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Alexandrino AV, Barcelos MP, Federico LB, da Silva TG, Cavalca LB, de Moraes CHA, Ferreira H, Taft CA, Behlau F, de Paula Silva CHT, Novo-Mansur MTM. GDP-mannose pyrophosphorylase is an efficient target in Xanthomonas citri for citrus canker control. Microbiol Spectr 2024; 12:e0367323. [PMID: 38722158 PMCID: PMC11237706 DOI: 10.1128/spectrum.03673-23] [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: 10/25/2023] [Accepted: 03/20/2024] [Indexed: 06/06/2024] Open
Abstract
Xanthomonas citri subsp. citri (Xcc) is a bacterium that causes citrus canker, an economically important disease that results in premature fruit drop and reduced yield of fresh fruit. In this study, we demonstrated the involvement of XanB, an enzyme with phosphomannose isomerase (PMI) and guanosine diphosphate-mannose pyrophosphorylase (GMP) activities, in Xcc pathogenicity. Additionally, we found that XanB inhibitors protect the host against Xcc infection. Besides being deficient in motility, biofilm production, and ultraviolet resistance, the xanB deletion mutant was unable to cause disease, whereas xanB complementation restored wild-type phenotypes. XanB homology modeling allowed in silico virtual screening of inhibitors from databases, three of them being suitable in terms of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) properties, which inhibited GMP (but not PMI) activity of the Xcc recombinant XanB protein in more than 50%. Inhibitors reduced citrus canker severity up to 95%, similarly to copper-based treatment. xanB is essential for Xcc pathogenicity, and XanB inhibitors can be used for the citrus canker control. IMPORTANCE Xcc causes citrus canker, a threat to citrus production, which has been managed with copper, being required a more sustainable alternative for the disease control. XanB was previously found on the surface of Xcc, interacting with the host and displaying PMI and GMP activities. We demonstrated by xanB deletion and complementation that GMP activity plays a critical role in Xcc pathogenicity, particularly in biofilm formation. XanB homology modeling was performed, and in silico virtual screening led to carbohydrate-derived compounds able to inhibit XanB activity and reduce disease symptoms by 95%. XanB emerges as a promising target for drug design for control of citrus canker and other economically important diseases caused by Xanthomonas sp.
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Affiliation(s)
- André Vessoni Alexandrino
- Laboratório de Bioquímica e Biologia Molecular Aplicada (LBBMA), Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Mariana Pegrucci Barcelos
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Leonardo Bruno Federico
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Tamiris Garcia da Silva
- Departamento de Pesquisa e Desenvolvimento, Fundo de Defesa da Citricultura, Fundecitrus, Araraquara, São Paulo, Brazil
| | - Lúcia Bonci Cavalca
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, UNESP, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Carlos Henrique Alves de Moraes
- Laboratório de Bioquímica e Biologia Molecular Aplicada (LBBMA), Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Henrique Ferreira
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, UNESP, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil
| | | | - Franklin Behlau
- Departamento de Pesquisa e Desenvolvimento, Fundo de Defesa da Citricultura, Fundecitrus, Araraquara, São Paulo, Brazil
| | | | - Maria Teresa Marques Novo-Mansur
- Laboratório de Bioquímica e Biologia Molecular Aplicada (LBBMA), Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
- Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular (PPGGEv), Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
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Durin Z, Houdou M, Legrand D, Foulquier F. Metalloglycobiology: The power of metals in regulating glycosylation. Biochim Biophys Acta Gen Subj 2023; 1867:130412. [PMID: 37348823 DOI: 10.1016/j.bbagen.2023.130412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023]
Abstract
The remarkable structural diversity of glycans that is exposed at the cell surface and generated along the secretory pathway is tightly regulated by several factors. The recent identification of human glycosylation diseases related to metal transporter defects opened a completely new field of investigation, referred to herein as "metalloglycobiology", on how metal changes can affect the glycosylation and hence the glycan structures that are produced. Although this field is in its infancy, this review aims to go through the different glycosylation steps/pathways that are metal dependent and that could be impacted by metal homeostasis dysregulations.
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Affiliation(s)
- Zoé Durin
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F- 59000 Lille, France
| | - Marine Houdou
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F- 59000 Lille, France
| | - Dominique Legrand
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F- 59000 Lille, France
| | - François Foulquier
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F- 59000 Lille, France.
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Ma S, Wang N, Liu R, Zhang R, Dang H, Wang Y, Wang S, Zeng Z, Ji M, Hou P. ZIP10 is a negative determinant for anti-tumor effect of mannose in thyroid cancer by activating phosphate mannose isomerase. J Exp Clin Cancer Res 2021; 40:387. [PMID: 34886901 PMCID: PMC8656095 DOI: 10.1186/s13046-021-02195-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022] Open
Abstract
Background Mannose, a natural hexose existing in daily food, has been demonstrated to preferentially inhibit the progression of tumors with low expression of phosphate mannose isomerase (PMI). However, its function in thyroid cancer still remains elusive. Methods MTT, colony formation and flow cytometry assays were performed to determine the response of thyroid cancer cells to mannose. Meanwhile, mouse models of subcutaneous xenograft and primary papillary thyroid cancer were established to determine in vivo anti-tumor activity of mannose. The underlying mechanism of mannose selectively killing thyroid cancer cells was clarified by a series of molecular and biochemical experiments. Results Our data demonstrated that mannose selectively suppressed the growth of thyroid cancer cells, and found that enzyme activity of PMI rather than its protein expression was negatively associated with the response of thyroid cancer cells to mannose. Besides, our data showed that zinc ion (Zn2+) chelator TPEN clearly increased the response of mannose-insensitive cells to mannose by inhibiting enzyme activity of PMI, while Zn2+ supplement could effectively reverse this effect. Further studies found that the expression of zinc transport protein ZIP10, which transport Zn2+ from extracellular area into cells, was negatively related to the response of thyroid cancer cells to mannose. Knocking down ZIP10 in mannose-insensitive cells significantly inhibited in vitro and in vivo growth of these cells by decreasing intracellular Zn2+ concentration and enzyme activity of PMI. Moreover, ectopic expression of ZIP10 in mannose-sensitive cells decrease their cellular response to mannose. Mechanistically, mannose exerted its anti-tumor effect by inhibiting cellular glycolysis; however, this effect was highly dependent on expression status of ZIP10. Conclusion The present study demonstrate that mannose selectively kills thyroid cancer cells dependent on enzyme activity of PMI rather than its expression, and provide a mechanistic rationale for exploring clinical use of mannose in thyroid cancer therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02195-z.
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Affiliation(s)
- Sharui Ma
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Na Wang
- Department of Endocrinology, Xi'an Central Hospital, Xi'an, 710003, People's Republic of China
| | - Rui Liu
- Department of Radio-Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Rui Zhang
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Hui Dang
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Yubo Wang
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Simeng Wang
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Zekun Zeng
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Meiju Ji
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China.
| | - Peng Hou
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China.
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Gene Amplification Uncovers Large Previously Unrecognized Cryptic Antibiotic Resistance Potential in E. coli. Microbiol Spectr 2021; 9:e0028921. [PMID: 34756069 PMCID: PMC8579933 DOI: 10.1128/spectrum.00289-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The activation of unrecognized antibiotic resistance genes in the bacterial cell can give rise to antibiotic resistance without the need for major mutations or horizontal gene transfer. We hypothesize that bacteria harbor an extensive array of diverse cryptic genes that can be activated in response to antibiotics via adaptive resistance. To test this hypothesis, we developed a plasmid assay to randomly manipulate gene copy numbers in Escherichia coli cells and identify genes that conferred resistance when amplified. We then tested for cryptic resistance to 18 antibiotics and identified genes conferring resistance. E. coli could become resistant to 50% of the antibiotics tested, including chloramphenicol, d-cycloserine, polymyxin B, and 6 beta-lactam antibiotics, following this manipulation. Known antibiotic resistance genes comprised 13% of the total identified genes, where 87% were unclassified (cryptic) antibiotic resistance genes. These unclassified genes encoded cell membrane proteins, stress response/DNA repair proteins, transporters, and miscellaneous or hypothetical proteins. Stress response/DNA repair genes have a broad antibiotic resistance potential, as this gene class, in aggregate, conferred cryptic resistance to nearly all resistance-positive antibiotics. We found that antibiotics that are hydrophilic, those that are amphipathic, and those that inhibit the cytoplasmic membrane or cell wall biosynthesis were more likely to induce cryptic resistance in E. coli. This study reveals a diversity of cryptic genes that confer an antibiotic resistance phenotype when present in high copy number. Thus, our assay can identify potential novel resistance genes while also describing which antibiotics are prone to induce cryptic antibiotic resistance in E. coli. IMPORTANCE Predicting where new antibiotic resistance genes will rise is a challenge and is especially important when new antibiotics are developed. Adaptive resistance allows sensitive bacterial cells to become transiently resistant to antibiotics. This provides an opportune time for cells to develop more efficient resistance mechanisms, such as tolerance and permanent resistance to higher antibiotic concentrations. The biochemical diversity harbored within bacterial genomes may lead to the presence of genes that could confer resistance when timely activated. Therefore, it is crucial to understand adaptive resistance to identify potential resistance genes and prolong antibiotics. Here, we investigate cryptic resistance, an adaptive resistance mechanism, and identify unknown (cryptic) antibiotic resistance genes that confer resistance when amplified in a laboratory strain of E. coli. We also pinpoint antibiotic characteristics that are likely to induce cryptic resistance. This study may help detect novel antibiotic resistance genes and provide the foundation to help develop more effective antibiotics.
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Gerdol M, Visintin A, Kaleb S, Spazzali F, Pallavicini A, Falace A. Gene expression response of the alga Fucus virsoides (Fucales, Ochrophyta) to glyphosate solution exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115483. [PMID: 32889518 DOI: 10.1016/j.envpol.2020.115483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Fucus virsoides is an ecologically important canopy-forming brown algae endemic to the Adriatic Sea. Once widespread in marine coastal areas, this species underwent a rapid population decline and is now confined to small residual areas. Although the reasons behind this progressive disappearance are still a matter of debate, F. virsoides may suffer, like other macroalgae, from the potential toxic effects of glyphosate-based herbicides. Here, through a transcriptomic approach, we investigate the molecular basis of the high susceptibility of this species to glyphosate solution, previously observed at the morphological and eco-physiological levels. By simulating runoff event in a factorial experiment, we exposed F. virsoides to glyphosate (Roundup® 2.0), either alone or in association with nutrient enrichment, highlighting significant alterations of gene expression profiles that were already visible after three days of exposure. In particular, glyphosate exposure determined the near-complete expression shutdown of several genes involved in photosynthesis, protein synthesis and stress response molecular pathways. Curiously, these detrimental effects were partially mitigated by nutrient supplementation, which may explain the survival of relict population in confined areas with high nutrient inputs.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Andrea Visintin
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Sara Kaleb
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Francesca Spazzali
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy; CoNISMa, Piazzale Flaminio 9, 00196, Roma, Italy; Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy
| | - Annalisa Falace
- Department of Life Sciences, University of Trieste, 34127, Trieste, Italy; CoNISMa, Piazzale Flaminio 9, 00196, Roma, Italy; Istituto Nazionale di Oceanografia e di Geofisica Sperimentale - OGS, Trieste, Italy.
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Transcriptional Profiling of the Probiotic Escherichia coli Nissle 1917 Strain under Simulated Microgravity. Int J Mol Sci 2020; 21:ijms21082666. [PMID: 32290466 PMCID: PMC7215827 DOI: 10.3390/ijms21082666] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/05/2020] [Accepted: 04/09/2020] [Indexed: 12/16/2022] Open
Abstract
Long-term space missions affect the gut microbiome of astronauts, especially the viability of some pathogens. Probiotics may be an effective solution for the management of gut microbiomes, but there is a lack of studies regarding the physiology of probiotics in microgravity. Here, we investigated the effects of microgravity on the probiotic Escherichia coli Nissle 1917 (EcN) by comparing transcriptomic data during exponential and stationary growth phases under simulated microgravity and normal gravity. Microgravity conditions affected several physiological features of EcN, including its growth profile, biofilm formation, stress responses, metal ion transport/utilization, and response to carbon starvation. We found that some changes, such as decreased adhesion ability and acid resistance, may be disadvantageous to EcN relative to gut pathogens under microgravity, indicating the need to develop probiotics optimized for space flight.
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7
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Sugar-Phosphate Metabolism Regulates Stationary-Phase Entry and Stalk Elongation in Caulobacter crescentus. J Bacteriol 2020; 202:JB.00468-19. [PMID: 31767777 DOI: 10.1128/jb.00468-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/17/2019] [Indexed: 12/28/2022] Open
Abstract
Bacteria have a variety of mechanisms for adapting to environmental perturbations. Changes in oxygen availability result in a switch between aerobic and anaerobic respiration, whereas iron limitation may lead to siderophore secretion. In addition to metabolic adaptations, many organisms respond by altering their cell shape. Caulobacter crescentus, when grown under phosphate-limiting conditions, dramatically elongates its polar stalk appendage. The stalk is hypothesized to facilitate phosphate uptake; however, the mechanistic details of stalk synthesis are not well characterized. We used a chemical mutagenesis approach to isolate and characterize stalk-deficient mutants, one of which had two mutations in the phosphomannose isomerase gene (manA) that were necessary and sufficient to inhibit stalk elongation. Transcription of the pho regulon was unaffected in the manA mutant; therefore, ManA plays a unique regulatory role in stalk synthesis. The mutant ManA had reduced enzymatic activity, resulting in a 5-fold increase in the intracellular fructose 6-phosphate/mannose 6-phosphate ratio. This metabolic imbalance impaired the synthesis of cellular envelope components derived from mannose 6-phosphate, namely, lipopolysaccharide O-antigen and exopolysaccharide. Furthermore, the manA mutations prevented C. crescentus cells from efficiently entering stationary phase. Deletion of the stationary-phase response regulator gene spdR inhibited stalk elongation in wild-type cells, while overproduction of the alarmone ppGpp, which triggers growth arrest and stationary-phase entry, increased stalk length in the manA mutant strain. These results demonstrate that sugar-phosphate metabolism regulates stalk elongation independently of phosphate starvation.IMPORTANCE Metabolic control of bacterial cell shape is an important mechanism for adapting to environmental perturbations. Caulobacter crescentus dramatically elongates its polar stalk appendage in response to phosphate starvation. To investigate the mechanism of this morphological adaptation, we isolated stalk-deficient mutants, one of which had mutations in the phosphomannose isomerase gene (manA) that blocked stalk elongation, despite normal activation of the phosphate starvation response. The mutant ManA resulted in an imbalance in sugar-phosphate concentrations, which had effects on the synthesis of cellular envelope components and entry into stationary phase. Due to the interconnectivity of metabolic pathways, our findings may suggest more generally that the modulation of bacterial cell shape involves the regulation of growth phase and the synthesis of cellular building blocks.
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Ahmad L, Plancqueel S, Dubosclard V, Lazar N, Ghattas W, Li de la Sierra‐Gallay I, Tilbeurgh H, Salmon L. Crystal structure of phosphomannose isomerase from
Candida albicans
complexed with 5‐phospho‐
d
‐arabinonhydrazide. FEBS Lett 2018; 592:1667-1680. [DOI: 10.1002/1873-3468.13059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Lama Ahmad
- Equipe de Chimie Bioorganique et Bioinorganique Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) CNRS UMR8182 LabEx LERMIT Université Paris‐Saclay Université Paris‐Sud Orsay France
| | - Stéphane Plancqueel
- Institut de Biologie Intégrative de la Cellule (I2BC) CNRS UMR9198 Université Paris‐Saclay Université Paris‐Sud Orsay France
| | - Virginie Dubosclard
- Equipe de Chimie Bioorganique et Bioinorganique Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) CNRS UMR8182 LabEx LERMIT Université Paris‐Saclay Université Paris‐Sud Orsay France
| | - Noureddine Lazar
- Institut de Biologie Intégrative de la Cellule (I2BC) CNRS UMR9198 Université Paris‐Saclay Université Paris‐Sud Orsay France
| | - Wadih Ghattas
- Equipe de Chimie Bioorganique et Bioinorganique Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) CNRS UMR8182 LabEx LERMIT Université Paris‐Saclay Université Paris‐Sud Orsay France
| | - Inès Li de la Sierra‐Gallay
- Institut de Biologie Intégrative de la Cellule (I2BC) CNRS UMR9198 Université Paris‐Saclay Université Paris‐Sud Orsay France
| | - Herman Tilbeurgh
- Institut de Biologie Intégrative de la Cellule (I2BC) CNRS UMR9198 Université Paris‐Saclay Université Paris‐Sud Orsay France
| | - Laurent Salmon
- Equipe de Chimie Bioorganique et Bioinorganique Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO) CNRS UMR8182 LabEx LERMIT Université Paris‐Saclay Université Paris‐Sud Orsay France
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Fuller DR, Glover MS, Pierson NA, Kim D, Russell DH, Clemmer DE. Cis→Trans Isomerization of Pro(7) in Oxytocin Regulates Zn(2+) Binding. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1376-82. [PMID: 27154022 PMCID: PMC5161230 DOI: 10.1007/s13361-016-1410-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/11/2016] [Accepted: 04/14/2016] [Indexed: 05/28/2023]
Abstract
Ion mobility/mass spectrometry techniques are employed to investigate the binding of Zn(2+) to the nine-residue peptide hormone oxytocin (OT, Cys(1)-Tyr(2)-Ile(3)-Gln(4)-Asn(5)-Cys(6)-Pro(7)-Leu(8)-Gly(9)-NH2, having a disulfide bond between Cys(1) and Cys(6) residues). Zn(2+) binding to OT is known to increase the affinity of OT for its receptor [Pearlmutter, A. F., Soloff, M. S.: Characterization of the metal ion requirement for oxytocin-receptor interaction in rat mammary gland membranes. J. Biol. Chem. 254, 3899-3906 (1979)]. In the absence of Zn(2+), we find evidence for two primary OT conformations, which arise because the Cys(6)-Pro(7) peptide bond exists in both the trans- and cis-configurations. Upon addition of Zn(2+), we determine binding constants in water of KA = 1.43 ± 0.24 and 0.42 ± 0.12 μM(-1), for the trans- and cis-configured populations, respectively. The Zn(2+) bound form of OT, having a cross section of Ω = 235 Å(2), has Pro(7) in the trans-configuration, which agrees with a prior report [Wyttenbach, T., Liu, D., Bowers, M. T.: Interactions of the hormone oxytocin with divalent metal ions. J. Am. Chem. Soc. 130, 5993-6000 (2008)], in which it was proposed that Zn(2+) binds to the peptide ring and is further coordinated by interaction of the C-terminal, Pro(7)-Leu(8)-Gly(9)-NH2, tail. The present work shows that the cis-configuration of OT isomerizes to the trans-configuration upon binding Zn(2+). In this way, the proline residue regulates Zn(2+) binding to OT and, hence, is important in receptor binding. Graphical Abstract ᅟ.
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Affiliation(s)
- Daniel R Fuller
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Matthew S Glover
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Nicholas A Pierson
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
- Merck Research Laboratories, Rahway, NJ, 07065, USA
| | - DoYong Kim
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA.
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Huang CJ, Lin H, Yang JX. A robust method for increasing Fc glycan high mannose level of recombinant antibodies. Biotechnol Bioeng 2015; 112:1200-9. [DOI: 10.1002/bit.25534] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/15/2014] [Accepted: 12/23/2014] [Indexed: 01/03/2023]
Affiliation(s)
- Chung-Jr Huang
- Cell Science & Technology; Process and Product Development; Amgen Inc.; One Amgen Center Drive Thousand Oaks California 91320
| | - Henry Lin
- Cell Science & Technology; Process and Product Development; Amgen Inc.; One Amgen Center Drive Thousand Oaks California 91320
| | - Jerry Xiaoming Yang
- Cell Science & Technology; Process and Product Development; Amgen Inc.; One Amgen Center Drive Thousand Oaks California 91320
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11
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Dunsmore CJ, Malone KJ, Bailey KR, Wear MA, Florance H, Shirran S, Barran PE, Page AP, Walkinshaw MD, Turner NJ. Design and synthesis of conformationally constrained cyclophilin inhibitors showing a cyclosporin-A phenotype in C. elegans. Chembiochem 2011; 12:802-10. [PMID: 21337480 DOI: 10.1002/cbic.201000413] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Indexed: 12/23/2022]
Abstract
Cyclophilin A (CypA) is a member of the immunophilin family of proteins and receptor for the immunosuppressant drug cyclosporin A (CsA). Here we describe the design and synthesis of a new class of small-molecule inhibitors for CypA that are based upon a dimedone template. Electrospray mass spectrometry is utilised as an initial screen to quantify the protein affinity of the ligands. Active inhibitors and fluorescently labelled derivatives are then used as chemical probes for investigating the biological role of cyclophilins in the nematode Caenorhabditis elegans.
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Affiliation(s)
- Colin J Dunsmore
- School of Chemistry, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3JJ, UK
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12
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Erba EB, Zenobi R. Mass spectrometric studies of dissociation constants of noncovalent complexes. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c1pc90006d] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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13
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Bosco GL, Baxa M, Sosnick TR. Metal binding kinetics of bi-histidine sites used in psi analysis: evidence of high-energy protein folding intermediates. Biochemistry 2009; 48:2950-9. [PMID: 19220047 DOI: 10.1021/bi802072u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The zinc-specific fluorophore, Zinpyr-1, is used in competition assays to determine the kinetic and thermodynamic parameters of Zn2+ binding to engineered bi-histidine sites located in ubiquitin and the B domain of protein A (BdpA). These binding sites are used in psi analysis studies to investigate structure formation in the folding transition state identified by the change in folding rate upon addition of metal ions. For ubiquitin, the on-rate binding constant and binding affinity for a site located along an alpha-helix are measured to be approximately 10(7) M-1 s-1 and 3 microM, respectively. For a site located across two beta-strands, the metal binding affinity was too weak to measure in the dye competition assays (Kd > 55 microM). The equilibrium-determined values for the Zn2+-induced stabilization of ubiquitin and BdpA match the values derived from changes in the global folding and unfolding rates. Therefore, metal ion binding is in fast equilibrium during the transit over the free energy barrier. Accordingly, the folding rate must be slower than the product of the fractional population of a high-energy intermediate with the metal site formed and the metal binding on-rate constant. The known folding rate of 20 s-1 at 1.5 M guanidinium chloride in 400 microM Zn2+ provides an upper bound for the stability of such intermediates (DeltaG(U-I) < 4 kcal/mol). These results support a view of the apparent two-state protein folding reaction surface as a fast pre-equilibrium between the denatured state and a series of high-energy species. The net folding rate is a product of the equilibrium constant of the highest-energy species and a transmission rate. For ubiquitin, we estimate the transmission rate to be approximately 10(4) s-1. Implications for the role of unfolded chain diffusion on folding rates and barrier heights are discussed.
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Affiliation(s)
- Gerra L Bosco
- The Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
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14
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Synthesis and evaluation of non-hydrolyzable D-mannose 6-phosphate surrogates reveal 6-deoxy-6-dicarboxymethyl-D-mannose as a new strong inhibitor of phosphomannose isomerases. Bioorg Med Chem 2009; 17:7100-7. [PMID: 19783448 DOI: 10.1016/j.bmc.2009.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Revised: 08/28/2009] [Accepted: 09/03/2009] [Indexed: 11/23/2022]
Abstract
Non-hydrolyzable d-mannose 6-phosphate analogues in which the phosphate group was replaced by a phosphonomethyl, a dicarboxymethyl, or a carboxymethyl group were synthesized and kinetically evaluated as substrate analogues acting as potential inhibitors of type I phosphomannose isomerases (PMIs) from Saccharomyces cerevisiae and Escherichia coli. While 6-deoxy-6-phosphonomethyl-d-mannose and 6-deoxy-6-carboxymethyl-D-mannose did not inhibit the enzymes significantly, 6-deoxy-6-dicarboxymethyl-D-mannose appeared as a new strong competitive inhibitor of both S. cerevisiae and E. coli PMIs with K(m)/K(i) ratios of 28 and 8, respectively. We thus report the first malonate-based inhibitor of an aldose-ketose isomerase to date. Phosphonomethyl mimics of the 1,2-cis-enediolate high-energy intermediate postulated for the isomerization reaction catalyzed by PMIs were also synthesized but behave as poor inhibitors of PMIs. A polarizable molecular mechanics (SIBFA) study was performed on the complexes of d-mannose 6-phosphate and two of its analogues with PMI from Candida albicans, an enzyme involved in yeast infection homologous to S. cerevisiae and E. coli PMIs. It shows that effective binding to the catalytic site occurs with retention of the Zn(II)-bound water molecule. Thus the binding of the hydroxyl group on C1 of the ligand to Zn(II) should be water-mediated. The kinetic study reported here also suggests the dianionic character of the phosphate surrogate as a likely essential parameter for strong binding of the inhibitor to the enzyme active site.
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15
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Gao H, Carroll KS, Chen H, Bertozzi CR, Leary J. Noncovalent complexes of APS reductase from M. tuberculosis: delineating a mechanistic model using ESI-FTICR MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:167-78. [PMID: 17023175 PMCID: PMC2755055 DOI: 10.1016/j.jasms.2006.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 08/16/2006] [Accepted: 08/17/2006] [Indexed: 05/12/2023]
Abstract
ESI-FTICR MS was utilized to characterize a 4Fe-4S containing protein Mycobacterium tuberculosis APS reductase. This enzyme catalyzes the reduction of APS to sulfite and AMP with reducing equivalents from the protein cofactor, thioredoxin. Under nondenaturing conditions, a distribution of the apoprotein, a 2Fe-2S intermediate, and the 4Fe-4S holoprotein were observed. Accurate mass measurements indicated an oxidation state of +2 for the 4Fe-4S cluster, with no disulfide bond in the holoenzyme. Gas-phase stability of the 4Fe-4S cluster was investigated using both in-source and collision induced dissociation, which provided information regarding the relative gas-phase binding strength of iron towards protein ligands and inorganic sulfides. Noncovalent complexes of the holoprotein with several ligands, including APS, thioredoxin, and AMP, were also investigated. Calculated values of dissociation constants for the complexes indicate that AMP binds with a higher affinity to the enzyme intermediate than to the free enzyme. The implications of the binary and ternary complexes observed by gas-phase noncovalent interactions in the mechanism of APS reduction are discussed.
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Affiliation(s)
- Hong Gao
- Section of Molecular Cell Biology and Department of Chemistry, University of California, Davis, CA 95616
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Kate S. Carroll
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Huiyi Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute
| | - Julie Leary
- Section of Molecular Cell Biology and Department of Chemistry, University of California, Davis, CA 95616
- Correspondence should be addressed to: Julie A. Leary, Genome Center, One Shields Ave, Davis, CA 95616, USA, , Tel: 530-754-4987, Fax: 530-754-8370
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16
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Lobinski R, Moulin C, Ortega R. Imaging and speciation of trace elements in biological environment. Biochimie 2006; 88:1591-604. [PMID: 17064836 DOI: 10.1016/j.biochi.2006.10.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2006] [Accepted: 10/03/2006] [Indexed: 11/24/2022]
Abstract
Mineral elements, often at the trace level, play a considerable role in physiology and pathology of biological systems. Metallogenomics, metalloproteomics, and metallomics are among the emerging disciplines which are critically dependent on spatially resolved concentration maps of trace elements in a cell or tissue, on information on chemical speciation, and on that on metal-binding coordination sites. The mini-review discusses recent progress in analytical techniques for element profiling on the genome scale, biological trace element imaging, and probing, identification and quantification of chemical species in the biological environment. Imaging of the element distribution in cells and tissue sections is becoming possible with sub-micrometer spatial resolution and picogram-level sensitivity owing to advances in laser ablation MS, ion beam and synchrotron radiation X-ray fluorescence microprobes. Progress in nanoflow chromatography and capillary electrophoresis coupled with element specific ICP MS and molecule-specific electrospray MS/MS and MALDI enables speciation of elements in microsamples in a complex biological environment. Laser ablation ICP MS, micro-SXRF, and micro-PIXE allow mapping of trace element distribution in 1D and 2D proteomics gels. The increasing sensitivity of EXAFS and XANES owing to the use of more intense synchrotron beams and efficient focusing optics provide information about oxidation state, fingerprint speciation of metal sites and metal-site structures.
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Affiliation(s)
- R Lobinski
- Equipe de chimie analytique bio-inorganique, CNRS UMR5034, Hélioparc, 2, avenue Professeur-Angot, 64053 Pau, France
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17
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Yu Y, Sweeney MD, Saad OM, Leary JA. Potential inhibitors of chemokine function: analysis of noncovalent complexes of CC chemokine and small polyanionic molecules by ESI FT-ICR mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:524-535. [PMID: 16503157 DOI: 10.1016/j.jasms.2005.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Revised: 12/08/2005] [Accepted: 12/14/2005] [Indexed: 05/06/2023]
Abstract
Chemokines play a critical role in inducing chemotaxis, extravasation, and activation of leukocytes both in routine immunosurveillance and autoimmune diseases. Traditionally, to disrupt chemokine function, strategies have focused on blockage of its interaction with the receptor. Recently, it has been demonstrated that binding to glycosaminoglycans (GAGs) is also required for the in vivo activity of many chemokines. Thus, interference with the GAG-binding of chemokines may offer an alternative, valid, anti-inflammatory strategy. However, the potential of using small polyanions to inhibit the interactions between chemokines and cell surface GAGs has not been fully explored. In this study, a mass spectrometry based filtration trapping assay was utilized to study the interactions between two CCR 2 ligands (MCP-1/CCL2 and MCP-3/CCL7) and a series of low molecular weight, polyanionic molecules. Findings were confirmed by using a hydrophobic trapping assay. The results indicated that Arixtra (fondaparinux sodium), sucrose octasulfate, and suramin were specific binders of the chemokines, while cyclodextrin sulfate, although the most highly sulfated molecule among the ones investigated, showed no binding. The binding stoichiometry of the small molecule ligand was determined from the measured molecular weight of the noncovalent complex. Furthermore, the dissociation constant between MCP-3 and Arixtra was determined by using electrospray ionization Fourier transform ion cyclotron resonance (ESI FT-ICR) mass spectrometry, which compared favorably with the result of the isothermal titration calorimetry (ITC) assay. The relative binding affinity of these ligands to MCP-3 was also determined using a competitive filtration trapping assay.
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Affiliation(s)
- Yonghao Yu
- Genome Center, Department of Chemistry and Molecular Cell Biology, University of California at Davis, One Shields Road, 95616, Davis, CA, USA
- the Department of Chemistry, University of California at Berkeley, Berkeley, CA
| | - Matthew D Sweeney
- Genome Center, Department of Chemistry and Molecular Cell Biology, University of California at Davis, One Shields Road, 95616, Davis, CA, USA
- the Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA
| | - Ola M Saad
- Genome Center, Department of Chemistry and Molecular Cell Biology, University of California at Davis, One Shields Road, 95616, Davis, CA, USA
| | - Julie A Leary
- Genome Center, Department of Chemistry and Molecular Cell Biology, University of California at Davis, One Shields Road, 95616, Davis, CA, USA.
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