scholarly journals Causes and consequences of mitochondrial proteome size-variation in animals

2019 ◽  
Author(s):  
Viraj Muthye ◽  
Dennis Lavrov
Keyword(s):  
Functional Significance ◽  
Size Variation ◽  
Mitochondrial Proteins ◽  
Mitochondrial Targeting ◽  
Factors Affecting ◽  
Mitochondrial Proteome ◽  
Mitochondrial Functions ◽  
Size Evolution ◽  
Targeting Signals ◽  
Gain And Loss

AbstractDespite a conserved set of core mitochondrial functions, animal mitochondrial proteomes show a large variation in size. In this study, we analyzed the putative mechanisms behind and functional significance of this variation using experimentally-verified mt-proteomes of four bilaterian animals and two non-animal outgroups. We found that, of several factors affecting mitochondrial proteome size, evolution of novel mitochondrial proteins in mammals and loss of ancestral proteins in protostomes were the main contributors. Interestingly, gain and loss of conventional mitochondrial targeting signals was not a significant factor in the proteome size evolution.

scholarly journals Coordinated Translocation of Presequence-Containing Precursor Proteins Across Two Mitochondrial Membranes: Knowns and Unknowns of How TOM and TIM23 Complexes Cooperate With Each Other

2022 ◽  
Vol 12 ◽  
Author(s):  
Marcel G. Genge ◽  
Dejana Mokranjac
Keyword(s):  
Protein Interactions ◽  
Nuclear Genome ◽  
Hydrophobic Surface ◽  
Mitochondrial Proteins ◽  
Intermembrane Space ◽  
Mitochondrial Targeting ◽  
Mitochondrial Membranes ◽  
Inner Mitochondrial Membrane ◽  
Precursor Proteins ◽  
Targeting Signals

The vast majority of mitochondrial proteins are encoded in the nuclear genome and synthesized on cytosolic ribosomes as precursor proteins with specific mitochondrial targeting signals. Mitochondrial targeting signals are very diverse, however, about 70% of mitochondrial proteins carry cleavable, N-terminal extensions called presequences. These amphipathic helices with one positively charged and one hydrophobic surface target proteins to the mitochondrial matrix with the help of the TOM and TIM23 complexes in the outer and inner membranes, respectively. Translocation of proteins across the two mitochondrial membranes does not take place independently of each other. Rather, in the intermembrane space, where the two complexes meet, components of the TOM and TIM23 complexes form an intricate network of protein–protein interactions that mediates initially transfer of presequences and then of the entire precursor proteins from the outer to the inner mitochondrial membrane. In this Mini Review, we summarize our current understanding of how the TOM and TIM23 complexes cooperate with each other and highlight some of the future challenges and unresolved questions in the field.

scholarly journals A high-density human mitochondrial proximity interaction network

2020 ◽  
Author(s):  
Hana Antonicka ◽  
Zhen-Yuan Lin ◽  
Alexandre Janer ◽  
Woranontee Weraarpachai ◽  
Anne-Claude Gingras ◽  
...  
Keyword(s):  
High Resolution ◽  
Correlation Analysis ◽  
Mitochondrial Protein ◽  
Interaction Network ◽  
Mitochondrial Proteins ◽  
Site Formation ◽  
List Type ◽  
Mitochondrial Proteome ◽  
Mitochondrial Functions ◽  
The Matrix

SummaryWe used BioID, a proximity-dependent biotinylation assay, to interrogate 100 mitochondrial baits from all mitochondrial sub-compartments to create a high resolution human mitochondrial proximity interaction network. We identified 1465 proteins, producing 15626 unique high confidence proximity interactions. Of these, 528 proteins were previously annotated as mitochondrial, nearly half of the mitochondrial proteome defined by Mitocarta 2.0. Bait-bait analysis showed a clear separation of mitochondrial compartments, and correlation analysis among preys across all baits allowed us to identify functional clusters involved in diverse mitochondrial functions, and to assign uncharacterized proteins to specific modules. We demonstrate that this analysis can assign isoforms of the same mitochondrial protein to different mitochondrial sub-compartments, and show that some proteins may have multiple cellular locations. Outer membrane baits showed specific proximity interactions with cytosolic proteins and proteins in other organellar membranes, suggesting specialization of proteins responsible for contact site formation between mitochondria and individual organelles. This proximity network will be a valuable resource for exploring the biology of uncharacterized mitochondrial proteins, the interactions of mitochondria with other cellular organelles, and will provide a framework to interpret alterations in sub-mitochondrial environments associated with mitochondrial disease.Bullet pointsWe created a high resolution human mitochondrial protein proximity map using BioIDBait-bait analysis showed that the map has sub-compartment resolution and correlation analysis of preys identified functional clusters and assigned proteins to specific modulesWe identified isoforms of matrix and IMS proteins with multiple cellular localizations and an endonuclease that localizes to both the matrix and the OMMOMM baits showed specific interactions with non-mitochondrial proteins reflecting organellar contact sites and protein dual localization

scholarly journals Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins

2019 ◽  
Vol 47 (11) ◽  
pp. 5777-5791 ◽  
Author(s):  
Geoffray Monteuuis ◽  
Anna Miścicka ◽  
Michał Świrski ◽  
Lounis Zenad ◽  
Olli Niemitalo ◽  
...  
Keyword(s):  
Translation Initiation ◽  
Single Gene ◽  
Protein Isoforms ◽  
Mitochondrial Proteins ◽  
Mitochondrial Targeting ◽  
Mitochondrial Proteome ◽  
Alternative Protein ◽  
Multiple Protein ◽  
Translation Start ◽  
Targeting Signal

Abstract Utilization of non-AUG alternative translation start sites is most common in bacteria and viruses, but it has been also reported in other organisms. This phenomenon increases proteome complexity by allowing expression of multiple protein isoforms from a single gene. In Saccharomyces cerevisiae, a few described cases concern proteins that are translated from upstream near-cognate start codons as N-terminally extended variants that localize to mitochondria. Using bioinformatics tools, we provide compelling evidence that in yeast the potential for producing alternative protein isoforms by non-AUG translation initiation is much more prevalent than previously anticipated and may apply to as many as a few thousand proteins. Several hundreds of candidates are predicted to gain a mitochondrial targeting signal (MTS), generating an unrecognized pool of mitochondrial proteins. We confirmed mitochondrial localization of a subset of proteins previously not identified as mitochondrial, whose standard forms do not carry an MTS. Our data highlight the potential of non-canonical translation initiation in expanding the capacity of the mitochondrial proteome and possibly also other cellular features.

scholarly journals Different environmental variables predict body and brain size evolution in Homo

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Manuel Will ◽  
Mario Krapp ◽  
Jay T. Stock ◽  
Andrea Manica
Keyword(s):  
Environmental Factors ◽  
Cognitive Abilities ◽  
Net Primary Productivity ◽  
Brain Size ◽  
Environmental Influence ◽  
Size Variation ◽  
Evolutionary Pattern ◽  
Statistical Framework ◽  
Size Evolution ◽  
Major Predictor

AbstractIncreasing body and brain size constitutes a key macro-evolutionary pattern in the hominin lineage, yet the mechanisms behind these changes remain debated. Hypothesized drivers include environmental, demographic, social, dietary, and technological factors. Here we test the influence of environmental factors on the evolution of body and brain size in the genus Homo over the last one million years using a large fossil dataset combined with global paleoclimatic reconstructions and formalized hypotheses tested in a quantitative statistical framework. We identify temperature as a major predictor of body size variation within Homo, in accordance with Bergmann’s rule. In contrast, net primary productivity of environments and long-term variability in precipitation correlate with brain size but explain low amounts of the observed variation. These associations are likely due to an indirect environmental influence on cognitive abilities and extinction probabilities. Most environmental factors that we test do not correspond with body and brain size evolution, pointing towards complex scenarios which underlie the evolution of key biological characteristics in later Homo.

scholarly journals Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain

2021 ◽  
Vol 22 (15) ◽  
pp. 8325
Author(s):  
Paola Zanfardino ◽  
Stefano Doccini ◽  
Filippo M. Santorelli ◽  
Vittoria Petruzzella
Keyword(s):  
Human Brain ◽  
Basic Function ◽  
Mitochondrial Proteome ◽  
Novel Proteins ◽  
Mitochondrial Functions ◽  
Organ Specific ◽  
Oxphos System ◽  
Mitochondrial Defects ◽  
Energy Dependent ◽  
The Brain

Oxidative phosphorylation (OxPhos) is the basic function of mitochondria, although the landscape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding details to the mitochondrial proteome and defining novel metabolic cellular interrelations, especially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition such as ‘mitoexome’, ‘mitoproteome’ and ‘mitointeractome’ have entered the field of ‘mitochondrial medicine’. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism, mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic origin of the OxPhos complexes is one of the reasons for the complexity of the genotype-phenotype correlation when facing human diseases associated with mitochondrial defects. Such complexity clinically manifests with extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the future directions of the multi-omics study of human brain disorders.

scholarly journals Comparative analysis reveals within-population genome size variation in a rotifer is driven by large genomic elements with highly abundant satellite DNA repeat elements

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
C. P. Stelzer ◽  
J. Blommaert ◽  
A. M. Waldvogel ◽  
M. Pichler ◽  
B. Hecox-Lea ◽  
...  
Keyword(s):  
Genome Size ◽  
Satellite Dna ◽  
Gc Content ◽  
Size Variation ◽  
Isolated Populations ◽  
Genome Size Variation ◽  
Variable Regions ◽  
Geographic Population ◽  
Genome Size Evolution ◽  
Size Evolution

Abstract Background Eukaryotic genomes are known to display an enormous variation in size, but the evolutionary causes of this phenomenon are still poorly understood. To obtain mechanistic insights into such variation, previous studies have often employed comparative genomics approaches involving closely related species or geographically isolated populations within a species. Genome comparisons among individuals of the same population remained so far understudied—despite their great potential in providing a microevolutionary perspective to genome size evolution. The rotifer Brachionus asplanchnoidis represents one of the most extreme cases of within-population genome size variation among eukaryotes, displaying almost twofold variation within a geographic population. Results Here, we used a whole-genome sequencing approach to identify the underlying DNA sequence differences by assembling a high-quality reference genome draft for one individual of the population and aligning short reads of 15 individuals from the same geographic population including the reference individual. We identified several large, contiguous copy number variable regions (CNVs), up to megabases in size, which exhibited striking coverage differences among individuals, and whose coverage overall scaled with genome size. CNVs were of remarkably low complexity, being mainly composed of tandemly repeated satellite DNA with only a few interspersed genes or other sequences, and were characterized by a significantly elevated GC-content. CNV patterns in offspring of two parents with divergent genome size and CNV patterns in several individuals from an inbred line differing in genome size demonstrated inheritance and accumulation of CNVs across generations. Conclusions By identifying the exact genomic elements that cause within-population genome size variation, our study paves the way for studying genome size evolution in contemporary populations rather than inferring patterns and processes a posteriori from species comparisons.

scholarly journals The nucleus is a quality control center for non-imported mitochondrial proteins

2020 ◽  
Author(s):  
Viplendra P.S. Shakya ◽  
William A. Barbeau ◽  
Tianyao Xiao ◽  
Christina S. Knutson ◽  
Adam L. Hughes
Keyword(s):  
Quality Control ◽  
Steady State ◽  
Nuclear Protein ◽  
Protein Quality ◽  
Mitochondrial Proteins ◽  
Mitochondrial Targeting ◽  
Mitochondrial Import ◽  
Control Center ◽  
Mitochondrial Impairment ◽  
Precursor Proteins

AbstractMitochondrial import deficiency causes cellular stress due to the accumulation of non-imported mitochondrial precursor proteins. Despite the burden mis-localized mitochondrial precursors place on cells, our understanding of the systems that dispose of these proteins is incomplete. Here, we catalog the location and steady-state abundance of mitochondrial precursor proteins during mitochondrial impairment in S. cerevisiae. We find that a number of non-imported mitochondrial proteins localize to the nucleus, where they are eliminated by proteasome-based nuclear protein quality control. Recognition of mitochondrial precursors by the nuclear quality control machinery requires the presence of an N-terminal mitochondrial targeting sequence (MTS), and impaired breakdown of precursors leads to their buildup in nuclear-associated foci. These results identify the nucleus as a key destination for the disposal of non-imported mitochondrial precursors.

scholarly journals Evolution of body size in anteaters and sloths (Xenarthra, Pilosa): phylogeny, metabolism, diet and substrate preferences

2015 ◽  
Vol 106 (4) ◽  
pp. 289-301 ◽  
Author(s):  
N. Toledo ◽  
M.S. Bargo ◽  
S.F. Vizcaíno ◽  
G. De Iuliis ◽  
F. Pujos
Keyword(s):  
Body Size ◽  
Fossil Record ◽  
Dietary Habits ◽  
Decomposition Analysis ◽  
Size Variation ◽  
The Body ◽  
Phylogenetic Pattern ◽  
Substrate Preferences ◽  
Size Evolution ◽  
Main Factor

ABSTRACTPilosa include anteaters (Vermilingua) and sloths (Folivora). Modern tree sloths are represented by two genera, Bradypus and Choloepus (both around 4–6 kg), whereas the fossil record is very diverse, with approximately 90 genera ranging in age from the Oligocene to the early Holocene. Fossil sloths include four main clades, Megalonychidae, Megatheriidae, Nothrotheriidae, and Mylodontidae, ranging in size from tens of kilograms to several tons. Modern Vermilingua are represented by three genera, Cyclopes, Tamandua and Myrmecophaga, with a size range from 0.25 kg to about 30 kg, and their fossil record is scarce and fragmentary. The dependence of the body size on phylogenetic pattern of Pilosa is analysed here, according to current cladistic hypotheses. Orthonormal decomposition analysis and Abouheif C-mean were performed. Statistics were significantly different from the null-hypothesis, supporting the hypothesis that body size variation correlates with the phylogenetic pattern. Most of the correlation is concentrated within Vermilingua, and less within Mylodontidae, Megatheriidae, Nothrotheriidae and Megalonychidae. Influence of basal metabolic rate (BMR), dietary habits and substrate preference is discussed. In anteaters, specialised insectivory is proposed as the primary constraint on body size evolution. In the case of sloths, mylodontids, megatheriids and nothrotheriids show increasing body size through time; whereas megalonychids retain a wider diversity of sizes. Interplay between BMR and dietary habits appears to be the main factor in shaping evolution of sloth body size.

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.

Plant mitochondrial protein import: mechanisms and control

1999 ◽  
Vol 26 (8) ◽  
pp. 725 ◽  
Author(s):  
James Whelan
Keyword(s):  
Protein Import ◽  
Current Knowledge ◽  
Mitochondrial Protein ◽  
Mitochondrial Proteins ◽  
Mitochondrial Protein Import ◽  
Future Directions ◽  
Receptor Structure ◽  
Processing Peptidase ◽  
Targeting Signals ◽  
And Control

The characterisation of components of the plant mitochondrial import apparatus along with the availability of over one hundred nuclear-encoded mitochondrial proteins allows the study of plant mitochondrial protein import in homologous systems. From these studies it has emerged that although similarities in the import process exist with other organisms, significance differences exist, such as receptor structure, location of processing peptidase and targeting signals. These differences mean that previous studies carried out in heterologous systems must be re-evaluated. Further studies into protein import in plants need to be directed at understanding the mechanism of import and how this process may be controlled. In this review the latter points will be dealt with in terms of summarising our current knowledge and possible future directions.

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