1
|
Cao L, Beiser M, Koos JD, Orlova M, Elashal HE, Schröder HV, Link AJ. Cellulonodin-2 and Lihuanodin: Lasso Peptides with an Aspartimide Post-Translational Modification. J Am Chem Soc 2021; 143:11690-11702. [PMID: 34283601 PMCID: PMC9206484 DOI: 10.1021/jacs.1c05017] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lasso peptides are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by their threaded structure. Besides the class-defining isopeptide bond, other post-translational modifications (PTMs) that further tailor lasso peptides have been previously reported. Using genome mining tools, we identified a subset of lasso peptide biosynthetic gene clusters (BGCs) that are colocalized with genes encoding protein l-isoaspartyl methyltransferase (PIMT) homologues. PIMTs have an important role in protein repair, restoring isoaspartate residues formed from asparagine deamidation to aspartate. Here we report a new function for PIMT enzymes in the post-translational modification of lasso peptides. The PIMTs associated with lasso peptide BGCs first methylate an l-aspartate side chain found within the ring of the lasso peptide. The methyl ester is then converted into a stable aspartimide moiety, endowing the lasso peptide ring with rigidity relative to its unmodified counterpart. We describe the heterologous expression and structural characterization of two examples of aspartimide-modified lasso peptides from thermophilic Gram-positive bacteria. The lasso peptide cellulonodin-2 is encoded in the genome of actinobacterium Thermobifida cellulosilytica, while lihuanodin is encoded in the genome of firmicute Lihuaxuella thermophila. Additional genome mining revealed PIMT-containing lasso peptide BGCs in 48 organisms. In addition to heterologous expression, we have reconstituted PIMT-mediated aspartimide formation in vitro, showing that lasso peptide-associated PIMTs transfer methyl groups very rapidly as compared to canonical PIMTs. Furthermore, in stark contrast to other characterized lasso peptide PTMs, the methyltransferase functions only on lassoed substrates.
Collapse
Affiliation(s)
- Li Cao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Moshe Beiser
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Joseph D. Koos
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
| | - Margarita Orlova
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Hader E. Elashal
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - Hendrik V. Schröder
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
| | - A. James Link
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, United States
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, United States
| |
Collapse
|
2
|
Liang R, Robb FT, Onstott TC. Aspartic acid racemization and repair in the survival and recovery of hyperthermophiles after prolonged starvation at high temperature. FEMS Microbiol Ecol 2021; 97:6330453. [PMID: 34323966 DOI: 10.1093/femsec/fiab112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/27/2021] [Indexed: 11/14/2022] Open
Abstract
Long-term survivability is well-known for microorganisms in nutrient-depleted environments, but the damage accrued by proteins and the associated repair processes during the starvation and recovery phase of microbial life still remain enigmatic. We focused on aspartic acid (Asp) racemization and repair in the survival of Pyrococcus furiosus and Thermococcus litoralis under starvation conditions at high temperature. Despite the dramatic decrease of viability over time, 0.002% of P. furiosus cells (2.1×103 cells/mL) and 0.23% of T. litoralis cells (2.3×105 cells/mL) remained viable after 25 and 50 days, respectively. The D/L Asp ratio in the starved cells was approximately half of those from the autoclaved cells, suggesting that the starving cells were capable of partially repairing racemized Asp. Transcriptomic analyses of the recovered cells of T. litoralis indicated that the gene encoding Protein-L-isoaspartate (D-aspartate) O-methyltransferase (PIMT) might be involved in the repair of damaged proteins by converting D-Asp back to L-Asp during the resuscitation of starved cells. Collectively, our results provided evidence that Asp underwent racemization in the surviving hyperthermophilic cells under starved conditions and PIMT played a critical role in the repair of abnormal aspartyl residues during the initial recovery of starved, yet still viable, cells.
Collapse
Affiliation(s)
- Renxing Liang
- Department of Geosciences, Princeton University, Princeton, New Jersey, 08544, USA
| | - Frank T Robb
- Institute of Marine and Environmental Technology, University of Maryland, Baltimore, Maryland, 21202, USA
- Department of Microbiology and Immunology, University of Maryland, Baltimore, Maryland, 21202, USA
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, New Jersey, 08544, USA
| |
Collapse
|
3
|
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.
Collapse
|
4
|
Riggs DL, Gomez SV, Julian RR. Sequence and Solution Effects on the Prevalence of d-Isomers Produced by Deamidation. ACS Chem Biol 2017; 12:2875-2882. [PMID: 28984444 PMCID: PMC5696650 DOI: 10.1021/acschembio.7b00686] [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] [Indexed: 11/30/2022]
Abstract
Deamidation of asparagine is a spontaneous and irreversible post-translational modification associated with a growing list of human diseases. While pervasive, deamidation is often overlooked because it represents a relatively minor chemical change. Structural and functional characterization of this modification is complicated because deamidation of asparagine yields four isomeric forms of Asp. Herein, radical directed dissociation (RDD), in conjunction with mass spectrometry, is used to identify and quantify all four isomers in a series of model peptides that were subjected to various deamidation conditions. Although primary sequence significantly influences the rate of deamidation, it has little impact on the relative proportions of the product isomers. Furthermore, the addition of ammonia can be used to increase the rate of deamidation without significantly perturbing isomer populations. Conversely, external factors such as buffer conditions and temperature alter product distributions but exhibit less dramatic effects on the deamidation rate. Strikingly, the common laboratory and biologically significant bicarbonate buffer is found to strongly promote racemization, yielding increased amounts of d-Asp and d-isoAsp. These outcomes following deamidation have broad implications in human aging and should be considered during the development of protein-based therapeutics.
Collapse
Affiliation(s)
- Dylan L. Riggs
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Sonia V. Gomez
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
| |
Collapse
|
5
|
Oda A, Noji I, Fukuyoshi S, Takahashi O. Prediction of binding modes between protein l-isoaspartyl (d-aspartyl) O-methyltransferase and peptide substrates including isomerized aspartic acid residues using in silico analytic methods for the substrate screening. J Pharm Biomed Anal 2015; 116:116-22. [DOI: 10.1016/j.jpba.2015.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 02/11/2015] [Accepted: 02/16/2015] [Indexed: 11/27/2022]
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Chatterjee T, Mukherjee D, Banerjee M, Chatterjee BK, Chakrabarti P. Crystal structure and activity of protein L-isoaspartyl-O-methyltransferase from Vibrio cholerae, and the effect of AdoHcy binding. Arch Biochem Biophys 2015; 583:140-9. [PMID: 26255776 DOI: 10.1016/j.abb.2015.08.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 11/17/2022]
Abstract
The repair enzyme Protein L-isoaspartyl-O-methyltransferase (PIMT) is widely distributed in various organisms. PIMT catalyzes S-adenosylmethionine (AdoMet) dependent methylation of abnormal L-isoaspartyl residues, formed by the deamidation of asparagines and isomerization of aspartates. We report the crystal structure of PIMT of Vibrio cholerae (VcPIMT), the aetiological agent for cholera, complexed with the demethylated cofactor S-adenosyl-L-homocysteine (AdoHcy) to 2.05 Å resolution. A stretch of residues (39-58), lining the substrate-binding site, is disordered. Urea-induced unfolding free energy for apo and VcPIMT-AdoHcy complex reveals greater stability for the cofactor-bound protein. The kinetic parameters for the methyltransferase activity of the recombinant VcPIMT was determined using a continuous spectrophotometric color-based assay using the peptide substrate [VYP(L-isoD)HA]. The enzyme exhibited activity higher than the Escherichia coli enzyme and closer to those from thermophilic bacteria and the mammalian source. The association constant for substrate binding is 2.29 × 10(6) M(-1), quite similar to that for AdoHcy. The crystal structure and the model of the peptide-bound structure indicate that the majority of the interactions used for cofactor/substrate binding are provided by the main-chain atoms. Evolutionary relationships derived based on a phylogenetic tree constructed using the PIMT sequences are in conformity with the crystal structures of nine AdoHcy-bound PIMTs.
Collapse
Affiliation(s)
- Tanaya Chatterjee
- Department of Biochemistry, Bose Institute, P1/12, CIT Scheme VIIM, Kolkata 700054, India
| | - Debadrita Mukherjee
- Bioinformatics Centre, Bose Institute, P1/12, CIT Scheme VIIM, Kolkata 700054, India
| | - Mousumi Banerjee
- Department of Biotechnology, West Bengal University of Technology, Kolkata 700064, India
| | - Barun K Chatterjee
- Department of Physics, Bose Institute, 93/1APC Road, Kolkata 700009, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P1/12, CIT Scheme VIIM, Kolkata 700054, India; Bioinformatics Centre, Bose Institute, P1/12, CIT Scheme VIIM, Kolkata 700054, India.
| |
Collapse
|
8
|
Computational investigation of the substrate recognition mechanism of protein d-aspartyl (l-isoaspartyl) O-methyltransferase by docking and molecular dynamics simulation studies and application to interpret size exclusion chromatography data. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3310-6. [DOI: 10.1016/j.jchromb.2011.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 06/03/2011] [Accepted: 06/14/2011] [Indexed: 11/19/2022]
|
9
|
Böhme L, Bär JW, Hoffmann T, Manhart S, Ludwig HH, Rosche F, Demuth HU. Isoaspartate residues dramatically influence substrate recognition and turnover by proteases. Biol Chem 2008. [DOI: 10.1515/bc.2008.123_bchm.just-accepted] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
10
|
16 Inhibition of mammalian protein methyltransferases by 5'-methylthioadenosine (MTA): A mechanism of action of dietary same? Enzymes 2007; 24:467-93. [PMID: 26718050 DOI: 10.1016/s1874-6047(06)80018-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
5'-deoxy-5'-methylthioadenosine (5'-methylthioadenosine, MTA) is a naturally occurring metabolite. As an experimental reagent, it has proved useful in providing investigators a window onto the role of protein methylation reactions in intact cells, although its mode of action is poorly understood in most cases. This chapter reevaluates its utility as a reagent. It appears now that MTA is at best a poor direct inhibitor of methyltransferases and that its effectiveness in intact cells may depend on its ability to inhibit S-adenosyl-l-homocysteine hydrolase. This chapter reviews recent evidence that points to an important role for MTA as an intermediary in the beneficial pharmaceutical action of orally ingested S-adenosyl-l-methionine (AdoMet, SAMe). These new results suggest that oral AdoMet may function not by enhancing the activity of cellular methyltransferases, as has been previously surmised, but by inhibiting their action. Such inhibition, particularly of protein methyltransferases involved in intracellular communication, may attenuate signal transduction pathways otherwise leading to inflammatory damage to tissues.
Collapse
|
11
|
Villa ST, Xu Q, Downie AB, Clarke SG. Arabidopsis Protein Repair L-Isoaspartyl Methyltransferases: Predominant Activities at Lethal Temperatures. PHYSIOLOGIA PLANTARUM 2006; 128:581-592. [PMID: 21076691 PMCID: PMC2980331 DOI: 10.1111/j.1399-3054.2006.00772.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein L-isoaspartyl (D-aspartyl) O-methyltransferases (EC 2.1.1.77; PIMT or PCMT) are enzymes that initiate the full or partial repair of damaged L-aspartyl and L-asparaginyl residues, respectively. These enzymes are found in most organisms and maintain a high degree of sequence conservation. Arabidopsis thaliana (Arabidopsis L. Heynh.) is unique among eukaryotes in that it contains two genes, rather than one, that encode PIMT isozymes. We describe a novel Arabidopsis PIMT isozyme, designated AtPIMT2αω, encoded by the PIMT2 gene (At5g50240). We characterized the enzymatic activity of the recombinant AtPIMT2αω in comparison to the other AtPIMT2 isozymes, AtPIMT1, and to the human PCMT ortholog, to better understand its role in Arabidopsis. All Arabidopsis PIMT isozymes are active over a relatively wide pH range. For AtPIMT2αω maximal activity is observed at 50 °C (a lethal temperature for Arabidopsis); this activity is almost ten times greater than the activity at the growth temperature of 25 °C. Interestingly, enzyme activity decreases after pre-incubation at temperatures above 30°C. A similar situation is found for the recombinant AtPIMT2ψ and the AtPIMT2ω isozymes, as well as for the AtPIMT1 and human PCMT1 enzymes. These results suggest that the short-term ability of these methyltransferases to initiate repair under extreme temperature conditions may be a common feature of both the plant and animal species.
Collapse
Affiliation(s)
- Sarah T Villa
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, Paul D. Boyer Hall, University of California, Los Angeles, California 90095-1569
| | | | | | | |
Collapse
|
12
|
O'Connor CM. 13 Protein L-isoaspartyl, D-aspartyl O-methyltransferases: Catalysts for protein repair. Enzymes 2006; 24:385-433. [PMID: 26718047 DOI: 10.1016/s1874-6047(06)80015-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Protein L-isoaspartyl, D-aspartyl O-methyltransferases (PIMTs) are ancient enzymes distributed through all phylogenetic domains. PIMTs catalyze the methylation of L-isoaspartyl, and to a lesser extent D-aspartyl, residues arising from the spontaneous deamidation and isomerization of protein asparaginyl and aspartyl residues. PIMTs catalyze the methylation of isoaspartyl residues in a large number of primary sequence configurations, which accounts for the broad specificity of the enzyme for protein substrates both in vitro and in vivo. PIMT-catalyzed methylation of isoaspartyl substrates initiates the repair of the polypeptide backbone in its damaged substrates by a spontaneous mechanism that involves a succinimidyl intermediate. The repair process catalyzed by PEVITs is not completely efficient, however, leaving open the possibility that unidentified enzymatic activities cooperate with PIMT in the repair process. Structurally, PIMTs are members of the class I family of AdoMet-dependent methyltransferases. PIMTs have a unique topological arrangement of strands in the central β sheet that provides a signature for this class of enzymes. The regulation and physiological significance of PIMT has been studied in several model organisms. PIMTs are constitutively synthesized by cells, but they can be upregulated in response to conditions that are potentially damaging to protein structures, or when proteins are stored for prolonged periods of time. Disruption of PIMT genes in bacteria and simple eukaryotes produces subtle phenotypes that are apparent only under stress. Loss of PIMT function in transgenic mice leads to fatalepilepsy, suggesting that PIMT function is particularly important to neurons in mammals.
Collapse
Affiliation(s)
- Clare M O'Connor
- Biology Department Boston College 140 Commonwealth Avenue Chestnut Hill, MA 02467, USA
| |
Collapse
|
13
|
Xu Q, Belcastro MP, Villa ST, Dinkins RD, Clarke SG, Downie AB. A second protein L-isoaspartyl methyltransferase gene in Arabidopsis produces two transcripts whose products are sequestered in the nucleus. PLANT PHYSIOLOGY 2004; 136:2652-64. [PMID: 15347786 PMCID: PMC523330 DOI: 10.1104/pp.104.046094] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Revised: 05/31/2004] [Accepted: 06/07/2004] [Indexed: 05/18/2023]
Abstract
The spontaneous and deleterious conversion of l-asparaginyl and l-aspartyl protein residues to l-iso-Asp or d-Asp occurs as proteins age and is accelerated under stressful conditions. Arabidopsis (Arabidopsis L. Heynh.) contains two genes (At3g48330 and At5g50240) encoding protein-l-isoaspartate methyltransferase (EC 2.1.1.77; PIMT), an enzyme capable of correcting this damage. The gene located on chromosome 5 (PIMT2) produces two proteins differing by three amino acids through alternative 3' splice site selection in the first intron. Recombinant protein from both splicing variants has PIMT activity. Subcellular localization using cell fractionation followed by immunoblot detection, as well as confocal visualization of PIMT:GFP fusions, demonstrated that PIMT1 is cytosolic while a canonical nuclear localization signal, present in PIMT2psi and the shorter PIMT2omega, is functional. Multiplex reverse transcription-PCR was used to establish PIMT1 and PIMT2 transcript presence and abundance, relative to beta-TUBULIN, in various tissues and under a variety of stresses imposed on seeds and seedlings. PIMT1 transcript is constitutively present but can increase, along with PIMT2, in developing seeds presumably in response to increasing endogenous abscisic acid (ABA). Transcript from PIMT2 also increases in establishing seedlings due to exogenous ABA and applied stress presumably through an ABA-dependent pathway. Furthermore, cleaved amplified polymorphic sequences from PIMT2 amplicons determined that ABA preferentially enhances the production of PIMT2omega transcript in leaves and possibly in tissues other than germinating seeds.
Collapse
Affiliation(s)
- Qilong Xu
- Department of Horticulture, University of Kentucky Agriculture Experiment Station, S129, Agriculture Science Center North, University of Kentucky, 800 Rose Street, Lexington, KY 40546-0312, USA
| | | | | | | | | | | |
Collapse
|
14
|
Tanaka Y, Tsumoto K, Yasutake Y, Umetsu M, Yao M, Fukada H, Tanaka I, Kumagai I. How Oligomerization Contributes to the Thermostability of an Archaeon Protein. J Biol Chem 2004; 279:32957-67. [PMID: 15169774 DOI: 10.1074/jbc.m404405200] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To study how oligomerization may contribute to the thermostability of archaeon proteins, we focused on a hexameric protein, protein L-isoaspartyl-O-methyltransferase from Sulfolobus tokodaii (StoPIMT). The crystal structure shows that StoPIMT has a distinctive hexameric structure composed of monomers consisting of two domains: an S-adenosylmethionine-dependent methyltransferase fold domain and a C-terminal alpha-helical domain. The hexameric structure includes three interfacial contact regions: major, minor, and coiled-coil. Several C-terminal deletion mutants were constructed and characterized. The hexameric structure and thermostability were retained when the C-terminal alpha-helical domain (Tyr(206)-Thr(231)) was deleted, suggesting that oligomerization via coiled-coil association using the C-terminal alpha-helical domains did not contribute critically to hexamerization or to the increased thermostability of the protein. Deletion of three additional residues located in the major contact region, Tyr(203)-Asp(204)-Asp(205), led to a significant decrease in hexamer stability and chemico/thermostability. Although replacement of Thr(146) and Asp(204), which form two hydrogen bonds in the interface in the major contact region, with Ala did not affect hexamer formation, these mutations led to a significant decrease in thermostability, suggesting that two residues in the major contact region make significant contributions to the increase in stability of the protein via hexamerization. These results suggest that cooperative hexamerization occurs via interactions of "hot spot" residues and that a couple of interfacial hot spot residues are responsible for enhancing thermostability via oligomerization.
Collapse
Affiliation(s)
- Yoshikazu Tanaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 07, Aoba-ku, Sendai 980-8579, Japan
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Clarke S. Aging as war between chemical and biochemical processes: protein methylation and the recognition of age-damaged proteins for repair. Ageing Res Rev 2003; 2:263-85. [PMID: 12726775 DOI: 10.1016/s1568-1637(03)00011-4] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Deamidated, isomerized, and racemized aspartyl and asparaginyl residues represent a significant part of the spontaneous damage to proteins that results from the aging process. The accumulation of these altered residues can lead to the loss of protein function and the consequent loss of cellular function. However, almost all cells in nature contain a methyltransferase that can recognize the major damaged form of the L-isoaspartyl residue, and some of these enzymes can also recognize the racemized D-aspartyl residue. The methyl esterification reaction can initiate the conversion of these altered residues to the normal L-aspartyl form, although there is no evidence yet that the L-asparaginyl form can be regenerated. This enzyme, the protein L-isoaspartate (D-aspartate) O-methyltransferase (EC 2.1.1.77), thus functions as a protein repair enzyme. The importance of this enzyme in attenuating age-related protein damage can be seen by the phenotypes of organisms where the gene encoding has been disrupted, or where its expression has been augmented.
Collapse
Affiliation(s)
- Steven Clarke
- Department of Chemistry and Biochemistry, the Molecular Biology Institute, University of California, Los Angeles, CA 90095-1569, USA.
| |
Collapse
|
16
|
Ryttersgaard C, Griffith SC, Sawaya MR, MacLaren DC, Clarke S, Yeates TO. Crystal structure of human L-isoaspartyl methyltransferase. J Biol Chem 2002; 277:10642-6. [PMID: 11792715 DOI: 10.1074/jbc.m200229200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzyme l-isoaspartyl methyltransferase initiates the repair of damaged proteins by recognizing and methylating isomerized and racemized aspartyl residues in aging proteins. The crystal structure of the human enzyme containing a bound S-adenosyl-l-homocysteine cofactor is reported here at a resolution of 2.1 A. A comparison of the human enzyme to homologs from two other species reveals several significant differences among otherwise similar structures. In all three structures, we find that three conserved charged residues are buried in the protein interior near the active site. Electrostatics calculations suggest that these buried charges might make significant contributions to the energetics of binding the charged S-adenosyl-l-methionine cofactor and to catalysis. We suggest a possible structural explanation for the observed differences in reactivity toward the structurally similar l-isoaspartyl and d-aspartyl residues in the human, archael, and eubacterial enzymes. Finally, the human structure reveals that the known genetic polymorphism at residue 119 (Val/Ile) maps to an exposed region away from the active site.
Collapse
Affiliation(s)
- Carsten Ryttersgaard
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA
| | | | | | | | | | | |
Collapse
|