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Lyon GJ, Longo J, Garcia A, Inusa F, Marchi E, Shi D, Dörfel M, Arnesen T, Aldabe R, Lyons S, Nashat MA, Bolton D. Evaluating possible maternal effect lethality and genetic background effects in Naa10 knockout mice. PLoS One 2024; 19:e0301328. [PMID: 38713657 PMCID: PMC11075865 DOI: 10.1371/journal.pone.0301328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 03/14/2024] [Indexed: 05/09/2024] Open
Abstract
Amino-terminal (Nt-) acetylation (NTA) is a common protein modification, affecting approximately 80% of all human proteins. The human essential X-linked gene, NAA10, encodes for the enzyme NAA10, which is the catalytic subunit in the N-terminal acetyltransferase A (NatA) complex. There is extensive genetic variation in humans with missense, splice-site, and C-terminal frameshift variants in NAA10. In mice, Naa10 is not an essential gene, as there exists a paralogous gene, Naa12, that substantially rescues Naa10 knockout mice from embryonic lethality, whereas double knockouts (Naa10-/Y Naa12-/-) are embryonic lethal. However, the phenotypic variability in the mice is nonetheless quite extensive, including piebaldism, skeletal defects, small size, hydrocephaly, hydronephrosis, and neonatal lethality. Here we replicate these phenotypes with new genetic alleles in mice, but we demonstrate their modulation by genetic background and environmental effects. We cannot replicate a prior report of "maternal effect lethality" for heterozygous Naa10-/X female mice, but we do observe a small amount of embryonic lethality in the Naa10-/y male mice on the inbred genetic background in this different animal facility.
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Affiliation(s)
- Gholson J. Lyon
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, United States of America
| | - Joseph Longo
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Andrew Garcia
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, United States of America
| | - Fatima Inusa
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Elaine Marchi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Daniel Shi
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - Max Dörfel
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Thomas Arnesen
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Rafael Aldabe
- Division of Gene Therapy and Regulation of Gene Expression, CIMA, University of Navarra, Pamplona, Spain
| | - Scott Lyons
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Woodbury, New York, United States of America
| | - Melissa A. Nashat
- Human Genetics Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
| | - David Bolton
- Molecular Biology Department, New York State Institute for Basic Research (IBR) in Developmental Disabilities, Staten Island, New York, United States of America
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Gomes KM, Nunn BL, Chappell PD, Jenkins BD. Subcellular proteomics for determining iron-limited remodeling of plastids in the model diatom Thalassiosira pseudonana (Bacillariophyta). JOURNAL OF PHYCOLOGY 2023; 59:1085-1099. [PMID: 37615442 DOI: 10.1111/jpy.13379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 08/25/2023]
Abstract
Diatoms are important primary producers in the world's oceans, yet their growth is constrained in large regions by low bioavailable iron (Fe). Low-Fe stress-induced limitation of primary production is due to requirements for Fe in components of essential metabolic pathways including photosynthesis and other chloroplast plastid functions. Studies have shown that under low-Fe stress, diatoms alter plastid-specific processes, including components of electron transport. These physiological changes suggest changes of protein content and in protein abundances within the diatom plastid. While in silico predictions provide putative information on plastid-localized proteins, knowledge of diatom plastid proteins remains limited in comparison to well-studied model photosynthetic organisms. To address this, we employed shotgun proteomics to investigate the proteome of subcellular plastid-enriched fractions from Thalassiosira pseudonana to gain a better understanding of how the plastid proteome is remodeled in response to Fe limitation. Using mass spectrometry-based peptide identification and quantification, we analyzed T. pseudonana grown under Fe-replete and -limiting conditions. Through these analyses, we inferred the relative quantities of each protein, revealing that Fe limitation regulates major metabolic pathways in the plastid, including the Calvin cycle. Additionally, we observed changes in the expression of light-harvesting proteins. In silico localization predictions of proteins identified in this plastid-enriched proteome allowed for an in-depth comparison of theoretical versus observed plastid-localization, providing evidence for the potential of additional protein import pathways into the diatom plastid.
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Affiliation(s)
- Kristofer M Gomes
- Department of Biological Sciences, University of Rhode Island, Rhode Island, Kingston, USA
| | - Brook L Nunn
- Department of Genome Sciences, University of Washington, Washington, Seattle, USA
| | - P Dreux Chappell
- College of Marine Science, University of South Florida, Florida, St. Petersburg, USA
| | - Bethany D Jenkins
- Department of Cell and Molecular Biology, University of Rhode Island, Rhode Island, Kingston, USA
- Graduate School of Oceanography, University of Rhode Island, Rhode Island, Narragansett, USA
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3
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Hanna R, Rozenberg A, Saied L, Ben-Yosef D, Lavy T, Kleifeld O. In-Depth Characterization of Apoptosis N-terminome Reveals a Link Between Caspase-3 Cleavage and Post-Translational N-terminal Acetylation. Mol Cell Proteomics 2023:100584. [PMID: 37236440 PMCID: PMC10362333 DOI: 10.1016/j.mcpro.2023.100584] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/16/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023] Open
Abstract
The N-termini of proteins contain information about their biochemical properties and functions. These N-termini can be processed by proteases, and can undergo other co- or post-translational modifications. We have developed LATE (LysN Amino Terminal Enrichment), a method that uses selective chemical derivatization of α-amines to isolate the N-terminal peptides, in order to improve N-terminome identification in conjunction with other enrichment strategies. We applied LATE alongside another N-terminomic method to study caspase-3 mediated proteolysis both in vitro and during apoptosis in cells. This has enabled us to identify many unreported caspase-3 cleavages, some of which cannot be identified by other methods. Moreover, we have found direct evidence that neo-N-termini generated by caspase-3 cleavage can be further modified by Nt-acetylation. Some of these neo-Nt-acetylation events occur in the early phase of the apoptotic process and may have a role in translation inhibition. This has provided a comprehensive overview of the caspase-3 degradome and has uncovered previously unrecognized crosstalk between post-translational Nt-acetylation and caspase proteolytic pathways.
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Affiliation(s)
- Rawad Hanna
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Layla Saied
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Daniel Ben-Yosef
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Tali Lavy
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Technion City, Haifa 3200003, Israel.
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Nawaly H, Tanaka A, Toyoshima Y, Tsuji Y, Matsuda Y. Localization and characterization θ carbonic anhydrases in Thalassiosira pseudonana. PHOTOSYNTHESIS RESEARCH 2023; 156:217-229. [PMID: 36862281 DOI: 10.1007/s11120-023-01007-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/12/2023] [Indexed: 05/03/2023]
Abstract
Carbonic anhydrase (CA) is a crucial component for the operation of CO2-concentrating mechanisms (CCMs) in the majority of aquatic photoautotrophs that maintain the global primary production. In the genome of the centric marine diatom, Thalassiosira pseudonana, there are four putative gene sequences that encode θ-type CA, which was a type of CA recently identified in marine diatoms and green algae. In the present study, specific subcellular locations of four θCAs, TpθCA1, TpθCA2, TpθCA3, and TpθCA4 were determined by expressing GFP-fused proteins of these TpθCAs in T. pseudonana. As a result, C-terminal GFP fusion proteins of TpθCA1, TpθCA2, and TpθCA3 were all localized in the chloroplast; TpθCA2 was at the central chloroplast area, and the other two TpθCAs were throughout the chloroplast. Immunogold-labeling transmission electron microscopy was further performed for the transformants expressing TpθCA1:GFP and TpθCA2:GFP with anti-GFP-monoclonal antibody. TpθCA1:GFP was localized in the free stroma area, including the peripheral pyrenoid area. TpθCA2:GFP was clearly located as a lined distribution at the central part of the pyrenoid structure, which was most likely the pyrenoid-penetrating thylakoid. Considering the presence of the sequence encoding the N-terminal thylakoid-targeting domain in the TpθCA2 gene, this localization was likely the lumen of the pyrenoid-penetrating thylakoid. On the other hand, TpθCA4:GFP was localized in the cytoplasm. Transcript analysis of these TpθCAs revealed that TpθCA2 and TpθCA3 were upregulated in atmospheric CO2 (0.04% CO2, LC) levels, while TpθCA1 and TpθCA4 were highly induced under 1% CO2 (HC) condition. The genome-editing knockout (KO) of TpθCA1, by CRISPR/Cas9 nickase, gave a silent phenotype in T. pseudonana under LC-HC conditions, which was in sharp agreement with the case of the previously reported TpθCA3 KO. In sharp contrast, TpθCA2 KO is so far unsuccessful, suggesting a housekeeping role of TpθCA2. The silent phenotype of KO strains of stromal CAs suggests that TpαCA1, TpθCA1, and TpθCA3 may have functional redundancy, but different transcript regulations in response to CO2 of these stromal CAs suggest in part their independent roles.
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Affiliation(s)
- Hermanus Nawaly
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Atsuko Tanaka
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara, 903-0213, Japan
| | - Yui Toyoshima
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Yoshinori Tsuji
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Yusuke Matsuda
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan.
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Michie KA, Harrop SJ, Rathbone HW, Wilk KE, Teng CY, Hoef‐Emden K, Hiller RG, Green BR, Curmi PMG. Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins. Protein Sci 2023; 32:e4586. [PMID: 36721353 PMCID: PMC9951199 DOI: 10.1002/pro.4586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/24/2023] [Accepted: 01/27/2023] [Indexed: 02/02/2023]
Abstract
In addition to their membrane-bound chlorophyll a/c light-harvesting antenna, the cryptophyte algae have evolved a unique phycobiliprotein antenna system located in the thylakoid lumen. The basic unit of this antenna consists of two copies of an αβ protomer where the α and β subunits scaffold different combinations of a limited number of linear tetrapyrrole chromophores. While the β subunit is highly conserved, encoded by a single plastid gene, the nuclear-encoded α subunits have evolved diversified multigene families. It is still unclear how this sequence diversity results in the spectral diversity of the mature proteins. By careful examination of three newly determined crystal structures in comparison with three previously obtained, we show how the α subunit amino acid sequences control chromophore conformations and hence spectral properties even when the chromophores are identical. Previously we have shown that α subunits control the quaternary structure of the mature αβ.αβ complex (either open or closed), however, each species appeared to only harbor a single quaternary form. Here we show that species of the Hemiselmis genus contain expressed α subunit genes that encode both distinct quaternary structures. Finally, we have discovered a common single-copy gene (expressed into protein) consisting of tandem copies of a small α subunit that could potentially scaffold pairs of light harvesting units. Together, our results show how the diversity of the multigene α subunit family produces a range of mature cryptophyte antenna proteins with differing spectral properties, and the potential for minor forms that could contribute to acclimation to varying light regimes.
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Affiliation(s)
- Katharine A. Michie
- School of PhysicsThe University of New South WalesSydneyNew South WalesAustralia
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyNew South WalesAustralia
- Mark Wainwright Analytical CentreUniversity of New South WalesSydneyNew South WalesAustralia
| | - Stephen J. Harrop
- School of PhysicsThe University of New South WalesSydneyNew South WalesAustralia
- MX Beamlines, Australian SynchrotronClaytonVictoriaAustralia
| | - Harry W. Rathbone
- School of PhysicsThe University of New South WalesSydneyNew South WalesAustralia
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyNew South WalesAustralia
| | - Krystyna E. Wilk
- School of PhysicsThe University of New South WalesSydneyNew South WalesAustralia
| | - Chang Ying Teng
- Department of BotanyUniversity of British ColumbiaVancouverCanada
| | | | - Roger G. Hiller
- Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | | | - Paul M. G. Curmi
- School of PhysicsThe University of New South WalesSydneyNew South WalesAustralia
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydneyNew South WalesAustralia
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6
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Meinnel T, Giglione C. N-terminal modifications, the associated processing machinery, and their evolution in plastid-containing organisms. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6013-6033. [PMID: 35768189 DOI: 10.1093/jxb/erac290] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The N-terminus is a frequent site of protein modifications. Referring primarily to knowledge gained from land plants, here we review the modifications that change protein N-terminal residues and provide updated information about the associated machinery, including that in Archaeplastida. These N-terminal modifications include many proteolytic events as well as small group additions such as acylation or arginylation and oxidation. Compared with that of the mitochondrion, the plastid-dedicated N-terminal modification landscape is far more complex. In parallel, we extend this review to plastid-containing Chromalveolata including Stramenopiles, Apicomplexa, and Rhizaria. We report a well-conserved machinery, especially in the plastid. Consideration of the two most abundant proteins on Earth-Rubisco and actin-reveals the complexity of N-terminal modification processes. The progressive gene transfer from the plastid to the nuclear genome during evolution is exemplified by the N-terminus modification machinery, which appears to be one of the latest to have been transferred to the nuclear genome together with crucial major photosynthetic landmarks. This is evidenced by the greater number of plastid genes in Paulinellidae and red algae, the most recent and fossil recipients of primary endosymbiosis.
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Affiliation(s)
- Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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7
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Oberleitner L, Perrar A, Macorano L, Huesgen PF, Nowack ECM. A bipartite chromatophore transit peptide and N-terminal protein processing in the Paulinella chromatophore. PLANT PHYSIOLOGY 2022; 189:152-164. [PMID: 35043947 PMCID: PMC9070848 DOI: 10.1093/plphys/kiac012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 12/06/2021] [Indexed: 05/19/2023]
Abstract
The amoeba Paulinella chromatophora contains photosynthetic organelles, termed chromatophores, which evolved independently from plastids in plants and algae. At least one-third of the chromatophore proteome consists of nucleus-encoded (NE) proteins that are imported across the chromatophore double envelope membranes. Chromatophore-targeted proteins exceeding 250 amino acids (aa) carry a conserved N-terminal extension presumably involved in protein targeting, termed the chromatophore transit peptide (crTP). Short imported proteins do not carry discernable targeting signals. To explore whether the import of proteins is accompanied by their N-terminal processing, here we identified N-termini of 208 chromatophore-localized proteins by a mass spectrometry-based approach. Our study revealed extensive N-terminal acetylation and proteolytic processing in both NE and chromatophore-encoded (CE) fractions of the chromatophore proteome. Mature N-termini of 37 crTP-carrying proteins were identified, of which 30 were cleaved in a common processing region. Surprisingly, only the N-terminal ∼50 aa (part 1) become cleaved upon import. This part contains a conserved adaptor protein-1 complex-binding motif known to mediate protein sorting at the trans-Golgi network followed by a predicted transmembrane helix, implying that part 1 anchors the protein co-translationally in the endoplasmic reticulum and mediates trafficking to the chromatophore via the Golgi. The C-terminal part 2 contains conserved secondary structural elements, remains attached to the mature proteins, and might mediate translocation across the chromatophore inner membrane. Short imported proteins remain largely unprocessed. Finally, this work illuminates N-terminal processing of proteins encoded in an evolutionary-early-stage organelle and suggests host-derived posttranslationally acting factors involved in regulation of the CE chromatophore proteome.
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Affiliation(s)
- Linda Oberleitner
- Department of Biology, Institute of Microbial Cell Biology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Andreas Perrar
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, 52425 Jülich, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases, CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany
| | - Luis Macorano
- Department of Biology, Institute of Microbial Cell Biology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, 52425 Jülich, Germany
- Cologne Excellence Cluster on Stress Responses in Ageing-Associated Diseases, CECAD, Medical Faculty and University Hospital, University of Cologne, 50931 Cologne, Germany
- Department of Chemistry, Institute of Biochemistry, University of Cologne, 50674 Cologne, Germany
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8
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Abstract
Protein N-termini provide unique and distinguishing information on proteolytically processed or N-terminally modified proteoforms. Also splicing, use of alternative translation initiation sites, and a variety of co- and post-translational N-terminal modifications generate distinct proteoforms that are unambiguously identified by their N-termini. However, N-terminal peptides are only a small fraction among all peptides generated in a shotgun proteome digest, are often of low stoichiometric abundance, and therefore require enrichment. Various protocols for enrichment of N-terminal peptides have been established and successfully been used for protease substrate discovery and profiling of N-terminal modification, but often require large amounts of proteome. We have recently established the High-efficiency Undecanal-based N-Termini EnRichment (HUNTER) as a fast and sensitive method to enable enrichment of protein N-termini from limited sample sources with as little as a few microgram proteome. Here we present our current HUNTER protocol for sensitive plant N-terminome profiling, including sample preparation, enrichment of N-terminal peptides, and mass spectrometry data analysis.
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Affiliation(s)
- Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Jülich, Germany
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Andreas Perrar
- Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Jülich, Germany
- Cologne Cluster of Excellence on Aging-related Disorders, CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Melissa Mantz
- Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Jülich, Germany
- Cologne Cluster of Excellence on Aging-related Disorders, CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Jülich, Germany.
- Cologne Cluster of Excellence on Aging-related Disorders, CECAD, Medical Faculty and University Hospital, University of Cologne, Cologne, Germany.
- Institute of Biochemistry, Department for Chemistry , University of Cologne, Cologne, Germany.
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Heidorn-Czarna M, Maziak A, Janska H. Protein Processing in Plant Mitochondria Compared to Yeast and Mammals. FRONTIERS IN PLANT SCIENCE 2022; 13:824080. [PMID: 35185991 PMCID: PMC8847149 DOI: 10.3389/fpls.2022.824080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 05/02/2023]
Abstract
Limited proteolysis, called protein processing, is an essential post-translational mechanism that controls protein localization, activity, and in consequence, function. This process is prevalent for mitochondrial proteins, mainly synthesized as precursor proteins with N-terminal sequences (presequences) that act as targeting signals and are removed upon import into the organelle. Mitochondria have a distinct and highly conserved proteolytic system that includes proteases with sole function in presequence processing and proteases, which show diverse mitochondrial functions with limited proteolysis as an additional one. In virtually all mitochondria, the primary processing of N-terminal signals is catalyzed by the well-characterized mitochondrial processing peptidase (MPP). Subsequently, a second proteolytic cleavage occurs, leading to more stabilized residues at the newly formed N-terminus. Lately, mitochondrial proteases, intermediate cleavage peptidase 55 (ICP55) and octapeptidyl protease 1 (OCT1), involved in proteolytic cleavage after MPP and their substrates have been described in the plant, yeast, and mammalian mitochondria. Mitochondrial proteins can also be processed by removing a peptide from their N- or C-terminus as a maturation step during insertion into the membrane or as a regulatory mechanism in maintaining their function. This type of limited proteolysis is characteristic for processing proteases, such as IMP and rhomboid proteases, or the general mitochondrial quality control proteases ATP23, m-AAA, i-AAA, and OMA1. Identification of processing protease substrates and defining their consensus cleavage motifs is now possible with the help of large-scale quantitative mass spectrometry-based N-terminomics, such as combined fractional diagonal chromatography (COFRADIC), charge-based fractional diagonal chromatography (ChaFRADIC), or terminal amine isotopic labeling of substrates (TAILS). This review summarizes the current knowledge on the characterization of mitochondrial processing peptidases and selected N-terminomics techniques used to uncover protease substrates in the plant, yeast, and mammalian mitochondria.
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Using Diatom and Apicomplexan Models to Study the Heme Pathway of Chromera velia. Int J Mol Sci 2021; 22:ijms22126495. [PMID: 34204357 PMCID: PMC8233740 DOI: 10.3390/ijms22126495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 12/20/2022] Open
Abstract
Heme biosynthesis is essential for almost all living organisms. Despite its conserved function, the pathway’s enzymes can be located in a remarkable diversity of cellular compartments in different organisms. This location does not always reflect their evolutionary origins, as might be expected from the history of their acquisition through endosymbiosis. Instead, the final subcellular localization of the enzyme reflects multiple factors, including evolutionary origin, demand for the product, availability of the substrate, and mechanism of pathway regulation. The biosynthesis of heme in the apicomonad Chromera velia follows a chimeric pathway combining heme elements from the ancient algal symbiont and the host. Computational analyses using different algorithms predict complex targeting patterns, placing enzymes in the mitochondrion, plastid, endoplasmic reticulum, or the cytoplasm. We employed heterologous reporter gene expression in the apicomplexan parasite Toxoplasma gondii and the diatom Phaeodactylum tricornutum to experimentally test these predictions. 5-aminolevulinate synthase was located in the mitochondria in both transfection systems. In T. gondii, the two 5-aminolevulinate dehydratases were located in the cytosol, uroporphyrinogen synthase in the mitochondrion, and the two ferrochelatases in the plastid. In P. tricornutum, all remaining enzymes, from ALA-dehydratase to ferrochelatase, were placed either in the endoplasmic reticulum or in the periplastidial space.
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Giglione C, Meinnel T. Evolution-Driven Versatility of N Terminal Acetylation in Photoautotrophs. TRENDS IN PLANT SCIENCE 2021; 26:375-391. [PMID: 33384262 DOI: 10.1016/j.tplants.2020.11.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/27/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
N terminal protein α-acetylation (NTA) is a pervasive protein modification that has recently attracted renewed interest. Early studies on NTA were mostly conducted in yeast and metazoans, providing a detailed portrait of the modification, which was indirectly applied to all eukaryotes. However, new findings originating from photosynthetic organisms have expanded our knowledge of this modification, revealing strong similarities as well as idiosyncratic features. Here, we review the most recent advances on NTA and its dedicated machinery in photosynthetic organisms. We discuss the cytosolic and unique plastid NTA machineries and their critical biological roles in development, stress responses, protein translocation, and stability. These new findings suggest that the multitasking plastid and cytosolic machineries evolved to support the specific needs of photoautotrophs.
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Affiliation(s)
- Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
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12
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Pyrih J, Žárský V, Fellows JD, Grosche C, Wloga D, Striepen B, Maier UG, Tachezy J. The iron-sulfur scaffold protein HCF101 unveils the complexity of organellar evolution in SAR, Haptista and Cryptista. BMC Ecol Evol 2021; 21:46. [PMID: 33740894 PMCID: PMC7980591 DOI: 10.1186/s12862-021-01777-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/08/2021] [Indexed: 11/22/2022] Open
Abstract
Background Nbp35-like proteins (Nbp35, Cfd1, HCF101, Ind1, and AbpC) are P-loop NTPases that serve as components of iron-sulfur cluster (FeS) assembly machineries. In eukaryotes, Ind1 is present in mitochondria, and its function is associated with the assembly of FeS clusters in subunits of respiratory Complex I, Nbp35 and Cfd1 are the components of the cytosolic FeS assembly (CIA) pathway, and HCF101 is involved in FeS assembly of photosystem I in plastids of plants (chHCF101). The AbpC protein operates in Bacteria and Archaea. To date, the cellular distribution of these proteins is considered to be highly conserved with only a few exceptions. Results We searched for the genes of all members of the Nbp35-like protein family and analyzed their targeting sequences. Nbp35 and Cfd1 were predicted to reside in the cytoplasm with some exceptions of Nbp35 localization to the mitochondria; Ind1was found in the mitochondria, and HCF101 was predicted to reside in plastids (chHCF101) of all photosynthetically active eukaryotes. Surprisingly, we found a second HCF101 paralog in all members of Cryptista, Haptista, and SAR that was predicted to predominantly target mitochondria (mHCF101), whereas Ind1 appeared to be absent in these organisms. We also identified a few exceptions, as apicomplexans possess mHCF101 predicted to localize in the cytosol and Nbp35 in the mitochondria. Our predictions were experimentally confirmed in selected representatives of Apicomplexa (Toxoplasma gondii), Stramenopila (Phaeodactylum tricornutum, Thalassiosira pseudonana), and Ciliophora (Tetrahymena thermophila) by tagging proteins with a transgenic reporter. Phylogenetic analysis suggested that chHCF101 and mHCF101 evolved from a common ancestral HCF101 independently of the Nbp35/Cfd1 and Ind1 proteins. Interestingly, phylogenetic analysis supports rather a lateral gene transfer of ancestral HCF101 from bacteria than its acquisition being associated with either α-proteobacterial or cyanobacterial endosymbionts. Conclusion Our searches for Nbp35-like proteins across eukaryotic lineages revealed that SAR, Haptista, and Cryptista possess mitochondrial HCF101. Because plastid localization of HCF101 was only known thus far, the discovery of its mitochondrial paralog explains confusion regarding the presence of HCF101 in organisms that possibly lost secondary plastids (e.g., ciliates, Cryptosporidium) or possess reduced nonphotosynthetic plastids (apicomplexans). Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01777-x.
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Affiliation(s)
- Jan Pyrih
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25250, Vestec, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25250, Vestec, Czech Republic
| | - Justin D Fellows
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Christopher Grosche
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany.,LOEWE Center for Synthetic Microbiology (Synmikro), Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Boris Striepen
- Department of Cellular Biology, University of Georgia, Athens, GA, USA.,Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, 380 South University Avenue, Philadelphia, PA, 19104, USA
| | - Uwe G Maier
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032, Marburg, Germany.,LOEWE Center for Synthetic Microbiology (Synmikro), Hans-Meerwein-Str. 6, 35032, Marburg, Germany
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25250, Vestec, Czech Republic.
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13
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Bienvenut WV, Brünje A, Boyer J, Mühlenbeck JS, Bernal G, Lassowskat I, Dian C, Linster E, Dinh TV, Koskela MM, Jung V, Seidel J, Schyrba LK, Ivanauskaite A, Eirich J, Hell R, Schwarzer D, Mulo P, Wirtz M, Meinnel T, Giglione C, Finkemeier I. Dual lysine and N-terminal acetyltransferases reveal the complexity underpinning protein acetylation. Mol Syst Biol 2020; 16:e9464. [PMID: 32633465 PMCID: PMC7339202 DOI: 10.15252/msb.20209464] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 01/02/2023] Open
Abstract
Protein acetylation is a highly frequent protein modification. However, comparatively little is known about its enzymatic machinery. N-α-acetylation (NTA) and ε-lysine acetylation (KA) are known to be catalyzed by distinct families of enzymes (NATs and KATs, respectively), although the possibility that the same GCN5-related N-acetyltransferase (GNAT) can perform both functions has been debated. Here, we discovered a new family of plastid-localized GNATs, which possess a dual specificity. All characterized GNAT family members display a number of unique features. Quantitative mass spectrometry analyses revealed that these enzymes exhibit both distinct KA and relaxed NTA specificities. Furthermore, inactivation of GNAT2 leads to significant NTA or KA decreases of several plastid proteins, while proteins of other compartments were unaffected. The data indicate that these enzymes have specific protein targets and likely display partly redundant selectivity, increasing the robustness of the acetylation process in vivo. In summary, this study revealed a new layer of complexity in the machinery controlling this prevalent modification and suggests that other eukaryotic GNATs may also possess these previously underappreciated broader enzymatic activities.
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Affiliation(s)
- Willy V Bienvenut
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Génétique Quantitative et ÉvolutionGif‐sur‐YvetteFrance
| | - Annika Brünje
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Jean‐Baptiste Boyer
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Jens S Mühlenbeck
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Gautier Bernal
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Institute of Plant Sciences Paris‐SaclayGif‐sur‐YvetteFrance
| | - Ines Lassowskat
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Cyril Dian
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Eric Linster
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Trinh V Dinh
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Minna M Koskela
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
- Present address:
Institute of MicrobiologyTřeboňCzech Republic
| | - Vincent Jung
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
- Present address:
Institute IMAGINEParisFrance
| | - Julian Seidel
- Interfaculty Institute of BiochemistryUniversity of TübingenTübingenGermany
| | - Laura K Schyrba
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Aiste Ivanauskaite
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
| | - Jürgen Eirich
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
| | - Rüdiger Hell
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Dirk Schwarzer
- Interfaculty Institute of BiochemistryUniversity of TübingenTübingenGermany
| | - Paula Mulo
- Department of BiochemistryMolecular Plant BiologyUniversity of TurkuTurkuFinland
| | - Markus Wirtz
- Centre for Organismal Studies HeidelbergUniversity of HeidelbergHeidelbergGermany
| | - Thierry Meinnel
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Carmela Giglione
- Université Paris‐SaclayCEACNRSInstitute for Integrative Biology of the Cell (I2BC)Gif‐sur‐YvetteFrance
| | - Iris Finkemeier
- Plant PhysiologyInstitute of Plant Biology and BiotechnologyUniversity of MuensterMuensterGermany
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14
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Falciatore A, Jaubert M, Bouly JP, Bailleul B, Mock T. Diatom Molecular Research Comes of Age: Model Species for Studying Phytoplankton Biology and Diversity. THE PLANT CELL 2020; 32:547-572. [PMID: 31852772 PMCID: PMC7054031 DOI: 10.1105/tpc.19.00158] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/18/2019] [Accepted: 12/13/2019] [Indexed: 05/08/2023]
Abstract
Diatoms are the world's most diverse group of algae, comprising at least 100,000 species. Contributing ∼20% of annual global carbon fixation, they underpin major aquatic food webs and drive global biogeochemical cycles. Over the past two decades, Thalassiosira pseudonana and Phaeodactylum tricornutum have become the most important model systems for diatom molecular research, ranging from cell biology to ecophysiology, due to their rapid growth rates, small genomes, and the cumulative wealth of associated genetic resources. To explore the evolutionary divergence of diatoms, additional model species are emerging, such as Fragilariopsis cylindrus and Pseudo-nitzschia multistriata Here, we describe how functional genomics and reverse genetics have contributed to our understanding of this important class of microalgae in the context of evolution, cell biology, and metabolic adaptations. Our review will also highlight promising areas of investigation into the diversity of these photosynthetic organisms, including the discovery of new molecular pathways governing the life of secondary plastid-bearing organisms in aquatic environments.
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Affiliation(s)
- Angela Falciatore
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Marianne Jaubert
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Jean-Pierre Bouly
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
- Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, UMR7238 Sorbonne Université, 75005 Paris, France
| | - Benjamin Bailleul
- Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae, UMR7141 Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, 75005 Paris, France
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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15
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RSH enzyme diversity for (p)ppGpp metabolism in Phaeodactylum tricornutum and other diatoms. Sci Rep 2019; 9:17682. [PMID: 31776430 PMCID: PMC6881373 DOI: 10.1038/s41598-019-54207-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 11/05/2019] [Indexed: 12/28/2022] Open
Abstract
The nucleotides guanosine tetraphosphate and pentaphosphate (together known as (p)ppGpp or magic spot) are produced in plant plastids from GDP/GTP and ATP by RelA-SpoT homologue (RSH) enzymes. In the model plant Arabidopsis (p)ppGpp regulates chloroplast transcription and translation to affect growth, and is also implicated in acclimation to stress. However, little is known about (p)ppGpp metabolism or its evolution in other photosynthetic eukaryotes. Here we studied (p)ppGpp metabolism in the marine diatom Phaeodactylum tricornutum. We identified three expressed RSH genes in the P. tricornutum genome, and determined the enzymatic activity of the corresponding enzymes by heterologous expression in bacteria. We showed that two P. tricornutum RSH are (p)ppGpp synthetases, despite substitution of a residue within the active site believed critical for activity, and that the third RSH is a bifunctional (p)ppGpp synthetase and hydrolase, the first of its kind demonstrated in a photosynthetic eukaryote. A broad phylogenetic analysis then showed that diatom RSH belong to novel algal RSH clades. Together our work significantly expands the horizons of (p)ppGpp signalling in the photosynthetic eukaryotes by demonstrating an unexpected functional, structural and evolutionary diversity in RSH enzymes from organisms with plastids derived from red algae.
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16
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Millar AH, Heazlewood JL, Giglione C, Holdsworth MJ, Bachmair A, Schulze WX. The Scope, Functions, and Dynamics of Posttranslational Protein Modifications. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:119-151. [PMID: 30786234 DOI: 10.1146/annurev-arplant-050718-100211] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Assessing posttranslational modification (PTM) patterns within protein molecules and reading their functional implications present grand challenges for plant biology. We combine four perspectives on PTMs and their roles by considering five classes of PTMs as examples of the broader context of PTMs. These include modifications of the N terminus, glycosylation, phosphorylation, oxidation, and N-terminal and protein modifiers linked to protein degradation. We consider the spatial distribution of PTMs, the subcellular distribution of modifying enzymes, and their targets throughout the cell, and we outline the complexity of compartmentation in understanding of PTM function. We also consider PTMs temporally in the context of the lifetime of a protein molecule and the need for different PTMs for assembly, localization, function, and degradation. Finally, we consider the combined action of PTMs on the same proteins, their interactions, and the challenge ahead of integrating PTMs into an understanding of protein function in plants.
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Affiliation(s)
- A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia;
| | - Joshua L Heazlewood
- School of BioSciences, University of Melbourne, Melbourne, Victoria 3010, Australia;
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell, CNRS UMR9198, F-91198 Gif-sur-Yvette Cedex, France;
| | - Michael J Holdsworth
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom;
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria;
| | - Waltraud X Schulze
- Systembiologie der Pflanze, Universität Hohenheim, 70599 Stuttgart, Germany;
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17
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Perrar A, Dissmeyer N, Huesgen PF. New beginnings and new ends: methods for large-scale characterization of protein termini and their use in plant biology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2021-2038. [PMID: 30838411 PMCID: PMC6460961 DOI: 10.1093/jxb/erz104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/27/2019] [Indexed: 05/17/2023]
Abstract
Dynamic regulation of protein function and abundance plays an important role in virtually every aspect of plant life. Diversifying mechanisms at the RNA and protein level result in many protein molecules with distinct sequence and modification, termed proteoforms, arising from a single gene. Distinct protein termini define proteoforms arising from translation of alternative transcripts, use of alternative translation initiation sites, and different co- and post-translational modifications of the protein termini. Also site-specific proteolytic processing by endo- and exoproteases generates truncated proteoforms, defined by distinct protease-generated neo-N- and neo-C-termini, that may exhibit altered activity, function, and localization compared with their precursor proteins. In eukaryotes, the N-degron pathway targets cytosolic proteins, exposing destabilizing N-terminal amino acids and/or destabilizing N-terminal modifications for proteasomal degradation. This enables rapid and selective removal not only of unfolded proteins, but also of substrate proteoforms generated by proteolytic processing or changes in N-terminal modifications. Here we summarize current protocols enabling proteome-wide analysis of protein termini, which have provided important new insights into N-terminal modifications and protein stability determinants, protein maturation pathways, and protease-substrate relationships in plants.
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Affiliation(s)
- Andreas Perrar
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB), Weinberg, Halle (Saale), Germany
- ScienceCampus Halle – Plant-based Bioeconomy, Halle (Saale), Germany
| | - Pitter F Huesgen
- Forschungszentrum Jülich, Central Institute for Engineering, Electronics and Analytics, ZEA-3 Analytics, Jülich, Germany
- Medical Faculty and University Hospital, University of Cologne, Cologne, Germany
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18
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Demir F, Niedermaier S, Villamor JG, Huesgen PF. Quantitative proteomics in plant protease substrate identification. THE NEW PHYTOLOGIST 2018; 218:936-943. [PMID: 28493421 DOI: 10.1111/nph.14587] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/07/2017] [Indexed: 05/17/2023]
Abstract
Contents Summary 936 I. Introduction 936 II. The quest for plant protease substrates - proteomics to the rescue? 937 III. Quantitative proteome comparison reveals candidate substrates 938 IV. Dynamic metabolic stable isotope labeling to measure protein turnover in vivo 938 V. Terminomics - large-scale identification of protease cleavage sites 939 VI. Substrate or not substrate, that is the question 940 VII. Concluding remarks 941 Acknowledgements 941 References 941 SUMMARY: Proteolysis is a central regulatory mechanism of protein homeostasis and protein function that affects all aspects of plant life. Higher plants encode for hundreds of proteases, but their physiological substrates and hence their molecular functions remain mostly unknown. Current quantitative mass spectrometry-based proteomics enables unbiased large-scale interrogation of the proteome and its modifications. Here we provide an overview of proteomics techniques that allow profiling of changes in protein abundance, measurement of proteome turnover rates, identification of protease cleavage sites in vivo and in vitro and determination of protease sequence specificity. We discuss how these techniques can help to reveal protease substrates and determine plant protease function, illustrated by recent studies on selected plant proteases.
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Affiliation(s)
- Fatih Demir
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Stefan Niedermaier
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Joji Grace Villamor
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
| | - Pitter Florian Huesgen
- ZEA-3 Analytics, Central Institute for Engineering, Electronics and Analytics, Forschungszentrum Jülich, Wilhelm-Johnen-Str., Jülich, 52425, Germany
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19
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Kieselbach T, Cheregi O, Green BR, Funk C. Proteomic analysis of the phycobiliprotein antenna of the cryptophyte alga Guillardia theta cultured under different light intensities. PHOTOSYNTHESIS RESEARCH 2018; 135:149-163. [PMID: 28540588 PMCID: PMC5784005 DOI: 10.1007/s11120-017-0400-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/16/2017] [Indexed: 06/01/2023]
Abstract
Plants and algae have developed various light-harvesting mechanisms for optimal delivery of excitation energy to the photosystems. Cryptophyte algae have evolved a novel soluble light-harvesting antenna utilizing phycobilin pigments to complement the membrane-intrinsic Chl a/c-binding LHC antenna. This new antenna consists of the plastid-encoded β-subunit, a relic of the ancestral phycobilisome, and a novel nuclear-encoded α-subunit unique to cryptophytes. Together, these proteins form the active α1β·α2β-tetramer. In all cryptophyte algae investigated so far, the α-subunits have duplicated and diversified into a large gene family. Although there is transcriptional evidence for expression of all these genes, the X-ray structures determined to date suggest that only two of the α-subunit genes might be significantly expressed at the protein level. Using proteomics, we show that in phycoerythrin 545 (PE545) of Guillardia theta, the only cryptophyte with a sequenced genome, all 20 α-subunits are expressed when the algae grow under white light. The expression level of each protein depends on the intensity of the growth light, but there is no evidence for a specific light-dependent regulation of individual members of the α-subunit family under the growth conditions applied. GtcpeA10 seems to be a special member of the α-subunit family, because it consists of two similar N- and C-terminal domains, which likely are the result of a partial tandem gene duplication. The proteomics data of this study have been deposited to the ProteomeXchange Consortium and have the dataset identifiers PXD006301 and 10.6019/PXD006301.
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Affiliation(s)
| | - Otilia Cheregi
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Beverley R. Green
- Botany Department, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Christiane Funk
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
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20
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Gruber A, Kroth PG. Intracellular metabolic pathway distribution in diatoms and tools for genome-enabled experimental diatom research. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160402. [PMID: 28717012 PMCID: PMC5516111 DOI: 10.1098/rstb.2016.0402] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2017] [Indexed: 11/12/2022] Open
Abstract
Diatoms are important primary producers in the oceans and can also dominate other aquatic habitats. One reason for the success of this phylogenetically relatively young group of unicellular organisms could be the impressive redundancy and diversity of metabolic isoenzymes in diatoms. This redundancy is a result of the evolutionary origin of diatom plastids by a eukaryote-eukaryote endosymbiosis, a process that implies temporary redundancy of functionally complete eukaryotic genomes. During the establishment of the plastids, this redundancy was partially reduced via gene losses, and was partially retained via gene transfer to the nucleus of the respective host cell. These gene transfers required re-assignment of intracellular targeting signals, a process that simultaneously altered the intracellular distribution of metabolic enzymes compared with the ancestral cells. Genome annotation, the correct assignment of the gene products and the prediction of putative function, strongly depends on the correct prediction of the intracellular targeting of a gene product. Here again diatoms are very peculiar, because the targeting systems for organelle import are partially different to those in land plants. In this review, we describe methods of predicting intracellular enzyme locations, highlight findings of metabolic peculiarities in diatoms and present genome-enabled approaches to study their metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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21
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Dorrell RG, Gile G, McCallum G, Méheust R, Bapteste EP, Klinger CM, Brillet-Guéguen L, Freeman KD, Richter DJ, Bowler C. Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. eLife 2017; 6. [PMID: 28498102 PMCID: PMC5462543 DOI: 10.7554/elife.23717] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 05/08/2017] [Indexed: 12/18/2022] Open
Abstract
Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25% of its phylogenetically tractable nucleus-encoded proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual-targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history. DOI:http://dx.doi.org/10.7554/eLife.23717.001 The cells of most plants and algae contain compartments called chloroplasts that enable them to capture energy from sunlight in a process known as photosynthesis. Chloroplasts are the remnants of photosynthetic bacteria that used to live freely in the environment until they were consumed by a larger cell. “Complex” chloroplasts can form if a cell that already has a chloroplast is swallowed by another cell. The most abundant algae in the oceans are known as diatoms. These algae belong to a group called the stramenopiles, which also includes giant seaweeds such as kelp. The stramenopiles have a complex chloroplast that they acquired from a red alga (a relative of the seaweed used in sushi). However, some of the proteins in their chloroplasts are from other sources, such as the green algal relatives of plants, and it was not clear how these chloroplast proteins have contributed to the evolution of this group. Many of the proteins that chloroplasts need to work properly are produced by the host cell and are then transported into the chloroplasts. Dorrell et al. studied the genetic material of many stramenopile species and identified 770 chloroplast-targeted proteins that are predicted to underpin the origins of this group. Experiments in a diatom called Phaeodactylum confirmed these predictions and show that many of these chloroplast-targeted proteins have been recruited from green algae, bacteria, and other compartments within the host cell to support the chloroplast. Further experiments suggest that another major group of algae called the haptophytes once had a stramenopile chloroplast. The current haptophyte chloroplast does not come from the stramenopiles so the haptophytes appear to have replaced their chloroplasts at least once in their evolutionary history. The findings show that algal chloroplasts are mosaics, supported by proteins from many different species. This helps us understand why certain species succeed in the wild and how they may respond to environmental changes in the oceans. In the future, these findings may help researchers to engineer new species of algae and plants for food and fuel production. DOI:http://dx.doi.org/10.7554/eLife.23717.002
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Affiliation(s)
- Richard G Dorrell
- IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Gillian Gile
- School of Life Sciences, Arizona State University, Tempe, United States
| | - Giselle McCallum
- IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Raphaël Méheust
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Paris, France
| | - Eric P Bapteste
- Institut de Biologie Paris-Seine, Université Pierre et Marie Curie, Paris, France
| | | | | | | | - Daniel J Richter
- Sorbonne Universités, Université Pierre et Marie Curie, CNRS UMR 7144.,Adaptation et Diversité en Milieu Marin, Équipe EPEP, Station Biologique de Roscoff, Roscoff, France
| | - Chris Bowler
- IBENS, Département de Biologie, École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
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Responses of the marine diatom Thalassiosira pseudonana to changes in CO 2 concentration: a proteomic approach. Sci Rep 2017; 7:42333. [PMID: 28181560 PMCID: PMC5299434 DOI: 10.1038/srep42333] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022] Open
Abstract
The concentration of CO2 in many aquatic systems is variable, often lower than the KM of the primary carboxylating enzyme Rubisco, and in order to photosynthesize efficiently, many algae operate a facultative CO2 concentrating mechanism (CCM). Here we measured the responses of a marine diatom, Thalassiosira pseudonana, to high and low concentrations of CO2 at the level of transcripts, proteins and enzyme activity. Low CO2 caused many metabolic pathways to be remodeled. Carbon acquisition enzymes, primarily carbonic anhydrase, stress, degradation and signaling proteins were more abundant while proteins associated with nitrogen metabolism, energy production and chaperones were less abundant. A protein with similarities to the Ca2+/ calmodulin dependent protein kinase II_association domain, having a chloroplast targeting sequence, was only present at low CO2. This protein might be a specific response to CO2 limitation since a previous study showed that other stresses caused its reduction. The protein sequence was found in other marine diatoms and may play an important role in their response to low CO2 concentration.
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23
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Demir F, Niedermaier S, Kizhakkedathu JN, Huesgen PF. Profiling of Protein N-Termini and Their Modifications in Complex Samples. Methods Mol Biol 2017; 1574:35-50. [PMID: 28315242 DOI: 10.1007/978-1-4939-6850-3_4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Protein N termini are a unique window to the functional state of the proteome, revealing translation initiation sites, co-translation truncation and modification, posttranslational maturation, and further proteolytic processing into different proteoforms with distinct functions. As a direct readout of proteolytic activity, protein N termini further reveal proteolytic regulation of diverse biological processes and provide a route to determine specific substrates and hence the physiological functions for any protease of interest. Here, we describe our current protocol of the successful Terminal Amine Isotope Labeling of Substrates (TAILS) technique, which enriches protein N-terminal peptides from complex proteome samples by negative selection. Genome-encoded N termini, protease-generated neo-N termini, and endogenously modified N termini are all enriched simultaneously. Subsequent mass spectrometric analysis therefore profiles all protein N termini and their modifications present in a complex sample in a single experiment. We further provide a detailed protocol for the TAILS-compatible proteome preparation from plant material and discuss specific considerations for N terminome data analysis and annotation.
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Affiliation(s)
- Fatih Demir
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, 52425, Jülich, Germany
| | - Stefan Niedermaier
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, 52425, Jülich, Germany
| | - Jayachandran N Kizhakkedathu
- Centre for Blood Research, Department of Pathology & Laboratory Medicine, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada, V6T 1Z3
- Department of Chemistry, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada, V6T 1Z3
| | - Pitter F Huesgen
- Central Institute for Engineering, Electronics and Analytics, ZEA-3, Forschungszentrum Jülich, Wilhelm-Johnen-Str, 52425, Jülich, Germany.
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24
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Dorrell RG, Klinger CM, Newby RJ, Butterfield ER, Richardson E, Dacks JB, Howe CJ, Nisbet ER, Bowler C. Progressive and Biased Divergent Evolution Underpins the Origin and Diversification of Peridinin Dinoflagellate Plastids. Mol Biol Evol 2016; 34:361-379. [DOI: 10.1093/molbev/msw235] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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25
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Canut H, Albenne C, Jamet E. Post-translational modifications of plant cell wall proteins and peptides: A survey from a proteomics point of view. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:983-90. [PMID: 26945515 DOI: 10.1016/j.bbapap.2016.02.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/12/2016] [Accepted: 02/24/2016] [Indexed: 12/21/2022]
Abstract
Plant cell wall proteins (CWPs) and peptides are important players in cell walls contributing to their assembly and their remodeling during development and in response to environmental constraints. Since the rise of proteomics technologies at the beginning of the 2000's, the knowledge of CWPs has greatly increased leading to the discovery of new CWP families and to the description of the cell wall proteomes of different organs of many plants. Conversely, cell wall peptidomics data are still lacking. In addition to the identification of CWPs and peptides by mass spectrometry (MS) and bioinformatics, proteomics has allowed to describe their post-translational modifications (PTMs). At present, the best known PTMs consist in proteolytic cleavage, N-glycosylation, hydroxylation of P residues into hydroxyproline residues (O), O-glycosylation and glypiation. In this review, the methods allowing the capture of the modified proteins based on the specific properties of their PTMs as well as the MS technologies used for their characterization are briefly described. A focus is done on proteolytic cleavage leading to protein maturation or release of signaling peptides and on O-glycosylation. Some new technologies, like top-down proteomics and terminomics, are described. They aim at a finer description of proteoforms resulting from PTMs or degradation mechanisms. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Hervé Canut
- Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Cécile Albenne
- Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Elisabeth Jamet
- Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France.
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26
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Breiman A, Fieulaine S, Meinnel T, Giglione C. The intriguing realm of protein biogenesis: Facing the green co-translational protein maturation networks. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:531-50. [PMID: 26555180 DOI: 10.1016/j.bbapap.2015.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 01/13/2023]
Abstract
The ribosome is the cell's protein-making factory, a huge protein-RNA complex, that is essential to life. Determining the high-resolution structures of the stable "core" of this factory was among the major breakthroughs of the past decades, and was awarded the Nobel Prize in 2009. Now that the mysteries of the ribosome appear to be more traceable, detailed understanding of the mechanisms that regulate protein synthesis includes not only the well-known steps of initiation, elongation, and termination but also the less comprehended features of the co-translational events associated with the maturation of the nascent chains. The ribosome is a platform for co-translational events affecting the nascent polypeptide, including protein modifications, folding, targeting to various cellular compartments for integration into membrane or translocation, and proteolysis. These events are orchestrated by ribosome-associated protein biogenesis factors (RPBs), a group of a dozen or more factors that act as the "welcoming committee" for the nascent chain as it emerges from the ribosome. In plants these factors have evolved to fit the specificity of different cellular compartments: cytoplasm, mitochondria and chloroplast. This review focuses on the current state of knowledge of these factors and their interaction around the exit tunnel of dedicated ribosomes. Particular attention has been accorded to the plant system, highlighting the similarities and differences with other organisms.
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Affiliation(s)
- Adina Breiman
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France; Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sonia Fieulaine
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Univ. Paris-Saclay 91198 Gif-sur-Yvette cedex, France.
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27
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Burkhart JM, Taskin AA, Zahedi RP, Vögtle FN. Quantitative Profiling for Substrates of the Mitochondrial Presequence Processing Protease Reveals a Set of Nonsubstrate Proteins Increased upon Proteotoxic Stress. J Proteome Res 2015; 14:4550-63. [PMID: 26446170 DOI: 10.1021/acs.jproteome.5b00327] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The majority of mitochondrial preproteins are targeted via N-terminal presequences that are cleaved upon import into the organelle. The essential mitochondrial processing protease (MPP) is assumed to cleave the majority of incoming precursors; however, only a small fraction of mitochondrial precursors have been experimentally analyzed limiting the information on MPP recognition and substrate specificity. Here we present the first systematic approach for identification of authentic MPP substrate proteins using a temperature-sensitive mutant of the MPP subunit Mas1. Inactivation of MPP at nonpermissive temperature leads to accumulation of immature precursors in mitochondria, which were measured by quantitative N-terminal ChaFRADIC. This led to the identification of 66 novel MPP substrates. Deduction of the cleaved presequences determines arginine in position -2 of the cleavage site as a main factor for MPP recognition. Interestingly, a set of nonprocessed proteins was also increased in mas1 mutant mitochondria. Additionally, mas1 mitochondria respond to temperature elevation with an increase in membrane potential and oxygen consumption. These changes might indicate that mas1 cells exert a response to balance the proteotoxic stress induced by MPP dysfunction.
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Affiliation(s)
- Julia M Burkhart
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Asli A Taskin
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg , Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- Faculty of Biology, Universität Freiburg , Schänzlestrasse 1, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, University of Freiburg , Albertstrasse 19A, 79104 Freiburg, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - F-Nora Vögtle
- Institut für Biochemie und Molekularbiologie, ZBMZ, Universität Freiburg , Stefan-Meier-Str. 17, 79104 Freiburg, Germany
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28
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Rowland E, Kim J, Bhuiyan NH, van Wijk KJ. The Arabidopsis Chloroplast Stromal N-Terminome: Complexities of Amino-Terminal Protein Maturation and Stability. PLANT PHYSIOLOGY 2015; 169:1881-96. [PMID: 26371235 PMCID: PMC4634096 DOI: 10.1104/pp.15.01214] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/14/2015] [Indexed: 05/10/2023]
Abstract
Protein amino (N) termini are prone to modifications and are major determinants of protein stability in bacteria, eukaryotes, and perhaps also in chloroplasts. Most chloroplast proteins undergo N-terminal maturation, but this is poorly understood due to insufficient experimental information. Consequently, N termini of mature chloroplast proteins cannot be accurately predicted. This motivated an extensive characterization of chloroplast protein N termini in Arabidopsis (Arabidopsis thaliana) using terminal amine isotopic labeling of substrates and mass spectrometry, generating nearly 14,000 tandem mass spectrometry spectra matching to protein N termini. Many nucleus-encoded plastid proteins accumulated with two or three different N termini; we evaluated the significance of these different proteoforms. Alanine, valine, threonine (often in N-α-acetylated form), and serine were by far the most observed N-terminal residues, even after normalization for their frequency in the plastid proteome, while other residues were absent or highly underrepresented. Plastid-encoded proteins showed a comparable distribution of N-terminal residues, but with a higher frequency of methionine. Infrequent residues (e.g. isoleucine, arginine, cysteine, proline, aspartate, and glutamate) were observed for several abundant proteins (e.g. heat shock proteins 70 and 90, Rubisco large subunit, and ferredoxin-glutamate synthase), likely reflecting functional regulation through their N termini. In contrast, the thylakoid lumenal proteome showed a wide diversity of N-terminal residues, including those typically associated with instability (aspartate, glutamate, leucine, and phenylalanine). We propose that, after cleavage of the chloroplast transit peptide by stromal processing peptidase, additional processing by unidentified peptidases occurs to avoid unstable or otherwise unfavorable N-terminal residues. The possibility of a chloroplast N-end rule is discussed.
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Affiliation(s)
- Elden Rowland
- Department of Plant Biology, Cornell University, Ithaca, New York 14850
| | - Jitae Kim
- Department of Plant Biology, Cornell University, Ithaca, New York 14850
| | - Nazmul H Bhuiyan
- Department of Plant Biology, Cornell University, Ithaca, New York 14850
| | - Klaas J van Wijk
- Department of Plant Biology, Cornell University, Ithaca, New York 14850
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29
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Muhseen ZT, Xiong Q, Chen Z, Ge F. Proteomics studies on stress responses in diatoms. Proteomics 2015; 15:3943-53. [PMID: 26364674 DOI: 10.1002/pmic.201500165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/09/2015] [Accepted: 09/09/2015] [Indexed: 01/09/2023]
Abstract
Diatoms are a highly diverse group of eukaryotic phytoplankton that are distributed throughout marine and freshwater environments and are believed to be responsible for approximately 40% of the total marine primary productivity. The ecological success of diatoms suggests that they have developed a range of strategies to cope with various biotic and abiotic stress factors. It is of great interest to understand the adaptive responses of diatoms to different stresses in the marine environment. Proteomic technologies have been applied to the adaptive responses of marine diatoms under different growth conditions in recent years such as nitrogen starvation, iron limitation and phosphorus deficiency. These studies have provided clues to elucidate the sophisticated sensing mechanisms that control their adaptive responses. Although only a very limited number of proteomic studies were conducted in diatoms, the obtained data have led to a better understanding of the biochemical processes that contribute to their ecological success. This review presents the current status of proteomic studies of diatom stress responses and discusses the novel developments and applications for the analysis of protein post-translational modification in diatoms. The potential future application of proteomics could contribute to a better understanding of the physiological mechanisms underlying diatom acclimation to a given stress and the acquisition of an enhanced diatom stress tolerance. Future challenges and research opportunities in the proteomics studies of diatoms are also discussed.
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Affiliation(s)
- Ziyad Tariq Muhseen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Zhuo Chen
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
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30
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The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
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31
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Köhler D, Montandon C, Hause G, Majovsky P, Kessler F, Baginsky S, Agne B. Characterization of chloroplast protein import without Tic56, a component of the 1-megadalton translocon at the inner envelope membrane of chloroplasts. PLANT PHYSIOLOGY 2015; 167:972-90. [PMID: 25588737 PMCID: PMC4348784 DOI: 10.1104/pp.114.255562] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 01/14/2015] [Indexed: 05/17/2023]
Abstract
We report on the characterization of Tic56, a unique component of the recently identified 1-MD translocon at the inner envelope membrane of chloroplasts (TIC) in Arabidopsis (Arabidopsis thaliana) comprising Tic20, Tic100, and Tic214. We isolated Tic56 by copurification with Tandem Affinity Purification-tagged Toc159 in the absence of precursor protein, indicating spontaneous and translocation-independent formation of the translocon at the outer envelope membrane of chloroplasts (TOC) and TIC supercomplexes. Tic56 mutant plants have an albino phenotype and are unable to grow without an external carbon source. Using specific enrichment of protein amino termini, we analyzed the tic56-1 and plastid protein import2 (toc159) mutants to assess the in vivo import capacity of plastids in mutants of an outer and inner envelope component of the anticipated TOC-TIC supercomplex. Inboth mutants, we observed processing of several import substrates belonging to various pathways. Our results suggest that despite the severe developmental defects, protein import into Tic56-deficient plastids is functional to a considerable degree, indicating the existence of alternative translocases at the inner envelope membrane.
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32
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Gruber A, Rocap G, Kroth PG, Armbrust EV, Mock T. Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:519-28. [PMID: 25438865 PMCID: PMC4329603 DOI: 10.1111/tpj.12734] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/19/2014] [Accepted: 11/26/2014] [Indexed: 05/19/2023]
Abstract
The plastids of ecologically and economically important algae from phyla such as stramenopiles, dinoflagellates and cryptophytes were acquired via a secondary endosymbiosis and are surrounded by three or four membranes. Nuclear-encoded plastid-localized proteins contain N-terminal bipartite targeting peptides with the conserved amino acid sequence motif 'ASAFAP'. Here we identify the plastid proteomes of two diatoms, Thalassiosira pseudonana and Phaeodactylum tricornutum, using a customized prediction tool (ASAFind) that identifies nuclear-encoded plastid proteins in algae with secondary plastids of the red lineage based on the output of SignalP and the identification of conserved 'ASAFAP' motifs and transit peptides. We tested ASAFind against a large reference dataset of diatom proteins with experimentally confirmed subcellular localization and found that the tool accurately identified plastid-localized proteins with both high sensitivity and high specificity. To identify nucleus-encoded plastid proteins of T. pseudonana and P. tricornutum we generated optimized sets of gene models for both whole genomes, to increase the percentage of full-length proteins compared with previous assembly model sets. ASAFind applied to these optimized sets revealed that about 8% of the proteins encoded in their nuclear genomes were predicted to be plastid localized and therefore represent the putative plastid proteomes of these algae.
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Affiliation(s)
- Ansgar Gruber
- Fachbereich Biologie, Universität KonstanzKonstanz, 78457, Germany
| | - Gabrielle Rocap
- School of Oceanography, Center for Environmental Genomics, University of WashingtonSeattle, WA, 98195, USA
| | - Peter G Kroth
- Fachbereich Biologie, Universität KonstanzKonstanz, 78457, Germany
| | - E Virginia Armbrust
- School of Oceanography, Center for Environmental Genomics, University of WashingtonSeattle, WA, 98195, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East AngliaNorwich Research Park, NR4 7TJ, Norwich, UK
- *
For correspondence (e-mail )
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33
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Köhler D, Dobritzsch D, Hoehenwarter W, Helm S, Steiner JM, Baginsky S. Identification of protein N-termini in Cyanophora paradoxa cyanelles: transit peptide composition and sequence determinants for precursor maturation. FRONTIERS IN PLANT SCIENCE 2015; 6:559. [PMID: 26257763 PMCID: PMC4510345 DOI: 10.3389/fpls.2015.00559] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 07/07/2015] [Indexed: 05/06/2023]
Abstract
Glaucophyta, rhodophyta, and chloroplastida represent the three main evolutionary lineages that diverged from a common ancestor after primary endosymbiosis. Comparative analyses between members of these three lineages are a rich source of information on ancestral plastid features. We analyzed the composition and the cleavage site of cyanelle transit peptides from the glaucophyte Cyanophora paradoxa by terminal amine labeling of substrates (TAILS), and compared their characteristics to those of representatives of the chloroplastida. Our data show that transit peptide architecture is similar between members of these two lineages. This entails a comparable modular structure, an overrepresentation of serine or alanine and similarities in the amino acid composition around the processing peptidase cleavage site. The most distinctive difference is the overrepresentation of phenylalanine in the N-terminal 1-10 amino acids of cyanelle transit peptides. A quantitative proteome analysis with periplasm-free cyanelles identified 42 out of 262 proteins without the N-terminal phenylalanine, suggesting that the requirement for phenylalanine in the N-terminal region is not absolute. Proteins in this set are on average of low abundance, suggesting that either alternative import pathways are operating specifically for low abundance proteins or that the gene model annotation is incorrect for proteins with fewer EST sequences. We discuss these two possibilities and provide examples for both interpretations.
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Affiliation(s)
- Daniel Köhler
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
| | - Dirk Dobritzsch
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
| | | | - Stefan Helm
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
| | - Jürgen M. Steiner
- Plant Physiology, Institute of Biology, Martin-Luther-University Halle-WittenbergHalle (Saale), Germany
| | - Sacha Baginsky
- Plant Biochemistry, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, BiozentrumHalle (Saale), Germany
- *Correspondence: Sacha Baginsky, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120 Halle (Saale), Germany
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34
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Sabir JSM, Yu M, Ashworth MP, Baeshen NA, Baeshen MN, Bahieldin A, Theriot EC, Jansen RK. Conserved gene order and expanded inverted repeats characterize plastid genomes of Thalassiosirales. PLoS One 2014; 9:e107854. [PMID: 25233465 PMCID: PMC4169464 DOI: 10.1371/journal.pone.0107854] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/14/2014] [Indexed: 12/28/2022] Open
Abstract
Diatoms are mostly photosynthetic eukaryotes within the heterokont lineage. Variable plastid genome sizes and extensive genome rearrangements have been observed across the diatom phylogeny, but little is known about plastid genome evolution within order- or family-level clades. The Thalassiosirales is one of the more comprehensively studied orders in terms of both genetics and morphology. Seven complete diatom plastid genomes are reported here including four Thalassiosirales: Thalassiosira weissflogii, Roundia cardiophora, Cyclotella sp. WC03_2, Cyclotella sp. L04_2, and three additional non-Thalassiosirales species Chaetoceros simplex, Cerataulina daemon, and Rhizosolenia imbricata. The sizes of the seven genomes vary from 116,459 to 129,498 bp, and their genomes are compact and lack introns. The larger size of the plastid genomes of Thalassiosirales compared to other diatoms is due primarily to expansion of the inverted repeat. Gene content within Thalassiosirales is more conserved compared to other diatom lineages. Gene order within Thalassiosirales is highly conserved except for the extensive genome rearrangement in Thalassiosira oceanica. Cyclotella nana, Thalassiosira weissflogii and Roundia cardiophora share an identical gene order, which is inferred to be the ancestral order for the Thalassiosirales, differing from that of the other two Cyclotella species by a single inversion. The genes ilvB and ilvH are missing in all six diatom plastid genomes except for Cerataulina daemon, suggesting an independent gain of these genes in this species. The acpP1 gene is missing in all Thalassiosirales, suggesting that its loss may be a synapomorphy for the order and this gene may have been functionally transferred to the nucleus. Three genes involved in photosynthesis, psaE, psaI, psaM, are missing in Rhizosolenia imbricata, which represents the first documented instance of the loss of photosynthetic genes in diatom plastid genomes.
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Affiliation(s)
- Jamal S. M. Sabir
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mengjie Yu
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
| | - Matt P. Ashworth
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Nabih A. Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad N. Baeshen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Edward C. Theriot
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Robert K. Jansen
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
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35
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Bland C, Hartmann EM, Christie-Oleza JA, Fernandez B, Armengaud J. N-Terminal-oriented proteogenomics of the marine bacterium roseobacter denitrificans Och114 using N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) labeling and diagonal chromatography. Mol Cell Proteomics 2014; 13:1369-81. [PMID: 24536027 DOI: 10.1074/mcp.o113.032854] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Given the ease of whole genome sequencing with next-generation sequencers, structural and functional gene annotation is now purely based on automated prediction. However, errors in gene structure are frequent, the correct determination of start codons being one of the main concerns. Here, we combine protein N termini derivatization using (N-Succinimidyloxycarbonylmethyl)tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP Ac-OSu) as a labeling reagent with the COmbined FRActional DIagonal Chromatography (COFRADIC) sorting method to enrich labeled N-terminal peptides for mass spectrometry detection. Protein digestion was performed in parallel with three proteases to obtain a reliable automatic validation of protein N termini. The analysis of these N-terminal enriched fractions by high-resolution tandem mass spectrometry allowed the annotation refinement of 534 proteins of the model marine bacterium Roseobacter denitrificans OCh114. This study is especially efficient regarding mass spectrometry analytical time. From the 534 validated N termini, 480 confirmed existing gene annotations, 41 highlighted erroneous start codon annotations, five revealed totally new mis-annotated genes; the mass spectrometry data also suggested the existence of multiple start sites for eight different genes, a result that challenges the current view of protein translation initiation. Finally, we identified several proteins for which classical genome homology-driven annotation was inconsistent, questioning the validity of automatic annotation pipelines and emphasizing the need for complementary proteomic data. All data have been deposited to the ProteomeXchange with identifier PXD000337.
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Affiliation(s)
- Céline Bland
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
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36
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Van Damme P, Støve SI, Glomnes N, Gevaert K, Arnesen T. A Saccharomyces cerevisiae model reveals in vivo functional impairment of the Ogden syndrome N-terminal acetyltransferase NAA10 Ser37Pro mutant. Mol Cell Proteomics 2014; 13:2031-41. [PMID: 24408909 DOI: 10.1074/mcp.m113.035402] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
N-terminal acetylation (Nt-acetylation) occurs on the majority of eukaryotic proteins and is catalyzed by N-terminal acetyltransferases (NATs). Nt-acetylation is increasingly recognized as a vital modification with functional implications ranging from protein degradation to protein localization. Although early genetic studies in yeast demonstrated that NAT-deletion strains displayed a variety of phenotypes, only recently, the first human genetic disorder caused by a mutation in a NAT gene was reported; boys diagnosed with the X-linked Ogden syndrome harbor a p.Ser37Pro (S37P) mutation in the gene encoding Naa10, the catalytic subunit of the NatA complex, and suffer from global developmental delays and lethality during infancy. Here, we describe a Saccharomyces cerevisiae model developed by introducing the human wild-type or mutant NatA complex into yeast lacking NatA (NatA-Δ). The wild-type human NatA complex phenotypically complemented the NatA-Δ strain, whereas only a partial rescue was observed for the Ogden mutant NatA complex suggesting that hNaa10 S37P is only partially functional in vivo. Immunoprecipitation experiments revealed a reduced subunit complexation for the mutant hNatA S37P next to a reduced in vitro catalytic activity. We performed quantitative Nt-acetylome analyses on a control yeast strain (yNatA), a yeast NatA deletion strain (yNatA-Δ), a yeast NatA deletion strain expressing wild-type human NatA (hNatA), and a yeast NatA deletion strain expressing mutant human NatA (hNatA S37P). Interestingly, a generally reduced degree of Nt-acetylation was observed among a large group of NatA substrates in the yeast expressing mutant hNatA as compared with yeast expressing wild-type hNatA. Combined, these data provide strong support for the functional impairment of hNaa10 S37P in vivo and suggest that reduced Nt-acetylation of one or more target substrates contributes to the pathogenesis of the Ogden syndrome. Comparative analysis between human and yeast NatA also provided new insights into the co-evolution of the NatA complexes and their substrates. For instance, (Met-)Ala- N termini are more prevalent in the human proteome as compared with the yeast proteome, and hNatA displays a preference toward these N termini as compared with yNatA.
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Affiliation(s)
- Petra Van Damme
- From the ‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium;
| | - Svein I Støve
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; **Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Nina Glomnes
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; ‖Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway; and
| | - Kris Gevaert
- From the ‡Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; §Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Thomas Arnesen
- ¶Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; **Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
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