Schallenberg-Rudinger M.,Abteilung Molekulare Evolution |
Lenz H.,Abteilung Molekulare Evolution |
Polsakiewicz M.,Abteilung Molekulare Evolution |
Gott J.M.,Center for Molecular Biology |
Knoop V.,Abteilung Molekulare Evolution
RNA biology | Year: 2013
The pentatricopeptide repeat modules of PPR proteins are key to their sequence-specific binding to RNAs. Gene families encoding PPR proteins are greatly expanded in land plants where hundreds of them participate in RNA maturation, mainly in mitochondria and chloroplasts. Many plant PPR proteins contain additional carboxyterminal domains and have been identified as essential factors for specific events of C-to-U RNA editing, which is abundant in the two endosymbiotic plant organelles. Among those carboxyterminal domain additions to plant PPR proteins, the so-called DYW domain is particularly interesting given its similarity to cytidine deaminases. The frequency of organelle C-to-U RNA editing and the diversity of DYW-type PPR proteins correlate well in plants and both were recently identified outside of land plants, in the protist Naegleria gruberi. Here we present a systematic survey of PPR protein genes and report on the identification of additional DYW-type PPR proteins in the protists Acanthamoeba castellanii, Malawimonas jakobiformis, and Physarum polycephalum. Moreover, DYW domains were also found in basal branches of multi-cellular lineages outside of land plants, including the alga Nitella flexilis and the rotifers Adineta ricciae and Philodina roseola. Intriguingly, the well-characterized and curious patterns of mitochondrial RNA editing in the slime mold Physarum also include examples of C-to-U changes. Finally, we identify candidate sites for mitochondrial RNA editing in Malawimonas, further supporting a link between DYW-type PPR proteins and C-to-U editing, which may have remained hitherto unnoticed in additional eukaryote lineages.
PubMed | J. Craig Venter Institute, Center for Molecular Biology and Case Western Reserve University
Type: | Journal: Human molecular genetics | Year: 2016
A defined set of genetic instructions encodes functionality in complex organisms. Delineating these unique genetic signatures is essential to understanding the formation and functionality of specialized tissues. Vision, one of the five central senses of perception, is initiated by the retina and has evolved over time to produce rod and cone photoreceptors that vary in a species-specific manner, and in some cases by geographical region resulting in higher order visual acuity in humans. RNA-sequencing and use of existing and de novo transcriptome assemblies allowed ocular transcriptome mapping from a diverse set of rodent and primate species. Global genomic refinements along with systems-based comparative and co-expression analyses of these transcriptome maps identified gene modules that correlated with specific features of rod versus cone retinal cellular composition. Organization of the ocular transcriptome demonstrated herein defines the molecular basis of photoreceptor architecture and functionality, providing a new paradigm for neurogenetic analyses of the mammalian retina in health and disease.
News Article | December 5, 2016
Nanotechnology - What You Should Know Top Scientific Minds You Probably Never Heard Of The Breakthrough Prizes 2017 were given away at an Oscars-like function in the NASA Ames Research Center in Mountain View on Sunday, Dec. 4, to honor outstanding research in life sciences, mathematics and fundamental physics. Attended by the Who's Who of the technology industry and scientific honchos, the award function was hosted by actor Morgan Freeman. At the ceremony, a total of $25 million was awarded to the winners. The event had Grammy winner Alicia Keys rendering live pop entertainment. "There has never been a more important time to support science," said Facebook founder Mark Zuckerberg, one of the patrons of the foundation. For conceiving the gala event in science, credit goes to Yuri Milner, the Russian billionaire and investor, and his wife, Julia, who instituted the debut award in 2012 to reward theoretical physicists for outstanding scientific achievements. Since then, the number of disciplines for awards expanded with more sponsors stepping in to support the cause. Among the new patrons are Google's Sergey Brin, Mark Zuckerberg of Facebook, biotech firm 23andMe's Anne Wojcicki and Jack Ma and his wife Cathy Zhang of Alibaba. The 2017 Breakthrough Prizes ceremony also marked the organization's fifth anniversary. Since 2012, the Breakthrough Prize has disbursed close to $200 million in honoring paradigm-shifting research in science. The awardees this year in life sciences, fundamental physics and mathematics are the following. These winners get individual $3 million in prizes. - Stephen J. Elledge, Professor of Genetics and Medicine in the Department of Genetics at Harvard Medical School, for probing the role of damage detection proteins in yielding mutated DNA replication and increasing cancer risk. - Harry F. Noller, Director, Center for Molecular Biology at the University of California. His work investigates the central role of RNA in the ribosome and origin of life. - Roeland Nusse, Professor at Stanford University. He explored the Wnt gene pathway and its implications in cancer. - Yoshinori Ohsumi, Honorary Professor, Institute of Innovative Research at Tokyo Institute of Technology. The work included the investigation of autophagy by which cells recycle their components to create nutrients. - Huda Yahya Zoghbi, Professor of Pediatrics, Baylor College of Medicine. The work was the discovery of biological underpinnings of spinocerebellar ataxia. The following three recipients shared a single $3 million award for their advances in string theory, quantum field theory and quantum gravity. - Joseph Polchinski, Professor of Physics at the University of California, Santa Barbara The following three winners shared a single $1 million prize, while $2 million was divided among 1,012 members of their research team. - Ronald Drever, Professor at the California Institute of Technology, Pasadena - Kip Thorne, Feynman Professor of Physics at the California Institute of Technology, Pasadena - Rainer Weiss, Professor at the Massachusetts Institute of Technology - Jean Bourgain, Professor, Institute for Advanced Study, Princeton, for contributions to high-dimensional geometry and other theoretical areas. One of the highlights of the awarding ceremony was the speeches by female students Antonella Masini, 18 (Peru) and Deanna See, 17 (Singapore). They were the winners of the Breakthrough Junior Challenge and got $250,000 for their inspiring science videos that promoted creative thinking on life sciences, physics and mathematics. © 2017 Tech Times, All rights reserved. Do not reproduce without permission.
Jungwirth U.,Medical University of Vienna |
Jungwirth U.,Institute of Cancer Research |
Gojo J.,Medical University of Vienna |
Tuder T.,Medical University of Vienna |
And 14 more authors.
Molecular Cancer Therapeutics | Year: 2014
On the basis of enhanced tumor accumulation and bone affinity, gallium compounds are under development as anticancer and antimetastatic agents. In this study, we analyzed molecular targets of one of the lead anticancer gallium complexes [KP46, Tris(8-quinolinolato)gallium(III)] focusing on colon and lung cancer. Within a few hours, KP46 treatment at low micromolar concentrations induced cell body contraction and loss of adhesion followed by prompt cell decomposition. This rapid KP46-induced cell death lacked classic apoptotic features and was insensitive toward a pan-caspase inhibitor. Surprisingly, however, it was accompanied by upregulation of proapoptotic Bcl-2 family members. Furthermore, a Bax- but not a p53-knockout HCT-116 subline exhibited significant KP46 resistance. Rapid KP46-induced detachment was accompanied by downregulation of focal adhesion proteins, including several integrin subunits. Loss of integrin-β1 and talin plasma membrane localization corresponded to reduced binding of RGD (Arg-Gly-Asp) peptides to KP46-treated cells. Accordingly, KP46-induced cell death and destabilization of integrins were enhanced by culture on collagen type I, a major integrin ligand. In contrast, KP46-mediated adhesion defects were partially rescued by Mg2+ ions, promoting integrin-mediated cell adhesion. Focal adhesion dynamics are regulated by calpains via cleavage of multiple cell adhesion molecules. Cotreatment with the cell-permeable calpain inhibitor PD150606 diminished KP46-mediated integrin destabilization and rapid cell death induction. KP46 treatment distinctly inhibited HCT-116 colon cancer xenograft in vivo by causing reduced integrin plasma membrane localization, tissue disintegration, and intense tumor necrosis. This study identifies integrin deregulation via a calpain-mediated mechanism as a novel mode of action for the anticancer gallium compound KP46. ©2014 AACR.
Liu F.,Nanjing Agricultural University |
Liu F.,Center for Molecular Biology |
Liu F.,Case Western Reserve University |
Putnam A.A.,Center for Molecular Biology |
And 2 more authors.
Biochemistry | Year: 2014
DEAD-box RNA helicases bind and remodel RNA and RNA-protein complexes in an ATP-dependent fashion. Several lines of evidence suggest that DEAD-box RNA helicases can also form stable, persistent complexes with RNA in a process referred to as RNA clamping. The molecular basis of RNA clamping is not well understood. Here we show that the yeast DEAD-box helicase Ded1p forms exceptionally long-lived complexes with RNA and the nonhydrolyzable ATP ground-state analogue ADP-BeFx or the nonhydrolyzable ATP transition state analogue ADP-AlFx. The complexes have lifetimes of several hours, and neither nucleotide nor Mg2+ is released during this period. Mutation of arginine 489, which stabilizes the transition state, prevents formation of long-lived complexes with the ATP transition state analogue, but not with the ground state analogue. We also show that two other yeast DEAD-box helicases, Mss116p and Sub2p, form comparably long-lived complexes with RNA and ADP-BeFx. Like Ded1p, Mss116p forms long-lived complexes with ADP-AlFx, but Sub2p does not. These data suggest that the ATP transition state might vary for distinct DEAD-box helicases, or that the transition state triggers differing RNA binding properties in these proteins. In the ATP ground state, however, all tested DEAD-box helicases establish a persistent grip on RNA, revealing an inherent capacity of the enzymes to function as potent, ATP-dependent RNA clamps. © 2013 American Chemical Society.
Moran V.A.,Center for Molecular Biology |
Perera R.J.,Sanford Burnham Institute for Medical Research |
Khalil A.M.,Center for Molecular Biology |
Khalil A.M.,Case Western Reserve University
Nucleic Acids Research | Year: 2012
The recent discovery that the human and other mammalian genomes produce thousands of long non-coding RNAs (lncRNAs) raises many fascinating questions. These mRNA-like molecules, which lack significant protein-coding capacity, have been implicated in a wide range of biological functions through diverse and as yet poorly understood molecular mechanisms. Despite some recent insights into how lncRNAs function in such diverse cellular processes as regulation of gene expression and assembly of cellular structures, by and large, the key questions regarding lncRNA mechanisms remain to be answered. In this review, we discuss recent advances in understanding the biology of lncRNAs and propose avenues of investigation that may lead to fundamental new insights into their functions and mechanisms of action. Finally, as numerous lncRNAs are dysregulated in human diseases and disorders, we also discuss potential roles for these molecules in human health. © The Author(s) 2012.
Hidalgo A.,Center for Molecular Biology |
Schliessmann A.,University of Greifswald |
Bornscheuer U.T.,University of Greifswald
Methods in Molecular Biology | Year: 2014
The OSCARR methodology (One-pot Simple methodology for CAssette Randomization and Recombination) bridges the gap between site-directed mutagenesis and full randomization by making use of carefully designed mutagenic cassettes and an optimized one-pot megaprimer PCR. The method is especially suited to construct libraries of up to ten randomized codons for focused directed evolution, exhibits up to 97 % efficiency in the amplification of mutated over wild-type products, and is sufficiently versatile to allow mutagenesis and recombination of several cassettes within the same gene. © 2014 Springer Science+Business Media New York.
Perriman R.,Center for Molecular Biology |
Ares Jr. M.,Center for Molecular Biology
Molecular Cell | Year: 2010
U2 snRNA-intron branchpoint pairing is a critical step in pre-mRNA recognition by the splicing apparatus, but the mechanism by which these two RNAs engage each other is unknown. Here, we identify a U2 snRNA structure, the branchpoint-interacting stem loop (BSL), which presents the U2 nucleotides that will contact the intron. We provide evidence that the BSL forms prior to interaction with the intron and is disrupted by the DExD/H protein Prp5p during engagement of the snRNA with the intron. In vitro splicing complex assembly in a BSL-destabilized mutant extract suggests that the BSL is required at a previously unrecognized step between commitment complex and prespliceosome formation. The extreme evolutionary conservation of the BSL suggests that it represents an ancient structural solution to the problem of intron branchpoint recognition by dynamic RNA elements that must serve multiple functions at other times during splicing. © 2010 Elsevier Inc. All rights reserved.
PubMed | Pennsylvania State University and Center for Molecular Biology
Type: Journal Article | Journal: Bioinformatics (Oxford, England) | Year: 2015
RNAs fold into complex structures that are integral to the diverse mechanisms underlying RNA regulation of gene expression. Recent development of transcriptome-wide RNA structure profiling through the application of structure-probing enzymes or chemicals combined with high-throughput sequencing has opened a new field that greatly expands the amount of in vitro and in vivo RNA structural information available. The resultant datasets provide the opportunity to investigate RNA structural information on a global scale. However, the analysis of high-throughput RNA structure profiling data requires considerable computational effort and expertise.We present a new platform, StructureFold, that provides an integrated computational solution designed specifically for large-scale RNA structure mapping and reconstruction across any transcriptome. StructureFold automates the processing and analysis of raw high-throughput RNA structure profiling data, allowing the seamless incorporation of wet-bench structural information from chemical probes and/or ribonucleases to restrain RNA secondary structure prediction via the RNAstructure and ViennaRNA package algorithms. StructureFold performs reads mapping and alignment, normalization and reactivity derivation, and RNA structure prediction in a single user-friendly web interface or via local installation. The variation in transcript abundance and length that prevails in living cells and consequently causes variation in the counts of structure-probing events between transcripts is accounted for. Accordingly, StructureFold is applicable to RNA structural profiling data obtained in vivo as well as to in vitro or in silico datasets. StructureFold is deployed via the Galaxy platform.StructureFold is freely available as a component of Galaxy available at: https://firstname.lastname@example.org or email@example.comSupplementary data are available at Bioinformatics online.
PubMed | Center for Molecular Biology
Type: Journal Article | Journal: Planta | Year: 2013
The cytological and intracellular localization of myrosinase (EC 188.8.131.52) has been studied by immunochemical techniques using paraffin-embedded sections of radicles and cotyledons from seeds of Brassica napus L. cv. Niklas. For immunolabelling, sections were sequentially incubated with a monoclonal anti-myrosinase antibody and with peroxidase-and fluorescein-isothiocyanate-conjugated secondary antibodies. Enzyme and fluorescence label was present in typical myrosin cells both in radicles and in cotyledons. With higher magnification, fluorescence label revealed that the intracellular localization of myrosinase was associated with the tonoplast-like membrane surrounding the myrosin grains in the myrosin cells. The results also indicate that a large proportion of the positive myrosin cells are located in the second-outermost cell layer of the peripheral cortex region of the radicles.