scholarly journals Mosaic nature of the mitochondrial proteome: Implications for the origin and evolution of mitochondria

2015 ◽  
Vol 112 (33) ◽  
pp. 10133-10138 ◽  
Author(s):  
Michael W. Gray
Keyword(s):  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Large Fraction ◽  
Mitochondrial Proteins ◽  
Surprising Result ◽  
Origin And Evolution ◽  
Mitochondrial Proteome ◽  
Mitochondrial Origin ◽  
Conserved Core ◽  
Evolution Of Mitochondria

Comparative studies of the mitochondrial proteome have identified a conserved core of proteins descended from the α-proteobacterial endosymbiont that gave rise to the mitochondrion and was the source of the mitochondrial genome in contemporary eukaryotes. A surprising result of phylogenetic analyses is the relatively small proportion (10–20%) of the mitochondrial proteome displaying a clear α-proteobacterial ancestry. A large fraction of mitochondrial proteins typically has detectable homologs only in other eukaryotes and is presumed to represent proteins that emerged specifically within eukaryotes. A further significant fraction of the mitochondrial proteome consists of proteins with homologs in prokaryotes, but without a robust phylogenetic signal affiliating them with specific prokaryotic lineages. The presumptive evolutionary source of these proteins is quite different in contending models of mitochondrial origin.

scholarly journals On the origin of mitochondria: a genomics perspective

2003 ◽  
Vol 358 (1429) ◽  
pp. 165-179 ◽  
Author(s):  
G. E. Andersson ◽  
Olof Karlberg ◽  
Björn Canbäck ◽  
Charles G. Kurland
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Nuclear Genome ◽  
Strong Relationship ◽  
Eukaryotic Cell ◽  
Mitochondrial Proteins ◽  
Origin And Evolution ◽  
Bacterial Genes

The availability of complete genome sequence data from both bacteria and eukaryotes provides information about the contribution of bacterial genes to the origin and evolution of mitochondria. Phylogenetic analyses based on genes located in the mitochondrial genome indicate that these genes originated from within the α–proteobacteria. A number of ancestral bacterial genes have also been transferred from the mitochondrial to the nuclear genome, as evidenced by the presence of orthologous genes in the mitochondrial genome in some species and in the nuclear genome of other species. However, a multitude of mitochondrial proteins encoded in the nucleus display no homology to bacterial proteins, indicating that these originated within the eukaryotic cell subsequent to the acquisition of the endosymbiont. An analysis of the expression patterns of yeast nuclear genes coding for mitochondrial proteins has shown that genes predicted to be of eukaryotic origin are mainly translated on polysomes that are free in the cytosol whereas those of putative bacterial origin are translated on polysomes attached to the mitochondrion. The strong relationship with α–proteobacterial genes observed for some mitochondrial genes, combined with the lack of such a relationship for others, indicates that the modern mitochondrial proteome is the product of both reductive and expansive processes.

scholarly journals Mosaic Genomes of the Six Major Primate Lentivirus Lineages Revealed by Phylogenetic Analyses

2003 ◽  
Vol 77 (13) ◽  
pp. 7202-7213 ◽  
Author(s):  
Marco Salemi ◽  
Tulio De Oliveira ◽  
Valerie Courgnaud ◽  
Vincent Moulton ◽  
Barbara Holland ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Statistical Tests ◽  
Phylogenetic Analyses ◽  
Decomposition Analysis ◽  
Phylogeny Reconstruction ◽  
Origin And Evolution ◽  
Immunodeficiency Virus ◽  
Primate Lentiviruses ◽  
Recombinant Fragments ◽  
Clustering Patterns

ABSTRACT To clarify the origin and evolution of the primate lentiviruses (PLVs), which include human immunodeficiency virus types 1 and 2 as well as their simian relatives, simian immunodeficiency viruses (SIVs), isolated from several host species, we investigated the phylogenetic relationships among the six supposedly nonrecombinant PLV lineages for which the full genome sequences are available. Employing bootscanning as an exploratory tool, we located several regions in the PLV genome that seem to have uncertain or conflicting phylogenetic histories. Phylogeny reconstruction based on distance and maximum-likelihood algorithms followed by a number of statistical tests confirms the existence of at least five putative recombinant fragments in the PLV genome with different clustering patterns. Split decomposition analysis also shows that phylogenetic relationships among PLVs may be better represented by network-based graphs, such as the ones produced by SplitsTree. Our findings not only imply that the six so-called pure PLV lineages have in fact mosaic genomes but also make more unlikely the hypothesis of cospeciation of SIVs and their simian hosts.

scholarly journals Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water

2021 ◽  
Vol 17 (7) ◽  
pp. e1009730
Author(s):  
Jialu Zheng ◽  
Jianhua Wang ◽  
Zhen Gong ◽  
Guan-Zhu Han
Keyword(s):  
Phylogenetic Analyses ◽  
Endogenous Retroviruses ◽  
Integration Time ◽  
Aquatic Environments ◽  
Ongoing Activity ◽  
Aquatic Life ◽  
Origin And Evolution ◽  
Molecular Fossils ◽  
Retroviral Infections

The ancestor of cetaceans underwent a macroevolutionary transition from land to water early in the Eocene Period >50 million years ago. However, little is known about how diverse retroviruses evolved during this shift from terrestrial to aquatic environments. Did retroviruses transition into water accompanying their hosts? Did retroviruses infect cetaceans through cross-species transmission after cetaceans invaded the aquatic environments? Endogenous retroviruses (ERVs) provide important molecular fossils for tracing the evolution of retroviruses during this macroevolutionary transition. Here, we use a phylogenomic approach to study the origin and evolution of ERVs in cetaceans. We identify a total of 8,724 ERVs within the genomes of 25 cetaceans, and phylogenetic analyses suggest these ERVs cluster into 315 independent lineages, each of which represents one or more independent endogenization events. We find that cetacean ERVs originated through two possible routes. 298 ERV lineages may derive from retrovirus endogenization that occurred before or during the transition from land to water of cetaceans, and most of these cetacean ERVs were reaching evolutionary dead-ends. 17 ERV lineages are likely to arise from independent retrovirus endogenization events that occurred after the split of mysticetes and odontocetes, indicating that diverse retroviruses infected cetaceans through cross-species transmission from non-cetacean mammals after the transition to aquatic life of cetaceans. Both integration time and synteny analyses support the recent or ongoing activity of multiple retroviral lineages in cetaceans, some of which proliferated into hundreds of copies within the host genomes. Although ERVs only recorded a proportion of past retroviral infections, our findings illuminate the complex evolution of retroviruses during one of the most marked macroevolutionary transitions in vertebrate history.

scholarly journals The Dual Origin of the Yeast Mitochondrial Proteome

Yeast ◽  
2000 ◽  
Vol 1 (3) ◽  
pp. 170-187 ◽  
Author(s):  
Olof Karlberg ◽  
Björn Canbäck ◽  
Charles G. Kurland ◽  
Siv G. E. Andersson
Keyword(s):  
Nuclear Genome ◽  
Mitochondrial Proteins ◽  
Mitochondrial Proteome ◽  
Phylogenetic Reconstructions ◽  
Eukaryotic Genes ◽  
Genes Encoding ◽  
Parallel Mode ◽  
Bacterial Genes ◽  
Dual Origin ◽  
Regulatory Functions

We propose a scheme for the origin of mitochondria based on phylogenetic reconstructions with more than 400 yeast nuclear genes that encode mitochondrial proteins. Half of the yeast mitochondrial proteins have no discernable bacterial homologues, while one-tenth are unequivocally of α-proteobacterial origin. These data suggest that the majority of genes encoding yeast mitochondrial proteins are descendants of two different genomic lineages that have evolved in different modes. First, the ancestral free-living α-proteobacterium evolved into an endosymbiont of an anaerobic host. Most of the ancestral bacterial genes were lost, but a small fraction of genes supporting bioenergetic and translational processes were retained and eventually transferred to what became the host nuclear genome. In a second, parallel mode, a larger number of novel mitochondrial genes were recruited from the nuclear genome to complement the remaining genes from the bacterial ancestor. These eukaryotic genes, which are primarily involved in transport and regulatory functions, transformed the endosymbiont into an ATP-exporting organelle.

Strangers in strange lands: mitochondrial proteins found at extra-mitochondrial locations

2019 ◽  
Vol 476 (1) ◽  
pp. 25-37 ◽  
Author(s):  
David P. Scanlon ◽  
Michael W. Salter
Keyword(s):  
Mitochondrial Genome ◽  
Mitochondrial Function ◽  
Mitochondrial Proteins ◽  
Dual Citizenship ◽  
Mitochondrial Proteome ◽  
Encoded Proteins

Abstract The mitochondrial proteome is estimated to contain ∼1100 proteins, the vast majority of which are nuclear-encoded, with only 13 proteins encoded by the mitochondrial genome. The import of these nuclear-encoded proteins into mitochondria was widely believed to be unidirectional, but recent discoveries have revealed that many these ‘mitochondrial’ proteins are exported, and have extra-mitochondrial activities divergent from their mitochondrial function. Surprisingly, three of the exported proteins discovered thus far are mitochondrially encoded and have significantly different extra-mitochondrial roles than those performed within the mitochondrion. In this review, we will detail the wide variety of proteins once thought to only reside within mitochondria, but now known to ‘emigrate’ from mitochondria in order to attain ‘dual citizenship’, present both within mitochondria and elsewhere.

scholarly journals Intragenic Conflict in Phylogenomic Data Sets

2020 ◽  
Vol 37 (11) ◽  
pp. 3380-3388
Author(s):  
Stephen A Smith ◽  
Nathanael Walker-Hale ◽  
Joseph F Walker
Keyword(s):  
Data Analysis ◽  
Empirical Data ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Simulated Data ◽  
Data Sets ◽  
Alignment Error ◽  
Biological Processes ◽  
Simple Method

Abstract Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.

scholarly journals Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase

2019 ◽  
Vol 400 (3) ◽  
pp. 367-381 ◽  
Author(s):  
Kristina Straub ◽  
Mona Linde ◽  
Cosimo Kropp ◽  
Samuel Blanquart ◽  
Patrick Babinger ◽  
...  
Keyword(s):  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Specific Property ◽  
Ancestral Sequence ◽  
Rational Approach ◽  
Ancestral Sequence Reconstruction ◽  
Representative Sequence ◽  
Sequence Selection ◽  
Sequence Reconstruction ◽  
Phosphate Synthase

Abstract For evolutionary studies, but also for protein engineering, ancestral sequence reconstruction (ASR) has become an indispensable tool. The first step of every ASR protocol is the preparation of a representative sequence set containing at most a few hundred recent homologs whose composition determines decisively the outcome of a reconstruction. A common approach for sequence selection consists of several rounds of manual recompilation that is driven by embedded phylogenetic analyses of the varied sequence sets. For ASR of a geranylgeranylglyceryl phosphate synthase, we additionally utilized FitSS4ASR, which replaces this time-consuming protocol with an efficient and more rational approach. FitSS4ASR applies orthogonal filters to a set of homologs to eliminate outlier sequences and those bearing only a weak phylogenetic signal. To demonstrate the usefulness of FitSS4ASR, we determined experimentally the oligomerization state of eight predecessors, which is a delicate and taxon-specific property. Corresponding ancestors deduced in a manual approach and by means of FitSS4ASR had the same dimeric or hexameric conformation; this concordance testifies to the efficiency of FitSS4ASR for sequence selection. FitSS4ASR-based results of two other ASR experiments were added to the Supporting Information. Program and documentation are available at https://gitlab.bioinf.ur.de/hek61586/FitSS4ASR.

scholarly journals Expanding magnetic organelle biogenesis in the domain Bacteria

Microbiome ◽  
2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Wei Lin ◽  
Wensi Zhang ◽  
Greig A. Paterson ◽  
Qiyun Zhu ◽  
Xiang Zhao ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Biological Significance ◽  
Gene Clusters ◽  
Magnetic Sensors ◽  
Evolutionary Origin ◽  
Phylogenomic Analysis ◽  
Organelle Biogenesis ◽  
Taxonomic Distribution ◽  
Origin And Evolution ◽  
Bacterial Phyla

Abstract Background The discovery of membrane-enclosed, metabolically functional organelles in Bacteria has transformed our understanding of the subcellular complexity of prokaryotic cells. Biomineralization of magnetic nanoparticles within magnetosomes by magnetotactic bacteria (MTB) is a fascinating example of prokaryotic organelles. Magnetosomes, as nano-sized magnetic sensors in MTB, facilitate cell navigation along the local geomagnetic field, a behaviour referred to as magnetotaxis or microbial magnetoreception. Recent discovery of novel MTB outside the traditionally recognized taxonomic lineages suggests that MTB diversity across the domain Bacteria are considerably underestimated, which limits understanding of the taxonomic distribution and evolutionary origin of magnetosome organelle biogenesis. Results Here, we perform the most comprehensive metagenomic analysis available of MTB communities and reconstruct metagenome-assembled MTB genomes from diverse ecosystems. Discovery of MTB in acidic peatland soils suggests widespread MTB occurrence in waterlogged soils in addition to subaqueous sediments and water bodies. A total of 168 MTB draft genomes have been reconstructed, which represent nearly a 3-fold increase over the number currently available and more than double the known MTB species at the genome level. Phylogenomic analysis reveals that these genomes belong to 13 Bacterial phyla, six of which were previously not known to include MTB. These findings indicate a much wider taxonomic distribution of magnetosome organelle biogenesis across the domain Bacteria than previously thought. Comparative genome analysis reveals a vast diversity of magnetosome gene clusters involved in magnetosomal biogenesis in terms of gene content and synteny residing in distinct taxonomic lineages. Phylogenetic analyses of core magnetosome proteins in this largest available and taxonomically diverse dataset support an unexpectedly early evolutionary origin of magnetosome biomineralization, likely ancestral to the origin of the domain Bacteria. Conclusions These findings expand the taxonomic and phylogenetic diversity of MTB across the domain Bacteria and shed new light on the origin and evolution of microbial magnetoreception. Potential biogenesis of the magnetosome organelle in the close descendants of the last bacterial common ancestor has important implications for our understanding of the evolutionary history of bacterial cellular complexity and emphasizes the biological significance of the magnetosome organelle.

scholarly journals Identifying the North American Plum Species Phylogenetic Signal Using Nuclear, Mitochondrial, and Chloroplast DNA Markers

2016 ◽  
Vol 141 (6) ◽  
pp. 623-644 ◽  
Author(s):  
Dario J. Chavez ◽  
Thomas G. Beckman ◽  
José X. Chaparro
Keyword(s):  
Chloroplast Dna ◽  
Prunus Persica ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Nuclear Gene ◽  
Its Region ◽  
Single Copy ◽  
Species Level ◽  
Species Relationships ◽  
The North

Prunus phylogeny has been extensively studied using chloroplast DNA (cpDNA) sequences. Chloroplast DNA has a slow rate of evolution, which is beneficial to determine species relationships at a deeper level. The chloroplast-based phylogenies have a limitation due to the transfer of this organelle by interspecific hybridization. This creates difficulties when studying species relationships. Interspecific hybrids in Prunus occur naturally and have been reported, which creates a problem when using cpDNA-based phylogenies to determine species relationships. The main goal of this project was to identify nuclear gene regions that could provide an improved phylogenetic signal at the species level in Prunus. A total of 11 species in Prunus and within section Prunocerasus were used. Two peach (Prunus persica) haploids were used to test the reliability of the molecular markers developed in this project to amplify single-copy genes. A total of 33 major genes associated with vernalization response, 16 with tree architecture, and 3 with isozymes, were tested. Similarly, 41 simple sequence repeat (SSR) markers, seven cpDNA regions, and the internal transcribed spacer (ITS) region, were used. Multiple gene regions were identified and provided the greatest number of characters, greatest variability, and improved phylogenetic signal at the species level in Prunus section Prunocerasus. Out of those, trnH-psbA, PGI, MAX4, AXR1, LFY, PHYE, and VRN1 are recommended for a phylogenetic analysis with a larger number of taxa. The use of potentially informative characters (PICS) as a measure of how informative a region will be for phylogenetic analyses has been previously reported beneficial in cpDNA regions and it clearly was important in this research. This will allow selecting the region(s), which can be used in phylogenetic studies with higher number of taxa.

scholarly journals Fast-evolving alignment sites are highly informative for reconstructions of deep Tree of Life phylogenies

2019 ◽  
Author(s):  
L. Thibério Rangel ◽  
Gregory P. Fournier
Keyword(s):  
Signal To Noise Ratio ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Phylogenetic Reconstruction ◽  
Tree Of Life ◽  
Signal To Noise ◽  
Fast Analysis ◽  
Substantial Impact ◽  
Substitution Saturation ◽  
Noise Ratio

AbstractThe trimming of fast-evolving sites, often known as “slow-fast” analysis, is broadly used in microbial phylogenetic reconstruction under assumption that fast-evolving sites do not retain accurate phylogenetic signal due to substitution saturation. Therefore, removing sites that have experienced multiple substitutions would improve the signal-to-noise ratio in phylogenetic analyses, with the remaining slower-evolving sites preserving a more reliable record of evolutionary relationships. Here we show that, contrary to this assumption, even the fastest evolving sites, present in conserved proteins often used in Tree of Life studies, contain reliable and valuable phylogenetic information, and that the trimming of such sites can negatively impact the accuracy of phylogenetic reconstruction. Simulated alignments modeled after ribosomal protein datasets used in Tree of Life studies consistently show that slow-evolving sites are less likely to recover true bipartitions than even the fastest-evolving sites. Furthermore, site specific substitution-rates are positively correlated with the frequency of accurately recovered short-branched bipartitions, as slowly evolving sites are less likely to have experienced substitutions along these intervals. Using published Tree of Life sequence alignment datasets, we additionally show that both slow-and fast-evolving sites contain similarly inconsistent phylogenetic signals, and that, for fast-evolving sites, this inconsistency can be attributed to poor alignment quality. Furthermore, trimming fast sites, slow sites, or both is shown to have substantial impact on phylogenetic reconstruction across multiple evolutionary models. This is perhaps most evident in the resulting placements of Eukarya and Asgardarchaeota groups, which are especially sensitive to the implementation of different trimming schemes.Significance StatementIt is common practice among comprehensive microbial phylogenetic studies to trim fast-evolving sites from the source alignment in the expectation to increase the signal to noise ratio. Here we show that despite fast-evolving sites being more sensitive to parameter misspecifications than mid-rate evolving sites, such sensitivity is comparable, if not smaller, than what we observe among slow-evolving sites. Through the use of both empirical and simulated datasets we also show that, besides the lack of evidences regarding the noisy nature of fast-evolving sites, such sites are of core importance for the reliable the reconstruction of short-branched bipartitions. Such points are exemplified by the variations in the Eukarya+Archaea Tree of Life when subjective alignment trimming strategies are employed.

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