We have published the dynamic extended folding (DEF) method, which is a RNA secondary structure prediction approach-to simulate the in vivo RNA co-transcriptional folding process. In order to verify the reliability of the method, we selected the X-ray-determined Tetrahymena group I intron as a sample to construct the framework of its folding secondary structure. Our prediction coincides well with the secondary structure predicted by T.R. Cech and the X-ray diffraction crystal structure determined by Lehnert V. Our results show that the DEF framework structure of Tetrahymena group I intron reflects its function sites in a concise and straightforward manner, and the scope of the simulation was expanded.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.jtbi.2010.09.001 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
The 'Janus A' gene encodes a polo-kinase whose loss creates a dorsal/ventral intracellular homeosis in the ciliate, .
bioRxiv
December 2024
Department of Cellular Biology, University of Georgia, Athens, GA.
Genetic studies on the protist, provide a glimpse into the unexpectedly rich world of intracellular patterning that unfolds within the ciliate cell cortex. Ciliate pattern studies provide a useful counterpoint to animal models of pattern formation in that the unicellular model draws attention away from fields of cells (or nuclei) as the principal players in the metazoan pattern paradigm, focusing instead on fields of ciliated basal bodies serving as sources of positional information. In this study, we identify , a Polo kinase of , that serves as an important factor driving global, circumferential pattern.
View Article and Find Full Text PDFA high-throughput search for intracellular factors that affect RNA folding identifies proteins PepA and YagL as RNA chaperones that promote RNA remodelling.
RNA Biol
January 2024
McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.
Article Synopsis
- General RNA chaperones are proteins that help RNA molecules fold correctly and avoid misfolding, which is crucial for bacteria, especially with large and complex RNA structures.
- Researchers adapted a technique to screen for factors affecting RNA folding and identified eight proteins that influence the folding of a specific RNA ribozyme when deleted.
- Among these, YagL and PepA were found to bind RNA and assist in the folding process, with YagL being especially effective in promoting correct refolding of misfolded RNA, thanks to a specific protein domain responsible for its activity.
The mitochondrial citrate synthase from Tetrahymena thermophila does not form an intermediate filament.
Eur J Protistol
October 2024
Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Karl-von-Frisch-Str. 14, 35043 Marburg, Germany; Department of Chemistry, Philipps-University Marburg, Hans-Meerwein-Str. 4, 35043 Marburg, Germany. Electronic address:
The mitochondrial citrate synthase (mCS) purified from the ciliate Tetrahymena thermophila has been reported to form intermediate-filament-like structures during conjugation and to self-assemble into fibers when recombinantly expressed. This would represent a rare example of a tractable and recent origin of a novel cytoskeletal element. In an attempt to investigate the evolutionary emergence of this behavior, we re-investigated the ability of Tetrahymena's mCS to form filaments in vivo.
View Article and Find Full Text PDFComplex evolutionary patterns within the tubulin gene family of ciliates, unicellular eukaryotes with diverse microtubular structures.
BMC Biol
August 2024
Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou, 510631, China.
Background: Tubulins are major components of the eukaryotic cytoskeletons that are crucial in many cellular processes. Ciliated protists comprise one of the oldest eukaryotic lineages possessing cilia over their cell surface and assembling many diverse microtubular structures. As such, ciliates are excellent model organisms to clarify the origin and evolution of tubulins in the early stages of eukaryote evolution.
View Article and Find Full Text PDFAnalyzing the Interaction between and Bacteria under Different Physicochemical Conditions When Infecting Guppy Using the eDNA Method.
Animals (Basel)
July 2024
Laboratory of Protozoology, Harbin Normal University, Harbin 150025, China.
Article Synopsis
- In the study of guppy fish in aquaculture, researchers looked at how bacteria and tiny parasites interact and how this affects fish health.
- Different water conditions, like temperature and pH, were tested to see how they impact these interactions.
- The findings showed that certain bacteria were linked to fish dying, and cooler temperatures with higher pH levels helped reduce diseases in the fish.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!