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Peyrane F, Denhez C, Guillaume D, Clivio P. Anti Regiospecificity in the Photosensitized Cycloaddition of 4-Tetrazolouracil Nucleoside †. Photochem Photobiol 2021; 98:640-648. [PMID: 34655494 DOI: 10.1111/php.13541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022]
Abstract
The [2 + 2] photocycloaddition of natural pyrimidine nucleobases is devoid of regioselectivity. Although modified pyrimidines have been developed to selectively obtain syn-cyclobutane isomers, the targeted formation of anti-cyclobutane isomers has not been addressed yet. Herein, using NMR analyses and DFT calculations, we demonstrate that the acetone photosensitized excitation of the 4-tetrazolouracil motif in the nucleoside series specifically provides anti-cyclobutane photoproducts in 51% yield. In addition, the cis stereomer formation is preferred over the trans-cyclobutane formation (71:29).
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Affiliation(s)
- Frédéric Peyrane
- Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | - Clément Denhez
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, Reims, France.,MaSCA, P3M, UFR des Sciences Exactes et Naturelles, Reims, France
| | - Dominique Guillaume
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, Reims, France
| | - Pascale Clivio
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, Reims, France
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2
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Abstract
Enterovirus 70 (EV70) is an emerging viral pathogen that remains viable in final treated effluent. Solar irradiation is, therefore, explored as a low-cost natural disinfection strategy to mitigate potential concerns. EV70 was exposed to simulated sunlight for 24 h at a fluence rate of 28.67 J/cm2/h in three different water matrices, namely, phosphate-buffered saline (PBS), treated wastewater effluent, and chlorinated effluent. In the presence of sunlight, EV70 decreased in infectivity by 1.7 log, 1.0 log, and 1.3 log in PBS, effluent, and chlorinated effluent, respectively. Irradiated EV70 was further introduced to host cell lines and was unable to infect the cell lines. In contrast, EV70 in dark microcosms replicated to titers 13.5, 3.3, and 4.2 times the initial inoculum. The reduction in EV70 infectivity was accompanied by a reduction in viral binding capacity to Vero cells. In addition, genome sequencing analysis revealed five nonsynonymous nucleotide substitutions in irradiated viruses after 10 days of infection in Vero cells, resulting in amino acid substitutions: Lys14Glu in the VP4 protein, Ala201Val in VP2, Gly71Ser in VP3, Glu50Gln in VP1, and Ile47Leu in 3Cpro. Overall, solar irradiation resulted in EV70 inactivation and an inhibition of viral activity in all parameters studied.
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3
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Chen L, Zhang YH, Wang S, Zhang Y, Huang T, Cai YD. Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways. PLoS One 2017; 12:e0184129. [PMID: 28873455 PMCID: PMC5584762 DOI: 10.1371/journal.pone.0184129] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/18/2017] [Indexed: 12/20/2022] Open
Abstract
Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes. Through the enrichment theory of GO and KEGG pathways, we encoded each essential/non-essential gene into a vector in which each component represented the relationship between the gene and one GO term or KEGG pathway. To analyze these relationships, the maximum relevance minimum redundancy (mRMR) was adopted. Then, the incremental feature selection (IFS) and support vector machine (SVM) were employed to extract important GO terms and KEGG pathways. A prediction model was built simultaneously using the extracted GO terms and KEGG pathways, which yielded nearly perfect performance, with a Matthews correlation coefficient of 0.951, for distinguishing essential and non-essential genes. To fully investigate the key factors influencing the fundamental roles of essential genes, the 21 most important GO terms and three KEGG pathways were analyzed in detail. In addition, several genes was provided in this study, which were predicted to be essential genes by our prediction model. We suggest that this study provides more functional and pathway information on the essential genes and provides a new way to investigate related problems.
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Affiliation(s)
- Lei Chen
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
- College of Information Engineering, Shanghai Maritime University, Shanghai, People’s Republic of China
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - ShaoPeng Wang
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - YunHua Zhang
- Anhui province key lab of farmland ecological conversation and pollution prevention, School of Resources and Environment, Anhui Agricultural University, Hefei, People’s Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
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4
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How Changes in Anti-SD Sequences Would Affect SD Sequences in Escherichia coli and Bacillus subtilis. G3-GENES GENOMES GENETICS 2017; 7:1607-1615. [PMID: 28364038 PMCID: PMC5427494 DOI: 10.1534/g3.117.039305] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The 3' end of the small ribosomal RNAs (ssu rRNA) in bacteria is directly involved in the selection and binding of mRNA transcripts during translation initiation via well-documented interactions between a Shine-Dalgarno (SD) sequence located upstream of the initiation codon and an anti-SD (aSD) sequence at the 3' end of the ssu rRNA. Consequently, the 3' end of ssu rRNA (3'TAIL) is strongly conserved among bacterial species because a change in the region may impact the translation of many protein-coding genes. Escherichia coli and Bacillus subtilis differ in their 3' ends of ssu rRNA, being GAUCACCUCCUUA3' in E. coli and GAUCACCUCCUUUCU3' or GAUCACCUCCUUUCUA3' in B. subtilis Such differences in 3'TAIL lead to species-specific SDs (designated SDEc for E. coli and SDBs for B. subtilis) that can form strong and well-positioned SD/aSD pairing in one species but not in the other. Selection mediated by the species-specific 3'TAIL is expected to favor SDBs against SDEc in B. subtilis, but favor SDEc against SDBs in E. coli Among well-positioned SDs, SDEc is used more in E. coli than in B. subtilis, and SDBs more in B. subtilis than in E. coli Highly expressed genes and genes of high translation efficiency tend to have longer SDs than lowly expressed genes and genes with low translation efficiency in both species, but more so in B. subtilis than in E. coli Both species overuse SDs matching the bolded part of the 3'TAIL shown above. The 3'TAIL difference contributes to the host specificity of phages.
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Posada LF, Alvarez JC, Hu CH, de-Bashan LE, Bashan Y. Construction of probe of the plant growth-promoting bacteria Bacillus subtilis useful for fluorescence in situ hybridization. J Microbiol Methods 2016; 128:125-129. [PMID: 27263830 DOI: 10.1016/j.mimet.2016.05.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/30/2016] [Accepted: 05/31/2016] [Indexed: 11/26/2022]
Abstract
Strains of Bacillus subtilis are plant growth-promoting bacteria (PGPB) of many crops and are used as inoculants. PGPB colonization is an important trait for success of a PGPB on plants. A specific probe, based on the 16 s rRNA of Bacillus subtilis, was designed and evaluated to distinguishing, by fluorescence in situ hybridization (FISH), between this species and the closely related Bacillus amyloliquefaciens. The selected target for the probe was between nucleotides 465 and 483 of the gene, where three different nucleotides can be identified. The designed probe successfully hybridized with several strains of Bacillus subtilis, but failed to hybridize not only with B. amyloliquefaciens, but also with other strains such as Bacillus altitudinis, Bacillus cereus, Bacillus gibsonii, Bacillus megaterium, Bacillus pumilus; and with the external phylogenetic strains Azospirillum brasilense Cd, Micrococcus sp. and Paenibacillus sp. The results showed the specificity of this molecular probe for B. subtilis.
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Affiliation(s)
- Luisa F Posada
- Department of Process Engineering, Cra 49 #7 sur-50, Universidad EAFIT, Medellín, Colombia
| | - Javier C Alvarez
- Departament of Biological Sciences, Cra 49 #7 sur-50, Universidad EAFIT, Medellín, Colombia
| | - Chia-Hui Hu
- Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Luz E de-Bashan
- The Bashan Institute of Science, 1730 Post Oak Ct., AL 36830, USA; Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Av. IPN 195, La Paz, B.C.S. 23096, Mexico; Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA
| | - Yoav Bashan
- The Bashan Institute of Science, 1730 Post Oak Ct., AL 36830, USA; Environmental Microbiology Group, Northwestern Center for Biological Research (CIBNOR), Av. IPN 195, La Paz, B.C.S. 23096, Mexico; Department of Entomology and Plant Pathology, Auburn University, 301 Funchess Hall, Auburn, AL 36849, USA.
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6
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Teixeira RT, Fortes AM, Pinheiro C, Pereira H. Comparison of good- and bad-quality cork: application of high-throughput sequencing of phellogenic tissue. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4887-905. [PMID: 24958897 DOI: 10.1093/jxb/eru252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cork is one of the most valuable non-wood forest products and plays an important role in Mediterranean economies. The production of high-quality cork is dependent on both genome and environment, posing constraints on the industry because an ever-growing amount of bad-quality cork (BQC) development has been observed. In order to identify genes responsible for production of cork of superior quality we performed a comparative analysis using the 454 pyrosequencing approach on phellogenic tissue of good- and bad-quality samples. The transcriptional profiling showed a high number of genes differentially expressed (8.48%) from which 78.8% displayed annotation. Genes more highly represented in BQC are involved in DNA synthesis, RNA processing, proteolysis, and transcription factors related to the abiotic stress response. Putative stomatal/lenticular-associated genes which may be responsible for the disadvantageous higher number of lenticular channels in BQC are also more highly represented. BQC also showed an elevated content of free phenolics. On the other hand, good-quality cork (GQC) can be distinguished by highly expressed genes encoding heat-shock proteins. Together the results provide valuable new information about the molecular events leading to cork formation and provide putative biomarkers associated with cork quality that can be useful in breeding programmes.
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Affiliation(s)
- Rita Teresa Teixeira
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade Técnica de Lisboa, 1349-017, Portugal
| | - Ana Margarida Fortes
- Center for Biodiversity, Functional and Integrative Genomics (BioFIG); Science Faculty, University of Lisbon, Campo Grande, 1749-016 Lisboa, Portugal
| | - Carla Pinheiro
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Helena Pereira
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade Técnica de Lisboa, 1349-017, Portugal
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7
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Kishore S, Luber S, Zavolan M. Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. Brief Funct Genomics 2010; 9:391-404. [PMID: 21127008 DOI: 10.1093/bfgp/elq028] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Eukaryotic cells express a large variety of ribonucleic acid-(RNA)-binding proteins (RBPs) with diverse affinity and specificity towards target RNAs that play a crucial role in almost every aspect of RNA metabolism. In addition, specific domains in RBPs impart catalytic activity or mediate protein-protein interactions, making RBPs versatile regulators of gene expression. In this review, we elaborate on recent experimental and computational approaches that have increased our understanding of RNA-protein interactions and their role in cellular function. We review aspects of gene expression that are modulated post-transcriptionally by RBPs, namely the stability of polymerase II-derived mRNA transcripts and their rate of translation into proteins. We further highlight the extensive regulatory networks of RBPs that implement a combinatorial control of gene expression. Taking cues from the recent development in the field, we argue that understanding spatio-temporal RNA-protein association on a transcriptome level will provide invaluable and unexpected insights into the regulatory codes that define growth, differentiation and disease.
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Huggins W, Ghosh SK, Wollenzien P. Hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16S rRNA in the 30S ribosome. BMC STRUCTURAL BIOLOGY 2009; 9:49. [PMID: 19643000 PMCID: PMC2731775 DOI: 10.1186/1472-6807-9-49] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Accepted: 07/30/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND Conformational flexibility in structured RNA frequently is critical to function. The 30S ribosomal subunit exists in different conformations in different functional states due to changes in the central part of the 16S rRNA. We are interested in evaluating the factors that might be responsible for restricting flexibility to specific parts of the 16S rRNA using biochemical data obtained from the 30S subunit in solution. This problem was approached taking advantage of the observation that there must be a high degree of conformational flexibility at sites where UV photocrosslinking occurs and a lack of flexibility inhibits photoreactivity at many other sites that are otherwise suitable for reaction. RESULTS We used 30S x-ray structures to quantify the properties of the nucleotide pairs at UV- and UVA-s4U-induced photocrosslinking sites in 16S rRNA and compared these to the properties of many hundreds of additional sites that have suitable geometry but do not undergo photocrosslinking. Five factors that might affect RNA flexibility were investigated - RNA interactions with ribosomal proteins, interactions with Mg2+ ions, the presence of long-range A minor motif interactions, hydrogen bonding and the count of neighboring heavy atoms around the center of each nucleobase to estimate the neighbor packing density. The two factors that are very different in the unreactive inflexible pairs compared to the reactive ones are the average number of hydrogen bonds and the average value for the number of neighboring atoms. In both cases, these factors are greater for the unreactive nucleotide pairs at a statistically very significant level. CONCLUSION The greater extent of hydrogen bonding and neighbor atom density in the unreactive nucleotide pairs is consistent with reduced flexibility at a majority of the unreactive sites. The reactive photocrosslinking sites are clustered in the 30S subunit and this indicates nonuniform patterns of hydrogen bonding and packing density in the 16S rRNA tertiary structure. Because this analysis addresses inter-nucleotide distances and geometry between nucleotides distant in the primary sequence, the results indicate regional and global flexibility of the rRNA.
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Affiliation(s)
- Wayne Huggins
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, USA
- RTI International, Research Triangle Park, USA
| | - Sujit K Ghosh
- Department of Statistics, North Carolina State University, Raleigh, USA
| | - Paul Wollenzien
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, USA
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9
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Abstract
Damage to RNA from ultraviolet light, oxidation, chlorination, nitration, and akylation can include chemical modifications to nucleobases as well as RNA-RNA and RNA-protein crosslinking. In vitro studies have described a range of possible damage products, some of which are supported as physiologically relevant by in vivo observations in normal growth, stress conditions, or disease states. Damage to both messenger RNA and noncoding RNA may have functional consequences, and work has begun to elucidate the role of RNA turnover pathways and specific damage recognition pathways in clearing cells of these damaged RNAs.
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10
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Abstract
RNA-RNA crosslinking provides a rapid means of obtaining evidence for the proximity of functional groups in structurally complex RNAs and ribonucleoproteins. Such evidence can be used to provide a physical context for interpreting structural information from other biochemical and biophysical methods and for the design of further experiments. The identification of crosslinks that accurately reflect the native conformation of the RNA of interest is strongly dependent on the position of the crosslinking agent, the conditions of the crosslinking reaction, and the method for mapping the crosslink position. Here, we provide an overview of protocols and experimental considerations for RNA-RNA crosslinking with the most commonly used long- and short-range photoaffinity reagents. Specifically, we describe the merits and strategies for random and site-specific incorporation of these reagents into RNA, the crosslinking reaction and isolation of crosslinked products, the mapping crosslinked sites, and assessment of the crosslinking data.
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Affiliation(s)
- Michael E Harris
- Center for RNA Molecular Biology, Department of Biochemistry, Case Western Reserve University Schoolof Medicine, Cleveland, Ohio, USA
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11
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A phage RNA-binding protein binds to a non-cognate structured RNA and stabilizes its core structure. Biochem Biophys Res Commun 2008; 378:168-73. [PMID: 19000653 PMCID: PMC7117394 DOI: 10.1016/j.bbrc.2008.10.160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 10/24/2008] [Indexed: 12/11/2022]
Abstract
Recent studies suggest that some RNA-binding proteins facilitate the folding of non-cognate RNAs. Here, we report that bacteriophage MS2 coat protein (MS2 CP) bound and promoted the catalytic activity of Candida group I ribozyme. Cloning of the MS2-bound RNA segments showed that this protein primarily interacts with the P5ab-P5 structure. Ultraviolet cross-linking and the T1 footprinting assay further showed that MS2 binding stabilized tertiary interactions, including the conserved L9-P5 interaction, and led to a more compact core structure. This mechanism is similar to that of the yeast mitochondrial tyrosyl-tRNA synthetase on other group I introns, suggesting that different RNA-binding proteins may use common mechanisms to support RNA structures.
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12
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Wang Y, Zhong X, Itaya A, Ding B. Evidence for the existence of the loop E motif of Potato spindle tuber viroid in vivo. J Virol 2006; 81:2074-7. [PMID: 17135317 PMCID: PMC1797592 DOI: 10.1128/jvi.01781-06] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
RNA motifs comprising nucleotides that interact through non-Watson-Crick base pairing play critical roles in RNA functions, often by serving as the sites for RNA-RNA, RNA-protein, or RNA small ligand interactions. The structures of viral and viroid RNA motifs are studied commonly by in vitro, computational, and mutagenesis approaches. Demonstration of the in vivo existence of a motif will help establish its biological significance and promote mechanistic studies on its functions. By using UV cross-linking and primer extension, we have obtained direct evidence for the in vivo existence of the loop E motif of Potato spindle tuber viroid. We present our findings and discuss their biological implications.
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Affiliation(s)
- Ying Wang
- Department of Plant Cellular and Molecular Biology, Ohio State University, 207 Rightmire Hall, 1060 Carmack Road, Columbus, OH 43210, USA
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13
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Huggins W, Ghosh SK, Nanda K, Wollenzien P. Internucleotide movements during formation of 16 S rRNA-rRNA photocrosslinks and their connection to the 30 S subunit conformational dynamics. J Mol Biol 2005; 354:358-74. [PMID: 16242153 DOI: 10.1016/j.jmb.2005.09.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2005] [Revised: 09/14/2005] [Accepted: 09/19/2005] [Indexed: 10/25/2022]
Abstract
UV light-induced RNA photocrosslinks are formed at a limited number of specific sites in the Escherichia coli and in other eubacterial 16 S rRNAs. To determine if unusually favorable internucleotide geometries could explain the restricted crosslinking patterns, parameters describing the internucleotide geometries were calculated from the Thermus thermophilus 30 S subunit X-ray structure and compared to crosslinking frequencies. Significant structural adjustments between the nucleotide pairs usually are needed for crosslinking. Correlations between the crosslinking frequencies and the geometrical parameters indicate that nucleotide pairs closer to the orientation needed for photoreaction have higher crosslinking frequencies. These data are consistent with transient conformational changes during crosslink formation in which the arrangements needed for photochemical reaction are attained during the electronic excitation times. The average structural rearrangement for UVA-4-thiouridine (s4U)-induced crosslinking is larger than that for UVB or UVC-induced crosslinking; this is associated with the longer excitation time for s4U and is also consistent with transient conformational changes. The geometrical parameters do not completely predict the crosslinking frequencies, implicating other aspects of the tertiary structure or conformational flexibility in determining the frequencies and the locations of the crosslinking sites. The majority of the UVB/C and UVA-s4U-induced crosslinks are located in four regions in the 30 S subunit, within or at the ends of RNA helix 34, in the tRNA P-site, in the distal end of helix 28 and in the helix 19/helix 27 region. These regions are implicated in different aspects of tRNA accommodation, translocation and in the termination reaction. These results show that photocrosslinking is an indicator for sites where there is internucleotide conformational flexibility and these sites are largely restricted to parts of the 30 S subunit associated with ribosome function.
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MESH Headings
- Base Pairing
- Base Sequence
- Binding Sites
- Cross-Linking Reagents
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/radiation effects
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation/radiation effects
- Nucleotides/chemistry
- Nucleotides/metabolism
- Nucleotides/radiation effects
- Photochemistry
- Protein Conformation/radiation effects
- Protein Subunits
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/radiation effects
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 16S/radiation effects
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/metabolism
- Ribosomes/radiation effects
- Ultraviolet Rays
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Affiliation(s)
- Wayne Huggins
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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14
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Ulm R, Nagy F. Signalling and gene regulation in response to ultraviolet light. CURRENT OPINION IN PLANT BIOLOGY 2005; 8:477-82. [PMID: 16039155 DOI: 10.1016/j.pbi.2005.07.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Accepted: 07/12/2005] [Indexed: 05/03/2023]
Abstract
In contrast to phytochrome-, cryptochrome- and phototropin-sensing systems, about which considerable knowledge has accumulated, the ultraviolet-B (UVB) photoreceptor is not yet known at the molecular level. Information about the downstream signalling events that underlie UVB-provoked physiological responses is limited. Recent whole-genome transcript profiling, isolation of mutants that are impaired in specific UVB-induced responses and detailed photobiological studies suggest that responses that are triggered by shorter wavelength UVB and longer wavelength UVB are mediated by two different sensory systems. The bZIP transcription factor HY5 was recently identified as an important player in the long-wavelength UVB-induced signal transduction cascade. Advances in the development of luciferase-reporter lines will make it feasible to perform high-throughput genetic screens to isolate novel mutants that are impaired in sensing or transducing signals downstream of the putative UVB photoreceptor(s).
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Affiliation(s)
- Roman Ulm
- Institute of Biology II/Botany, University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany.
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15
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Casati P, Walbot V. Crosslinking of ribosomal proteins to RNA in maize ribosomes by UV-B and its effects on translation. PLANT PHYSIOLOGY 2004; 136:3319-32. [PMID: 15466230 PMCID: PMC523391 DOI: 10.1104/pp.104.047043] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Ultraviolet-B (UV-B) photons can cause substantial cellular damage in biomolecules, as is well established for DNA. Because RNA has the same absorption spectrum for UV as DNA, we have investigated damage to this cellular constituent. In maize (Zea mays) leaves, UV-B radiation damages ribosomes by crosslinking cytosolic ribosomal proteins S14, L23a, and L32, and chloroplast ribosomal protein L29 to RNA. Ribosomal damage accumulated during a day of UV-B exposure correlated with a progressive decrease in new protein production; however, de novo synthesis of some ribosomal proteins is increased after 6 h of UV-B exposure. After 16 h without UV-B, damaged ribosomes were eliminated and translation was restored to normal levels. Ribosomal protein S6 and an S6 kinase are phosphorylated during UV-B exposure; these modifications are associated with selective translation of some ribosomal proteins after ribosome damage in mammalian fibroblast cells and may be an adaptation in maize. Neither photosynthesis nor pigment levels were affected significantly by UV-B, demonstrating that the treatment applied is not lethal and that maize leaf physiology readily recovers.
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Affiliation(s)
- Paula Casati
- Department of Biological Sciences, Stanford University, Stanford, California 94305-5020, USA.
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16
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Shapkina T, Lappi S, Franzen S, Wollenzien P. Efficiency and pattern of UV pulse laser-induced RNA-RNA cross-linking in the ribosome. Nucleic Acids Res 2004; 32:1518-26. [PMID: 14999094 PMCID: PMC390305 DOI: 10.1093/nar/gkh320] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2003] [Revised: 02/10/2004] [Accepted: 02/10/2004] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli ribosomes were irradiated with a KrF excimer laser (248 nm, 22 ns pulse) with incident pulse energies in the range of 10-40 mJ for a 1 cm2 area, corresponding to fluences of 4.5 to 18 x 10(9) W m(-2), to determine strand breakage yields and the frequency and pattern of RNA-RNA cross- linking in the 16S rRNA. Samples were irradiated in a cuvette with one laser pulse or in a flow cell with an average of 4.6 pulses per sample. The yield of strand breaks per photon was intensity dependent, with values of 0.7 to 1.3 x 10(-3) over the incident intensity range studied. The yield for RNA-RNA cross-linking was 3 x 10(-4) cross-links/photon at the intensity of 4.5 x 10(9) W m(-2), an approximately 4-fold higher yield per photon than obtained with a transilluminator. The cross-link yield/photon decreased at higher light intensities, probably due to intensity-dependent photoreversal. The pattern of cross-linking was similar to that observed with low intensity irradiation but with four additional long-range cross-links not previously seen in E.coli ribosomes. Cross- linking frequencies obtained with one laser pulse are more correlated to internucleotide distances than are frequencies obtained with transilluminator irradiation.
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Affiliation(s)
- Tatjana Shapkina
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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17
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Casati P, Walbot V. Rapid transcriptome responses of maize (Zea mays) to UV-B in irradiated and shielded tissues. Genome Biol 2004; 5:R16. [PMID: 15003119 PMCID: PMC395766 DOI: 10.1186/gb-2004-5-3-r16] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2003] [Revised: 12/15/2003] [Accepted: 01/22/2004] [Indexed: 11/10/2022] Open
Abstract
Profiling the transcriptional response of maize tissues to UV-B irradiation suggests that a signal is transmitted from irradiated to shielded tissue. The transcriptional response occurs rapidly, even in shielded tissue. Background Depletion of stratospheric ozone has raised terrestrial levels of ultraviolet-B radiation (UV-B), an environmental change linked to an increased risk of skin cancer and with potentially deleterious consequences for plants. To better understand the processes of UV-B acclimation that result in altered plant morphology and physiology, we investigated gene expression in different organs of maize at several UV-B fluence rates and exposure times. Results Microarray hybridization was used to assess UV-B responses in directly exposed maize organs and organs shielded by a plastic that absorbs UV-B. After 8 hours of high UV-B, the abundance of 347 transcripts was altered: 285 were increased significantly in at least one organ and 80 were downregulated. More transcript changes occurred in directly exposed than in shielded organs, and the levels of more transcripts were changed in adult compared to seedling tissues. The time course of transcript abundance changes indicated that the response kinetics to UV-B is very rapid, as some transcript levels were altered within 1 hour of exposure. Conclusions Most of the UV-B regulated genes are organ-specific. Because shielded tissues, including roots, immature ears, and leaves, displayed altered transcriptome profiles after exposure of the plant to UV-B, some signal(s) must be transmitted from irradiated to shielded tissues. These results indicate that there are integrated responses to UV-B radiation above normal levels. As the same total UV-B irradiation dose applied at three intensities elicited different transcript profiles, the transcriptome changes exhibit threshold effects rather than a reciprocal dose-effect response. Transcriptome profiling highlights possible signaling pathways and molecules for future research.
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Affiliation(s)
- Paula Casati
- Department of Biological Sciences, 385 Serra Mall, Stanford University, Stanford, CA 94305-5020, USA.
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Casati P, Walbot V. Gene expression profiling in response to ultraviolet radiation in maize genotypes with varying flavonoid content. PLANT PHYSIOLOGY 2003; 132:1739-54. [PMID: 12913132 PMCID: PMC181262 DOI: 10.1104/pp.103.022871] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2003] [Revised: 03/27/2003] [Accepted: 05/05/2003] [Indexed: 05/19/2023]
Abstract
Microarray hybridization was used to assess acclimation responses to four UV regimes by near isogenic maize (Zea mays) lines varying in flavonoid content. We found that 355 of the 2,500 cDNAs tested were regulated by UV radiation in at least one genotype. Among these, 232 transcripts are assigned putative functions, whereas 123 encode unknown proteins. UV-B increased expression of stress response and ribosomal protein genes, whereas photosynthesis-associated genes were down-regulated; lines lacking UV-absorbing pigments had more dramatic responses than did lines with these pigments, confirming the shielding role of these compounds. Sunlight filtered to remove UV-B or UV-B plus UV-A resulted in significant expression changes in many genes not previously associated with UV responses. Some pathways regulated by UV radiation are shared with defense, salt, and oxidative stresses; however, UV-B radiation can activate additional pathways not shared with other stresses.
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Affiliation(s)
- Paula Casati
- Department of Biological Sciences, 385 Serra Mall, Stanford University, Stanford, California 94305-5020, USA.
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Casati P, Walbot V. Gene expression profiling in response to ultraviolet radiation in maize genotypes with varying flavonoid content. PLANT PHYSIOLOGY 2003; 132:1739-1754. [PMID: 12913132 DOI: 10.1104/pp.103.022871.)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Microarray hybridization was used to assess acclimation responses to four UV regimes by near isogenic maize (Zea mays) lines varying in flavonoid content. We found that 355 of the 2,500 cDNAs tested were regulated by UV radiation in at least one genotype. Among these, 232 transcripts are assigned putative functions, whereas 123 encode unknown proteins. UV-B increased expression of stress response and ribosomal protein genes, whereas photosynthesis-associated genes were down-regulated; lines lacking UV-absorbing pigments had more dramatic responses than did lines with these pigments, confirming the shielding role of these compounds. Sunlight filtered to remove UV-B or UV-B plus UV-A resulted in significant expression changes in many genes not previously associated with UV responses. Some pathways regulated by UV radiation are shared with defense, salt, and oxidative stresses; however, UV-B radiation can activate additional pathways not shared with other stresses.
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Affiliation(s)
- Paula Casati
- Department of Biological Sciences, 385 Serra Mall, Stanford University, Stanford, California 94305-5020, USA.
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Zhirnov OV, Wollenzien P. Action spectra for UV-light induced RNA-RNA crosslinking in 16S ribosomal RNA in the ribosome. Photochem Photobiol Sci 2003; 2:688-93. [PMID: 12859155 DOI: 10.1039/b208677h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV irradiation induces intramolecular crosslinks in ribosomal RNA in the ribosome. These crosslinks occur between nucleotides distant in primary sequence and they are specific, limited in number and have crosslinking efficiencies sufficient to allow their use in monitoring conformational changes. In this work, the frequency of crosslinking for eight 16S rRNA crosslinks was determined as a function of wavelength of irradiation. For six of the crosslinks, the action spectra correspond to the absorption spectra of at least one of the participating nucleotides. For a crosslink between nucleotides C967 and C1400 the maximum frequency of crosslinking occurs at wavelengths blue-shifted from the absorbance maximum of cytidine and for a crosslink between C1402 and C1501 the maximum frequency of crosslinking is red-shifted. Photoreversal of the crosslinks was also studied by deproteinizing crosslinked RNA under mild conditions and then re-irradiating it with specific wavelengths under conditions in which the crosslinks were reversed but not formed. The different crosslinks exhibit significantly different extents of photoreversal versus wavelength profiles. The differences in the crosslinking action spectra can be accounted for in the absorbance spectra of the nucleotides that are involved in the crosslink as well as by the photoreversal action spectra.
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MESH Headings
- Base Sequence
- DNA/chemistry
- DNA/radiation effects
- Electrophoresis, Polyacrylamide Gel
- Escherichia coli/chemistry
- Molecular Sequence Data
- Nucleic Acid Conformation
- Photochemistry
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Bacterial/radiation effects
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 16S/radiation effects
- Ribosomes/radiation effects
- Spectrophotometry, Ultraviolet
- Ultraviolet Rays
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Affiliation(s)
- Oksana V Zhirnov
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
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Dolan MA, Babin P, Wollenzien P. Construction and analysis of base-paired regions of the 16S rRNA in the 30S ribosomal subunit determined by constraint satisfaction molecular modelling. J Mol Graph Model 2002; 19:495-513. [PMID: 11552678 DOI: 10.1016/s1093-3263(00)00097-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Structure models for each of the secondary structure regions from the Escherichia coli 16S rRNA (58 separate elements) were constructed using a constraint satisfaction modelling program to determine which helices deviated from classic A-form geometry. Constraints for each rRNA element included the comparative secondary structure, H-bonding conformations predicted from patterns of base-pair covariation, tertiary interactions predicted from covariation analysis, chemical probing data, rRNA-rRNA crosslinking information, and coordinates from solved structures. Models for each element were built using the MC-SYM modelling algorithm and subsequently were subjected to energy minimization to correct unfavorable geometry. Approximately two-thirds of the structures that result from the input data are very similar to A-form geometry. In the remaining instances, the presence of internal loops and bulges, some sequences (and sequence covariants) and accessory information require deviation from A-form geometry. The structures of regions containing more complex base-pairing arrangements including the central pseudoknot, the 530 region, and the pseudoknot involving base-pairing between G570-U571/A865-C866 and G861-C862/G867-C868 were predicted by this approach. These molecular models provide insight into the connection between patterns of H-bonding, the presence of unpaired nucleotides, and the overall geometry of each element.
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Affiliation(s)
- M A Dolan
- Department of Biochemistry, North Carolina State University, Raleigh, North Carolina 27695-762, USA
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Juzumiene D, Shapkina T, Kirillov S, Wollenzien P. Short-range RNA-RNA crosslinking methods to determine rRNA structure and interactions. Methods 2001; 25:333-43. [PMID: 11860287 DOI: 10.1006/meth.2001.1245] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We describe details of procedures to analyze RNA-RNA crosslinks made by far-UV irradiation (< 300 nm) or made by irradiation with near-UV light (320-365 nm) on RNA containing photosensitive nucleotides, in the present case containing 4-thiouridine. Zero-length crosslinks of these types must occur because of the close proximity of the participants through either specific interactions or transient contacts in the folded RNA structure, so they are valuable monitors of the conformation of the RNA. Procedures to produce crosslinks in the 16S ribosomal RNA and between the 16S rRNA and mRNA or tRNA are described. Gel electrophoresis conditions are described that separate the products according to their structure to allow the determination of the number and frequency of the crosslinking products. Gel electrophoresis together with an ultracentrifugation procedure for the efficient recovery of RNA from the polyacrylamide gels allows the purification of molecules containing different crosslinks. These separation techniques allow the analysis of the sites of crosslinking by primer extension and RNA sequencing techniques. The procedures are applicable to other types of RNA molecules with some differences to control levels of crosslinking and separation conditions.
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Affiliation(s)
- D Juzumiene
- Department of Molecular and Structural Biochemistry, North Carolina State University, 126 Polk Hall, Raleigh, North Carolina 27695, USA
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