RNA‐modifying machines in archaea

@article{Omer2003RNAmodifyingMI,
  title={RNA‐modifying machines in archaea},
  author={Arina D. Omer and Sonia M Ziesche and Wayne A. Decatur and Maurille J. Fournier and Patrick P. Dennis},
  journal={Molecular Microbiology},
  year={2003},
  volume={48}
}
It has been known for nearly half a century that coding and non‐coding RNAs (mRNA, and tRNAs and rRNAs respectively) play critical roles in the process of information transfer from DNA to protein. What is both surprising and exciting, are the discoveries in the last decade that cells, particularly eukaryotic cells, contain a plethora of non‐coding RNAs and that these RNAs can either possess catalytic activity or can function as integral components of dynamic ribonucleoprotein machines. These… 
Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification
TLDR
This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaealing sRNP components, their functions in nucleotide modification, and their structures.
RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP.
TLDR
This work reconstituted functional archaeal H/ACA RNPs from recombinant components, defined the components necessary and sufficient for function, and determined the direct RNA-protein and protein-protein interactions that occur between the components.
The structure and function of small nucleolar ribonucleoproteins
TLDR
Recent advances in the structure, assembly and function of the conserved C/D and H/ACA sno(s)RNPs are reviewed and insight is offered into the highly homologous eukaryotic snoRNPs.
Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum
TLDR
This review focuses on ncRNAs in the social amoeba Dictyostelium discoideum, an important genetically tractable model organism that has recently received renewed attention in terms of discovery, regulation and functional studies of nc RNAs.
Mechanisms and functions of RNA-guided RNA modification
TLDR
The authors are beginning to understand the basis for the importance of the RNA-guided modifications, which are well conserved and clustered in functionally important regions of RNAs.
The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA
TLDR
High resolution structures of the archaeal C/D and H/ACA sRNPs have not only provided a detailed understanding of the molecular architecture of these complexes but also produced key insights into substrate binding and product release.
H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes
TLDR
This review provides an overview of the current knowledge on H/ACA sRNPs from archaea, in particular their structure and function, and relates it to the understanding of the roles of eukaryotic H/ ACA sRNP during eUKaryotic ribosome synthesis and beyond.
Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution.
TLDR
KsgA orthologs from archaeabacteria and eukaryotes are able to complement for KsgA function in bacteria, both in vivo and in vitro, indicating that all of these enzymes can recognize a common ribosomal substrate, and that the recognition elements must be largely unchanged since the evolutionary split between the three domains of life.
RNA Metabolism and Gene Expression in Archaea
TLDR
This chapter discusses an integrated view of transcription from the molecular to the global level, and systems biology approaches have provided compelling insights into promoter and terminator DNA elements, the genome-wide distribution of transcription initiationand elongation factors and RNA polymerase, the archaeal transcriptome and chromatin organisation.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 108 REFERENCES
Small nucleolar RNA‐guided post‐transcriptional modification of cellular RNAs
  • T. Kiss
  • Biology, Chemistry
    The EMBO journal
  • 2001
TLDR
Post‐transcriptional modification of individual ribonucleotides, namely deamination of adenosines and cytidines, can also change the readout of mRNAs, and lack of ribosomal pseudouridines can reduce the growth rate or confer a selective disadvantage when it is competed against wild‐type ribosomes.
A guided tour: small RNA function in Archaea
TLDR
It is suggested that archaeal sRNAs may have two functions: to guide the deposition of methyl groups at the 2′‐O position of ribose, which is an important determinant in RNA structural stability, and to serve as a molecular chaperones to help orchestrate the folding of rRNAs and tRNAs at high temperature.
Small Nucleolar RNAs Guide the Ribose Methylations of Eukaryotic rRNAs
This chapter provides a progress report on developments that should set the stage for dissecting the rRNA-ribose methylation machinery and for deciphering the role of these modifications in ribosome
Ribosomal RNA introns in archaea and evidence for RNA conformational changes associated with splicing.
  • J. Kjems, R. Garrett
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1991
TLDR
The single 23S rRNA gene of the archaeon Staphylothermus marinus exhibits two introns which, at the RNA level, are located in highly conserved regions of domains IV and V, and parts of this structural feature that are essential for cleavage are defined using a phylogenetic sequence comparison approach.
In vitro reconstitution and activity of a C/D box methylation guide ribonucleoprotein complex
TLDR
The experiments define the minimal number of components and the conditions required to achieve in vitro RNA guide-directed 2′-O-methylation of ribose in a target RNA.
Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes.
TLDR
Archaeal genomes are searched for potential homologs of eukaryotic methylation guide small nucleolar RNAs, by combining searches for structured motifs with homology searches, and a family of 46 small RNAs is identified, conserved in the genomes of three hyperthermophile Pyrococcus species, which are experimentally characterized in PyrocOCcus abyssi.
The small nucleolar RNAs.
The present review summarizes key progress made in characterizing the small nucleolar RNAs (snoRNAs) of eukaryotic cells. Recent studies have shown snoRNA populations to be substantially more complex
...
1
2
3
4
5
...