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Genome-Wide Detection and Analysis of Copy Number Variation in Anhui Indigenous and Western Commercial Pig Breeds Using Porcine 80K SNP BeadChip. Genes (Basel) 2023; 14:genes14030654. [PMID: 36980927 PMCID: PMC10047991 DOI: 10.3390/genes14030654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Copy number variation (CNV) is an important class of genetic variations widely associated with the porcine genome, but little is known about the characteristics of CNVs in foreign and indigenous pig breeds. We performed a genome-wide comparison of CNVs between Anhui indigenous pig (AHIP) and Western commercial pig (WECP) breeds based on data from the Porcine 80K SNP BeadChip. After analysis using the PennCNV software, we detected 3863 and 7546 CNVs in the AHIP and WECP populations, respectively. We obtained 225 (loss: 178, gain: 47) and 379 (loss: 293, gain: 86) copy number variation regions (CNVRs) randomly distributed across the autosomes of the AHIP and WECP populations, accounting for 10.90% and 22.57% of the porcine autosomal genome, respectively. Functional enrichment analysis of genes in the CNVRs identified genes related to immunity (FOXJ1, FOXK2, MBL2, TNFRSF4, SIRT1, NCF1) and meat quality (DGAT1, NT5E) in the WECP population; these genes were a loss event in the WECP population. This study provides important information on CNV differences between foreign and indigenous pig breeds, making it possible to provide a reference for future improvement of these breeds and their production performance.
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Studying the Interaction of Neutrophils and Glaesserella Parasuis Indicates a Serotype Independent Benefit from Degradation of NETs. Pathogens 2022; 11:pathogens11080880. [PMID: 36015001 PMCID: PMC9415231 DOI: 10.3390/pathogens11080880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 02/04/2023] Open
Abstract
Glaesserella (G.) parasuis is one of the most important porcine pathogens causing Glaesser’s disease. Neutrophil granulocytes are the major counteracting cell type of the innate immune system, which contribute to the host defense by phagocytosis or the formation of neutrophil extracellular traps (NETs). Recently, NET-formation has been shown to facilitate the survival of bacteria from the Pasteurellaceae family. However, the interaction of NETs and G. parasuis is unclear so far. In this study, we investigated the interplay of three G. parasuis serotypes with porcine neutrophils. The production of reactive oxygen species by neutrophils after G. parasuis infection varied slightly among the serotypes but was generally low and not significantly influenced by the serotypes. Interestingly, we detected that independent of the serotype of G. parasuis, NET formation in neutrophils was induced to a small but significant extent. This phenomenon occurred despite the ability of G. parasuis to release nucleases, which can degrade NETs. Furthermore, the growth of Glaesserella was enhanced by external DNases and degraded NETs. This indicates that Glaesserella takes up degraded NET components, supplying them with nicotinamide adenine dinucleotide (NAD), as this benefit was diminished by inhibiting the 5′-nucleotidase, which metabolizes NAD. Our results indicate a serotype-independent interaction of Glaesserella with neutrophils by inducing NET-formation and benefiting from DNA degradation.
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Debiais M, Vasseur JJ, Smietana M. Applications of the Reversible Boronic Acids/Boronate Switch to Nucleic Acids. CHEM REC 2022; 22:e202200085. [PMID: 35641415 DOI: 10.1002/tcr.202200085] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Indexed: 11/09/2022]
Abstract
Over the last decades, boron and nucleic acids chemistries have gained a lot of attention for biological, medicinal and analytical applications. Our laboratory has a long-standing interest in both chemistries and owing to the ability of boronic acids to react with cis-diol function in aqueous media we developed over the years a variety of applications ranging from molecular recognition and sensing to the development of reversible dynamic systems in which the natural phosphodiester linkage was replaced by a boronate. In this account, we summarize research results from our group from our preliminary studies on molecular recognition of ribonucleosides to the dynamic assembly of functional DNAzymes. In particular, the various parameters influencing the dynamic nature of these reversible covalent bonds able to respond to external stimuli are discussed. Finally, current challenges and opportunities for boron-based nucleic acids are also addressed.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095, Montpellier, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095, Montpellier, France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 1919 route de Mende, 34095, Montpellier, France
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Cohen N, Kahana A, Schuldiner M. A Similarity-Based Method for Predicting Enzymatic Functions in Yeast Uncovers a New AMP Hydrolase. J Mol Biol 2022; 434:167478. [PMID: 35123996 PMCID: PMC9005783 DOI: 10.1016/j.jmb.2022.167478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 11/01/2022]
Abstract
Despite decades of research and the availability of the full genomic sequence of the baker's yeast Saccharomyces cerevisiae, still a large fraction of its genome is not functionally annotated. This hinders our ability to fully understand cellular activity and suggests that many additional processes await discovery. The recent years have shown an explosion of high-quality genomic and structural data from multiple organisms, ranging from bacteria to mammals. New computational methods now allow us to integrate these data and extract meaningful insights into the functional identity of uncharacterized proteins in yeast. Here, we created a database of sensitive sequence similarity predictions for all yeast proteins. We use this information to identify candidate enzymes for known biochemical reactions whose enzymes are unidentified, and show how this provides a powerful basis for experimental validation. Using one pathway as a test case we pair a new function for the previously uncharacterized enzyme Yhr202w, as an extra-cellular AMP hydrolase in the NAD degradation pathway. Yhr202w, which we now term Smn1 for Scavenger MonoNucleotidase 1, is a highly conserved protein that is similar to the human protein E5NT/CD73, which is associated with multiple cancers. Hence, our new methodology provides a paradigm, that can be adopted to other organisms, for uncovering new enzymatic functions of uncharacterized proteins.
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Affiliation(s)
- Nir Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Amit Kahana
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel. https://twitter.com/AmitKahana
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Komatsu T, Toita T, Uemoto Y. Estimates of genetic parameters for adenosine triphosphate-related compounds at different aging periods and NT5E genotypes in Japanese Black beef. Anim Sci J 2022; 93:e13748. [PMID: 35716373 DOI: 10.1111/asj.13748] [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: 03/13/2022] [Revised: 04/28/2022] [Accepted: 05/20/2022] [Indexed: 11/30/2022]
Abstract
Previous studies on Japanese Black beef showed that single nucleotide polymorphisms in the ecto-5'-nucleotidase (NT5E) gene affected the degradation rate of inosine 5'-monophosphate (IMP), which has contributed to the umami taste, especially between Postmortem Days 4 and 7. Therefore, this study estimated the genetic parameters of IMP and its degradation products on Postmortem Days 4 and 7 using the model with or without the NT5E genotype. The heritability estimates of IMP on Postmortem Days 4 and 7 were moderate by the model without the NT5E genotype (0.44 and 0.32, respectively). When the NT5E genotype was included in the model, the heritability of IMP on Postmortem Day 4 did not change, whereas that on Day 7 decreased from 0.32 to 0.08. The genetic correlation of IMP between Postmortem Days 4 and 7 was highly positive using the model with the NT5E genotype. Regarding the estimated breeding values (EBVs) of IMP, the ranking of EBVs among NT5E genotypes was not changed between Postmortem Days 4 and 7, when the model with the NT5E genotype was used. The study suggested that the model including NT5E genotype would allow for appropriate genetic parameter estimation and breeding value evaluation in adenosine triphosphate-related compounds (ATPRCs) under different aging periods.
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Affiliation(s)
- Tomohiko Komatsu
- Yamagata Prefectural Okitama Livestock Hygiene Service Center, Nanyo, Japan
| | - Tsuyoshi Toita
- Livestock Institute of Yamagata Integrated Agricultural Research Center, Shinjo, Japan
| | - Yoshinobu Uemoto
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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Nocentini A, Capasso C, Supuran CT. Small-molecule CD73 inhibitors for the immunotherapy of cancer: a patent and literature review (2017-present). Expert Opin Ther Pat 2021; 31:867-876. [PMID: 33909515 DOI: 10.1080/13543776.2021.1923694] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Hydrolysis of AMP to adenosine and inorganic phosphate is catalyzed by 5´-ectonucleotidase, e5NT, alias CD73, a metalloenzyme incorporating two zinc ions at its active site. e5NT is involved in crucial physiological and pathological processes, such as immune ho meostasis, inflammation, and tumor progression. CD73 inhibitors belonging to the monoclonal antibodies (MAbs) and small molecules started to be considered as candidates for the immunotherapy of tumors. AREAS COVERED We review the drug design landscape in the scientific and patent literature on CD73 inhibitors from 2017 to the present. Small-molecule inhibitors were mostly discussed, although the MAbs are also considered. EXPERT OPINION Considerable advances have been reported in the design of nucleotide/nucleoside-based CD73 inhibitors, after the X-ray crystal structure of the enzyme in complex with the non-hydrolyzable ADP analog, adenosine (α,β)-methylene diphosphate (AMPCP), was reported. A large number of highly effective such inhibitors are now available, through modifications of the nucleobase, sugar and zinc-binding groups of the lead. Few classes of non-nucleotide inhibitors were also reported, including flavones, anthraquinone ssulfonates, and primary sulfonamides. A highly potent ssmall-molecule CD73 inhibitor, AB680, is presently in the early phase of clinical trials as immunotherapeutic agents against various types of cancer.
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Affiliation(s)
- Alessio Nocentini
- Dipartimento Neurofarba, Sezione Di Scienze Farmaceutiche E Nutraceutiche, Università Degli Studi Di Firenze, Sesto Fiorentino (Florence), Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, CNR, Institute of Biosciences and Bioresources, Napoli, Italy
| | - Claudiu T Supuran
- Dipartimento Neurofarba, Sezione Di Scienze Farmaceutiche E Nutraceutiche, Università Degli Studi Di Firenze, Sesto Fiorentino (Florence), Italy
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Gupta R, Laxman S. Cycles, sources, and sinks: Conceptualizing how phosphate balance modulates carbon flux using yeast metabolic networks. eLife 2021; 10:e63341. [PMID: 33544078 PMCID: PMC7864628 DOI: 10.7554/elife.63341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/20/2021] [Indexed: 12/11/2022] Open
Abstract
Phosphates are ubiquitous molecules that enable critical intracellular biochemical reactions. Therefore, cells have elaborate responses to phosphate limitation. Our understanding of long-term transcriptional responses to phosphate limitation is extensive. Contrastingly, a systems-level perspective presenting unifying biochemical concepts to interpret how phosphate balance is critically coupled to (and controls) metabolic information flow is missing. To conceptualize such processes, utilizing yeast metabolic networks we categorize phosphates utilized in metabolism into cycles, sources and sinks. Through this, we identify metabolic reactions leading to putative phosphate sources or sinks. With this conceptualization, we illustrate how mass action driven flux towards sources and sinks enable cells to manage phosphate availability during transient/immediate phosphate limitations. We thereby identify how intracellular phosphate availability will predictably alter specific nodes in carbon metabolism, and determine signature cellular metabolic states. Finally, we identify a need to understand intracellular phosphate pools, in order to address mechanisms of phosphate regulation and restoration.
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Affiliation(s)
- Ritu Gupta
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
| | - Sunil Laxman
- Institute for Stem Cell Science and Regenerative Medicine (inStem)BangaloreIndia
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Du X, Moore J, Blank BR, Eksterowicz J, Sutimantanapi D, Yuen N, Metzger T, Chan B, Huang T, Chen X, Chen Y, Duong F, Kong W, Chang JH, Sun J, Zavorotinskaya T, Ye Q, Junttila MR, Ndubaku C, Friedman LS, Fantin VR, Sun D. Orally Bioavailable Small-Molecule CD73 Inhibitor (OP-5244) Reverses Immunosuppression through Blockade of Adenosine Production. J Med Chem 2020; 63:10433-10459. [PMID: 32865411 DOI: 10.1021/acs.jmedchem.0c01086] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The adenosinergic pathway represents an attractive new therapeutic approach in cancer immunotherapy. In this pathway, ecto-5-nucleotidase CD73 has the unique function of regulating production of immunosuppressive adenosine (ADO) through the hydrolysis of AMP. CD73 is overexpressed in many cancers, resulting in elevated levels of ADO that correspond to poor patient prognosis. Therefore, reducing the level of ADO via inhibition of CD73 is a potential strategy for treating cancers. Based on the binding mode of adenosine 5'-(α,β-methylene)diphosphate (AOPCP) with human CD73, we designed a series of novel monophosphonate small-molecule CD73 inhibitors. Among them, OP-5244 (35) proved to be a highly potent and orally bioavailable CD73 inhibitor. In preclinical studies, 35 completely inhibited ADO production in both human cancer cells and CD8+ T cells. Furthermore, 35 lowered the ratio of ADO/AMP significantly and reversed immunosuppression in mouse models, indicating its potential as an in vivo tool compound for further development.
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Affiliation(s)
- Xiaohui Du
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Jared Moore
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Brian R Blank
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - John Eksterowicz
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Dena Sutimantanapi
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Natalie Yuen
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Todd Metzger
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Brenda Chan
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Tom Huang
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Xi Chen
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Yuping Chen
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Frank Duong
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Wayne Kong
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Jae H Chang
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Jessica Sun
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Tatiana Zavorotinskaya
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Qiuping Ye
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Melissa R Junttila
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Chudi Ndubaku
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Lori S Friedman
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Valeria R Fantin
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
| | - Daqing Sun
- ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States
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Biochemical and Molecular Characterization of PvNTD2, a Nucleotidase Highly Expressed in Nodules from Phaseolus vulgaris. PLANTS 2020; 9:plants9020171. [PMID: 32024086 PMCID: PMC7076459 DOI: 10.3390/plants9020171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 01/28/2020] [Indexed: 12/30/2022]
Abstract
Nucleotides are molecules of great importance in plant physiology. In addition to being elementary units of the genetic material, nucleotides are involved in bio-energetic processes, play a role as cofactors, and are also components of secondary metabolites and the hormone cytokinin. The common bean (Phaseolus vulgaris) is a legume that transports the nitrogen fixed in nodules as ureides, compounds synthetized from purine nucleotides. The first step in this pathway is the removal of the 5’-phosphate group by a phosphatase. In this study, a gene that codes for a putative nucleotidase (PvNTD2) has been identified in P. vulgaris. The predicted peptide contains the conserved domains for haloacid dehalogenase-like hydrolase superfamily. The protein has been overexpressed in Escherichia coli, and the purified protein showed molybdate-resistant phosphatase activity with nucleoside monophosphates as substrates, confirming that the identified gene codes for a nucleotidase. The optimum pH for the activity was 7–7.5. The recombinant enzyme did not show special affinity for any particular nucleotide, although the behaviour with AMP was different from that with the other nucleotides. The activity was inhibited by adenosine, and a regulatory role for this nucleoside was proposed. The expression pattern of PvNTD2 shows that it is ubiquitously expressed in all the tissues analysed, with higher expression in nodules of adult plants. The expression was maintained during leaf ontogeny, and it was induced during seedling development. Unlike PvNTD1, another NTD previously described in common bean, the high expression of PvNTD2 was maintained during nodule development, and its possible role in this organ is discussed.
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Grant R, Berg J, Mestayer R, Braidy N, Bennett J, Broom S, Watson J. A Pilot Study Investigating Changes in the Human Plasma and Urine NAD+ Metabolome During a 6 Hour Intravenous Infusion of NAD. Front Aging Neurosci 2019; 11:257. [PMID: 31572171 PMCID: PMC6751327 DOI: 10.3389/fnagi.2019.00257] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/29/2019] [Indexed: 11/23/2022] Open
Abstract
Accumulating evidence suggests that active maintenance of optimal levels of the essential pyridine nucleotide, nicotinamide adenine dinucleotide (NAD+) is beneficial in conditions of either increased NAD+ turnover or inadequate synthesis, including Alzheimer's disease and other neurodegenerative disorders and the aging process. While studies have documented the efficacy of some NAD+ precursors such as nicotinamide riboside (NR) in raising plasma NAD+, no data are currently available on the fate of directly infused NAD+ in a human cohort. This study, therefore, documented changes in plasma and urine levels of NAD+ and its metabolites during and after a 6 h 3 μmol/min NAD+ intravenous (IV) infusion. Surprisingly, no change in plasma (NAD+) or metabolites [nicotinamide, methylnicotinamide, adenosine phosphoribose ribose (ADPR) and nicotinamide mononucleotide (NMN)] were observed until after 2 h. Increased urinary excretion of methylnicotinamide and NAD+ were detected at 6 h, however, no significant rise in urinary nicotinamide was observed. This study revealed for the first time that: (i) at an infusion rate of 3 μmol/min NAD+ is rapidly and completely removed from the plasma for at least the first 2 h; (ii) the profile of metabolites is consistent with NAD+ glycohydrolase and NAD+ pyrophosphatase activity; and (iii) urinary excretion products arising from an NAD+ infusion include NAD+ itself and methyl nicotinamide (meNAM) but not NAM.
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Affiliation(s)
- Ross Grant
- Australasian Research Institute, Sydney Adventist Hospital, Wahroonga, NSW, Australia
- Sydney Adventist Hospital Clinical School, University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Jade Berg
- Australasian Research Institute, Sydney Adventist Hospital, Wahroonga, NSW, Australia
| | - Richard Mestayer
- NAD+ Research Inc., Springfield, LA, United States
- Springfield Wellness Center, Springfield, LA, United States
| | - Nady Braidy
- School of Psychiatry, University of New South Wales, NPI, Euroa Centre, Randwick, NSW, Australia
| | - James Bennett
- Springfield Wellness Center, Springfield, LA, United States
| | - Susan Broom
- School of Natural and Behavioural Sciences, William Carey University, Hattiesburg, MS, United States
| | - James Watson
- Division of Plastic Surgery, Clinical Faculty, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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Degraded neutrophil extracellular traps promote the growth of Actinobacillus pleuropneumoniae. Cell Death Dis 2019; 10:657. [PMID: 31506432 PMCID: PMC6736959 DOI: 10.1038/s41419-019-1895-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/03/2019] [Accepted: 08/12/2019] [Indexed: 12/21/2022]
Abstract
Actinobacillus pleuropneumoniae (A.pp) causes severe pneumonia associated with enormous economic loss in pigs. Peracute diseased pigs die in <24 h with pneumonia. Neutrophils are the prominent innate immune cell in this infection that massively infiltrate the infected lung. Here we show that neutrophils release neutrophil extracellular traps (NETs) as response to A.pp infection. Numerous NET-markers were identified in bronchoalveolar lavage fluid (BALF) of A.pp-infected piglets in vivo, however, most NET fibers are degraded. Importantly, A.pp is able to enhance its growth rate in the presence of NETs that have been degraded by nucleases efficiently. A.pp itself releases no nuclease, but we identified host nucleases as sources that degrade NETs after A.pp infection. Furthermore, the nucleases of co-infecting pathogens like Streptococcus suis increase growth of A.pp in presence of porcine NETs. Thus, A.pp is not only evading the antimicrobial activity of NETs, A.pp is rather additionally using parts of NETs as growth factor thereby taking advantage of host nucleases as DNase1 or nucleases of co-infecting bacteria, which degrade NETs. This effect can be diminished by inhibiting the bacterial adenosine synthase indicating that degraded NETs serve as a source for NAD, which is required by A.pp for its growth. A similar phenotype was found for the human pathogen Haemophilus (H.) influenzae and its growth in the presence of human neutrophils. H. influenzae benefits from host nucleases in the presence of neutrophils. These data shed light on the detrimental effects of NETs during host immune response against certain bacterial species that require and/or efficiently take advantage of degraded DNA material, which has been provided by host nuclease or nucleases of other co-infecting bacteria, as growth source.
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The NT5E gene variant strongly affects the degradation rate of inosine 5'-monophosphate under postmortem conditions in Japanese Black beef. Meat Sci 2019; 158:107893. [PMID: 31401370 DOI: 10.1016/j.meatsci.2019.107893] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 01/31/2023]
Abstract
Inosine 5'-monophosphate (IMP) contributes to the umami taste in Japanese Black beef. In a previous study, it was suggested that single nucleotide polymorphisms (SNPs) in the ecto-5'-nucleotidase (NT5E) gene affect the concentration of IMP under postmortem conditions by regulating NT5E enzymatic activity in Japanese Black beef. The present study showed that the degradation rate of IMP in Japanese Black beef was significantly different among NT5E genotypes in the middle stage of postmortem, indicating a significant difference in the concentrations of IMP and its degradation products among NT5E genotypes. In addition, no significant difference was observed among NT5E genotypes in the concentrations of IMP precursors or other taste-active compounds. These results indicate the significant effect of the interaction between the NT5E genotype and the aging period on the degradation rate of IMP in beef.
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Limviphuvadh V, Tan CS, Konishi F, Jenjaroenpun P, Xiang JS, Kremenska Y, Mu YS, Syn N, Lee SC, Soo RA, Eisenhaber F, Maurer-Stroh S, Yong WP. Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy. BMC Cancer 2018; 18:555. [PMID: 29751792 PMCID: PMC5948914 DOI: 10.1186/s12885-018-4471-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 05/01/2018] [Indexed: 12/20/2022] Open
Abstract
Background Single Nucleotide Polymorphisms (SNPs) can influence patient outcome such as drug response and toxicity after drug intervention. The purpose of this study is to develop a systematic pathway approach to accurately and efficiently predict novel non-synonymous SNPs (nsSNPs) that could be causative to gemcitabine-based chemotherapy treatment outcome in Singaporean non-small cell lung cancer (NSCLC) patients. Methods Using a pathway approach that incorporates comprehensive protein-protein interaction data to systematically extend the gemcitabine pharmacologic pathway, we identified 77 related nsSNPs, common in the Singaporean population. After that, we used five computational criteria to prioritize the SNPs based on their importance for protein function. We specifically selected and screened six candidate SNPs in a patient cohort with NSCLC treated with gemcitabine-based chemotherapy. Result We performed survival analysis followed by hematologic toxicity analyses and found that three of six candidate SNPs are significantly correlated with the patient outcome (P < 0.05) i.e. ABCG2 Q141K (rs2231142), SLC29A3 S158F (rs780668) and POLR2A N764K (rs2228130). Conclusions Our computational SNP candidate enrichment workflow approach was able to identify several high confidence biomarkers predictive for personalized drug treatment outcome while providing a rationale for a molecular mechanism of the SNP effect. Trial registration NCT00695994. Registered 10 June, 2008 ‘retrospectively registered’. Electronic supplementary material The online version of this article (10.1186/s12885-018-4471-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vachiranee Limviphuvadh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Chee Seng Tan
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Fumikazu Konishi
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, Tokyo, Japan
| | - Piroon Jenjaroenpun
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Joy Shengnan Xiang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Yuliya Kremenska
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Yar Soe Mu
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Nicholas Syn
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Soo Chin Lee
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Ross A Soo
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, Singapore, 117543, Singapore.,School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore (NUS), 14 Science Drive 4, Singapore, 117543, Singapore
| | - Wei Peng Yong
- Department of Haematology-Oncology, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore.
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14
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Voloshchuk ON, Kopylchuk GP. The State of the Adenyl Nucleotide System in the Liver of Rats with Toxic Hepatitis under Conditions of Protein Deficiency. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350917060252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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Uemoto Y, Ohtake T, Sasago N, Takeda M, Abe T, Sakuma H, Kojima T, Sasaki S. Effect of two non-synonymous ecto-5'-nucleotidase variants on the genetic architecture of inosine 5'-monophosphate (IMP) and its degradation products in Japanese Black beef. BMC Genomics 2017; 18:874. [PMID: 29132308 PMCID: PMC5683534 DOI: 10.1186/s12864-017-4275-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/03/2017] [Indexed: 11/12/2022] Open
Abstract
Background Umami is a Japanese term for the fifth basic taste and is an important sensory property of beef palatability. Inosine 5′-monophosphate (IMP) contributes to umami taste in beef. Thus, the overall change in concentration of IMP and its degradation products can potentially affect the beef palatability. In this study, we investigated the genetic architecture of IMP and its degradation products in Japanese Black beef. First, we performed genome-wide association study (GWAS), candidate gene analysis, and functional analysis to detect the causal variants that affect IMP, inosine, and hypoxanthine. Second, we evaluated the allele frequencies in the different breeds, the contribution of genetic variance, and the effect on other economical traits using the detected variants. Results A total of 574 Japanese Black cattle were genotyped using the Illumina BovineSNP50 BeadChip and were then used for GWAS. The results of GWAS showed that the genome-wide significant single nucleotide polymorphisms (SNPs) on BTA9 were detected for IMP, inosine, and hypoxanthine. The ecto-5′-nucleotidase (NT5E) gene, which encodes the enzyme NT5E for the extracellular degradation of IMP to inosine, was located near the significant region on BTA9. The results of candidate gene analysis and functional analysis showed that two non-synonymous SNPs (c.1318C > T and c.1475 T > A) in NT5E affected the amount of IMP and its degradation products in beef by regulating the enzymatic activity of NT5E. The Q haplotype showed a positive effect on IMP and a negative effect on the enzymatic activity of NT5E in IMP degradation. The two SNPs were under perfect linkage disequilibrium in five different breeds, and different haplotype frequencies were seen among breeds. The two SNPs contribute to about half of the total genetic variance in IMP, and the results of genetic relationship between IMP and its degradation products showed that NT5E affected the overall concentration balance of IMP and its degradation products. In addition, the SNPs in NT5E did not have an unfavorable effect on the other economical traits. Conclusion Based on all the above findings taken together, two non-synonymous SNPs in NT5E would be useful for improving IMP and its degradation products by marker-assisted selection in Japanese Black cattle. Electronic supplementary material The online version of this article (doi: 10.1186/s12864-017-4275-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yoshinobu Uemoto
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.,Present address: Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845, Japan
| | - Tsuyoshi Ohtake
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Nanae Sasago
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Masayuki Takeda
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Tsuyoshi Abe
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Hironori Sakuma
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Takatoshi Kojima
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan
| | - Shinji Sasaki
- National Livestock Breeding Center, Nishigo, Fukushima, 961-8511, Japan.
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16
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Zakataeva NP, Romanenkov DV, Yusupova YR, Skripnikova VS, Asahara T, Gronskiy SV. Identification, Heterologous Expression, and Functional Characterization of Bacillus subtilis YutF, a HAD Superfamily 5'-Nucleotidase with Broad Substrate Specificity. PLoS One 2016; 11:e0167580. [PMID: 27907199 PMCID: PMC5132288 DOI: 10.1371/journal.pone.0167580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/16/2016] [Indexed: 11/25/2022] Open
Abstract
5'-nucleotidases (EC 3.1.3.5) catalyze the hydrolytic dephosphorylation of 5'-ribonucleotides and 5'-deoxyribonucleotides as well as complex nucleotides, such as uridine 5'-diphosphoglucose (UDP-glucose), nicotinamide adenine dinucleotide and flavin adenine dinucleotide, to their corresponding nucleosides plus phosphate. These enzymes have been found in diverse species in intracellular and membrane-bound, surface-localized forms. Soluble forms of 5'-nucleotidases belong to the ubiquitous haloacid dehalogenase superfamily (HADSF) and have been shown to be involved in the regulation of nucleotide, nucleoside and nicotinamide adenine dinucleotide (NAD+) pools. Despite the important role of 5'-nucleotidases in cellular metabolism, only a few of these enzymes have been characterized in the Gram-positive bacterium Bacillus subtilis, the workhorse industrial microorganism included in the Food and Drug Administration’s GRAS (generally regarded as safe) list. In the present study, we report the identification of a novel 5'-nucleotidase gene from B. subtilis, yutF, which comprises 771 bp encoding a 256-amino-acid protein belonging to the IIA subfamily of the HADSF. The gene product is responsible for the major p-nitrophenyl phosphatase activity in B. subtilis. The yutF gene was overexpressed in Escherichia coli, and its product fused to a polyhistidine tag was purified and biochemically characterized as a soluble 5'-nucleotidase with broad substrate specificity. The recombinant YutF protein was found to hydrolyze various purine and pyrimidine 5'-nucleotides, showing preference for 5'-nucleoside monophosphates and, specifically, 5'-XMP. Recombinant YutF also exhibited phosphohydrolase activity toward nucleotide precursors, ribose-5-phosphate and 5-phosphoribosyl-1-pyrophosphate. Determination of the kinetic parameters of the enzyme revealed a low substrate specificity (Km values in the mM concentration range) and modest catalytic efficiencies with respect to substrates. An initial study of the regulation of yutF expression showed that the yutF gene is a component of the yutDEF transcription unit and that YutF overproduction positively influences yutDEF expression.
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Affiliation(s)
| | | | | | | | - Takayuki Asahara
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, Japan
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17
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Genome Sequence of Lactobacillus fermentum Strain NCC2970 (CNCM I-5068). GENOME ANNOUNCEMENTS 2016; 4:4/6/e01254-16. [PMID: 27856580 PMCID: PMC5114372 DOI: 10.1128/genomea.01254-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Lactobacillus fermentum NCC2970 (CNCM I-5068) is a lactic acid bacterium originating from the Nestle Culture Collection. Here, we disclose its full 1.9-Gb genome sequence comprising one chromosome with no plasmid.
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18
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Suharti WS, Nose A, Zheng SH. Metabolomic study of two rice lines infected by Rhizoctonia solani in negative ion mode by CE/TOF-MS. JOURNAL OF PLANT PHYSIOLOGY 2016; 206:13-24. [PMID: 27688090 DOI: 10.1016/j.jplph.2016.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 09/16/2016] [Accepted: 09/18/2016] [Indexed: 05/03/2023]
Abstract
Rhizoctonia solani is a fungal pathogen that causes sheath blight disease in rice plants. In this study, metabolomic analysis using CE/TOF-MS in negative ion mode was used to investigate the resistance response of resistant and susceptible rice lines (32R and 29S, respectively) due to R. solani infection. Two rice lines showed different responses to the infection of R. solani. In 32R, R. solani infection induced significant increases in adenosine diphosphate (ADP), glyceric acid, mucic acid and jasmonic acid. In 29S, inosine monophosphate (IMP) was involved in the plant response to R. solani infection. Phenol compounds showed an increase as a response of the rice lines to R. solani infection. The study suggests that R. solani infection effects in 32R are associated with the induction of plant metabolic processes such as respiration, photorespiration, pectin synthesis, and lignin accumulation. In 29S, the R. solani infection is suggested to correlate with nitrogen metabolism.
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Affiliation(s)
- Woro Sri Suharti
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, 840-8502, Japan; Faculty of Agriculture, Jenderal Soedirman University, Purwokerto, Indonesia
| | - Akihiro Nose
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, 840-8502, Japan.
| | - Shao-Hui Zheng
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, 840-8502, Japan
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19
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Ma W, Zhang D, Li G, Liu J, He G, Zhang P, Yang L, Zhu H, Xu N, Liang S. Antibacterial mechanism of daptomycin antibiotic against Staphylococcus aureus based on a quantitative bacterial proteome analysis. J Proteomics 2016; 150:242-251. [PMID: 27693894 DOI: 10.1016/j.jprot.2016.09.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 09/06/2016] [Accepted: 09/26/2016] [Indexed: 02/05/2023]
Abstract
Daptomycin (DAP) is a novel lipopeptide antibiotic which exhibits excellent antibacterial activity against most clinically relevant Gram-positive bacteria, but the DAP-targeting protein molecules against host bacterial infection are far from clear. In order to discover bacterial protein response to DAP treatment, an iTRAQ-based quantitative proteomic analysis was applied to identify differential bacterial proteome profiling of Staphylococcus aureus (S. aureus) ATCC 25923 to 0.125μg/ml DAP exposure. Totally 51 bacterial proteins were significantly changed with DAP treatment, among which 34 proteins were obviously up-regulated and 17 proteins were down-regulated. Meanwhile, 139 bacterial cell membrane (CM) proteins were identified, and 7 CM proteins were significantly altered to decrease CM potential to disrupt bacterial cell membrane. Especially the up-regulation of NDK and down-regulation of NT5 in several S. aureus strains are validated to be a universal variation tendency response to DAP treatment. Under DAP exposure, bacterial membrane potential is decreased and cell membrane is disrupted, and bacterial chromosome is aggregated, which contributes to bacterial DNA rapid release and induces bacteria death within 2-5h. In general, multiple bacterial protein expressions are changed in response to DAP antibiotic exposure, which disrupts host bacterial physiology by multiple cellular levels. To our knowledge, this is the first time to exactly identify infectious bacterial proteins in response to DAP antibiotic action. Our findings help better understand DAP antibacterial mechanism and develop novel DAP derivatives against the upcoming antibiotic-resistant bacterial infection. BIOLOGICAL SIGNIFICANCE DAP is a novel lipopeptide antibiotic that it exhibits excellent in vitro activity against most clinically relevant Gram-positive bacteria, and the investigations on its pharmaceutical action mode of DAP have dramatically increased in the past decade due to its unique antimicrobial mechanism. However, the target molecules of DAP acting on the infectious bacteria, are far from clear. The state-of-the-art quantitative proteomic technologies provide new avenues to uncover underlying mechanism of antibiotics. Our research main aims to identify bacterial proteome profiling of host strain S. aureus response to DAP treatment through an iTRAQ-based quantitative proteomic analysis, which contributes to understand DAP efficient antibacterial activity and the microbial-antibiotic interactions.
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Affiliation(s)
- Wen Ma
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Dan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Guoshun Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Jingjing Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Gu He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Peng Zhang
- Department of Urinary Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, PR China
| | - Li Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China
| | - Hongxia Zhu
- Laboratory of Cell and Molecular Biology, State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing 100034, PR China
| | - Ningzhi Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China; Laboratory of Cell and Molecular Biology, State Key Laboratory of Molecular Oncology, Cancer Institute & Cancer Hospital, Chinese Academy of Medical Sciences, Beijing 100034, PR China
| | - Shufang Liang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University/Collaborative Innovation Center for Biotherapy, Chengdu 610041, PR China.
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20
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Nevedomskaya E, Perryman R, Solanki S, Syed N, Mayboroda OA, Keun HC. A Systems Oncology Approach Identifies NT5E as a Key Metabolic Regulator in Tumor Cells and Modulator of Platinum Sensitivity. J Proteome Res 2015; 15:280-90. [PMID: 26629888 DOI: 10.1021/acs.jproteome.5b00793] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Altered metabolism in tumor cells is required for rapid proliferation but also can influence other phenotypes that affect clinical outcomes such as metastasis and sensitivity to chemotherapy. Here, a genome-wide association study (GWAS)-guided integration of NCI-60 transcriptome and metabolome data identified ecto-5'-nucleotidase (NT5E or CD73) as a major determinant of metabolic phenotypes in cancer cells. NT5E expression and associated metabolome variations were also correlated with sensitivity to several chemotherapeutics including platinum-based treatment. NT5E mRNA levels were observed to be elevated in cells upon in vitro and in vivo acquisition of platinum resistance in ovarian cancer cells, and specific targeting of NT5E increased tumor cell sensitivity to platinum. We observed that tumor NT5E levels were prognostic for outcomes in ovarian cancer and were elevated after treatment with platinum, supporting the translational relevance of our findings. In this work, we integrated and analyzed a plethora of public data, demonstating the merit of such a systems oncology approach for the discovery of novel players in cancer biology and therapy. We experimentally validated the main findings of the NT5E gene being involved in both intrinsic and acquired resistance to platinum-based drugs. We propose that the efficacy of conventional chemotherapy could be improved by NT5E inhibition and that NT5E expression may be a useful prognostic and predictive clinical biomarker.
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Affiliation(s)
- Ekaterina Nevedomskaya
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , L4-Q, PO Box 9600, 2300RC Leiden, The Netherlands
| | - Richard Perryman
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital , London W12 0NN, United Kingdom.,Division of Brain Sciences, Department of Medicine, Imperial College London , London W12 0NN, United Kingdom
| | - Shyam Solanki
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital , London W12 0NN, United Kingdom
| | - Nelofer Syed
- Division of Brain Sciences, Department of Medicine, Imperial College London , London W12 0NN, United Kingdom
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC) , L4-Q, PO Box 9600, 2300RC Leiden, The Netherlands
| | - Hector C Keun
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital , London W12 0NN, United Kingdom
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21
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Responses to phosphate deprivation in yeast cells. Curr Genet 2015; 62:301-7. [PMID: 26615590 DOI: 10.1007/s00294-015-0544-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 01/10/2023]
Abstract
Inorganic phosphate is an essential nutrient because it is required for the biosynthesis of nucleotides, phospholipids and metabolites in energy metabolism. During phosphate starvation, phosphatases play a major role in phosphate acquisition by hydrolyzing phosphorylated macromolecules. In Saccharomyces cerevisiae, PHM8 (YER037W), a lysophosphatidic acid phosphatase, plays an important role in phosphate acquisition by hydrolyzing lysophosphatidic acid and nucleotide monophosphate that results in accumulation of triacylglycerol and nucleotides under phosphate limiting conditions. Under phosphate limiting conditions, it is transcriptionally regulated by Pho4p, a phosphate-responsive transcription factor. In this review, we focus on triacylglycerol metabolism in transcription factors deletion mutants involved in phosphate metabolism and propose a link between phosphate and triacylglycerol metabolism. Deletion of these transcription factors results in an increase in triacylglycerol level. Based on these observations, we suggest that PHM8 is responsible for the increase in triacylglycerol in phosphate metabolising gene deletion mutants.
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22
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Yadav KK, Singh N, Rajasekharan R. PHO4 transcription factor regulates triacylglycerol metabolism under low-phosphate conditions in Saccharomyces cerevisiae. Mol Microbiol 2015; 98:456-72. [PMID: 26179227 DOI: 10.1111/mmi.13133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2015] [Indexed: 02/01/2023]
Abstract
In Saccharomyces cerevisiae, PHM8 encodes a phosphatase that catalyses the dephosphorylation of lysophosphatidic acids to monoacylglycerol and nucleotide monophosphate to nucleoside and releases free phosphate. In this report, we investigated the role of PHM8 in triacylglycerol metabolism and its transcriptional regulation by a phosphate responsive transcription factor Pho4p under low-phosphate conditions. We found that the wild-type (BY4741) cells accumulate triacylglycerol and the expression of PHM8 was high under low-phosphate conditions. Overexpression of PHM8 in the wild-type, phm8Δ and quadruple phosphatase mutant (pah1Δdpp1Δlpp1Δapp1Δ) caused an increase in the triacylglycerol levels. However, the introduction of the PHM8 deletion into the quadruple phosphatase mutant resulted in a reduction in triacylglycerol levels and LPA phosphatase activity. The transcriptional activator Pho4p binds to the PHM8 promoter under low-phosphate conditions, activating PHM8 expression, which leads to the formation of monoacylglycerol from LPA. The synthesized monoacylglycerol is acylated to diacylglycerol by Dga1p, which is further acylated to triacylglycerol by the same enzyme.
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Affiliation(s)
- Kamlesh Kumar Yadav
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka, 570020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-CFTRI Campus
| | - Neelima Singh
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka, 570020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-CFTRI Campus
| | - Ram Rajasekharan
- Lipidomic Centre, Department of Lipid Science, CSIR-Central Food Technological Research Institute (CFTRI), Mysore, Karnataka, 570020, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-CFTRI Campus
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23
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Cabello-Díaz JM, Gálvez-Valdivieso G, Caballo C, Lambert R, Quiles FA, Pineda M, Piedras P. Identification and characterization of a gene encoding for a nucleotidase from Phaseolus vulgaris. JOURNAL OF PLANT PHYSIOLOGY 2015; 185:44-51. [PMID: 26276404 DOI: 10.1016/j.jplph.2015.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 07/07/2015] [Accepted: 07/07/2015] [Indexed: 06/04/2023]
Abstract
Nucleotidases are phosphatases that catalyze the removal of phosphate from nucleotides, compounds with an important role in plant metabolism. A phosphatase enzyme, with high affinity for nucleotides monophosphate previously identified and purified in embryonic axes from French bean, has been analyzed by MALDI TOF/TOF and two internal peptides have been obtained. The information of these peptide sequences has been used to search in the genome database and only a candidate gene that encodes for the phosphatase was identified (PvNTD1). The putative protein contains the conserved domains (motif I-IV) for haloacid dehalogenase-like hydrolases superfamily. The residues involved in the catalytic activity are also conserved. A recombinant protein overexpressed in Escherichia coli has shown molybdate resistant phosphatase activity with nucleosides monophosphate as substrate, confirming that the identified gene encodes for the phosphatase with high affinity for nucleotides purified in French bean embryonic axes. The activity of the purified protein was inhibited by adenosine. The expression of PvNTD1 gene was induced at the specific moment of radicle protrusion in embryonic axes. The gene was also highly expressed in young leaves whereas the level of expression in mature tissues was minimal.
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Affiliation(s)
- Juan Miguel Cabello-Díaz
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus Rabanales, Edif. Severo Ochoa, 1ª Planta, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Gregorio Gálvez-Valdivieso
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus Rabanales, Edif. Severo Ochoa, 1ª Planta, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Cristina Caballo
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus Rabanales, Edif. Severo Ochoa, 1ª Planta, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Rocío Lambert
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus Rabanales, Edif. Severo Ochoa, 1ª Planta, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Francisco Antonio Quiles
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus Rabanales, Edif. Severo Ochoa, 1ª Planta, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Manuel Pineda
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus Rabanales, Edif. Severo Ochoa, 1ª Planta, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Pedro Piedras
- Departamento de Botánica, Ecología y Fisiología Vegetal, Grupo de Fisiología Molecular y Biotecnología de Plantas, Campus Rabanales, Edif. Severo Ochoa, 1ª Planta, Universidad de Córdoba, 14071 Córdoba, Spain.
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24
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Nikiforov A, Kulikova V, Ziegler M. The human NAD metabolome: Functions, metabolism and compartmentalization. Crit Rev Biochem Mol Biol 2015; 50:284-97. [PMID: 25837229 PMCID: PMC4673589 DOI: 10.3109/10409238.2015.1028612] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The metabolism of NAD has emerged as a key regulator of cellular and organismal homeostasis. Being a major component of both bioenergetic and signaling pathways, the molecule is ideally suited to regulate metabolism and major cellular events. In humans, NAD is synthesized from vitamin B3 precursors, most prominently from nicotinamide, which is the degradation product of all NAD-dependent signaling reactions. The scope of NAD-mediated regulatory processes is wide including enzyme regulation, control of gene expression and health span, DNA repair, cell cycle regulation and calcium signaling. In these processes, nicotinamide is cleaved from NAD+ and the remaining ADP-ribosyl moiety used to modify proteins (deacetylation by sirtuins or ADP-ribosylation) or to generate calcium-mobilizing agents such as cyclic ADP-ribose. This review will also emphasize the role of the intermediates in the NAD metabolome, their intra- and extra-cellular conversions and potential contributions to subcellular compartmentalization of NAD pools.
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Affiliation(s)
- Andrey Nikiforov
- a Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University , St. Petersburg , Russia .,b Institute of Cytology, Russian Academy of Sciences , St. Petersburg , Russia , and
| | - Veronika Kulikova
- a Institute of Nanobiotechnologies, St. Petersburg State Polytechnical University , St. Petersburg , Russia
| | - Mathias Ziegler
- c Department of Molecular Biology , University of Bergen , Bergen , Norway
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25
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Kwon WS, Rahman MS, Lee JS, Yoon SJ, Park YJ, Pang MG. Discovery of predictive biomarkers for litter size in boar spermatozoa. Mol Cell Proteomics 2015; 14:1230-40. [PMID: 25693803 DOI: 10.1074/mcp.m114.045369] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Indexed: 11/06/2022] Open
Abstract
Conventional semen analysis has been used for prognosis and diagnosis of male fertility. Although this tool is essential for providing initial quantitative information about semen, it remains a subject of debate. Therefore, development of new methods for the prognosis and diagnosis of male fertility should be seriously considered for animal species of economic importance as well as for humans. In the present study, we applied a comprehensive proteomic approach to identify global protein biomarkers in boar spermatozoa in order to increase the precision of male fertility prognoses and diagnoses. We determined that l-amino acid oxidase, mitochondrial malate dehydrogenase 2, NAD (MDH2), cytosolic 5'-nucleotidase 1B, lysozyme-like protein 4, and calmodulin (CALM) were significantly and abundantly expressed in high-litter size spermatozoa. We also found that equatorin, spermadhesin AWN, triosephosphate isomerase (TPI), Ras-related protein Rab-2A (RAB2A), spermadhesin AQN-3, and NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 (NDUFS2) were significantly and abundantly expressed in low-litter size spermatozoa (>3-fold). Moreover, RAB2A, TPI, and NDUFS2 were negatively correlated with litter size, whereas CALM and MDH2 were positively correlated. This study provides novel biomarkers for the prediction of male fertility. To the best of our knowledge, this is the first work that shows significantly increased litter size using male fertility biomarkers in a field trial. Moreover, these protein markers may provide new developmental tools for the selection of superior sires as well as for the prognosis and diagnosis of male fertility.
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Affiliation(s)
- Woo-Sung Kwon
- From the ‡Department of Animal Science & Technology, Chung-Ang University, Anseong, Gyeonggi-do 456-756, Republic of Korea
| | - Md Saidur Rahman
- From the ‡Department of Animal Science & Technology, Chung-Ang University, Anseong, Gyeonggi-do 456-756, Republic of Korea
| | - June-Sub Lee
- From the ‡Department of Animal Science & Technology, Chung-Ang University, Anseong, Gyeonggi-do 456-756, Republic of Korea
| | - Sung-Jae Yoon
- From the ‡Department of Animal Science & Technology, Chung-Ang University, Anseong, Gyeonggi-do 456-756, Republic of Korea
| | - Yoo-Jin Park
- From the ‡Department of Animal Science & Technology, Chung-Ang University, Anseong, Gyeonggi-do 456-756, Republic of Korea
| | - Myung-Geol Pang
- From the ‡Department of Animal Science & Technology, Chung-Ang University, Anseong, Gyeonggi-do 456-756, Republic of Korea.
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26
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Ou Y, Wu J, Sandberg M, Weber SG. Electroosmotic perfusion of tissue: sampling the extracellular space and quantitative assessment of membrane-bound enzyme activity in organotypic hippocampal slice cultures. Anal Bioanal Chem 2014; 406:6455-68. [PMID: 25168111 DOI: 10.1007/s00216-014-8067-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/18/2014] [Accepted: 07/25/2014] [Indexed: 01/30/2023]
Abstract
This review covers recent advances in sampling fluid from the extracellular space of brain tissue by electroosmosis (EO). Two techniques, EO sampling with a single fused-silica capillary and EO push-pull perfusion, have been developed. These tools were used to investigate the function of membrane-bound enzymes with outward-facing active sites, or ectoenzymes, in modulating the activity of the neuropeptides leu-enkephalin and galanin in organotypic-hippocampal-slice cultures (OHSCs). In addition, the approach was used to determine the endogenous concentration of a thiol, cysteamine, in OHSCs. We have also investigated the degradation of coenzyme A in the extracellular space. The approach provides information on ectoenzyme activity, including Michaelis constants, in tissue, which, as far as we are aware, has not been done before. On the basis of computational evidence, EO push-pull perfusion can distinguish ectoenzyme activity with a ~100 μm spatial resolution, which is important for studies of enzyme kinetics in adjacent regions of the rat hippocampus.
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Affiliation(s)
- Yangguang Ou
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
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27
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Meurillon M, Marton Z, Hospital A, Jordheim LP, Béjaud J, Lionne C, Dumontet C, Périgaud C, Chaloin L, Peyrottes S. Structure-activity relationships of β-hydroxyphosphonate nucleoside analogues as cytosolic 5'-nucleotidase II potential inhibitors: synthesis, in vitro evaluation and molecular modeling studies. Eur J Med Chem 2014; 77:18-37. [PMID: 24607586 DOI: 10.1016/j.ejmech.2014.02.055] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 01/10/2014] [Accepted: 02/22/2014] [Indexed: 12/11/2022]
Abstract
The cytosolic 5'-nucleotidase II (cN-II) has been proposed as an attractive molecular target for the development of novel drugs circumventing resistance to cytotoxic nucleoside analogues currently used for treating leukemia and other malignant hemopathies. In the present work, synthesis of β-hydroxyphosphonate nucleoside analogues incorporating modifications either on the sugar residue or the nucleobase, and their in vitro evaluation towards the purified enzyme were carried out in order to determine their potency towards the inhibition of cN-II. In addition to the biochemical investigations, molecular modeling studies revealed important structural features for binding affinities towards the target enzyme.
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Affiliation(s)
- Maïa Meurillon
- Institut des biomolécules Max Mousseron (IBMM), UMR 5247 CNRS - UM1 - UM2, Université Montpellier 2, cc1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Zsuzsanna Marton
- Centre d'études d'agents pathogènes et biotechnologies pour la santé (CPBS), UMR 5236 CNRS - UM1 - UM2, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Audrey Hospital
- Institut des biomolécules Max Mousseron (IBMM), UMR 5247 CNRS - UM1 - UM2, Université Montpellier 2, cc1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Lars Petter Jordheim
- Université de Lyon 1, INSERM U1052 CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, 69000 Lyon, France
| | - Jérôme Béjaud
- Institut des biomolécules Max Mousseron (IBMM), UMR 5247 CNRS - UM1 - UM2, Université Montpellier 2, cc1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Corinne Lionne
- Centre d'études d'agents pathogènes et biotechnologies pour la santé (CPBS), UMR 5236 CNRS - UM1 - UM2, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Charles Dumontet
- Université de Lyon 1, INSERM U1052 CNRS UMR 5286, Centre de Recherche en Cancérologie de Lyon (CRCL), Centre Léon Bérard, 69000 Lyon, France
| | - Christian Périgaud
- Institut des biomolécules Max Mousseron (IBMM), UMR 5247 CNRS - UM1 - UM2, Université Montpellier 2, cc1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Laurent Chaloin
- Centre d'études d'agents pathogènes et biotechnologies pour la santé (CPBS), UMR 5236 CNRS - UM1 - UM2, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Institut des biomolécules Max Mousseron (IBMM), UMR 5247 CNRS - UM1 - UM2, Université Montpellier 2, cc1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France.
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28
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Santos CA, Saraiva AM, Toledo MAS, Beloti LL, Crucello A, Favaro MTP, Horta MAC, Santiago AS, Mendes JS, Souza AA, Souza AP. Initial biochemical and functional characterization of a 5'-nucleotidase from Xylella fastidiosa related to the human cytosolic 5'-nucleotidase I. Microb Pathog 2013; 59-60:1-6. [PMID: 23474016 DOI: 10.1016/j.micpath.2013.02.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 02/18/2013] [Accepted: 02/22/2013] [Indexed: 10/27/2022]
Abstract
The 5'-nucleotidases constitute a ubiquitous family of enzymes that catalyze either the hydrolysis or the transfer of esterified phosphate at the 5' position of nucleoside monophosphates. These enzymes are responsible for the regulation of nucleotide and nucleoside levels in the cell and can interfere with the phosphorylation-dependent activation of nucleoside analogs used in therapies targeting solid tumors and viral infections. In the present study, we report the initial biochemical and functional characterization of a 5'-nucleotidase from Xylella fastidiosa that is related to the human cytosolic 5'-nucleotidase I. X. fastidiosa is a plant pathogenic bacterium that is responsible for numerous economically important crop diseases. Biochemical assays confirmed the phosphatase activity of the recombinant purified enzyme and revealed metal ion dependence for full enzyme activity. In addition, we investigated the involvement of Xf5'-Nt in the formation of X. fastidiosa biofilms, which are structures that occlude the xylem vessels of susceptible plants and are strictly associated with bacterial pathogenesis. Using polyclonal antibodies against Xf5'-Nt, we observed an overexpression of Xf5'-Nt during the initial phases of X. fastidiosa biofilm formation that was not observed during X. fastidiosa planktonic growth. Our results demonstrate that the de/phosphorylation network catalyzed by 5'-nucleotidases may play an important role in bacterial biofilm formation, thereby contributing novel insights into bacterial nucleotide metabolism and pathogenicity.
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Affiliation(s)
- Clelton A Santos
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
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29
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El Amri C, Martin AR, Vasseur JJ, Smietana M. Borononucleotides as substrates/binders for human NMP kinases: enzymatic and spectroscopic evaluation. Chembiochem 2012; 13:1605-12. [PMID: 22733592 DOI: 10.1002/cbic.201200199] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Indexed: 11/06/2022]
Abstract
Borononucleotides are a family of natural nucleotide monophosphate analogues with a 5'-boronic acid function. As B-O-P linkages are known to be unstable in solution, we evaluated the ability of borononucleotides to be recognized by nucleoside monophosphate kinases and eventually foil the phosphorylation process. In this context, and with the idea of probing the influence of their size, shape, and flexibility, a library of borononucleotides were synthetized starting from the borononucleotide analogue of thymidine, which was shown to behave as a slow substrate of human TMP kinase. This study thus constitutes a good starting point for the development of new monophosphate mimics as potential substrates or ligands for NMP kinases.
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Affiliation(s)
- Chahrazade El Amri
- Groupe d'Enzymologie Moléculaire et Fonctionnelle, UR4-UPMC, Université Pierre et Marie Curie, Sorbonne Universités, case courrier 256, 7, quai St Bernard, 75252 Paris Cedex 05, France.
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