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Kurogi K, Suiko M, Sakakibara Y. Evolution and multiple functions of sulfonation and cytosolic sulfotransferases across species. Biosci Biotechnol Biochem 2024; 88:368-380. [PMID: 38271594 DOI: 10.1093/bbb/zbae008] [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: 11/07/2023] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
Organisms have conversion systems for sulfate ion to take advantage of the chemical features. The use of biologically converted sulfonucleotides varies in an evolutionary manner, with the universal use being that of sulfonate donors. Sulfotransferases have the ability to transfer the sulfonate group of 3'-phosphoadenosine 5'-phosphosulfate to a variety of molecules. Cytosolic sulfotransferases (SULTs) play a role in the metabolism of low-molecular-weight compounds in response to the host organism's living environment. This review will address the diverse functions of the SULT in evolution, including recent findings. In addition to the diversity of vertebrate sulfotransferases, the molecular aspects and recent studies on bacterial and plant sulfotransferases are also addressed.
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Affiliation(s)
- Katsuhisa Kurogi
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Miyazaki, Japan
| | - Masahito Suiko
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Miyazaki, Japan
| | - Yoichi Sakakibara
- Department of Biochemistry and Applied Biosciences, University of Miyazaki, Miyazaki, Japan
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2
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D’Antona AM, Lee JM, Zhang M, Friedman C, He T, Mosyak L, Bennett E, Lin L, Silverman M, Cometa F, Meade C, Hageman T, Sousa E, Cohen J, Marquette K, Ferguson D, Zhong X. Tyrosine Sulfation at Antibody Light Chain CDR-1 Increases Binding Affinity and Neutralization Potency to Interleukine-4. Int J Mol Sci 2024; 25:1931. [PMID: 38339208 PMCID: PMC10855961 DOI: 10.3390/ijms25031931] [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: 12/20/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Structure and function of therapeutic antibodies can be modulated by a variety of post-translational modifications (PTM). Tyrosine (Tyr) sulfation is a type of negatively charged PTM that occurs during protein trafficking through the Golgi. In this study, we discovered that an anti-interleukin (IL)-4 human IgG1, produced by transiently transfected HEK293 cells, contained a fraction of unusual negatively charged species. Interestingly, the isolated acidic species exhibited a two-fold higher affinity to IL-4 and a nearly four-fold higher potency compared to the main species. Mass spectrometry (MS) showed the isolated acidic species possessed an +80-Dalton from the expected mass, suggesting an occurrence of Tyr sulfation. Consistent with this hypothesis, we show the ability to control the acidic species during transient expression with the addition of Tyr sulfation inhibitor sodium chlorate or, conversely, enriched the acidic species from 30% to 92% of the total antibody protein when the IL-4 IgG was co-transfected with tyrosylprotein sulfotransferase genes. Further MS and mutagenesis analysis identified a Tyr residue at the light chain complementarity-determining region-1 (CDRL-1), which was sulfated specifically. These results together have demonstrated for the first time that Tyr sulfation at CDRL-1 could modulate antibody binding affinity and potency to a human immune cytokine.
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Affiliation(s)
- Aaron M. D’Antona
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Julie M. Lee
- Translational Clinical Sciences, Pfizer Discovery & Early Development, 610 Main Street, Cambridge, MA 02139, USA
| | - Melvin Zhang
- Inflammation and Immunology Research Unit, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA
| | - Clarence Friedman
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Tao He
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Lidia Mosyak
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Eric Bennett
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Laura Lin
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Maddison Silverman
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Funi Cometa
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Caryl Meade
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Tyler Hageman
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Eric Sousa
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Justin Cohen
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Kimberly Marquette
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Darren Ferguson
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
| | - Xiaotian Zhong
- BioMedicine Design, Pfizer Research & Development, 610 Main Street, Cambridge, MA 02139, USA (T.H.); (T.H.); (E.S.)
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3
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Bashyal A, Hui JO, Flick T, Dykstra AB, Zhang Q, Campuzano IDG, Brodbelt JS. Differentiation of Aspartic and Isoaspartic Acid Using 193 nm Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2023; 95:11510-11517. [PMID: 37458293 PMCID: PMC10588209 DOI: 10.1021/acs.analchem.3c02025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Spontaneous conversion of aspartic acid (Asp) to isoaspartic acid (isoAsp) is a ubiquitous modification that influences the structure and function of proteins. This modification of Asp impacts the stability of biotherapeutics and has been linked to the development of neurodegenerative diseases. We explored the use of 193 nm ultraviolet photodissociation (UVPD) to distinguish Asp and isoAsp in the protonated and deprotonated peptides. The differences in the relative abundances of several fragment ions uniquely generated by UVPD were used to differentiate isomeric peptide standards containing Asp or isoAsp. These fragment ions result from the cleavage of bonds N-terminal to Asp/isoAsp residues in addition to the side-chain losses from Asp/isoAsp or the losses of COOH, CO2, CO, or H2O from y-ions. Fragmentation of Asp-containing tryptic peptides using UVPD resulted in more enhanced w/w + 1/y - 1/x ions, while isoAsp-containing peptides yielded more enhanced y - 18/y - 45/y - 46 ions. UVPD was also used to identify an isomerized peptide from a tryptic digest of a monoclonal antibody. Moreover, UVPD of a protonated nontryptic peptide resulted in more enhanced y ions N- and C-terminal to isoAsp and differences in b/y ion ratios that were used to identify the isoAsp peptide.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - John O Hui
- Amgen Research, Molecular Analytics, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Tawnya Flick
- Process Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Andrew B Dykstra
- Process Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Qingchun Zhang
- Process Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Iain D G Campuzano
- Amgen Research, Molecular Analytics, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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4
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Shao Y, Tang G, Huang Y, Ke W, Wang S, Zheng D, Ruan L. Transcriptional regulator Sar regulates the multiple secretion systems in Xanthomonas oryzae. MOLECULAR PLANT PATHOLOGY 2023; 24:16-27. [PMID: 36177860 PMCID: PMC9742495 DOI: 10.1111/mpp.13272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Xanthomonas oryzae pv. oryzae (Xoo) is a notorious plant pathogen that causes leaf blight of rice cultivars. The pathogenic bacteria possess numerous transcriptional regulators to regulate various biological processes, such as pathogenicity in the host plant. Our previous study identified a new master regulator PXO_RS20790 that is involved in pathogenicity for Xoo against the host rice. However, the molecular functions of PXO_RS20790 are still unclear. Here, we demonstrate that transcriptional regulator Sar (PXO_RS20790) regulates multiple secretion systems. The RNA-sequencing analysis, bacterial one-hybrid assay, and electrophoretic mobility shift assay revealed that Sar enables binding of the promoters of the T1SS-related genes, the avirulence gene, raxX, and positively regulates these genes' expression. Meanwhile, we found that Sar positively regulated the T6SS-1 clusters but did not regulate the T6SS-2 clusters. Furthermore, we revealed that only T6SS-2 is involved in interbacterial competition. We also indicated that Sar could bind the promoters of the T3SS regulators, hrpG and hrpX, to activate these two genes' transcription. Our findings revealed that Sar is a crucial regulator of multiple secretion systems and virulence.
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Affiliation(s)
- Yanan Shao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Guiyu Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Yuanyuan Huang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Wenli Ke
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Shasha Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Dehong Zheng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- National Demonstration Center for Experimental Plant Science Education, College of AgricultureGuangxi UniversityNanningChina
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- College of Resources and EnvironmentTibet Agriculture & Animal Husbandry UniversityLinzhiChina
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5
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Coates RJ, Young MT, Scofield S. Optimising expression and extraction of recombinant proteins in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1074531. [PMID: 36570881 PMCID: PMC9773421 DOI: 10.3389/fpls.2022.1074531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Recombinant proteins are of paramount importance for research, industrial and medical use. Numerous expression chassis are available for recombinant protein production, and while bacterial and mammalian cell cultures are the most widely used, recent developments have positioned transgenic plant chassis as viable and often preferential options. Plant chassis are easily maintained at low cost, are hugely scalable, and capable of producing large quantities of protein bearing complex post-translational modification. Several protein targets, including antibodies and vaccines against human disease, have been successfully produced in plants, highlighting the significant potential of plant chassis. The aim of this review is to act as a guide to producing recombinant protein in plants, discussing recent progress in the field and summarising the factors that must be considered when utilising plants as recombinant protein expression systems, with a focus on optimising recombinant protein expression at the genetic level, and the subsequent extraction and purification of target proteins, which can lead to substantial improvements in protein stability, yield and purity.
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6
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Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210,Corresponding author:
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7
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Plant immunity: Rice XA21-mediated resistance to bacterial infection. Proc Natl Acad Sci U S A 2022; 119:2121568119. [PMID: 35131901 PMCID: PMC8872720 DOI: 10.1073/pnas.2121568119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2021] [Indexed: 12/27/2022] Open
Abstract
The mechanisms plants employ to resist infection were unknown until just a few decades ago. We now understand that plants utilize diverse classes of immune receptors to recognize and respond to pathogenic microbes and pests. This paper describes the development of the plant immunity field, from early studies on the genetics of disease resistance to our increasing knowledge of how plant receptors interact with their microbial ligands, with an emphasis on the rice immune receptor XA21 and its bacterial ligand. In this article, we describe the development of the plant immunity field, starting with efforts to understand the genetic basis for disease resistance, which ∼30 y ago led to the discovery of diverse classes of immune receptors that recognize and respond to infectious microbes. We focus on knowledge gained from studies of the rice XA21 immune receptor that recognizes RaxX (required for activation of XA21 mediated immunity X), a sulfated microbial peptide secreted by the gram-negative bacterium Xanthomonas oryzae pv. oryzae. XA21 is representative of a large class of plant and animal immune receptors that recognize and respond to conserved microbial molecules. We highlight the complexity of this large class of receptors in plants, discuss a possible role for RaxX in Xanthomonas biology, and draw attention to the important role of sulfotyrosine in mediating receptor–ligand interactions.
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8
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Joe A, Stewart V, Ronald PC. The HrpX Protein Activates Synthesis of the RaxX Sulfopeptide, Required for Activation of XA21-Mediated Immunity to Xanthomonas oryzae pv. oryzae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1307-1315. [PMID: 34731589 DOI: 10.1094/mpmi-05-21-0124-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Upon encountering a susceptible plant host, a bacterial pathogen expresses specific virulence factors. For example, in planta, the Xanthomonas HrpX protein activates transcription of roughly 150 genes encoding components of the type III secretion system or its translocated effectors, as well as other secreted proteins implicated in pathogenesis. Here, we show that X. oryzae pv. oryzae growth in planta or in HrpX-inducing XOM2 media resulted in HrpX-dependent transcription of the raxX and raxST genes that control production of the RaxX sulfopeptide, exported through a type I secretion system. The RaxX protein is required for activation of XA21-mediated immunity in Xa21+ rice lines. We identified potential plant-inducible promoter elements upstream of the likely 5' ends of the raxX and raxST transcripts. Deletions and nucleotide substitutions confirmed that these elements are required for HrpX-dependent expression of raxX and raxST. We conclude that raxX-raxST gene expression is induced by HrpX during growth in planta and, therefore, is coordinately expressed with other genes required for pathogenesis.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Anna Joe
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Valley Stewart
- Department of Microbiology & Molecular Genetics, University of California, Davis, CA 95616, U.S.A
| | - Pamela C Ronald
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
- Genome Center, University of California, Davis, CA 95616, U.S.A
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9
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LeBlanc BM, Moreno RY, Escobar EE, Venkat Ramani MK, Brodbelt JS, Zhang Y. What's all the phos about? Insights into the phosphorylation state of the RNA polymerase II C-terminal domain via mass spectrometry. RSC Chem Biol 2021; 2:1084-1095. [PMID: 34458825 PMCID: PMC8341212 DOI: 10.1039/d1cb00083g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/03/2021] [Indexed: 12/31/2022] Open
Abstract
RNA polymerase II (RNAP II) is one of the primary enzymes responsible for expressing protein-encoding genes and some small nuclear RNAs. The enigmatic carboxy-terminal domain (CTD) of RNAP II and its phosphorylation state are critically important in regulating transcription in vivo. Early methods of identifying phosphorylation on the CTD heptad were plagued by issues of low specificity and ambiguous signals. However, advancements in the field of mass spectrometry (MS) have presented the opportunity to gain new insights into well-studied processes as well as explore new frontiers in transcription. By using MS, residues which are modified within the CTD heptad and across repeats are now able to be pinpointed. Likewise, identification of kinase and phosphatase specificity towards residues of the CTD has reached a new level of accuracy. Now, MS is being used to investigate the crosstalk between modified residues of the CTD and may be a critical technique for understanding how phosphorylation plays a role in the new LLPS model of transcription. Herein, we discuss the development of various MS techniques and evaluate their capabilities. By highlighting the pros and cons of each technique, we aim to provide future investigators with a comprehensive overview of how MS can be used to investigate the complexities of RNAP-II mediated transcription.
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Affiliation(s)
- Blase M LeBlanc
- Department of Molecular Biosciences, University of Texas Austin USA
| | - R Yvette Moreno
- Department of Molecular Biosciences, University of Texas Austin USA
| | | | | | | | - Yan Zhang
- Department of Molecular Biosciences, University of Texas Austin USA
- Institute of Cellular and Molecular Biology, University of Texas Austin USA
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Venkat Ramani MK, Yang W, Irani S, Zhang Y. Simplicity is the Ultimate Sophistication-Crosstalk of Post-translational Modifications on the RNA Polymerase II. J Mol Biol 2021; 433:166912. [PMID: 33676925 PMCID: PMC8184622 DOI: 10.1016/j.jmb.2021.166912] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 12/19/2022]
Abstract
The highly conserved C-terminal domain (CTD) of the largest subunit of RNA polymerase II comprises a consensus heptad (Y1S2P3T4S5P6S7) repeated multiple times. Despite the simplicity of its sequence, the essential CTD domain orchestrates eukaryotic transcription and co-transcriptional processes, including transcription initiation, elongation, and termination, and mRNA processing. These distinct facets of the transcription cycle rely on specific post-translational modifications (PTM) of the CTD, in which five out of the seven residues in the heptad repeat are subject to phosphorylation. A hypothesis termed the "CTD code" has been proposed in which these PTMs and their combinations generate a sophisticated landscape for spatiotemporal recruitment of transcription regulators to Pol II. In this review, we summarize the recent experimental evidence understanding the biological role of the CTD, implicating a context-dependent theme that significantly enhances the ability of accurate transcription by RNA polymerase II. Furthermore, feedback communication between the CTD and histone modifications coordinates chromatin states with RNA polymerase II-mediated transcription, ensuring the effective and accurate conversion of information into cellular responses.
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Affiliation(s)
| | - Wanjie Yang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States
| | - Seema Irani
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States
| | - Yan Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, United States; The Institute for Cellular and Molecular Biology. University of Texas at Austin, Austin, TX 78712, United States.
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The Xanthomonas RaxH-RaxR Two-Component Regulatory System Is Orthologous to the Zinc-Responsive Pseudomonas ColS-ColR System. Microorganisms 2021; 9:microorganisms9071458. [PMID: 34361895 PMCID: PMC8306577 DOI: 10.3390/microorganisms9071458] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 01/08/2023] Open
Abstract
Genome sequence comparisons to infer likely gene functions require accurate ortholog assignments. In Pseudomonas spp., the sensor-regulator ColS-ColR two-component regulatory system responds to zinc and other metals to control certain membrane-related functions, including lipid A remodeling. In Xanthomonas spp., three different two-component regulatory systems, RaxH-RaxR, VgrS-VgrR, and DetS-DetR, have been denoted as ColS-ColR in several different genome annotations and publications. To clarify these assignments, we compared the sensor periplasmic domain sequences and found that those from Pseudomonas ColS and Xanthomonas RaxH share a similar size as well as the location of a Glu-X-X-Glu metal ion-binding motif. Furthermore, we determined that three genes adjacent to raxRH are predicted to encode enzymes that remodel the lipid A component of lipopolysaccharide. The modifications catalyzed by lipid A phosphoethanolamine transferase (EptA) and lipid A 1-phosphatase (LpxE) previously were detected in lipid A from multiple Xanthomonas spp. The third gene encodes a predicted lipid A glycosyl transferase (ArnT). Together, these results indicate that the Xanthomonas RaxH-RaxR system is orthologous to the Pseudomonas ColS-ColR system that regulates lipid A remodeling. To avoid future confusion, we recommend that the terms ColS and ColR no longer be applied to Xanthomonas spp., and that the Vgr, Rax, and Det designations be used instead.
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12
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Structure and Function of Piezophilic Hyperthermophilic Pyrococcus yayanosii pApase. Int J Mol Sci 2021; 22:ijms22137159. [PMID: 34281213 PMCID: PMC8268124 DOI: 10.3390/ijms22137159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 12/03/2022] Open
Abstract
3’-Phosphoadenosine 5’-monophosphate (pAp) is a byproduct of sulfate assimilation and coenzyme A metabolism. pAp can inhibit the activity of 3′-phosphoadenosine 5′-phosphosulfate (PAPS) reductase and sulfotransferase and regulate gene expression under stress conditions by inhibiting XRN family of exoribonucleases. In metazoans, plants, yeast, and some bacteria, pAp can be converted into 5’-adenosine monophosphate (AMP) and inorganic phosphate by CysQ. In some bacteria and archaea, nanoRNases (Nrn) from the Asp-His-His (DHH) phosphoesterase superfamily are responsible for recycling pAp. In addition, histidinol phosphatase from the amidohydrolase superfamily can hydrolyze pAp. The bacterial enzymes for pAp turnover and their catalysis mechanism have been well studied, but these processes remain unclear in archaea. Pyrococcus yayanosii, an obligate piezophilic hyperthermophilic archaea, encodes a DHH family pApase homolog (PyapApase). Biochemical characterization showed that PyapApase can efficiently convert pAp into AMP and phosphate. The resolved crystal structure of apo-PyapApase is similar to that of bacterial nanoRNaseA (NrnA), but they are slightly different in the α-helix linker connecting the DHH and Asp-His-His associated 1 (DHHA1) domains. The longer α-helix of PyapApase leads to a narrower substrate-binding cleft between the DHH and DHHA1 domains than what is observed in bacterial NrnA. Through mutation analysis of conserved amino acid residues involved in coordinating metal ion and binding substrate pAp, it was confirmed that PyapApase has an ion coordination pattern similar to that of NrnA and slightly different substrate binding patterns. The results provide combined structural and functional insight into the enzymatic turnover of pAp, implying the potential function of sulfate assimilation in hyperthermophilic cells.
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13
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Maxwell JW, Payne RJ. Revealing the functional roles of tyrosine sulfation using synthetic sulfopeptides and sulfoproteins. Curr Opin Chem Biol 2020; 58:72-85. [DOI: 10.1016/j.cbpa.2020.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022]
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14
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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15
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Kaufmann C, Sauter M. Sulfated plant peptide hormones. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4267-4277. [PMID: 31231771 PMCID: PMC6698702 DOI: 10.1093/jxb/erz292] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/11/2019] [Indexed: 05/08/2023]
Abstract
Sulfated peptides are plant hormones that are active at nanomolar concentrations. The sulfation at one or more tyrosine residues is catalysed by tyrosylprotein sulfotransferase (TPST), which is encoded by a single-copy gene. The sulfate group is provided by the co-substrate 3´-phosphoadenosine 5´-phosphosulfate (PAPS), which links synthesis of sulfated signaling peptides to sulfur metabolism. The precursor proteins share a conserved DY-motif that is implicated in specifying tyrosine sulfation. Several sulfated peptides undergo additional modification such as hydroxylation of proline and glycosylation of hydroxyproline. The modifications render the secreted signaling molecules active and stable. Several sulfated signaling peptides have been shown to be perceived by leucine-rich repeat receptor-like kinases (LRR-RLKs) but have signaling pathways that, for the most part, are yet to be elucidated. Sulfated peptide hormones regulate growth and a wide variety of developmental processes, and intricately modulate immunity to pathogens. While basic research on sulfated peptides has made steady progress, their potential in agricultural and pharmaceutical applications has yet to be explored.
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Affiliation(s)
- Christine Kaufmann
- Plant Developmental Biology and Physiology, University of Kiel, Am Botanischen Garten, Kiel, Germany
- Correspondence:
| | - Margret Sauter
- Plant Developmental Biology and Physiology, University of Kiel, Am Botanischen Garten, Kiel, Germany
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16
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Thomas PW, Cammarata M, Brodbelt JS, Monzingo AF, Pratt RF, Fast W. A Lysine-Targeted Affinity Label for Serine-β-Lactamase Also Covalently Modifies New Delhi Metallo-β-lactamase-1 (NDM-1). Biochemistry 2019; 58:2834-2843. [PMID: 31145588 DOI: 10.1021/acs.biochem.9b00393] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The divergent sequences, protein structures, and catalytic mechanisms of serine- and metallo-β-lactamases hamper the development of wide-spectrum β-lactamase inhibitors that can block both types of enzymes. The O-aryloxycarbonyl hydroxamate inactivators of Enterobacter cloacae P99 class C serine-β-lactamase are unusual covalent inhibitors in that they target both active-site Ser and Lys residues, resulting in a cross-link consisting of only two atoms. Many clinically relevant metallo-β-lactamases have an analogous active-site Lys residue used to bind β-lactam substrates, suggesting a common site to target with covalent inhibitors. Here, we demonstrate that an O-aryloxycarbonyl hydroxamate inactivator of serine-β-lactamases can also serve as a classical affinity label for New Delhi metallo-β-lactamase-1 (NDM-1). Rapid dilution assays, site-directed mutagenesis, and global kinetic fitting are used to map covalent modification at Lys211 and determine KI (140 μM) and kinact (0.045 min-1) values. Mass spectrometry of the intact protein and the use of ultraviolet photodissociation for extensive fragmentation confirm stoichiometric covalent labeling that occurs specifically at Lys211. A 2.0 Å resolution X-ray crystal structure of inactivated NDM-1 reveals that the covalent adduct is bound at the substrate-binding site but is not directly coordinated to the active-site zinc cluster. These results indicate that Lys-targeted affinity labels might be a successful strategy for developing compounds that can inactivate both serine- and metallo-β-lactamases.
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Affiliation(s)
| | | | | | | | - R F Pratt
- Department of Chemistry , Wesleyan University , Middletown , Connecticut 06459 , United States
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17
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Liu F, McDonald M, Schwessinger B, Joe A, Pruitt R, Erickson T, Zhao X, Stewart V, Ronald PC. Variation and inheritance of the Xanthomonas raxX-raxSTAB gene cluster required for activation of XA21-mediated immunity. MOLECULAR PLANT PATHOLOGY 2019; 20:656-672. [PMID: 30773771 PMCID: PMC6637879 DOI: 10.1111/mpp.12783] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The rice XA21-mediated immune response is activated on recognition of the RaxX peptide produced by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). The 60-residue RaxX precursor is post-translationally modified to form a sulfated tyrosine peptide that shares sequence and functional similarity with the plant sulfated tyrosine (PSY) peptide hormones. The 5-kb raxX-raxSTAB gene cluster of Xoo encodes RaxX, the RaxST tyrosylprotein sulfotransferase, and the RaxA and RaxB components of a predicted type I secretion system. To assess raxX-raxSTAB gene cluster evolution and to determine its phylogenetic distribution, we first identified rax gene homologues in other genomes. We detected the complete raxX-raxSTAB gene cluster only in Xanthomonas spp., in five distinct lineages in addition to X. oryzae. The phylogenetic distribution of the raxX-raxSTAB gene cluster is consistent with the occurrence of multiple lateral (horizontal) gene transfer events during Xanthomonas speciation. RaxX natural variants contain a restricted set of missense substitutions, as expected if selection acts to maintain peptide hormone-like function. Indeed, eight RaxX variants tested all failed to activate the XA21-mediated immune response, yet retained peptide hormone activity. Together, these observations support the hypothesis that the XA21 receptor evolved specifically to recognize Xoo RaxX.
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Affiliation(s)
- Furong Liu
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Megan McDonald
- Research School of BiologyAustralian National UniversityCanberra0200Australia
| | - Benjamin Schwessinger
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
- Research School of BiologyAustralian National UniversityCanberra0200Australia
| | - Anna Joe
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Rory Pruitt
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Teresa Erickson
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Xiuxiang Zhao
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
| | - Valley Stewart
- Department of Microbiology & Molecular GeneticsUniversity of CaliforniaDavisCA95616USA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCA95616USA
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18
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Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptor. Proc Natl Acad Sci U S A 2019; 116:8525-8534. [PMID: 30948631 DOI: 10.1073/pnas.1818275116] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The rice immune receptor XA21 is activated by the sulfated microbial peptide required for activation of XA21-mediated immunity X (RaxX) produced by Xanthomonas oryzae pv. oryzae (Xoo). Mutational studies and targeted proteomics revealed that the RaxX precursor peptide (proRaxX) is processed and secreted by the protease/transporter RaxB, the function of which can be partially fulfilled by a noncognate peptidase-containing transporter component B (PctB). proRaxX is cleaved at a Gly-Gly motif, yielding a mature peptide that retains the necessary elements for RaxX function as an immunogen and host peptide hormone mimic. These results indicate that RaxX is a prokaryotic member of a previously unclassified and understudied group of eukaryotic tyrosine sulfated ribosomally synthesized, posttranslationally modified peptides (RiPPs). We further demonstrate that sulfated RaxX directly binds XA21 with high affinity. This work reveals a complete, previously uncharacterized biological process: bacterial RiPP biosynthesis, secretion, binding to a eukaryotic receptor, and triggering of a robust host immune response.
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19
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Kim H, Joe A, Lee M, Yang S, Ma X, Ronald PC, Lee I. A Genome-Scale Co-Functional Network of Xanthomonas Genes Can Accurately Reconstruct Regulatory Circuits Controlled by Two-Component Signaling Systems. Mol Cells 2019; 42:166-174. [PMID: 30759970 PMCID: PMC6399010 DOI: 10.14348/molcells.2018.0403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/09/2018] [Accepted: 12/19/2018] [Indexed: 01/24/2023] Open
Abstract
Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.
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Affiliation(s)
- Hanhae Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul,
Korea
- Bio and Basic Science R&D Coordination Division, Korea Institute of S&T Evaluation and Planning, Seoul,
Korea
| | - Anna Joe
- Department of Plant Pathology and the Genome Center, University of California, CA 95616,
USA
- Feedstocks Division, Joint Bioenergy Institute, CA 94608,
USA
| | - Muyoung Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul,
Korea
| | - Sunmo Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul,
Korea
| | - Xiaozhi Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou,
China
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome Center, University of California, CA 95616,
USA
- Feedstocks Division, Joint Bioenergy Institute, CA 94608,
USA
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul,
Korea
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20
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Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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21
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Greer SM, Sidoli S, Coradin M, Schack Jespersen M, Schwämmle V, Jensen ON, Garcia BA, Brodbelt JS. Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy. Anal Chem 2018; 90:10425-10433. [PMID: 30063333 PMCID: PMC6383154 DOI: 10.1021/acs.analchem.8b02320] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The ability to map combinatorial patterns of post-translational modifications (PTMs) of proteins remains challenging for traditional bottom-up mass spectrometry workflows. There are also hurdles associated with top-down approaches related to limited data analysis options for heavily modified proteoforms. These shortcomings have accelerated interest in middle-down MS methods that focus on analysis of large peptides generated by specific proteases in conjunction with validated bioinformatics strategies to allow quantification of isomeric histoforms. Mapping multiple PTMs simultaneously requires the ability to obtain high sequence coverage to allow confident localization of the modifications, and 193 nm ultraviolet photodissociation (UVPD) has been shown to cause extensive fragmentation for large peptides and proteins. Histones are an ideal system to test the ability of UVPD to characterize multiple modifications, as the combinations of PTMs are the underpinning of the biological significance of histones and at the same time create an imposing challenge for characterization. The present study focuses on applying 193 nm UVPD to the identification and localization of PTMs on histones by UVPD and comparison to a popular alternative, electron-transfer dissociation (ETD), via a high-throughput middle-down LC/MS/MS strategy. Histone Coder and IsoScale, bioinformatics tools for verification of PTM assignments and quantification of histone peptides, were adapted for UVPD data and applied in the present study. In total, over 300 modified forms were identified, and the distributions of PTMs were quantified between UVPD and ETD. Significant differences in patterns of PTMs were found for histones from HeLa cells prior to and after treatment with a deacetylase inhibitor. Additional fragment ion types generated by UVPD proved essential for extensive characterization of the most heavily modified forms (>5 PTMs).
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Affiliation(s)
- Sylvester M Greer
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Mariel Coradin
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Malena Schack Jespersen
- Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense , Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense , Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense , Denmark
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
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22
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Gallo C, Nuzzo G, d'Ippolito G, Manzo E, Sardo A, Fontana A. Sterol Sulfates and Sulfotransferases in Marine Diatoms. Methods Enzymol 2018; 605:101-138. [PMID: 29909823 DOI: 10.1016/bs.mie.2018.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Sterol sulfates are widely occurring molecules in marine organisms. Their importance has been so far underestimated although many of these compounds are crucial mediators of physiological and ecological functions in other organisms. Biosynthesis of sterol sulfates is controlled by cytosolic sulfotransferases (SULTs), a varied family of enzymes that catalyze the transfer of a sulfo residue (-SO3H) from the universal donor 3'-phosphoadenosine-5'-phosphosulfate to the hydroxyl function at C-3 of the steroid skeleton. The absence of molecular tools has been the main impediment to the development of a biosynthetic study of this class of compounds in marine organisms. In fact, there is very limited information about these enzymes in marine environments. SULT activity has, however, been reported in several marine species, and, recently, the production of sterol sulfates has been linked to the control of growth in marine diatoms. In this chapter, we describe methods for the study of sterol sulfates in this lineage of marine microalgae. The main aim is to provide the tools useful to deal with the biosynthesis and regulation of these compounds and to circumvent the bottleneck of the lack of molecular information. The protocols have been designed for marine diatoms, but most of the procedures can be used for other marine organisms.
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Affiliation(s)
- Carmela Gallo
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy
| | - Genoveffa Nuzzo
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy
| | - Giuliana d'Ippolito
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy.
| | - Emiliano Manzo
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy
| | - Angela Sardo
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy
| | - Angelo Fontana
- National Research Council of Italy, Institute of Biomolecular Chemistry, Pozzuoli, Naples, Italy.
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23
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Moreira IS, Bessa VS, Murgolo S, Piccirillo C, Mascolo G, Castro PML. Biodegradation of Diclofenac by the bacterial strain Labrys portucalensis F11. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 152:104-113. [PMID: 29407776 DOI: 10.1016/j.ecoenv.2018.01.040] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 06/07/2023]
Abstract
Diclofenac (DCF) is a widely used non-steroidal anti-inflammatory pharmaceutical which is detected in the environment at concentrations which can pose a threat to living organisms. In this study, biodegradation of DCF was assessed using the bacterial strain Labrys portucalensis F11. Biotransformation of 70% of DCF (1.7-34 μM), supplied as the sole carbon source, was achieved in 30 days. Complete degradation was reached via co-metabolism with acetate, over a period of 6 days for 1.7 µM and 25 days for 34 μM of DCF. The detection and identification of biodegradation intermediates was performed by UPLC-QTOF/MS/MS. The chemical structure of 12 metabolites is proposed. DCF degradation by strain F11 proceeds mainly by hydroxylation reactions; the formation of benzoquinone imine species seems to be a central step in the degradation pathway. Moreover, this is the first report that identified conjugated metabolites, resulting from sulfation reactions of DCF by bacteria. Stoichiometric liberation of chlorine and no detection of metabolites at the end of the experiments are strong indications of complete degradation of DCF by strain F11. To the best of our knowledge this is the first report that points to complete degradation of DCF by a single bacterial strain isolated from the environment.
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Affiliation(s)
- Irina S Moreira
- CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal.
| | - Vânia S Bessa
- CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Sapia Murgolo
- CNR, Istituto di Ricerca Sulle Acque, Via F. De Blasio 5, 70132 Bari, Italy
| | - Clara Piccirillo
- CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
| | - Giuseppe Mascolo
- CNR, Istituto di Ricerca Sulle Acque, Via F. De Blasio 5, 70132 Bari, Italy
| | - Paula M L Castro
- CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, 172, 4200-374 Porto, Portugal
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24
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The Ax21 protein influences virulence and biofilm formation in Stenotrophomonas maltophilia. Arch Microbiol 2017; 200:183-187. [PMID: 28965241 PMCID: PMC5758655 DOI: 10.1007/s00203-017-1433-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/07/2017] [Accepted: 09/19/2017] [Indexed: 01/01/2023]
Abstract
Stenotrophomonas maltophilia is an antibiotic-resistant Gram-negative pathogen, which is associated with hospital-acquired infection. The genome encodes a protein highly related to the Ax21 protein of Xanthomonas oryzae that is implicated in interactions of this plant pathogen with rice. Here, we report on the pleiotropic nature of ax21 mutation in S. maltophilia and the effects of addition of the Ax21 protein on the restoration of the wild-type phenotype. We show that loss by mutation of Ax21 leads to reduced motility, reduced biofilm formation, reduced tolerance to the antibiotic tobramycin and reduced virulence to larvae of Galleria mellonella, as well as alteration in the expression of specific genes associated with virulence or antibiotic resistance. Addition of the Ax21protein restored motility and the level of gene expression towards wild type. These findings are consistent with the notion that the Ax21 protein is involved in intraspecies communication, although other interpretations cannot be discounted.
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25
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Mayfield JE, Robinson MR, Cotham VC, Irani S, Matthews WL, Ram A, Gilmour DS, Cannon JR, Zhang YJ, Brodbelt JS. Mapping the Phosphorylation Pattern of Drosophila melanogaster RNA Polymerase II Carboxyl-Terminal Domain Using Ultraviolet Photodissociation Mass Spectrometry. ACS Chem Biol 2017; 12:153-162. [PMID: 28103682 DOI: 10.1021/acschembio.6b00729] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Phosphorylation of the C-terminal domain of RNA polymerase II (CTD) plays an essential role in eukaryotic transcription by recruiting transcriptional regulatory factors to the active polymerase. However, the scarcity of basic residues and repetitive nature of the CTD sequence impose a huge challenge for site-specific characterization of phosphorylation, hindering our understanding of this crucial biological process. Herein, we apply LC-UVPD-MS methods to analyze post-translational modification along native sequence CTDs. Application of our method to the Drosophila melanogaster CTD reveals the phosphorylation pattern of this model organism for the first time. The divergent nature of fly CTD allows us to derive rules defining how flanking residues affect phosphorylation choice by CTD kinases. Our data support the use of LC-UVPD-MS to decipher the CTD code and determine rules that program its function.
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Affiliation(s)
| | | | | | | | | | | | - David S. Gilmour
- Department
of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802, United States
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26
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27
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Robinson MR, Brodbelt JS. Integrating Weak Anion Exchange and Ultraviolet Photodissociation Mass Spectrometry with Strategic Modulation of Peptide Basicity for the Enrichment of Sulfopeptides. Anal Chem 2016; 88:11037-11045. [PMID: 27768275 DOI: 10.1021/acs.analchem.6b02899] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Tyrosine sulfation is an important post-translational modification but remains difficult to detect in biological samples owing to its low stoichiometric abundance and the lack of effective enrichment methods. In the present study, weak anion exchange (WAX) is evaluated for the enrichment of sulfopeptides that have been modified via carbamylation to convert all primary amines to less basic carbamates. The decrease in basicity enhanced the binding of carbamylated sulfopeptides to WAX resin relative to nonsulfated peptides. Upon elution and electrospray ionization in the negative mode, ultraviolet photodissociation (UVPD) was applied for peptide sequencing. Application of the method to a tryptic digest of bovine coagulation factor V resulted in identification of sulfation on tyrosine 1513.
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Affiliation(s)
- Michelle R Robinson
- Department of Chemistry, The University of Texas , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas , Austin, Texas 78712, United States
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28
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Restriction of Aerobic Metabolism by Acquired or Innate Arylsulfatase B Deficiency: A New Approach to the Warburg Effect. Sci Rep 2016; 6:32885. [PMID: 27605497 PMCID: PMC5015117 DOI: 10.1038/srep32885] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/16/2016] [Indexed: 11/09/2022] Open
Abstract
Aerobic respiration is required for optimal efficiency of metabolism in mammalian cells. Under circumstances when oxygen utilization is impaired, cells survive by anerobic metabolism. The malignant cell has cultivated the use of anerobic metabolism in an aerobic environment, the Warburg effect, but the explanation for this preference is not clear. This paper presents evidence that deficiency of the enzyme arylsulfatase B (ARSB; N-acetylgalactosamine 4-sulfatase), either innate or acquired, helps to explain the Warburg phenomenon. ARSB is the enzyme that removes 4-sulfate groups from the non-reducing end of chondroitin 4-sulfate and dermatan sulfate. Previous reports indicated reduced ARSB activity in malignancy and replication of the effects of hypoxia by decline in ARSB. Hypoxia reduced ARSB activity, since molecular oxygen is needed for post-translational modification of ARSB. In this report, studies were performed in human HepG2 cells and in hepatocytes from ARSB-deficient and normal C57BL/6J control mice. Decline of ARSB, in the presence of oxygen, profoundly reduced the oxygen consumption rate and increased the extracellular acidification rate, indicating preference for aerobic glycolysis. Specific study findings indicate that decline in ARSB activity enhanced aerobic glycolysis and impaired normal redox processes, consistent with a critical role of ARSB and sulfate reduction in mammalian metabolism.
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29
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Robinson MR, Taliaferro JM, Dalby KN, Brodbelt JS. 193 nm Ultraviolet Photodissociation Mass Spectrometry for Phosphopeptide Characterization in the Positive and Negative Ion Modes. J Proteome Res 2016; 15:2739-48. [PMID: 27425180 DOI: 10.1021/acs.jproteome.6b00289] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) have permitted phosphoproteomic analysis on a grand scale, but ongoing challenges specifically associated with confident phosphate localization continue to motivate the development of new fragmentation techniques. In the present study, ultraviolet photodissociation (UVPD) at 193 nm is evaluated for the characterization of phosphopeptides in both positive and negative ion modes. Compared to the more standard higher energy collisional dissociation (HCD), UVPD provided more extensive fragmentation with improved phosphate retention on product ions. Negative mode UVPD showed particular merit for detecting and sequencing highly acidic phosphopeptides from alpha and beta casein, but was not as robust for larger scale analysis because of lower ionization efficiencies in the negative mode. HeLa and HCC70 cell lysates were analyzed by both UVPD and HCD. While HCD identified more phosphopeptides and proteins compared to UVPD, the unique matches from UVPD analysis could be combined with the HCD data set to improve the overall depth of coverage compared to either method alone.
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Affiliation(s)
- Michelle R Robinson
- Department of Chemistry, and ‡Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, The University of Texas Austin, Texas 78712, United States
| | - Juliana M Taliaferro
- Department of Chemistry, and ‡Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, The University of Texas Austin, Texas 78712, United States
| | - Kevin N Dalby
- Department of Chemistry, and ‡Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, The University of Texas Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, and ‡Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, The University of Texas Austin, Texas 78712, United States
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Park HJ, Park CJ, Bae N, Han SW. Deciphering the Role of Tyrosine Sulfation in Xanthomonas oryzae pv. oryzae Using Shotgun Proteomic Analysis. THE PLANT PATHOLOGY JOURNAL 2016; 32:266-272. [PMID: 27298602 PMCID: PMC4892823 DOI: 10.5423/ppj.nt.12.2015.0273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/23/2016] [Accepted: 02/23/2016] [Indexed: 05/31/2023]
Abstract
A bacterial tyrosine sulfotransferase, RaxST, is required for activation of rice XA21-mediated immunity, and it catalyzes sulfation of tyrosine residues of Omp1X and RaxX in Xanthomonas oryzae pv. oryzae, a causal agent of bacterial blight in rice. Although RaxST is biochemically well-characterized, biological functions of tyrosine sulfation have not been fully elucidated. We compared protein expression patterns between the wildtype and a raxST knockout mutant using shotgun proteomic analysis. Forty nine proteins displayed a more than 1.5-fold difference in their expression between the wildtype and the mutant strains. Clusters of orthologous groups analysis revealed that proteins involved in cell motility were most abundant, and phenotypic observation also showed that the twitching motility of the mutant was dramatically changed. These results indicate that tyrosine sulfation by RaxST is essential for Xoo movement, and they provide new insights into the biological roles of RaxST in cellular processes.
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Affiliation(s)
- Hye-Jee Park
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17546,
Korea
| | - Chang-Jin Park
- Department of Plant Biotechnology and Plant Engineering Research Institute, Sejong University, Seoul 05006,
Korea
| | - Nahee Bae
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17546,
Korea
| | - Sang-Wook Han
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17546,
Korea
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31
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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32
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Schwessinger B, Li X, Ellinghaus TL, Chan LJG, Wei T, Joe A, Thomas N, Pruitt R, Adams PD, Chern MS, Petzold CJ, Liu CC, Ronald PC. A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection. Integr Biol (Camb) 2015; 8:542-5. [PMID: 26611838 DOI: 10.1039/c5ib00232j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Posttranslational modification (PTM) of proteins and peptides is important for diverse biological processes in plants and animals. The paucity of heterologous expression systems for PTMs and the technical challenges associated with chemical synthesis of these modified proteins has limited detailed molecular characterization and therapeutic applications. Here we describe an optimized system for expression of tyrosine-sulfated proteins in Escherichia coli and its application in a bio-based crop protection strategy in rice.
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Affiliation(s)
- Benjamin Schwessinger
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA.
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33
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Vale N, Carvalho Veloso R, Gomes P. Exploring the Solid-Phase Synthesis of Sulfotyrosine Peptides. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500715] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Pruitt RN, Schwessinger B, Joe A, Thomas N, Liu F, Albert M, Robinson MR, Chan LJG, Luu DD, Chen H, Bahar O, Daudi A, De Vleesschauwer D, Caddell D, Zhang W, Zhao X, Li X, Heazlewood JL, Ruan D, Majumder D, Chern M, Kalbacher H, Midha S, Patil PB, Sonti RV, Petzold CJ, Liu CC, Brodbelt JS, Felix G, Ronald PC. The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium. SCIENCE ADVANCES 2015; 1:e1500245. [PMID: 26601222 PMCID: PMC4646787 DOI: 10.1126/sciadv.1500245] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/14/2015] [Indexed: 05/18/2023]
Abstract
Surveillance of the extracellular environment by immune receptors is of central importance to eukaryotic survival. The rice receptor kinase XA21, which confers robust resistance to most strains of the Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo), is representative of a large class of cell surface immune receptors in plants and animals. We report the identification of a previously undescribed Xoo protein, called RaxX, which is required for activation of XA21-mediated immunity. Xoo strains that lack RaxX, or carry mutations in the single RaxX tyrosine residue (Y41), are able to evade XA21-mediated immunity. Y41 of RaxX is sulfated by the prokaryotic tyrosine sulfotransferase RaxST. Sulfated, but not nonsulfated, RaxX triggers hallmarks of the plant immune response in an XA21-dependent manner. A sulfated, 21-amino acid synthetic RaxX peptide (RaxX21-sY) is sufficient for this activity. Xoo field isolates that overcome XA21-mediated immunity encode an alternate raxX allele, suggesting that coevolutionary interactions between host and pathogen contribute to RaxX diversification. RaxX is highly conserved in many plant pathogenic Xanthomonas species. The new insights gained from the discovery and characterization of the sulfated protein, RaxX, can be applied to the development of resistant crop varieties and therapeutic reagents that have the potential to block microbial infection of both plants and animals.
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Affiliation(s)
- Rory N. Pruitt
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Benjamin Schwessinger
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The Australian National University, Research School of Biology, Acton ACT 2601, Australia
- Corresponding author. E-mail: (B.S.); (P.C.R.)
| | - Anna Joe
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas Thomas
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Furong Liu
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Markus Albert
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
| | - Michelle R. Robinson
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
| | - Leanne Jade G. Chan
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dee Dee Luu
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Huamin Chen
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Ofir Bahar
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Arsalan Daudi
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - David De Vleesschauwer
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Daniel Caddell
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Weiguo Zhang
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Xiuxiang Zhao
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Xiang Li
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Joshua L. Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deling Ruan
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dipali Majumder
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Mawsheng Chern
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tübingen, 72074 Tübingen, Germany
| | - Samriti Midha
- Council of Scientific & Industrial Research (CSIR)–Institute of Microbial Technology, Chandigarh 160036, India
| | - Prabhu B. Patil
- Council of Scientific & Industrial Research (CSIR)–Institute of Microbial Technology, Chandigarh 160036, India
| | - Ramesh V. Sonti
- CSIR–Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christopher J. Petzold
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Georg Felix
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Corresponding author. E-mail: (B.S.); (P.C.R.)
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Greer SM, Parker WR, Brodbelt JS. Impact of Protease on Ultraviolet Photodissociation Mass Spectrometry for Bottom-up Proteomics. J Proteome Res 2015; 14:2626-32. [DOI: 10.1021/acs.jproteome.5b00165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
| | - W. Ryan Parker
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
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36
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Greer S, Cannon JR, Brodbelt JS. Improvement of shotgun proteomics in the negative mode by carbamylation of peptides and ultraviolet photodissociation mass spectrometry. Anal Chem 2014; 86:12285-90. [PMID: 25420043 PMCID: PMC4270407 DOI: 10.1021/ac5035314] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Accepted: 11/24/2014] [Indexed: 02/08/2023]
Abstract
Although acidic peptides compose a substantial portion of many proteomes, their less efficient ionization during positive polarity electrospray ionization (ESI) impedes their detection in bottom-up mass spectrometry workflows. We have implemented a derivatization strategy based on carbamylation which converts basic amine sites (Lys, N-termini) to less basic amides for enhanced analysis in the negative mode. Ultraviolet photodissociation (UVPD) is used to analyze the resulting peptide anions, as demonstrated for tryptic peptides from bovine serum albumin and Halobacterium salinarum in a high throughput liquid chromatography/tandem mass spectrometry (LC/MS/MS) mode. LC/UVPD-MS of a carbamylated H. salinarum digest resulted in 45% more identified peptides and 25% more proteins compared to the unmodified digest analyzed in the negative mode.
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Affiliation(s)
- Sylvester
M. Greer
- Department of Chemistry, University of
Texas at Austin, Austin, Texas 78712, United
States
| | - Joe R. Cannon
- Department of Chemistry, University of
Texas at Austin, Austin, Texas 78712, United
States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of
Texas at Austin, Austin, Texas 78712, United
States
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37
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Nedumpully-Govindan P, Li L, Alexov EG, Blenner MA, Ding F. Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. Bioinformatics 2014; 30:2302-9. [PMID: 24794930 DOI: 10.1093/bioinformatics/btu309] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Tyrosine sulfation is a type of post-translational modification (PTM) catalyzed by tyrosylprotein sulfotransferases (TPST). The modification plays a crucial role in mediating protein-protein interactions in many biologically important processes. There is no well-defined sequence motif for TPST sulfation, and the underlying determinants of TPST sulfation specificity remains elusive. Here, we perform molecular modeling to uncover the structural and energetic determinants of TPST sulfation specificity. RESULTS We estimate the binding affinities between TPST and peptides around tyrosines of both sulfated and non-sulfated proteins to differentiate them. We find that better differentiation is achieved after including energy costs associated with local unfolding of the tyrosine-containing peptide in a host protein, which depends on both the peptide's secondary structures and solvent accessibility. Local unfolding renders buried peptide-with ordered structures-thermodynamically available for TPST binding. Our results suggest that both thermodynamic availability of the peptide and its binding affinity to the enzyme are important for TPST sulfation specificity, and their interplay results into great variations in sequences and structures of sulfated peptides. We expect our method to be useful in predicting potential sulfation sites and transferable to other TPST variants. Our study may also shed light on other PTM systems without well-defined sequence and structural specificities. AVAILABILITY AND IMPLEMENTATION All the data and scripts used in the work are available at http://dlab.clemson.edu/research/Sulfation.
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Affiliation(s)
- Praveen Nedumpully-Govindan
- Department of Physics and Astronomy and Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA
| | - Lin Li
- Department of Physics and Astronomy and Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA
| | - Emil G Alexov
- Department of Physics and Astronomy and Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA
| | - Mark A Blenner
- Department of Physics and Astronomy and Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA
| | - Feng Ding
- Department of Physics and Astronomy and Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA
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38
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Robinson MR, Moore KL, Brodbelt JS. Direct identification of tyrosine sulfation by using ultraviolet photodissociation mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1461-71. [PMID: 24845354 PMCID: PMC4108549 DOI: 10.1007/s13361-014-0910-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/30/2014] [Accepted: 04/05/2014] [Indexed: 05/25/2023]
Abstract
Sulfation is a common post-translational modification of tyrosine residues in eukaryotes; however, detection using traditional liquid chromatography-mass spectrometry (LC-MS) methods is challenging based on poor ionization efficiency in the positive ion mode and facile neutral loss upon collisional activation. In the present study, 193 nm ultraviolet photodissociation (UVPD) is applied to sulfopeptide anions to generate diagnostic sequence ions, which do not undergo appreciable neutral loss of sulfate even using higher energy photoirradiation parameters. At the same time, neutral loss of SO₃ is observed from the precursor and charge-reduced precursor ions, a spectral feature that is useful for differentiating tyrosine sulfation from the nominally isobaric tyrosine phosphorylation. LC-MS detection limits for UVPD analysis in the negative mode were determined to be around 100 fmol for three sulfated peptides, caerulein, cionin, and leu-enkephalin. The LC-UVPD-MS method was applied for analysis of bovine fibrinogen, and its key sulfated peptide was confidently identified.
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Affiliation(s)
- Michelle R Robinson
- Department of Chemistry, The University of Texas at Austin, 1 University Station A5300, Austin, TX, 78712, USA
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39
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Tripathi JN, Lorenzen J, Bahar O, Ronald P, Tripathi L. Transgenic expression of the rice Xa21 pattern-recognition receptor in banana (Musa sp.) confers resistance to Xanthomonas campestris pv. musacearum. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:663-73. [PMID: 24612254 PMCID: PMC4110157 DOI: 10.1111/pbi.12170] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/20/2013] [Accepted: 01/09/2014] [Indexed: 05/04/2023]
Abstract
Banana Xanthomonas wilt (BXW), caused by the bacterium Xanthomonas campestris pv. musacearum (Xcm), is the most devastating disease of banana in east and central Africa. The spread of BXW threatens the livelihood of millions of African farmers who depend on banana for food security and income. There are no commercial chemicals, biocontrol agents or resistant cultivars available to control BXW. Here, we take advantage of the robust resistance conferred by the rice pattern-recognition receptor (PRR), XA21, to the rice pathogen Xanthomonas oryzae pv. oryzae (Xoo). We identified a set of genes required for activation of Xa21-mediated immunity (rax) that were conserved in both Xoo and Xcm. Based on the conservation, we hypothesized that intergeneric transfer of Xa21 would confer resistance to Xcm. We evaluated 25 transgenic lines of the banana cultivar 'Gonja manjaya' (AAB) using a rapid bioassay and 12 transgenic lines in the glasshouse for resistance against Xcm. About 50% of the transgenic lines showed complete resistance to Xcm in both assays. In contrast, all of the nontransgenic control plants showed severe symptoms that progressed to complete wilting. These results indicate that the constitutive expression of the rice Xa21 gene in banana results in enhanced resistance against Xcm. Furthermore, this work demonstrates the feasibility of PRR gene transfer between monocotyledonous species and provides a valuable new tool for controlling the BXW pandemic of banana, a staple food for 100 million people in east Africa.
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Affiliation(s)
| | - Jim Lorenzen
- International Institute of Tropical Agriculture (IITA), Arusha, Tanzania
| | - Ofir Bahar
- Department of Pathology and the Genome Center, University of California, Davis, USA
| | - Pamela Ronald
- Department of Pathology and the Genome Center, University of California, Davis, USA
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
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40
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Brodbelt JS. Photodissociation mass spectrometry: new tools for characterization of biological molecules. Chem Soc Rev 2014; 43:2757-83. [PMID: 24481009 PMCID: PMC3966968 DOI: 10.1039/c3cs60444f] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photodissociation mass spectrometry combines the ability to activate and fragment ions using photons with the sensitive detection of the resulting product ions by mass spectrometry. This combination affords a versatile tool for characterization of biological molecules. The scope and breadth of photodissociation mass spectrometry have increased substantially over the past decade as new research groups have entered the field and developed a number of innovative applications that illustrate the ability of photodissociation to produce rich fragmentation patterns, to cleave bonds selectively, and to target specific molecules based on incorporation of chromophores. This review focuses on many of the key developments in photodissociation mass spectrometry over the past decade with a particular emphasis on its applications to biological molecules.
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41
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Gault J, Malosse C, Machata S, Millien C, Podglajen I, Ploy MC, Costello CE, Duménil G, Chamot-Rooke J. Complete posttranslational modification mapping of pathogenic Neisseria meningitidis pilins requires top-down mass spectrometry. Proteomics 2014; 14:1141-51. [PMID: 24459079 DOI: 10.1002/pmic.201300394] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 09/04/2013] [Accepted: 10/11/2013] [Indexed: 12/13/2022]
Abstract
In pathogenic bacteria, posttranslationally modified proteins have been found to promote bacterial survival, replication, and evasion from the host immune system. In the human pathogen Neisseria meningitidis, the protein PilE (15-18 kDa) is the major building block of type IV pili, extracellular filamentous organelles that play a major role in mediating pathogenesis. Previous reports have shown that PilE can be expressed as a number of different proteoforms, each harboring its own set of PTMs and that specific proteoforms are key in promoting bacterial virulence. Efficient tools that allow complete PTM mapping of proteins involved in bacterial infection are therefore strongly needed. As we show in this study, a simple combination of mass profiling and bottom-up proteomics is fundamentally unable to achieve this goal when more than two proteoforms are present simultaneously. In a N. meningitidis strain isolated from a patient with meningitis, mass profiling revealed the presence of four major proteoforms of PilE, in a 1:1:1:1 ratio. Due to the complexity of the sample, a top-down approach was required to achieve complete PTM mapping for all four proteoforms, highlighting an unprecedented extent of glycosylation. Top-down MS therefore appears to be a promising tool for the analysis of highly posttranslationally modified proteins involved in bacterial virulence.
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Affiliation(s)
- Joseph Gault
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France; Laboratoire des Mécanismes Réactionnels (DCMR), Département de Chimie, École Polytechnique, CNRS, Palaiseau, France
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42
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Bahar O, Pruitt R, Luu DD, Schwessinger B, Daudi A, Liu F, Ruan R, Fontaine-Bodin L, Koebnik R, Ronald P. The Xanthomonas Ax21 protein is processed by the general secretory system and is secreted in association with outer membrane vesicles. PeerJ 2014; 2:e242. [PMID: 24482761 PMCID: PMC3897388 DOI: 10.7717/peerj.242] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 12/19/2013] [Indexed: 01/05/2023] Open
Abstract
Pattern recognition receptors (PRRs) play an important role in detecting invading pathogens and mounting a robust defense response to restrict infection. In rice, one of the best characterized PRRs is XA21, a leucine rich repeat receptor-like kinase that confers broad-spectrum resistance to multiple strains of the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo). In 2009 we reported that an Xoo protein, called Ax21, is secreted by a type I-secretion system and that it serves to activate XA21-mediated immunity. This report has recently been retracted. Here we present data that corrects our previous model. We first show that Ax21 secretion does not depend on the predicted type I secretion system and that it is processed by the general secretion (Sec) system. We further show that Ax21 is an outer membrane protein, secreted in association with outer membrane vesicles. Finally, we provide data showing that ax21 knockout strains do not overcome XA21-mediated immunity.
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Affiliation(s)
- Ofir Bahar
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
| | - Rory Pruitt
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
| | - Dee Dee Luu
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
| | - Benjamin Schwessinger
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
| | - Arsalan Daudi
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
| | - Furong Liu
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
| | - Randy Ruan
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA
| | - Lisa Fontaine-Bodin
- UMR 186 IRD-Cirad-Université Montpellier 2 "Résistance des Plantes aux Bioaggresseurs", Montpellier, France
| | - Ralf Koebnik
- UMR 186 IRD-Cirad-Université Montpellier 2 "Résistance des Plantes aux Bioaggresseurs", Montpellier, France
| | - Pamela Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, USA.,UMR 186 IRD-Cirad-Université Montpellier 2 "Résistance des Plantes aux Bioaggresseurs", Montpellier, France
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43
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Ronald PC. The Role of RaxST, a Prokaryotic Sulfotransferase, and RaxABC, a Putative Type I Secretion System, in Activation of the Rice XA21-Mediated Immune Response. SCIENTIFICA 2014; 2014:532816. [PMID: 25386383 PMCID: PMC4216712 DOI: 10.1155/2014/532816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 05/07/2023]
Abstract
Tyrosine sulfation is an important posttranslational modification that determines the outcome of serious diseases in plants and animals. We have recently demonstrated that the plant pathogen Xanthomonas oryzae pv. oryzae (Xoo) carries a functional sulfotransferase (RaxST). raxST is required for activation of rice Xa21-mediated immunity indicating the critical, but unknown, function of raxST in mediating the Xoo/rice interaction. The raxST gene resides in the same operon (raxSTAB) as components of a predicted type I secretion and processing system (RaxA and RaxB). These observations suggest a model where RaxST sulfates a molecule that contains a leader peptide, which is cleaved by the peptidase domain of the RaxB protein and secreted outside the bacterial cell by the RaxABC T1SS.
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Affiliation(s)
- Pamela C. Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
- *Pamela C. Ronald:
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Arrieta-Ortiz ML, Rodríguez-R LM, Pérez-Quintero ÁL, Poulin L, Díaz AC, Arias Rojas N, Trujillo C, Restrepo Benavides M, Bart R, Boch J, Boureau T, Darrasse A, David P, Dugé de Bernonville T, Fontanilla P, Gagnevin L, Guérin F, Jacques MA, Lauber E, Lefeuvre P, Medina C, Medina E, Montenegro N, Muñoz Bodnar A, Noël LD, Ortiz Quiñones JF, Osorio D, Pardo C, Patil PB, Poussier S, Pruvost O, Robène-Soustrade I, Ryan RP, Tabima J, Urrego Morales OG, Vernière C, Carrere S, Verdier V, Szurek B, Restrepo S, López C, Koebnik R, Bernal A. Genomic survey of pathogenicity determinants and VNTR markers in the cassava bacterial pathogen Xanthomonas axonopodis pv. Manihotis strain CIO151. PLoS One 2013; 8:e79704. [PMID: 24278159 PMCID: PMC3838355 DOI: 10.1371/journal.pone.0079704] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/24/2013] [Indexed: 11/24/2022] Open
Abstract
Xanthomonas axonopodis pv. manihotis (Xam) is the causal agent of bacterial blight of cassava, which is among the main components of human diet in Africa and South America. Current information about the molecular pathogenicity factors involved in the infection process of this organism is limited. Previous studies in other bacteria in this genus suggest that advanced draft genome sequences are valuable resources for molecular studies on their interaction with plants and could provide valuable tools for diagnostics and detection. Here we have generated the first manually annotated high-quality draft genome sequence of Xam strain CIO151. Its genomic structure is similar to that of other xanthomonads, especially Xanthomonas euvesicatoria and Xanthomonas citri pv. citri species. Several putative pathogenicity factors were identified, including type III effectors, cell wall-degrading enzymes and clusters encoding protein secretion systems. Specific characteristics in this genome include changes in the xanthomonadin cluster that could explain the lack of typical yellow color in all strains of this pathovar and the presence of 50 regions in the genome with atypical nucleotide composition. The genome sequence was used to predict and evaluate 22 variable number of tandem repeat (VNTR) loci that were subsequently demonstrated as polymorphic in representative Xam strains. Our results demonstrate that Xanthomonas axonopodis pv. manihotis strain CIO151 possesses ten clusters of pathogenicity factors conserved within the genus Xanthomonas. We report 126 genes that are potentially unique to Xam, as well as potential horizontal transfer events in the history of the genome. The relation of these regions with virulence and pathogenicity could explain several aspects of the biology of this pathogen, including its ability to colonize both vascular and non-vascular tissues of cassava plants. A set of 16 robust, polymorphic VNTR loci will be useful to develop a multi-locus VNTR analysis scheme for epidemiological surveillance of this disease.
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Affiliation(s)
- Mario L. Arrieta-Ortiz
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Luis M. Rodríguez-R
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | | | - Lucie Poulin
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Ana C. Díaz
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Nathalia Arias Rojas
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Cesar Trujillo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | | | - Rebecca Bart
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Jens Boch
- Department of Genetics, Martin Luther University, Halle-Wittenberg, Germany
| | - Tristan Boureau
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Armelle Darrasse
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Perrine David
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Thomas Dugé de Bernonville
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Paula Fontanilla
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Lionel Gagnevin
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Fabien Guérin
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Marie-Agnès Jacques
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
| | - Emmanuelle Lauber
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Pierre Lefeuvre
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Cesar Medina
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Edgar Medina
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Nathaly Montenegro
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Alejandra Muñoz Bodnar
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Laurent D. Noël
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Juan F. Ortiz Quiñones
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniela Osorio
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Carolina Pardo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Prabhu B. Patil
- Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh, India
| | - Stéphane Poussier
- Institut National de la Recherche Agronomique, UMR45 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 Quasav, PRES L'UNAM, Beaucouzé, France
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Beaucouzé, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
| | - Olivier Pruvost
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Isabelle Robène-Soustrade
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Robert P. Ryan
- College of Life Sciences, University of Dundee, Dundee, Scotland
| | - Javier Tabima
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Oscar G. Urrego Morales
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Christian Vernière
- Unite Mixte de Recherche Peuplement Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération internationale en recherche agronomique pour le développement, La Réunion, France
| | - Sébastien Carrere
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan-Microorganismes, Institut National de la Recherche Agronomique. Toulouse, France
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 2594, Centre National de la Recherche Scientifique, Castanet-Tolosan, France
| | - Valérie Verdier
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado, United States of America
| | - Boris Szurek
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
| | - Camilo López
- Manihot-Biotec, Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Ralf Koebnik
- Unité Mixte de Recherche Résistance des Plantes aux Bioaggresseurs, Institut de Recherche pour le Développement, Montpellier, France
| | - Adriana Bernal
- Laboratorio de Micología y Fitopatología Uniandes (LAMFU), Universidad de Los Andes, Bogotá, Colombia
- * E-mail:
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Ellefson JW, Meyer AJ, Hughes RA, Cannon JR, Brodbelt JS, Ellington AD. Directed evolution of genetic parts and circuits by compartmentalized partnered replication. Nat Biotechnol 2013; 32:97-101. [DOI: 10.1038/nbt.2714] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/05/2013] [Indexed: 11/09/2022]
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Robotham SA, Kluwe C, Cannon JR, Ellington A, Brodbelt JS. De novo sequencing of peptides using selective 351 nm ultraviolet photodissociation mass spectrometry. Anal Chem 2013; 85:9832-8. [PMID: 24050806 DOI: 10.1021/ac402309h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Although in silico database search methods remain more popular for shotgun proteomics methods, de novo sequencing offers the ability to identify peptides derived from proteins lacking sequenced genomes and ones with subtle splice variants or truncations. Ultraviolet photodissociation (UVPD) of peptides derivatized by selective attachment of a chromophore at the N-terminus generates a characteristic series of y ions. The UVPD spectra of the chromophore-labeled peptides are simplified and thus amenable to de novo sequencing. This method resulted in an observed sequence coverage of 79% for cytochrome C (eight peptides), 47% for β-lactoglobulin (five peptides), 25% for carbonic anhydrase (six peptides), and 51% for bovine serum albumin (33 peptides). This strategy also allowed differentiation of proteins with high sequence homology as evidenced by de novo sequencing of two variants of green fluorescent protein.
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Affiliation(s)
- Scott A Robotham
- Department of Chemistry, University of Texas , Austin, Texas 78712, United States
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Luo Y, Yogesha SD, Cannon JR, Yan W, Ellington AD, Brodbelt JS, Zhang Y. novel modifications on C-terminal domain of RNA polymerase II can fine-tune the phosphatase activity of Ssu72. ACS Chem Biol 2013; 8:2042-52. [PMID: 23844594 DOI: 10.1021/cb400229c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The C-terminal domain of RNA polymerase II (CTD) modulates the process of transcription through sequential phosphorylation/dephosphorylation of its heptide repeats, through which it recruits various transcription regulators. Ssu72 is the first characterized cis-specific CTD phosphatase that dephosphorylates Ser5 with a requirement for the adjacent Pro6 in a cis conformation. The recent discovery of Thr4 phosphorylation in the CTD calls into question whether such a modification can interfere with Ssu72 binding via the elimination of a conserved intramolecular hydrogen bond in the CTD that is potentially essential for recognition. To test if Thr4 phosphorylation will abolish Ser5 dephosphorylation by Ssu72, we determined the kinetic and structural properties of Drosophila Ssu72-symplekin in complex with the CTD peptide with consecutive phosphorylated Thr4 and Ser5. Our mass spectrometric and kinetic data established that Ssu72 does not dephosphorylate Thr4, but the existence of phosphoryl-Thr4 next to Ser5 reduces the activity of Ssu72 toward the CTD peptide by 4-fold. To our surprise, even though the intramolecular hydrogen bond is eliminated due to the phosphorylation of Thr4, the CTD adopts an almost identical conformation to be recognized by Ssu72 with Ser5 phosphorylated alone or both Thr4/Ser5 phosphorylated. Our results indicate that Thr4 phosphorylation will not abolish the essential Ssu72 activity, which is needed for cell survival. Instead, the phosphatase activity of Ssu72 is fine-tuned by Thr4 phosphorylation and eventually may lead to changes in transcription. Overall, we report the first case of structural and kinetic effects of phosphorylated Thr4 on CTD modifying enzymes. Our results support a model in which a combinatorial cascade of CTD modification can modulate transcription.
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Affiliation(s)
- Yonghua Luo
- Department
of Chemistry and Biochemistry and ‡Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin,
Texas 78712, United States
| | - S. D. Yogesha
- Department
of Chemistry and Biochemistry and ‡Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin,
Texas 78712, United States
| | - Joe R. Cannon
- Department
of Chemistry and Biochemistry and ‡Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin,
Texas 78712, United States
| | - Wupeng Yan
- Department
of Chemistry and Biochemistry and ‡Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin,
Texas 78712, United States
| | - Andrew D. Ellington
- Department
of Chemistry and Biochemistry and ‡Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin,
Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department
of Chemistry and Biochemistry and ‡Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin,
Texas 78712, United States
| | - Yan Zhang
- Department
of Chemistry and Biochemistry and ‡Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin,
Texas 78712, United States
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48
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Madsen JA, Ko BJ, Xu H, Iwashkiw JA, Robotham SA, Shaw JB, Feldman MF, Brodbelt JS. Concurrent automated sequencing of the glycan and peptide portions of O-linked glycopeptide anions by ultraviolet photodissociation mass spectrometry. Anal Chem 2013; 85:9253-61. [PMID: 24006841 DOI: 10.1021/ac4021177] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
O-Glycopeptides are often acidic owing to the frequent occurrence of acidic saccharides in the glycan, rendering traditional proteomic workflows that rely on positive mode tandem mass spectrometry (MS/MS) less effective. In this report, we demonstrate the utility of negative mode ultraviolet photodissociation (UVPD) MS for the characterization of acidic O-linked glycopeptide anions. This method was evaluated for a series of singly and multiply deprotonated glycopeptides from the model glycoprotein kappa casein, resulting in production of both peptide and glycan product ions that afforded 100% sequence coverage of the peptide and glycan moieties from a single MS/MS event. The most abundant and frequent peptide sequence ions were a/x-type products which, importantly, were found to retain the labile glycan modifications. The glycan-specific ions mainly arose from glycosidic bond cleavages (B, Y, C, and Z ions) in addition to some less common cross-ring cleavages. On the basis of the UVPD fragmentation patterns, an automated database searching strategy (based on the MassMatrix algorithm) was designed that is specific for the analysis of glycopeptide anions by UVPD. This algorithm was used to identify glycopeptides from mixtures of glycosylated and nonglycosylated peptides, sequence both glycan and peptide moieties simultaneously, and pinpoint the correct site(s) of glycosylation. This methodology was applied to uncover novel site-specificity of the O-linked glycosylated OmpA/MotB from the "superbug" A. baumannii to help aid in the elucidation of the functional role that protein glycosylation plays in pathogenesis.
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Affiliation(s)
- James A Madsen
- Department of Chemistry, The University of Texas at Austin , 1 University Station A5300, Austin, Texas, 78712 United States
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Henderson JC, O'Brien JP, Brodbelt JS, Trent MS. Isolation and chemical characterization of lipid A from gram-negative bacteria. J Vis Exp 2013:e50623. [PMID: 24084191 DOI: 10.3791/50623] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Lipopolysaccharide (LPS) is the major cell surface molecule of gram-negative bacteria, deposited on the outer leaflet of the outer membrane bilayer. LPS can be subdivided into three domains: the distal O-polysaccharide, a core oligosaccharide, and the lipid A domain consisting of a lipid A molecular species and 3-deoxy-D-manno-oct-2-ulosonic acid residues (Kdo). The lipid A domain is the only component essential for bacterial cell survival. Following its synthesis, lipid A is chemically modified in response to environmental stresses such as pH or temperature, to promote resistance to antibiotic compounds, and to evade recognition by mediators of the host innate immune response. The following protocol details the small- and large-scale isolation of lipid A from gram-negative bacteria. Isolated material is then chemically characterized by thin layer chromatography (TLC) or mass-spectrometry (MS). In addition to matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS, we also describe tandem MS protocols for analyzing lipid A molecular species using electrospray ionization (ESI) coupled to collision induced dissociation (CID) and newly employed ultraviolet photodissociation (UVPD) methods. Our MS protocols allow for unequivocal determination of chemical structure, paramount to characterization of lipid A molecules that contain unique or novel chemical modifications. We also describe the radioisotopic labeling, and subsequent isolation, of lipid A from bacterial cells for analysis by TLC. Relative to MS-based protocols, TLC provides a more economical and rapid characterization method, but cannot be used to unambiguously assign lipid A chemical structures without the use of standards of known chemical structure. Over the last two decades isolation and characterization of lipid A has led to numerous exciting discoveries that have improved our understanding of the physiology of gram-negative bacteria, mechanisms of antibiotic resistance, the human innate immune response, and have provided many new targets in the development of antibacterial compounds.
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Affiliation(s)
- Jeremy C Henderson
- Section of Molecular Genetics and Microbiology, The University of Texas at Austin
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50
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Westmuckett AD, Siefert JC, Tesiram YA, Pinson DM, Moore KL. Salivary gland hypofunction in tyrosylprotein sulfotransferase-2 knockout mice is due to primary hypothyroidism. PLoS One 2013; 8:e71822. [PMID: 23951251 PMCID: PMC3737198 DOI: 10.1371/journal.pone.0071822] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/09/2013] [Indexed: 12/14/2022] Open
Abstract
Background Protein-tyrosine sulfation is a post-translational modification of an unknown number of secreted and membrane proteins mediated by two known Golgi tyrosylprotein sulfotransferases (TPST-1 and TPST-2). We reported that Tpst2-/- mice have mild-moderate primary hypothyroidism, whereas Tpst1-/- mice are euthyroid. While using magnetic resonance imaging (MRI) to look at the thyroid gland we noticed that the salivary glands in Tpst2-/- mice appeared smaller than in wild type mice. This prompted a detailed analysis to compare salivary gland structure and function in wild type, Tpst1-/-, and Tpst2 -/- mice. Methodology/Principal Findings Quantitative MRI imaging documented that salivary glands in Tpst2-/- females were ≈ 30% smaller than wild type or Tpst1-/- mice and that the granular convoluted tubules in Tpst2-/- submandibular glands were less prominent and were almost completely devoid of exocrine secretory granules compared to glands from wild type or Tpst1-/- mice. In addition, pilocarpine–induced salivary flow and salivary α-amylase activity in Tpst2-/- mice of both sexes was substantially lower than in wild type and Tpst1-/- mice. Anti-sulfotyrosine Western blots of salivary gland extracts and saliva showed no differences between wild type, Tpst1-/-, and Tpst2-/- mice, suggesting that the salivary gland hypofunction is due to factor(s) extrinsic to the salivary glands. Finally, we found that all indicators of hypothyroidism (serum T4, body weight) and salivary gland hypofunction (salivary flow, salivary α-amylase activity, histological changes) were restored to normal or near normal by thyroid hormone supplementation. Conclusions/Significance Our findings conclusively demonstrate that low body weight and salivary gland hypofunction in Tpst2-/- mice is due solely to primary hypothyroidism.
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Affiliation(s)
- Andrew D Westmuckett
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America.
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