Dynamic evolution of mitochondrial ribosomal proteins in Holozoa

Scheel, Bettina M.; Hausdorf, Bernhard

doi:10.1016/j.ympev.2014.03.005

Cited by 12 publications

(10 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, we are unaware of any existing quantitative approach that identifies the evolutionary pressures behind the highly variable patterns of the presence and absence of mtDNA genes across the whole of the eukaryotic tree of life. Although important progress has been made at a sequence level, Scheel and Hausdorf (2014) take a phylogenetic approach in studying the sequence evolution of mitochondrial ribosomes across a diverse range of taxa), molecular phylogenies are not necessarily the optimal tools to answer broader questions about the evolution of genome structure (Keeling et al, 2005), particularly given the broad range of taxa (and consequent differences in encodings and sequence properties), and the possible parallel evolutionary pathways involved (Adams et al, 2002;Maier et al, 2013). To make progress with this evolutionary problem, we developed highly generalizable stochastic and statistical machinery for inference of evolutionary dynamics and applied it to a large dataset of over 2,000 sequenced mtDNA genomes across eukaryotic life, reconstructing the evolutionary history of mitochondrial genomes.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention

2016

View full text Add to dashboard Cite

Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species.

show abstract

Section: Introductionmentioning

confidence: 99%

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention

2016

View full text Add to dashboard Cite

show abstract

“…Furthermore, as we have shown here, the new OXPHOS subunits in the Metazoa are in general, although part of the membrane arm, not located specifically close to where the deletions in the mitochondrial encoded subunits occurred. There is thus no compelling evidence for the prosthetic hypothesis at the level of complete proteins, in contrast to the level of individual amino acid changes where evidence for co‐evolution has been documented . At the level of protein function, results are more encouraging.…”

Section: Coevolution Of the Mitochondrial Proteome With The Mitochondmentioning

confidence: 97%

Does mitochondrial DNA evolution in metazoa drive the origin of new mitochondrial proteins?

Esveld

Huynen

2018

IUBMB Life

View full text Add to dashboard Cite

Most eukaryotic cells contain mitochondria with a genome that evolved from their α-proteobacterial ancestor. In the course of eukaryotic evolution, the mitochondrial genome underwent a dramatic reduction in size, caused by the loss and translocation of genes. This required adjustments in mitochondrial gene expression mechanisms and resulted in a complex collaborative system of mitochondrially encoded transfer RNAs and ribosomal RNAs with nuclear encoded proteins to express the mitochondrial encoded oxidative phosphorylation (OXPHOS) proteins. In this review, we examine mitochondrial gene expression from an evolutionary point of view: to what extent can we correlate changes in the mitochondrial genome in the evolutionary lineage leading to human with the origin of new nuclear encoded proteins. We dated the evolutionary origin of mitochondrial proteins that interact with mitochondrial DNA or its RNA and/or protein products in a systematic manner and compared them with documented changes in the mitochondrial DNA. We find anecdotal but accumulating evidence that metazoan RNA-interacting proteins arose in conjunction with changes of the mitochondrial DNA. We find no substantial evidence for such compensatory evolution in new OXPHOS proteins, which appear to be constrained by the ability to form supercomplexes.

show abstract

“…FcC-G represents an advancement of FASconCAT [ 44 ], an already commonly used tool in phylogenetic studies (e.g. [ 45 - 53 ]).…”

Section: Introductionmentioning

confidence: 99%

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

2014

View full text Add to dashboard Cite

BackgroundPhylogenetic and population genetic studies often deal with multiple sequence alignments that require manipulation or processing steps such as sequence concatenation, sequence renaming, sequence translation or consensus sequence generation. In recent years phylogenetic data sets have expanded from single genes to genome wide markers comprising hundreds to thousands of loci. Processing of these large phylogenomic data sets is impracticable without using automated process pipelines. Currently no stand-alone or pipeline compatible program exists that offers a broad range of manipulation and processing steps for multiple sequence alignments in a single process run.ResultsHere we present FASconCAT-G, a system independent editor, which offers various processing options for multiple sequence alignments. The software provides a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation between nucleotide and amino acid states, consensus generation of specific sequence blocks, sequence concatenation, model selection of amino acid replacement with ProtTest, two types of RY coding as well as site exclusions and extraction of parsimony informative sites. Convieniently, most options can be invoked in combination and performed during a single process run. Additionally, FASconCAT-G prints useful information regarding alignment characteristics and editing processes such as base compositions of single in- and outfiles, sequence areas in a concatenated supermatrix, as well as paired stem and loop regions in secondary structure sequence strings.ConclusionsFASconCAT-G is a command-line driven Perl program that delivers computationally fast and user-friendly processing of multiple sequence alignments for phylogenetic and population genetic applications and is well suited for incorporation into analysis pipelines.Electronic supplementary materialThe online version of this article (doi:10.1186/s12983-014-0081-x) contains supplementary material, which is available to authorized users.

show abstract

Dynamic evolution of mitochondrial ribosomal proteins in Holozoa

Cited by 12 publications

References 54 publications

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention

Does mitochondrial DNA evolution in metazoa drive the origin of new mitochondrial proteins?

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

Contact Info

Product

Resources

About