1
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Fréville A, Ressurreição M, van Ooij C. Identification of a non-exported Plasmepsin V substrate that functions in the parasitophorous vacuole of malaria parasites. mBio 2024; 15:e0122323. [PMID: 38078758 PMCID: PMC10790765 DOI: 10.1128/mbio.01223-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/26/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE In the manuscript, the authors investigate the role of the protease Plasmepsin V in the parasite-host interaction. Whereas processing by Plasmepsin V was previously thought to target a protein for export into the host cell, the authors now show that there are proteins cleaved by this protease that are not exported but instead function at the host-parasite interface. This changes the view of this protease, which turns out to have a much broader role than anticipated. The result shows that the protease may have a function much more similar to that of related organisms. The authors also investigate the requirements for protein export by analyzing exported and non-exported proteins and find commonalities between the proteins of each set that further our understanding of the requirements for protein export.
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Affiliation(s)
- Aline Fréville
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Margarida Ressurreição
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Christiaan van Ooij
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
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2
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Chloroplasts evolved an additional layer of translational regulation based on non-AUG start codons for proteins with different turnover rates. Sci Rep 2023; 13:896. [PMID: 36650197 PMCID: PMC9845219 DOI: 10.1038/s41598-022-27347-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
Chloroplasts have evolved from photosynthetic cyanobacteria-like progenitors through endosymbiosis. The chloroplasts of present-day land plants have their own transcription and translation systems that show several similarities with prokaryotic organisms. A remarkable feature of the chloroplast translation system is the use of non-AUG start codons in the protein synthesis of certain genes that are evolutionarily conserved from Algae to angiosperms. However, the biological significance of such use of non-AUG codons is not fully understood. The present study was undertaken to unravel the significance of non-AUG start codons in vivo using the chloroplast genetic engineering approach. For this purpose, stable transplastomic tobacco plants expressing a reporter gene i.e. uidA (GUS) under four different start codons (AUG/UUG/GUG/CUG) were generated and β-glucuronidase (GUS) expression was compared. To investigate further the role of promoter sequences proximal to the start codon, uidA was expressed under two different chloroplast gene promoters psbA and psbC that use AUG and a non-AUG (GUG) start codons, respectively, and also showed significant differences in the DNA sequence surrounding the start codon. Further, to delineate the role of RNA editing that creates AUG start codon by editing non-AUG codons, if any, which is another important feature of the chloroplast transcription and translation system, transcripts were sequenced. In addition, a proteomic approach was used to identify the translation initiation site(s) of GUS and the N-terminal amino acid encoded when expressed under different non-AUG start codons. The results showed that chloroplasts use non-AUG start codons in combination with the translation initiation site as an additional layer of gene regulation to over-express proteins that are required at high levels due to their high rates of turnover.
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3
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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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4
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Ahlqvist J, Linares-Pastén JA, Håkansson M, Jasilionis A, Kwiatkowska-Semrau K, Friðjónsson ÓH, Kaczorowska AK, Dabrowski S, Ævarsson A, Hreggviðsson GÓ, Al-Karadaghi S, Kaczorowski T, Nordberg Karlsson E. Crystal structure and initial characterization of a novel archaeal-like Holliday junction-resolving enzyme from Thermus thermophilus phage Tth15-6. Acta Crystallogr D Struct Biol 2022; 78:212-227. [PMID: 35102887 PMCID: PMC8805305 DOI: 10.1107/s2059798321012298] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
This study describes the production, characterization and structure determination of a novel Holliday junction-resolving enzyme. The enzyme, termed Hjc_15-6, is encoded in the genome of phage Tth15-6, which infects Thermus thermophilus. Hjc_15-6 was heterologously produced in Escherichia coli and high yields of soluble and biologically active recombinant enzyme were obtained in both complex and defined media. Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA–Holliday junctions (Hjs). The crystal structure of Hjc_15-6 was determined to 2.5 Å resolution using the selenomethionine single-wavelength anomalous dispersion method. To our knowledge, this is the first crystal structure of an Hj-resolving enzyme originating from a bacteriophage that can be classified as an archaeal type of Hj-resolving enzyme. As such, it represents a new fold for Hj-resolving enzymes from phages. Characterization of the structure of Hjc_15-6 suggests that it may form a dimer, or even a homodimer of dimers, and activity studies show endonuclease activity towards Hjs. Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E–SD–EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages.
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5
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Ahrens CH, Wade JT, Champion MM, Langer JD. A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry. J Bacteriol 2022; 204:e0035321. [PMID: 34748388 PMCID: PMC8765459 DOI: 10.1128/jb.00353-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms. Mass spectrometry (MS) has great potential for the discovery, validation, and functional characterization of small proteins. However, standard MS approaches are poorly suited to the identification of both known and novel small proteins due to limitations at each step of a typical proteomics workflow, i.e., sample preparation, protease digestion, liquid chromatography, MS data acquisition, and data analysis. Here, we outline the major MS-based workflows and bioinformatic pipelines used for small protein discovery and validation. Special emphasis is placed on highlighting the adjustments required to improve detection and data quality for small proteins. We discuss both the unbiased detection of small proteins and the targeted analysis of small proteins of interest. Finally, we provide guidelines to prioritize novel small proteins, and an outlook on methods with particular potential to further improve comprehensive discovery and characterization of small proteins.
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Affiliation(s)
- Christian H. Ahrens
- Agroscope, Method Development and Analytics & SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Joseph T. Wade
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, USA
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Julian D. Langer
- Mass Spectrometry and Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Proteomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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6
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Parks AR, Escalante-Semerena JC. Protein N-terminal acylation: An emerging field in bacterial cell physiology. CURRENT TRENDS IN MICROBIOLOGY 2022; 16:1-18. [PMID: 37009250 PMCID: PMC10062008 DOI: 10.31300/ctmb.16.2022.1-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
N-terminal (Nt)-acylation is the irreversible addition of an acyl moiety to the terminal alpha amino group of a peptide chain. This type of modification alters the nature of the N terminus, which can interfere with the function of the modified protein by disrupting protein interactions, function, localization, degradation, hydrophobicity, or charge. Nt acylation is found in all domains of life and is a highly common occurrence in eukaryotic cells. However, in prokaryotes very few cases of Nt acylation have been reported. It was once thought that Nt acylation of proteins, other than ribosomal proteins, was uncommon in prokaryotes, but recent evidence suggests that this modification may be more common than once realized. In this review, we discuss what is known about prokaryotic Nt acetylation and the acetyltransferases that are responsible, as well as recent advancements in this field and currently used methods to study Nt acetylation.
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Affiliation(s)
- Anastacia R. Parks
- Department of Microbiology, University of Georgia, Athens, GA 30606, USA
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7
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Chen P, Paschoal Sobreira TJ, Hall MC, Hazbun TR. Discovering the N-Terminal Methylome by Repurposing of Proteomic Datasets. J Proteome Res 2021; 20:4231-4247. [PMID: 34382793 DOI: 10.1021/acs.jproteome.1c00009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein α-N-methylation is an underexplored post-translational modification involving the covalent addition of methyl groups to the free α-amino group at protein N-termini. To systematically explore the extent of α-N-terminal methylation in yeast and humans, we reanalyzed publicly accessible proteomic datasets to identify N-terminal peptides contributing to the α-N-terminal methylome. This repurposing approach found evidence of α-N-methylation of established and novel protein substrates with canonical N-terminal motifs of established α-N-terminal methyltransferases, including human NTMT1/2 and yeast Tae1. NTMT1/2 are implicated in cancer and aging processes but have unclear and context-dependent roles. Moreover, α-N-methylation of noncanonical sequences was surprisingly prevalent, suggesting unappreciated and cryptic methylation events. Analysis of the amino acid frequencies of α-N-methylated peptides revealed a [S]1-[S/A/Q]2 pattern in yeast and [A/N/G]1-[A/S/V]2-[A/G]3 in humans, which differs from the canonical motif. We delineated the distribution of the two types of prevalent N-terminal modifications, acetylation and methylation, on amino acids at the first position. We tested three potentially methylated proteins and confirmed the α-N-terminal methylation of Hsp31 by additional proteomic analysis and immunoblotting. The other two proteins, Vma1 and Ssa3, were found to be predominantly acetylated, indicating that proteomic searching for α-N-terminal methylation requires careful consideration of mass spectra. This study demonstrates the feasibility of reprocessing proteomic data for global α-N-terminal methylome investigations.
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Affiliation(s)
- Panyue Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | | | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tony R Hazbun
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States.,Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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8
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Abstract
KRAS is one of the most commonly mutated oncogene and a negative predictive factor for a number of targeted therapies. Therefore, the development of targeting strategies against mutant KRAS is urgently needed. One potential strategy involves disruption of K-Ras membrane localization, which is necessary for its proper function. In this review, we summarize the current data about the importance of membrane-anchorage of K-Ras and provide a critical evaluation of this targeting paradigm focusing mainly on prenylation inhibition. Additionally, we performed a RAS mutation-specific analysis of prenylation-related drug sensitivity data from a publicly available database (https://depmap.org/repurposing/) of three classes of prenylation inhibitors: statins, N-bisphosphonates, and farnesyl-transferase inhibitors. We observed significant differences in sensitivity to N-bisphosphonates and farnesyl-transferase inhibitors depending on KRAS mutational status and tissue of origin. These observations emphasize the importance of factors affecting efficacy of prenylation inhibition, like distinct features of different KRAS mutations, tissue-specific mutational patterns, K-Ras turnover, and changes in regulation of prenylation process. Finally, we enlist the factors that might be responsible for the large discrepancy between the outcomes in preclinical and clinical studies including methodological pitfalls, the incomplete understanding of K-Ras protein turnover, and the variation of KRAS dependency in KRAS mutant tumors.
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9
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Wang YY, Zhang J, Liu XM, Li Y, Sui J, Dong MQ, Ye K, Du LL. Molecular and structural mechanisms of ZZ domain-mediated cargo selection by Nbr1. EMBO J 2021; 40:e107497. [PMID: 34169534 DOI: 10.15252/embj.2020107497] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/17/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast Schizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.
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Affiliation(s)
- Ying-Ying Wang
- College of Life Sciences, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Jianxiu Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, Beijing, China
| | - Yulu Li
- National Institute of Biological Sciences, Beijing, China
| | - Jianhua Sui
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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10
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Collier MP, Moreira KB, Li KH, Chen YC, Itzhak D, Samant R, Leitner A, Burlingame A, Frydman J. Native mass spectrometry analyses of chaperonin complex TRiC/CCT reveal subunit N-terminal processing and re-association patterns. Sci Rep 2021; 11:13084. [PMID: 34158536 PMCID: PMC8219831 DOI: 10.1038/s41598-021-91086-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/05/2021] [Indexed: 11/14/2022] Open
Abstract
The eukaryotic chaperonin TRiC/CCT is a large ATP-dependent complex essential for cellular protein folding. Its subunit arrangement into two stacked eight-membered hetero-oligomeric rings is conserved from yeast to man. A recent breakthrough enables production of functional human TRiC (hTRiC) from insect cells. Here, we apply a suite of mass spectrometry techniques to characterize recombinant hTRiC. We find all subunits CCT1-8 are N-terminally processed by combinations of methionine excision and acetylation observed in native human TRiC. Dissociation by organic solvents yields primarily monomeric subunits with a small population of CCT dimers. Notably, some dimers feature non-canonical inter-subunit contacts absent in the initial hTRiC. This indicates individual CCT monomers can promiscuously re-assemble into dimers, and lack the information to assume the specific interface pairings in the holocomplex. CCT5 is consistently the most stable subunit and engages in the greatest number of non-canonical dimer pairings. These findings confirm physiologically relevant post-translational processing and function of recombinant hTRiC and offer quantitative insight into the relative stabilities of TRiC subunits and interfaces, a key step toward reconstructing its assembly mechanism. Our results also highlight the importance of assigning contacts identified by native mass spectrometry after solution dissociation as canonical or non-canonical when investigating multimeric assemblies.
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Affiliation(s)
| | | | - Kathy H Li
- Department of Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Yu-Chan Chen
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Rahul Samant
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Alma Burlingame
- Department of Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA.
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11
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Production and Membrane Binding of N-Terminally Acetylated, C-Terminally Farnesylated and Carboxymethylated KRAS4b. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:105-116. [PMID: 33977473 DOI: 10.1007/978-1-0716-1190-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recombinant mammalian proteins are routinely produced in E. coli and thus lack post-translational modifications. KRAS4b is processed at both the N- and C-terminus, resulting in an acetylation of the N-terminus (at Thr, after aminopeptidase removal of the original N-term Met) and farnesylation/carboxymethylation of the C-terminal Cys (after proteolytic cleavage of the original C-terminal three amino acids, Val-Iso-Met). Processing of KRAS enables it to associate with the plasma membrane and fulfill its function in cell signaling. We describe here the production of recombinant KRAS4b from our modified baculovirus/insect cell expression system that accurately incorporates these in vivo modifications to allow experiments that anchor KRAS4b to membrane mimetics (e.g., nanodiscs and liposomes).
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12
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Tian F, Shi J, Li Y, Gao H, Chang L, Zhang Y, Gao L, Xu P, Tang S. Proteogenomics Study of Blastobotrys adeninivorans TMCC 70007-A Dominant Yeast in the Fermentation Process of Pu-erh Tea. J Proteome Res 2021; 20:3290-3304. [PMID: 34008989 DOI: 10.1021/acs.jproteome.1c00205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Blastobotrys adeninivorans plays an essential role in pile-fermenting of Pu-erh tea. Its ability to assimilate various carbon and nitrogen sources makes it available for application in a wide range of industry sectors. The genome of B. adeninivorans TMCC 70007 isolated from pile-fermented Pu-erh tea was sequenced and assembled. Proteomics analysis indicated that 4900 proteins in TMCC 70007 were expressed under various culture conditions. Proteogenomics mapping revealed 48 previously unknown genes and corrected 118 gene models predicted by GeneMark-ES. Ortho-proteogenomics analysis identified 17 previously unidentified genes in B. adeninivorans LS3, the first strain with a sequenced genome among the genus Blastobotrys as well. More importantly, five species specific genes were identified from TMCC 70007, which could serve as a barcode for strain typing and were applicable for fermentation process protection of this industrial species. The datasets generated from tea aqueous extract culture not only increased the proteome coverage and accuracy but also contributed to the identification of proteins related to polyphenols and caffeine, which were considered to change greatly during the microbial fermentation of Pu-erh tea. This study provides a proteome perspective on TMCC 70007, which was considered to be an important strain in the production of Pu-erh tea. The systematic proteogenomics analysis not only made a better annotation on the genome of B. adeninivorans TMCC 70007 as previous proteogenomics study but also provided solution for fermentation process protection on valuable industrial species with species specific genes uniquely identified from proteogenomics study.
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Affiliation(s)
- Fei Tian
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jiahui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.,Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Huiying Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Linrui Gao
- Yunnan Pu-erh Tea Fermentation Engineering Research Center, Yunnan TAETEA Microbial Technology Co., Ltd., Kunming 650217, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Research Unit of Proteomics & Research and Development of New Drug, Chinese Academy of Medical Sciences, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China.,Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding 071002, China
| | - Shukun Tang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming 650091, China.,Yunnan Pu-erh Tea Fermentation Engineering Research Center, Yunnan TAETEA Microbial Technology Co., Ltd., Kunming 650217, China
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13
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Supekar NT, Shajahan A, Gleinich AS, Rouhani DS, Heiss C, Chapla DG, Moremen KW, Azadi P. Variable post-translational modifications of SARS-CoV-2 nucleocapsid protein. Glycobiology 2021; 31:1080-1092. [PMID: 33997890 PMCID: PMC8241430 DOI: 10.1093/glycob/cwab044] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/19/2021] [Accepted: 04/30/2021] [Indexed: 12/27/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), started in 2019 in China and quickly spread into a global pandemic. Nucleocapsid protein (N protein) is highly conserved and is the most abundant protein in coronaviruses and is thus a potential target for both vaccine and point-of-care diagnostics. N Protein has been suggested in the literature as having posttranslational modifications (PTMs), and accurately defining these PTMs is critical for its potential use in medicine. Reports of phosphorylation of N protein have failed to provide detailed site-specific information. We have performed comprehensive glycomics, glycoproteomics and proteomics experiments on two different N protein preparations. Both were expressed in HEK293 cells; one was in-house expressed and purified without a signal peptide (SP) sequence, and the other was commercially produced with a SP channeling it through the secretory pathway. Our results show completely different PTMs on the two N protein preparations. The commercial product contained extensive N- and O-linked glycosylation as well as O-phosphorylation on site Thr393. Conversely, the native N Protein model had O-phosphorylation at Ser176 and no glycosylation, highlighting the importance of knowing the provenance of any commercial protein to be used for scientific or clinical studies. Recent studies have indicated that N protein can serve as an important diagnostic marker for COVID-19 and as a major immunogen by priming protective immune responses. Thus, detailed structural characterization of N protein may provide useful insights for understanding the roles of PTMs on viral pathogenesis, vaccine design and development of point-of-care diagnostics.
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Affiliation(s)
- Nitin T Supekar
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602
| | - Asif Shajahan
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602
| | - Anne S Gleinich
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602
| | - Daniel S Rouhani
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602
| | - Christian Heiss
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602
| | | | - Kelley W Moremen
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, The University of Georgia, Athens, GA 30602
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14
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Nymark M, Grønbech Hafskjold MC, Volpe C, Fonseca DDM, Sharma A, Tsirvouli E, Serif M, Winge P, Finazzi G, Bones AM. Functional studies of CpSRP54 in diatoms show that the mechanism of thylakoid protein insertion differs from that in plants and green algae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:113-132. [PMID: 33372269 DOI: 10.1111/tpj.15149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
The chloroplast signal recognition particle 54 kDa (CpSRP54) protein is a member of the CpSRP pathway known to target proteins to thylakoid membranes in plants and green algae. Loss of CpSRP54 in the marine diatom Phaeodactylum tricornutum lowers the accumulation of a selection of chloroplast-encoded subunits of photosynthetic complexes, indicating a role in the co-translational part of the CpSRP pathway. In contrast to plants and green algae, absence of CpSRP54 does not have a negative effect on the content of light-harvesting antenna complex proteins and pigments in P. tricornutum, indicating that the diatom CpSRP54 protein has not evolved to function in the post-translational part of the CpSRP pathway. Cpsrp54 KO mutants display altered photophysiological responses, with a stronger induction of photoprotective mechanisms and lower growth rates compared to wild type when exposed to increased light intensities. Nonetheless, their phenotype is relatively mild, thanks to the activation of mechanisms alleviating the loss of CpSRP54, involving upregulation of chaperones. We conclude that plants, green algae, and diatoms have evolved differences in the pathways for co-translational and post-translational insertion of proteins into the thylakoid membranes.
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Affiliation(s)
- Marianne Nymark
- Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Marthe Caroline Grønbech Hafskjold
- Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Charlotte Volpe
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Davi de Miranda Fonseca
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, N-7491, Norway
- Proteomics and Modomics Experimental Core Facility (PROMEC), NTNU and Central Administration, St Olavs Hospital, The University Hospital in Trondheim, Trondheim, Norway
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, N-7491, Norway
- Proteomics and Modomics Experimental Core Facility (PROMEC), NTNU and Central Administration, St Olavs Hospital, The University Hospital in Trondheim, Trondheim, Norway
| | - Eirini Tsirvouli
- Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Manuel Serif
- Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Per Winge
- Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Giovanni Finazzi
- Université Grenoble Alpes (UGA), Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Interdisciplinary Research Institute of Grenoble (IRIG), CEA-Grenoble, Grenoble, 38000, France
| | - Atle Magnar Bones
- Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
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15
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Alpha-Bazin B, Gorlas A, Lagorce A, Joulié D, Boyer JB, Dutertre M, Gaillard JC, Lopes A, Zivanovic Y, Dedieu A, Confalonieri F, Armengaud J. Lysine-specific acetylated proteome from the archaeon Thermococcus gammatolerans reveals the presence of acetylated histones. J Proteomics 2020; 232:104044. [PMID: 33161166 DOI: 10.1016/j.jprot.2020.104044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 11/20/2022]
Abstract
Thermococcus gammatolerans EJ3 is an extremophile archaeon which was revealed as one of the most radioresistant organisms known on Earth, withstanding up to 30 kGy gamma-ray radiations. While its theoretical proteome is rather small, T. gammatolerans may enhance its toolbox by post-translational modification of its proteins. Here, we explored its extent of Nε-acetylation of lysines. For this, we immunopurified with two acetylated-lysine antibodies the acetylated peptides resulting from a proteolysis of soluble proteins with trypsin. The comparison of acetylated proteomes of two archaea highlights some common acetylation patterns but only 4 out of 26 orthologous proteins found to be acetylated in both species, are acetylated on the same lysine site. We evidenced that histone B is acetylated in T. gammatolerans at least at two different sites (K27 and K36), and a peptide common at the C-terminus of histones A and B is also acetylated. We verified that acetylation of histones is a common trait among Thermococcales after recording data on Thermococcus kodakaraensis histones and identifying three acetylated sites. This discovery reinforces the strong evolutionary link between Archaea and Eukaryotes and should be an incentive for further investigation on the extent and role of acetylation of histones in Archaea. SIGNIFICANCE: Acetylation is an important post-translational modification of proteins that has been extensively described in Eukaryotes, and more recently in Bacteria. Here, we report for the first time ever that histones in Archaea are also modified by acetylation after a systematic survey of acetylated peptides in Thermococcus gammatolerans. Structural models of histones A and B indicates that acetylation of the identified modified residues may play an important role in histone assembly and/or interaction with DNA. The in-depth protein acetylome landscape in T. gammatolerans includes at least 181 unique protein sequences, some of them being modified on numerous residues. Proteins involved in metabolic processes, information storage and processing mechanisms are over-represented categories in this dataset, highlighting the ancient role of this protein post-translational modification in primitive cells.
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Affiliation(s)
- Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Aurore Gorlas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Arnaud Lagorce
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan, Via Domitia, Perpignan, France
| | - Damien Joulié
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Murielle Dutertre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Anne Lopes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Yvan Zivanovic
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Alain Dedieu
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Fabrice Confalonieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France.
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16
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Choong WK, Wang JH, Sung TY. MinProtMaxVP: Generating a minimized number of protein variant sequences containing all possible variant peptides for proteogenomic analysis. J Proteomics 2020; 223:103819. [PMID: 32407886 DOI: 10.1016/j.jprot.2020.103819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 12/12/2022]
Abstract
Identifying single-amino-acid variants (SAVs) from mass spectrometry-based experiments is critical for validating single-nucleotide variants (SNVs) at the protein level to facilitate biomedical research. Currently, two approaches are usually applied to convert SNV annotations into SAV-harboring protein sequences. One approach generates one sequence containing exactly one SAV, and the other all SAVs. However, they may neglect the possibility of SAV combinations, e.g., haplotypes, existing in bio-samples. Therefore, it is necessary to consider all SAV combinations of a protein when generating SAV-harboring protein sequences. In this paper, we propose MinProtMaxVP, a novel approach which selects a minimized number of SAV-harboring protein sequences generated from the exhaustive approach, while still accommodating all possible variant peptides, by solving a classic set covering problem. Our study on known haplotype variations of TAS2R38 justifies the necessity for MinProtMaxVP to consider all combinations of SAVs. The performance of MinProtMaxVP is demonstrated by an in silico study on OR2T27 with five SAVs and real experimental data of the HEK293 cell line. Furthermore, assuming simulated somatic and germline variants of OR2T27 in tumor and normal tissues demonstrates that when adopting the appropriate somatic and germline SAV integration strategy, MinProtMaxVP is adaptable to labeling and label-free mass spectrometry-based experiments. SIGNIFICANCE: We present MinProtMaxVP, a novel approach to generate SAV-harboring protein sequences for constructing a customized protein sequence database, which is used in database searching for variant peptide identification. This approach outperforms the existing approaches in generating all possible variant peptides to be included in protein sequences and possibly leading to identification of more variant peptides in proteogenomic analysis.
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Affiliation(s)
- Wai-Kok Choong
- Institute of Information Science, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Jen-Hung Wang
- Institute of Information Science, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica, Nankang, Taipei 11529, Taiwan.
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17
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Li Z, Dogra V, Lee KP, Li R, Li M, Li M, Kim C. N-Terminal Acetylation Stabilizes SIGMA FACTOR BINDING PROTEIN1 Involved in Salicylic Acid-Primed Cell Death. PLANT PHYSIOLOGY 2020; 183:358-370. [PMID: 32139475 PMCID: PMC7210619 DOI: 10.1104/pp.19.01417] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/24/2020] [Indexed: 05/14/2023]
Abstract
N-terminal (Nt) acetylation (NTA) is an ample and irreversible cotranslational protein modification catalyzed by ribosome-associated Nt-acetyltransferases. NTA on specific proteins can act as a degradation signal (called an Ac/N-degron) for proteolysis in yeast and mammals. However, in plants, the biological relevance of NTA remains largely unexplored. In this study, we reveal that Arabidopsis (Arabidopsis thaliana) SIGMA FACTOR-BINDING PROTEIN1 (SIB1), a transcription coregulator and a positive regulator of salicylic acid-primed cell death, undergoes an absolute NTA on the initiator Met; Nt-acetyltransferase B (NatB) partly contributes to this modification. While NTA results in destabilization of certain target proteins, our genetic and biochemical analyses revealed that plant NatB-involved NTA instead renders SIB1 more stable. Given that the ubiquitin/proteasome system stimulates SIB1 degradation, it seems that the NTA-conferred stability ensures the timely expression of SIB1-dependent genes, mostly related to immune responses. Taking our findings together, here we report a noncanonical NTA-driven protein stabilization in land plants.
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Affiliation(s)
- Zihao Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Vivek Dogra
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Keun Pyo Lee
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Rongxia Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mingyue Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Mengping Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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18
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Cao J, Wang T, Wang Q, Zheng X, Huang L. Functional Insights Into Protein Acetylation in the Hyperthermophilic Archaeon Sulfolobus islandicus. Mol Cell Proteomics 2019; 18:1572-1587. [PMID: 31182439 PMCID: PMC6683002 DOI: 10.1074/mcp.ra119.001312] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/02/2019] [Indexed: 01/03/2023] Open
Abstract
Proteins undergo acetylation at the Nε-amino group of lysine residues and the Nα-amino group of the N terminus in Archaea as in Bacteria and Eukarya. However, the extent, pattern and roles of the modifications in Archaea remain poorly understood. Here we report the proteomic analyses of a wild-type Sulfolobus islandicus strain and its mutant derivative strains lacking either a homolog of the protein acetyltransferase Pat (ΔSisPat) or a homolog of the Nt-acetyltransferase Ard1 (ΔSisArd1). A total of 1708 Nε-acetylated lysine residues in 684 proteins (26% of the total proteins), and 158 Nt-acetylated proteins (44% of the identified proteins) were found in S. islandicus ΔSisArd1 grew more slowly than the parental strain, whereas ΔSisPat showed no significant growth defects. Only 24 out of the 1503 quantifiable Nε-acetylated lysine residues were differentially acetylated, and all but one of the 24 residues were less acetylated by >1.3 fold in ΔSisPat than in the parental strain, indicating the narrow substrate specificity of the enzyme. Six acyl-CoA synthetases were the preferred substrates of SisPat in vivo, suggesting that Nε-acetylation by the acetyltransferase is involved in maintaining metabolic balance in the cell. Acetylation of acyl-CoA synthetases by SisPat occurred at a sequence motif conserved among all three domains of life. On the other hand, 92% of the acetylated N termini identified were acetylated by SisArd1 in the cell. The enzyme exhibited broad substrate specificity and could modify nearly all types of the target N termini of human NatA-NatF. The deletion of the SisArd1 gene altered the cellular levels of 18% of the quantifiable proteins (1518) by >1.5 fold. Consistent with the growth phenotype of ΔSisArd1, the cellular levels of proteins involved in cell division and cell cycle control, DNA replication, and purine synthesis were significantly lowered in the mutant than those in the parental strain.
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Affiliation(s)
- Jingjing Cao
- ‡State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China; §College of Life Science, University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Tongkun Wang
- ‡State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China; §College of Life Science, University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qian Wang
- ¶Core Facility of Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China
| | - Xiaowei Zheng
- ‡State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China; §College of Life Science, University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Li Huang
- ‡State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, P. R. China; §College of Life Science, University of Chinese Academy of Sciences, Beijing, P. R. China.
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19
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Dharmaiah S, Tran TH, Messing S, Agamasu C, Gillette WK, Yan W, Waybright T, Alexander P, Esposito D, Nissley DV, McCormick F, Stephen AG, Simanshu DK. Structures of N-terminally processed KRAS provide insight into the role of N-acetylation. Sci Rep 2019; 9:10512. [PMID: 31324887 PMCID: PMC6642148 DOI: 10.1038/s41598-019-46846-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 07/04/2019] [Indexed: 01/19/2023] Open
Abstract
Although post-translational modification of the C-terminus of RAS has been studied extensively, little is known about N-terminal processing. Mass spectrometric characterization of KRAS expressed in mammalian cells showed cleavage of the initiator methionine (iMet) and N-acetylation of the nascent N-terminus. Interestingly, structural studies on GDP- and GMPPNP-bound KRAS lacking the iMet and N-acetylation resulted in Mg2+-free structures of KRAS with flexible N-termini. In the Mg2+-free KRAS-GDP structure, the flexible N-terminus causes conformational changes in the interswitch region resulting in a fully open conformation of switch I. In the Mg2+-free KRAS-GMPPNP structure, the flexible N-terminus causes conformational changes around residue A59 resulting in the loss of Mg2+ and switch I in the inactive state 1 conformation. Structural studies on N-acetylated KRAS-GDP lacking the iMet revealed the presence of Mg2+ and a conformation of switch regions also observed in the structure of GDP-bound unprocessed KRAS with the iMet. In the absence of the iMet, the N-acetyl group interacts with the central beta-sheet and stabilizes the N-terminus and the switch regions. These results suggest there is crosstalk between the N-terminus and the Mg2+ binding site, and that N-acetylation plays an important role by stabilizing the N-terminus of RAS upon excision of the iMet.
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Affiliation(s)
- Srisathiyanarayanan Dharmaiah
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Timothy H Tran
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Simon Messing
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Constance Agamasu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - William K Gillette
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Wupeng Yan
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Timothy Waybright
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Patrick Alexander
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Dominic Esposito
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Dwight V Nissley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
- Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Andrew G Stephen
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA.
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20
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Formylated N-terminal methionine is absent from the Mycoplasma hyopneumoniae proteome: Implications for translation initiation. Int J Med Microbiol 2019; 309:288-298. [PMID: 31126750 DOI: 10.1016/j.ijmm.2019.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/28/2019] [Accepted: 03/17/2019] [Indexed: 12/31/2022] Open
Abstract
N-terminal methionine excision (NME) is a proteolytic pathway that cleaves the N-termini of proteins, a process that influences where proteins localise in the cell and their turnover rates. In bacteria, protein biosynthesis is initiated by formylated methionine start tRNA (fMet-tRNAfMet). The formyl group is attached by formyltransferase (FMT) and is subsequently removed by peptide deformylase (PDF) in most but not all proteins. Methionine aminopeptidase then cleaves deformylated methionine to complete the process. Components of NME, particularly PDF, are promising therapeutic targets for bacterial pathogens. In Mycoplasma hyopneumoniae, a genome-reduced, major respiratory pathogen of swine, pdf and fmt are absent from its genome. Our bioinformatic analysis uncovered additional enzymes involved in formylated N-terminal methionine (fnMet) processing missing in fourteen mycoplasma species, including M. hyopneumoniae but not in Mycoplasma pneumoniae, a major respiratory pathogen of humans. Consistent with our bioinformatic studies, an analysis of in-house tryptic peptide libraries confirmed the absence of fnMet in M. hyopneumoniae proteins but, as expected fnMet peptides were detected in the proteome of M. pneumoniae. Additionally, computational molecular modelling of M. hyopneumoniae translation initiation factors reveal structural and sequence differences in areas known to interact with fMet-tRNAfMet. Our data suggests that some mycoplasmas have evolved a translation process that does not require fnMet.
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21
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Dissmeyer N. Conditional Protein Function via N-Degron Pathway-Mediated Proteostasis in Stress Physiology. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:83-117. [PMID: 30892918 DOI: 10.1146/annurev-arplant-050718-095937] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The N-degron pathway, formerly the N-end rule pathway, regulates functions of regulatory proteins. It impacts protein half-life and therefore directs the actual presence of target proteins in the cell. The current concept holds that the N-degron pathway depends on the identity of the amino (N)-terminal amino acid and many other factors, such as the follow-up sequence at the N terminus, conformation, flexibility, and protein localization. It is evolutionarily conserved throughout the kingdoms. One possible entry point for substrates of the N-degron pathway is oxidation of N-terminal Cys residues. Oxidation of N-terminal Cys is decisive for further enzymatic modification of various neo-N termini by arginylation that generates potentially neofunctionalized or instable proteoforms. Here, I focus on the posttranslational modifications that are encompassed by protein degradation via the Cys/Arg branch of the N-degron pathway-part of the PROTEOLYSIS 6 (PRT6)/N-degron pathway-as well as the underlying physiological principles of this branch and its biological significance in stress response.
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Affiliation(s)
- Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB) and ScienceCampus Halle-Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany; ; Twitter: @NDissmeyer
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22
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Nguyen KT, Kim JM, Park SE, Hwang CS. N-terminal methionine excision of proteins creates tertiary destabilizing N-degrons of the Arg/N-end rule pathway. J Biol Chem 2019; 294:4464-4476. [PMID: 30674553 DOI: 10.1074/jbc.ra118.006913] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/18/2019] [Indexed: 11/06/2022] Open
Abstract
All organisms begin protein synthesis with methionine (Met). The resulting initiator Met of nascent proteins is irreversibly processed by Met aminopeptidases (MetAPs). N-terminal (Nt) Met excision (NME) is an evolutionarily conserved and essential process operating on up to two-thirds of proteins. However, the universal function of NME remains largely unknown. MetAPs have a well-known processing preference for Nt-Met with Ala, Ser, Gly, Thr, Cys, Pro, or Val at position 2, but using CHX-chase assays to assess protein degradation in yeast cells, as well as protein-binding and RT-qPCR assays, we demonstrate here that NME also occurs on nascent proteins bearing Met-Asn or Met-Gln at their N termini. We found that the NME at these termini exposes the tertiary destabilizing Nt residues (Asn or Gln) of the Arg/N-end rule pathway, which degrades proteins according to the composition of their Nt residues. We also identified a yeast DNA repair protein, MQ-Rad16, bearing a Met-Gln N terminus, as well as a human tropomyosin-receptor kinase-fused gene (TFG) protein, MN-TFG, bearing a Met-Asn N terminus as physiological, MetAP-processed Arg/N-end rule substrates. Furthermore, we show that the loss of the components of the Arg/N-end rule pathway substantially suppresses the growth defects of naa20Δ yeast cells lacking the catalytic subunit of NatB Nt acetylase at 37 °C. Collectively, the results of our study reveal that NME is a key upstream step for the creation of the Arg/N-end rule substrates bearing tertiary destabilizing residues in vivo.
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Affiliation(s)
- Kha The Nguyen
- From the Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jeong-Mok Kim
- From the Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Sang-Eun Park
- From the Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Cheol-Sang Hwang
- From the Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
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23
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Kaushal P, Kwon Y, Ju S, Lee C. An SDS-PAGE based proteomic approach for N-terminome profiling. Analyst 2019; 144:7001-7009. [DOI: 10.1039/c9an01616c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Schematic diagram of the SDS-PAGE based N-termini enrichment (GelNrich) workflow.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
| | - Yumi Kwon
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Shinyeong Ju
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Department of Life Science and Research Institute for Natural Sciences
| | - Cheolju Lee
- Center for Theragnosis
- Korea Institute of Science and Technology
- Seoul 02792
- Korea
- Division of Bio-Medical Science & Technology
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24
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Mandad S, Rahman RU, Centeno TP, Vidal RO, Wildhagen H, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Kirli K, Benito E, Fischer A, Yousefi RY, Dennerlein S, Rehling P, Feussner I, Urlaub H, Bonn S, Rizzoli SO, Fornasiero EF. The codon sequences predict protein lifetimes and other parameters of the protein life cycle in the mouse brain. Sci Rep 2018; 8:16913. [PMID: 30443017 PMCID: PMC6237891 DOI: 10.1038/s41598-018-35277-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 11/02/2018] [Indexed: 12/14/2022] Open
Abstract
The homeostasis of the proteome depends on the tight regulation of the mRNA and protein abundances, of the translation rates, and of the protein lifetimes. Results from several studies on prokaryotes or eukaryotic cell cultures have suggested that protein homeostasis is connected to, and perhaps regulated by, the protein and the codon sequences. However, this has been little investigated for mammals in vivo. Moreover, the link between the coding sequences and one critical parameter, the protein lifetime, has remained largely unexplored, both in vivo and in vitro. We tested this in the mouse brain, and found that the percentages of amino acids and codons in the sequences could predict all of the homeostasis parameters with a precision approaching experimental measurements. A key predictive element was the wobble nucleotide. G-/C-ending codons correlated with higher protein lifetimes, protein abundances, mRNA abundances and translation rates than A-/U-ending codons. Modifying the proportions of G-/C-ending codons could tune these parameters in cell cultures, in a proof-of-principle experiment. We suggest that the coding sequences are strongly linked to protein homeostasis in vivo, albeit it still remains to be determined whether this relation is causal in nature.
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Affiliation(s)
- Sunit Mandad
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, 37077, Göttingen, Germany
| | - Raza-Ur Rahman
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Tonatiuh Pena Centeno
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - Ramon O Vidal
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - Hanna Wildhagen
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Burkhard Rammner
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Sarva Keihani
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Felipe Opazo
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany
| | - Inga Urban
- Genes and Behavior Department, Max Planck Institute of Biophysical Chemistry, 37073, Göttingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University, 37073, Göttingen, Germany
| | - Koray Kirli
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, 37073, Göttingen, Germany
| | - Eva Benito
- Laboratory of Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
| | - André Fischer
- Laboratory of Epigenetics in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Roya Y Yousefi
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
| | - Sven Dennerlein
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, 37073, Germany
- Max Planck Institute for Biophysical Chemistry, 37073, Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute, Georg-August-University, 37073, Göttingen, Germany
| | - Henning Urlaub
- Department of Clinical Chemistry, University Medical Center Göttingen, 37077, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute of Biophysical Chemistry, 37077, Göttingen, Germany
| | - Stefan Bonn
- Laboratory of Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany.
- Institute of Medical Systems Biology, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany.
- German Center for Neurodegenerative Diseases (DZNE), 72076, Tübingen, Germany.
| | - Silvio O Rizzoli
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany.
- Center for Biostructural Imaging of Neurodegeneration (BIN), 37075, Göttingen, Germany.
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, 37073, Göttingen, Germany.
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25
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Thompson CR, Champion MM, Champion PA. Quantitative N-Terminal Footprinting of Pathogenic Mycobacteria Reveals Differential Protein Acetylation. J Proteome Res 2018; 17:3246-3258. [PMID: 30080413 DOI: 10.1021/acs.jproteome.8b00373] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
N-terminal acetylation (NTA) is a post-transcriptional modification of proteins that is conserved from bacteria to humans. In bacteria, the enzymes that mediate protein NTA also promote antimicrobial resistance. In pathogenic mycobacteria, which cause human tuberculosis and other chronic infections, NTA has been linked to pathogenesis and stress response, yet the fundamental biology underlying NTA of mycobacterial proteins remains unclear. We enriched, defined, and quantified the NT-acetylated populations of both cell-associated and secreted proteins from both the human pathogen, Mycobacterium tuberculosis, and the nontuberculous opportunistic pathogen, Mycobacterium marinum. We used a parallel N-terminal enrichment strategy from proteolytic digests coupled to charge-based selection and stable isotope ratio mass spectrometry. We show that NTA of the mycobacterial proteome is abundant, diverse, and primarily on Thr residues, which is unique compared with other bacteria. We isolated both the acetylated and unacetylated forms of 256 proteins, indicating that NTA of mycobacterial proteins is homeostatic. We identified 16 mycobacterial proteins with differential levels of NTA on the cytoplasmic and secreted forms, linking protein modification and localization. Our findings reveal novel biology underlying the NTA of mycobacterial proteins, which may provide a basis to understand NTA in mycobacterial physiology, pathogenesis, and antimicrobial resistance.
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26
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Abrahams L, Hurst LD. Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts. Mol Biol Evol 2018; 34:3064-3080. [PMID: 28961919 PMCID: PMC5850271 DOI: 10.1093/molbev/msx223] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Beyond selection for optimal protein functioning, coding sequences (CDSs) are under selection at the RNA and DNA levels. Here, we identify a possible signature of “dual-coding,” namely extensive adenine (A) enrichment at bacterial CDS fourth sites. In 99.07% of studied bacterial genomes, fourth site A use is greater than expected given genomic A-starting codon use. Arguing for nucleotide level selection, A-starting serine and arginine second codons are heavily utilized when compared with their non-A starting synonyms. Several models have the ability to explain some of this trend. In part, A-enrichment likely reduces 5′ mRNA stability, promoting translation initiation. However T/U, which may also reduce stability, is avoided. Further, +1 frameshifts on the initiating ATG encode a stop codon (TGA) provided A is the fourth residue, acting either as a frameshift “catch and destroy” or a frameshift stop and adjust mechanism and hence implicated in translation initiation. Consistent with both, genomes lacking TGA stop codons exhibit weaker fourth site A-enrichment. Sequences lacking a Shine–Dalgarno sequence and those without upstream leader genes, that may be more error prone during initiation, have greater utilization of A, again suggesting a role in initiation. The frameshift correction model is consistent with the notion that many genomic features are error-mitigation factors and provides the first evidence for site-specific out of frame stop codon selection. We conjecture that the NTG universal start codon may have evolved as a consequence of TGA being a stop codon and the ability of NTGA to rapidly terminate or adjust a ribosome.
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Affiliation(s)
- Liam Abrahams
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Laurence D Hurst
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
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27
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Sandrin TR, Demirev PA. Characterization of microbial mixtures by mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:321-349. [PMID: 28509357 DOI: 10.1002/mas.21534] [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: 11/23/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 05/27/2023]
Abstract
MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.
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Affiliation(s)
- Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona
| | - Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland
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28
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Zhang H, Gannon L, Hassall KL, Deery MJ, Gibbs DJ, Holdsworth MJ, van der Hoorn RAL, Lilley KS, Theodoulou FL. N-terminomics reveals control of Arabidopsis seed storage proteins and proteases by the Arg/N-end rule pathway. THE NEW PHYTOLOGIST 2018; 218:1106-1126. [PMID: 29168982 PMCID: PMC5947142 DOI: 10.1111/nph.14909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/23/2017] [Indexed: 05/04/2023]
Abstract
The N-end rule pathway of targeted protein degradation is an important regulator of diverse processes in plants but detailed knowledge regarding its influence on the proteome is lacking. To investigate the impact of the Arg/N-end rule pathway on the proteome of etiolated seedlings, we used terminal amine isotopic labelling of substrates with tandem mass tags (TMT-TAILS) for relative quantification of N-terminal peptides in prt6, an Arabidopsis thaliana N-end rule mutant lacking the E3 ligase PROTEOLYSIS6 (PRT6). TMT-TAILS identified over 4000 unique N-terminal peptides representing c. 2000 protein groups. Forty-five protein groups exhibited significantly increased N-terminal peptide abundance in prt6 seedlings, including cruciferins, major seed storage proteins, which were regulated by Group VII Ethylene Response Factor (ERFVII) transcription factors, known substrates of PRT6. Mobilisation of endosperm α-cruciferin was delayed in prt6 seedlings. N-termini of several proteases were downregulated in prt6, including RD21A. RD21A transcript, protein and activity levels were downregulated in a largely ERFVII-dependent manner. By contrast, cathepsin B3 protein and activity were upregulated by ERFVIIs independent of transcript. We propose that the PRT6 branch of the pathway regulates protease activities in a complex manner and optimises storage reserve mobilisation in the transition from seed to seedling via control of ERFVII action.
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Affiliation(s)
- Hongtao Zhang
- Plant Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
| | - Lucy Gannon
- Plant Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
| | - Kirsty L. Hassall
- Computational and Analytical Sciences DepartmentRothamsted ResearchHarpendenAL5 2JQUK
| | - Michael J. Deery
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
| | - Daniel J. Gibbs
- School of BiosciencesUniversity of BirminghamEdgbastonB15 2TTUK
| | | | | | - Kathryn S. Lilley
- Cambridge Centre for ProteomicsDepartment of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridge, CB2 1QRUK
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29
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Jonckheere V, Fijałkowska D, Van Damme P. Omics Assisted N-terminal Proteoform and Protein Expression Profiling On Methionine Aminopeptidase 1 (MetAP1) Deletion. Mol Cell Proteomics 2018; 17:694-708. [PMID: 29317475 DOI: 10.1074/mcp.ra117.000360] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 12/12/2017] [Indexed: 12/14/2022] Open
Abstract
Excision of the N-terminal initiator methionine (iMet) residue from nascent peptide chains is an essential and omnipresent protein modification carried out by methionine aminopeptidases (MetAPs) that accounts for a major source of N-terminal proteoform diversity. Although MetAP2 is known to be implicated in processes such as angiogenesis and proliferation in mammals, the physiological role of MetAP1 is much less clear. In this report we studied the omics-wide effects of human MetAP1 deletion and general MetAP inhibition. The levels of iMet retention are inversely correlated with cellular proliferation rates. Further, despite the increased MetAP2 expression on MetAP1 deletion, MetAP2 was unable to restore processing of Met-Ser-, Met-Pro-, and Met-Ala- starting N termini as inferred from the iMet retention profiles observed, indicating a higher activity of MetAP1 over these N termini. Proteome and transcriptome expression profiling point to differential expression of proteins implicated in lipid metabolism, cytoskeleton organization, cell proliferation and protein synthesis upon perturbation of MetAP activity.
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Affiliation(s)
- Veronique Jonckheere
- From the ‡VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,§Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Daria Fijałkowska
- From the ‡VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium.,§Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Petra Van Damme
- From the ‡VIB-UGent Center for Medical Biotechnology, B-9000 Ghent, Belgium; .,§Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
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30
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Zhang M, Xu JY, Hu H, Ye BC, Tan M. Systematic Proteomic Analysis of Protein Methylation in Prokaryotes and Eukaryotes Revealed Distinct Substrate Specificity. Proteomics 2017; 18. [PMID: 29150981 DOI: 10.1002/pmic.201700300] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/25/2017] [Indexed: 11/07/2022]
Abstract
The studies of protein methylation mainly focus on lysine and arginine residues due to their diverse roles in essential cellular processes from gene expression to signal transduction. Nevertheless, atypical protein methylation occurring on amino acid residues, such as glutamine and glutamic acid, is largely neglected until recently. In addition, the systematic analysis for the distribution of methylation on different amino acids in various species is still lacking, which hinders our understanding of its functional roles. In this study, we deeply explored the methylated sites in three species Escherichia coli, Saccharomyces cerevisiae, and HeLa cells by employing MS-based proteomic approach coupled with heavy methyl SILAC method. We identify a total of 234 methylated sites on 187 proteins with high localization confidence, including 94 unreported methylated sites on nine different amino acid residues. KEGG and gene ontology analysis show the pathways enriched with methylated proteins are mainly involved in central metabolism for E. coli and S. cerevisiae, but related to spliceosome for HeLa cells. The analysis of methylation preference on different amino acids is conducted in three species. Protein N-terminal methylation is dominant in E. coli while methylated lysines and arginines are widely identified in S. cerevisiae and HeLa cells, respectively. To study whether some atypical protein methylation has biological relevance in the pathological process in mammalian cells, we focus on histone methylation in diet-induced obese (DIO) mouse. Two glutamate methylation sites showed statistical significance in DIO mice compared with chow-fed mice, suggesting their potential roles in diabetes and obesity. Together, these findings expanded the methylome database from microbes to mammals, which will benefit our further appreciation for the protein methylation as well as its possible functions on disease.
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Affiliation(s)
- Min Zhang
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Yu Xu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hao Hu
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Bang-Ce Ye
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
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31
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Post-Translational Modification of Human Histone by Wide Tolerance of Acetylation. Cells 2017; 6:cells6040034. [PMID: 29023412 PMCID: PMC5753069 DOI: 10.3390/cells6040034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 12/16/2022] Open
Abstract
Histone acetylation adds an acetyl group on the lysine residue commonly found within the N-terminal tail protruding from the histone core of the nucleosome, and is important for chromosome structure and function in gene transcription and chromatin remodeling. Acetylation may also occur on other residues additional to lysine, but have not been thoroughly investigated at the proteomics level. Here we report a wide tolerance acetylation study mimicking the addition of 42 ± 0.5 Da delta mass modification on undefined amino acid residues of histones by shotgun proteomics using liquid chromatography–tandem mass spectrometry. A multi-blind spectral alignment algorithm with a wide peptide tolerance revealed frequent occurrence of 42 ± 0.5 Da modifications at lysine (K), serine (S) and threonine (T) residues in human histones from kidney tissues. Precision delta mass analysis identified acetylation (42.011 ± 0.004 Da) and trimethylation (42.047 ± 0.002 Da) modifications within the delta mass range. A specific antibody was produced to validate the acetylated T22 of human histone H3 (H3T22ac) by immune assays. Thus, we demonstrated that the wide tolerance acetylation approach identified histone acetylation as well as modification variants commonly associated with acetylation at undefined residues additional to lysine.
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32
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Berry IJ, Jarocki VM, Tacchi JL, Raymond BBA, Widjaja M, Padula MP, Djordjevic SP. N-terminomics identifies widespread endoproteolysis and novel methionine excision in a genome-reduced bacterial pathogen. Sci Rep 2017; 7:11063. [PMID: 28894154 PMCID: PMC5593965 DOI: 10.1038/s41598-017-11296-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/21/2017] [Indexed: 12/12/2022] Open
Abstract
Proteolytic processing alters protein function. Here we present the first systems-wide analysis of endoproteolysis in the genome-reduced pathogen Mycoplasma hyopneumoniae. 669 N-terminal peptides from 164 proteins were identified, demonstrating that functionally diverse proteins are processed, more than half of which 75 (53%) were accessible on the cell surface. Multiple cleavage sites were characterised, but cleavage with arginine in P1 predominated. Putative functions for a subset of cleaved fragments were assigned by affinity chromatography using heparin, actin, plasminogen and fibronectin as bait. Binding affinity was correlated with the number of cleavages in a protein, indicating that novel binding motifs are exposed, and protein disorder increases, after a cleavage event. Glyceraldehyde 3-phosphate dehydrogenase was used as a model protein to demonstrate this. We define the rules governing methionine excision, show that several aminopeptidases are involved, and propose that through processing, genome-reduced organisms can expand protein function.
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Affiliation(s)
- Iain J Berry
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Veronica M Jarocki
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Jessica L Tacchi
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Benjamin B A Raymond
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Michael Widjaja
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Matthew P Padula
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Steven P Djordjevic
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia. .,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.
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33
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Kuhlmann NJ, Chien P. Selective adaptor dependent protein degradation in bacteria. Curr Opin Microbiol 2017; 36:118-127. [PMID: 28458096 DOI: 10.1016/j.mib.2017.03.013] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/12/2017] [Accepted: 03/29/2017] [Indexed: 11/30/2022]
Abstract
Energy dependent proteolysis is essential for all life, but uncontrolled degradation leads to devastating consequences. In bacteria, oligomeric AAA+ proteases are responsible for controlling protein destruction and are regulated in part by adaptor proteins. Adaptors are regulatory factors that shape protease substrate choice by either restricting or enhancing substrate recognition in several ways. In some cases, protease activity or assembly itself requires adaptor binding. Adaptors can also alter specificity by acting as scaffolds to tether particular substrates to already active proteases. Finally, hierarchical assembly of adaptors can use combinations of several activities to enhance the protease's selectivity. Because the lifetime of the constituent proteins directly affects the duration of a particular signaling pathway, regulated proteolysis impacts almost all cellular responses. In this review, we describe recent progress in regulated protein degradation, focusing on fundamental principles of adaptors and how they perform critical biological functions, such as promoting cell cycle progression and quality control.
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Affiliation(s)
- Nathan J Kuhlmann
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States
| | - Peter Chien
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, United States; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, United States.
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34
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Abstract
Protein synthesis is initiated by methionine in eukaryotes and by formylmethionine in prokaryotes. N-terminal methionine can be co-translationally cleaved by the enzyme methionine aminopeptidase (MAP). When recombinant proteins are expressed in bacterial and mammalian expression systems, there is a simple universal rule that predicts whether the initiating methionine will be processed by MAP based on the size of the residue adjacent (penultimate) to the N-methionine. In general, if the side chains of the penultimate residues have a radius of gyration of 1.29 Å or less, methionine is cleaved. © 2017 by John Wiley & Sons, Inc.
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35
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Abstract
Determination of the general capacity of proteolytic activity of a certain cell or tissue type can be crucial for an assessment of various features of an organism's growth and development and also for the optimization of biotechnological applications. Here, we describe the use of chimeric protein stability reporters that can be detected by standard laboratory techniques such as histological staining, selection using selective media or fluorescence microscopy. Dependent on the expression of the reporters due to the promoters applied, cell- and tissue-specific questions can be addressed. Here, we concentrate on methods which can be used for large-scale screening for protein stability changes rather than for detailed protein stability studies.
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Affiliation(s)
- Pavel Reichman
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB) and Science Campus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB) and Science Campus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany.
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36
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Armengaud J. Defining Diagnostic Biomarkers Using Shotgun Proteomics and MALDI-TOF Mass Spectrometry. Methods Mol Biol 2017; 1616:107-120. [PMID: 28600764 DOI: 10.1007/978-1-4939-7037-7_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Whole-cell MALDI-TOF has become a robust and widely used tool to quickly identify any pathogen. In addition to being routinely used in hospitals, it is also useful for low cost dereplication in large scale screening procedures of new environmental isolates for environmental biotechnology or taxonomical applications. Here, I describe how specific biomarkers can be defined using shotgun proteomics and whole-cell MALDI-TOF mass spectrometry. Based on MALDI-TOF spectra recorded on a given set of pathogens with internal calibrants, m/z values of interest are extracted. The proteins which contribute to these peaks are deduced from label-free shotgun proteomics measurements carried out on the same sample. Quantitative information based on the spectral count approach allows ranking the most probable candidates. Proteogenomic approaches help to define whether these proteins give the same m/z values along the whole taxon under consideration or result in heterogeneous lists. These specific biomarkers nicely complement conventional profiling approaches and may help to better define groups of organisms, for example at the subspecies level.
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Affiliation(s)
- Jean Armengaud
- CEA-Marcoule, DRF/JOLIOT/DMTS/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostics", BP 17171, 30200, Bagnols-sur-Cèze, France.
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37
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Bienvenut WV, Giglione C, Meinnel T. SILProNAQ: A Convenient Approach for Proteome-Wide Analysis of Protein N-Termini and N-Terminal Acetylation Quantitation. Methods Mol Biol 2017; 1574:17-34. [PMID: 28315241 DOI: 10.1007/978-1-4939-6850-3_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Protein N-terminal modifications have recently been involved in overall proteostasis through their impact on cell fate and protein life time. This explains the development of new approaches to characterize more precisely the N-terminal end of mature proteins. Although few approaches are available to perform N-terminal enrichment based on positive or negative discriminations, these methods are usually restricted to the enrichment in N-terminal peptides and their characterization by mass spectrometry. Recent investigation highlights both (1) the knowledge of the N-terminal acetylation status of most cytosolic proteins and (2) post-translational addition of this modification on the N-terminus of nuclear coded chloroplast proteins imported in the plastid and after the cleavage of the transit peptide. The workflow involves stable isotope labeling to assess N-acetylation rates followed by Strong Cation eXchange (SCX ) fractionation of the samples to provide protein N-terminal enriched fractions. Combined with mass spectrometry analyses, the technology finally requires extensive data processing. This last step aims first at discriminating the most relevant mature N-termini from the characterized peptides, next at determining its experimental position and then at calculating the N-terminal acetylation yield. Stable-Isotope Protein N-terminal Acetylation Quantification (SILProNAQ) is a complete workflow combining wet-lab techniques together with dry-lab processing to determine the N-terminal acetylation yield of mature proteins for a clearly defined localization.
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Affiliation(s)
- Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Bâtiment 21, Avenue de la Terrassee, 91198, Gif-sur-Yvette cedex, France.
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Bâtiment 21, Avenue de la Terrassee, 91198, Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris Saclay, Bâtiment 21, Avenue de la Terrassee, 91198, Gif-sur-Yvette cedex, France
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38
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Makins C, Ghosh S, Román-Meléndez GD, Malec PA, Kennedy RT, Marsh ENG. Does Viperin Function as a Radical S-Adenosyl-l-methionine-dependent Enzyme in Regulating Farnesylpyrophosphate Synthase Expression and Activity? J Biol Chem 2016; 291:26806-26815. [PMID: 27834682 DOI: 10.1074/jbc.m116.751040] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/31/2016] [Indexed: 01/09/2023] Open
Abstract
Viperin is an endoplasmic reticulum-associated antiviral responsive protein that is highly up-regulated in eukaryotic cells upon viral infection through both interferon-dependent and independent pathways. Viperin is predicted to be a radical S-adenosyl-l-methionine (SAM) enzyme, but it is unknown whether viperin actually exploits radical SAM chemistry to exert its antiviral activity. We have investigated the interaction of viperin with its most firmly established cellular target, farnesyl pyrophosphate synthase (FPPS). Numerous enveloped viruses utilize cholesterol-rich lipid rafts to bud from the host cell membrane, and it is thought that by inhibiting FPPS activity (and therefore cholesterol synthesis), viperin retards viral budding from infected cells. We demonstrate that, consistent with this hypothesis, overexpression of viperin in human embryonic kidney cells reduces the intracellular rate of accumulation of FPPS but does not inhibit or inactivate FPPS. The endoplasmic reticulum-localizing, N-terminal amphipathic helix of viperin is specifically required for viperin to reduce cellular FPPS levels. However, although viperin reductively cleaves SAM to form 5'-deoxyadenosine in a slow, uncoupled reaction characteristic of radical SAM enzymes, this cleavage reaction is independent of FPPS. Furthermore, mutation of key cysteinyl residues ligating the catalytic [Fe4S4] cluster in the radical SAM domain, surprisingly, does not abolish the inhibitory activity of viperin against FPPS; indeed, some mutations potentiate viperin activity. These observations imply that viperin does not act as a radical SAM enzyme in regulating FPPS.
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Affiliation(s)
- Caitlyn Makins
- From the Departments of Chemistry and.,Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
| | | | | | | | | | - E Neil G Marsh
- From the Departments of Chemistry and .,Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055
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39
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Trempe JF, Šašková KG, Sivá M, Ratcliffe CDH, Veverka V, Hoegl A, Ménade M, Feng X, Shenker S, Svoboda M, Kožíšek M, Konvalinka J, Gehring K. Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family. Sci Rep 2016; 6:33671. [PMID: 27646017 PMCID: PMC5028754 DOI: 10.1038/srep33671] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/01/2016] [Indexed: 12/16/2022] Open
Abstract
The eukaryotic Ddi1 family is defined by a conserved retroviral aspartyl protease-like (RVP) domain found in association with a ubiquitin-like (UBL) domain. Ddi1 from Saccharomyces cerevisiae additionally contains a ubiquitin-associated (UBA) domain. The substrate specificity and role of the protease domain in the biological functions of the Ddi family remain unclear. Yeast Ddi1 has been implicated in the regulation of cell cycle progression, DNA-damage repair, and exocytosis. Here, we investigated the multi-domain structure of yeast Ddi1 using X-ray crystallography, nuclear magnetic resonance, and small-angle X-ray scattering. The crystal structure of the RVP domain sheds light on a putative substrate recognition site involving a conserved loop. Isothermal titration calorimetry confirms that both UBL and UBA domains bind ubiquitin, and that Ddi1 binds K48-linked diubiquitin with enhanced affinity. The solution NMR structure of a helical domain that precedes the protease displays tertiary structure similarity to DNA-binding domains from transcription regulators. Our structural studies suggest that the helical domain could serve as a landing platform for substrates in conjunction with attached ubiquitin chains binding to the UBL and UBA domains.
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Affiliation(s)
- Jean-François Trempe
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Klára Grantz Šašková
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 120 00 Prague 2, Czech Republic
| | - Monika Sivá
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 120 00 Prague 2, Czech Republic.,First Faculty of Medicine, Charles University in Prague, Katerinska 32, 121 08, Prague 2, Czech Republic
| | - Colin D H Ratcliffe
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Václav Veverka
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Annabelle Hoegl
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Marie Ménade
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Xin Feng
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Solomon Shenker
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
| | - Michal Svoboda
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic.,Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, 120 00 Prague 2, Czech Republic
| | - Milan Kožíšek
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Jan Konvalinka
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Flemingovo n. 2, 166 10 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 8, 120 00 Prague 2, Czech Republic
| | - Kalle Gehring
- Groupe de Recherche Axé sur la Structure des Protéines, Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Montreal, QC, H3G 0B1, Canada
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40
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Drazic A, Myklebust LM, Ree R, Arnesen T. The world of protein acetylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1372-401. [PMID: 27296530 DOI: 10.1016/j.bbapap.2016.06.007] [Citation(s) in RCA: 514] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 12/30/2022]
Abstract
Acetylation is one of the major post-translational protein modifications in the cell, with manifold effects on the protein level as well as on the metabolome level. The acetyl group, donated by the metabolite acetyl-coenzyme A, can be co- or post-translationally attached to either the α-amino group of the N-terminus of proteins or to the ε-amino group of lysine residues. These reactions are catalyzed by various N-terminal and lysine acetyltransferases. In case of lysine acetylation, the reaction is enzymatically reversible via tightly regulated and metabolism-dependent mechanisms. The interplay between acetylation and deacetylation is crucial for many important cellular processes. In recent years, our understanding of protein acetylation has increased significantly by global proteomics analyses and in depth functional studies. This review gives a general overview of protein acetylation and the respective acetyltransferases, and focuses on the regulation of metabolic processes and physiological consequences that come along with protein acetylation.
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Affiliation(s)
- Adrian Drazic
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Line M Myklebust
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Rasmus Ree
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway; Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - 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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41
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Kentache T, Jouenne T, Dé E, Hardouin J. Proteomic characterization of Nα- and Nε-acetylation in Acinetobacter baumannii. J Proteomics 2016; 144:148-58. [PMID: 27222042 DOI: 10.1016/j.jprot.2016.05.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/12/2016] [Accepted: 05/18/2016] [Indexed: 12/25/2022]
Abstract
Nα- and Nε-acetylation represent a pivotal post-translational modification used by both eukaryotes and prokaryotes to modulate diverse biological processes. Acinetobacter baumannii has been described as an important nosocomial pathogen for the past 30 years, frequently involved in ventilator-associated pneumonia, bloodstream and urinary tract infections. Many aspects of the biology of A. baumannii remain elusive, in particular the extent and function of N-acetylation. We investigated here N-acetylation in A. baumannii strain ATCC 17978 by proteomic analysis, and we showed the usefulness of using different analytical approaches. Overall, we identified 525 N-acetylated proteins in which, 145 were Nα-acetylated and 411 were Nε-acetylated. Among them, 41 proteins carried both types of N-acetylation. We found that N-acetylation may play a role in biofilm formation, bacterial virulence (e.g. in several iron acquisition pathways), as well as a number of phenotypes, such as, stress adaptation and drug resistance. BIOLOGICAL SIGNIFICANCE This study is the first to perform the N-acetylome of A. baumannii using different analytical approaches. Each analytical tool permitted to characterize distinctive modified peptides. The combination of all these methods allowed us to identify 145 and 411 Nα- and Nε-acetylated proteins. Besides the fact that acetylation was involved in central metabolism as previously described in other bacteria, some N-acetylated proteins showed interesting role in bacterial virulence (iron acquisition), biofilm formation, stress adaptation and drug resistance of A. baumannii.
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Affiliation(s)
- Takfarinas Kentache
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Emmanuelle Dé
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76821 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO proteomic facility, IRIB, F-76821 Mont-Saint-Aignan, France.
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42
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Bienvenut WV, Giglione C, Meinnel T. Proteome-wide analysis of the amino terminal status of Escherichia coli proteins at the steady-state and upon deformylation inhibition. Proteomics 2016; 15:2503-18. [PMID: 26017780 DOI: 10.1002/pmic.201500027] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/18/2015] [Accepted: 05/21/2015] [Indexed: 12/14/2022]
Abstract
A proteome wide analysis was performed in Escherichia coli to identify the impact on protein N-termini of actinonin, an antibiotic specifically inhibiting peptide deformylase (PDF). A strategy and tool suite (SILProNaQ) was employed to provide large-scale quantitation of N-terminal modifications. In control conditions, more than 1000 unique N-termini were identified with 56% showing initiator methionine removal. Additional modifications corresponded to partial or complete Nα-acetylation (10%) and N-formyl retention (5%). Among the proteins undergoing these N-terminal modifications, 140 unique N-termini from translocated membrane proteins were highlighted. The very early time-course impact of actinonin was followed after addition of bacteriostatic concentrations of the drug. Under these conditions, 26% of all proteins did not undergo deformylation any longer after 10 min, a value reaching more than 60% of all characterized proteins after 40 min of treatment. The N-formylation ratio measured on individual proteins increased with the same trend. Upon early PDF inhibition, two major categories of proteins retained their N-formyl group: a large number of inner membrane proteins and many proteins involved in protein synthesis including factors assisting the nascent chains in early cotranslational events. All MS data have been deposited in the ProteomeXchange with identifiers PXD001979, PXD002012 and PXD001983 (http://proteomecentral.proteomexchange.org/dataset/PXD001979, http://proteomecentral.proteomexchange.org/dataset/PXD002012 and http://proteomecentral.proteomexchange.org/dataset/PXD001983).
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Affiliation(s)
- Willy V Bienvenut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Carmela Giglione
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
| | - Thierry Meinnel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France
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43
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Venne AS, Solari FA, Faden F, Paretti T, Dissmeyer N, Zahedi RP. An improved workflow for quantitative N-terminal charge-based fractional diagonal chromatography (ChaFRADIC) to study proteolytic events in Arabidopsis thaliana. Proteomics 2016; 15:2458-69. [PMID: 26010716 DOI: 10.1002/pmic.201500014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/28/2015] [Accepted: 05/20/2015] [Indexed: 11/11/2022]
Abstract
We applied an extended charge-based fractional diagonal chromatography (ChaFRADIC) workflow to analyze the N-terminal proteome of Arabidopsis thaliana seedlings. Using iTRAQ protein labeling and a multi-enzyme digestion approach including trypsin, GluC, and subtilisin, a total of 200 μg per enzyme, and measuring only one third of each ChaFRADIC-enriched fraction by LC-MS, we quantified a total of 2791 unique N-terminal peptides corresponding to 2249 different unique N-termini from 1270 Arabidopsis proteins. Our data indicate the power, reproducibility, and sensitivity of the applied strategy that might be applicable to quantify proteolytic events from as little as 20 μg of protein per condition across up to eight different samples. Furthermore, our data clearly reflect the methionine excision dogma as well as the N-end rule degradation pathway (NERP) discriminating into a stabilizing or destabilizing function of N-terminal amino acid residues. We found bona fide NERP destabilizing residues underrepresented, and the list of neo N-termini from wild type samples may represent a helpful resource during the evaluation of NERP substrate candidates. All MS data have been deposited in the ProteomeXchange with identifier PXD001855 (http://proteomecentral.proteomexchange.org/dataset/PXD001855).
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Affiliation(s)
- A Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Frederik Faden
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - Tomasso Paretti
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany.,Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, Italy
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
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44
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Ouidir T, Jouenne T, Hardouin J. Post-translational modifications in Pseudomonas aeruginosa revolutionized by proteomic analysis. Biochimie 2016; 125:66-74. [PMID: 26952777 DOI: 10.1016/j.biochi.2016.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 03/01/2016] [Indexed: 11/25/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes severe infections in vulnerable individuals. It is known that post-translational modifications (PTMs) play a key role in bacterial physiology. Their characterization is still challenging and the recent advances in proteomics allow large-scale and high-throughput analyses of PTMs. Here, we provide an overview of proteomic data about the modified proteins in P. aeruginosa. We emphasize the significant contribution of proteomics in knowledge enhancement of PTMs (phosphorylation, N-acetylation and glycosylation) and we discuss their importance in P. aeruginosa physiology.
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Affiliation(s)
- Tassadit Ouidir
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Thierry Jouenne
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères, Surfaces Laboratory, F-76820 Mont-Saint-Aignan, France; Normandie Univ, UR, France; PISSARO Proteomic Facility, IRIB, F-76820 Mont-Saint-Aignan, France.
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45
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Abstract
In the past decade, proteogenomics has emerged as a valuable technique that contributes to the state-of-the-art in genome annotation; however, previous proteogenomic studies were limited to bottom-up mass spectrometry and did not take advantage of top-down approaches. We show that top-down proteogenomics allows one to address the problems that remained beyond the reach of traditional bottom-up proteogenomics. In particular, we show that top-down proteogenomics leads to the discovery of previously unannotated genes even in extensively studied bacterial genomes and present SpectroGene, a software tool for genome annotation using top-down tandem mass spectra. We further show that top-down proteogenomics searches (against the six-frame translation of a genome) identify nearly all proteoforms found in traditional top-down proteomics searches (against the annotated proteome). SpectroGene is freely available at http://github.com/fenderglass/SpectroGene .
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Affiliation(s)
- Mikhail Kolmogorov
- Department of Computer Science and Engineering, UCSD, 9500 Gilman Drive, La Jolla, CA, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, IUPUI, 719 Indiana Ave, Suite 304, Indianapolis, IN, USA
| | - Pavel A. Pevzner
- Department of Computer Science and Engineering, UCSD, 9500 Gilman Drive, La Jolla, CA, USA
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46
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Ouidir T, Kentache T, Hardouin J. Protein lysine acetylation in bacteria: Current state of the art. Proteomics 2015; 16:301-9. [DOI: 10.1002/pmic.201500258] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/11/2015] [Accepted: 09/15/2015] [Indexed: 12/28/2022]
Affiliation(s)
- Tassadit Ouidir
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
| | - Takfarinas Kentache
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
| | - Julie Hardouin
- CNRS, UMR 6270, Polymères, Biopolymères; Surfaces Laboratory; Mont-Saint-Aignan France
- Normandie University; UR France
- PISSARO proteomic facility; IRIB; Mont-Saint-Aignan France
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47
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Chang YY, Hsu CH. Multiple Conformations of the Loop Region Confers Heat-Resistance on SsArd1, a Thermophilic NatA. Chembiochem 2015; 17:214-7. [PMID: 26593285 DOI: 10.1002/cbic.201500568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Indexed: 11/10/2022]
Abstract
Structural comparison indicates that the loop region between β3 and β4 of SsArd1 is extended relative to the corresponding region in mesophilic Nats, and forms a plastic hydrogen-bond network mainly at two serine residues. Strikingly, two single-point mutants showed ∼3 °C decrease in melting temperature, and two other variants showed ∼7 °C decrease; this correlated with significantly reduced enzymatic activity. To our knowledge, this is the first discovery of a loop region capable of remarkably improving protein thermostability. This provides a novel route to engineer heat-resistant proteins.
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Affiliation(s)
- Yu-Yung Chang
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, Center for Systems Biology, Genome and Systems Biology Degree Program, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
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48
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Schmidt A, Kochanowski K, Vedelaar S, Ahrné E, Volkmer B, Callipo L, Knoops K, Bauer M, Aebersold R, Heinemann M. The quantitative and condition-dependent Escherichia coli proteome. Nat Biotechnol 2015; 34:104-10. [PMID: 26641532 PMCID: PMC4888949 DOI: 10.1038/nbt.3418] [Citation(s) in RCA: 480] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 10/28/2015] [Indexed: 12/26/2022]
Abstract
Measuring precise concentrations of proteins can provide insights into biological processes. Here, we use efficient protein extraction and sample fractionation and state-of-the-art quantitative mass spectrometry techniques to generate a comprehensive, condition-dependent protein abundance map of Escherichia coli. We measure cellular protein concentrations for 55% of predicted E. coli genes (>2300 proteins) under 22 different experimental conditions and identify methylation and N-terminal protein acetylations previously not known to be prevalent in bacteria. We uncover system-wide proteome allocation, expression regulation, and post-translational adaptations. These data provide a valuable resource for the systems biology and broader E. coli research communities.
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Affiliation(s)
| | - Karl Kochanowski
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Silke Vedelaar
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Erik Ahrné
- Biozentrum, University of Basel, Basel, Switzerland
| | - Benjamin Volkmer
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Luciano Callipo
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Kèvin Knoops
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Manuel Bauer
- Biozentrum, University of Basel, Basel, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Matthias Heinemann
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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49
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Berry IJ, Steele JR, Padula MP, Djordjevic SP. The application of terminomics for the identification of protein start sites and proteoforms in bacteria. Proteomics 2015; 16:257-72. [DOI: 10.1002/pmic.201500319] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/21/2015] [Accepted: 09/30/2015] [Indexed: 01/11/2023]
Affiliation(s)
- Iain J. Berry
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Joel R. Steele
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Matthew P. Padula
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
| | - Steven P. Djordjevic
- The ithree Institute; University of Technology Sydney; Broadway NSW Australia
- Proteomics Core Facility; University of Technology Sydney; Broadway NSW Australia
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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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