UV-induced crosslinks in the 16S rRNAs of Escherichia coli, Bacillus subtilis and Thermus aquaticus and their implications for ribosome structure and photochemistry

Noah, James W.; Shapkina, Tatjana; Wollenzien, Paul

doi:10.1093/nar/28.19.3785

Cited by 26 publications

(29 citation statements)

References 35 publications

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“…A major component of DNA damage is UV-B-induced base dimerization. In a similar way, UV-B could damage ribosomes by forming cross-links in ribosomal RNA or between mRNA, tRNA, rRNA, and proteins (Noah et al, 2000). As a consequence, coordinate up-regulation of ribosomal protein synthesis is likely to be important for the maintenance of this crucial cellular function.…”

Section: Discussionmentioning

confidence: 99%

Gene Expression Profiling in Response to Ultraviolet Radiation in Maize Genotypes with Varying Flavonoid Content

2003

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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.UV radiation is divided into three classes: UV-C, UV-B, and UV-A. Highly energetic UV-C (wavelengths Յ280 nm) is strongly absorbed by oxygen and ozone in the stratosphere such that none of this sterilizing radiation is present in terrestrial sunlight. Potentially harmful UV-B (280-315 nm) is strongly absorbed by atmospheric ozone, but approximately 4% of terrestrial radiation is UV-B from 290 to 315 nm. UV-A (315-400 nm) is not attenuated by atmospheric ozone, and this less damaging radiation is an important photomorphogenic signal in plant development (Bjorn, 1994). Chlorofluorocarbons and other pollutants have catalyzed depletion of the stratospheric ozone layer; consequently, terrestrial levels of UV-B are increasing with potentially deleterious consequences for all living organisms, particularly for plant development and physiology Searles et al., 2001;Paul and Gwynn-Jones, 2003).UV-B radiation induces diverse morphological and physiological responses in plants (for reviews, see Ballaré et al., 2001;Searles et al., 2001;Paul and Gwynn-Jones, 2003), but the underlying mechanisms governing these integrated responses are unknown. Concurrent with exposure, UV-B photons cause cellular damage by generating photoproducts in DNA (Britt, 1996) and direct damage to proteins (Gerhardt et al., 1999). In response to the inevitable exposure to damaging UV-B radiation, plants have evolved UVinduced mechanisms of protection and repair, such as accumulation of UV-absorbing pigments (Stapleton and Walbot, 1994;Mazza et al., 2000;Bieza and Lois, 2001) and use of UV-A photons to repair most UV-B-induced DNA damage (Britt, 1996). Because of its absorption spectrum, DNA is a major target of UV-B damage; even low doses of radiation can kill mutants lacking specific DNA repair pathways (Britt et al., 1993;Britt, 1996;Landry et al., 1997). In flowering plants, flavonoids, including anthocyanins, accumulate in the vacuoles of epidermal cells where they attenuate the UV component of sunlight with minimal absorption of photosynthetically active radiation (Stapleton and Walbot, 1...

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Section: Discussionmentioning

confidence: 99%

Gene Expression Profiling in Response to Ultraviolet Radiation in Maize Genotypes with Varying Flavonoid Content

2003

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“…UV cross-linking has been used for detecting tertiary interactions in vitro in a wide range of RNAs, for example, hepatitis delta virus (5,7,9), tRNAs (4), small nuclear RNAs (32), hairpin ribozymes (8), ribosomal RNAs (22), and Peach latent mosaic viroid (16). As shown here, this approach may be extended to investigate the in vivo existence of these tertiary interactions.…”

Section: Fig 3 Rna Gel Blotmentioning

confidence: 99%

Evidence for the Existence of the Loop E Motif of Potato Spindle Tuber Viroid In Vivo

Wang¹,

Zhong²,

Itaya³

et al. 2007

J Virol

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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.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 interactions with proteins, other RNA motifs, or small ligands (19). For viral and viroid RNAs, such interactions are crucial for the establishment of infection. The structures of RNA motifs of viral and viroid RNAs have been generally studied by in vitro chemical/ enzymatic mapping, thermodynamic calculations using minimum free energy, biophysical characterization, and mutational analyses. It has been shown experimentally that some structural features of RNAs deduced by in vitro and in silico methods may not be identical to those found in vivo, likely because of the influence of cellular factors that interact with the RNAs (2, 26, 30). Therefore, to further establish the biological significance of findings from in vitro and in silico approaches, the in vivo existence of an RNA motif should be directly demonstrated.We are interested in using viroid infection as a model system to investigate the structure-function relationships of RNA motifs. Viroids are the smallest known nucleic acid-based infectious agents and self-replicating genetic units. Their genomes consist of single-stranded, circular RNAs ranging in size from 250 to 400 nucleotides (12, 13, 33). Viroids do not encode proteins, do not have encapsidation mechanisms, and do not require helper viruses. Nonetheless, they can replicate efficiently and spread throughout an infected plant (13, 33). Thus, viroid infection provides an excellent experimental system to investigate the basic RNA structure-function relationships for infection as well as for RNA biology (18).One of the best-studied viroid RNA motifs is the so-called loop E located in the central conserved region of Potato spindle tuber viroid (PSTVd). The loop E is a recurrent motif found in many RNAs, including 5S, 16S, and 23S rRNAs, group I and group II introns, bacterial RNase P, ribozyme of Tobacco ringspot virus satellite RNA (20), and lysine riboswitches (15,31), where it plays critical roles in RNA-RNA and RNA-protein interactions. UV-induced cross-linking between G98 and U260 in vitro provided the first evidence for the existence of local tertiary structure in the loop E of PSTVd resembling that of the loop E of 5S rRNA from HeLa cells (6) ...

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“…However, UVBinduced crosslinking has also been done in Bacillus subtilis and Thermus aquaticus 19 and the majority of the crosslinking sites seen in the E. coli 16 S rRNA was also observed in those other organisms. T. aquaticus shares an identical pattern of crosslinking with Thermus thermophilus as assayed by gel electrophoresis (P.W., unpublished results) and 11 of 13 crosslinking sites in T. aquaticus are the same as sites in E. coli with the remaining sites involving neighboring nucleotides.…”

Section: Introductionmentioning

confidence: 99%

Internucleotide Movements during Formation of 16 S rRNA–rRNA Photocrosslinks and their Connection to the 30 S Subunit Conformational Dynamics

Huggins

Ghosh

Nanda

et al. 2005

Journal of Molecular Biology

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UV-induced crosslinks in the 16S rRNAs of Escherichia coli, Bacillus subtilis and Thermus aquaticus and their implications for ribosome structure and photochemistry

Cited by 26 publications

References 35 publications

Gene Expression Profiling in Response to Ultraviolet Radiation in Maize Genotypes with Varying Flavonoid Content

Gene Expression Profiling in Response to Ultraviolet Radiation in Maize Genotypes with Varying Flavonoid Content

Evidence for the Existence of the Loop E Motif of Potato Spindle Tuber Viroid In Vivo

Internucleotide Movements during Formation of 16 S rRNA–rRNA Photocrosslinks and their Connection to the 30 S Subunit Conformational Dynamics

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