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Ichioka R, Kitazawa Y, Taguchi G, Shimosaka M. A novel N-acetylglucosamine-6-phosphate deacetylase that is essential for chitin utilization in the chitinolytic bacterium, Chitiniphilus shinanonensis. J Appl Microbiol 2024; 135:lxae117. [PMID: 38724455 DOI: 10.1093/jambio/lxae117] [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: 02/18/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
AIMS We aimed to investigate the function of an unidentified gene annotated as a PIG-L domain deacetylase (cspld) in Chitiniphilus shinanonensis SAY3. cspld was identified using transposon mutagenesis, followed by negatively selecting a mutant incapable of growing on chitin, a polysaccharide consisting of N-acetyl-d-glucosamine (GlcNAc). We focused on the physiological role of CsPLD protein in chitin utilization. METHODS AND RESULTS Recombinant CsPLD expressed in Escherichia coli exhibited GlcNAc-6-phosphate deacetylase (GPD) activity, which is involved in the metabolism of amino sugars. However, SAY3 possesses two genes (csnagA1 and csnagA2) in its genome that code for proteins whose primary sequences are homologous to those of typical GPDs. Recombinant CsNagA1 and CsNagA2 also exhibited GPD activity with 23 and 1.6% of catalytic efficiency (kcat/Km), respectively, compared to CsPLD. The gene-disrupted mutant, Δcspld was unable to grow on chitin or GlcNAc, whereas the three mutants, ΔcsnagA1, ΔcsnagA2, and ΔcsnagA1ΔcsnagA2 grew similarly to SAY3. The determination of GPD activity in the crude extracts of each mutant revealed that CsPLD is a major enzyme that accounts for almost all cellular activities. CONCLUSIONS Deacetylation of GlcNAc-6P catalyzed by CsPLD (but not by typical GPDs) is essential for the assimilation of chitin and its constituent monosaccharide, GlcNAc, as a carbon and energy source in C. shinanonensis.
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Affiliation(s)
- Ryotaro Ichioka
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda, Nagano 386-8567, Japan
| | - Yuri Kitazawa
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda, Nagano 386-8567, Japan
| | - Goro Taguchi
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda, Nagano 386-8567, Japan
| | - Makoto Shimosaka
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda, Nagano 386-8567, Japan
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2
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Utter DR, He X, Cavanaugh CM, McLean JS, Bor B. The saccharibacterium TM7x elicits differential responses across its host range. THE ISME JOURNAL 2020; 14:3054-3067. [PMID: 32839546 PMCID: PMC7784981 DOI: 10.1038/s41396-020-00736-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/01/2020] [Accepted: 08/03/2020] [Indexed: 12/28/2022]
Abstract
Host range is a fundamental component of symbiotic interactions, yet it remains poorly characterized for the prevalent yet enigmatic subcategory of bacteria/bacteria symbioses. The recently characterized obligate bacterial epibiont Candidatus Nanosynbacter lyticus TM7x with its bacterial host Actinomyces odontolyticus XH001 offers an ideal system to study such a novel relationship. In this study, the host range of TM7x was investigated by coculturing TM7x with various related Actinomyces strains and characterizing their growth dynamics from initial infection through subsequent co-passages. Of the twenty-seven tested Actinomyces, thirteen strains, including XH001, could host TM7x, and further classified into "permissive" and "nonpermissive" based on their varying initial responses to TM7x. Ten permissive strains exhibited growth/crash/recovery phases following TM7x infection, with crash timing and extent dependent on initial TM7x dosage. Meanwhile, three nonpermissive strains hosted TM7x without a growth-crash phase despite high TM7x dosage. The physical association of TM7x with all hosts, including nonpermissive strains, was confirmed by microscopy. Comparative genomic analyses revealed distinguishing genomic features between permissive and nonpermissive hosts. Our results expand the concept of host range beyond a binary to a wider spectrum, and the varying susceptibility of Actinomyces strains to TM7x underscores how small genetic differences between hosts can underly divergent selective trajectories.
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Affiliation(s)
- Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, 02142, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, 02115, USA
| | - Colleen M Cavanaugh
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA, 98119, USA
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, 02142, USA.
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, 02115, USA.
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3
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Pascual S, Planas A. Carbohydrate de-N-acetylases acting on structural polysaccharides and glycoconjugates. Curr Opin Chem Biol 2020; 61:9-18. [PMID: 33075728 DOI: 10.1016/j.cbpa.2020.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022]
Abstract
Deacetylation of N-acetylhexosamine residues in structural polysaccharides and glycoconjugates is catalyzed by different families of carbohydrate esterases that, despite different structural folds, share a common metal-assisted acid/base mechanism with the metal cation coordinated with a conserved Asp-His-His triad. These enzymes serve diverse biological functions in the modification of cell-surface polysaccharides in bacteria and fungi as well as in the metabolism of hexosamines in the biosynthesis of cellular glycoconjugates. Focusing on carbohydrate de-N-acetylases, this article summarizes the background of the different families from a structural and functional viewpoint and covers advances in the characterization of novel enzymes over the last 2-3 years. Current research is addressed to the identification of new deacetylases and unravel their biological functions as they are candidate targets for the design of antimicrobials against pathogenic bacteria and fungi. Likewise, some families are also used as biocatalysts for the production of defined glycostructures with diverse applications.
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Affiliation(s)
- Sergi Pascual
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017, Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, 08017, Barcelona, Spain.
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4
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GlcNAc De- N-Acetylase from the Hyperthermophilic Archaeon Sulfolobus solfataricus. Appl Environ Microbiol 2019; 85:AEM.01879-18. [PMID: 30446550 DOI: 10.1128/aem.01879-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/04/2018] [Indexed: 01/17/2023] Open
Abstract
Sulfolobus solfataricus is an aerobic crenarchaeal hyperthermophile with optimum growth at temperatures greater than 80°C and pH 2 to 4. Within the crenarchaeal group of Sulfolobales, N-acetylglucosamine (GlcNAc) has been shown to be a component of exopolysaccharides, forming their biofilms, and of the N-glycan decorating some proteins. The metabolism of GlcNAc is still poorly understood in Archaea, and one approach to gaining additional information is through the identification and functional characterization of carbohydrate active enzymes (CAZymes) involved in the modification of GlcNAc. The screening of S. solfataricus extracts allowed the detection of a novel α-N-acetylglucosaminidase (α-GlcNAcase) activity, which has never been identified in Archaea Mass spectrometry analysis of the purified activity showed a protein encoded by the sso2901 gene. Interestingly, the purified recombinant enzyme, which was characterized in detail, revealed a novel de-N-acetylase activity specific for GlcNAc and derivatives. Thus, assays to identify an α-GlcNAcase found a GlcNAc de-N-acetylase instead. The α-GlcNAcase activity observed in S. solfataricus extracts did occur when SSO2901 was used in combination with an α-glucosidase. Furthermore, the inspection of the genomic context and the preliminary characterization of a putative glycosyltransferase immediately upstream of sso2901 (sso2900) suggest the involvement of these enzymes in the GlcNAc metabolism in S. solfataricus IMPORTANCE In this study, a preliminary screening of cellular extracts of S. solfataricus allowed the identification of an α-N-acetylglucosaminidase activity. However, the characterization of the corresponding recombinant enzyme revealed a novel GlcNAc de-N-acetylase, which, in cooperation with the α-glucosidase, catalyzed the hydrolysis of O-α-GlcNAc glycosides. In addition, we show that the product of a gene flanking the one encoding the de-N-acetylase is a putative glycosyltransferase, suggesting the involvement of the two enzymes in the metabolism of GlcNAc. The discovery and functional analysis of novel enzymatic activities involved in the modification of this essential sugar represent a powerful strategy to shed light on the physiology and metabolism of Archaea.
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Song W, Wang S, Shen J, Zhu B. Complete Genome Sequence of Massilia oculi sp. nov. CCUG 43427 T (=DSM 26321 T), the Type Strain of M. oculi, and Comparison with Genome Sequences of Other Massilia Strains. Curr Microbiol 2018; 76:1082-1086. [PMID: 30443686 DOI: 10.1007/s00284-018-1597-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/08/2018] [Indexed: 11/26/2022]
Abstract
Massilia oculi sp. nov. of type strain CCUG 43427T is a Gram-negative, rod-shaped, nonspore-forming bacterium, which was recently isolated from the eye of a patient suffering from endophthalmitis and was described as novel species in Massilia genus. In this study, we present the complete genome sequence of this strain by using Pacbio SMRT cell platform and compare this sequence with the genomes of 30 Massilia representative strains. Also, a comprehensive search was conducted for genes and proteins involved in antibiotic resistance and pathogenicity. The genome of CCUG 43427T is 5,844,653 bp with 65.55% GC content. This genome contains four prophages and four genomic islands (GIs). The cobalt/zinc/cadmium transporter locus CzcABCD is included in these GIs. This GI was predicted to play important role in bacterial heavy-metal tolerance. The in silico genome analysis also revealed that this strain contains a lot of antibiotic resistance and pathogenicity related genes. This result suggested that this strain may has evolved a wide arsenal of weapons for pathogenicity and survival. Genome comparison among CCUG 43427T and other 30 Massilia strains revealed that more than 400 genes are unique in CCUG 43427T. Among these, one gene cluster, which was annotated to be important for LOS biosynthesis, catalytic mechanism and the substrate specificity of the enzyme, was predicted to be horizontally transferred by using phylogenies and biased GC content.
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Affiliation(s)
- WeiJie Song
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Sai Wang
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- College of Life Sciences, Zhejiang Sci-Tech University, Road 2, Hangzhou, 310018, Zhejiang, China
| | - Jian Shen
- Blood Transfusion Department of Zhejiang Province People's Hospital, Hangzhou, 310014, Zhejiang, China.
| | - Bo Zhu
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Beijing, China.
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6
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Lee BD, Apel WA, Sheridan PP, DeVeaux LC. Glycoside hydrolase gene transcription by Alicyclobacillus acidocaldarius during growth on wheat arabinoxylan and monosaccharides: a proposed xylan hydrolysis mechanism. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:110. [PMID: 29686728 PMCID: PMC5901876 DOI: 10.1186/s13068-018-1110-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 04/06/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Metabolism of carbon bound in wheat arabinoxylan (WAX) polysaccharides by bacteria requires a number of glycoside hydrolases active toward different bonds between sugars and other molecules. Alicyclobacillus acidocaldarius is a Gram-positive thermoacidophilic bacterium capable of growth on a variety of mono-, di-, oligo-, and polysaccharides. Nineteen proposed glycoside hydrolases have been annotated in the A. acidocaldarius Type Strain ATCC27009/DSM 446 genome. Experiments were performed to understand the effect of monosaccharides on gene expression during growth on the polysaccharide, WAX. RESULTS Molecular analysis using high-density oligonucleotide microarrays was performed on A. acidocaldarius strain ATCC27009 when growing on WAX. When a culture growing exponentially at the expense of arabinoxylan saccharides was challenged with glucose or xylose, most glycoside hydrolases were downregulated. Interestingly, regulation was more intense when xylose was added to the culture than when glucose was added, showing a clear departure from classical carbon catabolite repression demonstrated by many Gram-positive bacteria. In silico analyses of the regulated glycoside hydrolases, along with the results from the microarray analyses, yielded a potential mechanism for arabinoxylan metabolism by A. acidocaldarius. Glycoside hydrolases expressed by this strain may have broad substrate specificity, and initial hydrolysis is catalyzed by an extracellular xylanase, while subsequent steps are likely performed inside the growing cell. CONCLUSIONS Glycoside hydrolases, for the most part, appear to be found in clusters, throughout the A. acidocaldarius genome. Not all of the glycoside hydrolase genes found at loci within these clusters were regulated during the experiment, indicating that a specific subset of the 19 glycoside hydrolase genes found in A. acidocaldarius were used during metabolism of WAX. While specific functions of the glycoside hydrolases were not tested as part of the research discussed, many of the glycoside hydrolases found in the A. acidocaldarius Type Strain appear to have a broader substrate range than that represented by the glycoside hydrolase family in which the enzymes were categorized.
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Affiliation(s)
- Brady D. Lee
- Biological Systems Department, Idaho National Laboratory, P. O. Box 1625, Idaho Falls, ID 83415 USA
- Department of Biological Sciences, Idaho State University, Campus Box 8007, Pocatello, ID 83209 USA
- Present Address: Pacific Northwest National Laboratory, Energy and Environment Directorate, Richland, WA USA
| | - William A. Apel
- Biological Systems Department, Idaho National Laboratory, P. O. Box 1625, Idaho Falls, ID 83415 USA
| | - Peter P. Sheridan
- Department of Biological Sciences, Idaho State University, Campus Box 8007, Pocatello, ID 83209 USA
| | - Linda C. DeVeaux
- Department of Biology, New Mexico Institute of Mining and Technology, 801 Leroy Pl, Socorro, NM 87801 USA
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7
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Fadouloglou VE, Balomenou S, Aivaliotis M, Kotsifaki D, Arnaouteli S, Tomatsidou A, Efstathiou G, Kountourakis N, Miliara S, Griniezaki M, Tsalafouta A, Pergantis SA, Boneca IG, Glykos NM, Bouriotis V, Kokkinidis M. Unusual α-Carbon Hydroxylation of Proline Promotes Active-Site Maturation. J Am Chem Soc 2017; 139:5330-5337. [DOI: 10.1021/jacs.6b12209] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Stavroula Balomenou
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Michalis Aivaliotis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Dina Kotsifaki
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Sofia Arnaouteli
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Anastasia Tomatsidou
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Giorgos Efstathiou
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Nikos Kountourakis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Sofia Miliara
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
| | - Marianna Griniezaki
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Aleka Tsalafouta
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Spiros A. Pergantis
- Department
of Chemistry, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Ivo G. Boneca
- Biology
and Genetics of the Bacterial Cell Wall Unit, Institut Pasteur, 75015 Paris, France
- INSERM, Equipe Avenir, Paris, France
| | - Nicholas M. Glykos
- Department
of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, 68100 Alexandroupolis, Greece
| | - Vassilis Bouriotis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
| | - Michael Kokkinidis
- Institute of Molecular Biology and Biotechnology, 70013 Heraklion, Crete, Greece
- Department
of Biology, University of Crete, Voutes University Campus, 70013 Heraklion, Crete, Greece
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8
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Nakamura T, Yonezawa Y, Tsuchiya Y, Niiyama M, Ida K, Oshima M, Morita J, Uegaki K. Substrate recognition of N,N′-diacetylchitobiose deacetylase from Pyrococcus horikoshii. J Struct Biol 2016; 195:286-293. [DOI: 10.1016/j.jsb.2016.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 10/21/2022]
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Crystal structure of the Bacillus-conserved MazG protein, a nucleotide pyrophosphohydrolase. Biochem Biophys Res Commun 2016; 472:237-42. [DOI: 10.1016/j.bbrc.2016.02.097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 02/22/2016] [Indexed: 11/22/2022]
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10
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Perera VR, Newton GL, Pogliano K. Bacillithiol: a key protective thiol in Staphylococcus aureus. Expert Rev Anti Infect Ther 2015; 13:1089-107. [PMID: 26184907 DOI: 10.1586/14787210.2015.1064309] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacillithiol is a low-molecular-weight thiol analogous to glutathione and is found in several Firmicutes, including Staphylococcus aureus. Since its discovery in 2009, bacillithiol has been a topic of interest because it has been found to contribute to resistance during oxidative stress and detoxification of electrophiles, such as the antibiotic fosfomycin, in S. aureus. The rapid increase in resistance of methicillin-resistant Staphylococcus aureus (MRSA) to available therapeutic agents is a great health concern, and many research efforts are focused on identifying new drugs and targets to combat this organism. This review describes the discovery of bacillithiol, studies that have elucidated the physiological roles of this molecule in S. aureus and other Bacilli, and the contribution of bacillithiol to S. aureus fitness during pathogenesis. Additionally, the bacillithiol biosynthesis pathway is evaluated as a novel drug target that can be utilized in combination with existing therapies to treat S. aureus infections.
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Affiliation(s)
- Varahenage R Perera
- Division of Biological Sciences, University of California at San Diego, 9500 Gilman Drive, Natural Sciences Building 4113, La Jolla, CA 92093-0377, USA
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Identity of cofactor bound to mycothiol conjugate amidase (Mca) influenced by expression and purification conditions. Biometals 2015; 28:755-63. [DOI: 10.1007/s10534-015-9864-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/24/2015] [Indexed: 10/23/2022]
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12
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Guo Z, Li J, Qin H, Wang M, Lv X, Li X, Chen Y. Biosynthesis of the CarbamoylatedD-Gulosamine Moiety of Streptothricins: Involvement of a Guanidino-N-glycosyltransferase and anN-Acetyl-D-gulosamine Deacetylase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201412190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Guo Z, Li J, Qin H, Wang M, Lv X, Li X, Chen Y. Biosynthesis of the CarbamoylatedD-Gulosamine Moiety of Streptothricins: Involvement of a Guanidino-N-glycosyltransferase and anN-Acetyl-D-gulosamine Deacetylase. Angew Chem Int Ed Engl 2015; 54:5175-8. [DOI: 10.1002/anie.201412190] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 11/06/2022]
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14
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Viars S, Valentine J, Hernick M. Structure and function of the LmbE-like superfamily. Biomolecules 2014; 4:527-45. [PMID: 24970229 PMCID: PMC4101496 DOI: 10.3390/biom4020527] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/18/2014] [Accepted: 04/18/2014] [Indexed: 11/17/2022] Open
Abstract
The LmbE-like superfamily is comprised of a series of enzymes that use a single catalytic metal ion to catalyze the hydrolysis of various substrates. These substrates are often key metabolites for eukaryotes and prokaryotes, which makes the LmbE-like enzymes important targets for drug development. Herein we review the structure and function of the LmbE-like proteins identified to date. While this is the newest superfamily of metallohydrolases, a growing number of functionally interesting proteins from this superfamily have been characterized. Available crystal structures of LmbE-like proteins reveal a Rossmann fold similar to lactate dehydrogenase, which represented a novel fold for (zinc) metallohydrolases at the time the initial structure was solved. The structural diversity of the N-acetylglucosamine containing substrates affords functional diversity for the LmbE-like enzyme superfamily. The majority of enzymes identified to date are metal-dependent deacetylases that catalyze the hydrolysis of a N-acetylglucosamine moiety on substrate using a combination of amino acid side chains and a single bound metal ion, predominantly zinc. The catalytic zinc is coordinated to proteins via His2-Asp-solvent binding site. Additionally, studies indicate that protein dynamics play important roles in regulating access to the active site and facilitating catalysis for at least two members of this protein superfamily.
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Affiliation(s)
- Shane Viars
- Department of Pharmaceutical Sciences, Appalachian College of Pharmacy, Oakwood, VA 24631, USA.
| | - Jason Valentine
- Department of Pharmaceutical Sciences, Appalachian College of Pharmacy, Oakwood, VA 24631, USA.
| | - Marcy Hernick
- Department of Pharmaceutical Sciences, Appalachian College of Pharmacy, Oakwood, VA 24631, USA.
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15
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Liebens V, Defraine V, Van der Leyden A, De Groote VN, Fierro C, Beullens S, Verstraeten N, Kint C, Jans A, Frangipani E, Visca P, Marchal K, Versées W, Fauvart M, Michiels J. A putative de-N-acetylase of the PIG-L superfamily affects fluoroquinolone tolerance in Pseudomonas aeruginosa. Pathog Dis 2014; 71:39-54. [PMID: 24692291 DOI: 10.1111/2049-632x.12174] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 03/13/2014] [Accepted: 03/21/2014] [Indexed: 11/29/2022] Open
Abstract
A major cause of treatment failure of infections caused by Pseudomonas aeruginosa is the presence of antibiotic-insensitive persister cells. The mechanism of persister formation in P. aeruginosa is largely unknown, and so far, only few genetic determinants have been linked to P. aeruginosa persistence. Based on a previous high-throughput screening, we here present dnpA (de-N-acetylase involved in persistence; gene locus PA14_66140/PA5002) as a new gene involved in noninherited fluoroquinolone tolerance in P. aeruginosa. Fluoroquinolone tolerance of a dnpA mutant is strongly reduced both in planktonic culture and in a biofilm model, whereas overexpression of dnpA in the wild-type strain increases the persister fraction. In addition, the susceptibility of the dnpA mutant to different classes of antibiotics is not affected. dnpA is part of the conserved LPS core oligosaccharide biosynthesis gene cluster. Based on primary sequence analysis, we predict that DnpA is a de-N-acetylase, acting on an unidentified substrate. Site-directed mutagenesis suggests that this enzymatic activity is essential for DnpA-mediated persistence. A transcriptome analysis indicates that DnpA primarily affects the expression of genes involved in surface-associated processes. We discuss the implications of these findings for future antipersister therapies targeted at chronic P. aeruginosa infections.
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Affiliation(s)
- Veerle Liebens
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
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16
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Cross-functionalities of Bacillus deacetylases involved in bacillithiol biosynthesis and bacillithiol-S-conjugate detoxification pathways. Biochem J 2013; 454:239-47. [PMID: 23758290 DOI: 10.1042/bj20130415] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BshB, a key enzyme in bacillithiol biosynthesis, hydrolyses the acetyl group from N-acetylglucosamine malate to generate glucosamine malate. In Bacillus anthracis, BA1557 has been identified as the N-acetylglucosamine malate deacetylase (BshB); however, a high content of bacillithiol (~70%) was still observed in the B. anthracis ∆BA1557 strain. Genomic analysis led to the proposal that another deacetylase could exhibit cross-functionality in bacillithiol biosynthesis. In the present study, BA1557, its paralogue BA3888 and orthologous Bacillus cereus enzymes BC1534 and BC3461 have been characterized for their deacetylase activity towards N-acetylglucosamine malate, thus providing biochemical evidence for this proposal. In addition, the involvement of deacetylase enzymes is also expected in bacillithiol-detoxifying pathways through formation of S-mercapturic adducts. The kinetic analysis of bacillithiol-S-bimane conjugate favours the involvement of BA3888 as the B. anthracis bacillithiol-S-conjugate amidase (Bca). The high degree of specificity of this group of enzymes for its physiological substrate, along with their similar pH-activity profile and Zn²⁺-dependent catalytic acid-base reaction provides further evidence for their cross-functionalities.
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Mining of a streptothricin gene cluster from Streptomyces sp. TP-A0356 genome via heterologous expression. SCIENCE CHINA-LIFE SCIENCES 2013; 56:619-27. [DOI: 10.1007/s11427-013-4504-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 05/28/2013] [Indexed: 12/29/2022]
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Collins C, Keane TM, Turner DJ, O'Keeffe G, Fitzpatrick DA, Doyle S. Genomic and proteomic dissection of the ubiquitous plant pathogen, Armillaria mellea: toward a new infection model system. J Proteome Res 2013; 12:2552-70. [PMID: 23656496 PMCID: PMC3679558 DOI: 10.1021/pr301131t] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
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Armillaria mellea is a major plant
pathogen. Yet, no large-scale “-omics” data are available
to enable new studies, and limited experimental models are available
to investigate basidiomycete pathogenicity. Here we reveal that the A. mellea genome comprises 58.35 Mb, contains 14473 gene
models, of average length 1575 bp (4.72 introns/gene). Tandem mass
spectrometry identified 921 mycelial (n = 629 unique)
and secreted (n = 183 unique) proteins. Almost 100
mycelial proteins were either species-specific or previously unidentified
at the protein level. A number of proteins (n = 111)
was detected in both mycelia and culture supernatant extracts. Signal
sequence occurrence was 4-fold greater for secreted (50.2%) compared
to mycelial (12%) proteins. Analyses revealed a rich reservoir of
carbohydrate degrading enzymes, laccases, and lignin peroxidases in
the A. mellea proteome, reminiscent of both basidiomycete
and ascomycete glycodegradative arsenals. We discovered that A. mellea exhibits a specific killing effect against Candida albicans during coculture. Proteomic investigation
of this interaction revealed the unique expression of defensive and
potentially offensive A. mellea proteins (n = 30). Overall, our data reveal new insights into the
origin of basidiomycete virulence and we present a new model system
for further studies aimed at deciphering fungal pathogenic mechanisms.
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Affiliation(s)
- Cassandra Collins
- Department of Biology, National University of Ireland Maynooth, Maynooth, Co Kildare, Ireland
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The genome and proteome of a Campylobacter coli bacteriophage vB_CcoM-IBB_35 reveal unusual features. Virol J 2012; 9:35. [PMID: 22284308 PMCID: PMC3322345 DOI: 10.1186/1743-422x-9-35] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 01/27/2012] [Indexed: 12/22/2022] Open
Abstract
Background Campylobacter is the leading cause of foodborne diseases worldwide. Bacteriophages (phages) are naturally occurring predators of bacteria, ubiquitous in the environment, with high host specificity and thus considered an appealing option to control bacterial pathogens. Nevertheless for an effective use of phages as antimicrobial agents, it is important to understand phage biology which renders crucial the analysis of phage genomes and proteomes. The lack of sequence data from Campylobacter phages adds further importance to these studies. Methods vB_CcoM-IBB_35 is a broad lytic spectrum Myoviridae Campylobacter phage with high potential for therapeutic use. The genome of this phage was obtained by pyrosequencing and the sequence data was further analyzed. The proteomic analysis was performed by SDS-PAGE and Mass spectrometry. Results and conclusions The DNA sequence data of vB_CcoM-IBB_35 consists of five contigs for a total of 172,065 bp with an average GC content of 27%. Attempts to close the gaps between contigs were unsuccessful since the DNA preparations appear to contain substances that inhibited Taq and ϕ29 polymerases. From the 210 identified ORFs, around 60% represent proteins that were not functionally assigned. Homology exists with members of the Teequatrovirinae namely for T4 proteins involved in morphogenesis, nucleotide metabolism, transcription, DNA replication and recombination. Tandem mass spectrometric analysis revealed 38 structural proteins as part of the mature phage particle. Conclusions Genes encoding proteins involved in the carbohydrate metabolism along with several incidences of gene duplications, split genes with inteins and introns have been rarely found in other phage genomes yet are found in this phage. We identified the genes encoding for tail fibres and for the lytic cassette, this later, expressing enzymes for bacterial capsular polysaccharides (CPS) degradation, which has not been reported before for Campylobacter phages.
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Kokkinidis M, Glykos N, Fadouloglou V. Protein Flexibility and Enzymatic Catalysis. STRUCTURAL AND MECHANISTIC ENZYMOLOGY - BRINGING TOGETHER EXPERIMENTS AND COMPUTING 2012; 87:181-218. [DOI: 10.1016/b978-0-12-398312-1.00007-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Rangarajan ES, Ruane KM, Proteau A, Schrag JD, Valladares R, Gonzalez CF, Gilbert M, Yakunin AF, Cygler M. Structural and enzymatic characterization of NanS (YjhS), a 9-O-Acetyl N-acetylneuraminic acid esterase from Escherichia coli O157:H7. Protein Sci 2011; 20:1208-19. [PMID: 21557376 DOI: 10.1002/pro.649] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 04/15/2011] [Accepted: 04/18/2011] [Indexed: 11/08/2022]
Abstract
There is a high prevalence of sialic acid in a number of different organisms, resulting in there being a myriad of different enzymes that can exploit it as a fermentable carbon source. One such enzyme is NanS, a carbohydrate esterase that we show here deacetylates the 9 position of 9-O-sialic acid so that it can be readily transported into the cell for catabolism. Through structural studies, we show that NanS adopts a SGNH hydrolase fold. Although the backbone of the structure is similar to previously characterized family members, sequence comparisons indicate that this family can be further subdivided into two subfamilies with somewhat different fingerprints. NanS is the founding member of group II. Its catalytic center contains Ser19 and His301 but no Asp/Glu is present to form the classical catalytic triad. The contribution of Ser19 and His301 to catalysis was confirmed by mutagenesis. In addition to structural characterization, we have mapped the specificity of NanS using a battery of substrates.
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Parsonage D, Newton GL, Holder RC, Wallace BD, Paige C, Hamilton CJ, Dos Santos PC, Redinbo MR, Reid SD, Claiborne A. Characterization of the N-acetyl-α-D-glucosaminyl l-malate synthase and deacetylase functions for bacillithiol biosynthesis in Bacillus anthracis . Biochemistry 2010; 49:8398-414. [PMID: 20799687 DOI: 10.1021/bi100698n] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bacillithiol (Cys-GlcN-malate, BSH) has recently been identified as a novel low-molecular weight thiol in Bacillus anthracis, Staphylococcus aureus, and several other Gram-positive bacteria lacking glutathione and mycothiol. We have now characterized the first two enzymes for the BSH biosynthetic pathway in B. anthracis, which combine to produce α-d-glucosaminyl l-malate (GlcN-malate) from UDP-GlcNAc and l-malate. The structure of the GlcNAc-malate intermediate has been determined, as have the kinetic parameters for the BaBshA glycosyltransferase (→GlcNAc-malate) and the BaBshB deacetylase (→GlcN-malate). BSH is one of only two natural products reported to contain a malyl glycoside, and the crystal structure of the BaBshA-UDP-malate ternary complex, determined in this work at 3.3 Å resolution, identifies several active-site interactions important for the specific recognition of l-malate, but not other α-hydroxy acids, as the acceptor substrate. In sharp contrast to the structures reported for the GlcNAc-1-d-myo-inositol-3-phosphate synthase (MshA) apo and ternary complex forms, there is no major conformational change observed in the structures of the corresponding BaBshA forms. A mutant strain of B. anthracis deficient in the BshA glycosyltransferase fails to produce BSH, as predicted. This B. anthracis bshA locus (BA1558) has been identified in a transposon-site hybridization study as required for growth, sporulation, or germination [Day, W. A., Jr., Rasmussen, S. L., Carpenter, B. M., Peterson, S. N., and Friedlander, A. M. (2007) J. Bacteriol. 189, 3296-3301], suggesting that the biosynthesis of BSH could represent a target for the development of novel antimicrobials with broad-spectrum activity against Gram-positive pathogens like B. anthracis. The metabolites that function in thiol redox buffering and homeostasis in Bacillus are not well understood, and we present a composite picture based on this and other recent work.
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Affiliation(s)
- Derek Parsonage
- Center for Structural Biology, Wake Forest University School of Medicine,Winston-Salem, North Carolina 27157, USA
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