1
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Fineide FA, Tashbayev B, Elgstøen KBP, Sandås EM, Rootwelt H, Hynne H, Chen X, Ræder S, Vehof J, Dartt D, Jensen JL, Utheim TP. Tear and Saliva Metabolomics in Evaporative Dry Eye Disease in Females. Metabolites 2023; 13:1125. [PMID: 37999221 PMCID: PMC10673540 DOI: 10.3390/metabo13111125] [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: 09/28/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023] Open
Abstract
Accurate diagnosis of dry eye disease (DED) is challenging, and even today there is no gold standard biomarker of DED. Hypothesis-free global metabolomic studies of tears from DED patients have great potential to discover metabolites and pathways affected in the pathophysiology of DED, and to identify possible future biomarkers. These metabolites and biomarkers could be important for diagnosing and monitoring disease as well as for new therapeutic targets and strategies. As DED is associated with dry mouth, this study aimed to perform metabolomic analyses of tears and saliva from patients with decreased tear film break-up time but normal Schirmer test, and age-matched controls with both tear production and stability within physiological range. We applied strict inclusion criteria to reduce sampling bias in the metabolomic analyses and selected only age-matched females with Schirmer test values between 10-15 mm/5 min. The tear film analysis arm included 19 patients (with tear film break-up time 0-5 s) and 12 controls (with tear film break-up time 10-30 s), while the salivary analysis arm consisted of a subset which included 18 patients and six controls. Metabolomic analyses were performed using liquid chromatography and high-resolution mass spectrometry. Analyses using a global database search detected a total of 56 metabolites in tear samples that were significantly different between the groups. Of these, several have known associations with DED. These metabolites are present in meibum and have anti-oxidative characteristics or associations with the ocular microbiome, and altered concentrations suggest that they may play a significant role in DED associated with decreased tear film stability. In saliva, hypotaurine levels were lower among patients with tear film instability. In this pilot study, we found different levels of several metabolites in patients with decreased tear film break-up time that may have associations with DED. Future studies are required to replicate our findings and clarify the exact roles of these metabolites.
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Affiliation(s)
- Fredrik A. Fineide
- The Norwegian Dry Eye Clinic, 0366 Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, 0450 Oslo, Norway
- Department of Computer Science, Oslo Metropolitan University, 0130 Oslo, Norway
| | - Behzod Tashbayev
- The Norwegian Dry Eye Clinic, 0366 Oslo, Norway
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, 0313 Oslo, Norway
| | | | - Elise M. Sandås
- Department of Medical Biochemistry, Oslo University Hospital, 0450 Oslo, Norway
| | - Helge Rootwelt
- Department of Medical Biochemistry, Oslo University Hospital, 0450 Oslo, Norway
| | - Håvard Hynne
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, 0313 Oslo, Norway
| | - Xiangjun Chen
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, 0313 Oslo, Norway
- Department of Ophthalmology, Drammen Hospital Trust, 3004 Drammen, Norway
- Department of Ophthalmology, Sørlandet Hospital Trust, 4838 Arendal, Norway
| | - Sten Ræder
- The Norwegian Dry Eye Clinic, 0366 Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, 0450 Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, 0450 Oslo, Norway
| | - Jelle Vehof
- Departments of Ophthalmology and Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands
| | - Darlene Dartt
- Schepens Eye Research Institute/Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, 20 Staniford St., Boston, MA 02114, USA
| | - Janicke L. Jensen
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, 0313 Oslo, Norway
| | - Tor P. Utheim
- Department of Medical Biochemistry, Oslo University Hospital, 0450 Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, 0450 Oslo, Norway
- Department of Oral Biology, Faculty of Dentistry, University of Oslo, 0313 Oslo, Norway
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2
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Daniel-Ivad PG, Van Lanen S, Ryan KS. Structure of the Oxygen, Pyridoxal Phosphate-Dependent Capuramycin Biosynthetic Protein Cap15. Biochemistry 2023; 62:2611-2621. [PMID: 37556254 DOI: 10.1021/acs.biochem.3c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Pyridoxal phosphate-dependent enzymes able to use oxygen as a co-substrate have emerged in multiple protein families. Here, we use crystallography to solve the 2.40 Å resolution crystal structure of Cap15, a nucleoside biosynthetic enzyme that catalyzes the oxidative decarboxylation of glycyl uridine. Our structural study captures the internal aldimine, pinpointing the active site lysine as K230 and showing the site of phosphate binding. Our docking studies reveal how Cap15 is able to catalyze a stereoselective deprotonation reaction, and bioinformatic analysis reveals active site residues that distinguish Cap15 from the structurally related d-glucosaminate-6-phosphate ammonia lyase and l-seryl-tRNA(Sec) selenium transferase (SelA). Our work provides the structural basis for further mechanistic investigation of a unique biosynthetic enzyme and provides a blueprint for understanding how oxygen reactivity emerged in the SelA-like protein family.
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Affiliation(s)
- Phillip G Daniel-Ivad
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Steven Van Lanen
- Pharmaceutical Sciences Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Katherine S Ryan
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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3
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Srivastava J, Balaji PV. Clues to reaction specificity in
PLP
‐dependent fold type I aminotransferases of monosaccharide biosynthesis. Proteins 2022; 90:1247-1258. [DOI: 10.1002/prot.26305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Jaya Srivastava
- Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Mumbai India
| | - Petety V. Balaji
- Department of Biosciences and Bioengineering Indian Institute of Technology Bombay Mumbai India
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4
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Seltzner CA, Ferek JD, Thoden JB, Holden HM. Characterization of an aminotransferase from Acanthamoeba polyphaga Mimivirus. Protein Sci 2021; 30:1882-1894. [PMID: 34076307 DOI: 10.1002/pro.4139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 01/03/2023]
Abstract
Acanthamoeba polyphaga Mimivirus, a complex virus that infects amoeba, was first reported in 2003. It is now known that its DNA genome encodes for nearly 1,000 proteins including enzymes that are required for the biosynthesis of the unusual sugar 4-amino-4,6-dideoxy-d-glucose, also known as d-viosamine. As observed in some bacteria, the pathway for the production of this sugar initiates with a nucleotide-linked sugar, which in the Mimivirus is thought to be UDP-d-glucose. The enzyme required for the installment of the amino group at the C-4' position of the pyranosyl moiety is encoded in the Mimivirus by the L136 gene. Here, we describe a structural and functional analysis of this pyridoxal 5'-phosphate-dependent enzyme, referred to as L136. For this analysis, three high-resolution X-ray structures were determined: the wildtype enzyme/pyridoxamine 5'-phosphate/dTDP complex and the site-directed mutant variant K185A in the presence of either UDP-4-amino-4,6-dideoxy-d-glucose or dTDP-4-amino-4,6-dideoxy-d-glucose. Additionally, the kinetic parameters of the enzyme utilizing either UDP-d-glucose or dTDP-d-glucose were measured and demonstrated that L136 is efficient with both substrates. This is in sharp contrast to the structurally related DesI from Streptomyces venezuelae, whose three-dimensional architecture was previously reported by this laboratory. As determined in this investigation, DesI shows a profound preference in its catalytic efficiency for the dTDP-linked sugar substrate. This difference can be explained in part by a hydrophobic patch in DesI that is missing in L136. Notably, the structure of L136 reported here represents the first three-dimensional model for a virally encoded PLP-dependent enzyme and thus provides new information on sugar aminotransferases in general.
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Affiliation(s)
- Chase A Seltzner
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Justin D Ferek
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
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5
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Han X, Sun R, Sandalova T, Achour A. Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in Streptococcus pneumoniae. Open Biol 2019; 8:rsob.170248. [PMID: 29669826 PMCID: PMC5936713 DOI: 10.1098/rsob.170248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/23/2018] [Indexed: 11/28/2022] Open
Abstract
Spr1654 from Streptococcus pneumoniae plays a key role in the production of unusual sugars, presumably functioning as a pyridoxal-5′-phosphate (PLP)-dependent aminotransferase. Spr1654 was predicted to catalyse the transferring of amino group to form the amino sugar 2-acetamido-4-amino-2, 4, 6-trideoxygalactose moiety (AATGal), representing a crucial step in biosynthesis of teichoic acids in S. pneumoniae. We have determined the crystal structures of the apo-, PLP- and PMP-bound forms of Spr1654. Spr1654 forms a homodimer, in which each monomer contains one active site. Using spectrophotometry and based on absorbance profiles of PLP- and PMP-formed enzymes, our results indicate that l-glutamate is most likely the preferred amino donor. Structural superposition of the crystal structures of Spr1654 on previously determined structures of other sugar aminotransferases in complex with glutamate and/or UDP-activated sugar allowed us to identify key Spr1654 residues for ligand binding and catalysis. The crystal structures of Spr1654 and in complex with PLP and PMP can direct the future rational design of novel therapeutic compounds against S. pneumoniae.
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Affiliation(s)
- Xiao Han
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden.,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine Solna, Karolinska Institute, Solna, 17176 Stockholm, Sweden .,Division of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden
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6
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Uddin R, Rafi S. Structural and functional characterization of a unique hypothetical protein (WP_003901628.1) of Mycobacterium tuberculosis: a computational approach. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1822-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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7
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Cui L, Zhu Y, Guan X, Deng Z, Bai L, Feng Y. De Novo Biosynthesis of β-Valienamine in Engineered Streptomyces hygroscopicus 5008. ACS Synth Biol 2016; 5:15-20. [PMID: 26436873 DOI: 10.1021/acssynbio.5b00138] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The C7N aminocyclitol β-valienamine is a lead compound for the development of new biologically active β-glycosidase inhibitors as chemical chaperone therapeutic agents for lysosomal storage diseases. Its chemical synthesis is challenging due to the presence of multichiral centers in the structure. Herein, we took advantage of a heterogeneous aminotransferase with stereospecificity and designed a novel pathway for producing β-valienamine in Streptomyces hygroscopicus 5008, a validamycin producer. The aminotransferase BtrR from Bacillus circulans was able to convert valienone to β-valienamine with an optical purity of up to >99.9% enantiomeric excess value in vitro. When the aminotransferase gene was introduced into a mutant of S. hygroscopicus 5008 accumulating valienone, 20 mg/L of β-valienamine was produced after 96 h cultivation in shaking flasks. This work provides a powerful alternative for preparing the chiral intermediates for pharmaceutical development.
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Affiliation(s)
- Li Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, and Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Zhu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, and Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoqing Guan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, and Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, and Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, and Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, and Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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8
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Lee M, Sousa MC. Structural basis for substrate specificity in ArnB. A key enzyme in the polymyxin resistance pathway of Gram-negative bacteria. Biochemistry 2014; 53:796-805. [PMID: 24460375 PMCID: PMC3985747 DOI: 10.1021/bi4015677] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Cationic Antimicrobial Peptides (CAMPs)
represent a first line
of defense against bacterial colonization. When fighting Gram-negative
bacteria, CAMPs initially interact electrostatically with the negatively
charged phosphate groups in lipid A and are thought to kill bacteria
by disrupting their membrane integrity. However, many human pathogens,
including Salmonella and Pseudomonas, have evolved lipid A modification mechanisms
that result in resistance to CAMPs and related antibiotics such as
Colistin. The addition of 4-amino-4-deoxy-l-Arabinose (Ara4N)
to a phosphate group in lipid A is one such modification, frequently
found in Pseudomonas isolated from
cystic fibrosis patients. The pathway for biosynthesis of Ara4N-lipid
A requires conversion of UDP-Glucuronic acid into UDP-Ara4N and subsequent
transfer of the amino-sugar to lipid A. ArnB is a pyridoxal-phosphate
(PLP) dependent transaminase that catalyzes a crucial step in the
pathway: synthesis of UDP-Ara4N from UDP-4-keto-pentose. Here we present
the 2.3 Å resolution crystal structure of an active site mutant
of ArnB (K188A) in complex with the reaction intermediate aldimine
formed by UDP-Ara4N and PLP. The sugar–nucleotide binding site
is in a cleft between the subunits of the ArnB dimer with the uracil
buried at the interface and the UDP ribose and phosphate groups exposed
to the solvent. The Ara4N moiety is found in the 4C1 conformation and its positioning, stabilized by interactions
with both the protein and cofactor, is compatible with catalysis.
The structure suggests strategies for the development of specific
inhibitors that may prove useful in the treatment of resistant bacteria
such as Pseudomonas found in cystic
fibrosis patients.
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Affiliation(s)
- Myeongseon Lee
- Department of Chemistry and Biochemistry, University of Colorado at Boulder , Boulder, Colorado 80309-0596, United States
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9
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Bello M, Martínez-Archundia M, Correa-Basurto J. Automated docking for novel drug discovery. Expert Opin Drug Discov 2013; 8:821-34. [DOI: 10.1517/17460441.2013.794780] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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10
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Chopra S, Ramkissoon K, Anderson DC. A systematic quantitative proteomic examination of multidrug resistance in Acinetobacter baumannii. J Proteomics 2013; 84:17-39. [PMID: 23542354 DOI: 10.1016/j.jprot.2013.03.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/18/2013] [Accepted: 03/17/2013] [Indexed: 12/29/2022]
Abstract
UNLABELLED Multidrug-resistant Acinetobacter baumannii strains have been examined at the DNA sequence level, but seldom using large-scale quantitative proteomics. We have compared the proteome of the multidrug resistant strain BAA-1605, with the proteome of the drug-sensitive strain ATCC 17978, using iTRAQ labeling and online 2D LC/MS/MS for peptide/protein identification. Of 1484 proteins present in at least 2 of 4 independent experiments, 114 are 2-fold to 66-fold more abundant in BAA-1605, and 99 are 2-fold to 50-fold less abundant. Proteins with 2-fold or greater abundance in the multidrug resistant strain include drug-, antibiotic-, and heavy metal-resistance proteins, stress-related proteins, porins, membrane transporters, proteins important for acquisition of foreign DNA, biofilm-related proteins, cell-wall and exopolysaccharide-related proteins, lipoproteins, metabolic proteins, and many with no annotated function. The porin CarO, inactivated in carbapenem-resistant strains, is 2.3-fold more abundant in BAA-1605. Likewise, the porin OmpW, less abundant in carbapenem- and colistin-resistant A. baumannii strains, is 3-fold more abundant in BAA-1605. Nine proteins, all present in the drug-sensitive strain but from 2.2-fold to 16-fold more abundant in the MDR strain, can potentially account for the observed resistance of BAA-1605 to 18 antibiotics. BIOLOGICAL SIGNIFICANCE Multidrug resistant (MDR) strains of the pathogen Acinetobacter baumannii are a significant cause of hospital-acquired infections, are associated with increased mortality and length of stay, and may be a major factor underlying the spread of this pathogen, which is difficult to eradicate from clinical settings. To obtain a better understanding of antimicrobial resistance mechanisms in MDR A. baumannii, we report the first large scale 2D LC/MS/MS-based quantitative proteomics comparison of a drug-sensitive strain and an MDR strain of this pathogen. Ca. 20% of the expressed proteome changes 2-fold or more between the compared strains, including 42 proteins with literature or informatics annotations related to resistance mechanisms, modification of xenobiotics, or drug transport. Other categories of proteins differing 2-fold or more between strains include stress-response related proteins, porins, OMPs, transporters and secretion-related proteins, cell wall- and expolysaccharide-related proteins, lipoproteins, and DNA- and plasmid-related proteins. While the compared strains also differ in other aspects than multi-drug resistance, the observed differences, combined with protein functional annotation, suggest that complex protein expression changes may accompany the MDR phenotype. Expression changes of nine proteins in the MDR strain can potentially account for the observed resistance to 18 antibiotics.
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Affiliation(s)
- Sidharth Chopra
- Center for Infectious Disease and Biodefense Research, SRI International, 333 Ravenswood, Avenue, Menlo Park, CA 94025, USA
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11
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Singh S, Phillips GN, Thorson JS. The structural biology of enzymes involved in natural product glycosylation. Nat Prod Rep 2012; 29:1201-37. [PMID: 22688446 DOI: 10.1039/c2np20039b] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glycosylation of microbial natural products often dramatically influences the biological and/or pharmacological activities of the parental metabolite. Over the past decade, crystal structures of several enzymes involved in the biosynthesis and attachment of novel sugars found appended to natural products have emerged. In many cases, these studies have paved the way to a better understanding of the corresponding enzyme mechanism of action and have served as a starting point for engineering variant enzymes to facilitate to production of differentially-glycosylated natural products. This review specifically summarizes the structural studies of bacterial enzymes involved in biosynthesis of novel sugar nucleotides.
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Affiliation(s)
- Shanteri Singh
- Laboratory for Biosynthetic Chemistry, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
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12
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Piacente F, Marin M, Molinaro A, De Castro C, Seltzer V, Salis A, Damonte G, Bernardi C, Claverie JM, Abergel C, Tonetti M. Giant DNA virus mimivirus encodes pathway for biosynthesis of unusual sugar 4-amino-4,6-dideoxy-D-glucose (Viosamine). J Biol Chem 2012; 287:3009-18. [PMID: 22157758 PMCID: PMC3270958 DOI: 10.1074/jbc.m111.314559] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mimivirus is one the largest DNA virus identified so far, infecting several Acanthamoeba species. Analysis of its genome revealed the presence of a nine-gene cluster containing genes potentially involved in glycan formation. All of these genes are co-expressed at late stages of infection, suggesting their role in the formation of the long fibers covering the viral surface. Among them, we identified the L136 gene as a pyridoxal phosphate-dependent sugar aminotransferase. This enzyme was shown to catalyze the formation of UDP-4-amino-4,6-dideoxy-D-glucose (UDP-viosamine) from UDP-4-keto-6-deoxy-D-glucose, a key compound involved also in the biosynthesis of L-rhamnose. This finding further supports the hypothesis that Mimivirus encodes a glycosylation system that is completely independent of the amoebal host. Viosamine, together with rhamnose, (N-acetyl)glucosamine, and glucose, was found as a major component of the viral glycans. Most of the sugars were associated with the fibers, confirming a capsular-like nature of the viral surface. Phylogenetic analysis clearly indicated that L136 was not a recent acquisition from bacteria through horizontal gene transfer, but it was acquired very early during evolution. Implications for the origin of the glycosylation machinery in giant DNA virus are also discussed.
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Affiliation(s)
- Francesco Piacente
- Department of Experimental Medicine and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV/1, 16132 Genova, Italy
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13
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Romo AJ, Liu HW. Mechanisms and structures of vitamin B(6)-dependent enzymes involved in deoxy sugar biosynthesis. BIOCHIMICA ET BIOPHYSICA ACTA 2011; 1814:1534-47. [PMID: 21315852 PMCID: PMC3115481 DOI: 10.1016/j.bbapap.2011.02.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 01/08/2011] [Accepted: 02/01/2011] [Indexed: 10/18/2022]
Abstract
PLP is well-regarded for its role as a coenzyme in a number of diverse enzymatic reactions. Transamination, deoxygenation, and aldol reactions mediated by PLP-dependent enzymes enliven and enrich deoxy sugar biosynthesis, endowing these compounds with unique structures and contributing to their roles as determinants of biological activity in many natural products. The importance of deoxy aminosugars in natural product biosynthesis has spurred several recent structural investigations of sugar aminotransferases. The structure of a PMP-dependent enzyme catalyzing the C-3 deoxygenation reaction in the biosynthesis of ascarylose was also determined. These studies, and the crystal structures they have provided, offer a wealth of new insights regarding the enzymology of PLP/PMP-dependent enzymes in deoxy sugar biosynthesis. In this review, we consider these recent achievements in the structural biology of deoxy sugar biosynthetic enzymes and the important implications they hold for understanding enzyme catalysis and natural product biosynthesis in general. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.
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Affiliation(s)
- Anthony J. Romo
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712
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14
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Holden HM, Cook PD, Thoden JB. Biosynthetic enzymes of unusual microbial sugars. Curr Opin Struct Biol 2010; 20:543-50. [PMID: 20832292 DOI: 10.1016/j.sbi.2010.08.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 05/07/2010] [Accepted: 08/11/2010] [Indexed: 11/18/2022]
Abstract
The biological importance of proteins and nucleic acids in the natural world is undeniable, and research efforts on these macromolecules have often overshadowed those directed at carbohydrates. It is now known, however, that carbohydrates not only play roles in energy storage and plant cell wall structure, but are also intimately involved in such processes as fertilization, the immune response, and cell adhesion. Indeed, recent years have seen an explosion in research efforts directed at uncovering and understanding new sugar moieties. The dideoxysugars and trideoxysugars, which are synthesized by a variety of bacteria, fungi, and plants, represent an especially intriguing class of carbohydrates. They are found, for example, on the lipopolysaccharides of some Gram-negative bacteria or on antibacterial agents such as erythromycin. Many of them are formed from simple monosaccharides such as glucose-6-phosphate or fructose-6-phosphate via a myriad of enzymatic reactions including acetylations, aminations, dehydrations, epimerizations, reductions, and methylations. In this review we focus on the recent structural investigations of the bacterial N-acetyltransferases and the PLP-dependent aminotransferases that function on nucleotide-linked sugar substrates.
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Affiliation(s)
- Hazel M Holden
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.
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15
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Hutchinson E, Murphy B, Dunne T, Breen C, Rawlings B, Caffrey P. Redesign of polyene macrolide glycosylation: engineered biosynthesis of 19-(O)-perosaminyl-amphoteronolide B. ACTA ACUST UNITED AC 2010; 17:174-82. [PMID: 20189107 DOI: 10.1016/j.chembiol.2010.01.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 12/03/2009] [Accepted: 01/11/2010] [Indexed: 11/17/2022]
Abstract
Most polyene macrolide antibiotics are glycosylated with mycosamine (3,6-dideoxy-3-aminomannose). In the amphotericin B producer, Streptomyces nodosus, mycosamine biosynthesis begins with AmphDIII-catalyzed conversion of GDP-mannose to GDP-4-keto-6-deoxymannose. This is converted to GDP-3-keto-6-deoxymannose, which is transaminated to GDP-mycosamine by the AmphDII protein. The glycosyltransferase AmphDI transfers mycosamine to amphotericin aglycones (amphoteronolides). The aromatic heptaene perimycin is unusual among polyenes in that the sugar is perosamine (4,6-dideoxy-4-aminomannose), which is synthesized by direct transamination of GDP-4-keto-6-deoxymannose. Here, we use the Streptomyces aminophilus perDII perosamine synthase and perDI perosaminyltransferase genes to engineer biosynthesis of perosaminyl-amphoteronolide B in S. nodosus. Efficient production required a hybrid glycosyltransferase containing an N-terminal region of AmphDI and a C-terminal region of PerDI. This work will assist efforts to generate glycorandomized amphoteronolides for drug discovery.
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Affiliation(s)
- Eve Hutchinson
- School of Biomolecular and Biomedical Science and Centre for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
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Cook PD, Kubiak RL, Toomey DP, Holden HM. Two site-directed mutations are required for the conversion of a sugar dehydratase into an aminotransferase. Biochemistry 2009; 48:5246-53. [PMID: 19402712 DOI: 10.1021/bi9005545] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
L-colitose and d-perosamine are unusual sugars found in the O-antigens of some Gram-negative bacteria such as Escherichia coli, Vibrio cholerae, and Salmonella enterica, among others. The biosynthetic pathways for these two sugars begin with the formation of GDP-mannose from d-mannose 1-phosphate and GTP followed by the subsequent dehydration and oxidation of GDP-mannose to yield GDP-4-keto-6-deoxymannose. Following the production of GDP-4-keto-6-deoxymannose, the two pathways diverge. In the case of GDP-perosamine biosynthesis, the next step involves an amination reaction at the C-4' position of the sugar, whereas in GDP-colitose production, the 3'-hydroxyl group is removed. The enzymes catalyzing these reactions are GDP-perosamine synthase and GDP-4-keto-6-deoxymannose-3-dehydratase (ColD), respectively. Both of these enzymes are pyridoxal 5'-phosphate (PLP) dependent, and their three-dimensional structures place them into the well-characterized aspartate aminotransferase superfamily. A comparison of the active site architecture of ColD from E. coli (strain 5a, type O55:H7) to that of GDP-perosamine synthase from Caulobacter crescentus CB15 suggested that only two mutations would be required to convert ColD into an aminotransferase. Here we present a combined structural and functional analysis of the ColD S187N/H188K mutant protein that, indeed, has been converted from a sugar dehydratase into an aminotransferase.
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Affiliation(s)
- Paul D Cook
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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