scholarly journals The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules

2019 ◽  
Vol 20 (1) ◽  
pp. 140 ◽  
Author(s):  
Robert Root-Bernstein ◽  
Meredith Root-Bernstein
Keyword(s):  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Relevant Literature ◽  
Messenger Rnas ◽  
Rna Sequences ◽  
Transfer Rnas ◽  
Cell Functions ◽  
Cellular Evolution ◽  
Full Complement ◽  
Reading Frames

We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.

scholarly journals The complete mitochondrial genome of the lipid-producing yeast Rhodotorula toruloides

2020 ◽  
Vol 20 (6) ◽  
Author(s):  
Renhui Zhou ◽  
Zhiwei Zhu ◽  
Sufang Zhang ◽  
Zongbao Kent Zhao
Keyword(s):  
Mitochondrial Genome ◽  
Ribosomal Rna ◽  
Complete Mitochondrial Genome ◽  
Nuclear Genome ◽  
Open Reading Frames ◽  
Circular Dna ◽  
Transfer Rnas ◽  
Fundamental Information ◽  
Significant Genetic Divergence ◽  
Reading Frames

ABSTRACT Mitochondria are semi-autonomous organelles with their own genome and crucial to cellular material and energy metabolism. Here, we report the complete mitochondrial genome of a lipid-producing basidiomycetous yeast Rhodotorula toruloides NP11. The mitochondrial genome of R. toruloides NP11 was assembled into a circular DNA molecule of 125937bp, encoding 15 proteins, 28 transfer RNAs, 2 ribosomal RNA subunits and 10 open reading frames with unknown function. The G + C content (41%) of the mitochondrial genome is substantially lower than that of the nuclear genome (62%) of R. toruloides NP11. Further reanalysis of the transcriptome data confirmed the transcription of four mitochondrial genes. The comparison of the mitochondrial genomes of R. toruloides NP11 and NBRC0880 revealed a significant genetic divergence. These data can complement our understanding of the genetic background of R. toruloides and provide fundamental information for further genetic engineering of this strain.

scholarly journals Inosine in Biology and Disease

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 600
Author(s):  
Sundaramoorthy Srinivasan ◽  
Adrian Gabriel Torres ◽  
Lluís Ribas de Pouplana
Keyword(s):  
Human Health ◽  
Purine Biosynthesis ◽  
Messenger Rnas ◽  
Transfer Rnas ◽  
Functional Roles ◽  
Codon Recognition ◽  
Wobble Position ◽  
Biosynthesis Gene ◽  
The Stability ◽  
Cell Signaling Pathways

The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health.

scholarly journals Base Pairing Constraints Drive Structural Epistasis in Ribosomal RNA Sequences

2010 ◽  
Vol 27 (8) ◽  
pp. 1868-1876 ◽  
Author(s):  
Julien Y. Dutheil ◽  
Fabrice Jossinet ◽  
Eric Westhof
Keyword(s):  
Ribosomal Rna ◽  
Base Pairing ◽  
Rna Sequences ◽  
Ribosomal Rna Sequences

PHYLOGENETIC RELATIONSHIPS IN GREEN PLANTS—A COMMENT ON THE USE OF 5S RIBOSOMAL RNA SEQUENCES BY BREMER ET AL.

Taxon ◽  
1988 ◽  
Vol 37 (1) ◽  
pp. 135-138 ◽  
Author(s):  
Kelly P. Steele ◽  
Kent E. Holsinger ◽  
Robert K. Jansen ◽  
David W. Taylor
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Relationships ◽  
Rna Sequences ◽  
5S Ribosomal Rna ◽  
Green Plants ◽  
Ribosomal Rna Sequences

Phylogenetic Study of Haloanaerobic Bacteria by 16S Ribosomal RNA Sequences Analysis

1995 ◽  
Vol 18 (2) ◽  
pp. 189-195 ◽  
Author(s):  
Tatjana P. Tourova ◽  
Eugenia S. Boulygina ◽  
Tatjana N. Zhilina ◽  
Richard S. Hanson ◽  
George A. Zavarzin
Keyword(s):  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
Phylogenetic Study ◽  
Rna Sequences ◽  
Ribosomal Rna Sequences ◽  
Sequences Analysis

scholarly journals The modifying enzyme Tsr3 establishes the hierarchy of Rio kinase activity in 40S ribosome assembly

2021 ◽  
Author(s):  
Haina Huang ◽  
Melissa Parker ◽  
Katrin Karbstein
Keyword(s):  
Quality Control ◽  
Binding Site ◽  
Ribosomal Rna ◽  
Ribosomal Proteins ◽  
Kinase Activity ◽  
Ribosomal Subunit ◽  
Ribosome Assembly ◽  
Small Ribosomal Subunit ◽  
Yeast Strains

AbstractRibosome assembly is an intricate process, which in eukaryotes is promoted by a large machinery comprised of over 200 assembly factors (AF) that enable the modification, folding, and processing of the ribosomal RNA (rRNA) and the binding of the 79 ribosomal proteins. While some early assembly steps occur via parallel pathways, the process overall is highly hierarchical, which allows for the integration of maturation steps with quality control processes that ensure only fully and correctly assembled subunits are released into the translating pool. How exactly this hierarchy is established, in particular given that there are many instances of RNA substrate “handover” from one highly related AF to another remains to be determined. Here we have investigated the role of Tsr3, which installs a universally conserved modification in the P-site of the small ribosomal subunit late in assembly. Our data demonstrate that Tsr3 separates the activities of the Rio kinases, Rio2 and Rio1, with whom it shares a binding site. By binding after Rio2 dissociation, Tsr3 prevents rebinding of Rio2, promoting forward assembly. After rRNA modification is complete, Tsr3 dissociates, thereby allowing for recruitment of Rio1. Inactive Tsr3 blocks Rio1, which can be rescued using mutants that bypass the requirement for Rio1 activity. Finally, yeast strains lacking Tsr3 randomize the binding of the two kinases, leading to the release of immature ribosomes into the translating pool. These data demonstrate a role for Tsr3 and its modification activity in establishing a hierarchy for the function of the Rio kinases.

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