An evaluation of mitochondrial tRNA gene evolution and its relation to the genetic code

1982 ◽  
Vol 60 (4) ◽  
pp. 475-479 ◽  
Author(s):  
R. J. Cedergren
Keyword(s):  
Genetic Code ◽  
Trna Gene ◽  
Gene Evolution ◽  
Sequence Data ◽  
Cellular Systems ◽  
Trna Genes ◽  
Gene Structures ◽  
And Function ◽  
First Time ◽  
Mitochondrial Trna Gene

Extensive sequence data on mitochondrial (mt) tRNAs give for the first time an opportunity to evaluate tRNA gene evolution in this organelle. Deductions from these gene structures relate to the evolution of tRNA genes in other cellular systems and to the origin of the genetic code. Mt tRNAs, in contrast to the prokaryotic nature of chloroplastic tRNA structure, can not at the present time be definitely related to either prokaryotic or eukaryotic tRNAs, probably because of a higher mutation rate in mitochondria.Fungal mt tRNAs having the same anticodon and function are generally similar enough to be considered homologous. Comparisons of all mt tRNA sequences contained in the same mitochondrion indicate that some tRNAs originated by duplication of a prototypic gene which, after divergence, led to tRNAs having different amino acid specificities. The deviant mt genetic code, although admittedly permitting a simpler decoding mechanism, is not useful in determining whether the origin of mitochondria had preceded or was derived from prokaryotes or eukaryotes, since the genetic code is variable even among mitochondria. Variants of the mt genetic code lead to speculation on the nature of die primordial code and its relation to the present "universal" code.

scholarly journals Transfer RNA genes experience exceptionally elevated mutation rates

2018 ◽  
Vol 115 (36) ◽  
pp. 8996-9001 ◽  
Author(s):  
Bryan P. Thornlow ◽  
Josh Hough ◽  
Jacquelyn M. Roger ◽  
Henry Gong ◽  
Todd M. Lowe ◽  
...  
Keyword(s):  
Mutation Rate ◽  
Trna Gene ◽  
Gene Evolution ◽  
Purifying Selection ◽  
Mutation Rates ◽  
Model Organisms ◽  
Biological Synthesis ◽  
Human Populations ◽  
Trna Genes ◽  
Simple Method

Transfer RNAs (tRNAs) are a central component for the biological synthesis of proteins, and they are among the most highly conserved and frequently transcribed genes in all living things. Despite their clear significance for fundamental cellular processes, the forces governing tRNA evolution are poorly understood. We present evidence that transcription-associated mutagenesis and strong purifying selection are key determinants of patterns of sequence variation within and surrounding tRNA genes in humans and diverse model organisms. Remarkably, the mutation rate at broadly expressed cytosolic tRNA loci is likely between 7 and 10 times greater than the nuclear genome average. Furthermore, evolutionary analyses provide strong evidence that tRNA genes, but not their flanking sequences, experience strong purifying selection acting against this elevated mutation rate. We also find a strong correlation between tRNA expression levels and the mutation rates in their immediate flanking regions, suggesting a simple method for estimating individual tRNA gene activity. Collectively, this study illuminates the extreme competing forces in tRNA gene evolution and indicates that mutations at tRNA loci contribute disproportionately to mutational load and have unexplored fitness consequences in human populations.

scholarly journals The MG-RAST API explorer: an on-ramp for RESTful query composition

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Tobias Paczian ◽  
William L. Trimble ◽  
Wolfgang Gerlach ◽  
Travis Harrison ◽  
Andreas Wilke ◽  
...  
Keyword(s):  
Sequence Data ◽  
Web Interface ◽  
Function Data ◽  
Barrier To Entry ◽  
And Function ◽  
First Time ◽  
The Web

Abstract Background The MG-RAST API provides search capabilities and delivers organism and function data as well as raw or annotated sequence data via the web interface and its RESTful API. For casual users, however, RESTful APIs are hard to learn and work with. Results We created the graphical MG-RAST API explorer to help researchers more easily build and export API queries; understand the data abstractions and indices available in MG-RAST; and use the results presented in-browser for exploration, development, and debugging. Conclusions The API explorer lowers the barrier to entry for occasional or first-time MG-RAST API users.

scholarly journals Tracing the evolution of the plastome and mitogenome in the Chloropicophyceae uncovered convergent tRNA gene losses and a variant plastid genetic code

2019 ◽  
Author(s):  
Monique Turmel ◽  
Adriana Lopes dos Santos ◽  
Christian Otis ◽  
Roxanne Sergerie ◽  
Claude Lemieux
Keyword(s):  
Genetic Code ◽  
Trna Gene ◽  
Marine Phytoplankton ◽  
Trna Genes ◽  
Protein Coding ◽  
Organelle Genomes ◽  
Phytoplankton Communities ◽  
Plastid Protein ◽  
Intergenic Regions ◽  
Phylogenetic Affinities

AbstractThe tiny green algae belonging to the Chloropicophyceae play a key role in marine phytoplankton communities; this newly erected class of prasinophytes comprises two genera (Chloropicon and Chloroparvula) containing each several species. We sequenced the plastomes and mitogenomes of eight Chloropicon and five Chloroparvula species to better delineate the phylogenetic affinities of these taxa and to infer the suite of changes that their organelle genomes sustained during evolution. The relationships resolved in organelle-based phylogenomic trees were essentially congruent with previously reported rRNA trees, and similar evolutionary trends but distinct dynamics were identified for the plastome and mitogenome. Although the plastome sustained considerable changes in gene content and order at the time the two genera split, subsequently it remained stable and maintained a very small size. The mitogenome, however, was remodeled more gradually and showed more fluctuation in size, mainly as a result of expansions/contractions of intergenic regions. Remarkably, the plastome and mitogenome lost a common set of three tRNA genes, with the trnI(cau) and trnL(uaa) losses being accompanied with important variations in codon usage. Unexpectedly, despite the disappearance of trnI(cau) from the plastome in the Chloroparvula lineage, AUA codons (the codons recognized by this gene product) were detected in certain plastid genes. By comparing the sequences of plastid protein-coding genes from chloropicophycean and phylogenetically diverse chlorophyte algae with those of the corresponding predicted proteins, we discovered that the AUA codon was reassigned from isoleucine to methionine in Chloroparvula. This noncanonical genetic code has not previously been uncovered in plastids.

scholarly journals Genome Size Reduction and Transposon Activity Impact tRNA Gene Diversity While Ensuring Translational Stability in Birds

2021 ◽  
Vol 13 (4) ◽  
Author(s):  
Jente Ottenburghs ◽  
Keyi Geng ◽  
Alexander Suh ◽  
Claudia Kutter
Keyword(s):  
Trna Gene ◽  
Gene Evolution ◽  
Phenotypic Diversity ◽  
Gene Diversity ◽  
Phylogenetic Analyses ◽  
Genetic Regulation ◽  
Bird Species ◽  
Protein Translation ◽  
Trna Genes ◽  
Avian Genomes

Abstract As a highly diverse vertebrate class, bird species have adapted to various ecological systems. How this phenotypic diversity can be explained genetically is intensively debated and is likely grounded in differences in the genome content. Larger and more complex genomes could allow for greater genetic regulation that results in more phenotypic variety. Surprisingly, avian genomes are much smaller compared to other vertebrates but contain as many protein-coding genes as other vertebrates. This supports the notion that the phenotypic diversity is largely determined by selection on non-coding gene sequences. Transfer RNAs (tRNAs) represent a group of non-coding genes. However, the characteristics of tRNA genes across bird genomes have remained largely unexplored. Here, we exhaustively investigated the evolution and functional consequences of these crucial translational regulators within bird species and across vertebrates. Our dense sampling of 55 avian genomes representing each bird order revealed an average of 169 tRNA genes with at least 31% being actively used. Unlike other vertebrates, avian tRNA genes are reduced in number and complexity but are still in line with vertebrate wobble pairing strategies and mutation-driven codon usage. Our detailed phylogenetic analyses further uncovered that new tRNA genes can emerge through multiplication by transposable elements. Together, this study provides the first comprehensive avian and cross-vertebrate tRNA gene analyses and demonstrates that tRNA gene evolution is flexible albeit constrained within functional boundaries of general mechanisms in protein translation.

scholarly journals Rapid shifts in mitochondrial tRNA import in a plant lineage with extensive mitochondrial tRNA gene loss

2021 ◽  
Author(s):  
Jessica Marie Warren ◽  
Thalia Salinas-Giegé ◽  
Deborah A. Triant ◽  
Douglas R. Taylor ◽  
Laurence Drouard ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Loss ◽  
Trna Gene ◽  
Flowering Plant ◽  
Trna Genes ◽  
Evolutionary Divergence ◽  
Mitochondrial Trna ◽  
Trna Import ◽  
History Of ◽  
Mitochondrial Trna Gene

In most eukaryotes, transfer RNAs (tRNAs) are one of the very few classes of genes remaining in the mitochondrial genome, but some mitochondria have lost these vestiges of their prokaryotic ancestry. Sequencing of mitogenomes from the flowering plant genus Silene previously revealed a large range in tRNA gene content, suggesting rapid and ongoing gene loss/replacement. Here, we use this system to test longstanding hypotheses about how mitochondrial tRNA genes are replaced by importing nuclear-encoded tRNAs. We traced the evolutionary history of these gene loss events by sequencing mitochondrial genomes from key outgroups (Agrostemma githago and Silene [=Lychnis] chalcedonica). We then performed the first global sequencing of purified plant mitochondrial tRNA populations to characterize the expression of mitochondrial-encoded tRNAs and the identity of imported nuclear-encoded tRNAs. We also confirmed the utility of high-throughput sequencing methods for the detection of tRNA import by sequencing mitochondrial tRNA populations in a species (Solanum tuberosum) with known tRNA trafficking patterns. Mitochondrial tRNA sequencing in Silene revealed substantial shifts in the abundance of some nuclear-encoded tRNAs in conjunction with their recent history of mt-tRNA gene loss and surprising cases where tRNAs with anticodons still encoded in the mitochondrial genome also appeared to be imported. These data suggest that nuclear-encoded counterparts are likely replacing mitochondrial tRNAs even in systems with recent mitochondrial tRNA gene loss, and the redundant import of a nuclear-encoded tRNA may provide a mechanism for functional replacement between translation systems separated by billions of years of evolutionary divergence.

scholarly journals Rapid Shifts in Mitochondrial tRNA Import in a Plant Lineage with Extensive Mitochondrial tRNA Gene Loss

2021 ◽  
Author(s):  
Jessica M Warren ◽  
Thalia Salinas-Giegé ◽  
Deborah A Triant ◽  
Douglas R Taylor ◽  
Laurence Drouard ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Loss ◽  
Trna Gene ◽  
Flowering Plant ◽  
Trna Genes ◽  
Evolutionary Divergence ◽  
Mitochondrial Trna ◽  
Trna Import ◽  
History Of ◽  
Mitochondrial Trna Gene

Abstract In most eukaryotes, transfer RNAs (tRNAs) are one of the very few classes of genes remaining in the mitochondrial genome, but some mitochondria have lost these vestiges of their prokaryotic ancestry. Sequencing of mitogenomes from the flowering plant genus Silene previously revealed a large range in tRNA gene content, suggesting rapid and ongoing gene loss/replacement. Here, we use this system to test longstanding hypotheses about how mitochondrial tRNA genes are replaced by importing nuclear-encoded tRNAs. We traced the evolutionary history of these gene loss events by sequencing mitochondrial genomes from key outgroups (Agrostemma githago and Silene [=Lychnis] chalcedonica). We then performed the first global sequencing of purified plant mitochondrial tRNA populations to characterize the expression of mitochondrial-encoded tRNAs and the identity of imported nuclear-encoded tRNAs. We also confirmed the utility of high-throughput sequencing methods for the detection of tRNA import by sequencing mitochondrial tRNA populations in a species (Solanum tuberosum) with known tRNA trafficking patterns. Mitochondrial tRNA sequencing in Silene revealed substantial shifts in the abundance of some nuclear-encoded tRNAs in conjunction with their recent history of mt-tRNA gene loss and surprising cases where tRNAs with anticodons still encoded in the mitochondrial genome also appeared to be imported. These data suggest that nuclear-encoded counterparts are likely replacing mitochondrial tRNAs even in systems with recent mitochondrial tRNA gene loss, and the redundant import of a nuclear-encoded tRNA may provide a mechanism for functional replacement between translation systems separated by billions of years of evolutionary divergence.

PHYLOGENETIC ANALYSES OF FRINGILLIDAE (AVES: PASSERIFORMES) USING MITOCHONDRIAL tRNA GENE SEQUENCES AND SECONDARY STRUCTURE

2006 ◽  
Vol 14 (03) ◽  
pp. 413-424
Author(s):  
BO CUI ◽  
FEI MA ◽  
XIANG WANG ◽  
YI SUN ◽  
LI YU ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Trna Gene ◽  
Structural Characteristics ◽  
Phylogenetic Analyses ◽  
Likelihood Method ◽  
Trna Genes ◽  
Gene Sequences ◽  
Mitochondrial Trna ◽  
Mitochondrial Trna Genes ◽  
Mitochondrial Trna Gene

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

Strategies for Oral Delivery of Metal-Saturated Lactoferrin

2019 ◽  
Vol 20 (11) ◽  
pp. 1046-1051 ◽  
Author(s):  
Przemysław Gajda-Morszewski ◽  
Klaudyna Śpiewak-Wojtyła ◽  
Maria Oszajca ◽  
Małgorzata Brindell
Keyword(s):  
Biological Activity ◽  
Oral Delivery ◽  
Therapeutic Potential ◽  
Structure And Function ◽  
The Difference ◽  
And Function ◽  
First Time

Lactoferrin was isolated and purified for the first time over 50-years ago. Since then, extensive studies on the structure and function of this protein have been performed and the research is still being continued. In this mini-review we focus on presenting recent scientific efforts towards the elucidation of the role and therapeutic potential of lactoferrin saturated with iron(III) or manganese(III) ions. The difference in biological activity of metal-saturated lactoferrin vs. the unmetalated one is emphasized. The strategies for oral delivery of lactoferrin, are also reviewed, with particular attention to the metalated protein.

scholarly journals Frequent tRNA gene translocation towards the boundaries with control regions contributes to the highly dynamic mitochondrial genome organization of the parasitic lice of mammals

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wen-Ge Dong ◽  
Yalun Dong ◽  
Xian-Guo Guo ◽  
Renfu Shao
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Genome Organization ◽  
Trna Gene ◽  
Trna Genes ◽  
Single Chromosome ◽  
Gene Translocation ◽  
Sucking Lice ◽  
Different Types ◽  
Mt Genome

Abstract Background The typical single-chromosome mitochondrial (mt) genome of animals has fragmented into multiple minichromosomes in the lineage Mitodivisia, which contains most of the parasitic lice of eutherian mammals. These parasitic lice differ from each other even among congeneric species in mt karyotype, i.e. the number of minichromosomes, and the gene content and gene order in each minichromosome, which is in stark contrast to the extremely conserved single-chromosome mt genomes across most animal lineages. How fragmented mt genomes evolved is still poorly understood. We use Polyplax sucking lice as a model to investigate how tRNA gene translocation shapes the dynamic mt karyotypes. Results We sequenced the full mt genome of the Asian grey shrew louse, Polyplax reclinata. We then inferred the ancestral mt karyotype for Polyplax lice and compared it with the mt karyotypes of the three Polyplax species sequenced to date. We found that tRNA genes were entirely responsible for mt karyotype variation among these three species of Polyplax lice. Furthermore, tRNA gene translocation observed in Polyplax lice was only between different types of minichromosomes and towards the boundaries with the control region. A similar pattern of tRNA gene translocation can also been seen in other sucking lice with fragmented mt genomes. Conclusions We conclude that inter-minichromosomal tRNA gene translocation orientated towards the boundaries with the control region is a major contributing factor to the highly dynamic mitochondrial genome organization in the parasitic lice of mammals.

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