1
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Sharon I, Schmeing TM. Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation. Sci Rep 2023; 13:8314. [PMID: 37221236 PMCID: PMC10206079 DOI: 10.1038/s41598-023-34587-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023] Open
Abstract
Cyanophycin is a bacterial biopolymer used for storage of fixed nitrogen. It is composed of a backbone of L-aspartate residues with L-arginines attached to each of their side chains. Cyanophycin is produced by cyanophycin synthetase 1 (CphA1) using Arg, Asp and ATP, and is degraded in two steps. First, cyanophycinase breaks down the backbone peptide bonds, releasing β-Asp-Arg dipeptides. Then, these dipeptides are broken down into free Asp and Arg by enzymes with isoaspartyl dipeptidase activity. Two bacterial enzymes are known to possess promiscuous isoaspartyl dipeptidase activity: isoaspartyl dipeptidase (IadA) and isoaspartyl aminopeptidase (IaaA). We performed a bioinformatic analysis to investigate whether genes for cyanophycin metabolism enzymes cluster together or are spread around the microbial genomes. Many genomes showed incomplete contingents of known cyanophycin metabolizing genes, with different patterns in various bacterial clades. Cyanophycin synthetase and cyanophycinase are usually clustered together when recognizable genes for each are found within a genome. Cyanophycinase and isoaspartyl dipeptidase genes typically cluster within genomes lacking cphA1. About one-third of genomes with genes for CphA1, cyanophycinase and IaaA show these genes clustered together, while the proportion is around one-sixth for CphA1, cyanophycinase and IadA. We used X-ray crystallography and biochemical studies to characterize an IadA and an IaaA from two such clusters, in Leucothrix mucor and Roseivivax halodurans, respectively. The enzymes retained their promiscuous nature, showing that being associated with cyanophycin-related genes did not make them specific for β-Asp-Arg dipeptides derived from cyanophycin degradation.
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Affiliation(s)
- Itai Sharon
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - T Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.
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2
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Gelder K, Oliveira-Filho ER, García-García JD, Hu Y, Bruner SD, Hanson AD. Directed Evolution of Aerotolerance in Sulfide-Dependent Thiazole Synthases. ACS Synth Biol 2023; 12:963-970. [PMID: 36920242 PMCID: PMC10127261 DOI: 10.1021/acssynbio.2c00512] [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: 09/26/2022] [Indexed: 03/16/2023]
Abstract
Sulfide-dependent THI4 thiazole synthases could potentially be used to replace plant cysteine-dependent suicide THI4s, whose high protein turnover rates make thiamin synthesis exceptionally energy-expensive. However, sulfide-dependent THI4s are anaerobic or microoxic enzymes and hence unadapted to the aerobic conditions in plants; they are also slow enzymes (kcat < 1 h-1). To improve aerotolerance and activity, we applied continuous directed evolution under aerobic conditions in the yeast OrthoRep system to two sulfide-dependent bacterial THI4s. Seven beneficial single mutations were identified, of which five lie in the active-site cleft predicted by structural modeling and two recapitulate features of naturally aerotolerant THI4s. That single mutations gave substantial improvements suggests that further advance under selection will be possible by stacking mutations. This proof-of-concept study established that the performance of sulfide-dependent THI4s in aerobic conditions is evolvable and, more generally, that yeast OrthoRep provides a plant-like bridge to adapt nonplant enzymes to work better in plants.
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Affiliation(s)
- Kristen
Van Gelder
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | - Edmar R. Oliveira-Filho
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
| | | | - You Hu
- Chemistry
Department, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D. Bruner
- Chemistry
Department, University of Florida, Gainesville, Florida 32611, United States
| | - Andrew D. Hanson
- Horticultural
Sciences Department, University of Florida, Gainesville, Florida 32611, United States
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3
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Warmack RA, Pang EZ, Peluso E, Lowenson JD, Ong JY, Torres JZ, Clarke SG. Human Protein-l-isoaspartate O-Methyltransferase Domain-Containing Protein 1 (PCMTD1) Associates with Cullin-RING Ligase Proteins. Biochemistry 2022; 61:879-894. [PMID: 35486881 PMCID: PMC9875861 DOI: 10.1021/acs.biochem.2c00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The spontaneous l-isoaspartate protein modification has been observed to negatively affect protein function. However, this modification can be reversed in many proteins in reactions initiated by the protein-l-isoaspartyl (d-aspartyl) O-methyltransferase (PCMT1). It has been hypothesized that an additional mechanism exists in which l-isoaspartate-damaged proteins are recognized and proteolytically degraded. Herein, we describe the protein-l-isoaspartate O-methyltransferase domain-containing protein 1 (PCMTD1) as a putative E3 ubiquitin ligase substrate adaptor protein. The N-terminal domain of PCMTD1 contains l-isoaspartate and S-adenosylmethionine (AdoMet) binding motifs similar to those in PCMT1. This protein also has a C-terminal domain containing suppressor of cytokine signaling (SOCS) box ubiquitin ligase recruitment motifs found in substrate receptor proteins of the Cullin-RING E3 ubiquitin ligases. We demonstrate specific PCMTD1 binding to the canonical methyltransferase cofactor S-adenosylmethionine (AdoMet). Strikingly, while PCMTD1 is able to bind AdoMet, it does not demonstrate any l-isoaspartyl methyltransferase activity under the conditions tested here. However, this protein is able to associate with the Cullin-RING proteins Elongins B and C and Cul5 in vitro and in human cells. The previously uncharacterized PCMTD1 protein may therefore provide an alternate maintenance pathway for modified proteins in mammalian cells by acting as an E3 ubiquitin ligase adaptor protein.
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Affiliation(s)
- Rebeccah A Warmack
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Eric Z Pang
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Esther Peluso
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Jonathan D Lowenson
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Joseph Y Ong
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and Molecular Biology Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095, United States
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4
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Soliman R, Cordero-Maldonado ML, Martins TG, Moein M, Conrotte JF, Warmack RA, Skupin A, Crawford AD, Clarke SG, Linster CL. l-Isoaspartyl Methyltransferase Deficiency in Zebrafish Leads to Impaired Calcium Signaling in the Brain. Front Genet 2021; 11:612343. [PMID: 33552132 PMCID: PMC7859441 DOI: 10.3389/fgene.2020.612343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/21/2020] [Indexed: 11/13/2022] Open
Abstract
Isomerization of l-aspartyl and l-asparaginyl residues to l-isoaspartyl residues is one type of protein damage that can occur under physiological conditions and leads to conformational changes, loss of function, and enhanced protein degradation. Protein l-isoaspartyl methyltransferase (PCMT) is a repair enzyme whose action initiates the reconversion of abnormal l-isoaspartyl residues to normal l-aspartyl residues in proteins. Many lines of evidence support a crucial role for PCMT in the brain, but the mechanisms involved remain poorly understood. Here, we investigated PCMT activity and function in zebrafish, a vertebrate model that is particularly well-suited to analyze brain function using a variety of techniques. We characterized the expression products of the zebrafish PCMT homologous genes pcmt and pcmtl. Both zebrafish proteins showed a robust l-isoaspartyl methyltransferase activity and highest mRNA transcript levels were found in brain and testes. Zebrafish morphant larvae with a knockdown in both the pcmt and pcmtl genes showed pronounced morphological abnormalities, decreased survival, and increased isoaspartyl levels. Interestingly, we identified a profound perturbation of brain calcium homeostasis in these morphants. An abnormal calcium response upon ATP stimulation was also observed in mouse hippocampal HT22 cells knocked out for Pcmt1. This work shows that zebrafish is a promising model to unravel further facets of PCMT function and demonstrates, for the first time in vivo, that PCMT plays a pivotal role in the regulation of calcium fluxes.
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Affiliation(s)
- Remon Soliman
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Teresa G Martins
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Mahsa Moein
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jean-François Conrotte
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rebeccah A Warmack
- Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.,University of California, San Diego, La Jolla, CA, United States
| | - Alexander D Crawford
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, Oslo, Norway.,Institute for Orphan Drug Discovery, Bremer Innovations- und Technologiezentrum, Bremen, Germany
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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5
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Guo X, Ramirez I, Garcia YA, Velasquez EF, Gholkar AA, Cohn W, Whitelegge JP, Tofig B, Damoiseaux R, Torres JZ. DUSP7 regulates the activity of ERK2 to promote proper chromosome alignment during cell division. J Biol Chem 2021; 296:100676. [PMID: 33865857 PMCID: PMC8131738 DOI: 10.1016/j.jbc.2021.100676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 12/20/2022] Open
Abstract
Human cell division is a highly regulated process that relies on the accurate capture and movement of chromosomes to the metaphase plate. Errors in the fidelity of chromosome congression and alignment can lead to improper chromosome segregation, which is correlated with aneuploidy and tumorigenesis. These processes are known to be regulated by extracellular signal-regulated kinase 2 (ERK2) in other species, but the role of ERK2 in mitosis in mammals remains unclear. Here, we have identified the dual-specificity phosphatase 7 (DUSP7), known to display selectivity for ERK2, as important in regulating chromosome alignment. During mitosis, DUSP7 bound to ERK2 and regulated the abundance of active phospho-ERK2 through its phosphatase activity. Overexpression of DUSP7, but not catalytically inactive mutants, led to a decrease in the levels of phospho-ERK2 and mitotic chromosome misalignment, while knockdown of DUSP7 also led to defective chromosome congression that resulted in a prolonged mitosis. Consistently, knockdown or chemical inhibition of ERK2 or chemical inhibition of the MEK kinase that phosphorylates ERK2 led to chromosome alignment defects. Our results support a model wherein MEK-mediated phosphorylation and DUSP7-mediated dephosphorylation regulate the levels of active phospho-ERK2 to promote proper cell division.
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Affiliation(s)
- Xiao Guo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Ivan Ramirez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Yenni A Garcia
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Erick F Velasquez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Ankur A Gholkar
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Whitaker Cohn
- Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, California, USA; Molecular Biology Institute, University of California, Los Angeles, California, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, USA
| | - Bobby Tofig
- California NanoSystems Institute, University of California, Los Angeles, California, USA
| | - Robert Damoiseaux
- California NanoSystems Institute, University of California, Los Angeles, California, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, California, USA
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA; Molecular Biology Institute, University of California, Los Angeles, California, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, USA.
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6
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PROTEIN l-ISOASPARTYL METHYLTRANSFERASE (PIMT) in plants: regulations and functions. Biochem J 2020; 477:4453-4471. [PMID: 33245750 DOI: 10.1042/bcj20200794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023]
Abstract
Proteins are essential molecules that carry out key functions in a cell. However, as a result of aging or stressful environments, the protein undergoes a range of spontaneous covalent modifications, including the formation of abnormal l-isoaspartyl residues from aspartyl or asparaginyl residues, which can disrupt the protein's inherent structure and function. PROTEIN l-ISOASPARTYL METHYLTRANSFERASE (PIMT: EC 2.1.1.77), an evolutionarily conserved ancient protein repairing enzyme (PRE), converts such abnormal l-isoaspartyl residues to normal l-aspartyl residues and re-establishes the protein's native structure and function. Although originally discovered in animals as a PRE, PIMT emerged as a key PRE in plants, particularly in seeds, in which PIMT plays a predominant role in preserving seed vigor and viability for prolonged periods of time. Interestingly, higher plants encode a second PIMT (PIMT2) protein which possesses a unique N-terminal extension, and exhibits several distinct features and far more complexity than non-plant PIMTs. Recent studies indicate that the role of PIMT is not restricted to preserving seed vigor and longevity but is also implicated in enhancing the growth and survivability of plants under stressful environments. Furthermore, expression studies indicate the tantalizing possibility that PIMT is involved in various physiological processes apart from its role in seed vigor, longevity and plant's survivability under abiotic stress. This review article particularly describes new insights and emerging interest in all facets of this enzyme in plants along with a concise comparative overview on isoAsp formation, and the role and regulation of PIMTs across evolutionary diverse species. Additionally, recent methods and their challenges in identifying isoaspartyl containing proteins (PIMT substrates) are highlighted.
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7
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Lorenzo JR, Leonetti CO, Alonso LG, Sánchez IE. NGOME-Lite: Proteome-wide prediction of spontaneous protein deamidation highlights differences between taxa. Methods 2020; 200:15-22. [PMID: 33189829 DOI: 10.1016/j.ymeth.2020.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/01/2020] [Accepted: 11/10/2020] [Indexed: 12/31/2022] Open
Abstract
Asparagines in proteins deamidate spontaneously, which changes the chemical structure of a protein and often affects its function. Current prediction algorithms for asparagine deamidation require a structure as an input or are too slow to be applied at a proteomic scale. We present NGOME-Lite, a new version of our sequence-based predictor for spontaneous asparagine deamidation that is faster by over two orders of magnitude at a similar degree of accuracy. The algorithm takes into account intrinsic sequence propensities and slowing down of deamidation by local structure. NGOME-Lite can run in a proteomic analysis mode that provides the half-time of the intact form of each protein, predicted by taking into account sequence propensities and structural protection or sequence propensities only, and a structure protection factor. The detailed analysis mode also provides graphical output for all Asn residues in the query sequence. We applied NGOME-Lite to over 257,000 sequences in 38 proteomes and found that different taxa differ in their predicted deamidation dynamics. Spontaneous protein deamidation is faster in Eukarya than in Bacteria because of a higher degree of structural protection in the latter. Predicted protein deamidation half-lifes correlate with protein turnover in human, mouse, rat, C. elegans and budding yeast but not in two plants and two bacteria. NGOME-Lite is implemented in a docker container available at https://ngome.proteinphysiologylab.org.
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Affiliation(s)
- Juan R Lorenzo
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Buenos Aires, Argentina; Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro (FCV-UNCPBA), Tandil, Argentina
| | - César O Leonetti
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Buenos Aires, Argentina
| | - Leonardo G Alonso
- Instituto de Nanobiotecnología (NANOBIOTEC), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Ignacio E Sánchez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, Laboratorio de Fisiología de Proteínas, Buenos Aires, Argentina.
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8
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Sze SK, JebaMercy G, Ngan SC. Profiling the 'deamidome' of complex biosamples using mixed-mode chromatography-coupled tandem mass spectrometry. Methods 2020; 200:31-41. [PMID: 32418626 DOI: 10.1016/j.ymeth.2020.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 04/26/2020] [Accepted: 05/06/2020] [Indexed: 12/14/2022] Open
Abstract
Deamidation is a spontaneous degenerative protein modification (DPM) that disrupts the structure and function of both endogenous proteins and various therapeutic agents. While deamidation has long been recognized as a critical event in human aging and multiple degenerative diseases, research progress in this field has been restricted by the technical challenges associated with studying this DPM in complex biological samples. Asparagine (Asn) deamidation generates L-aspartic acid (L-Asp), D-aspartic acid (D-Asp), L-isoaspartic acid (L-isoAsp) or D-isoaspartic acid (D-isoAsp) residues at the same position of Asn in the affected protein, but each of these amino acids displays similar hydrophobicity and cannot be effectively separated by reverse phase liquid chromatography. The Asp and isoAsp isoforms are also difficult to resolve using mass spectrometry since they have the same mass and fragmentation pattern in MS/MS. Moreover, the 13C peaks of the amidated peptide are often misassigned as monoisotopic peaks of the corresponding deamidated peptides in protein database searches. Furthermore, typical protein isolation and proteomic sample preparation methods induce artificial deamidation that cannot be distinguished from the physiological forms. To better understand the role of deamidation in biological aging and degenerative pathologies, new technologies are now being developed to address these analytical challenges, including mixed mode electrostatic-interaction modified hydrophilic interaction liquid chromatography (emHILIC). When coupled to high resolution, high accuracy tandem mass spectrometry this technology enables unprecedented, proteome-wide study of the 'deamidome' of complex samples. The current article therefore reviews recent advances in sample preparation methods, emHILIC-MS/MS technology, and MS instrumentation / data processing approaches to achieving accurate and reliable characterization of protein deamidation in complex biological and clinical samples.
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Affiliation(s)
- Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Gnanasekaran JebaMercy
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - SoFong Cam Ngan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
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9
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Warmack RA, Shawa H, Liu K, Lopez K, Loo JA, Horwitz J, Clarke SG. The l-isoaspartate modification within protein fragments in the aging lens can promote protein aggregation. J Biol Chem 2019; 294:12203-12219. [PMID: 31239355 DOI: 10.1074/jbc.ra119.009052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/05/2019] [Indexed: 01/15/2023] Open
Abstract
Transparency in the lens is accomplished by the dense packing and short-range order interactions of the crystallin proteins in fiber cells lacking organelles. These features are accompanied by a lack of protein turnover, leaving lens proteins susceptible to a number of damaging modifications and aggregation. The loss of lens transparency is attributed in part to such aggregation during aging. Among the damaging post-translational modifications that accumulate in long-lived proteins, isomerization at aspartate residues has been shown to be extensive throughout the crystallins. In this study of the human lens, we localize the accumulation of l-isoaspartate within water-soluble protein extracts primarily to crystallin peptides in high-molecular weight aggregates and show with MS that these peptides are from a variety of crystallins. To investigate the consequences of aspartate isomerization, we investigated two αA crystallin peptides 52LFRTVLDSGISEVR65 and 89VQDDFVEIH98, identified within this study, with the l-isoaspartate modification introduced at Asp58 and Asp91, respectively. Importantly, whereas both peptides modestly increase protein precipitation, the native 52LFRTVLDSGISEVR65 peptide shows higher aggregation propensity. In contrast, the introduction of l-isoaspartate within a previously identified anti-chaperone peptide from water-insoluble aggregates, αA crystallin 66SDRDKFVIFL(isoAsp)VKHF80, results in enhanced amyloid formation in vitro The modification of this peptide also increases aggregation of the lens chaperone αB crystallin. These findings may represent multiple pathways within the lens wherein the isomerization of aspartate residues in crystallin peptides differentially results in peptides associating with water-soluble or water-insoluble aggregates. Here the eye lens serves as a model for the cleavage and modification of long-lived proteins within other aging tissues.
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Affiliation(s)
- Rebeccah A Warmack
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Harrison Shawa
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Kate Liu
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Katia Lopez
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Joseph Horwitz
- Molecular Biology Institute, UCLA, Los Angeles, California 90095; Jules Stein Eye Institute, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095.
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10
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Yin L, Harwood CS. Functional divergence of annotated l-isoaspartate O-methyltransferases in an α-proteobacterium. J Biol Chem 2019; 294:2854-2861. [PMID: 30578298 DOI: 10.1074/jbc.ra118.006546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/14/2018] [Indexed: 12/28/2022] Open
Abstract
Spontaneous formation of isoaspartates (isoDs) often causes protein damage. l-Isoaspartate O-methyltransferase (PIMT) repairs isoD residues by catalyzing the formation of an unstable l-isoaspartyl methyl ester that spontaneously converts to an l-aspartyl residue. PIMTs are widely distributed in all three domains of life and have been studied most intensively in connection with their role in protein repair and aging in plants and animals. Studies of bacterial PIMTs have been limited to Escherichia coli, which has one PIMT. The α-proteobacterium Rhodopseudomonas palustris has three annotated PIMT genes, one of which (rpa2580) has been found to be important for cellular longevity in a growth-arrested state. However, the biochemical activities of these three R. palustris PIMTs are unknown. Here, we expressed and characterized all three annotated PIMT proteins, finding that two of them, RPA0376 and RPA2838, had PIMT activity, whereas RPA2580 did not. RPA0376 and RPA2838 single- and double-deletion mutants did not differ in longevity from WT R. palustris and did not exhibit elevated levels of isoD residues in aged cells. Comparative sequence analyses revealed that RPA2580 belongs to a separate phylogenetic group of annotated PIMT proteins present in the α-proteobacteria. Our results suggest that this group of proteins is not involved in repair of protein isoD residues. In addition, the bona fide bacterial PIMT enzymes may play a different or subtler role in bacterial physiology than previously suggested.
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Affiliation(s)
- Liang Yin
- From the Department of Microbiology, University of Washington, Seattle, Washington 98195
| | - Caroline S Harwood
- From the Department of Microbiology, University of Washington, Seattle, Washington 98195
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11
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Hao P, Adav SS, Gallart-Palau X, Sze SK. Recent advances in mass spectrometric analysis of protein deamidation. MASS SPECTROMETRY REVIEWS 2017; 36:677-692. [PMID: 26763661 DOI: 10.1002/mas.21491] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 12/28/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
Protein deamidation has been proposed to represent a "molecular clock" that progressively disrupts protein structure and function in human degenerative diseases and natural aging. Importantly, this spontaneous process can also modify therapeutic proteins by altering their purity, stability, bioactivity, and antigenicity during drug synthesis and storage. Deamidation occurs non-enzymatically in vivo, but can also take place spontaneously in vitro, hence artificial deamidation during proteomic sample preparation can hamper efforts to identify and quantify endogenous deamidation of complex proteomes. To overcome this, mass spectrometry (MS) can be used to conduct rigorous site-specific characterization of protein deamidation due to the high sensitivity, speed, and specificity offered by this technique. This article reviews recent progress in MS analysis of protein deamidation and discusses the strengths and limitations of common "top-down" and "bottom-up" approaches. Recent advances in sample preparation methods, chromatographic separation, MS technology, and data processing have for the first time enabled the accurate and reliable characterization of protein modifications in complex biological samples, yielding important new data on how deamidation occurs across the entire proteome of human cells and tissues. These technological advances will lead to a better understanding of how deamidation contributes to the pathology of biological aging and major degenerative diseases. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:677-692, 2017.
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Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Sunil S Adav
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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12
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Monocyte adhesion to atherosclerotic matrix proteins is enhanced by Asn-Gly-Arg deamidation. Sci Rep 2017; 7:5765. [PMID: 28720870 PMCID: PMC5515959 DOI: 10.1038/s41598-017-06202-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/09/2017] [Indexed: 12/25/2022] Open
Abstract
Atherosclerosis arises from leukocyte infiltration and thickening of the artery walls and constitutes a major component of vascular disease pathology, but the molecular events underpinning this process are not fully understood. Proteins containing an Asn-Gly-Arg (NGR) motif readily undergo deamidation of asparagine to generate isoDGR structures that bind to integrin αvβ3 on circulating leukocytes. Here we report the identification of isoDGR motifs in human atherosclerotic plaque components including extracellular matrix (ECM) proteins fibronectin and tenascin C, which have been strongly implicated in human atherosclerosis. We further demonstrate that deamidation of NGR motifs in fibronectin and tenascin C leads to increased adhesion of the monocytic cell line U937 and enhanced binding of primary human monocytes, except in the presence of a αvβ3-blocking antibody or the αv-selective inhibitor cilengitide. In contrast, under the same deamidating conditions monocyte-macrophages displayed only weak binding to the alternative ECM component vitronectin which lacks NGR motifs. Together, these findings confirm a critical role for isoDGR motifs in mediating leukocyte adhesion to the ECM via integrin αvβ3 and suggest that protein deamidation may promote the pathological progression of human atherosclerosis by enhancing monocyte recruitment to developing plaques.
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13
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Faserl K, Sarg B, Maurer V, Lindner HH. Exploiting charge differences for the analysis of challenging post-translational modifications by capillary electrophoresis-mass spectrometry. J Chromatogr A 2017; 1498:215-223. [DOI: 10.1016/j.chroma.2017.01.086] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 01/25/2017] [Accepted: 01/29/2017] [Indexed: 12/27/2022]
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14
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Wang J, Rajbhandari P, Damianov A, Han A, Sallam T, Waki H, Villanueva CJ, Lee SD, Nielsen R, Mandrup S, Reue K, Young SG, Whitelegge J, Saez E, Black DL, Tontonoz P. RNA-binding protein PSPC1 promotes the differentiation-dependent nuclear export of adipocyte RNAs. J Clin Invest 2017; 127:987-1004. [PMID: 28192372 DOI: 10.1172/jci89484] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/15/2016] [Indexed: 12/14/2022] Open
Abstract
A highly orchestrated gene expression program establishes the properties that define mature adipocytes, but the contribution of posttranscriptional factors to the adipocyte phenotype is poorly understood. Here we have shown that the RNA-binding protein PSPC1, a component of the paraspeckle complex, promotes adipogenesis in vitro and is important for mature adipocyte function in vivo. Cross-linking and immunoprecipitation followed by RNA sequencing revealed that PSPC1 binds to intronic and 3'-untranslated regions of a number of adipocyte RNAs, including the RNA encoding the transcriptional regulator EBF1. Purification of the paraspeckle complex from adipocytes further showed that PSPC1 associates with the RNA export factor DDX3X in a differentiation-dependent manner. Remarkably, PSPC1 relocates from the nucleus to the cytoplasm during differentiation, coinciding with enhanced export of adipogenic RNAs. Mice lacking PSPC1 in fat displayed reduced lipid storage and adipose tissue mass and were resistant to diet-induced obesity and insulin resistance due to a compensatory increase in energy expenditure. These findings highlight a role for PSPC1-dependent RNA maturation in the posttranscriptional control of adipose development and function.
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15
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Singh SK, Hasan SS, Zakharov SD, Naurin S, Cohn W, Ma J, Whitelegge JP, Cramer WA. Trans-membrane Signaling in Photosynthetic State Transitions: REDOX- AND STRUCTURE-DEPENDENT INTERACTION IN VITRO BETWEEN STT7 KINASE AND THE CYTOCHROME b6f COMPLEX. J Biol Chem 2016; 291:21740-21750. [PMID: 27539852 DOI: 10.1074/jbc.m116.732545] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/01/2016] [Indexed: 12/11/2022] Open
Abstract
Trans-membrane signaling involving a serine/threonine kinase (Stt7 in Chlamydomonas reinhardtii) directs light energy distribution between the two photosystems of oxygenic photosynthesis. Oxidation of plastoquinol mediated by the cytochrome b6f complex on the electrochemically positive side of the thylakoid membrane activates the kinase domain of Stt7 on the trans (negative) side, leading to phosphorylation and redistribution ("state transition") of the light-harvesting chlorophyll proteins between the two photosystems. The molecular description of the Stt7 kinase and its interaction with the cytochrome b6f complex are unknown or unclear. In this study, Stt7 kinase has been cloned, expressed, and purified in a heterologous host. Stt7 kinase is shown to be active in vitro in the presence of reductant and purified as a tetramer, as determined by analytical ultracentrifugation, electron microscopy, and electrospray ionization mass spectrometry, with a molecular weight of 332 kDa, consisting of an 83.41-kDa monomer. Far-UV circular dichroism spectra show Stt7 to be mostly α-helical and document a physical interaction with the b6f complex through increased thermal stability of Stt7 secondary structure. The activity of wild-type Stt7 and its Cys-Ser mutant at positions 68 and 73 in the presence of a reductant suggest that the enzyme does not require a disulfide bridge for its activity as suggested elsewhere. Kinase activation in vivo could result from direct interaction between Stt7 and the b6f complex or long-range reduction of Stt7 by superoxide, known to be generated in the b6f complex by quinol oxidation.
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Affiliation(s)
| | | | | | | | - Whitaker Cohn
- the Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90024
| | - Jia Ma
- Biophysical Analysis Laboratory, Bindley Bioscience Center,Purdue University, West Lafayette, Indiana 47907 and
| | - Julian P Whitelegge
- the Pasarow Mass Spectrometry Laboratory, NPI-Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90024
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16
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(p)ppGpp-Dependent Persisters Increase the Fitness of Escherichia coli Bacteria Deficient in Isoaspartyl Protein Repair. Appl Environ Microbiol 2016; 82:5444-54. [PMID: 27371580 DOI: 10.1128/aem.00623-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/16/2016] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED The l-isoaspartyl protein carboxyl methyltransferase (PCM) repairs protein damage resulting from spontaneous conversion of aspartyl or asparaginyl residues to isoaspartate and increases long-term stationary-phase survival of Escherichia coli under stress. In the course of studies intended to examine PCM function in metabolically inactive cells, we identified pcm as a gene whose mutation influences the formation of ofloxacin-tolerant persisters. Specifically, a Δpcm mutant produced persisters for an extended period in stationary phase, and a ΔglpD mutation drastically increased persisters in a Δpcm background, reaching 23% of viable cells. The high-persister double mutant showed much higher competitive fitness than the pcm mutant in competition with wild type during long-term stationary phase, suggesting a link between persistence and the mitigation of unrepaired protein damage. We hypothesized that reduced metabolism in the high-persister strain might retard protein damage but observed no gross differences in metabolism relative to wild-type or single-mutant strains. However, methylglyoxal, which accumulates in glpD mutants, also increased fitness, suggesting a possible mechanism. High-level persister formation in the Δpcm ΔglpD mutant was dependent on guanosine pentaphosphate [(p)ppGpp] and polyphosphate. In contrast, persister formation in the Δpcm mutant was (p)ppGpp independent and thus may occur by a distinct pathway. We also observed an increase in conformationally unstable proteins in the high-persister strain and discuss this as a possible trigger for persistence as a response to unrepaired protein damage. IMPORTANCE Protein damage is an important factor in the survival and function of cells and organisms. One specific form of protein damage, the formation of the abnormal amino acid isoaspartate, can be repaired by a nearly universally conserved enzyme, PCM. PCM-directed repair is associated with stress survival and longevity in bacteria, insects, worms, plants, mice, and humans, but much remains to be learned about the specific effects of protein damage and repair. This paper identifies an unexpected connection between isoaspartyl protein damage and persisters, subpopulations in bacterial cultures showing increased tolerance to antibiotics. In the absence of PCM, the persister population in Escherichia coli bacteria increased, especially if the metabolic gene glpD was also mutated. High levels of persisters in pcm glpD double mutants correlated with increased fitness of the bacteria in a competition assay, and the fitness was dependent on the signal molecule (p)ppGpp; this may represent an alternative pathway for responding to protein damage.
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17
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Deuteration protects asparagine residues against racemization. Amino Acids 2016; 48:2189-96. [PMID: 27169868 DOI: 10.1007/s00726-016-2250-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/02/2016] [Indexed: 12/24/2022]
Abstract
Racemization in proteins and peptides at sites of L-asparaginyl and L-aspartyl residues contributes to their spontaneous degradation, especially in the biological aging process. Amino acid racemization involves deprotonation of the alpha carbon and replacement of the proton in the opposite stereoconfiguration; this reaction is much faster for aspartate/asparagine than for other amino acids because these residues form a succinimide ring in which resonance stabilizes the carbanion resulting from proton loss. To determine if the replacement of the hydrogen atom on the alpha carbon with a deuterium atom might decrease the rate of racemization and thus stabilize polypeptides, we synthesized a hexapeptide, VYPNGA, in which the three carbon-bound protons in the asparaginyl residue were replaced with deuterium atoms. Upon incubation of this peptide in pH 7.4 buffer at 37 °C, we found that the rate of deamidation via the succinimide intermediate was unchanged by the presence of the deuterium atoms. However, the accumulation of the D-aspartyl and D-isoaspartyl-forms resulting from racemization and hydrolysis of the succinimide was decreased more than five-fold in the deuterated peptide over a 20 day incubation at physiological temperature and pH. Additionally, we found that the succinimide intermediate arising from the degradation of the deuterated asparaginyl peptide was slightly less likely to open to the isoaspartyl configuration than was the protonated succinimide. These findings suggest that the kinetic isotope effect resulting from the presence of deuteriums in asparagine residues can limit the accumulation of at least some of the degradation products that arise as peptides and proteins age.
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18
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Warmack RA, Mansilla E, Goya RG, Clarke SG. Racemized and Isomerized Proteins in Aging Rat Teeth and Eye Lens. Rejuvenation Res 2016; 19:309-17. [PMID: 26650547 DOI: 10.1089/rej.2015.1778] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The quantification of aspartic acid racemization in the proteins of nonmetabolically active tissues can be used as a measure of chronological aging in humans and other long-lived organisms. However, very few studies have been conducted in shorter-lived animals such as rodents, which are increasingly used as genetic and metabolic models of aging. An initial study had reported significant changes in the ratio of d- to l-aspartate in rat molars with age. Using a sensitive HPLC method for the determination of d- and l-aspartate from protein hydrolysates, we found no accumulation of d-aspartate in the molars of 17 rats that ranged in age from 2 to 44 months, and the amount of d-aspartate per molar did not correspond with molar eruption date as had been previously reported. However, developing an alternate approach, we found significant accumulation of isomerized aspartyl residues in eye lens proteins that are also formed by spontaneous degradation processes. In this study, we used the human protein l-isoaspartate/d-aspartate O-methyltransferase (PCMT1) as an analytical reagent in a sensitive and convenient procedure that could be used to rapidly examine multiple samples simultaneously. We found levels of isomerized aspartyl residues to be about 35 times higher in the lens extracts of 18-month-old rats versus 2-month-old rats, suggesting that isomerization may be an effective marker for biological aging in this range of ages. Importantly, we found that the accumulation appeared to plateau in rats of 18 months and older, indicating that potentially novel mechanisms for removing altered proteins may develop with age.
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Affiliation(s)
- Rebeccah A Warmack
- 1 Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California , Los Angeles, Los Angeles, California
| | - Eduardo Mansilla
- 2 Tissue Engineering, Regenerative Medicine and Cell Therapies Laboratory, CUCAIBA, Buenos Aires Province Ministry of Public Health , Buenos Aires, Argentina
| | - Rodolfo G Goya
- 3 Institute for Biochemical Research (INIBIOLP)-Cathedra of Histology B, Cathedra of Pathology B, School of Medicine, National University of La Plata , La Plata, Argentina
| | - Steven G Clarke
- 1 Department of Chemistry and Biochemistry, The Molecular Biology Institute, University of California , Los Angeles, Los Angeles, California
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19
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Mildly acidic conditions eliminate deamidation artifact during proteolysis: digestion with endoprotease Glu-C at pH 4.5. Amino Acids 2016; 48:1059-1067. [PMID: 26748652 DOI: 10.1007/s00726-015-2166-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/25/2015] [Indexed: 10/22/2022]
Abstract
Common yet often overlooked, deamidation of peptidyl asparagine (Asn or N) generates aspartic acid (Asp or D) or isoaspartic acid (isoAsp or isoD). Being a spontaneous, non-enzymatic protein post-translational modification, deamidation artifact can be easily introduced during sample preparation, especially proteolysis where higher-order structures are removed. This artifact not only complicates the analysis of bona fide deamidation but also affects a wide range of chemical and enzymatic processes; for instance, the newly generated Asp and isoAsp residues may block or introduce new proteolytic sites, and also convert one Asn peptide into multiple species that affect quantification. While the neutral to mildly basic conditions for common proteolysis favor deamidation, mildly acidic conditions markedly slow down the process. Unlike other commonly used endoproteases, Glu-C remains active under mildly acid conditions. As such, as demonstrated herein, deamidation artifact during proteolysis was effectively eliminated by simply performing Glu-C digestion at pH 4.5 in ammonium acetate, a volatile buffer that is compatible with mass spectrometry. Moreover, nearly identical sequence specificity was observed at both pH's (8.0 for ammonium bicarbonate), rendering Glu-C as effective at pH 4.5. In summary, this method is generally applicable for protein analysis as it requires minimal sample preparation and uses the readily available Glu-C protease.
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20
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Gholkar AA, Senese S, Lo YC, Vides E, Contreras E, Hodara E, Capri J, Whitelegge JP, Torres JZ. The X-Linked-Intellectual-Disability-Associated Ubiquitin Ligase Mid2 Interacts with Astrin and Regulates Astrin Levels to Promote Cell Division. Cell Rep 2015; 14:180-8. [PMID: 26748699 DOI: 10.1016/j.celrep.2015.12.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 10/13/2015] [Accepted: 12/04/2015] [Indexed: 12/13/2022] Open
Abstract
Mid1 and Mid2 are ubiquitin ligases that regulate microtubule dynamics and whose mutation is associated with X-linked developmental disorders. We show that astrin, a microtubule-organizing protein, co-purifies with Mid1 and Mid2, has an overlapping localization with Mid1 and Mid2 at intercellular bridge microtubules, is ubiquitinated by Mid2 on lysine 409, and is degraded during cytokinesis. Mid2 depletion led to astrin stabilization during cytokinesis, cytokinetic defects, multinucleated cells, and cell death. Similarly, expression of a K409A mutant astrin in astrin-depleted cells led to the accumulation of K409A on intercellular bridge microtubules and an increase in cytokinetic defects, multinucleated cells, and cell death. These results indicate that Mid2 regulates cell division through the ubiquitination of astrin on K409, which is critical for its degradation and proper cytokinesis. These results could help explain how mutation of MID2 leads to misregulation of microtubule organization and the downstream disease pathology associated with X-linked intellectual disabilities.
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Affiliation(s)
- Ankur A Gholkar
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Silvia Senese
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yu-Chen Lo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Program in Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Edmundo Vides
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ely Contreras
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emmanuelle Hodara
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joseph Capri
- Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory, The Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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21
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Prediction of Spontaneous Protein Deamidation from Sequence-Derived Secondary Structure and Intrinsic Disorder. PLoS One 2015; 10:e0145186. [PMID: 26674530 PMCID: PMC4682632 DOI: 10.1371/journal.pone.0145186] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/01/2015] [Indexed: 02/07/2023] Open
Abstract
Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www.embnet.qb.fcen.uba.ar/ in the subpage “Protein and nucleic acid structure and sequence analysis”.
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22
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Banerjee S, Dutta T, Lahiri S, Sengupta S, Gangopadhyay A, Kumar Karri S, Chakraborty S, Bhattacharya D, Ghosh AK. Enzymatic attributes of an l-isoaspartyl methyltransferase from Candida utilis and its role in cell survival. Biochem Biophys Rep 2015; 4:59-75. [PMID: 29124188 PMCID: PMC5668901 DOI: 10.1016/j.bbrep.2015.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/23/2015] [Accepted: 08/24/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUNDS Spontaneous deamidation and isoaspartate (IsoAsp) formation contributes to aging and reduced longevity in cells. A protein-l-isoaspartate (d-aspartate) O-methyltransferase (PCMT) is responsible for minimizing IsoAsp moieties in most organisms. METHODS PCMT was purified in its native form from yeast Candida utilis. The role of the native PCMT in cell survival and protein repair was investigated by manipulating intracellular PCMT levels with Oxidized Adenosine (AdOx) and Lithium Chloride (LiCl). Proteomic Identification of possible cellular targets was carried out using 2-dimensional gel electrophoresis, followed by on-Blot methylation and mass spectrometric analysis. RESULTS The 25.4 kDa native PCMT from C. utilis was found to have a Km of 3.5 µM for AdoMet and 33.36 µM for IsoAsp containing Delta Sleep Inducing Peptide (DSIP) at pH 7.0. Native PCMT comprises of 232 amino acids which is coded by a 698 bp long nucleotide sequence. Phylogenetic comparison revealed the PCMT to be related more closely with the prokaryotic homologs. Increase in PCMT levels in vivo correlated with increased cell survival under physiological stresses. PCMT expression was seen to be linked with increased intracellular reactive oxygen species (ROS) concentration. Proteomic identification of possible cellular substrates revealed that PCMT interacts with proteins mainly involved with cellular housekeeping. PCMT effected both functional and structural repair in aged proteins in vitro. GENERAL SIGNIFICANCE Identification of PCMT in unicellular eukaryotes like C. utilis promises to make investigations into its control machinery easier owing to the familiarity and flexibility of the system.
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Affiliation(s)
- Shakri Banerjee
- Drug Development, Diagnostics and Biotechnology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Trina Dutta
- Drug Development, Diagnostics and Biotechnology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Sagar Lahiri
- Drug Development, Diagnostics and Biotechnology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Shinjinee Sengupta
- Drug Development, Diagnostics and Biotechnology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Anushila Gangopadhyay
- Drug Development, Diagnostics and Biotechnology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Suresh Kumar Karri
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Sandeep Chakraborty
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Debasish Bhattacharya
- Structural Biology and Bioinformatics Division, CSIR- Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
| | - Anil K. Ghosh
- Drug Development, Diagnostics and Biotechnology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, India
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23
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Gholkar AA, Senese S, Lo YC, Capri J, Deardorff WJ, Dharmarajan H, Contreras E, Hodara E, Whitelegge JP, Jackson PK, Torres JZ. Tctex1d2 associates with short-rib polydactyly syndrome proteins and is required for ciliogenesis. Cell Cycle 2015; 14:1116-25. [PMID: 25830415 PMCID: PMC4614626 DOI: 10.4161/15384101.2014.985066] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 10/28/2014] [Accepted: 11/03/2014] [Indexed: 12/26/2022] Open
Abstract
Short-rib polydactyly syndromes (SRPS) arise from mutations in genes involved in retrograde intraflagellar transport (IFT) and basal body homeostasis, which are critical for cilia assembly and function. Recently, mutations in WDR34 or WDR60 (candidate dynein intermediate chains) were identified in SRPS. We have identified and characterized Tctex1d2, which associates with Wdr34, Wdr60 and other dynein complex 1 and 2 subunits. Tctex1d2 and Wdr60 localize to the base of the cilium and their depletion causes defects in ciliogenesis. We propose that Tctex1d2 is a novel dynein light chain important for trafficking to the cilium and potentially retrograde IFT and is a new molecular link to understanding SRPS pathology.
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Affiliation(s)
- Ankur A. Gholkar
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Silvia Senese
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Yu-Chen Lo
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
- Program in Bioengineering; University of California; Los Angeles, CA USA
| | - Joseph Capri
- Pasarow Mass Spectrometry Laboratory; The Jane and Terry Semel Institute for Neuroscience and Human Behavior; David Geffen School of Medicine; University of California; Los Angeles, CA USA
| | - William J Deardorff
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Harish Dharmarajan
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Ely Contreras
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Emmanuelle Hodara
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory; The Jane and Terry Semel Institute for Neuroscience and Human Behavior; David Geffen School of Medicine; University of California; Los Angeles, CA USA
- Molecular Biology Institute; University of California; Los Angeles, CA USA
| | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology; Department of Microbiology & Immunology; Stanford University School of Medicine; Stanford, CA USA
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry; University of California; Los Angeles, CA USA
- Molecular Biology Institute; University of California; Los Angeles, CA USA
- Jonsson Comprehensive Cancer Center; University of California; Los Angeles, CA USA
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24
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Dimitrijevic A, Qin Z, Aswad DW. Isoaspartyl formation in creatine kinase B is associated with loss of enzymatic activity; implications for the linkage of isoaspartate accumulation and neurological dysfunction in the PIMT knockout mouse. PLoS One 2014; 9:e100622. [PMID: 24955845 PMCID: PMC4067349 DOI: 10.1371/journal.pone.0100622] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 05/29/2014] [Indexed: 01/12/2023] Open
Abstract
Isoaspartate (isoAsp) formation is a common type of spontaneous protein damage that is normally kept in check by the repair enzyme protein-L-isoaspartyl methyltransferase (PIMT). PIMT-KO (knockout) mice exhibit a pronounced neuropathology highlighted by death from an epileptic seizure at 30 to 60 days after birth. The mechanisms by which isoaspartyl damage disrupts normal brain function are incompletely understood. Proteomic analysis of the PIMT-KO mouse brain has shown that a number of key neuronal proteins accumulate high levels of isoAsp, but the extent to which their cellular functions is altered has yet to be determined. One of the major neuronal targets of PIMT is creatine kinase B (CKB), a well-characterized enzyme whose activity is relatively easy to assay. We show here that (1) the specific activity of CKB is significantly reduced in the brains of PIMT-deficient mice, (2) that in vitro aging of recombinant CKB results in significant accumulation of isoAsp sites with concomitant loss of enzymatic activity, and (3) that incubation of in vitro aged CKB with PIMT and its methyl donor S-adenosyl-L-methionine substantially repairs the aged CKB with regard to both its isoAsp content and its enzymatic activity. These results, combined with similarity in phenotypes of PIMT-KO and CKB-KO mice, suggests that loss of normal CKB structure and function contributes to the mechanisms by which isoAsp accumulation leads to CNS dysfunction in the PIMT-KO mouse.
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Affiliation(s)
- Aleksandra Dimitrijevic
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Zhenxia Qin
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
| | - Dana W Aswad
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, California, United States of America
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