-dependent RNA polymerase (RdRp) in two states pertaining to transcription. In addition to the previously discovered universal "hand-shaped" polymerase core domain shared by DNA polymerases and telomerases, our results show the function of N- and C-terminal domains of RdRp: the former opens the genome duplex to isolate the template strand; the latter splits the emerging template-transcript hybrid, guides genome reannealing to form a transcription bubble, and opens a capsid shell protein (CSP) to release the transcript. These two "helicase" domains also extensively interact with CSP, which has a switchable N-terminal helix that, like cellular transcriptional factors, either inhibits or promotes RdRp activity. The in situ structures of RdRp, CSP, and RNA in action inform mechanisms of not only transcription, but also replication.
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Affiliation(s)
- Ke Ding
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Cristina C Celma
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Xing Zhang
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Thomas Chang
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Wesley Shen
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
| | - Ivo Atanasov
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - Polly Roy
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Z Hong Zhou
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA.
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA.
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18
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Hernández-Ibarra NK, Morelos RM, Ramírez JL, Cruz P, Leitch AR, Ibarra AM. Chromosomal and molecular characterization of 5S rRNA genes in the North American abalones Haliotis rufescens Swainson (red abalone) and H. fulgens Philippi (blue abalone). Gene 2019; 695:65-74. [PMID: 30738966 DOI: 10.1016/j.gene.2019.02.003] [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: 02/23/2018] [Revised: 01/17/2019] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Abstract
Abalone is an extremely valuable food source derived from cultured and wild animals, the later from populations under intense fishing exploitation and of high conservation value. As part of a long-term study to characterize genes from abalone that can be used as markers for hybrids certification, we characterised 5S ribosomal DNA (5S rDNA) in red abalone (Haliotis rufescens) and blue abalone (H. fulgens). The 5S rDNA arrays occur to a single pair of metacentric chromosomes at interstitial positions in both species. Two types of 5S genes were found, named types I and II, each associated with different non-transcribed spacer (NTS) sequences. The structure of the 5S rRNA genes and the NTS indicate incomplete homogenisation of the 5S rDNA arrays. The divergence of the 5S genes between species provide polymorphisms which can be used to distinguish red from blue abalone in forensic analysis of commercial production.
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Affiliation(s)
- Norma K Hernández-Ibarra
- Aquaculture Genetics & Breeding Laboratory, Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Sta. Rita, La Paz, BCS 23096, Mexico
| | - Rosa M Morelos
- Aquaculture Genetics & Breeding Laboratory, Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Sta. Rita, La Paz, BCS 23096, Mexico
| | - José L Ramírez
- Aquaculture Genetics & Breeding Laboratory, Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Sta. Rita, La Paz, BCS 23096, Mexico
| | - Pedro Cruz
- Aquaculture Genetics & Breeding Laboratory, Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Sta. Rita, La Paz, BCS 23096, Mexico
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Ana M Ibarra
- Aquaculture Genetics & Breeding Laboratory, Centro de Investigaciones Biológicas del Noroeste, Av. Instituto Politécnico Nacional 195, Col. Playa Palo de Sta. Rita, La Paz, BCS 23096, Mexico.
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19
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Thornlow BP, Hough J, Roger JM, Gong H, Lowe TM, Corbett-Detig RB. Transfer RNA genes experience exceptionally elevated mutation rates. Proc Natl Acad Sci U S A 2018; 115:8996-9001. [PMID: 30127029 PMCID: PMC6130373 DOI: 10.1073/pnas.1801240115] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Transfer RNAs (tRNAs) are a central component for the biological synthesis of proteins, and they are among the most highly conserved and frequently transcribed genes in all living things. Despite their clear significance for fundamental cellular processes, the forces governing tRNA evolution are poorly understood. We present evidence that transcription-associated mutagenesis and strong purifying selection are key determinants of patterns of sequence variation within and surrounding tRNA genes in humans and diverse model organisms. Remarkably, the mutation rate at broadly expressed cytosolic tRNA loci is likely between 7 and 10 times greater than the nuclear genome average. Furthermore, evolutionary analyses provide strong evidence that tRNA genes, but not their flanking sequences, experience strong purifying selection acting against this elevated mutation rate. We also find a strong correlation between tRNA expression levels and the mutation rates in their immediate flanking regions, suggesting a simple method for estimating individual tRNA gene activity. Collectively, this study illuminates the extreme competing forces in tRNA gene evolution and indicates that mutations at tRNA loci contribute disproportionately to mutational load and have unexplored fitness consequences in human populations.
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Affiliation(s)
- Bryan P Thornlow
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
| | - Josh Hough
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
| | - Jacquelyn M Roger
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
| | - Henry Gong
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064;
- Genomics Institute, University of California, Santa Cruz, CA 95064
| | - Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064;
- Genomics Institute, University of California, Santa Cruz, CA 95064
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20
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Probing the evolutionary conserved residues Y204, F259, S400 and W590 that shape the catalytic groove of human TDP1 for 3'- and 5'-phosphodiester-DNA bond cleavage. DNA Repair (Amst) 2018; 66-67:64-71. [PMID: 29747024 DOI: 10.1016/j.dnarep.2018.05.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/10/2018] [Accepted: 05/01/2018] [Indexed: 11/20/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (TDP1) is an ubiquitous DNA repair enzyme present in yeast, plants and animals. It removes a broad range of blocking lesions at the ends of DNA breaks. The catalytic core of TDP1 consists in a pair of conserved histidine-lysine-asparagine (HKN) motifs. Analysis of the human TDP1 (hTDP1) crystal structure reveals potential involvement of additional residues that shape the substrate binding site. In this biochemical study, we analyzed four such conserved residues, tyrosine 204 (Y204), phenylalanine 259 (F259), serine 400 (S400) and tryptophan 590 (W590). We show that the F259 residue of hTDP1 is critical for both 3'- and 5'-phosphodiesterase catalysis. We propose that the double π-π interactions of the F259 residue with the -2 and -3 nucleobases serve to position the nucleopeptide substrate in phase with the active site histidines of hTDP1. Mutating Y204 of hTDP1 to phenylalanine (Y204F), as in fly and yeast TDP1 enzymes, had minor impact on TDP1 activity. In constrast, we find that S400 enhances 3'-processing activity while it suppresses 5'-processing activity, thereby promoting specificity for 3'-substrates. W590 is selectively important for 5'-processing. These results reveal the impact of conserved amino acid residues that participate in defining the DNA binding groove around the dual HKN catalytic core motif of TDP1, and their differential roles in facilitating the 3'- vs 5'-end processing activities of hTDP1.
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21
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Kinyanyi D, Obiero G, Obiero GFO, Amwayi P, Mwaniki S, Wamalwa M. In silico structural and functional prediction of African swine fever virus protein-B263R reveals features of a TATA-binding protein. PeerJ 2018; 6:e4396. [PMID: 29492339 PMCID: PMC5825884 DOI: 10.7717/peerj.4396] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/30/2018] [Indexed: 11/26/2022] Open
Abstract
African swine fever virus (ASFV) is the etiological agent of ASF, a fatal hemorrhagic fever that affects domestic pigs. There is currently no vaccine against ASFV, making it a significant threat to the pork industry. The ASFV genome sequence has been published; however, about half of ASFV open reading frames have not been characterized in terms of their structure and function despite being essential for our understanding of ASFV pathogenicity. The present study reports the three-dimensional structure and function of uncharacterized protein, pB263R (NP_042780.1), an open reading frame found in all ASFV strains. Sequence-based profiling and hidden Markov model search methods were used to identify remote pB263R homologs. Iterative Threading ASSEmbly Refinement (I-TASSER) was used to model the three-dimensional structure of pB263R. The posterior probability of fold family assignment was calculated using TM-fold, and biological function was assigned using TM-site, RaptorXBinding, Gene Ontology, and TM-align. Our results suggests that pB263R has the features of a TATA-binding protein and is thus likely to be involved in viral gene transcription.
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Affiliation(s)
- Dickson Kinyanyi
- Department of Biochemistry and Biotechnology, Technical University of Kenya, Nairobi, Kenya
| | - George Obiero
- Center for Biotechnology and Bioinformatics, University Of Nairobi, Nairobi, Kenya
| | - George F O Obiero
- Department of Biochemistry and Biotechnology, Technical University of Kenya, Nairobi, Kenya
| | - Peris Amwayi
- Department of Biochemistry and Biotechnology, Technical University of Kenya, Nairobi, Kenya
| | - Stephen Mwaniki
- Department of Biochemistry and Biotechnology, Technical University of Kenya, Nairobi, Kenya
| | - Mark Wamalwa
- Department of Biochemistry and Biotechnology, Kenyatta University, Ruiru, Kenya
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22
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Peterson EJ, Daniel AG, Katner SJ, Bohlmann L, Chang CW, Bezos A, Parish CR, von Itzstein M, Berners-Price SJ, Farrell NP. Antiangiogenic platinum through glycan targeting. Chem Sci 2017; 8:241-252. [PMID: 28451171 PMCID: PMC5355868 DOI: 10.1039/c6sc02515c] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/12/2016] [Indexed: 01/17/2023] Open
Abstract
Heparan sulfate is identified as a ligand receptor for polynuclear platinum anti-cancer agents through sulfate cluster binding. We present a new biological role for platinum and coordination compounds and a new target for metal-based drugs while presenting a new chemotype for heparanase and growth factor inhibition through modulation (metalloshielding) of their interactions. Masking of extracellular (ECM)-resident heparan sulfate (HS) through metalloshielding results in very effective inhibition of physiologically critical HS functions including enzyme (heparanase, HPSE) and protein growth factor recognition. The interaction of the highly cationic polynuclear platinum complexes (PPCs) with the highly sulfated pentasaccharide Fondaparinux (FPX, in this case as a model HS-like substrate) results in inhibition of its cleavage by the HS-related enzyme heparanase. Binding of the fibroblast growth factor FGF-2 to HS is also inhibited with consequences for downstream signalling events as measured by a reduction in accumulation of phospho-S6 ribosomal protein in human colon tumor HCT-116 cells. The end-point of inhibition of HPSE activity and growth factor growth factor signaling is the prevention of cell invasion and angiogenesis. Finally these events culminate in inhibition of HCT-116 cell invasion at sub-cytotoxic concentrations and the process of angiogenesis. A competition assay shows that Fondaparinux can sequester the 8+ TriplatinNC from bound DNA, emphasising the strength of PPC-HS interactions. Altering the profile of platinum agents from cytotoxic to anti-metastatic has profound implications for future directions in the development of platinum-based chemotherapeutics.
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Affiliation(s)
- Erica J Peterson
- Department of Chemistry , Virginia Commonwealth University , Richmond VA 23284 , Virginia , USA .
- The Massey Cancer Center , Virginia Commonwealth University , Richmond 23294 , Virginia , USA
| | - A Gerard Daniel
- Department of Chemistry , Virginia Commonwealth University , Richmond VA 23284 , Virginia , USA .
- The Massey Cancer Center , Virginia Commonwealth University , Richmond 23294 , Virginia , USA
| | - Samantha J Katner
- Department of Chemistry , Virginia Commonwealth University , Richmond VA 23284 , Virginia , USA .
- The Massey Cancer Center , Virginia Commonwealth University , Richmond 23294 , Virginia , USA
| | - Lisa Bohlmann
- Institute for Glycomics , Griffith University , Gold Coast Campus , Southport , Queensland 4222 , Australia
| | - Chih-Wei Chang
- Institute for Glycomics , Griffith University , Gold Coast Campus , Southport , Queensland 4222 , Australia
| | - Anna Bezos
- John Curtin School of Medical Research , The Australian National University , Canberra , Australia
| | - Christopher R Parish
- John Curtin School of Medical Research , The Australian National University , Canberra , Australia
| | - Mark von Itzstein
- Institute for Glycomics , Griffith University , Gold Coast Campus , Southport , Queensland 4222 , Australia
| | - Susan J Berners-Price
- Institute for Glycomics , Griffith University , Gold Coast Campus , Southport , Queensland 4222 , Australia
| | - Nicholas P Farrell
- Department of Chemistry , Virginia Commonwealth University , Richmond VA 23284 , Virginia , USA .
- The Massey Cancer Center , Virginia Commonwealth University , Richmond 23294 , Virginia , USA
- Institute for Glycomics , Griffith University , Gold Coast Campus , Southport , Queensland 4222 , Australia
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23
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Hantsche M, Cramer P. Strukturelle Grundlage der Transkription: 10 Jahre nach dem Chemie-Nobelpreis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Merle Hantsche
- Abteilung für Molekularbiologie; Max-Planck-Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
| | - Patrick Cramer
- Abteilung für Molekularbiologie; Max-Planck-Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Deutschland
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24
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Il'icheva IA, Khodikov MV, Poptsova MS, Nechipurenko DY, Nechipurenko YD, Grokhovsky SL. Structural features of DNA that determine RNA polymerase II core promoter. BMC Genomics 2016; 17:973. [PMID: 27884105 PMCID: PMC5123417 DOI: 10.1186/s12864-016-3292-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/15/2016] [Indexed: 01/02/2023] Open
Abstract
Background The general structure and action of all eukaryotic and archaeal RNA polymerases machinery have an astonishing similarity despite the diversity of core promoter sequences in different species. The goal of our work is to find common characteristics of DNA region that define it as a promoter for the RNA polymerase II (Pol II). Results The profiles of a large number of physical and structural characteristics, averaged over representative sets of the Pol II minimal core promoters of the evolutionary divergent species from animals, plants and unicellular fungi were analysed. In addition to the characteristics defined at the base-pair steps, we, for the first time, use profiles of the ultrasonic cleavage and DNase I cleavage indexes, informative for internal properties of each complementary strand. Conclusions DNA of the core promoters of metazoans and Schizosaccharomyces pombe has similar structural organization. Its mechanical and 3D structural characteristics have singular properties at the positions of TATA-box. The minor groove is broadened and conformational motion is decreased in that region. Special characteristics of conformational behavior are revealed in metazoans at the region, which connects the end of TATA-box and the transcription start site (TSS). The intensities of conformational motions in the complementary strands are periodically changed in opposite phases. They are noticeable, best of all, in mammals. Such conformational features are lacking in the core promoters of S. pombe. The profiles of Saccharomyces cerevisiae core promoters significantly differ: their singular region is shifted down thus pointing to the uniqueness of their structural organization. Obtained results may be useful in genetic engineering for artificial modulation of the promoter strength. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3292-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irina A Il'icheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Mingian V Khodikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Yury D Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei L Grokhovsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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25
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Romero Romero ML, Rabin A, Tawfik DS. Funktionelle Proteine aus kurzen Peptiden: 50 Jahre nach Margaret Dayhoffs Hypothese. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609977] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- M. Luisa Romero Romero
- Department of Biomolecular Sciences; The Weizmann Institute of Science; Rehovot 76100 Israel
| | - Avigayel Rabin
- Derzeitige Adresse: Department of Biological Chemistry, Alexander Silberman Inst. of Life Sciences; The Hebrew University of Jerusalem; Edmond J. Safra Campus Jerusalem 91904 Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences; The Weizmann Institute of Science; Rehovot 76100 Israel
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26
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Romero Romero ML, Rabin A, Tawfik DS. Functional Proteins from Short Peptides: Dayhoff's Hypothesis Turns 50. Angew Chem Int Ed Engl 2016; 55:15966-15971. [PMID: 27865046 DOI: 10.1002/anie.201609977] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 01/08/2023]
Abstract
First and foremost: Margaret Dayhoff's 1966 hypothesis on the origin of proteins is now an accepted model for the emergence of large, globular, functional proteins from short, simple peptides. However, the fundamental question of how the first protein(s) emerged still stands. The tools and hypotheses pioneered by Dayhoff, and the over 65 million protein sequences and 12 000 structures known today, enable those who follow in her footsteps to address this question.
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Affiliation(s)
- M Luisa Romero Romero
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Avigayel Rabin
- Current address: Department of Biological Chemistry the Alexander Silberman Inst. of Life Sciences, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 91904, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, 76100, Israel
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27
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Hantsche M, Cramer P. The Structural Basis of Transcription: 10 Years After the Nobel Prize in Chemistry. Angew Chem Int Ed Engl 2016; 55:15972-15981. [DOI: 10.1002/anie.201608066] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Merle Hantsche
- Abteilung für Molekularbiologie; Max Planck Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
| | - Patrick Cramer
- Abteilung für Molekularbiologie; Max Planck Institut für biophysikalische Chemie; Am Fassberg 11 37077 Göttingen Germany
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28
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Muskhelishvili G, Travers A. The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity. Biophys Rev 2016; 8:5-22. [PMID: 28510220 PMCID: PMC5425797 DOI: 10.1007/s12551-016-0237-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 10/21/2016] [Indexed: 01/06/2023] Open
Abstract
We argue that dynamic changes in DNA supercoiling in vivo determine both how DNA is packaged and how it is accessed for transcription and for other manipulations such as recombination. In both bacteria and eukaryotes, the principal generators of DNA superhelicity are DNA translocases, supplemented in bacteria by DNA gyrase. By generating gradients of superhelicity upstream and downstream of their site of activity, translocases enable the differential binding of proteins which preferentially interact with respectively more untwisted or more writhed DNA. Such preferences enable, in principle, the sequential binding of different classes of protein and so constitute an essential driver of chromatin organization.
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Affiliation(s)
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.
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29
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Uncovering ancient transcription systems with a novel evolutionary indicator. Sci Rep 2016; 6:27922. [PMID: 27307191 PMCID: PMC4910066 DOI: 10.1038/srep27922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 05/26/2016] [Indexed: 11/08/2022] Open
Abstract
TBP and TFIIB are evolutionarily conserved transcription initiation factors in archaea and eukaryotes. Information about their ancestral genes would be expected to provide insight into the origin of the RNA polymerase II-type transcription apparatus. In obtaining such information, the nucleotide sequences of current genes of both archaea and eukaryotes should be included in the analysis. However, the present methods of evolutionary analysis require that a subset of the genes should be excluded as an outer group. To overcome this limitation, we propose an innovative concept for evolutionary analysis that does not require an outer group. This approach utilizes the similarity in intramolecular direct repeats present in TBP and TFIIB as an evolutionary measure revealing the degree of similarity between the present offspring genes and their ancestors. Information on the properties of the ancestors and the order of emergence of TBP and TFIIB was also revealed. These findings imply that, for evolutionarily early transcription systems billions of years ago, interaction of RNA polymerase II with transcription initiation factors and the regulation of its enzymatic activity was required prior to the accurate positioning of the enzyme. Our approach provides a new way to discuss mechanistic and system evolution in a quantitative manner.
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30
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Zanegina O, Aksianov E, Alexeevski AV, Karyagina A, Spirin S. Conserved features of complexes of TATA-box binding proteins with DNA. J Bioinform Comput Biol 2016; 14:1641007. [PMID: 27122319 DOI: 10.1142/s0219720016410079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A comparative analysis of all available structures of complexes of TATA-box binding proteins (TBPs) with DNA is performed. Conserved features of DNA-protein interaction are described, including nine amino acid residues that form conserved hydrogen bonds, 13 residues participating in formation of two conserved hydrophobic clusters at DNA-protein interface, and four conserved water-mediated contacts. Partial symmetry of conserved contacts reflects quasi-symmetry of TBP structure.
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Affiliation(s)
- Olga Zanegina
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1 Leninskiye Gory, bld.40, Moscow 119991, Russia
| | - Evgeniy Aksianov
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1 Leninskiye Gory, bld.40, Moscow 119991, Russia
| | - Andrei V Alexeevski
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1 Leninskiye Gory, bld.40, Moscow 119991, Russia.,† Institute of System Studies, 36 Nakhimovski Prospect Corp. 1, Moscow 117218, Russia
| | - Anna Karyagina
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1 Leninskiye Gory, bld.40, Moscow 119991, Russia.,‡ Gamaleya Center of Epidemiology and Microbiology, 18 Gamaleya st., Moscow 123098, Russia.,§ Institute of Agricultural Biotechnology, 42 Timiryazevskaya st., Moscow 127422, Russia
| | - Sergei Spirin
- * Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 1 Leninskiye Gory, bld.40, Moscow 119991, Russia.,† Institute of System Studies, 36 Nakhimovski Prospect Corp. 1, Moscow 117218, Russia
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31
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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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Rodríguez-Lima O, García-Gutierrez P, Jiménez L, Zarain-Herzberg Á, Lazzarini R, Landa A. Molecular Cloning of a cDNA Encoding for Taenia solium TATA-Box Binding Protein 1 (TsTBP1) and Study of Its Interactions with the TATA-Box of Actin 5 and Typical 2-Cys Peroxiredoxin Genes. PLoS One 2015; 10:e0141818. [PMID: 26529408 PMCID: PMC4631506 DOI: 10.1371/journal.pone.0141818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 10/13/2015] [Indexed: 11/18/2022] Open
Abstract
TATA-box binding protein (TBP) is an essential regulatory transcription factor for the TATA-box and TATA-box-less gene promoters. We report the cloning and characterization of a full-length cDNA that encodes a Taenia solium TATA-box binding protein 1 (TsTBP1). Deduced amino acid composition from its nucleotide sequence revealed that encodes a protein of 238 residues with a predicted molecular weight of 26.7 kDa, and a theoretical pI of 10.6. The NH2-terminal domain shows no conservation when compared with to pig and human TBP1s. However, it shows high conservation in size and amino acid identity with taeniids TBP1s. In contrast, the TsTBP1 COOH-terminal domain is highly conserved among organisms, and contains the amino acids involved in interactions with the TATA-box, as well as with TFIIA and TFIIB. In silico TsTBP1 modeling reveals that the COOH-terminal domain forms the classical saddle structure of the TBP family, with one α-helix at the end, not present in pig and human. Native TsTBP1 was detected in T. solium cysticerci´s nuclear extract by western blot using rabbit antibodies generated against two synthetic peptides located in the NH2 and COOH-terminal domains of TsTBP1. These antibodies, through immunofluorescence technique, identified the TBP1 in the nucleus of cells that form the bladder wall of cysticerci of Taenia crassiceps, an organism close related to T. solium. Electrophoretic mobility shift assays using nuclear extracts from T. solium cysticerci and antibodies against the NH2-terminal domain of TsTBP1 showed the interaction of native TsTBP1 with the TATA-box present in T. solium actin 5 (pAT5) and 2-Cys peroxiredoxin (Ts2-CysPrx) gene promoters; in contrast, when antibodies against the anti-COOH-terminal domain of TsTBP1 were used, they inhibited the binding of TsTBP1 to the TATA-box of the pAT5 promoter gene.
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Affiliation(s)
- Oscar Rodríguez-Lima
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | | | - Lucía Jiménez
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | - Ángel Zarain-Herzberg
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
| | - Roberto Lazzarini
- Departamento de Biología Experimental, Universidad Autónoma Metropolitana–Iztapalapa, México D.F., México
| | - Abraham Landa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., México
- * E-mail:
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Sjaarda CP, Abubaker KS, Castle AJ. Induction of lcc2 expression and activity by Agaricus bisporus provides defence against Trichoderma aggressivum toxic extracts. Microb Biotechnol 2015; 8:918-29. [PMID: 25824278 PMCID: PMC4621445 DOI: 10.1111/1751-7915.12277] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/16/2015] [Indexed: 12/25/2022] Open
Abstract
Laccases are used by fungi for several functions including defence responses to stresses associated with attack by other fungi. Laccase activity changes and the induction of two laccase genes, lcc1 and lcc2, in Agaricus bisporus were measured in response to toxic extracts of medium in which Trichoderma aggressivum, the cause of green mould disease, was grown. A strain of A. bisporus that shows resistance to the extracts showed higher basal levels and greater enzymatic activity after extract exposure than did a sensitive strain. Furthermore, pre-incubation of T. aggressivum extract with laccases reduced toxicity. Faster induction and greater numbers of lcc2 transcripts in response to the extract were noted in the resistant strain than in the sensitive strain. The timing and increase in lcc2 transcript abundance mirrored changes in total laccase activity. No correlation between resistance and lcc1 transcription was apparent. Transcript abundance in transformants with a siRNA construct homologous to both genes varied widely. A strong negative correlation between transcript abundance and sensitivity of the transformant to toxic extract was observed in plate assays. These results indicated that laccase activity and in particular that encoded by lcc2 contributes to toxin metabolism and by extension green mould disease resistance.
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Affiliation(s)
- Calvin P Sjaarda
- Department of Biological Sciences, Brock UniversitySt Catharines, ON, L2S 3A1, Canada
| | - Kamal S Abubaker
- Department of Biological Sciences, Brock UniversitySt Catharines, ON, L2S 3A1, Canada
| | - Alan J Castle
- Department of Biological Sciences, Brock UniversitySt Catharines, ON, L2S 3A1, Canada
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Applying Thymine Isostere 2,4-Difluoro-5-Methylbenzene as a NMR Assignment Tool and Probe of Homopyrimidine/Homopurine Tract Structural Dynamics. Methods Enzymol 2015; 566:89-110. [PMID: 26791977 DOI: 10.1016/bs.mie.2015.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Proton assignment of nuclear magnetic resonance (NMR) spectra of homopyrimidine/homopurine tract oligonucleotides becomes extremely challenging with increasing helical length due to severe cross-peak overlap. As an alternative to the more standard practice of (15)N and (13)C labeling of oligonucleotides, here, we describe a method for assignment of highly redundant DNA sequences that uses single-site substitution of the thymine isostere 2,4-difluoro-5-methylbenzene (dF). The impact of this approach in facilitating the assignment of intractable spectra and analyzing oligonucleotide structure and dynamics is demonstrated using A-tract and TATA box DNA and two polypurine tract-containing RNA:DNA hybrids derived from HIV-1 and the Saccharomyces cerevisiae long-terminal repeat-containing retrotransposon Ty3. Only resonances proximal to the site of dF substitution exhibit sizable chemical shift changes, providing spectral dispersion while still allowing chemical shift mapping of resonances from unaffected residues distal to the site of modification directly back to the unmodified sequence. It is further illustrated that dF incorporation can subtly alter the conformation and dynamics of homopyrimidine/homopurine tract oligonucleotides, and how these NMR observations can be correlated, in the cases of the TATA box DNA, with modulation in the TATA box-binding protein interaction using an orthogonal gel assay.
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35
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Balaji S. Internal symmetry in protein structures: prevalence, functional relevance and evolution. Curr Opin Struct Biol 2015; 32:156-66. [PMID: 26093245 DOI: 10.1016/j.sbi.2015.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
Abstract
Symmetry has been found at various levels of biological organization in the protein structural universe. Numerous evolutionary studies have proposed connections between internal symmetry within protein tertiary structures, quaternary associations and protein functions. Recent computational methods, such as SymD and CE-Symm, facilitate a large-scale detection of internal symmetry in protein structures. Based on the results from these methods, about 20% of SCOP folds, superfamilies and families are estimated to have structures with internal symmetry (Figure 1d). All-β and membrane proteins fold classes contain a relatively high number of unique instances of internal symmetry. In addition to the axis of symmetry, anecdotal evidence suggests that, the region of connection or contact between symmetric units could coincide with functionally relevant sites within a fold. General principles that underlie protein internal symmetry and their connections to protein structural integrity and functions remain to be elucidated.
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Affiliation(s)
- Santhanam Balaji
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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36
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Abstract
Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter.
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37
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Farrell NP. Multi-platinum anti-cancer agents. Substitution-inert compounds for tumor selectivity and new targets. Chem Soc Rev 2015; 44:8773-85. [DOI: 10.1039/c5cs00201j] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Substitution-inert polynuclear platinum complexes are inherently dual-function anti-cancer agents combining extra and intra-cellular effects in one structural chemotype.
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Affiliation(s)
- N. P. Farrell
- Department of Chemistry
- Virginia Commonwealth University
- Richmond
- USA
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Affiliation(s)
- Robert K McGinty
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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39
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Contribution of phenylalanine side chain intercalation to the TATA-box binding protein–DNA interaction: molecular dynamics and dispersion-corrected density functional theory studies. J Mol Model 2014; 20:2499. [DOI: 10.1007/s00894-014-2499-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
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Pasi M, Maddocks JH, Beveridge D, Bishop TC, Case DA, Cheatham T, Dans PD, Jayaram B, Lankas F, Laughton C, Mitchell J, Osman R, Orozco M, Pérez A, Petkevičiūtė D, Spackova N, Sponer J, Zakrzewska K, Lavery R. μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA. Nucleic Acids Res 2014; 42:12272-83. [PMID: 25260586 PMCID: PMC4231739 DOI: 10.1093/nar/gku855] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We present the results of microsecond molecular dynamics simulations carried out by the ABC group of laboratories on a set of B-DNA oligomers containing the 136 distinct tetranucleotide base sequences. We demonstrate that the resulting trajectories have extensively sampled the conformational space accessible to B-DNA at room temperature. We confirm that base sequence effects depend strongly not only on the specific base pair step, but also on the specific base pairs that flank each step. Beyond sequence effects on average helical parameters and conformational fluctuations, we also identify tetranucleotide sequences that oscillate between several distinct conformational substates. By analyzing the conformation of the phosphodiester backbones, it is possible to understand for which sequences these substates will arise, and what impact they will have on specific helical parameters.
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Affiliation(s)
- Marco Pasi
- Section de Mathématiques, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - John H. Maddocks
- Section de Mathématiques, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
- To whom correspondence should be addressed. Tel: +41 21 693 27 62; Fax: +41 21 693 55 30;
| | - David Beveridge
- Department of Chemistry, Wesleyan University, Middletown, CT 06459, USA
| | - Thomas C. Bishop
- Departments of Chemistry and Physics, Louisiana Tech University, Ruston, LA 71270, USA
| | - David A. Case
- BioMaPS Institute and Deptartment of Chemistry and Chemical Biology, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
| | - Thomas Cheatham
- Department of Medicinal Chemistry, University of Utah, Skaggs 307, Salt Lake City, UT 84112, USA
| | - Pablo D. Dans
- Joint BSC-CRG-IRB Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
- Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain
- Departament de Bioquímica, Facultat de Biología, Avgda Diagonal 647, Barcelona 08028, Spain
| | - B. Jayaram
- Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Filip Lankas
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Praha 6, Czech Republic
| | - Charles Laughton
- School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, NG7 2RD, UK
| | - Jonathan Mitchell
- Section de Mathématiques, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Roman Osman
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Modesto Orozco
- Joint BSC-CRG-IRB Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
- Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain
- Departament de Bioquímica, Facultat de Biología, Avgda Diagonal 647, Barcelona 08028, Spain
| | - Alberto Pérez
- Joint BSC-CRG-IRB Program on Computational Biology, Institute of Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain
- Barcelona Supercomputing Centre, Jordi Girona 31, Edifici Torre Girona, Barcelona 08034, Spain
- Departament de Bioquímica, Facultat de Biología, Avgda Diagonal 647, Barcelona 08028, Spain
| | - Daiva Petkevičiūtė
- Section de Mathématiques, Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland
| | - Nada Spackova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- CEITEC—Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Krystyna Zakrzewska
- Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UMR 5086/Université Lyon I, IBCP, 7 Passage du Vercors, 69367 Lyon, France
| | - Richard Lavery
- Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UMR 5086/Université Lyon I, IBCP, 7 Passage du Vercors, 69367 Lyon, France
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Singh V, Kumari B, Maity B, Seth D, Das P. Direct observation of preferential processing of clustered abasic DNA damages with APE1 in TATA box and CpG island by reaction kinetics and fluorescence dynamics. Mutat Res 2014; 766-767:56-65. [PMID: 25847273 DOI: 10.1016/j.mrfmmm.2014.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 05/16/2014] [Accepted: 06/16/2014] [Indexed: 06/04/2023]
Abstract
Sequences like the core element of TATA box and CpG island are frequently encountered in the genome and related to transcription. The fate of repair of clustered abasic sites in such sequences of genomic importance is largely unknown. This prompted us to investigate the sequence dependence of cleavage efficiency of APE1 enzyme at abasic sites within the core sequences of TATA box and CpG island using fluorescence dynamics and reaction kinetics. Simultaneous molecular dynamics study through steady state and time resolved fluorescence spectroscopy using unique ethidium bromide dye release assay confirmed an elevated amount of abasic site cleavage of the TATA box sequence as compared to the core CpG island. Reaction kinetics showed that catalytic efficiency of APE1 for abasic site cleavage of core CpG island sequence was ∼4 times lower as compared to that of the TATA box. Higher value of Km was obtained from the core CpG island sequence than the TATA box sequence. This suggests a greater binding effect of APE1 enzyme on TATA sequence that signifies a prominent role of the sequence context of the DNA substrate. Evidently, a faster response from APE1 was obtained for clustered abasic damage repair of TATA box core sequences than CpG island consensus sequences. The neighboring bases of the abasic sites in the complementary DNA strand were found to have significant contribution in addition to the flanking bases in modulating APE1 activity. The repair refractivity of the bistranded clustered abasic sites arise from the slow processing of the second abasic site, consequently resulting in decreased overall production of potentially lethal double strand breaks.
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Affiliation(s)
- Vandana Singh
- Department of Chemistry, Indian Institute of Technology Patna, Govt. Polytechnic Campus, Patliputra Colony, Patna 800013, Bihar, India
| | - Bhavini Kumari
- Department of Chemistry, Indian Institute of Technology Patna, Govt. Polytechnic Campus, Patliputra Colony, Patna 800013, Bihar, India
| | - Banibrata Maity
- Department of Chemistry, Indian Institute of Technology Patna, Govt. Polytechnic Campus, Patliputra Colony, Patna 800013, Bihar, India
| | - Debabrata Seth
- Department of Chemistry, Indian Institute of Technology Patna, Govt. Polytechnic Campus, Patliputra Colony, Patna 800013, Bihar, India
| | - Prolay Das
- Department of Chemistry, Indian Institute of Technology Patna, Govt. Polytechnic Campus, Patliputra Colony, Patna 800013, Bihar, India.
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42
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Myers-Turnbull D, Bliven SE, Rose PW, Aziz ZK, Youkharibache P, Bourne PE, Prlić A. Systematic detection of internal symmetry in proteins using CE-Symm. J Mol Biol 2014; 426:2255-68. [PMID: 24681267 DOI: 10.1016/j.jmb.2014.03.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 11/26/2022]
Abstract
Symmetry is an important feature of protein tertiary and quaternary structures that has been associated with protein folding, function, evolution, and stability. Its emergence and ensuing prevalence has been attributed to gene duplications, fusion events, and subsequent evolutionary drift in sequence. This process maintains structural similarity and is further supported by this study. To further investigate the question of how internal symmetry evolved, how symmetry and function are related, and the overall frequency of internal symmetry, we developed an algorithm, CE-Symm, to detect pseudo-symmetry within the tertiary structure of protein chains. Using a large manually curated benchmark of 1007 protein domains, we show that CE-Symm performs significantly better than previous approaches. We use CE-Symm to build a census of symmetry among domain superfamilies in SCOP and note that 18% of all superfamilies are pseudo-symmetric. Our results indicate that more domains are pseudo-symmetric than previously estimated. We establish a number of recurring types of symmetry-function relationships and describe several characteristic cases in detail. With the use of the Enzyme Commission classification, symmetry was found to be enriched in some enzyme classes but depleted in others. CE-Symm thus provides a methodology for a more complete and detailed study of the role of symmetry in tertiary protein structure [availability: CE-Symm can be run from the Web at http://source.rcsb.org/jfatcatserver/symmetry.jsp. Source code and software binaries are also available under the GNU Lesser General Public License (version 2.1) at https://github.com/rcsb/symmetry. An interactive census of domains identified as symmetric by CE-Symm is available from http://source.rcsb.org/jfatcatserver/scopResults.jsp].
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Affiliation(s)
- Douglas Myers-Turnbull
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Spencer E Bliven
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Peter W Rose
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Zaid K Aziz
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Philip E Bourne
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Andreas Prlić
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA.
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43
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Kumar R, Moure CM, Khan SH, Callaway C, Grimm SL, Goswami D, Griffin PR, Edwards DP. Regulation of the structurally dynamic N-terminal domain of progesterone receptor by protein-induced folding. J Biol Chem 2013; 288:30285-30299. [PMID: 23995840 DOI: 10.1074/jbc.m113.491787] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The N-terminal domain (NTD) of steroid receptors harbors a transcriptional activation function (AF1) that is composed of an intrinsically disordered polypeptide. We examined the interaction of the TATA-binding protein (TBP) with the NTD of the progesterone receptor (PR) and its ability to regulate AF1 activity through coupled folding and binding. As assessed by solution phase biophysical methods, the isolated NTD of PR contains a large content of random coil, and it is capable of adopting secondary α-helical structure and more stable tertiary folding either in the presence of the natural osmolyte trimethylamine-N-oxide or through a direct interaction with TBP. Hydrogen-deuterium exchange coupled with mass spectrometry confirmed the highly dynamic intrinsically disordered property of the NTD within the context of full-length PR. Deletion mapping and point mutagenesis defined a region of the NTD (amino acids 350-428) required for structural folding in response to TBP interaction. Overexpression of TBP in cells enhanced transcriptional activity mediated by the PR NTD, and deletion mutations showed that a region (amino acids 327-428), similar to that required for TBP-induced folding, was required for functional response. TBP also increased steroid receptor co-activator 1 (SRC-1) interaction with the PR NTD and cooperated with SRC-1 to stimulate NTD-dependent transcriptional activity. These data suggest that TBP can mediate structural reorganization of the NTD to facilitate the binding of co-activators required for maximal transcriptional activation.
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Affiliation(s)
- Raj Kumar
- the Department of Basic Sciences, Commonwealth Medical College, Scranton, Pennsylvania 18509
| | - Carmen M Moure
- From the Departments of Molecular and Cellular Biology and
| | - Shagufta H Khan
- the Department of Basic Sciences, Commonwealth Medical College, Scranton, Pennsylvania 18509
| | | | - Sandra L Grimm
- From the Departments of Molecular and Cellular Biology and
| | - Devrishi Goswami
- the Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, and
| | - Patrick R Griffin
- the Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458, and
| | - Dean P Edwards
- From the Departments of Molecular and Cellular Biology and; Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030,.
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44
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Nardini M, Gnesutta N, Donati G, Gatta R, Forni C, Fossati A, Vonrhein C, Moras D, Romier C, Bolognesi M, Mantovani R. Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination. Cell 2013; 152:132-43. [PMID: 23332751 DOI: 10.1016/j.cell.2012.11.047] [Citation(s) in RCA: 184] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 09/29/2012] [Accepted: 11/20/2012] [Indexed: 12/16/2022]
Abstract
The sequence-specific transcription factor NF-Y binds the CCAAT box, one of the sequence elements most frequently found in eukaryotic promoters. NF-Y is composed of the NF-YA and NF-YB/NF-YC subunits, the latter two hosting histone-fold domains (HFDs). The crystal structure of NF-Y bound to a 25 bp CCAAT oligonucleotide shows that the HFD dimer binds to the DNA sugar-phosphate backbone, mimicking the nucleosome H2A/H2B-DNA assembly. NF-YA both binds to NF-YB/NF-YC and inserts an α helix deeply into the DNA minor groove, providing sequence-specific contacts to the CCAAT box. Structural considerations and mutational data indicate that NF-YB ubiquitination at Lys138 precedes and is equivalent to H2B Lys120 monoubiquitination, important in transcriptional activation. Thus, NF-Y is a sequence-specific transcription factor with nucleosome-like properties of nonspecific DNA binding and helps establish permissive chromatin modifications at CCAAT promoters. Our findings suggest that other HFD-containing proteins may function in similar ways.
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Affiliation(s)
- Marco Nardini
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
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Savinkova L, Drachkova I, Arshinova T, Ponomarenko P, Ponomarenko M, Kolchanov N. An experimental verification of the predicted effects of promoter TATA-box polymorphisms associated with human diseases on interactions between the TATA boxes and TATA-binding protein. PLoS One 2013; 8:e54626. [PMID: 23424617 PMCID: PMC3570547 DOI: 10.1371/journal.pone.0054626] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 12/13/2012] [Indexed: 11/18/2022] Open
Abstract
Human genome sequencing has resulted in a great body of data, including a stunningly large number of single nucleotide polymorphisms (SNPs) with unknown phenotypic manifestations. Identification and comprehensive analysis of regulatory SNPs in human gene promoters will help quantify the effects of these SNPs on human health. Based on our experimental and computer-aided study of SNPs in TATA boxes and the use of literature data, we have derived an equation for TBP/TATA equilibrium binding in three successive steps: TATA-binding protein (TBP) sliding along DNA due to their nonspecific affinity for each other ↔ recognition of the TATA box ↔ stabilization of the TBP/TATA complex. Using this equation, we have analyzed TATA boxes containing SNPs associated with human diseases and made in silico predictions of changes in TBP/TATA affinity. An electrophoretic mobility shift assay (EMSA)-based experimental study performed under the most standardized conditions demonstrates that the experimentally measured values are highly correlated with the predicted values: the coefficient of linear correlation, r, was 0.822 at a significance level of α<10⁻⁷ for equilibrium K(D) values, (-ln K(D)), and 0.785 at a significance level of α<10⁻³ for changes in equilibrium K(D) (δ) due to SNPs in the TATA boxes (δ= -ln[K(D,TATAMut)]-(-ln[K(D,TATAMut)])). It has been demonstrated that the SNPs associated with increased risk of human diseases such as α-, β- and δ-thalassemia, myocardial infarction and thrombophlebitis, changes in immune response, amyotrophic lateral sclerosis, lung cancer and hemophilia B Leyden cause 2-4-fold changes in TBP/TATA affinity in most cases. The results obtained strongly suggest that the TBP/TATA equilibrium binding equation derived can be used for analysis of TATA-box sequences and identification of SNPs with a potential of being functionally important.
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Affiliation(s)
- Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia.
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46
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Yueh H, Yu H, Theile CS, Pal A, Horhota A, Greco N, Christianson CV, McLaughlin LW. Synthesis and properties of DNA containing cyclonucleosides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2013; 31:661-79. [PMID: 23004930 DOI: 10.1080/15257770.2012.716189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Here, we present efficient syntheses of the R and S diastereomers of 8,5'-cyclo-2'-deoxyadenosine and 6,5'-cyclo-2'-deoxyuridine. We incorporated these interesting nucleosides into DNA to study how the cyclo linkage affects the stability of duplex formation.
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Affiliation(s)
- Han Yueh
- Department of Chemistry, Boston College, Merkert Chemistry Center, Chestnut Hill, Massachusetts, USA
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Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters. BMC Genomics 2012; 13:512. [PMID: 23020586 PMCID: PMC3549790 DOI: 10.1186/1471-2164-13-512] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Accepted: 09/13/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The main function of gene promoters appears to be the integration of different gene products in their biological pathways in order to maintain homeostasis. Generally, promoters have been classified in two major classes, namely TATA and CpG. Nevertheless, many genes using the same combinatorial formation of transcription factors have different gene expression patterns. Accordingly, we tried to ask ourselves some fundamental questions: Why certain genes have an overall predisposition for higher gene expression levels than others? What causes such a predisposition? Is there a structural relationship of these sequences in different tissues? Is there a strong phylogenetic relationship between promoters of closely related species? RESULTS In order to gain valuable insights into different promoter regions, we obtained a series of image-based patterns which allowed us to identify 10 generic classes of promoters. A comprehensive analysis was undertaken for promoter sequences from Arabidopsis thaliana, Drosophila melanogaster, Homo sapiens and Oryza sativa, and a more extensive analysis of tissue-specific promoters in humans. We observed a clear preference for these species to use certain classes of promoters for specific biological processes. Moreover, in humans, we found that different tissues use distinct classes of promoters, reflecting an emerging promoter network. Depending on the tissue type, comparisons made between these classes of promoters reveal a complementarity between their patterns whereas some other classes of promoters have been observed to occur in competition. Furthermore, we also noticed the existence of some transitional states between these classes of promoters that may explain certain evolutionary mechanisms, which suggest a possible predisposition for specific levels of gene expression and perhaps for a different number of factors responsible for triggering gene expression. Our conclusions are based on comprehensive data from three different databases and a new computer model whose core is using Kappa index of coincidence. CONCLUSIONS To fully understand the connections between gene promoters and gene expression, we analyzed thousands of promoter sequences using our Kappa Index of Coincidence method and a specialized Optical Character Recognition (OCR) neural network. Under our criteria, 10 classes of promoters were detected. In addition, the existence of "transitional" promoters suggests that there is an evolutionary weighted continuum between classes, depending perhaps upon changes in their gene products.
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Preus S, Kilså K, Miannay FA, Albinsson B, Wilhelmsson LM. FRETmatrix: a general methodology for the simulation and analysis of FRET in nucleic acids. Nucleic Acids Res 2012; 41:e18. [PMID: 22977181 PMCID: PMC3592456 DOI: 10.1093/nar/gks856] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Förster resonance energy transfer (FRET) is a technique commonly used to unravel the structure and conformational changes of biomolecules being vital for all living organisms. Typically, FRET is performed using dyes attached externally to nucleic acids through a linker that complicates quantitative interpretation of experiments because of dye diffusion and reorientation. Here, we report a versatile, general methodology for the simulation and analysis of FRET in nucleic acids, and demonstrate its particular power for modelling FRET between probes possessing limited diffusional and rotational freedom, such as our recently developed nucleobase analogue FRET pairs (base–base FRET). These probes are positioned inside the DNA/RNA structures as a replacement for one of the natural bases, thus, providing unique control of their position and orientation and the advantage of reporting from inside sites of interest. In demonstration studies, not requiring molecular dynamics modelling, we obtain previously inaccessible insight into the orientation and nanosecond dynamics of the bases inside double-stranded DNA, and we reconstruct high resolution 3D structures of kinked DNA. The reported methodology is accompanied by a freely available software package, FRETmatrix, for the design and analysis of FRET in nucleic acid containing systems.
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Affiliation(s)
- Søren Preus
- Department of Chemistry, University of Copenhagen, Copenhagen DK-2100, Denmark
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Elder RM, Jayaraman A. Role of structure and dynamics of DNA with cisplatin and oxaliplatin adducts in various sequence contexts on binding of HMGB1a. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2011.654208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Gómez-Ruiz S, Maksimović-Ivanić D, Mijatović S, Kaluđerović GN. On the discovery, biological effects, and use of Cisplatin and metallocenes in anticancer chemotherapy. Bioinorg Chem Appl 2012; 2012:140284. [PMID: 22844263 PMCID: PMC3401524 DOI: 10.1155/2012/140284] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Accepted: 05/19/2012] [Indexed: 01/08/2023] Open
Abstract
The purpose of this paper is to summarize mode of action of cisplatin on the tumor cells, a brief outlook on the metallocene compounds as antitumor drugs as well as the future tendencies for the use of the latter in anticancer chemotherapy. Molecular mechanisms of cisplatin interaction with DNA, DNA repair mechanisms, and cellular proteins are discussed. Molecular background of the sensitivity and resistance to cisplatin, as well as its influence on the efficacy of the antitumor immune response was evaluated. Furthermore, herein are summarized some metallocenes (titanocene, vanadocene, molybdocene, ferrocene, and zirconocene) with high antitumor activity.
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Affiliation(s)
- Santiago Gómez-Ruiz
- Departamento de Química Inorgánica y Analítica, E.S.C.E.T., Universidad Rey Juan Carlos, 28933 Móstoles, Spain
| | - Danijela Maksimović-Ivanić
- Institute for Biological Research “Sinisa Stankovic”, University of Belgrade, Boulevard of Despot Stefan 142, 11060 Belgrade, Serbia
| | - Sanja Mijatović
- Institute for Biological Research “Sinisa Stankovic”, University of Belgrade, Boulevard of Despot Stefan 142, 11060 Belgrade, Serbia
| | - Goran N. Kaluđerović
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Straße 2, 06120 Halle, Germany
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