A prioritized and validated resource of mitochondrial proteins in Plasmodium identifies leads to unique biology

AbstractPlasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by anti-malarial drugs. Most proteins are imported into this organelle and our picture of the Plasmodium mitochondrial proteome remains incomplete. Many data sources contain information about mitochondrial localization, including proteome and gene expression profiles, orthology to mitochondrial proteins from other species, co-evolutionary relationships, and amino acid sequences, each with different coverage and reliability. To obtain a comprehensive, prioritized list of Plasmodium falciparum mitochondrial proteins, we rigorously analyzed and integrated eight datasets using Bayesian statistics into a predictive score per protein for mitochondrial localization. At a corrected false discovery rate of 25%, we identified 295 proteins with a sensitivity of 65% and a specificity of 98%. They include proteins that have not been identified as mitochondrial in other eukaryotes but have characterized homologs in bacteria that are involved in metabolism or translation. Mitochondrial localization of seven Plasmodium berghei orthologs was confirmed by epitope labeling and co-localization with a mitochondrial marker protein. One of these belongs to a newly identified apicomplexan mitochondrial protein family that in P. falciparum has four members. With the experimentally validated mitochondrial proteins and the complete ranked P. falciparum proteome, which we have named PlasmoMitoCarta, we present a resource to study unique proteins of Plasmodium mitochondria.

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The human SIRT3 protein deacetylase is exclusively mitochondrial

Biochemical Journal ◽

10.1042/bj20071624 ◽

2008 ◽

Vol 411 (2) ◽

pp. 279-285 ◽

Cited By ~ 87

Author(s):

Helen M. Cooper ◽

Johannes N. Spelbrink

Keyword(s):

Cellular Stress ◽

Mitochondrial Protein ◽

Subcellular Fractionation ◽

Precursor Protein ◽

Mitochondrial Proteins ◽

Lysine Acetylation ◽

Crucial Importance ◽

Mitochondrial Localization ◽

Genome Databases ◽

Protein Deacetylase

It has recently been suggested that perhaps as many as 20% of all mitochondrial proteins are regulated through lysine acetylation while SIRT3 has been implicated as an important mitochondrial protein deacetylase. It is therefore of crucial importance that the mitochondrial localization of potential protein deacetylases is unambiguously established. Although mouse SIRT3 was recently shown to be mitochondrial, HsSIRT3 (human SIRT3) was reported to be both nuclear and mitochondrial and to relocate from the nucleus to the mitochondrion upon cellular stress. In the present study we show, using various HsSIRT3 expression constructs and a combination of immunofluorescence and careful subcellular fractionation, that in contrast with earlier reports HsSIRT3 is exclusively mitochondrial. We discuss possible experimental explanations for these discrepancies. In addition we suggest, on the basis of the analysis of public genome databases, that the full-length mouse SIRT3 protein is a 37 kDa mitochondrial precursor protein contrary to the previously suggested 29 kDa protein.

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New Short Term Prediction Method for Chemical Carcinogenicity by Hepatic Transcript Profiling following 28-Day Toxicity Tests in Rats

Cancer Informatics ◽

10.4137/cin.s7789 ◽

2011 ◽

Vol 10 ◽

pp. CIN.S7789 ◽

Cited By ~ 4

Author(s):

Hiroshi Matsumoto ◽

Yoshikuni Yakabe ◽

Fumiyo Saito ◽

Koichi Saito ◽

Kayo Sumida ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Prediction Method ◽

Predictive Score ◽

Toxicity Tests ◽

Support Vector ◽

Total System ◽

Prediction Formula ◽

Group 1

We have previously shown the hepatic gene expression profiles of carcinogens in 28-day toxicity tests were clustered into three major groups (Group-1 to 3). Here, we developed a new prediction method for Group-1 carcinogens which consist mainly of genotoxic rat hepatocarcinogens. The prediction formula was generated by a support vector machine using 5 selected genes as the predictive genes and predictive score was introduced to judge carcinogenicity. It correctly predicted the carcinogenicity of all 17 Group-1 chemicals and 22 of 24 non-carcinogens regardless of genotoxicity. In the dose-response study, the prediction score was altered from negative to positive as the dose increased, indicating that the characteristic gene expression profile emerged over a range of carcinogen-specific doses. We conclude that the prediction formula can quantitatively predict the carcinogenicity of Group-1 carcinogens. The same method may be applied to other groups of carcinogens to build a total system for prediction of carcinogenicity.

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Temporal Profiling of the Cortical Synaptic Mitochondrial Proteome Identifies Ageing Associated Regulators of Stability

Cells ◽

10.3390/cells10123403 ◽

2021 ◽

Vol 10 (12) ◽

pp. 3403

Author(s):

Laura C. Graham ◽

Rachel A. Kline ◽

Douglas J. Lamont ◽

Thomas H. Gillingwater ◽

Neil A. Mabbott ◽

...

Keyword(s):

Protein Expression ◽

Expression Profiles ◽

Mitochondrial Protein ◽

Wild Type Mouse ◽

Proteomic Profiling ◽

Temporal Regulation ◽

Mitochondrial Proteome ◽

Age Dependent ◽

Protein Expression Profiles

Synapses are particularly susceptible to the effects of advancing age, and mitochondria have long been implicated as organelles contributing to this compartmental vulnerability. Despite this, the mitochondrial molecular cascades promoting age-dependent synaptic demise remain to be elucidated. Here, we sought to examine how the synaptic mitochondrial proteome (including strongly mitochondrial associated proteins) was dynamically and temporally regulated throughout ageing to determine whether alterations in the expression of individual candidates can influence synaptic stability/morphology. Proteomic profiling of wild-type mouse cortical synaptic and non-synaptic mitochondria across the lifespan revealed significant age-dependent heterogeneity between mitochondrial subpopulations, with aged organelles exhibiting unique protein expression profiles. Recapitulation of aged synaptic mitochondrial protein expression at the Drosophila neuromuscular junction has the propensity to perturb the synaptic architecture, demonstrating that temporal regulation of the mitochondrial proteome may directly modulate the stability of the synapse in vivo.

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Mitochondrial diseases caused by dysfunctional mitochondrial protein import

Biochemical Society Transactions ◽

10.1042/bst20180239 ◽

2018 ◽

Vol 46 (5) ◽

pp. 1225-1238 ◽

Cited By ~ 8

Author(s):

Thomas Daniel Jackson ◽

Catherine Sarah Palmer ◽

Diana Stojanovski

Keyword(s):

Mitochondrial Disease ◽

Genetic Disease ◽

Molecular Basis ◽

Protein Import ◽

Mitochondrial Protein ◽

Mitochondrial Diseases ◽

Mitochondrial Proteins ◽

Eukaryotic Cells ◽

Mitochondrial Protein Import ◽

Mitochondrial Proteome

Mitochondria are essential organelles which perform complex and varied functions within eukaryotic cells. Maintenance of mitochondrial health and functionality is thus a key cellular priority and relies on the organelle's extensive proteome. The mitochondrial proteome is largely encoded by nuclear genes, and mitochondrial proteins must be sorted to the correct mitochondrial sub-compartment post-translationally. This essential process is carried out by multimeric and dynamic translocation and sorting machineries, which can be found in all four mitochondrial compartments. Interestingly, advances in the diagnosis of genetic disease have revealed that mutations in various components of the human import machinery can cause mitochondrial disease, a heterogenous and often severe collection of disorders associated with energy generation defects and a multisystem presentation often affecting the cardiovascular and nervous systems. Here, we review our current understanding of mitochondrial protein import systems in human cells and the molecular basis of mitochondrial diseases caused by defects in these pathways.

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Abstract MP252: Genetic Architecture Of Heart Mitochondrial Proteome Influencing Cardiac Hypertrophy

Circulation Research ◽

10.1161/res.129.suppl_1.mp252 ◽

2021 ◽

Vol 129 (Suppl_1) ◽

Author(s):

Karthickeyan Chella Krishnan ◽

Elie-Julien El Hachem ◽

Christine Light ◽

Varun Shravah ◽

Diana Anum ◽

...

Keyword(s):

High Resolution ◽

Ribosomal Proteins ◽

Heart Function ◽

Mitochondrial Protein ◽

Strong Support ◽

Mitochondrial Proteins ◽

Heart Hypertrophy ◽

Genetic Loci ◽

Mouse Population ◽

Mitochondrial Proteome

Our lab studies how natural genetic variations affect common diseases using a mouse population called hybrid mouse diversity panel (HMDP). In this study, we have explored the genetic regulation of mitochondrial pathways and their contribution to heart function using an integrative proteomics approach. We first performed a whole heart proteomic analysis in the HMDP (72 strains, n=2-3 mice) and surveyed mitochondrial localization using MitoCarta2.0. We retrieved 840 of these proteins (quantified in ≥50 strains) and performed high-resolution association mapping on their respective abundance levels to the HMDP genotypes. Our analyses identified three genetic loci, located on chromosome (chr) 7, chr13 and chr17, that control distinct classes of mitochondrial proteins as well as heart hypertrophy. Follow-up high resolution regional mapping identified NDUFS4, LRPPRC and COQ7 as the candidate genes for chr13, chr17 and chr7 loci, respectively. All three are associated with heart mass in two independent heart stress models, namely, isoproterenol (ISO)-induced heart failure and diet-induced obesity (DIO) models. Next, to identify the aspects of mitochondrial metabolism regulated by these loci, we constructed co-expression protein networks using weighted gene co-expression network analysis (WGCNA) and identified five modules. Eigengenes, representing the first principal component of two of these modules (Brown and Green), mapped to the same regions as the chr13 and chr17 loci, respectively. DAVID enrichment analyses revealed that the Brown module (72 proteins, 96% overlap with chr13) was highly enriched for complex-I proteins (35 proteins, P = 8.8E-74) and the Green module (44 proteins, 73% overlap with chr17) for mitochondrial ribosomal proteins (25 proteins, P = 1.3E-53). The proteins in the chr7 locus were found primarily in the Turquoise module (393 proteins, 81% overlap) but this module was not enriched for any single mitochondrial protein complex. In summary, we now report the identification of three genetic loci that control distinct classes of mitochondrial proteins as well as heart hypertrophy. Our results provide strong support for a role of the mitochondrial proteome in heart pathophysiology.

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Generation of a mitochondrial protein compendium in Dictyostelium discoideum

10.1101/2021.11.08.467494 ◽

2021 ◽

Author(s):

Hong Xu

Keyword(s):

Dictyostelium Discoideum ◽

Mitochondrial Protein ◽

Metabolic Reprogramming ◽

Mitochondrial Proteins ◽

Mitochondrial Proteome ◽

Cellular Processes ◽

Proteomic Approach ◽

The Social ◽

Cellular Pathways ◽

Alpha Proteobacteria

The social amoeba Dictyostelium discoideum is a well-established model to study numerous cellular processes including cell motility, chemotaxis, and differentiation. As energy metabolism is involved in these processes, mitochondrial genetics and bioenergetics are of interest, though many features of Dictyostelium mitochondria differ from metazoans. A comprehensive inventory of mitochondrial proteins is critical to understanding mitochondrial processes and their involvement in various cellular pathways. Here, we utilized high-throughput multiplexed protein quantitation and homology analyses to generate a high-confidence mitochondrial protein compendium. Our proteomic approach, which utilizes quantitative mass spectrometry in combination with mathematical modeling, was validated through mitochondrial targeting sequence prediction and live-cell imaging. Our final compendium consists of 1082 proteins. Within our D. discoideum mitochondrial proteome, we identify many proteins that are not present in humans, yeasts, or the ancestral alpha-proteobacteria, which can serve as a foundation for future investigations into the unique mitochondria of Dictyostelium. Additionally, we leverage our compendium to highlight the complexity of metabolic reprogramming during starvation-induced development. Our compendium lays a foundation to investigate mitochondrial processes that are unique in protists, as well as for future studies to understand the functions of conserved mitochondrial proteins in health and diseases using D. discoideum as the model.

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Generation of a Mitochondrial Protein Compendium in Dictyostelium Discoideum

10.21203/rs.3.rs-1054199/v1 ◽

2021 ◽

Author(s):

Anna V Freitas ◽

Jake T Herb ◽

Miao Pan ◽

Yong Cheng ◽

Marjan Gucek ◽

...

Keyword(s):

Dictyostelium Discoideum ◽

Mitochondrial Protein ◽

Metabolic Reprogramming ◽

Mitochondrial Proteins ◽

Mitochondrial Proteome ◽

Cellular Processes ◽

Proteomic Approach ◽

The Social ◽

Cellular Pathways ◽

Alpha Proteobacteria

Abstract The social amoeba Dictyostelium discoideum is a well-established model to study numerous cellular processes including cell motility, chemotaxis, and differentiation. As energy metabolism is involved in these processes, mitochondrial genetics and bioenergetics are of interest, though many features of Dictyostelium mitochondria differ from metazoans. A comprehensive inventory of mitochondrial proteins is critical to understanding mitochondrial processes and their involvement in various cellular pathways. Here, we utilized high-throughput multiplexed protein quantitation and homology analyses to generate a high-confidence mitochondrial protein compendium. Our proteomic approach, which utilizes quantitative mass spectrometry in combination with mathematical modeling, was validated through mitochondrial targeting sequence prediction and live-cell imaging. Our final compendium consists of 1082 proteins. Within our D. discoideum mitochondrial proteome, we identify many proteins that are not present in humans, yeasts, or the ancestral alpha-proteobacteria, which can serve as a foundation for future investigations into the unique mitochondria of Dictyostelium. Additionally, we leverage our compendium to highlight the complexity of metabolic reprogramming during starvation-induced development. Our compendium lays a foundation to investigate mitochondrial processes that are unique in protists, as well as for future studies to understand the functions of conserved mitochondrial proteins in health and diseases using D. discoideum as the model.

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A high-density human mitochondrial proximity interaction network

10.1101/2020.04.01.020479 ◽

2020 ◽

Cited By ~ 4

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

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Comparing transcriptome profiles of human embryo cultured in closed and standard incubators

PeerJ ◽

10.7717/peerj.9738 ◽

2020 ◽

Vol 8 ◽

pp. e9738

Author(s):

Jingyu Li ◽

Jiayu Huang ◽

Wei Han ◽

Xiaoli Shen ◽

Ying Gao ◽

...

Keyword(s):

Rna Splicing ◽

Positive Impact ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Enrichment Analysis ◽

Time Lapse ◽

Human Embryos ◽

Rna Seq ◽

False Discovery ◽

Time Lapse Imaging

It is necessary to compare the transcriptomic profiles of human embryos cultured in time-lapse imaging (TLI) incubators and standard incubators (SI) in order to determine whether a closed culture system has a positive impact on embryos. In this study, we used RNA-sequencing (RNA-Seq) to characterize and compare the gene expression profiles of eight-cell embryos of the same quality grade cultured in TLI and SI. We sequenced a total of 580,952,620 reads for zygotes, TLI-cultured, and SI-cultured eight-cell embryos. The global transcriptomic profiles of the TLI embryos were similar to those of the SI embryos and were highly distinct from the zygotes. We also detected 539 genes showing differential expression between the TLI and SI groups with a false discovery rate (FDR) < 0.05. Using gene ontology enrichment analysis, we found that the highly expressed SI genes tended to execute functions such as transcription, RNA splicing, and DNA repair, and that the highly expressed TLI genes were enriched in the cell differentiation and methyltransferase activity pathways. This study, the first to use transcriptome analysis to compare SI and TLI, will serve as a basis for assessing the safety of TLI application in assisted reproductive technology.

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Gene expression profiles of bovine caruncular and intercaruncular endometrium at implantation

Physiological Genomics ◽

10.1152/physiolgenomics.90404.2008 ◽

2009 ◽

Vol 39 (1) ◽

pp. 14-27 ◽

Cited By ~ 106

Author(s):

Nadéra Mansouri-Attia ◽

Julie Aubert ◽

Pierrette Reinaud ◽

Corinne Giraud-Delville ◽

Géraldine Taghouti ◽

...

Keyword(s):

False Discovery Rate ◽

Cellular Localization ◽

Target Genes ◽

Expression Profiles ◽

Primary Cultures ◽

Gene Expression Profiles ◽

Oligonucleotide Array ◽

Endometrial Cells ◽

False Discovery ◽

The Impact

At implantation the endometrium undergoes modifications necessary for its physical interactions with the trophoblast as well as the development of the conceptus. We aim to identify endometrial factors and pathways essential for a successful implantation in the caruncular (C) and the intercaruncular (IC) areas in cattle. Using a 13,257-element bovine oligonucleotide array, we established expression profiles at day 20 of the estrous cycle or pregnancy (implantation), revealing 446 and 1,295 differentially expressed genes (DEG) in C and IC areas, respectively (false discovery rate = 0.08). The impact of the conceptus was higher on the immune response function in C but more prominent on the regulation of metabolism function in IC. The C vs. IC direct comparison revealed 1,177 and 453 DEG in cyclic and pregnant animals respectively (false discovery rate = 0.05), with a major impact of the conceptus on metabolism and cell adhesion. We selected 15 genes including C11ORF34, CXCL12, CXCR4, PLAC8, SCARA5, and NPY and confirmed their differential expression by quantitative RT-PCR. The cellular localization was analyzed by in situ hybridization and, upon pregnancy, showed gene-specific patterns of cell distribution, including a high level of expression in the luminal epithelium for C11ORF34 and MX1. Using primary cultures of bovine endometrial cells, we identified PTN, PLAC8, and CXCL12 as interferon-τ (IFNT) target genes and MSX1 and CXCR7 as IFNT-regulated genes, whereas C11ORF34 was not an IFNT-regulated gene. Our transcriptomic data provide novel molecular insights accounting for the biological functions related to the C or IC endometrial areas and may contribute to the identification of potential biomarkers for normal and perturbed early pregnancy.

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