RNA-guided nucleotide modification of ribosomal and non-ribosomal RNAs in Archaea

Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures.

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Conformational Transitions in Escherichia coli Ribosomal RNAs as Visualized by Dedicated STEM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100102961 ◽

1988 ◽

Vol 46 ◽

pp. 176-177

Author(s):

J.S. Wall ◽

V. Maridiyan ◽

S. Tumminia ◽

J. Hairifeld ◽

M. Boublik

Keyword(s):

Ionic Strength ◽

Three Dimensional ◽

Conformational Transitions ◽

Dark Field ◽

Dimensional Structure ◽

Ribosomal Rnas ◽

Field Mode ◽

Freeze Dried ◽

High Resolution Images ◽

Low Ionic Strength

The high contrast in the dark-field mode of dedicated STEM, specimen deposition by the wet film technique and low radiation dose (1 e/Å2) at -160°C make it possible to obtain high resolution images of unstained freeze-dried macromolecules with minimal structural distortion. Since the image intensity is directly related to the local projected mass of the specimen it became feasible to determine the molecular mass and mass distribution within individual macromolecules and from these data to calculate the linear density (M/L) and the radii of gyration.2 This parameter (RQ), reflecting the three-dimensional structure of the macromolecular particles in solution, has been applied to monitor the conformational transitions in E. coli 16S and 23S ribosomal RNAs in solutions of various ionic strength.In spite of the differences in mass (550 kD and 1050 kD, respectively), both 16S and 23S RNA appear equally sensitive to changes in buffer conditions. In deionized water or conditions of extremely low ionic strength both appear as filamentous structures (Fig. la and 2a, respectively) possessing a major backbone with protruding branches which are more frequent and more complex in 23S RNA (Fig. 2a).

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Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa018 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

John W Davey ◽

Carolina M C Catta-Preta ◽

Sally James ◽

Sarah Forrester ◽

Maria Cristina M Motta ◽

...

Keyword(s):

Chromosome Number ◽

Noncoding Rnas ◽

Nuclear Genome ◽

Supernumerary Chromosome ◽

Ribosomal Rnas ◽

Protein Coding ◽

Transfer Rnas ◽

Protein Coding Genes ◽

Oxford Nanopore ◽

Genome Assemblies

Abstract Angomonas deanei is an endosymbiont-bearing trypanosomatid with several highly fragmented genome assemblies and unknown chromosome number. We present an assembly of the A. deanei nuclear genome based on Oxford Nanopore sequence that resolves into 29 complete or close-to-complete chromosomes. The assembly has several previously unknown special features; it has a supernumerary chromosome, a chromosome with a 340-kb inversion, and there is a translocation between two chromosomes. We also present an updated annotation of the chromosomal genome with 10,365 protein-coding genes, 59 transfer RNAs, 26 ribosomal RNAs, and 62 noncoding RNAs.

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