1
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Wang L, Han X, Wang Y, Wei X, Liu S, Shao S, Yang S, Sun L, Xin F. Rational Design for Broadened Substrate Specificity and Enhanced Activity of a Novel Acetyl Xylan Esterase from Bacteroides thetaiotaomicron. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:6665-6675. [PMID: 34074097 DOI: 10.1021/acs.jafc.1c00750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gut bacteria-derived enzymes play important roles in the metabolism of dietary fiber through enabling the hydrolysis of polysaccharides. In this study, we identified and characterized a 29 kDa novel acetyl xylan esterase, BTAxe1, from Bacteroides thetaiotaomicron VPI5482. Then, we solved the structure of BTAxe1 and performed the rational design. Mutants N65S and N65A increased the activities toward short-chain (pNPA, pNPB) to near four-fold, and gained the activities toward longer-chain substrate (pNPO). Molecular docking analysis showed that the mutant N65S had a larger substrate binding pocket than the wild type. Hydrolysis studies using natural substrates showed that either N65S or N65A showed higher activity of that of wild-type, yielding 131.31 and 136.09 mM of acetic acid from xylan. This is the first study on the rational design of gut bacteria-derived Axes with broadened substrate specificity and enhanced activity, which can be referenced by other acetyl esterases or gut-derived enzymes.
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Affiliation(s)
- Luyao Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Han
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar 161000, China
| | - Yulu Wang
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Wei
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shujun Liu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuli Shao
- College of Life Science and Agriculture Forestry, Qiqihar University, Qiqihar 161000, China
| | - Shaoqing Yang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Lichao Sun
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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2
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Choi WS, Liu B, Shen Z, Yang W. Structure of human BCCIP and implications for binding and modification of partner proteins. Protein Sci 2021; 30:693-699. [PMID: 33452718 DOI: 10.1002/pro.4026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 11/09/2022]
Abstract
BCCIP was isolated based on its interactions with tumor suppressors BRCA2 and p21. Knockdown or knockout of BCCIP causes embryonic lethality in mice. BCCIP deficient cells exhibit impaired cell proliferation and chromosome instability. BCCIP also plays a key role in biogenesis of ribosome 60S subunits. BCCIP is conserved from yeast to humans, but it has no discernible sequence similarity to proteins of known structures. Here we report two crystal structures of an N-terminal truncated human BCCIPβ, consisting of residues 61-314. Structurally BCCIP is similar to GCN5-related acetyltransferases (GNATs) but contains different sequence motifs. Moreover, both acetyl-CoA and substrate-binding grooves are altered in BCCIP. A large 19-residue flap over the putative CoA binding site adopts either an open or closed conformation in BCCIP. The substrate binding groove is significantly reduced in size and is positively charged despite the acidic isoelectric point of BCCIP. BCCIP has potential binding sites for partner proteins and may have enzymatic activity.
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Affiliation(s)
- Woo Suk Choi
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, USA
| | - Bochao Liu
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, USA
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3
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Chang YY, Hagawa S, Hsu CH. Adaptation of thermophilic acetyltransferase to a water-mediated catalytic mechanism. Chem Commun (Camb) 2020; 56:10537-10540. [PMID: 32780067 DOI: 10.1039/d0cc04305b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The common mechanism of N-acetyltransferases (NATs) is a water-mediated catalysis, which is not conducive to thermophilic acetyltransferases. The crystal structure of SsArd1 shows an ordered catalytic water molecule in a trap formed by the residues H88 and E127. Structure-guided mutagenesis, kinetic studies and MD simulation indicated that the turnover rates of H88A, E127A and H88A/E127A mutants were low, but that of the H88E/E127H mutant could be restored to the level of the wild type.
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Affiliation(s)
- Yu-Yung Chang
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan.
| | - Sora Hagawa
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan. and Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
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4
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Protein N-Terminal Acetylation: Structural Basis, Mechanism, Versatility, and Regulation. Trends Biochem Sci 2020; 46:15-27. [PMID: 32912665 DOI: 10.1016/j.tibs.2020.08.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/15/2022]
Abstract
N-terminal acetylation (NTA) is one of the most widespread protein modifications, which occurs on most eukaryotic proteins, but is significantly less common on bacterial and archaea proteins. This modification is carried out by a family of enzymes called N-terminal acetyltransferases (NATs). To date, 12 NATs have been identified, harboring different composition, substrate specificity, and in some cases, modes of regulation. Recent structural and biochemical analysis of NAT proteins allows for a comparison of their molecular mechanisms and modes of regulation, which are described here. Although sharing an evolutionarily conserved fold and related catalytic mechanism, each catalytic subunit uses unique elements to mediate substrate-specific activity, and use NAT-type specific auxiliary and regulatory subunits, for their cellular functions.
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5
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The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nat Commun 2020; 11:3145. [PMID: 32561711 PMCID: PMC7305310 DOI: 10.1038/s41467-020-16784-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/18/2020] [Indexed: 11/08/2022] Open
Abstract
While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii, we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.
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6
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Abboud A, Bédoucha P, Byška J, Arnesen T, Reuter N. Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases. Comput Struct Biotechnol J 2020; 18:532-547. [PMID: 32206212 PMCID: PMC7078549 DOI: 10.1016/j.csbj.2020.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
N-terminal acetyltransferases (NATs) belong to the superfamily of acetyltransferases. They are enzymes catalysing the transfer of an acetyl group from acetyl coenzyme A to the N-terminus of polypeptide chains. N-terminal acetylation is one of the most common protein modifications. To date, not much is known on the molecular basis for the exclusive substrate specificity of NATs. All NATs share a common fold called GNAT. A characteristic of NATs is the β6β7 hairpin loop covering the active site and forming with the α1α2 loop a narrow tunnel surrounding the catalytic site in which cofactor and polypeptide meet and exchange an acetyl group. We investigated the dynamics-function relationships of all available structures of NATs covering the three domains of Life. Using an elastic network model and normal mode analysis, we found a common dynamics pattern conserved through the GNAT fold; a rigid V-shaped groove formed by the β4 and β5 strands and splitting the fold in two dynamical subdomains. Loops α1α2, β3β4 and β6β7 all show clear displacements in the low frequency normal modes. We characterized the mobility of the loops and show that even limited conformational changes of the loops along the low-frequency modes are able to significantly change the size and shape of the ligand binding sites. Based on the fact that these movements are present in most low-frequency modes, and common to all NATs, we suggest that the α1α2 and β6β7 loops may regulate ligand uptake and the release of the acetylated polypeptide.
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Affiliation(s)
- Angèle Abboud
- Department of Informatics, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Pierre Bédoucha
- Department of Informatics, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Jan Byška
- Department of Informatics, University of Bergen, Bergen, Norway
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Thomas Arnesen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Department of Surgery, Haukeland University Hospital, Bergen, Norway
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Chemistry, University of Bergen, Bergen, Norway
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7
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Chien MH, Lee WJ, Yang YC, Tan P, Pan KF, Liu YC, Tsai HC, Hsu CH, Wen YC, Hsiao M, Hua KT. N-α-acetyltransferase 10 protein promotes metastasis by stabilizing matrix metalloproteinase-2 protein in human osteosarcomas. Cancer Lett 2018; 433:86-98. [PMID: 29960050 DOI: 10.1016/j.canlet.2018.06.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/21/2018] [Accepted: 06/23/2018] [Indexed: 01/10/2023]
Abstract
N-α-Acetyltransferase 10 protein (Naa10p) mediates N-terminal acetylation of nascent proteins. Oncogenic or tumor suppressive roles of Naa10p were reported in cancers. Here, we report an oncogenic role of Naa10p in promoting metastasis of osteosarcomas. Higher NAA10 transcripts were observed in metastatic osteosarcoma tissues compared to non-metastatic tissues and were also correlated with a worse prognosis of patients. Knockdown and overexpression of Naa10p in osteosarcoma cells respectively led to decreased and increased cell migratory/invasive abilities. Re-expression of Naa10p, but not an enzymatically inactive mutant, relieved suppression of the invasive ability in vitro and metastasis in vivo imposed by Naa10p-knockdown. According to protease array screening, we identified that matrix metalloproteinase (MMP)-2 was responsible for the Naa10p-induced invasive phenotype. Naa10p was directly associated with MMP-2 protein through its acetyltransferase domain and maintained MMP-2 protein stability via NatA complex activity. MMP-2 expression levels were also significantly correlated with Naa10p levels in osteosarcoma tissues. These results reveal a novel function of Naa10p in the regulation of cell invasiveness by preventing MMP-2 protein degradation that is crucial during osteosarcoma metastasis.
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Affiliation(s)
- Ming-Hsien Chien
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Medical Education and Research, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
| | - Wei-Jiunn Lee
- Department of Medical Education and Research, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Department of Urology, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Chieh Yang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; The Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Peng Tan
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ke-Fan Pan
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Cheng Liu
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsiao-Chi Tsai
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yu-Ching Wen
- Department of Urology, School of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Urology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Michael Hsiao
- The Genomics Research Center, Academia Sinica, Taipei, Taiwan; Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kuo-Tai Hua
- Graduate Institute of Toxicology, College of Medicine, National Taiwan University, Taipei, Taiwan.
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8
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Chen J, Li H, Wang T, Sun S, Liu J, Chen J. Production of N α-acetyl Tα1-HSA through in vitro acetylation by RimJ. Oncotarget 2017; 8:95247-95255. [PMID: 29221124 PMCID: PMC5707018 DOI: 10.18632/oncotarget.20259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/13/2017] [Indexed: 01/12/2023] Open
Abstract
Thymosin alpha 1 (Tα1) is an important immunomodulating agent with various clinical applications. The natural form of Tα1 is Nα -acetylated, which was supposed to be related to in vivo stability of the hormone. In this study, fusion protein Tα1-HSA was constructed and expressed in Pichia pastoris. RimJ, a Nα -acetyltransferase from E.coli, was also overexpressed and purified to homogeneity. In vitro acetylation of Tα1-HSA in the presence of RimJ and acetyl coenzyme A resulted in Nα -acetyl Tα1-HSA. The Nα -acetylation was determined by LC-MS/MS. Kinetic assay indicated that RimJ had a higher affinity to desacetyl Tα1 than to Tα1-HSA. Bioactivity assay revealed fully retained activity of Tα1 when the hormone was connected to the N-terminus of the fusion protein, while the activity was compromised in our previously constructed HSA-Tα1. With fully retained activity and N-terminal acetylation, Nα -acetyl Tα1-HSA was expected to be a more promising pharmaceutical agent than Tα1.
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Affiliation(s)
- Jing Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Haibin Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Tao Wang
- Department of Neurosurgery, Shanghai 5th People's Hospital, Shanghai Medical College, Fudan University, Shanghai 200240, China
| | - Shuyang Sun
- Overseas Education College, Nanjing Tech University, Nanjing 211816, China
| | - Jia Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Jianhua Chen
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
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9
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Hong H, Cai Y, Zhang S, Ding H, Wang H, Han A. Molecular Basis of Substrate Specific Acetylation by N-Terminal Acetyltransferase NatB. Structure 2017; 25:641-649.e3. [PMID: 28380339 DOI: 10.1016/j.str.2017.03.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/24/2017] [Accepted: 03/09/2017] [Indexed: 11/29/2022]
Abstract
The NatB N-terminal acetyltransferase specifically acetylates the N-terminal group of substrate protein peptides starting with Met-Asp/Glu/Asn/Gln. How NatB recognizes and acetylates these substrates remains unknown. Here, we report crystal structures of a NatB holoenzyme from Candida albicans in the presence of its co-factor CoA and substrate peptides. The auxiliary subunit Naa25 of NatB forms a horseshoe-like deck to hold specifically its catalytic subunit Naa20. The first two amino acids Met and Asp of a substrate peptide mediate the major interactions with the active site in the Naa20 subunit. The hydrogen bonds between the substrate Asp and pocket residues of Naa20 are essential to determine the NatB substrate specificity. Moreover, a hydrogen bond between the amino group of the substrate Met and a carbonyl group in the Naa20 active site directly anchors the substrate toward acetyl-CoA. Together, these structures define a unique molecular mechanism of specific N-terminal acetylation acted by NatB.
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Affiliation(s)
- Haiyan Hong
- State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Shijun Zhang
- State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Hongyan Ding
- State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China
| | - Haitao Wang
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, Department of Biomedical Sciences, School of Life Sciences, Xiamen University, Xiang'an, Xiamen 361102, China.
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10
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Homology modeling and prediction of the amino acid residues participating in the transfer of acetyl-CoA to arylalkylamine by the N-acetyltransferase from Chryseobacterium sp. Biotechnol Lett 2017; 39:1699-1707. [PMID: 28721586 DOI: 10.1007/s10529-017-2399-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVES To predict the amino acid residues playing important roles in acetyl-CoA and substrate binding and to study the acetyl group transfer mechanism of Chryseobacterium sp. 5-3B N-acetyltransferase (5-3B NatA). RESULTS A 3-dimensional homology model of 5-3B NatA was constructed to compare the theoretical structure of this compound with the structures of previously reported proteins belonging to the bacterial GCN5 N-acetyltransferase family. Homology modeling of the 5-3B NatA structure and a characterization of the enzyme's kinetic parameters identified the essential amino acid residues involved in binding and acetyl-group transfer. 126Leu, 132Leu, and 135Lys were implicated in the binding of phosphopantothenic acid, and 100Tyr and 131Lys in that of adenosyl biphosphate. The data supported the participation of 83Glu and 133Tyr in catalyzing acetyl-group transfer to L-2-phenylglycine. CONCLUSIONS 5-3B NatA catalyzes the enantioselective N-acetylation of L-2-phenylglycine via a ternary complex comprising the enzyme, acetyl-CoA, and the substrate.
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11
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Shin S, Choe J. Crystal structure of Pseudomonas aeruginosa N-acetyltransferase PA4534. Biochem Biophys Res Commun 2017; 487:236-240. [PMID: 28412357 DOI: 10.1016/j.bbrc.2017.04.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/10/2017] [Indexed: 11/29/2022]
Abstract
The GCN5-related N-acetyltransferase (GNAT) superfamily includes a large and diverse group of enzymes that catalyzes the transfer of an acetyl group from acetyl coenzyme A (Ac-CoA) to the amine group of a substrate. Substrates include protein N-terminus, lysine of histone tails, and other small molecules such as aminoglycoside, serotonin, and glucose-6-phosphate. GNAT superfamily of proteins is involved in many physiologically important reactions in eukaryotes and prokaryotes. However, functions of many GNATs remain unknown and PA4534 is one of those uncharacterized GNAT proteins from Pseudomonas aeruginosa. To investigate functions of the PA4534, we determined the apo and Ac-CoA bound PA4534 structures. Our structures showed that PA4534 shared common characteristic structures with other GNAT family N-acetyltransferases and contained a potential substrate binding tunnel close to the bound Ac-CoA.
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Affiliation(s)
- Sungwook Shin
- Department of Life Science, University of Seoul, Seoul 130-743, South Korea
| | - Jungwoo Choe
- Department of Life Science, University of Seoul, Seoul 130-743, South Korea.
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12
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Vorontsov EA, Rensen E, Prangishvili D, Krupovic M, Chamot-Rooke J. Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics. Mol Cell Proteomics 2016; 15:3388-3404. [PMID: 27555370 PMCID: PMC5098037 DOI: 10.1074/mcp.m116.058073] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 07/06/2016] [Indexed: 12/18/2022] Open
Abstract
Protein post-translational methylation has been reported to occur in archaea, including members of the genus Sulfolobus, but has never been characterized on a proteome-wide scale. Among important Sulfolobus proteins carrying such modification are the chromatin proteins that have been described to be methylated on lysine side chains, resembling eukaryotic histones in that aspect. To get more insight into the extent of this modification and its dynamics during the different growth steps of the thermoacidophylic archaeon S. islandicus LAL14/1, we performed a global and deep proteomic analysis using a combination of high-throughput bottom-up and top-down approaches on a single high-resolution mass spectrometer. 1,931 methylation sites on 751 proteins were found by the bottom-up analysis, with methylation sites on 526 proteins monitored throughout three cell culture growth stages: early-exponential, mid-exponential, and stationary. The top-down analysis revealed 3,978 proteoforms arising from 681 proteins, including 292 methylated proteoforms, 85 of which were comprehensively characterized. Methylated proteoforms of the five chromatin proteins (Alba1, Alba2, Cren7, Sul7d1, Sul7d2) were fully characterized by a combination of bottom-up and top-down data. The top-down analysis also revealed an increase of methylation during cell growth for two chromatin proteins, which had not been evidenced by bottom-up. These results shed new light on the ubiquitous lysine methylation throughout the S. islandicus proteome. Furthermore, we found that S. islandicus proteins are frequently acetylated at the N terminus, following the removal of the N-terminal methionine. This study highlights the great value of combining bottom-up and top-down proteomics for obtaining an unprecedented level of accuracy in detecting differentially modified intact proteoforms. The data have been deposited to the ProteomeXchange with identifiers PXD003074 and PXD004179.
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Affiliation(s)
- Egor A Vorontsov
- From the ‡Structural Mass Spectrometry and Proteomics Unit, Structural Biology and Chemistry Department, Institut Pasteur, 75015 Paris, France
| | - Elena Rensen
- §Unit of the Molecular Biology of Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - David Prangishvili
- §Unit of the Molecular Biology of Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - Mart Krupovic
- §Unit of the Molecular Biology of Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015 Paris, France; julia.chamot-rooke@pasteur
| | - Julia Chamot-Rooke
- From the ‡Structural Mass Spectrometry and Proteomics Unit, Structural Biology and Chemistry Department, Institut Pasteur, 75015 Paris, France; julia.chamot-rooke@pasteur
- ¶UMR3528 CNRS, Paris, France
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13
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Young BH, Caldwell TA, McKenzie AM, Kokhan O, Berndsen CE. Characterization of the structure and catalytic activity of Legionella pneumophila VipF. Proteins 2016; 84:1422-30. [PMID: 27315603 DOI: 10.1002/prot.25087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/31/2016] [Accepted: 06/13/2016] [Indexed: 11/05/2022]
Abstract
The pathogenic bacteria Legionella pneumophila is known to cause Legionnaires' Disease, a severe pneumonia that can be fatal to immunocompromised individuals and the elderly. Shohdy et al. identified the L. pneumophila vacuole sorting inhibitory protein VipF as a putative N-acetyltransferase based on sequence homology. We have characterized the basic structural and functional properties of VipF to confirm this original functional assignment. Sequence conservation analysis indicates two putative CoA-binding regions within VipF. Homology modeling and small angle X-ray scattering suggest a monomeric, dual-domain structure joined by a flexible linker. Each domain contains the characteristic beta-splay motif found in many acetyltransferases, suggesting that VipF may contain two active sites. Docking experiments suggest reasonable acetyl-CoA binding locations within each beta-splay motif. Broad substrate screening indicated that VipF is capable of acetylating chloramphenicol and both domains are catalytically active. Given that chloramphenicol is not known to be N-acetylated, this is a surprising finding suggesting that VipF is capable of O-acetyltransferase activity. Proteins 2016; 84:1422-1430. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Byron H Young
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Tracy A Caldwell
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Aidan M McKenzie
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Christopher E Berndsen
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807.
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14
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Pathak D, Bhat AH, Sapehia V, Rai J, Rao A. Biochemical evidence for relaxed substrate specificity of Nα-acetyltransferase (Rv3420c/rimI) of Mycobacterium tuberculosis. Sci Rep 2016; 6:28892. [PMID: 27353550 PMCID: PMC4926160 DOI: 10.1038/srep28892] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/08/2016] [Indexed: 12/11/2022] Open
Abstract
Nα-acetylation is a naturally occurring irreversible modification of N-termini of proteins catalyzed by Nα-acetyltransferases (NATs). Although present in all three domains of life, it is little understood in bacteria. The functional grouping of NATs into six types NatA - NatF, in eukaryotes is based on subunit requirements and stringent substrate specificities. Bacterial orthologs are phylogenetically divergent from eukaryotic NATs, and only a couple of them are characterized biochemically. Accordingly, not much is known about their substrate specificities. Rv3420c of Mycobacterium tuberculosis is a NAT ortholog coding for RimI(Mtb). Using in vitro peptide-based enzyme assays and mass-spectrometry methods, we provide evidence that RimI(Mtb) is a protein Nα-acetyltransferase of relaxed substrate specificity mimicking substrate specificities of eukaryotic NatA, NatC and most competently that of NatE. Also, hitherto unknown acetylation of residues namely, Asp, Glu, Tyr and Leu by a bacterial NAT (RimI(Mtb)) is elucidated, in vitro. Based on in vivo acetylation status, in vitro assay results and genetic context, a plausible cellular substrate for RimI(Mtb) is proposed.
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Affiliation(s)
- Deepika Pathak
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
| | - Aadil Hussain Bhat
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
| | - Vandana Sapehia
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
| | - Jagdish Rai
- Institute of Forensic Science & Criminology, Panjab University, Sector 14, Chandigarh, 160014, India
| | - Alka Rao
- CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh, 160036, India
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15
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Rathore OS, Faustino A, Prudêncio P, Van Damme P, Cox CJ, Martinho RG. Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms. Sci Rep 2016; 6:21304. [PMID: 26861501 PMCID: PMC4748286 DOI: 10.1038/srep21304] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/18/2016] [Indexed: 11/09/2022] Open
Abstract
Protein N-terminal acetylation is an ancient and ubiquitous co-translational modification catalyzed by a highly conserved family of N-terminal acetyltransferases (NATs). Prokaryotes have at least 3 NATs, whereas humans have six distinct but highly conserved NATs, suggesting an increase in regulatory complexity of this modification during eukaryotic evolution. Despite this, and against our initial expectations, we determined that NAT diversification did not occur in the eukaryotes, as all six major human NATs were most likely present in the Last Eukaryotic Common Ancestor (LECA). Furthermore, we also observed that some NATs were actually secondarily lost during evolution of major eukaryotic lineages; therefore, the increased complexity of the higher eukaryotic proteome occurred without a concomitant diversification of NAT complexes.
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Affiliation(s)
- Om Singh Rathore
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,ProRegeM-PhD Program in Mechanisms of Disease and Regenerative Medicine, Faro, Portugal
| | - Alexandra Faustino
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal
| | - Pedro Prudêncio
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2781-901, Portugal
| | - Petra Van Damme
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Cymon J Cox
- Center of Marine Sciences, University of Algarve, Faro, Portugal
| | - Rui Gonçalo Martinho
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2781-901, Portugal
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16
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Qin Z, Xiao Y, Yang X, Mesters JR, Yang S, Jiang Z. A unique GCN5-related glucosamine N-acetyltransferase region exist in the fungal multi-domain glycoside hydrolase family 3 β-N-acetylglucosaminidase. Sci Rep 2015; 5:18292. [PMID: 26669854 PMCID: PMC4680927 DOI: 10.1038/srep18292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 11/16/2015] [Indexed: 11/17/2022] Open
Abstract
Glycoside hydrolase (GH) family 3 β-N-acetylglucosaminidases widely exist in the filamentous fungi, which may play a key role in chitin metabolism of fungi. A multi-domain GH family 3 β-N-acetylglucosaminidase from Rhizomucor miehei (RmNag), exhibiting a potential N-acetyltransferase region, has been recently reported to show great potential in industrial applications. In this study, the crystal structure of RmNag was determined at 2.80 Å resolution. The three-dimensional structure of RmNag showed four distinctive domains, which belong to two distinguishable functional regions — a GH family 3 β-N-acetylglucosaminidase region (N-terminal) and a N-acetyltransferase region (C-terminal). From structural and functional analysis, the C-terminal region of RmNag was identified as a unique tandem array linking general control non-derepressible 5 (GCN5)-related N-acetyltransferase (GNAT), which displayed glucosamine N-acetyltransferase activity. Structural analysis of this glucosamine N-acetyltransferase region revealed that a unique glucosamine binding pocket is located in the pantetheine arm binding terminal region of the conserved CoA binding pocket, which is different from all known GNAT members. This is the first structural report of a glucosamine N-acetyltransferase, which provides novel structural information about substrate specificity of GNATs. The structural and functional features of this multi-domain β-N-acetylglucosaminidase could be useful in studying the catalytic mechanism of GH family 3 proteins.
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Affiliation(s)
- Zhen Qin
- College of Food Science and Nutritional Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100083, China
| | - Yibei Xiao
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Xinbin Yang
- College of Food Science and Nutritional Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100083, China
| | - Jeroen R Mesters
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Shaoqing Yang
- College of Food Science and Nutritional Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100083, China
| | - Zhengqiang Jiang
- College of Food Science and Nutritional Engineering, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100083, China
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17
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Chang YY, Hsu CH. Multiple Conformations of the Loop Region Confers Heat-Resistance on SsArd1, a Thermophilic NatA. Chembiochem 2015; 17:214-7. [PMID: 26593285 DOI: 10.1002/cbic.201500568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Indexed: 11/10/2022]
Abstract
Structural comparison indicates that the loop region between β3 and β4 of SsArd1 is extended relative to the corresponding region in mesophilic Nats, and forms a plastic hydrogen-bond network mainly at two serine residues. Strikingly, two single-point mutants showed ∼3 °C decrease in melting temperature, and two other variants showed ∼7 °C decrease; this correlated with significantly reduced enzymatic activity. To our knowledge, this is the first discovery of a loop region capable of remarkably improving protein thermostability. This provides a novel route to engineer heat-resistant proteins.
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Affiliation(s)
- Yu-Yung Chang
- Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, Center for Systems Biology, Genome and Systems Biology Degree Program, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.
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18
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The biological functions of Naa10 - From amino-terminal acetylation to human disease. Gene 2015; 567:103-31. [PMID: 25987439 DOI: 10.1016/j.gene.2015.04.085] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/07/2023]
Abstract
N-terminal acetylation (NTA) is one of the most abundant protein modifications known, and the N-terminal acetyltransferase (NAT) machinery is conserved throughout all Eukarya. Over the past 50 years, the function of NTA has begun to be slowly elucidated, and this includes the modulation of protein-protein interaction, protein-stability, protein function, and protein targeting to specific cellular compartments. Many of these functions have been studied in the context of Naa10/NatA; however, we are only starting to really understand the full complexity of this picture. Roughly, about 40% of all human proteins are substrates of Naa10 and the impact of this modification has only been studied for a few of them. Besides acting as a NAT in the NatA complex, recently other functions have been linked to Naa10, including post-translational NTA, lysine acetylation, and NAT/KAT-independent functions. Also, recent publications have linked mutations in Naa10 to various diseases, emphasizing the importance of Naa10 research in humans. The recent design and synthesis of the first bisubstrate inhibitors that potently and selectively inhibit the NatA/Naa10 complex, monomeric Naa10, and hNaa50 further increases the toolset to analyze Naa10 function.
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