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Lee JK, Wang X, Wang J, Rosales JL, Lee KY. PKA inhibition kills L-asparaginase-resistant leukemic cells from relapsed acute lymphoblastic leukemia patients. Cell Death Discov 2024; 10:257. [PMID: 38802344 PMCID: PMC11130271 DOI: 10.1038/s41420-024-02028-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
Despite the success in treating newly diagnosed pediatric acute lymphoblastic leukemia (aLL), the long-term cure rate for the 20% of children who relapse is poor, making relapsed aLL the primary cause of cancer death in children. By unbiased genome-wide retroviral RNAi screening and knockdown studies, we previously discovered opioid receptor mu 1 (OPRM1) as a new aLL cell resistance biomarker for the aLL chemotherapeutic drug, L-asparaginase, i.e., OPRM1 loss triggers L-asparaginase resistance. Indeed, aLL cell OPRM1 level is inversely proportional to L-asparaginase IC50: the lower the OPRM1 level, the higher the L-asparaginase IC50, indicating that aLL cells expressing reduced OPRM1 levels show resistance to L-asparaginase. In the current study, we utilized OPRM1-expressing and -knockdown aLL cells as well as relapsed patient aLL cells to identify candidate targeted therapy for L-asparaginase-resistant aLL. In OPRM1-expressing cells, L-asparaginase induces apoptosis via a cascade of events that include OPRM1-mediated decline in [cAMP]i, downregulation of PKA-mediated BAD S118 phosphorylation that can be reversed by 8-CPT-cAMP, cyt C release from the mitochondria, and subsequent caspase activation and PARP1 cleavage. The critical role of PKA inhibition due to a decrease in [cAMP]i in this apoptotic process is evident in the killing of OPRM1-knockdown and low OPRM1-expressing relapsed patient aLL cells by the PKA inhibitors, H89 and 14-22 amide. These findings demonstrate for the first time that PKA can be targeted to kill aLL cells resistant to L-asparaginase due to OPRM1 loss, and that H89 and 14-22 amide may be utilized to destroy L-asparaginase-resistant patient aLL cells.
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Affiliation(s)
- Jung Kwon Lee
- Department of Cell Biology & Anatomy, Arnie Charbonneau Cancer and Alberta Children's Hospital Research Institutes, University of Calgary, Calgary, AB, Canada
| | - Xidi Wang
- Department of Pathogen Biology and Immunology, Health Science Center, Ningbo University, Ningbo, China
| | - Jinghua Wang
- Department of Hematology, Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jesusa L Rosales
- Department of Cell Biology & Anatomy, Arnie Charbonneau Cancer and Alberta Children's Hospital Research Institutes, University of Calgary, Calgary, AB, Canada
| | - Ki-Young Lee
- Department of Cell Biology & Anatomy, Arnie Charbonneau Cancer and Alberta Children's Hospital Research Institutes, University of Calgary, Calgary, AB, Canada.
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2
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Zhang D, Czapinska H, Bochtler M, Wlodawer A, Lubkowski J. RrA, an enzyme from Rhodospirillum rubrum, is a prototype of a new family of short-chain L-asparaginases. Protein Sci 2024; 33:e4920. [PMID: 38501449 PMCID: PMC10949315 DOI: 10.1002/pro.4920] [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: 11/22/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 03/20/2024]
Abstract
L-Asparaginases (ASNases) catalyze the hydrolysis of L-Asn to L-Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300-400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum, reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N-terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L-Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short-chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild-type RrA, both with and without bound L-Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand-alone subfamily of ASNases that can catalyze the hydrolysis of L-Asn to L-Asp despite the lack of the C-terminal domain that is present in all ASNases described structurally to date.
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Affiliation(s)
- Di Zhang
- Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
| | - Honorata Czapinska
- Laboratory of Structural BiologyInternational Institute of Molecular and Cell BiologyWarsawPoland
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Matthias Bochtler
- Laboratory of Structural BiologyInternational Institute of Molecular and Cell BiologyWarsawPoland
- Institute of Biochemistry and BiophysicsPolish Academy of SciencesWarsawPoland
| | - Alexander Wlodawer
- Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
| | - Jacek Lubkowski
- Center for Structural BiologyNational Cancer InstituteFrederickMarylandUSA
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3
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Sharon I, Hilvert D, Schmeing TM. Cyanophycin and its biosynthesis: not hot but very cool. Nat Prod Rep 2023; 40:1479-1497. [PMID: 37231979 DOI: 10.1039/d2np00092j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Covering: 1878 to early 2023Cyanophycin is a biopolymer consisting of a poly-aspartate backbone with arginines linked to each Asp sidechain through isopeptide bonds. Cyanophycin is made by cyanophycin synthetase 1 or 2 through ATP-dependent polymerization of Asp and Arg, or β-Asp-Arg, respectively. It is degraded into dipeptides by exo-cyanophycinases, and these dipeptides are hydrolyzed into free amino acids by general or dedicated isodipeptidase enzymes. When synthesized, chains of cyanophycin coalesce into large, inert, membrane-less granules. Although discovered in cyanobacteria, cyanophycin is made by species throughout the bacterial kingdom, and cyanophycin metabolism provides advantages for toxic bloom forming algae and some human pathogens. Some bacteria have developed dedicated schemes for cyanophycin accumulation and use, which include fine temporal and spatial regulation. Cyanophycin has also been heterologously produced in a variety of host organisms to a remarkable level, over 50% of the host's dry mass, and has potential for a variety of green industrial applications. In this review, we summarize the progression of cyanophycin research, with an emphasis on recent structural studies of enzymes in the cyanophycin biosynthetic pathway. These include several unexpected revelations that show cyanophycin synthetase to be a very cool, multi-functional macromolecular machine.
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Affiliation(s)
- Itai Sharon
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada, H3G 0B1.
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - T Martin Schmeing
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada, H3G 0B1.
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4
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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 DOI: 10.1038/s41598-023-34587-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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5
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Sharon I, McKay GA, Nguyen D, Schmeing TM. Discovery of cyanophycin dipeptide hydrolase enzymes suggests widespread utility of the natural biopolymer cyanophycin. Proc Natl Acad Sci U S A 2023; 120:e2216547120. [PMID: 36800389 PMCID: PMC9974463 DOI: 10.1073/pnas.2216547120] [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: 09/29/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Cyanophycin is a bacterial polymer mainly used for nitrogen storage. It is composed of a peptide backbone of L-aspartate residues with L-arginines attached to their side chains through isopeptide bonds. Cyanophycin is degraded in two steps: Cyanophycinase cleaves the polymer into β-Asp-Arg dipeptides, which are hydrolyzed into free Asp and Arg by enzymes possessing isoaspartyl dipeptide hydrolase activity. Two unrelated enzymes with this activity, isoaspartyl dipeptidase (IadA) and isoaspartyl aminopeptidase (IaaA) have been shown to degrade β-Asp-Arg dipeptides, but bacteria which encode cyanophycin-metabolizing genes can lack iaaA and iadA genes. In this study, we investigate a previously uncharacterized enzyme whose gene can cluster with cyanophycin-metabolizing genes. This enzyme, which we name cyanophycin dipeptide hydrolase (CphZ), is specific for dipeptides derived from cyanophycin degradation. Accordingly, a co-complex structure of CphZ and β-Asp-Arg shows that CphZ, unlike IadA or IaaA, recognizes all portions of its β-Asp-Arg substrate. Bioinformatic analyses showed that CphZ is found in very many proteobacteria and is homologous to an uncharacterized protein encoded in the "arginine/ornithine transport" (aot) operon of many pseudomonas species, including Pseudomonas aeruginosa. In vitro assays show that AotO is indeed a CphZ, and in cellulo growth experiments show that this enzyme and the aot operon allow P. aeruginosa to take up and use β-Asp-Arg as a sole carbon and nitrogen source. Together the results establish the novel, highly specific enzyme subfamily of CphZs, suggesting that cyanophycin is potentially used by a much wider range of bacteria than previously appreciated.
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Affiliation(s)
- Itai Sharon
- Department of Biochemistry, McGill University, Montréal, QCH3G 0B1, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, QCH3G 0B1, Canada
| | - Geoffrey A. McKay
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montréal, QCH4A 3J1, Canada
| | - Dao Nguyen
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Centre, Montréal, QCH4A 3J1, Canada
| | - T. Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QCH3G 0B1, Canada
- Centre de recherche en biologie structurale, McGill University, Montréal, QCH3G 0B1, Canada
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Van Trimpont M, Schalk AM, De Visser Y, Nguyen HA, Reunes L, Vandemeulebroecke K, Peeters E, Su Y, Lee H, Lorenzi PL, Chan WK, Mondelaers V, De Moerloose B, Lammens T, Goossens S, Van Vlierberghe P, Lavie A. In vivo stabilization of a less toxic asparaginase variant leads to a durable antitumor response in acute leukemia. Haematologica 2022; 108:409-419. [PMID: 35979719 PMCID: PMC9890011 DOI: 10.3324/haematol.2022.281390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2002] [Indexed: 02/03/2023] Open
Abstract
Asparagine is a non-essential amino acid since it can either be taken up via the diet or synthesized by asparagine synthetase. Acute lymphoblastic leukemia (ALL) cells do not express asparagine synthetase or express it only minimally, which makes them completely dependent on extracellular asparagine for their growth and survival. This dependency makes ALL cells vulnerable to treatment with L-asparaginase, an enzyme that hydrolyzes asparagine. To date, all clinically approved L-asparaginases have significant L-glutaminase co-activity, associated with non-immune related toxic side effects observed during therapy. Therefore, reduction of L-glutaminase co-activity with concomitant maintenance of its anticancer L-asparaginase effect may effectively improve the tolerability of this unique drug. Previously, we designed a new alternative variant of Erwinia chrysanthemi (ErA; Erwinaze) with decreased L-glutaminase co-activity, while maintaining its L-asparaginase activity, by the introduction of three key mutations around the active site (ErA-TM). However, Erwinaze and our ErA-TM variant have very short half-lives in vivo. Here, we show that the fusion of ErA-TM with an albumin binding domain (ABD)-tag significantly increases its in vivo persistence. In addition, we evaluated the in vivo therapeutic efficacy of ABD-ErA-TM in a B-ALL xenograft model of SUP-B15. Our results show a comparable long-lasting durable antileukemic effect between the standard-of-care pegylated-asparaginase and ABD-ErA-TM L-asparaginase, but with fewer co-glutaminase-related acute side effects. Since the toxic side effects of current L-asparaginases often result in treatment discontinuation in ALL patients, this novel ErA-TM variant with ultra-low L-glutaminase co-activity and long in vivo persistence may have great clinical potential.
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Affiliation(s)
- Maaike Van Trimpont
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Amanda M. Schalk
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Yanti De Visser
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Hien Anh Nguyen
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Lindy Reunes
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Katrien Vandemeulebroecke
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Evelien Peeters
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Ying Su
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago (UIC), Chicago, IL, USA,Biophysics Core at Research Resources Center, University of Illinois at Chicago (UIC), Chicago, IL, USA
| | - Philip L. Lorenzi
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wai-Kin Chan
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Veerle Mondelaers
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Barbara De Moerloose
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Tim Lammens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium,Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Steven Goossens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium,#PVV and AL contributed equally as co-senior authors
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, USA; The Jesse Brown VA Medical Center, Chicago, IL.
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7
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Sharon I, Grogg M, Hilvert D, Schmeing TM. The structure of cyanophycinase in complex with a cyanophycin degradation intermediate. Biochim Biophys Acta Gen Subj 2022; 1866:130217. [PMID: 35905922 DOI: 10.1016/j.bbagen.2022.130217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/07/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Cyanophycinases are serine protease family enzymes which are required for the metabolism of cyanophycin, the natural polymer multi-L-arginyl-poly(L-aspartic acid). Cyanophycinases degrade cyanophycin to β-Asp-Arg dipeptides, which enables use of this important store of fixed nitrogen. METHODS We used genetic code expansion to incorporate diaminopropionic acid into cyanophycinase in place of the active site serine, and determined a high-resolution structure of the covalent acyl-enzyme intermediate resulting from attack of cyanophycinase on a short cyanophycin segment. RESULTS The structure indicates that cyanophycin dipeptide residues P1 and P1' bind shallow pockets adjacent to the catalytic residues. We observe many cyanophycinase - P1 dipeptide interactions in the co-complex structure. Calorimetry measurements show that at least two cyanophycin dipeptides are needed for high affinity binding to cyanophycinase. We also characterized a putative cyanophycinase which we found to be structurally very similar but that shows no activity and could not be activated by mutation of its active site. GENERAL SIGNIFICANCE Despite its peptidic structure, cyanophycin is resistant to degradation by peptidases and other proteases. Our results help show how cyanophycinase can specifically bind and degrade this important polymer.
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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
| | - Marcel Grogg
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - T Martin Schmeing
- Department of Biochemistry and Centre de recherche en biologie structurale, McGill University, Montréal, QC H3G 0B1, Canada.
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8
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Andersen S, Nawrocki A, Johansen AE, Herrero-Fresno A, Menéndez VG, Møller-Jensen J, Olsen JE. Proteomes of Uropathogenic Escherichia coli Growing in Human Urine and in J82 Urinary Bladder Cells. Proteomes 2022; 10:proteomes10020015. [PMID: 35645373 PMCID: PMC9149909 DOI: 10.3390/proteomes10020015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 12/17/2022] Open
Abstract
Uropathogenic Escherichia coli (UPEC) are the most common cause of urinary tract infection (UTI). UPEC normally reside in the intestine, and during establishment of UTI, they undergo metabolic adaptations, first to urine and then upon tissue invasion to the bladder cell interior. To understand these adaptations, we used quantitative proteomic profiling to characterize protein expression of the UPEC strain UTI89 growing in human urine and when inside J82 bladder cells. In order to facilitate detection of UPEC proteins over the excess amount of eukaryotic proteins in bladder cells, we developed a method where proteins from UTI89 grown in MOPS and urine was spiked-in to enhance detection of bacterial proteins. More than 2000 E. coli proteins were detected. During growth in urine, proteins associated with iron acquisition and several amino acid uptake and biosynthesis systems, most prominently arginine metabolism, were significantly upregulated. During growth in J82 cells, proteins related to iron uptake and arginine metabolisms were likewise upregulated together with proteins involved in sulfur compound turnover. Ribosomal proteins were downregulated relative to growth in MOPS in this environment. There was no direct correlation between upregulated proteins and proteins reported to be essential for infections, showing that upregulation during growth does not signify that the proteins are essential for growth under a condition.
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Affiliation(s)
- Sisse Andersen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark; (S.A.); (A.E.J.); (A.H.-F.); (V.G.M.)
| | - Arkadiusz Nawrocki
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (A.N.); (J.M.-J.)
| | - Andreas Eske Johansen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark; (S.A.); (A.E.J.); (A.H.-F.); (V.G.M.)
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark; (S.A.); (A.E.J.); (A.H.-F.); (V.G.M.)
| | - Vanesa García Menéndez
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark; (S.A.); (A.E.J.); (A.H.-F.); (V.G.M.)
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (A.N.); (J.M.-J.)
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark; (S.A.); (A.E.J.); (A.H.-F.); (V.G.M.)
- Correspondence:
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9
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Chakdar H, Thapa S, Srivastava A, Shukla P. Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127609. [PMID: 34772552 DOI: 10.1016/j.jhazmat.2021.127609] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/16/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Heavy metals (HMs) pose a global ecological threat due to their toxic effects on aquatic and terrestrial life. Effective remediation of HMs from the environment can help to restore soil's fertility and ecological vigor, one of the key Sustainable Development Goals (SDG) set by the United Nations. The cyanobacteria have emerged as a potential option for bioremediation of HMs due to their unique adaptations and robust metabolic machineries. Generally, cyanobacteria deploy multifarious mechanisms such as biosorption, bioaccumulation, activation of metal transporters, biotransformation and induction of detoxifying enzymes to sequester and minimize the toxic effects of heavy metals. Therefore, understanding the physiological responses and regulation of adaptation mechanisms at molecular level is necessary to unravel the candidate genes and proteins which can be manipulated to improve the bioremediation efficiency of cyanobacteria. Chaperons, cellular metabolites (extracellular polymers, biosurfactants), transcriptional regulators, metal transporters, phytochelatins and metallothioneins are some of the potential targets for strain engineering. In the present review, we have discussed the potential of cyanobacteria for HM bioremediation and provided a deeper insight into their genomic and proteomic regulation of various tolerance mechanisms. These approaches might pave new possibilities of implementing genetic engineering strategies for improving bioremediation efficiency with a future perspective.
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Affiliation(s)
- Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Shobit Thapa
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Amit Srivastava
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, ID 47907-2048, United States
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
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10
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Dumina M, Zhgun A, Pokrovskaya M, Aleksandrova S, Zhdanov D, Sokolov N, El’darov M. Highly Active Thermophilic L-Asparaginase from Melioribacter roseus Represents a Novel Large Group of Type II Bacterial L-Asparaginases from Chlorobi-Ignavibacteriae-Bacteroidetes Clade. Int J Mol Sci 2021; 22:13632. [PMID: 34948436 PMCID: PMC8709496 DOI: 10.3390/ijms222413632] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 02/07/2023] Open
Abstract
L-asparaginase (L-ASNase) is a biotechnologically relevant enzyme for the pharmaceutical, biosensor and food industries. Efforts to discover new promising L-ASNases for different fields of biotechnology have turned this group of enzymes into a growing family with amazing diversity. Here, we report that thermophile Melioribacter roseus from Ignavibacteriae of the Bacteroidetes/Chlorobi group possesses two L-ASNases-bacterial type II (MrAII) and plant-type (MrAIII). The current study is focused on a novel L-ASNase MrAII that was expressed in Escherichia coli, purified and characterized. The enzyme is optimally active at 70 °C and pH 9.3, with a high L-asparaginase activity of 1530 U/mg and L-glutaminase activity ~19% of the activity compared with L-asparagine. The kinetic parameters KM and Vmax for the enzyme were 1.4 mM and 5573 µM/min, respectively. The change in MrAII activity was not significant in the presence of 10 mM Ni2+, Mg2+ or EDTA, but increased with the addition of Cu2+ and Ca2+ by 56% and 77%, respectively, and was completely inhibited by Zn2+, Fe3+ or urea solutions 2-8 M. MrAII displays differential cytotoxic activity: cancer cell lines K562, Jurkat, LnCap, and SCOV-3 were more sensitive to MrAII treatment, compared with normal cells. MrAII represents the first described enzyme of a large group of uncharacterized counterparts from the Chlorobi-Ignavibacteriae-Bacteroidetes clade.
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Affiliation(s)
- Maria Dumina
- Group of Fungal Genetic Engineering, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 117312 Moscow, Russia;
| | - Alexander Zhgun
- Group of Fungal Genetic Engineering, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 117312 Moscow, Russia;
| | - Marina Pokrovskaya
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (M.P.); (S.A.); (D.Z.); (N.S.)
| | - Svetlana Aleksandrova
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (M.P.); (S.A.); (D.Z.); (N.S.)
| | - Dmitry Zhdanov
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (M.P.); (S.A.); (D.Z.); (N.S.)
| | - Nikolay Sokolov
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, 119121 Moscow, Russia; (M.P.); (S.A.); (D.Z.); (N.S.)
| | - Michael El’darov
- Group of Fungal Genetic Engineering, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 117312 Moscow, Russia;
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Zhang ZC, Wang K, Hao FH, Shang JL, Tang HR, Qiu BS. New types of ATP-grasp ligase are associated with the novel pathway for complicated mycosporine-like amino acid production in desiccation-tolerant cyanobacteria. Environ Microbiol 2021; 23:6420-6432. [PMID: 34459073 DOI: 10.1111/1462-2920.15732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Mycosporine-like amino acids (MAAs) were widespread in diverse organisms to attenuate UV radiation. We recently characterized the large, complicated MAA mycosporine-2-(4-deoxygadusolyl-ornithine) in desert cyanobacterium Nostoc flagelliforme. Synthesis of this MAA requires the five-gene cluster mysABDC2C3. Here, bioinformatic analysis indicated that mysC duplication within five-gene mys clusters is strictly limited to drought-tolerant cyanobacteria. Phylogenic analysis distinguished these duplicated MysCs into two clades that separated from canonical MysCs. Heterologous expression of N. flagelliforme mys genes in Escherichia coli showed that MysAB produces 4-deoxygadusol. The ATP-grasp ligase of MysC3 catalyses the linkage of the δ- or ε-amino group of ornithine/lysine to 4-deoxygadusol, yielding mycosporine-ornithine or mycosporine-lysine respectively. The ATP-grasp ligase of MysC2 strictly condenses the α-amino group of mycosporine-ornithine to another 4-deoxygadusol. MysD (D-Ala-D-Ala ligase) functions following MysC2 to catalyse the formation of mycosporine-2-(4-deoxygadusolyl-ornithine). High arginine content likely provides a greater pool of ornithine over other amino acids during rehydration of desiccated N. flagelliforme. Duplication of ATP-grasp ligases is specific for the use of substrates that have two amino groups (such as ornithine) for the production of complicated MAAs with multiple chromophores. This five-enzyme biosynthesis pathway for complicated MAAs is a novel adaptation of cyanobacteria for UV tolerance in drought environments.
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Affiliation(s)
- Zhong-Chun Zhang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Kai Wang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Fu-Hua Hao
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Jin-Long Shang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Hui-Ru Tang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Collaborative Innovation Center for Genetics and Development, Ministry of Education Key Laboratory of Contemporary Anthropology, Metabonomics and Systems Biology Laboratory, Fudan University, Shanghai, 200438, China
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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Loch JI, Jaskolski M. Structural and biophysical aspects of l-asparaginases: a growing family with amazing diversity. IUCRJ 2021; 8:514-531. [PMID: 34258001 PMCID: PMC8256714 DOI: 10.1107/s2052252521006011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
l-Asparaginases have remained an intriguing research topic since their discovery ∼120 years ago, especially after their introduction in the 1960s as very efficient antileukemic drugs. In addition to bacterial asparaginases, which are still used to treat childhood leukemia, enzymes of plant and mammalian origin are now also known. They have all been structurally characterized by crystallography, in some cases at outstanding resolution. The structural data have also shed light on the mechanistic details of these deceptively simple enzymes. Yet, despite all this progress, no better therapeutic agents have been found to beat bacterial asparaginases. However, a new option might arise with the discovery of yet another type of asparaginase, those from symbiotic nitrogen-fixing Rhizobia, and with progress in the protein engineering of enzymes with desired properties. This review surveys the field of structural biology of l-asparaginases, focusing on the mechanistic aspects of the well established types and speculating about the potential of the new members of this amazingly diversified family.
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Affiliation(s)
- Joanna I. Loch
- Department of Crystal Chemistry and Crystal Physics, Faculty of Chemistry, Jagiellonian University, Cracow, Poland
| | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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da Silva LS, Doonan LB, Pessoa A, de Oliveira MA, Long PF. Structural and functional diversity of asparaginases: Overview and recommendations for a revised nomenclature. Biotechnol Appl Biochem 2021; 69:503-513. [PMID: 33624365 DOI: 10.1002/bab.2127] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022]
Abstract
Asparaginases (ASNases) are a large and structurally diverse group of enzymes ubiquitous amongst archaea, bacteria and eukaryotes, that catalyze hydrolysis of asparagine to aspartate and ammonia. Bacterial ASNases are important biopharmaceuticals for the treatment of acute lymphoblastic leukemia, although some patients experience adverse allergic side effects during treatment with these protein therapeutics. ASNases are currently divided into three families: plant-type ASNases, Rhizobium etli-type ASNases and bacterial-type ASNases. This system is outdated as both bacterial-type and plant-type families also include archaeal, bacterial and eukaryotic enzymes, each with their own distinct characteristics. Herein, phylogenetic studies allied to tertiary structural analyses are described with the aim of proposing a revised and more robust classification system that considers the biochemical diversity of ASNases. Accordingly, based on distinct peptide domains, phylogenetic data, structural analysis and functional characteristics, we recommend that ASNases now be divided into three new distinct classes containing subgroups according to structural and functional aspects. Using this new classification scheme, 25 ASNases were identified as candidates for future new lead discovery.
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Affiliation(s)
- Leonardo Schultz da Silva
- Instituto de Biociências, Universidade Estadual Paulista (UNESP), São Vicente, São Paulo, Brazil.,Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, UK
| | - Liam B Doonan
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, UK
| | - Adalberto Pessoa
- Departamento de Tecnologia Tecnologia Bioquímico-Farmacêuticas, Faculdade de Ciencias Farmaceuticas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | | | - Paul F Long
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, UK.,Departamento de Tecnologia Tecnologia Bioquímico-Farmacêuticas, Faculdade de Ciencias Farmaceuticas, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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Elbahloul Y, Steinbüchel A. Characterization of an efficient extracellular cyanophycinase and its encoding cphE Strept. gene from Streptomyces pratensis strain YSM. J Biotechnol 2020; 319:15-24. [PMID: 32473189 DOI: 10.1016/j.jbiotec.2020.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/22/2020] [Accepted: 05/19/2020] [Indexed: 11/16/2022]
Abstract
Until now, no enzymes were described that hydrolyze cyanophycin granular protein (CGP) from a species of the genus Streptomyces. An isolate able to hydrolyze CGP was identified as Streptomyces pratensis strain YSM. The CGPase from S. pratensis strain YSM had an optimum activity at 42 °C and pH 8.5, and was able to degrade CGP at a rate of 12 ± 0.3 μg/mL min. Additionally, this CGPase hydrolyzes water-soluble CGP significantly faster than water-insoluble CGP. The molecular mass of CGPase subunits from S. pratensis strain YSM as determined by SDS-PAGE was about 43 kDa, and the enzyme was entirely inhibited by serine-protease inhibitors. The CGPase coding gene (cphEStrept.) was amplified from genomic DNA using primers designed form consensus sequence of putative CGPase sequences. The cphEStrept. was 1427 bp encoding a CGPase of 420 amino acids that showed about 44% and 22% similarities to CGPase from Pseudomonas anguilliseptica BI and Synechocystis sp. PCC 6803, respectively. The catalytic triad and serine-protease residues (GXSXG) were identified in the CphEStrept. sequence. Dipeptides and tetrapeptides were identified as hydrolysis products. Biotechnological exploitation of S. pratensis strain YSM for CGPase production might have an advantage due to the reduction of separation costs and its ability to degrade CGP in phosphate buffer saline using actively growing or resting cells.
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Affiliation(s)
- Yasser Elbahloul
- Biology Department, College of Science, Taibah University, Almadinah Almunawarah, Saudi Arabia; Botany and Microbiology Department, Faculty of Science, Alexandria University, 21511, Alexandria, Egypt; Institut Für Molekulare Mikrobiologie Und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Corrensstraße 3, 48149, Münster, Germany.
| | - Alexander Steinbüchel
- Institut Für Molekulare Mikrobiologie Und Biotechnologie, Westfälische Wilhelms-Universität, Münster, Corrensstraße 3, 48149, Münster, Germany; Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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Lee H, Rhee S. Structural and mutational analyses of the bifunctional arginine dihydrolase and ornithine cyclodeaminase AgrE from the cyanobacterium Anabaena. J Biol Chem 2020; 295:5751-5760. [PMID: 32198136 PMCID: PMC7186175 DOI: 10.1074/jbc.ra120.012768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/17/2020] [Indexed: 01/07/2023] Open
Abstract
In cyanobacteria, metabolic pathways that use the nitrogen-rich amino acid arginine play a pivotal role in nitrogen storage and mobilization. The N-terminal domains of two recently identified bacterial enzymes: ArgZ from Synechocystis and AgrE from Anabaena, have been found to contain an arginine dihydrolase. This enzyme provides catabolic activity that converts arginine to ornithine, resulting in concomitant release of CO2 and ammonia. In Synechocystis, the ArgZ-mediated ornithine-ammonia cycle plays a central role in nitrogen storage and remobilization. The C-terminal domain of AgrE contains an ornithine cyclodeaminase responsible for the formation of proline from ornithine and ammonia production, indicating that AgrE is a bifunctional enzyme catalyzing two sequential reactions in arginine catabolism. Here, the crystal structures of AgrE in three different ligation states revealed that it has a tetrameric conformation, possesses a binding site for the arginine dihydrolase substrate l-arginine and product l-ornithine, and contains a binding site for the coenzyme NAD(H) required for ornithine cyclodeaminase activity. Structure-function analyses indicated that the structure and catalytic mechanism of arginine dihydrolase in AgrE are highly homologous with those of a known bacterial arginine hydrolase. We found that in addition to other active-site residues, Asn-71 is essential for AgrE's dihydrolase activity. Further analysis suggested the presence of a passage for substrate channeling between the two distinct AgrE active sites, which are situated ∼45 Å apart. These results provide structural and functional insights into the bifunctional arginine dihydrolase-ornithine cyclodeaminase enzyme AgrE required for arginine catabolism in Anabaena.
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Affiliation(s)
- Haehee Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea
| | - Sangkee Rhee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 151-921, Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
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17
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Zhang H, Yang C. Arginine and nitrogen mobilization in cyanobacteria. Mol Microbiol 2019; 111:863-867. [DOI: 10.1111/mmi.14204] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Hao Zhang
- CAS‐Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai 200032China
| | - Chen Yang
- CAS‐Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences Shanghai 200032China
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Cyanophycin Synthesis Optimizes Nitrogen Utilization in the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6803. Appl Environ Microbiol 2018; 84:AEM.01298-18. [PMID: 30120117 DOI: 10.1128/aem.01298-18] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/09/2018] [Indexed: 11/20/2022] Open
Abstract
Cyanophycin is a carbon/nitrogen storage polymer widely distributed in most cyanobacterial strains and in a few heterotrophic bacteria. It is a nonribosomal polypeptide consisting of equimolar amounts of aspartate and arginine. Here, we focused on the physiological function and cell biology of cyanophycin in the unicellular nondiazotrophic cyanobacterium Synechocystis sp. strain PCC 6803. To study the cellular localization of the cyanophycin-synthesizing enzyme CphA during cyanophycin synthesis and degradation, we fused it to green fluorescent protein. When CphA was inactive, it localized diffusely in the cytoplasm. When cyanophycin synthesis was triggered, CphA first aggregated into foci and later localized on the surface of cyanophycin granules. In the corresponding cell extracts, localization of CphA on the cyanophycin granule surface required Mg2+ During cyanophycin degradation, CphA dissociated from the granule surface and returned to its inactive form in the cytoplasm. To investigate the physiological role of cyanophycin, we compared wild-type cells with a CphA-deficient mutant. Under standard laboratory conditions, the ability to synthesize cyanophycin did not confer a growth advantage. To mimic the situation in natural habitats, cells were cultured with a fluctuating and limiting nitrogen supplementation and/or day/night cycles. Under all of these conditions, cyanophycin provided a fitness advantage to the wild type over the mutant lacking cyanophycin. During resuscitation from nitrogen starvation, wild-type cells accumulated cyanophycin during the night and used it as an internal nitrogen source during the day. This demonstrates that cyanophycin can be used as a temporary nitrogen storage to uncouple nitrogen assimilation from photosynthesis.IMPORTANCE We clarified the elusive biological function of cyanophycin in the nondiazotrophic cyanobacterium Synechocystis sp. PCC 6803. Cyanophycin is a dynamic carbon/nitrogen storage polymer (multi-arginyl-l-polyaspartate) that is conditionally present in most cyanobacteria and a few heterotrophic bacteria as cellular inclusion granules. Here, we show that the cyanophycin-synthesizing enzyme CphA in the nonactive state localizes diffusely in the cytoplasm. When cyanophycin synthesis is triggered, active CphA first aggregates into foci and then covers the surface of mature cyanophycin granules, which in vitro requires Mg2+ as a cofactor. Cyanophycin accumulation enables Synechocystis sp. to optimize nitrogen assimilation under nitrogen-poor conditions, in particular when the nitrogen supply fluctuates and during day/night cycles, by allowing continuous nitrogen assimilation and storage. Therefore, cyanophycin provides the wild-type cyanobacterium with a clear fitness advantage over non-cyanophycin-producing cells in natural environments with fluctuating nitrogen supply.
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Proteomics reveals key proteins participating in growth difference between fall dormant and non-dormant alfalfa in terminal buds. J Proteomics 2017; 173:126-138. [PMID: 29229487 DOI: 10.1016/j.jprot.2017.11.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/18/2017] [Accepted: 11/30/2017] [Indexed: 12/14/2022]
Abstract
To explore the molecular mechanism of growth differences between fall dormant (FD) and non-FD alfalfa, we conducted iTRAQ-based quantitative proteomics on terminal buds of Maverick (FD) and Cuf101 (non-FD) cultivars, identified differential abundance protein species (DAPS) and verified expression profiling of certain corresponding mRNA by qRT-PCR. A total of 3872 protein species were annotated. Of the 90 DAPS, 56 and 34 were respectively up- and down-accumulated in Maverick, compared to Cuf101. They were grouped into 35 functional categories and enriched in seven pathways. Of which, auxin polar transport was up-regulated, while phenylpropanoid biosynthesis, pyruvate metabolism and transportation, vitamin B1 synthesis process and flavonoid biosynthesis were down-regulated in Maverick, comparing with Cuf101. In Maverick, mRNA abundances of l-asparaginase, chalcone and stilbene synthase family protein, cinnamyl alcohol dehydrogenase-like protein, thiazole biosynthetic enzyme, pyruvate dehydrogenase E1 beta subunit, and aldo/keto reductase family oxidoreductase were significantly lower at FD than at other stages, and lower than in Cuf101. We also observed opposite mRNA profiles of thiazole biosynthetic enzyme, chalcone and stilbene synthase family protein, pyruvate dehydrogenase E1 beta subunit in both cultivars from summer to autumn. Our results suggest that these DAPS could play important roles in growth difference between FD and non-FD alfalfa. BIOLOGICAL SIGNIFICANCE Up to now, as far as we know, currently the proteins related with the growth differences between FD and non-FD alfalfa cultivars in autumn have not yet been identified in terminal buds. This study identified the protein species expressed in alfalfa terminal buds, selected differentially abundant protein species in terminal buds between Maverick (FD) and Cuf101 (non-FD) cultivars in autumn and identified the important protein species participated in the growth differences. This study lays a foundation for further investigation of the molecular mechanism of the growth differences between FD and non-FD alfalfa and the cultivation of advanced alfalfa cultivars.
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Yabuki Y, Ohashi M, Imagawa F, Ishiyama K, Beier MP, Konishi N, Umetsu-Ohashi T, Hayakawa T, Yamaya T, Kojima S. A temporal and spatial contribution of asparaginase to asparagine catabolism during development of rice grains. RICE (NEW YORK, N.Y.) 2017; 10:3. [PMID: 28124210 PMCID: PMC5267587 DOI: 10.1186/s12284-017-0143-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/19/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Asparagine is one of the most dominant organic nitrogen compounds in phloem and xylem sap in a wide range of plant species. Asparaginase (ASNase; EC, 3.5.1.1) catabolizes asparagine into aspartate and ammonium; therefore, it is suggested to play a key role in asparagine metabolism within legume sink organs. However, the metabolic fate of asparagine in source and sink organs during rice seed production remains to be elucidated. Therefore, the main objective of this study is to investigate the asparagine metabolism in a temporal and spatial manner during rice seed production. RESULTS For this purpose, the expression of genes involved in asparagine catabolism, such as asparaginase1 (OsASNase1) and 2 (OsASNase2), were quantitatively measured, and contents of asparagine, aspartate and ammonium ions were determined in sink and source organs during spikelet ripening. Quantitative real-time PCR and in situ localization studies determined that OsASNase2 is expressed in the dorsal vascular bundles and nucellar projection of developing grains, as well as in mesophyll and phloem companion cells of senescent flag leaves. Amino acid measurements revealed that the aspartate concentration is higher than asparagine in both source and sink organs. CONCLUSION This work suggests that asparaginase dependent asparagine catabolism occurred not only in sink but also in source organs.
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Affiliation(s)
- Yui Yabuki
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 9800845 Japan
| | - Miwa Ohashi
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 9800845 Japan
| | - Fumi Imagawa
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 9800845 Japan
| | - Keiki Ishiyama
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 9800845 Japan
| | - Marcel Pascal Beier
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 9800845 Japan
| | - Noriyuki Konishi
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 9800845 Japan
| | - Toshiko Umetsu-Ohashi
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 9800845 Japan
| | - Toshihiko Hayakawa
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 9800845 Japan
| | - Tomoyuki Yamaya
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 9800845 Japan
| | - Soichi Kojima
- Graduate School of Agricultural Science, Tohoku University, 468-1 Aoba, Aramaki, Sendai, 9800845 Japan
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Park SY, Scranton MA, Stajich JE, Yee A, Walling LL. Chlorophyte aspartyl aminopeptidases: Ancient origins, expanded families, new locations, and secondary functions. PLoS One 2017; 12:e0185492. [PMID: 29023459 PMCID: PMC5638241 DOI: 10.1371/journal.pone.0185492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/13/2017] [Indexed: 11/19/2022] Open
Abstract
M18 aspartyl aminopeptidases (DAPs) are well characterized in microbes and animals with likely functions in peptide processing and vesicle trafficking. In contrast, there is a dearth of knowledge on plant aminopeptidases with a preference for proteins and peptides with N-terminal acidic residues. During evolution of the Plantae, there was an expansion and diversification of the M18 DAPs. After divergence of the ancestral green algae from red and glaucophyte algae, a duplication yielded the DAP1 and DAP2 lineages. Subsequently DAP1 genes were lost in chlorophyte algae. A duplication of DAP2-related genes occurred early in green plant evolution. DAP2 genes were retained in land plants and picoeukaryotic algae and lost in green algae. In contrast, DAP2-like genes persisted in picoeukaryotic and green algae, while this lineage was lost in land plants. Consistent with this evolutionary path, Arabidopsis thaliana has two DAP gene lineages (AtDAP1 and AtDAP2). Similar to animal and yeast DAPs, AtDAP1 is localized to the cytosol or vacuole; while AtDAP2 harbors an N-terminal transit peptide and is chloroplast localized. His6-DAP1 and His6-DAP2 expressed in Escherichia coli were enzymatically active and dodecameric with masses exceeding 600 kDa. His6-DAP1 and His6-DAP2 preferentially hydrolyzed Asp-p-nitroanilide and Glu-p-nitroanilide. AtDAPs are highly conserved metallopeptidases activated by MnCl2 and inhibited by ZnCl2 and divalent ion chelators. The protease inhibitor PMSF inhibited and DTT stimulated both His6-DAP1 and His6-DAP2 activities suggesting a role for thiols in the AtDAP catalytic mechanism. The enzymes had distinct pH and temperature optima, as well as distinct kinetic parameters. Both enzymes had high catalytic efficiencies (kcat/Km) exceeding 1.0 x 107 M-1 sec-1. Using established molecular chaperone assays, AtDAP1 and AtDAP2 prevented thermal denaturation. AtDAP1 also prevented protein aggregation and promoted protein refolding. Collectively, these data indicate that plant DAPs have a complex evolutionary history and have evolved new biochemical features that may enable their role in vivo.
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Affiliation(s)
- Sang-Youl Park
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, United States of America
| | - Melissa A. Scranton
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, United States of America
| | - Jason E. Stajich
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, University of California, Riverside, California, United States of America
| | - Ashley Yee
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, United States of America
| | - Linda L. Walling
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- * E-mail:
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Rigouin C, Nguyen HA, Schalk AM, Lavie A. Discovery of human-like L-asparaginases with potential clinical use by directed evolution. Sci Rep 2017; 7:10224. [PMID: 28860480 PMCID: PMC5579231 DOI: 10.1038/s41598-017-10758-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/14/2017] [Indexed: 11/15/2022] Open
Abstract
L-asparaginase is a chemotherapy drug used to treat acute lymphoblastic leukemia (ALL). The main prerequisite for clinical efficacy of L-asparaginases is micromolar KM for asparagine to allow for complete depletion of this amino acid in the blood. Since currently approved L-asparaginases are of bacterial origin, immunogenicity is a challenge, which would be mitigated by a human enzyme. However, all human L-asparaginases have millimolar KM for asparagine. We recently identified the low KM guinea pig L-asparaginase (gpASNase1). Because gpASNase1 and human L-asparaginase 1 (hASNase1) share ~70% amino-acid identity, we decided to humanize gpASNase1 by generating chimeras with hASNase1 through DNA shuffling. To identify low KM chimeras we developed a suitable bacterial selection system (E. coli strain BW5Δ). Transforming BW5Δ with the shuffling libraries allowed for the identification of several low KM clones. To further humanize these clones, the C-terminal domain of gpASNase1 was replaced with that of hASNase1. Two of the identified clones, 63N-hC and 65N-hC, share respectively 85.7% and 87.1% identity with the hASNase1 but have a KM similar to gpASNase1. These clones possess 100-140 fold enhanced catalytic efficiency compared to hASNase1. Notably, we also show that these highly human-like L-asparaginases maintain their in vitro ALL killing potential.
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Affiliation(s)
- Coraline Rigouin
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Hien Anh Nguyen
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
- The Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Amanda M Schalk
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America.
- The Jesse Brown VA Medical Center, Chicago, Illinois, United States of America.
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Ponndorf D, Ehmke S, Walliser B, Thoss K, Unger C, Görs S, Daş G, Metges CC, Broer I, Nausch H. Stable production of cyanophycinase in Nicotiana benthamiana and its functionality to hydrolyse cyanophycin in the murine intestine. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:605-613. [PMID: 27808470 PMCID: PMC5399006 DOI: 10.1111/pbi.12658] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/05/2016] [Accepted: 10/30/2016] [Indexed: 05/09/2023]
Abstract
Food supplementation with the conditionally essential amino acid arginine (Arg) has been shown to have nutritional benefits. Degradation of cyanophycin (CGP), a peptide polymer used for nitrogen storage by cyanobacteria, requires cyanophycinase (CGPase) and results in the release of β-aspartic acid (Asp)-Arg dipeptides. The simultaneous production of CGP and CGPase in plants could be a convenient source of Arg dipeptides. Different variants of the cphB coding region from Thermosynechococcus elongatus BP-1 were transiently expressed in Nicotiana benthamiana plants. Translation and enzyme stability were optimized to produce high amounts of active CGPase. Protein stability was increased by the translational fusion of CGPase to the green fluorescent protein (GFP) or to the transit peptide of the small subunit of RuBisCO for peptide production in the chloroplasts. Studies in mice showed that plant-expressed CGP fed in combination with plant-made CGPase was hydrolysed in the intestine, and high levels of ß-Asp-Arg dipeptides were found in plasma, demonstrating dipeptide absorption. However, the lack of an increase in Asp and Arg or its metabolite ornithine in plasma suggests that Arg from CGP was not bioavailable in this mouse group. Intestinal degradation of CGP by CGPase led to low intestinal CGP content 4 h after consumption, but after ingestion of CGP alone, high CGP concentrations remained in the large intestine; this indicated that intact CGP was transported from the small to the large intestine and that CGP was resistant to colonic microbes.
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Affiliation(s)
- Daniel Ponndorf
- Faculty of Agricultural and Environmental SciencesDepartment of Agrobiotechnology and Risk Assessment for Bio‐ and Gene TechnologyUniversity of RostockRostockGermany
| | - Sven Ehmke
- Faculty of Agricultural and Environmental SciencesDepartment of Agrobiotechnology and Risk Assessment for Bio‐ and Gene TechnologyUniversity of RostockRostockGermany
- Present address: Paraxel International GmbHKlinikum am Westend, Haus 18, SpandauerDamm 130, 14050BerlinGermany
| | - Benjamin Walliser
- Faculty of Agricultural and Environmental SciencesDepartment of Agrobiotechnology and Risk Assessment for Bio‐ and Gene TechnologyUniversity of RostockRostockGermany
| | - Kerstin Thoss
- Faculty of Agricultural and Environmental SciencesDepartment of Agrobiotechnology and Risk Assessment for Bio‐ and Gene TechnologyUniversity of RostockRostockGermany
| | - Christoph Unger
- Faculty of Agricultural and Environmental SciencesDepartment of Agrobiotechnology and Risk Assessment for Bio‐ and Gene TechnologyUniversity of RostockRostockGermany
| | - Solvig Görs
- Leibniz Institute for Farm Animal Biology (FBN)Institute of Nutritional Physiology ‘Oskar Kellner’DummerstorfGermany
| | - Gürbüz Daş
- Leibniz Institute for Farm Animal Biology (FBN)Institute of Nutritional Physiology ‘Oskar Kellner’DummerstorfGermany
| | - Cornelia C. Metges
- Leibniz Institute for Farm Animal Biology (FBN)Institute of Nutritional Physiology ‘Oskar Kellner’DummerstorfGermany
| | - Inge Broer
- Faculty of Agricultural and Environmental SciencesDepartment of Agrobiotechnology and Risk Assessment for Bio‐ and Gene TechnologyUniversity of RostockRostockGermany
| | - Henrik Nausch
- Faculty of Agricultural and Environmental SciencesDepartment of Agrobiotechnology and Risk Assessment for Bio‐ and Gene TechnologyUniversity of RostockRostockGermany
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24
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Rehman HM, Shah ZH, Nawaz MA, Ahmad MQ, Yang SH, Kho KH, Chung G. RETRACTED ARTICLE: Beta-cyanoalanine synthase pathway as a homeostatic mechanism for cyanide detoxification as well as growth and development in higher plants. PLANTA 2017; 245:235. [PMID: 27744484 DOI: 10.1007/s00425-016-2606-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/09/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, King Abdul-Aziz University, Jeddah, 21577, Saudi Arabia
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Muhammad Qadir Ahmad
- Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan, 6000, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Kang Hee Kho
- Department of Aquatic Biology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, South Korea.
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25
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Van Kerckhoven SH, de la Torre FN, Cañas RA, Avila C, Cantón FR, Cánovas FM. Characterization of Three L-Asparaginases from Maritime Pine ( Pinus pinaster Ait.). FRONTIERS IN PLANT SCIENCE 2017; 8:1075. [PMID: 28690619 PMCID: PMC5481357 DOI: 10.3389/fpls.2017.01075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/06/2017] [Indexed: 05/15/2023]
Abstract
Asparaginases (ASPG, EC 3.5.1.1) catalyze the hydrolysis of the amide group of L-asparagine producing L-aspartate and ammonium. Three ASPG, PpASPG1, PpASPG2, and PpASPG3, have been identified in the transcriptome of maritime pine (Pinus pinaster Ait.) that were transiently expressed in Nicotiana benthamiana by agroinfection. The three recombinant proteins were processed in planta to active enzymes and it was found that all mature forms exhibited double activity asparaginase/isoaspartyl dipeptidase but only PpASPG1 was able to catalyze efficiently L-asparagine hydrolysis. PpASPG1 contains a variable region of 77 amino acids that is critical for proteolytic processing of the precursor and is retained in the mature enzyme. Furthermore, the functional analysis of deletion mutants demonstrated that this protein fragment is required for specific recognition of the substrate and favors enzyme stability. Potassium has a limited effect on the activation of maritime pine ASPG what is consistent with the lack of a critical residue essential for interaction of cation. Taken together, the results presented here highlight the specific features of ASPG from conifers when compared to the enzymes from angiosperms.
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26
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Gaufichon L, Rothstein SJ, Suzuki A. Asparagine Metabolic Pathways in Arabidopsis. PLANT & CELL PHYSIOLOGY 2016; 57:675-89. [PMID: 26628609 DOI: 10.1093/pcp/pcv184] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/18/2015] [Indexed: 05/03/2023]
Abstract
Inorganic nitrogen in the form of ammonium is assimilated into asparagine via multiple steps involving glutamine synthetase (GS), glutamate synthase (GOGAT), aspartate aminotransferase (AspAT) and asparagine synthetase (AS) in Arabidopsis. The asparagine amide group is liberated by the reaction catalyzed by asparaginase (ASPG) and also the amino group of asparagine is released by asparagine aminotransferase (AsnAT) for use in the biosynthesis of amino acids. Asparagine plays a primary role in nitrogen recycling, storage and transport in developing and germinating seeds, as well as in vegetative and senescence organs. A small multigene family encodes isoenzymes of each step of asparagine metabolism in Arabidopsis, except for asparagine aminotransferase encoded by a single gene. The aim of this study is to highlight the structure of the genes and encoded enzyme proteins involved in asparagine metabolic pathways; the regulation and role of different isogenes; and kinetic and physiological properties of encoded enzymes in different tissues and developmental stages.
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Affiliation(s)
- Laure Gaufichon
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
| | - Steven J Rothstein
- University of Guelph, Department of Molecular and Cellular Biology, Guelph, Ontario, Canada N1G 2W1
| | - Akira Suzuki
- INRA, IJPB, UMR1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France
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27
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Klemke F, Nürnberg DJ, Ziegler K, Beyer G, Kahmann U, Lockau W, Volkmer T. CphA2 is a novel type of cyanophycin synthetase in N2-fixing cyanobacteria. Microbiology (Reading) 2016; 162:526-536. [DOI: 10.1099/mic.0.000241] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Friederike Klemke
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestraße 117, 10115 Berlin, Germany
| | - Dennis J. Nürnberg
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestraße 117, 10115 Berlin, Germany
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Karl Ziegler
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestraße 117, 10115 Berlin, Germany
| | - Gabriele Beyer
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestraße 117, 10115 Berlin, Germany
| | - Uwe Kahmann
- Zentrum für Ultrastrukturelle Diagnostik im IIT, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Wolfgang Lockau
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestraße 117, 10115 Berlin, Germany
| | - Thomas Volkmer
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestraße 117, 10115 Berlin, Germany
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28
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Schalk AM, Antansijevic A, Caffrey M, Lavie A. Experimental Data in Support of a Direct Displacement Mechanism for Type I/II L-Asparaginases. J Biol Chem 2016; 291:5088-100. [PMID: 26733195 DOI: 10.1074/jbc.m115.699884] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 01/02/2023] Open
Abstract
Bacterial L-asparaginases play an important role in the treatment of certain types of blood cancers. We are exploring the guinea pig L-asparaginase (gpASNase1) as a potential replacement of the immunogenic bacterial enzymes. The exact mechanism used by L-asparaginases to catalyze the hydrolysis of asparagine into aspartic acid and ammonia has been recently put into question. Earlier experimental data suggested that the reaction proceeds via a covalent intermediate using a ping-pong mechanism, whereas recent computational work advocates the direct displacement of the amine by an activated water. To shed light on this controversy, we generated gpASNase1 mutants of conserved active site residues (T19A, T116A, T19A/T116A, K188M, and Y308F) suspected to play a role in hydrolysis. Using x-ray crystallography, we determined the crystal structures of the T19A, T116A, and K188M mutants soaked in asparagine. We also characterized their steady-state kinetic properties and analyzed the conversion of asparagine to aspartate using NMR. Our structures reveal bound asparagine in the active site that has unambiguously not formed a covalent intermediate. Kinetic and NMR assays detect significant residual activity for all of the mutants. Furthermore, no burst of ammonia production was observed that would indicate covalent intermediate formation and the presence of a ping-pong mechanism. Hence, despite using a variety of techniques, we were unable to obtain experimental evidence that would support the formation of a covalent intermediate. Consequently, our observations support a direct displacement rather than a ping-pong mechanism for l-asparaginases.
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Affiliation(s)
- Amanda M Schalk
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607 and
| | - Aleksandar Antansijevic
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607 and
| | - Michael Caffrey
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607 and
| | - Arnon Lavie
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607 and the Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
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29
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Requirement of Fra proteins for communication channels between cells in the filamentous nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120. Proc Natl Acad Sci U S A 2015. [PMID: 26216997 DOI: 10.1073/pnas.1512232112] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The filamentous nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120 differentiates specialized cells, heterocysts, that fix atmospheric nitrogen and transfer the fixed nitrogen to adjacent vegetative cells. Reciprocally, vegetative cells transfer fixed carbon to heterocysts. Several routes have been described for metabolite exchange within the filament, one of which involves communicating channels that penetrate the septum between adjacent cells. Several fra gene mutants were isolated 25 y ago on the basis of their phenotypes: inability to fix nitrogen and fragmentation of filaments upon transfer from N+ to N- media. Cryopreservation combined with electron tomography were used to investigate the role of three fra gene products in channel formation. FraC and FraG are clearly involved in channel formation, whereas FraD has a minor part. Additionally, FraG was located close to the cytoplasmic membrane and in the heterocyst neck, using immunogold labeling with antibody raised to the N-terminal domain of the FraG protein.
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30
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Prihanto AA, Nonomura Y, Takagi K, Naohara R, Umekawa M, Wakayama M. Novel properties of γ-glutamyltransferase from Pseudomonas syringae with β-aspartyltransferase activity. Biotechnol Lett 2015; 37:2255-63. [DOI: 10.1007/s10529-015-1906-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 06/29/2015] [Indexed: 01/08/2023]
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31
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Schalk AM, Nguyen HA, Rigouin C, Lavie A. Identification and structural analysis of an L-asparaginase enzyme from guinea pig with putative tumor cell killing properties. J Biol Chem 2014; 289:33175-86. [PMID: 25320094 PMCID: PMC4246078 DOI: 10.1074/jbc.m114.609552] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/09/2014] [Indexed: 12/18/2022] Open
Abstract
The initial observation that guinea pig serum kills lymphoma cells marks the serendipitous discovery of a new class of anti-cancer agents. The serum cell killing factor was shown to be an enzyme with L-asparaginase (ASNase) activity. As a direct result of this observation, several bacterial L-asparaginases were developed and are currently approved by the Food and Drug Administration for the treatment of the subset of hematological malignancies that are dependent on the extracellular pool of the amino acid asparagine. As drugs, these enzymes act to hydrolyze asparagine to aspartate, thereby starving the cancer cells of this amino acid. Prior to the work presented here, the precise identity of this guinea pig enzyme has not been reported in the peer-reviewed literature. We discovered that the guinea pig enzyme annotated as H0W0T5_CAVPO, which we refer to as gpASNase1, has the required low Km property consistent with that possessed by the cell-killing guinea pig serum enzyme. Elucidation of the ligand-free and aspartate complex gpASNase1 crystal structures allows a direct comparison with the bacterial enzymes and serves to explain the lack of L-glutaminase activity in the guinea pig enzyme. The structures were also used to generate a homology model for the human homolog hASNase1 and to help explain its vastly different kinetic properties compared with gpASNase1, despite a 70% sequence identity. Given that the bacterial enzymes frequently present immunogenic and other toxic side effects, this work suggests that gpASNase1 could be a promising alternative to these bacterial enzymes.
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Affiliation(s)
- Amanda M Schalk
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Hien-Anh Nguyen
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Coraline Rigouin
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
| | - Arnon Lavie
- From the Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607
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32
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Burnat M, Flores E. Inactivation of agmatinase expressed in vegetative cells alters arginine catabolism and prevents diazotrophic growth in the heterocyst-forming cyanobacterium Anabaena. Microbiologyopen 2014; 3:777-92. [PMID: 25209059 PMCID: PMC4234267 DOI: 10.1002/mbo3.207] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/08/2014] [Accepted: 07/22/2014] [Indexed: 11/12/2022] Open
Abstract
Arginine decarboxylase produces agmatine, and arginase and agmatinase are ureohydrolases that catalyze the production of ornithine and putrescine from arginine and agmatine, respectively, releasing urea. In the genome of the filamentous, heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120, ORF alr2310 putatively encodes an ureohydrolase. Cells of Anabaena supplemented with [14C]arginine took up and catabolized this amino acid generating a set of labeled amino acids that included ornithine, proline, and glutamate. In an alr2310 deletion mutant, an agmatine spot appeared and labeled glutamate increased with respect to the wild type, suggesting that Alr2310 is an agmatinase rather than an arginase. As determined in cell-free extracts, agmatinase activity could be detected in the wild type but not in the mutant. Thus, alr2310 is the Anabaena speB gene encoding agmatinase. The Δalr2310 mutant accumulated large amounts of cyanophycin granule polypeptide, lacked nitrogenase activity, and did not grow diazotrophically. Growth tests in solid media showed that agmatine is inhibitory for Anabaena, especially under diazotrophic conditions, suggesting that growth of the mutant is inhibited by non-metabolized agmatine. Measurements of incorporation of radioactivity from [14C]leucine into macromolecules showed, however, a limited inhibition of protein synthesis in the Δalr2310 mutant. Analysis of an Anabaena strain producing an Alr2310-GFP (green fluorescent protein) fusion showed expression in vegetative cells but much less in heterocysts, implying compartmentalization of the arginine decarboxylation pathway in the diazotrophic filaments of this heterocyst-forming cyanobacterium.
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Affiliation(s)
- Mireia Burnat
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, E-41092, Seville, Spain
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33
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Karamitros CS, Konrad M. Human 60-kDa lysophospholipase contains an N-terminal L-asparaginase domain that is allosterically regulated by L-asparagine. J Biol Chem 2014; 289:12962-75. [PMID: 24657844 PMCID: PMC4036312 DOI: 10.1074/jbc.m113.545038] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/02/2014] [Indexed: 11/06/2022] Open
Abstract
The structural and functional characterization of human enzymes that are of potential medical and therapeutic interest is of prime significance for translational research. One of the most notable examples of a therapeutic enzyme is L-asparaginase, which has been established as an antileukemic protein drug for more than four decades. Up until now, only bacterial enzymes have been used in therapy despite a plethora of undesired side effects mainly attributed to the bacterial origins of these enzymes. Therefore, the replacement of the currently approved bacterial drugs by human homologs aiming at the elimination of adverse effects is of great importance. Recently, we structurally and biochemically characterized the enzyme human L-asparaginase 3 (hASNase3), which possesses L-asparaginase activity and belongs to the N-terminal nucleophile superfamily of enzymes. Inspired by the necessity for the development of a protein drug of human origin, in the present study, we focused on the characterization of another human L-asparaginase, termed hASNase1. This bacterial-type cytoplasmic L-asparaginase resides in the N-terminal subdomain of an overall 573-residue protein previously reported to function as a lysophospholipase. Our kinetic, mutagenesis, structural modeling, and fluorescence labeling data highlight allosteric features of hASNase1 that are similar to those of its Escherichia coli homolog, EcASNase1. Differential scanning fluorometry and urea denaturation experiments demonstrate the impact of particular mutations on the structural and functional integrity of the L-asparaginase domain and provide a direct comparison of sites critical for the conformational stability of the human and E. coli enzymes.
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Affiliation(s)
- Christos S. Karamitros
- From the Enzyme Biochemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen D-37077, Germany
| | - Manfred Konrad
- From the Enzyme Biochemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen D-37077, Germany
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34
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Patananan AN, Capri J, Whitelegge JP, Clarke SG. Non-repair pathways for minimizing protein isoaspartyl damage in the yeast Saccharomyces cerevisiae. J Biol Chem 2014; 289:16936-53. [PMID: 24764295 DOI: 10.1074/jbc.m114.564385] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The spontaneous degradation of asparaginyl and aspartyl residues to isoaspartyl residues is a common type of protein damage in aging organisms. Although the protein-l-isoaspartyl (d-aspartyl) O-methyltransferase (EC 2.1.1.77) can initiate the repair of l-isoaspartyl residues to l-aspartyl residues in most organisms, no gene homolog or enzymatic activity is present in the budding yeast Saccharomyces cerevisiae. Therefore, we used biochemical approaches to elucidate how proteins containing isoaspartyl residues are metabolized in this organism. Surprisingly, the level of isoaspartyl residues in yeast proteins (50-300 pmol of isoaspartyl residues/mg of protein extract) is comparable with organisms with protein-l-isoaspartyl (d-aspartyl) O-methyltransferase, suggesting a novel regulatory pathway. Interfering with common protein quality control mechanisms by mutating and inhibiting the proteasomal and autophagic pathways in vivo did not increase isoaspartyl residue levels compared with wild type or uninhibited cells. However, the inhibition of metalloproteases in in vitro aging experiments by EDTA resulted in an ∼3-fold increase in the level of isoaspartyl-containing peptides. Characterization by mass spectrometry of these peptides identified several proteins involved in metabolism as targets of isoaspartyl damage. Further analysis of these peptides revealed that many have an N-terminal isoaspartyl site and originate from proteins with short half-lives. These results suggest that one or more metalloproteases participate in limiting isoaspartyl formation by robust proteolysis.
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Affiliation(s)
- Alexander N Patananan
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute and
| | - Joseph Capri
- the Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | - Julian P Whitelegge
- the Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute and
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35
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Nomme J, Su Y, Lavie A. Elucidation of the specific function of the conserved threonine triad responsible for human L-asparaginase autocleavage and substrate hydrolysis. J Mol Biol 2014; 426:2471-85. [PMID: 24768817 DOI: 10.1016/j.jmb.2014.04.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/14/2014] [Accepted: 04/15/2014] [Indexed: 02/05/2023]
Abstract
Our long-term goal is the design of a human l-asparaginase (hASNase3) variant, suitable for use in cancer therapy without the immunogenicity problems associated with the currently used bacterial enzymes. Asparaginases catalyze the hydrolysis of the amino acid asparagine to aspartate and ammonia. The key property allowing for the depletion of blood asparagine by bacterial asparaginases is their low micromolar KM value. In contrast, human enzymes have a millimolar KM for asparagine. Toward the goal of engineering an hASNase3 variant with micromolar KM, we conducted a structure/function analysis of the conserved catalytic threonine triad of this human enzyme. As a member of the N-terminal nucleophile family, to become enzymatically active, hASNase3 must undergo autocleavage between residues Gly167 and Thr168. To determine the individual contribution of each of the three conserved active-site threonines (threonine triad Thr168, Thr186, Thr219) for the enzyme-activating autocleavage and asparaginase reactions, we prepared the T168S, T186V and T219A/V mutants. These mutants were tested for their ability to cleave and to catalyze asparagine hydrolysis, in addition to being examined structurally. We also elucidated the first N-terminal nucleophile plant-type asparaginase structure in the covalent intermediate state. Our studies indicate that, while not all triad threonines are required for the cleavage reaction, all are essential for the asparaginase activity. The increased understanding of hASNase3 function resulting from these studies reveals the key regions that govern cleavage and the asparaginase reaction, which may inform the design of variants that attain a low KM for asparagine.
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Affiliation(s)
- Julian Nomme
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Ying Su
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Arnon Lavie
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA.
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Schalk AM, Lavie A. Structural and kinetic characterization of guinea pig L-asparaginase type III. Biochemistry 2014; 53:2318-28. [PMID: 24669941 PMCID: PMC4004260 DOI: 10.1021/bi401692v] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated whether an uncharacterized protein from guinea pig could be the enzyme behind Kidd's serendipitous discovery, made over 60 years ago, that guinea pig serum has cell killing ability. It has been long known that an enzyme with l-asparaginase activity is responsible for cell killing, although astonishingly, its identity remains unclear. Bacterial asparaginases with similar cell killing properties have since become a mainstay therapy of certain cancers such as acute lymphoblastic leukemia. By hydrolyzing asparagine to aspartate and ammonia, these drugs deplete the asparagine present in the blood, killing cancer cells that rely on extracellular asparagine uptake for survival. However, bacterial asparaginases can elicit an adverse immune response. We propose that replacement of bacterial enzymes with the guinea pig asparaginase responsible for serum activity, by its virtue of being more closely related to human enzymes, will be less immunogenic. To this goal, we investigated whether an uncharacterized protein from guinea pig with putative asparaginase activity, which we call gpASNase3, could be that enzyme. We examined its self-activation process (gpASNase3 requires autocleavage to become active), kinetically characterized it for asparaginase and β-aspartyl dipeptidase activity, and elucidated its crystal structure in both the uncleaved and cleaved states. This work reveals that gpASNase3 is not the enzyme responsible for the antitumor effects of guinea pig serum. It exhibits a low affinity for asparagine as measured by a high Michaelis constant, KM, in the millimolar range, in contrast to the low KM (micromolar range) required for asparaginase to be effective as an anticancer agent.
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Affiliation(s)
- Amanda M Schalk
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago , 900 S. Ashland, Chicago , Illinois 60607, United States
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Compartmentalized cyanophycin metabolism in the diazotrophic filaments of a heterocyst-forming cyanobacterium. Proc Natl Acad Sci U S A 2014; 111:3823-8. [PMID: 24550502 DOI: 10.1073/pnas.1318564111] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterocyst-forming cyanobacteria are multicellular organisms in which growth requires the activity of two metabolically interdependent cell types, the vegetative cells that perform oxygenic photosynthesis and the dinitrogen-fixing heterocysts. Vegetative cells provide the heterocysts with reduced carbon, and heterocysts provide the vegetative cells with fixed nitrogen. Heterocysts conspicuously accumulate polar granules made of cyanophycin [multi-L-arginyl-poly (L-aspartic acid)], which is synthesized by cyanophycin synthetase and degraded by the concerted action of cyanophycinase (that releases β-aspartyl-arginine) and isoaspartyl dipeptidase (that produces aspartate and arginine). Cyanophycin synthetase and cyanophycinase are present at high levels in the heterocysts. Here we created a deletion mutant of gene all3922 encoding isoaspartyl dipeptidase in the model heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. The mutant accumulated cyanophycin and β-aspartyl-arginine, and was impaired specifically in diazotrophic growth. Analysis of an Anabaena strain bearing an All3922-GFP (green fluorescent protein) fusion and determination of the enzyme activity in specific cell types showed that isoaspartyl dipeptidase is present at significantly lower levels in heterocysts than in vegetative cells. Consistently, isolated heterocysts released substantial amounts of β-aspartyl-arginine. These observations imply that β-aspartyl-arginine produced from cyanophycin in the heterocysts is transferred intercellularly to be hydrolyzed, producing aspartate and arginine in the vegetative cells. Our results showing compartmentalized metabolism of cyanophycin identify the nitrogen-rich molecule β-aspartyl-arginine as a nitrogen vehicle in the unique multicellular system represented by the heterocyst-forming cyanobacteria.
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Pandey S, Rai R, Rai LC. Proteomics combines morphological, physiological and biochemical attributes to unravel the survival strategy of Anabaena sp. PCC7120 under arsenic stress. J Proteomics 2011; 75:921-37. [PMID: 22057044 DOI: 10.1016/j.jprot.2011.10.011] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 09/13/2011] [Accepted: 10/17/2011] [Indexed: 11/30/2022]
Abstract
Proteomics in conjunction with morphological, physiological and biochemical variables has been employed for the first time to unravel survival strategies of the diazotrophic cyanobacterium Anabaena sp. PCC7120 under Arsenic (As) stress. Significant reduction in growth, carbon fixation, nitrogenase activity and chlorophyll content after 1 day (1d) and recovery after 15 days (15d) of As exposure indicates the acclimation of the test organism against As stress. The formation of akinete like structures is a novel observation never reported before in Anabaena sp. PCC7120. Proteomic characterization using 2-DE showed average 537, 422 and 439 spots in control, 1 and 15d treatment respectively. MALDI-TOF and LC-MS of As-treated Anabaena revealed a total of 45 differentially expressed proteins, of which 13 were novel (hypothetical) ones. Down-regulation of phosphoglycerate kinase (PGK), fructose bisphosphate aldolase II (FBA II), fructose 1,6 bisphosphatase (FBPase), transketolase (TK), and ATP synthase on day 1 and their significant recovery on the 15th day presumably maintained the glycolysis, pentose phosphate pathway (PPP) and turnover rate of Calvin cycle, hence survival of the test organism. Up-regulation of catalase (CAT), peroxiredoxin (Prx), thioredoxin (Trx) and oxidoreductase appears to protect the cells from oxidative stress. Appreciable induction in phytochelatin content (2.4 fold), GST activity (2.3 fold), and transcripts of phytochelatin synthase (5.0 fold), arsenate reductase (8.5 fold) and arsenite efflux genes - asr1102 (5.0 fold), alr1097 (4.7 fold) reiterates their role in As sequestration and shielding of the organism from As toxicity. While up-regulated metabolic and antioxidative defense proteins, phytochelatin and GST work synchronously, the ars genes play a central role in detoxification and survival of Anabaena under As stress. The proposed hypothetical model explains the interaction of metabolic proteins associated with the survival of Anabaena sp. PCC7120 under As stress.
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Affiliation(s)
- Sarita Pandey
- Molecular Biology Section, Laboratory of Algal Biology, Center of Advanced Study in Botany, Banaras Hindu University, Varanasi-221005, India
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Heterologous expression of Anabaena sp. PCC7120 cyanophycin metabolism genes cphA1 and cphB1 in Sinorhizobium (Ensifer) meliloti 1021. Appl Microbiol Biotechnol 2010; 89:1177-92. [DOI: 10.1007/s00253-010-2891-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 09/17/2010] [Accepted: 09/21/2010] [Indexed: 10/19/2022]
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Cantor JR, Stone EM, Chantranupong L, Georgiou G. The human asparaginase-like protein 1 hASRGL1 is an Ntn hydrolase with beta-aspartyl peptidase activity. Biochemistry 2009; 48:11026-31. [PMID: 19839645 PMCID: PMC2782781 DOI: 10.1021/bi901397h] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein we report the bacterial expression, purification, and enzymatic characterization of the human asparaginase-like protein 1 (hASRGL1). We present evidence that hASRGL1 exhibits beta-aspartyl peptidase activity consistent with enzymes designated as plant-type asparaginases, which had thus far been found in only plants and bacteria. Similar to nonmammalian plant-type asparaginases, hASRGL1 is shown to be an Ntn hydrolase for which Thr168 serves as the essential N-terminal nucleophile for intramolecular processing and catalysis, corroborated in part by abolishment of both activities through the Thr168Ala point mutation. In light of the activity profile reported here, ASRGL1s may act synergistically with protein l-isoaspartyl methyl transferase to relieve accumulation of potentially toxic isoaspartyl peptides in mammalian brain and other tissues.
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Affiliation(s)
- Jason R. Cantor
- Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
| | - Everett M. Stone
- Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
| | | | - George Georgiou
- Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
- Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712, USA
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Lo HF, Chou WM, Chen PJ, Lin LL. Influence of signal-peptide truncations on the functional expression of Escherichia coli gamma -glutamyltranspeptidase. J Basic Microbiol 2008; 48:260-8. [PMID: 18720502 DOI: 10.1002/jobm.200700325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The full-length Escherichia coli gamma -glutamyltranspeptidase (EcGGT) gene and five truncations lacking 33, 51, 54, 60, and 78 bp respectively at the 5' end were prepared by polymerase chain reaction and cloned into the expression vector pQE-30. Isopropyl-beta -D-thiogalactopyranoside induction of E. coli M15 cells bearing the recombinant plasmids resulted in the intracellular production of the expressed proteins, EcGGT, EcGGT/DeltaN11, EcGGT/DeltaN17, EcGGT/DeltaN18, EcGGT/DeltaN20, and EcGGT/DeltaN26. The overexpressed enzymes were purified to near homogeneity by Ni(2+)-NTA resin. The specific activity for EcGGT, EcGGT/DeltaN11 and EcGGT/DeltaN17 was 5.3, 4.9, and 4.8 U/mg protein respectively, whereas the rest three enzymes had shown no GGT activity under the enzyme assay conditions. More than 94% of the activity was found in the cytoplasmic fraction of E. coli M15 cells harboring pQE-EcGGT, pQE-EcGGT/DeltaN11 or pQE-EcGGT/DeltaN17. Western blot analysis confirmed that the majority of N-terminally truncated enzymes were present in the cytoplasm.
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Affiliation(s)
- Huei-Fen Lo
- Department of Food and Nutrition, Hungkuang University, Shalu, Taichung, Taiwan
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Anaerobic and aerobic degradation of cyanophycin by the denitrifying bacterium Pseudomonas alcaligenes strain DIP1 and role of three other coisolates in a mixed bacterial consortium. Appl Environ Microbiol 2008; 74:3434-43. [PMID: 18424548 DOI: 10.1128/aem.02575-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Four bacterial strains were isolated from a cyanophycin granule polypeptide (CGP)-degrading anaerobic consortium, identified by 16S rRNA gene sequencing, and assigned to species of the genera Pseudomonas, Enterococcus, Clostridium, and Paenibacillus. The consortium member responsible for CGP degradation was assigned as Pseudomonas alcaligenes strain DIP1. The growth of and CGP degradation by strain DIP1 under anaerobic conditions were enhanced but not dependent on the presence of nitrate as an electron acceptor. CGP was hydrolyzed to its constituting beta-Asp-Arg dipeptides, which were then completely utilized within 25 and 4 days under anaerobic and aerobic conditions, respectively. The end products of CGP degradation by strain DIP1 were alanine, succinate, and ornithine as determined by high-performance liquid chromatography analysis. The facultative anaerobic Enterococcus casseliflavus strain ELS3 and the strictly anaerobic Clostridium sulfidogenes strain SGB2 were coisolates and utilized the beta-linked isodipeptides from the common pool available to the mixed consortium, while the fourth isolate, Paenibacillus odorifer strain PNF4, did not play a direct role in the biodegradation of CGP. Several syntrophic interactions affecting CGP degradation, such as substrate utilization, the reduction of electron acceptors, and aeration, were elucidated. This study demonstrates the first investigation of CGP degradation under both anaerobic and aerobic conditions by one bacterial strain, with regard to the physiological role of other bacteria in a mixed consortium.
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Füser G, Steinbüchel A. Analysis of genome sequences for genes of cyanophycin metabolism: identifying putative cyanophycin metabolizing prokaryotes. Macromol Biosci 2007; 7:278-96. [PMID: 17390395 DOI: 10.1002/mabi.200600207] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
CGP, a copolymer of aspartate and arginine, serves as a storage compound for nitrogen, carbon and energy in many cyanobacteria. Analysis of available genome sequences from prokaryotes identified ORFs putatively encoding proteins of high similarity to known cyanophycin synthetases and cyanophycinases from cyanobacteria in various strains of bacteria belonging to different phylogenetic taxa and not closely related to cyanobacteria. Genes of CGP metabolism occur in a wide range of bacteria exhibiting diverse metabolic capabilities, including aerobic and anaerobic respiration, fermentation, phototrophy and chemolithoautotrophy. This study identified different groups of cyanophycin synthetases and cyanophycinases, respectively, and proposes a collective terminology for the putative genes and enzymes of cyanophycin metabolism. Among 570 different microbial strains, whose genomes have been partially or completely sequenced and are publicly accessible, we identified 44 prokaryotes which possess a cyanophycin synthetase and are putatively able to synthesize CGP. From these, 31 prokaryotes harbor also a cyanophycinase enabling them to degrade CGP to dipeptides. From the latter, 24 strains possess in addition a dipeptidase necessary to hydrolyze beta-Asp-Arg dipeptides, thereby enabling them to completely utilize CGP. Therefore, CGP seems to have a much wider distribution among prokaryotes than previously recognized. Genes putatively encoding cyanophycin synthetase homologues were not identified in the genomes of Eukarya and Archaea and are therefore obviously only occurring in Eubacteria. In addition, the outcome of this detailed in silico analysis proposes to distinguish 10 different groups of cyanophycin synthetases.
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Affiliation(s)
- Gregor Füser
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, Münster, Germany
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Cañas RA, de la Torre F, Cánovas FM, Cantón FR. Coordination of PsAS1 and PsASPG expression controls timing of re-allocated N utilization in hypocotyls of pine seedlings. PLANTA 2007; 225:1205-19. [PMID: 17123103 DOI: 10.1007/s00425-006-0431-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2006] [Accepted: 10/13/2006] [Indexed: 05/11/2023]
Abstract
During pine seed germination, a large amount of N mobilized from the storage proteins is re-allocated in the hypocotyl as free asparagine, as a result of the high levels of asparagine synthetase (AS) encoded by the PsAS1 gene. To determine the role of this re-allocated N reserve, a full-length cDNA encoding L: -asparaginase (ASPG) has been cloned from Scots pine (Pinus sylvestris L.) seedlings and characterized. Like other N-terminal nucleophile hydrolases, pine ASPG requires a post-translational processing to exhibit enzymatic activity. However, in contrast to previous reports on other plant ASPGs, purified recombinant pine ASPG does not undergo autoproteolytic cleavage in vitro. Our results suggest that the processing requires accessory proteins to assist in the proteolysis or in the proper folding before autocleavage in a divalent cation-dependent manner. Sequence comparison analysis revealed that the pine protein is included in the K+-dependent subfamily of plant ASPGs. The expression of the ASPG-encoding gene (PsASPG) was higher in organs with extensive secondary development of the vascular system. The increase in transcript abundance observed at advanced stages of hypocotyl development was concomitant with a decrease of PsAS1 transcript abundance and a remarkable increase in the number of xylem elements and highly lignified cell walls. These results, together with the precise localization of PsASPG transcripts in cells of the cambial region, suggest that the expression of PsAS1 and PsASPG is temporally coordinated, to control the re-allocation of N from seed storage proteins toward the hypocotyl to be later used during early development of secondary vascular system.
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Affiliation(s)
- Rafael A Cañas
- Departamento Biología Molecular y Bioquímica, Universidad de Málaga, Campus de Teatinos s/n, 29071 Málaga, Spain
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Bruneau L, Chapman R, Marsolais F. Co-occurrence of both L-asparaginase subtypes in Arabidopsis: At3g16150 encodes a K+-dependent L-asparaginase. PLANTA 2006; 224:668-79. [PMID: 16705405 DOI: 10.1007/s00425-006-0245-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Accepted: 02/08/2006] [Indexed: 05/09/2023]
Abstract
L-asparaginases (EC 3.5.1.1) are hypothesized to play an important role in nitrogen supply to sink tissues, especially in legume-developing seeds. Two plant L-asparaginase subtypes were previously identified according to their K(+)-dependence for catalytic activity. An L-asparaginase homologous to Lupinus K(+)-independent enzymes with activity towards beta-aspartyl dipeptides, At5g08100, has been previously characterized as a member of the N-terminal nucleophile amidohydrolase superfamily in Arabidopsis. In this study, a K(+)-dependent L-asparaginase from Arabidopsis, At3g16150, is characterized. The recombinants At3g16150 and At5g08100 share a similar subunit structure and conserved autoproteolytic pentapeptide cleavage site, commencing with the catalytic Thr nucleophile, as determined by ESI-MS. The catalytic activity of At3g16150 was enhanced approximately tenfold in the presence of K(+). At3g16150 was strictly specific for L-Asn, and had no activity towards beta-aspartyl dipeptides. At3g16150 also had an approximately 80-fold higher catalytic efficiency with L-Asn relative to At5g08100. Among the beta-aspartyl dipeptides tested, At5g08100 had a preference for beta-aspartyl-His, with catalytic efficiency comparable to that with L-Asn. The phylogenetic analysis revealed that At3g16150 and At5g08100 belong to two distinct subfamilies. The transcript levels of At3g16150 and At5g08100 were highest in sink tissues, especially in flowers and siliques, early in development, as determined by quantitative RT-PCR. The overlapping spatial patterns of expression argue for a partially redundant function of the enzymes. However, the high catalytic efficiency suggests that the K(+)-dependent enzyme may metabolize L-Asn more efficiently under conditions of high metabolic demand for N.
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Affiliation(s)
- Luanne Bruneau
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, 1391 Sandford Street, London, Ontario, Canada N5V 4T3
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Michalska K, Bujacz G, Jaskolski M. Crystal Structure of Plant Asparaginase. J Mol Biol 2006; 360:105-16. [PMID: 16725155 DOI: 10.1016/j.jmb.2006.04.066] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2006] [Revised: 04/25/2006] [Accepted: 04/27/2006] [Indexed: 11/28/2022]
Abstract
In plants, specialized enzymes are required to catalyze the release of ammonia from asparagine, which is the main nitrogen-relocation molecule in these organisms. In addition, K+-independent plant asparaginases are also active in splitting the aberrant isoaspartyl peptide bonds, which makes these proteins important for seed viability and germination. Here, we present the crystal structure of potassium-independent L-asparaginase from yellow lupine (LlA) and confirm the classification of this group of enzymes in the family of Ntn-hydrolases. The alpha- and beta-subunits that form the mature (alphabeta)2 enzyme arise from autoproteolytic cleavage of two copies of a precursor protein. In common with other Ntn-hydrolases, the (alphabeta) heterodimer has a sandwich-like fold with two beta-sheets flanked by two layers of alpha-helices (alphabetabetaalpha). The nucleophilic Thr193 residue, which is liberated in the autocatalytic event at the N terminus of subunit beta, is part of an active site that is similar to that observed in a homologous bacterial enzyme. An unusual sodium-binding loop of the bacterial protein, necessary for proper positioning of all components of the active site, shows strictly conserved conformation and metal coordination in the plant enzyme. A chloride anion complexed in the LlA structure marks the position of the alpha-carboxylate group of the L-aspartyl substrate/product moiety. Detailed analysis of the active site suggests why the plant enzyme hydrolyzes asparagine and its beta-peptides but is inactive towards substrates accepted by similar Ntn-hydrolases, such as taspase1, an enzyme implicated in some human leukemias. Structural comparisons of LlA and taspase1 provide interesting insights into the role of small inorganic ions in the latter enzyme.
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Affiliation(s)
- Karolina Michalska
- Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
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Maheswaran M, Ziegler K, Lockau W, Hagemann M, Forchhammer K. PII-regulated arginine synthesis controls accumulation of cyanophycin in Synechocystis sp. strain PCC 6803. J Bacteriol 2006; 188:2730-4. [PMID: 16547064 PMCID: PMC1428389 DOI: 10.1128/jb.188.7.2730-2734.2006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanophycin (multi-L-arginyl-poly-L-aspartic acid) is a nitrogen storage polymer found in most cyanobacteria and some heterotrophic bacteria. The cyanobacterium Synechocystis sp. strain PCC 6803 accumulates cyanophycin following a transition from nitrogen-limited to nitrogen-excess conditions. Here we show that the accumulation of cyanophycin depends on the activation of the key enzyme of arginine biosynthesis, N-acetyl-L-glutamate kinase, by signal transduction protein PII.
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Affiliation(s)
- Mani Maheswaran
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig Universität Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
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Azevedo RA, Lancien M, Lea PJ. The aspartic acid metabolic pathway, an exciting and essential pathway in plants. Amino Acids 2006; 30:143-62. [PMID: 16525757 DOI: 10.1007/s00726-005-0245-2] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2005] [Accepted: 06/20/2005] [Indexed: 10/24/2022]
Abstract
Aspartate is the common precursor of the essential amino acids lysine, threonine, methionine and isoleucine in higher plants. In addition, aspartate may also be converted to asparagine, in a potentially competing reaction. The latest information on the properties of the enzymes involved in the pathways and the genes that encode them is described. An understanding of the overall regulatory control of the flux through the pathways is undisputedly of great interest, since the nutritive value of all cereal and legume crops is reduced due to low concentrations of at least one of the aspartate-derived amino acids. We have reviewed the recent literature and discussed in this paper possible methods by which the concentrations of the limiting amino acids may be increased in the seeds.
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Affiliation(s)
- R A Azevedo
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil.
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Martí-Arbona R, Thoden JB, Holden HM, Raushel FM. Functional significance of Glu-77 and Tyr-137 within the active site of isoaspartyl dipeptidase. Bioorg Chem 2005; 33:448-58. [PMID: 16289685 DOI: 10.1016/j.bioorg.2005.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2005] [Revised: 10/01/2005] [Accepted: 10/03/2005] [Indexed: 11/22/2022]
Abstract
Isoaspartyl dipeptidase (IAD) is a binuclear metalloenzyme and a member of the amidohydrolase superfamily. This enzyme catalyzes the hydrolytic cleavage of beta-aspartyl dipeptides. The pH-rate profiles for the hydrolysis of beta-Asp-Leu indicates that catalysis is dependent on the ionization of two groups; one that ionizes at a pH approximately 6 and the other approximately 9. The group that must be ionized for catalysis is directly dependent on the identity of the metal ion bound to the active site. This result is consistent with the ionization of the hydroxide that bridges the two divalent cations. In addition to the residues that interact directly with the divalent cations there are two other residues that are highly conserved and found within the active site: Glu-77 and Tyr-137. Mutation of Tyr-137 to phenylalanine reduced the rate of catalysis by three orders of magnitude. The three dimensional X-ray structure of the Y137F mutant did not show any significant conformation changes relative to the three dimensional structure of the wild-type enzyme. The positioning of the side-chain phenolic group of Tyr-137 in the active site of IAD is consistent with the stabilization of the tetrahedral adduct concomitant with nucleophilic attack by the hydroxide that bridges the two divalent cations. Mutation of Glu-77 resulted in the reduction of catalytic activity by five orders of magnitude. The three dimensional structure of the E77Q mutant did not show any significant conformational changes in the mutant relative to the three dimensional structure of the wild-type enzyme. The positioning of the side-chain carboxylate of Glu-77 is consistent with the formation of an ion pair interaction with the free alpha-amino group of the substrate.
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Obst M, Krug A, Luftmann H, Steinbüchel A. Degradation of cyanophycin by Sedimentibacter hongkongensis strain KI and Citrobacter amalonaticus strain G Isolated from an anaerobic bacterial consortium. Appl Environ Microbiol 2005; 71:3642-52. [PMID: 16000772 PMCID: PMC1169039 DOI: 10.1128/aem.71.7.3642-3652.2005] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2004] [Accepted: 02/02/2005] [Indexed: 11/20/2022] Open
Abstract
Using a combination of various enrichment techniques, the strictly anaerobic, gram-positive, endospore-forming bacterium Sedimentibacter hongkongensis strain KI as revealed by 16S rRNA analysis and the gram-negative enterobacterium Citrobacter amalonaticus strain G as revealed by physiological tests were isolated from an anaerobic cyanophycin (CGP)-degrading bacterial consortium. S. hongkongensis strain KI is the first anaerobic bacterium with the ability to hydrolyze CGP to beta-Asp-Arg and beta-Asp-Lys dipeptides, as revealed by electrospray ionization-mass spectrometry and reversed-phase high-performance liquid chromatography analysis. However, these primary accumulated hydrolysis products were only partially used by S. hongkongensis strain KI, and significant growth on CGP did not occur. On the other hand, C. amalonaticus strain G did not degrade CGP but grew on the beta-linked iso-dipeptides formed in vitro by enzymatic CGP degradation or in vivo by metabolic activity of S. hongkongensis strain KI. Dipeptide utilization occurred at the highest rate if both strains were used in cocultivation experiments with CGP, indicating that cooperation between different bacteria occurs in anaerobic natural environments for complete CGP turnover. The amino acids obtained from the cleavage of dipeptides were fermented to ethanol, acetic acid, and succinic acid, as revealed by gas chromatographic analysis and by spectrophotometric enzyme assays.
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Affiliation(s)
- Martin Obst
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, 48149 Münster, Germany.
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