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Maayan Y, Pandaranayaka EPJ, Srivastava DA, Lapidot M, Levin I, Dombrovsky A, Harel A. Using genomic analysis to identify tomato Tm-2 resistance-breaking mutations and their underlying evolutionary path in a new and emerging tobamovirus. Arch Virol 2018; 163:1863-1875. [PMID: 29582165 DOI: 10.1007/s00705-018-3819-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/05/2018] [Indexed: 12/20/2022]
Abstract
In September 2014, a new tobamovirus was discovered in Israel that was able to break Tm-2-mediated resistance in tomato that had lasted 55 years. The virus was isolated, and sequencing of its genome showed it to be tomato brown rugose fruit virus (ToBRFV), a new tobamovirus recently identified in Jordan. Previous studies on mutant viruses that cause resistance breaking, including Tm-2-mediated resistance, demonstrated that this phenotype had resulted from only a few mutations. Identification of important residues in resistance breakers is hindered by significant background variation, with 9-15% variability in the genomic sequences of known isolates. To understand the evolutionary path leading to the emergence of this resistance breaker, we performed a comprehensive phylogenetic analysis and genomic comparison of different tobamoviruses, followed by molecular modeling of the viral helicase. The phylogenetic location of the resistance-breaking genes was found to be among host-shifting clades, and this, together with the observation of a relatively low mutation rate, suggests that a host shift contributed to the emergence of this new virus. Our comparative genomic analysis identified twelve potential resistance-breaking mutations in the viral movement protein (MP), the primary target of the related Tm-2 resistance, and nine in its replicase. Finally, molecular modeling of the helicase enabled the identification of three additional potential resistance-breaking mutations.
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Affiliation(s)
- Yonatan Maayan
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, 7505101, Rishon LeZion, Israel
| | - Eswari P J Pandaranayaka
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, 7505101, Rishon LeZion, Israel
| | - Dhruv Aditya Srivastava
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, 7505101, Rishon LeZion, Israel
| | - Moshe Lapidot
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, 7505101, Rishon LeZion, Israel
| | - Ilan Levin
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, 7505101, Rishon LeZion, Israel
| | - Aviv Dombrovsky
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, 7505101, Rishon LeZion, Israel
| | - Arye Harel
- Department of Vegetable and Field Crop Research, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, 7505101, Rishon LeZion, Israel.
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102
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Wani R, Murray BW. Analysis of Cysteine Redox Post-Translational Modifications in Cell Biology and Drug Pharmacology. Methods Mol Biol 2018; 1558:191-212. [PMID: 28150239 DOI: 10.1007/978-1-4939-6783-4_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Reversible cysteine oxidation is an emerging class of protein post-translational modification (PTM) that regulates catalytic activity, modulates conformation, impacts protein-protein interactions, and affects subcellular trafficking of numerous proteins. Redox PTMs encompass a broad array of cysteine oxidation reactions with different half-lives, topographies, and reactivities such as S-glutathionylation and sulfoxidation. Recent studies from our group underscore the lesser known effect of redox protein modifications on drug binding. To date, biological studies to understand mechanistic and functional aspects of redox regulation are technically challenging. A prominent issue is the lack of tools for labeling proteins oxidized to select chemotype/oxidant species in cells. Predictive computational tools and curated databases of oxidized proteins are facilitating structural and functional insights into regulation of the network of oxidized proteins or redox proteome. In this chapter, we discuss analytical platforms for studying protein oxidation, suggest computational tools currently available in the field to determine redox sensitive proteins, and begin to illuminate roles of cysteine redox PTMs in drug pharmacology.
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Affiliation(s)
- Revati Wani
- Oncology Research Unit, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, CA, 92121, USA
| | - Brion W Murray
- Oncology Research Unit, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, CA, 92121, USA.
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103
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Kozic M, Fox SJ, Thomas JM, Verma CS, Rigden DJ. Large scale ab initio modeling of structurally uncharacterized antimicrobial peptides reveals known and novel folds. Proteins 2018; 86:548-565. [DOI: 10.1002/prot.25473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/16/2018] [Accepted: 01/29/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Mara Kozic
- Institute of Integrative Biology, University of Liverpool; Liverpool L69 7ZB U.K
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute; Singapore
| | - Stephen J. Fox
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute; Singapore
| | - Jens M. Thomas
- Institute of Integrative Biology, University of Liverpool; Liverpool L69 7ZB U.K
| | - Chandra S. Verma
- Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute; Singapore
- Department of Biological Sciences; National University of Singapore; Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore
| | - Daniel J. Rigden
- Institute of Integrative Biology, University of Liverpool; Liverpool L69 7ZB U.K
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104
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Christie AE, Cieslak MC, Roncalli V, Lenz PH, Major KM, Poynton HC. Prediction of a peptidome for the ecotoxicological model Hyalella azteca (Crustacea; Amphipoda) using a de novo assembled transcriptome. Mar Genomics 2018; 38:67-88. [PMID: 29395622 DOI: 10.1016/j.margen.2017.12.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 11/29/2017] [Accepted: 12/05/2017] [Indexed: 02/05/2023]
Abstract
Due to its sensitivity to many environmental and anthropogenic stressors, including a wide range of chemical compounds, Hyalella azteca, a freshwater amphipod, has emerged as one of the most commonly used invertebrates for ecotoxicological assessment.Peptidergic signaling systems are key components in the control of organism-environment interactions, and there is a growing literature suggesting that they are targets of a number of aquatic toxicants.Interestingly, and despite its model species status in the field of ecotoxicology, little is known about the peptide hormones of H. azteca.Here, a transcriptome was produced for this species using the de novo assembler Trinity and mined for sequences encoding putative peptide precursors; the transcriptome was assembled from 460,291,636 raw reads and consists of 133,486 unique transcripts.Seventy-six sequences encoding peptide pre/preprohormones were identified from this transcriptome, allowing for the prediction of 202 distinct peptides, which included members of the allatostatin A, allatostatin B, allatostatin C, allatotropin, bursicon, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/molt-inhibiting hormone, ecdysis-triggering hormone, eclosion hormone, elevenin, FMRFamide-like peptide, glycoprotein hormone, GSEFLamide, inotocin, leucokinin, myosuppressin, neuropeptide F, orcokinin, orcomyotropin, pigment dispersing hormone, proctolin, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, SIFamide, sulfakinin, tachykinin-related peptide and trissin families.These peptides expand the known peptidome for H. azteca approximately nine-fold, forming a strong foundation for future studies of peptidergic control, including disruption by aquatic toxicants, in this important ecotoxicological model.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
| | - Matthew C Cieslak
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Vittoria Roncalli
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Petra H Lenz
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Kaley M Major
- School for the Environment, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA
| | - Helen C Poynton
- School for the Environment, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA.
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105
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Pandey V, Krishnan V, Basak N, Marathe A, Thimmegowda V, Dahuja A, Jolly M, Sachdev A. Molecular modeling and in silico characterization of GmABCC5: a phytate transporter and potential target for low-phytate crops. 3 Biotech 2018; 8:54. [PMID: 29354365 DOI: 10.1007/s13205-017-1053-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/17/2017] [Indexed: 02/06/2023] Open
Abstract
Designing low-phytate crops without affecting the developmental process in plants had led to the identification of ABCC5 gene in soybean. The GmABCC5 gene was identified and a partial gene sequence was cloned from popular Indian soybean genotype Pusa16. Conserved domains and motifs unique to ABC transporters were identified in the 30 homologous sequences retrieved by BLASTP analysis. The homologs were analyzed for their evolutionary relationship and physiochemical properties. Conserved domains, transmembrane architecture and secondary structure of GmABCC5 were predicted with the aid of computational tools. Analysis identified 53 alpha helices and 31 beta strands, predicting 60% residues in alpha conformation. A three-dimensional (3D) model for GmABCC5 was developed based on 5twv.1.B (Homo sapiens) template homology to gain better insight into its molecular mechanism of transport and sequestration. Spatio-temporal real-time PCR analysis identified mid-to-late seed developmental stages as the time window for the maximum GmABCC5 gene expression, a potential target stage for phytate reduction. Results of this study provide valuable insights into the structural and functional characteristics of GmABCC5, which may be further utilized for the development of nutritionally enriched low-phytate soybean with improved mineral bioavailability.
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Affiliation(s)
- Vanita Pandey
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Quality and Basic Sciences, ICAR-Indian Institute of Wheat and Barley Research, Karnal, New Delhi 132 001 India
| | - Veda Krishnan
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Nabaneeta Basak
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
- Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, 753006 India
| | - Ashish Marathe
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Vinutha Thimmegowda
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Anil Dahuja
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Monica Jolly
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Archana Sachdev
- 1Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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106
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Oliveira G, Viviani VR. Comparison of the thermostability of recombinant luciferases from Brazilian bioluminescent beetles: Relationship with kinetics and bioluminescence colours. LUMINESCENCE 2017; 33:282-288. [DOI: 10.1002/bio.3411] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 08/23/2017] [Accepted: 08/30/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Gabriela Oliveira
- Laboratory of Biochemistry and Biotechnology of Bioluminescence, Graduate Program of Biotechnology and Environmental Monitoring, Department of Chemistry, Physics and Mathematics; Federal University of São Carlos (UFSCar); Campus of Sorocaba Sorocaba SP Brazil
- Department of Evolutive Genetics and Molecular Biology; Federal University of São Carlos (UFSCar); São Carlos SP Brazil
| | - Vadim R. Viviani
- Laboratory of Biochemistry and Biotechnology of Bioluminescence, Graduate Program of Biotechnology and Environmental Monitoring, Department of Chemistry, Physics and Mathematics; Federal University of São Carlos (UFSCar); Campus of Sorocaba Sorocaba SP Brazil
- Department of Evolutive Genetics and Molecular Biology; Federal University of São Carlos (UFSCar); São Carlos SP Brazil
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107
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Christie AE. Neuropeptide discovery in Proasellus cavaticus: Prediction of the first large-scale peptidome for a member of the Isopoda using a publicly accessible transcriptome. Peptides 2017; 97:29-45. [PMID: 28893643 DOI: 10.1016/j.peptides.2017.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/01/2017] [Accepted: 09/03/2017] [Indexed: 11/29/2022]
Abstract
In silico transcriptome mining is one of the most effective methods for neuropeptide discovery in crustaceans, particularly for species that are small, rare or from geographically inaccessible habitats that make obtaining the large pools of tissue needed for other peptide discovery platforms impractical. Via this approach, large peptidomes have recently been described for members of many of the higher crustacean taxa, one notable exception being the Isopoda; no peptidome has been predicted for any member of this malacostracan order. Using a publicly accessible transcriptome for the isopod Proasellus cavaticus, a subcentimeter subterranean ground water dweller, the first in silico-predicted peptidome for a member of the Isopoda is presented here. BLAST searches employing known arthropod neuropeptide pre/preprohormone queries identified 49 transcripts as encoding putative homologs within the P. cavaticus transcriptome. The proteins deduced from these transcripts allowed for the prediction of 171 distinct mature neuropeptides. The P. cavaticus peptidome includes members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, allatotropin, bursicon α, bursicon β, CCHamide, crustacean cardioactive peptide, crustacean hyperglycemic hormone/molt-inhibiting hormone, diuretic hormone 31, eclosion hormone, elevenin, FMRFamide-like peptide, glycoprotein hormone α2, leucokinin, myosuppressin, neuroparsin, neuropeptide F, pigment dispersing hormone, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, sulfakinin, tachykinin-related peptide and trissin families, as well as many linker/precursor-related sequences that may or may not represent additional bioactive molecules. Interestingly, many of the predicted P. cavaticus neuropeptides possess structures identical (or nearly so) to those previously described from members of several other malacostracan orders, i.e., the Decapoda, Amphipoda and Euphausiacea, a finding that suggests broad phylogenetic conservation of bioactive peptide structures, and possibly functions, may exist within the Malacostraca.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822 USA, USA.
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108
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Navarrete-Perea J, Isasa M, Paulo JA, Corral-Corral R, Flores-Bautista J, Hernández-Téllez B, Bobes RJ, Fragoso G, Sciutto E, Soberón X, Gygi SP, Laclette JP. Quantitative multiplexed proteomics of Taenia solium cysts obtained from the skeletal muscle and central nervous system of pigs. PLoS Negl Trop Dis 2017; 11:e0005962. [PMID: 28945737 PMCID: PMC5634658 DOI: 10.1371/journal.pntd.0005962] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/10/2017] [Accepted: 09/13/2017] [Indexed: 01/01/2023] Open
Abstract
In human and porcine cysticercosis caused by the tapeworm Taenia solium, the larval stage (cysts) can infest several tissues including the central nervous system (CNS) and the skeletal muscles (SM). The cyst’s proteomics changes associated with the tissue localization in the host tissues have been poorly studied. Quantitative multiplexed proteomics has the power to evaluate global proteome changes in response to different conditions. Here, using a TMT-multiplexed strategy we identified and quantified over 4,200 proteins in cysts obtained from the SM and CNS of pigs, of which 891 were host proteins. To our knowledge, this is the most extensive intermixing of host and parasite proteins reported for tapeworm infections.Several antigens in cysticercosis, i.e., GP50, paramyosin and a calcium-binding protein were enriched in skeletal muscle cysts. Our results suggested the occurrence of tissue-enriched antigen that could be useful in the improvement of the immunodiagnosis for cysticercosis. Using several algorithms for epitope detection, we selected 42 highly antigenic proteins enriched for each tissue localization of the cysts. Taking into account the fold changes and the antigen/epitope contents, we selected 10 proteins and produced synthetic peptides from the best epitopes. Nine peptides were recognized by serum antibodies of cysticercotic pigs, suggesting that those peptides are antigens. Mixtures of peptides derived from SM and CNS cysts yielded better results than mixtures of peptides derived from a single tissue location, however the identification of the ‘optimal’ tissue-enriched antigens remains to be discovered. Through machine learning technologies, we determined that a reliable immunodiagnostic test for porcine cysticercosis required at least five different antigenic determinants. Human and porcine cysticercosis caused by Taenia solium is a parasite disease still endemic in developing countries. The cysts can be located in different host tissues, including different organs of the central nervous system and the skeletal muscles. The molecular mechanisms associated with the tissue localization of the cysts are not well understood. Here, we described the proteome changes of the cysts obtained from different host tissues from infected pigs using quantitative multiplex proteomics. We explored the diversity of host proteins identified in the cyst’s protein extracts and we also explored the immune-localization of several host-related proteins within the cysts, and propose their possible function. We identified several proteins and antigens enriched for a given tissue localization. Several synthetic peptides designed from these tissue-enriched antigens were tested trough ELISA. Using a combination of peptide mixtures and machine learning technologies we were able to distinguish non cysticercotic and cysticercotic pig’s sera. The tissue-enriched proteins/antigens could be useful for the development of improved immuno-diagnostic tests capable of discriminate the tissue-localization of the cysts.
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Affiliation(s)
- José Navarrete-Perea
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Marta Isasa
- Dept. of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joao A Paulo
- Dept. of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ricardo Corral-Corral
- Dept. of Biochemistry and Structural Biology, Institute of Cell Physiology, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Jeanette Flores-Bautista
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Beatriz Hernández-Téllez
- Dept. of Tissue and Cell Biology, School of Medicine, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Raúl J Bobes
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Gladis Fragoso
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Edda Sciutto
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica, Ciudad de México, México.,Dept. of Biocatalysis and Cellular Engineering, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, México
| | - Steven P Gygi
- Dept. of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Juan P Laclette
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
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109
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Spider's venom phospholipases D: A structural review. Int J Biol Macromol 2017; 107:1054-1065. [PMID: 28951301 DOI: 10.1016/j.ijbiomac.2017.09.081] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/25/2017] [Accepted: 09/20/2017] [Indexed: 12/28/2022]
Abstract
Spider venoms are complex mixtures of proteins, peptides and small organic and inorganic molecules. Among the proteins, phospholipases D (PLDs) present the major portion, and till now they are the most studied enzymes in spider venom. These PLDs have been divided into two classes, I and II, based on their primary and tertiary structure. Currently, crystal structures of both classes of these enzymes are available in the Protein Data Bank (PDB). Their three-dimensional structure is composed of eight α-helices and eight β-strands forming the ubiquitous fold called triosephosphate isomerase (TIM) barrel. These enzymes use general acid-base catalysis to hydrolyzes their substrate. In this review, we have described the structural features, structure-based mechanisms of catalysis, maturation, and inhibition of these enzymes using the synthetic inhibitor.
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110
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Kist AM, Lampert A, O'Reilly AO. DIsulfide Mapping PLanner Software Tool. J Comput Biol 2017; 25:430-434. [PMID: 28817312 DOI: 10.1089/cmb.2017.0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Disulfide bridges are side-chain-mediated covalent bonds between cysteines that stabilize many protein structures. Disulfide mapping experiments to resolve these linkages typically involve proteolytic cleavage of the protein of interest followed by mass spectroscopy to identify fragments corresponding to linked peptides. Here we report the sequence-based "DIMPL" web tool to facilitate the planning and analysis steps of experimental mapping studies. The software tests permutations of user-selected proteases to determine an optimal peptic digest that produces cleavage between cysteine residues, thus separating each to an individual peptide fragment. The webserver returns fragment sequence and mass data that can be dynamically ordered to enable straightforward comparative analysis with mass spectroscopy results, facilitating dipeptide identification.
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Affiliation(s)
- Andreas M Kist
- 1 Institute of Physiology and Pathophysiology, Friedrich-Alexander-University , Erlangen-Nuremberg, Erlangen, Germany .,2 Max-Planck-Institute of Neurobiology , Martinsried, Germany
| | - Angelika Lampert
- 1 Institute of Physiology and Pathophysiology, Friedrich-Alexander-University , Erlangen-Nuremberg, Erlangen, Germany .,3 Institute of Physiology , Uniklinik RWTH Aachen, 52074 Aachen, Germany
| | - Andrias O O'Reilly
- 1 Institute of Physiology and Pathophysiology, Friedrich-Alexander-University , Erlangen-Nuremberg, Erlangen, Germany .,4 School of Natural Sciences and Psychology, Liverpool John Moores University , Liverpool, United Kingdom
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111
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Raffaello T, Asiegbu FO. Small secreted proteins from the necrotrophic conifer pathogen Heterobasidion annosum s.l. (HaSSPs) induce cell death in Nicotiana benthamiana. Sci Rep 2017; 7:8000. [PMID: 28801666 PMCID: PMC5554239 DOI: 10.1038/s41598-017-08010-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/05/2017] [Indexed: 01/07/2023] Open
Abstract
The basidiomycete Heterobasidion annosum sensu lato (s.l.) is considered to be one of the most destructive conifer pathogens in the temperate forests of the northern hemisphere. H. annosum is characterized by a dual fungal lifestyle. The fungus grows necrotrophically on living plant cells and saprotrophically on dead wood material. In this study, we screened the H. annosum genome for small secreted proteins (HaSSPs) that could potentially be involved in promoting necrotrophic growth during the fungal infection process. The final list included 58 HaSSPs that lacked predictable protein domains. The transient expression of HaSSP encoding genes revealed the ability of 8 HaSSPs to induce cell chlorosis and cell death in Nicotiana benthamiana. In particular, one protein (HaSSP30) could induce a rapid, strong, and consistent cell death within 2 days post-infiltration. HaSSP30 also increased the transcription of host-defence-related genes in N. benthamiana, which suggested a necrotrophic-specific immune response. This is the first line of evidence demonstrating that the H. annosum genome encodes HaSSPs with the capability to induce plant cell death in a non-host plant.
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Affiliation(s)
- Tommaso Raffaello
- Department of Forest Sciences, University of Helsinki, Faculty of Agriculture and Forestry, Latokartanonkaari 7, 00014, Helsinki, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, University of Helsinki, Faculty of Agriculture and Forestry, Latokartanonkaari 7, 00014, Helsinki, Finland.
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112
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Abstract
Cysteine thiols are among the most reactive functional groups in proteins, and their pairing in disulfide linkages is a common post-translational modification in proteins entering the secretory pathway. This modest amino acid alteration, the mere removal of a pair of hydrogen atoms from juxtaposed cysteine residues, contrasts with the substantial changes that characterize most other post-translational reactions. However, the wide variety of proteins that contain disulfides, the profound impact of cross-linking on the behavior of the protein polymer, the numerous and diverse players in intracellular pathways for disulfide formation, and the distinct biological settings in which disulfide bond formation can take place belie the simplicity of the process. Here we lay the groundwork for appreciating the mechanisms and consequences of disulfide bond formation in vivo by reviewing chemical principles underlying cysteine pairing and oxidation. We then show how enzymes tune redox-active cofactors and recruit oxidants to improve the specificity and efficiency of disulfide formation. Finally, we discuss disulfide bond formation in a cellular context and identify important principles that contribute to productive thiol oxidation in complex, crowded, dynamic environments.
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Affiliation(s)
- Deborah Fass
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 7610001, Israel
| | - Colin Thorpe
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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113
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Zimmer RK, Ferrier GA, Kim SJ, Ogorzalek Loo RR, Zimmer CA, Loo JA. Keystone predation and molecules of keystone significance. Ecology 2017; 98:1710-1721. [PMID: 28376248 DOI: 10.1002/ecy.1849] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 01/24/2017] [Accepted: 03/27/2017] [Indexed: 11/09/2022]
Abstract
Keystone species structure ecological communities and are major determinants of biodiversity. A synthesis of research on keystone species is nonetheless missing a critical component - the sensory mechanisms for behavioral interactions that determine population- and community-wide attributes. Here, we establish the chemosensory basis for keystone predation by sea stars (Pisaster ochraceus) on mussels. This consumer-resource interaction is prototypic of top-down driven trophic cascades. Each mussel species (Mytilus californianus and M. galloprovincialis) secretes a glycoprotein orthologue (29.6 and 28.1 kDa, respectively) that acts, singularly, to evoke the sea star predatory response. The orthologues (named "KEYSTONEin") are localized in the epidermis, extrapallial fluid, and organic shell coating (periostracum) of live, intact mussels. Thus, KEYSTONEin contacts chemosensory receptors on tube feet as sea stars crawl over rocky surfaces in search of prey. The complete nucleotide sequences reveal that KEYSTONEin shares 87% (M. californianus) or 98% (M. galloprovincialis) homology with a calcium-binding protein in the shell matrix of a closely related congener, M. edulis. All three molecules cluster tightly within the Complement Component 1 Domain Containing (C1qDC) protein family; each exhibits a large globular domain, low complexity region(s), coiled coil, and at least four of five histidine-aspartic acid tandem motifs. Collective results support the hypothesis that KEYSTONEin evolved ancestrally in immunological, and later, in biomineralization roles. More recently, the substance has become exploited by sea stars as a contact cue for prey recognition. As the first identified compound to evoke keystone predation, KEYSTONEin provides valuable sensory information, promotes biodiversity, and shapes community structure and function. Without this molecule, there would be no predation by sea stars on mussels.
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Affiliation(s)
- Richard K Zimmer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA.,Moreton Bay Research Station, Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Graham A Ferrier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA
| | - Steven J Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, USA
| | - Rachel R Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, 90095, USA.,UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, 90095, USA
| | - Cheryl Ann Zimmer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, 90095, USA.,Moreton Bay Research Station, Centre for Marine Science, School of Biological Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, 90095, USA.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, 90095, USA.,UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, California, 90095, USA
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Oeser B, Kind S, Schurack S, Schmutzer T, Tudzynski P, Hinsch J. Cross-talk of the biotrophic pathogen Claviceps purpurea and its host Secale cereale. BMC Genomics 2017; 18:273. [PMID: 28372538 PMCID: PMC5379732 DOI: 10.1186/s12864-017-3619-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/10/2017] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The economically important Ergot fungus Claviceps purpurea is an interesting biotrophic model system because of its strict organ specificity (grass ovaries) and the lack of any detectable plant defense reactions. Though several virulence factors were identified, the exact infection mechanisms are unknown, e.g. how the fungus masks its attack and if the host detects the infection at all. RESULTS We present a first dual transcriptome analysis using an RNA-Seq approach. We studied both, fungal and plant gene expression in young ovaries infected by the wild-type and two virulence-attenuated mutants. We can show that the plant recognizes the fungus, since defense related genes are upregulated, especially several phytohormone genes. We present a survey of in planta expressed fungal genes, among them several confirmed virulence genes. Interestingly, the set of most highly expressed genes includes a high proportion of genes encoding putative effectors, small secreted proteins which might be involved in masking the fungal attack or interfering with host defense reactions. As known from several other phytopathogens, the C. purpurea genome contains more than 400 of such genes, many of them clustered and probably highly redundant. Since the lack of effective defense reactions in spite of recognition of the fungus could very well be achieved by effectors, we started a functional analysis of some of the most highly expressed candidates. However, the redundancy of the system made the identification of a drastic effect of a single gene most unlikely. We can show that at least one candidate accumulates in the plant apoplast. Deletion of some candidates led to a reduced virulence of C. purpurea on rye, indicating a role of the respective proteins during the infection process. CONCLUSIONS We show for the first time that- despite the absence of effective plant defense reactions- the biotrophic pathogen C. purpurea is detected by its host. This points to a role of effectors in modulation of the effective plant response. Indeed, several putative effector genes are among the highest expressed genes in planta.
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Affiliation(s)
- Birgitt Oeser
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, D-48143 Münster, Germany
| | - Sabine Kind
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, D-48143 Münster, Germany
| | - Selma Schurack
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, D-48143 Münster, Germany
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Paul Tudzynski
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, D-48143 Münster, Germany
| | - Janine Hinsch
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, D-48143 Münster, Germany
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115
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Christie AE, Roncalli V, Cieslak MC, Pascual MG, Yu A, Lameyer TJ, Stanhope ME, Dickinson PS. Prediction of a neuropeptidome for the eyestalk ganglia of the lobster Homarus americanus using a tissue-specific de novo assembled transcriptome. Gen Comp Endocrinol 2017; 243:96-119. [PMID: 27823957 PMCID: PMC5796769 DOI: 10.1016/j.ygcen.2016.11.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/03/2016] [Indexed: 11/19/2022]
Abstract
In silico transcriptome mining is a powerful tool for crustacean peptidome prediction. Using homology-based BLAST searches and a simple bioinformatics workflow, large peptidomes have recently been predicted for a variety of crustaceans, including the lobster, Homarus americanus. Interestingly, no in silico studies have been conducted on the eyestalk ganglia (lamina ganglionaris, medulla externa, medulla interna and medulla terminalis) of the lobster, although the eyestalk is the location of a major neuroendocrine complex, i.e., the X-organ-sinus gland system. Here, an H. americanus eyestalk ganglia-specific transcriptome was produced using the de novo assembler Trinity. This transcriptome was generated from 130,973,220 Illumina reads and consists of 147,542 unique contigs. Eighty-nine neuropeptide-encoding transcripts were identified from this dataset, allowing for the deduction of 62 distinct pre/preprohormones. Two hundred sixty-two neuropeptides were predicted from this set of precursors; the peptides include members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, bursicon α, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone (CHH), CHH precursor-related peptide, diuretic hormone 31, diuretic hormone 44, eclosion hormone, elevenin, FMRFamide-like peptide, glycoprotein hormone α2, glycoprotein hormone β5, GSEFLamide, intocin, leucokinin, molt-inhibiting hormone, myosuppressin, neuroparsin, neuropeptide F, orcokinin, orcomyotropin, pigment dispersing hormone, proctolin, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, SIFamide, sulfakinin, tachykinin-related peptide and trissin families. The predicted peptides expand the H. americanus eyestalk ganglia neuropeptidome approximately 7-fold, and include 78 peptides new to the lobster. The transcriptome and predicted neuropeptidome described here provide new resources for investigating peptidergic signaling within/from the lobster eyestalk ganglia.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
| | - Vittoria Roncalli
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Matthew C Cieslak
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Micah G Pascual
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Andy Yu
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Tess J Lameyer
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04672, USA
| | - Meredith E Stanhope
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04672, USA
| | - Patsy S Dickinson
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, ME 04672, USA
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116
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Christie AE, Hull JJ, Richer JA, Geib SM, Tassone EE. Prediction of a peptidome for the western tarnished plant bug Lygus hesperus. Gen Comp Endocrinol 2017; 243:22-38. [PMID: 27789347 DOI: 10.1016/j.ygcen.2016.10.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/08/2016] [Accepted: 10/20/2016] [Indexed: 12/28/2022]
Abstract
Many strategies for controlling insect pests require an understanding of their hormonal signaling agents, peptides being the largest and most diverse single class of these molecules. Lygus hesperus is a pest species of particular concern, as it is responsible for significant damage to a wide variety of commercially important plant crops. At present, little is known about the peptide hormones of L. hesperus. Here, transcriptomic data were used to predict a peptidome for L. hesperus. Fifty-three L. hesperus transcripts encoding peptide precursors were identified, with a subset amplified by PCR for sequence verification. The proteins deduced from these transcripts allowed for the prediction of a 119-sequence peptidome for L. hesperus. The predicted peptides include isoforms of allatostatin A, allatostatin B (AST-B), allatostatin C, allatotropin, bursicon, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/ion transport peptide, diuretic hormone 31, GSEFLamide, insulin-like peptide, myosuppressin, neuroparsin, neuropeptide F, orcokinin, orcomyotropin, pyrokinin, short neuropeptide F, SIFamide, sulfakinin and tachykinin-related peptide. Of note were several isoforms of AST-B that possess -WX7Wamide carboxyl-termini rather than the stereotypical -WX6Wamide (e.g., KWQDMQNPGWamide), an allatotropin ending in -SARGFamide rather than -TARGFamide (GLKNGPLNSARGFamide), a GSEFLamide ending in -GTEFLamide (TVGTEFLamide), several orcokinins with PMDEIDR- rather than NFDEIDR- amino-termini (e.g., PMDEIDRAGFTHFV), and an eight rather than 12 amino acid long isoform of SIFamide (PPFNGSIFamide). Collectively, the L. hesperus peptidome predicted here provides a resource for initiating physiological investigations of peptidergic signaling in this species, including studies directed at the biological control of this agricultural pest.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - J Joe Hull
- Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ 85138, USA
| | - Josh A Richer
- Pest Management and Biocontrol Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ 85138, USA
| | - Scott M Geib
- Tropical Crop and Commodity Protection Research Unit, Daniel K. Inouye Pacific Basin Agricultural Research Center, USDA Agricultural Research Services, Hilo, HI 96720, USA
| | - Erica E Tassone
- Plant Physiology and Genetics Research Unit, US Arid Land Agricultural Research Center, USDA Agricultural Research Services, Maricopa, AZ 85138, USA
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117
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Spit J, Philips A, Wynant N, Santos D, Plaetinck G, Vanden Broeck J. Knockdown of nuclease activity in the gut enhances RNAi efficiency in the Colorado potato beetle, Leptinotarsa decemlineata, but not in the desert locust, Schistocerca gregaria. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 81:103-116. [PMID: 28093313 DOI: 10.1016/j.ibmb.2017.01.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/02/2017] [Accepted: 01/13/2017] [Indexed: 05/21/2023]
Abstract
The responsiveness towards orally delivered dsRNA and the potency of a subsequent environmental RNA interference (RNAi) response strongly differs between different insect species. While some species are very sensitive to dsRNA delivery through the diet, others are not. The underlying reasons for this may vary, but degradation of dsRNA by nucleases in the gut lumen is believed to play a crucial role. The Colorado potato beetle, Leptinotarsa decemlineata, is a voracious defoliator of potato crops worldwide, and is currently under investigation for novel control methods based on dsRNA treatments. Here we describe the identification and characterization of two nuclease genes exclusively expressed in the gut of this pest species. Removal of nuclease activity in adults increased the sensitivity towards dsRNA and resulted in improved protection of potato plants. A similar strategy in the desert locust, Schistocerca gregaria, for which we show a far more potent nuclease activity in the gut juice, did however not lead to an improvement of the RNAi response. Possible reasons for this are discussed. Taken together, the present data confirm a negative effect of nucleases in the gut on the environmental RNAi response, and further suggest that interfering with this activity is a strategy worth pursuing for improving RNAi efficacy in insect pest control applications.
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Affiliation(s)
- Jornt Spit
- KU Leuven, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59, 3000 Leuven, Belgium; Syngenta Ghent Innovation Center, Technologiepark 30, 9052 Zwijnaarde, Belgium.
| | - Annelies Philips
- Syngenta Ghent Innovation Center, Technologiepark 30, 9052 Zwijnaarde, Belgium
| | - Niels Wynant
- KU Leuven, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59, 3000 Leuven, Belgium
| | - Dulce Santos
- KU Leuven, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59, 3000 Leuven, Belgium
| | - Geert Plaetinck
- Syngenta Ghent Innovation Center, Technologiepark 30, 9052 Zwijnaarde, Belgium
| | - Jozef Vanden Broeck
- KU Leuven, Research Group of Molecular Developmental Physiology and Signal Transduction, Naamsestraat 59, 3000 Leuven, Belgium
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Carneiro RF, Torres RCF, Chaves RP, de Vasconcelos MA, de Sousa BL, Goveia ACR, Arruda FV, Matos MNC, Matthews-Cascon H, Freire VN, Teixeira EH, Nagano CS, Sampaio AH. Purification, Biochemical Characterization, and Amino Acid Sequence of a Novel Type of Lectin from Aplysia dactylomela Eggs with Antibacterial/Antibiofilm Potential. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:49-64. [PMID: 28150103 DOI: 10.1007/s10126-017-9728-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 01/08/2017] [Indexed: 06/06/2023]
Abstract
A new lectin from Aplysia dactylomela eggs (ADEL) was isolated by affinity chromatography on HCl-activated Sepharose™ media. Hemagglutination caused by ADEL was inhibited by several galactosides, mainly galacturonic acid (Ka = 6.05 × 106 M-1). The primary structure of ADEL consists of 217 residues, including 11 half-cystines involved in five intrachain and one interchain disulfide bond, resulting in a molecular mass of 57,228 ± 2 Da, as determined by matrix-assisted laser desorption/ionization time of flight mass spectrometry. ADEL showed high similarity with lectins isolated from Aplysia eggs, but not with other known lectins, indicating that these lectins could be grouped into a new family of animal lectins. Three glycosylation sites were found in its polypeptide backbone. Data from peptide-N-glycosidase F digestion and MS suggest that all oligosaccharides attached to ADEL are high in mannose. The secondary structure of ADEL is predominantly β-sheet, and its tertiary structure is sensitive to the presence of ligands, as observed by CD. A 3D structure model of ADEL was created and shows two domains connected by a short loop. Domain A is composed of a flat three-stranded and a curved five-stranded β-sheet, while domain B presents a flat three-stranded and a curved four-stranded β-sheet. Molecular docking revealed favorable binding energies for interactions between lectin and galacturonic acid, lactose, galactosamine, and galactose. Moreover, ADEL was able to agglutinate and inhibit biofilm formation of Staphylococcus aureus, suggesting that this lectin may be a potential alternative to conventional use of antimicrobial agents in the treatment of infections caused by Staphylococcal biofilms.
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Affiliation(s)
- Rômulo Farias Carneiro
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, Av. Mister Hull, Box 6043, Fortaleza, Ceará, 60440-970, Brazil
| | - Renato Cézar Farias Torres
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, Av. Mister Hull, Box 6043, Fortaleza, Ceará, 60440-970, Brazil
| | - Renata Pinheiro Chaves
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, Av. Mister Hull, Box 6043, Fortaleza, Ceará, 60440-970, Brazil
| | - Mayron Alves de Vasconcelos
- Laboratório Integrado de Biomoléculas - LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, Fortaleza, Ceará, 60430-160, Brazil
| | - Bruno Lopes de Sousa
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, Fortaleza, Ceará, 60440-970, Brazil
| | - André Castelo Rodrigues Goveia
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, Av. Mister Hull, Box 6043, Fortaleza, Ceará, 60440-970, Brazil
| | - Francisco Vassiliepe Arruda
- Laboratório Integrado de Biomoléculas - LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, Fortaleza, Ceará, 60430-160, Brazil
| | - Maria Nágila Carneiro Matos
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, Av. Mister Hull, Box 6043, Fortaleza, Ceará, 60440-970, Brazil
| | - Helena Matthews-Cascon
- Laboratório de Invertebrados Marinhos do Ceará - LIMCE, Departamento de Biologia, Universidade Federal do Ceará, Campus do Pici s/n, bloco 906, Fortaleza, CE, 60455-760, Brazil
| | - Valder Nogueira Freire
- Departamento de Física, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, Fortaleza, Ceará, 60440-970, Brazil
| | - Edson Holanda Teixeira
- Laboratório Integrado de Biomoléculas - LIBS, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Monsenhor Furtado, s/n, Fortaleza, Ceará, 60430-160, Brazil
| | - Celso Shiniti Nagano
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, Av. Mister Hull, Box 6043, Fortaleza, Ceará, 60440-970, Brazil
| | - Alexandre Holanda Sampaio
- Laboratório de Biotecnologia Marinha - BioMar-Lab, Departamento de Engenharia de Pesca, Universidade Federal do Ceará, Campus do Pici s/n, bloco 871, Av. Mister Hull, Box 6043, Fortaleza, Ceará, 60440-970, Brazil.
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119
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Anjos L, Morgado I, Guerreiro M, Cardoso JCR, Melo EP, Power DM. Cartilage acidic protein 1, a new member of the beta-propeller protein family with amyloid propensity. Proteins 2016; 85:242-255. [DOI: 10.1002/prot.25210] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/06/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Liliana Anjos
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve; Campus de Gambelas Faro 8005-139 Portugal
| | - Isabel Morgado
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve; Campus de Gambelas Faro 8005-139 Portugal
| | - Marta Guerreiro
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve; Campus de Gambelas Faro 8005-139 Portugal
| | - João C. R. Cardoso
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve; Campus de Gambelas Faro 8005-139 Portugal
| | - Eduardo P. Melo
- Campus de Gambelas, Center for Biomedical Research, University of Algarve; Faro 8005-139 Portugal
| | - Deborah M. Power
- Comparative Endocrinology and Integrative Biology Group (CEIB), Centro de Ciencias do Mar (CCMAR), University of Algarve; Campus de Gambelas Faro 8005-139 Portugal
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120
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Sharma V, Salwan R, Sharma P, Kanwar S. Molecular cloning and characterization of ech 46 endochitinase from Trichoderma harzianum. Int J Biol Macromol 2016; 92:615-624. [DOI: 10.1016/j.ijbiomac.2016.07.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/17/2016] [Accepted: 07/21/2016] [Indexed: 01/24/2023]
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121
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Structural and dynamic insights into the C-terminal extension of cysteine proteinase B from Leishmania amazonensis. J Mol Graph Model 2016; 70:30-39. [DOI: 10.1016/j.jmgm.2016.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/14/2016] [Accepted: 08/12/2016] [Indexed: 11/20/2022]
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122
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Christie AE, Pascual MG. Peptidergic signaling in the crab Cancer borealis: Tapping the power of transcriptomics for neuropeptidome expansion. Gen Comp Endocrinol 2016; 237:53-67. [PMID: 27497705 DOI: 10.1016/j.ygcen.2016.08.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 11/21/2022]
Abstract
The crab Cancer borealis has long been used as a model for understanding neural control of rhythmic behavior. One significant discovery made through its use is that even numerically simple neural circuits are capable of producing an essentially infinite array of distinct motor outputs via the actions of locally released and circulating neuromodulators, the largest class being peptides. While much work has focused on elucidating the peptidome of C. borealis, no investigation has used in silico transcriptome mining for peptide discovery in this species, a strategy proven highly effective for identifying neuropeptides in other crustaceans. Here, we mined a C. borealis neural transcriptome for putative peptide-encoding transcripts, and predicted 200 distinct mature neuropeptides from the proteins deduced from these sequences. The identified peptides include isoforms of allatostatin A, allatostatin B, allatostatin C, CCHamide, crustacean cardioactive peptide, crustacean hyperglycemic hormone, diuretic hormone 31 (DH31), diuretic hormone 44 (DH44), FMRFamide-like peptide, GSEFLamide, HIGSLYRamide, insulin-like peptide (ILP), intocin, leucokinin, neuroparsin, pigment dispersing hormone, pyrokinin, red pigment concentrating hormone, short neuropeptide F and SIFamide. While some of the predicted peptides were known previously from C. borealis, most (159) are new discoveries for the species, e.g., the isoforms of CCHamide, DH31, DH44, GSEFLamide, ILP, intocin and neuroparsin, which are the first members of these peptide families identified from C. borealis. Collectively, the peptides predicted here approximately double the peptidome known for C. borealis, and in so doing provide an expanded platform from which to launch new investigations of peptidergic neuromodulation in this species.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822 USA.
| | - Micah G Pascual
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822 USA
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123
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Christie AE. Expansion of the neuropeptidome of the globally invasive marine crab Carcinus maenas. Gen Comp Endocrinol 2016; 235:150-169. [PMID: 27179880 DOI: 10.1016/j.ygcen.2016.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 10/21/2022]
Abstract
Carcinus maenas is widely recognized as one of the world's most successful marine invasive species; its success as an invader is due largely to its ability to thrive under varied environmental conditions. The physiological/behavioral control systems that allow C. maenas to adapt to new environments are undoubtedly under hormonal control, the largest single class of hormones being peptides. While numerous studies have focused on identifying native C. maenas peptides, none has taken advantage of mining transcriptome shotgun assembly (TSA) sequence data, a strategy proven highly successful for peptide discovery in other crustaceans. Here, a C. maenas peptidome was predicted via in silico transcriptome mining. Thirty-seven peptide families were searched for in the extant TSA database, with transcripts encoding precursors for 29 groups identified. The pre/preprohormones deduced from the identified sequences allowed for the prediction of 263 distinct mature peptides, 193 of which are new discoveries for C. maenas. The predicted peptides include isoforms of adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, bursicon, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone, diuretic hormone 31, diuretic hormone 44, eclosion hormone, FMRFamide-like peptide, HIGSLYRamide, intocin, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, pigment dispersing hormone, proctolin, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, SIFamide, and tachykinin-related peptide. This peptidome is the largest predicted from any single crustacean using the in silico approach, and provides a platform for investigating peptidergic signaling in C. maenas, including control of the processes that allow for its success as a global marine invader.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
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Expression, purification and biochemical characterization of AtFUT1, a xyloglucan-specific fucosyltransferase from Arabidopsis thaliana. Biochimie 2016; 128-129:183-92. [PMID: 27580247 DOI: 10.1016/j.biochi.2016.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/25/2016] [Indexed: 12/29/2022]
Abstract
Efforts to identify genes and characterize enzymes involved in the biosynthesis of plant cell wall polysaccharides have yet to produce and purify to homogeneity an active plant cell wall synthesizing enzyme suitable for structural studies. In Arabidopsis, the last step of xyloglucan (XG) biosynthesis is catalyzed by fucosyltransferase 1 (AtFUT1), which transfers l-fucose from GDP-β-l-fucose to a specific galactose on the XG core. Here, we describe the production of a soluble form of AtFUT1 (HisΔ68-AtFUT1) and its purification to milligram quantities. An active form of AtFUT1 was produced in an insect cell culture medium, using a large-scale expression system, and purified in a two-step protocol. Characterization of purified HisΔ68-AtFUT1 revealed that the enzyme behaves as a non-covalent homodimer in solution. A bioluminescent transferase assay confirmed HisΔ68-AtFUT1 activity on its substrates, namely GDP-fucose and tamarind XG, with calculated Km values of 42 μM and 0.31 μM, respectively. Moreover, the length of the XG-derived acceptor quantitatively affected fucosyltransferase activity in a size-dependent manner. The affinity of HisΔ68-AtFUT1 for tamarind XG and GDP was determined using isothermal titration calorimetry (ITC). Interestingly, ITC data suggest that HisΔ68-AtFUT1 undergoes conformational changes in the presence of its first co-substrate (XG or GDP), which then confers greater affinity for the second co-substrate. The procedure described in this study can potentially be transferred to other enzymes involved in plant cell wall synthesis.
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Wong YH, Yu L, Zhang G, He LS, Qian PY. In Silico Prediction of Neuropeptides/Peptide Hormone Transcripts in the Cheilostome Bryozoan Bugula neritina. PLoS One 2016; 11:e0160271. [PMID: 27537380 PMCID: PMC4990251 DOI: 10.1371/journal.pone.0160271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/15/2016] [Indexed: 11/18/2022] Open
Abstract
The bryozoan Bugula neritina has a biphasic life cycle that consists of a planktonic larval stage and a sessile juvenile/adult stage. The transition between these two stages is crucial for the development and recruitment of B. neritina. Metamorphosis in B. neritina is mediated by both the nervous system and the release of developmental signals. However, no research has been conducted to investigate the expression of neuropeptides (NP)/peptide hormones in B. neritina larvae. Here, we report a comprehensive study of the NP/peptide hormones in the marine bryozoan B. neritina based on in silico identification methods. We recovered 22 transcripts encompassing 11 NP/peptide hormone precursor transcript sequences. The transcript sequences of the 11 isolated NP precursors were validated by cDNA cloning using gene-specific primers. We also examined the expression of three peptide hormone precursor transcripts (BnFDSIG, BnILP1, BnGPB) in the coronate larvae of B. neritina, demonstrating their distinct expression patterns in the larvae. Overall, our findings serve as an important foundation for subsequent investigations of the peptidergic control of bryozoan larval behavior and settlement.
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Affiliation(s)
- Yue Him Wong
- Division of Life Science, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Li Yu
- Division of Life Science, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Gen Zhang
- Division of Life Science, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Li-Sheng He
- Division of Life Science, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, San Ya, Hai Nan, China
| | - Pei-Yuan Qian
- Division of Life Science, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Sanya Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, San Ya, Hai Nan, China
- * E-mail:
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126
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Ashfaq UA, Ahmed B. De Novo Structural Modeling and Conserved Epitopes Prediction of Zika Virus Envelop Protein for Vaccine Development. Viral Immunol 2016; 29:436-43. [PMID: 27438351 DOI: 10.1089/vim.2016.0033] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Zika virus (Zika V) is a positive single-stranded RNA virus that is transmitted by mosquito bites. Zika V Envelop protein is antigenic and is involved in fusion and entry of viral particles into the cell. Till date, there is no vaccine and antiviral drug available against Zika V. Thus, there is a need to develop a vaccine against Zika V. This study was designed for the prediction of B cell and T cell epitopes that can be helpful in diagnosis and vaccine designing against this emerging threat. For this purpose, several B cell and T cell epitopes were predicted that are conserved among Zika virus genomes taken from 12 different countries. Peptides QTLTPVGRL, in case of major histocompatibility complex (MHC) class I, and IRCIGVSNRDFV, in case of MHC class II, are highly antigenic among T cell epitopes. Molecular docking was performed to study the interactions of B cell epitopes with HLA-B7. However, these predicted epitopes could play a constructive role in designing of a vaccine against Zika V.
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Affiliation(s)
- Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF) , Faisalabad, Pakistan
| | - Bilal Ahmed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF) , Faisalabad, Pakistan
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Simpkin AJ, Rigden DJ. GP0.4 from bacteriophage T7: in silico characterisation of its structure and interaction with E. coli FtsZ. BMC Res Notes 2016; 9:343. [PMID: 27411831 PMCID: PMC4944311 DOI: 10.1186/s13104-016-2149-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/06/2016] [Indexed: 01/21/2023] Open
Abstract
Background Proteins produced by bacteriophages can have potent antimicrobial activity. The study of phage-host interactions can therefore inform small molecule drug discovery by revealing and characterising new drug targets. Here we characterise in silico the predicted interaction of gene protein 0.4 (GP0.4) from the Escherichia coli (E. coli) phage T7 with E. coli filamenting temperature-sensitive mutant Z division protein (FtsZ). FtsZ is a tubulin homolog which plays a key role in bacterial cell division and that has been proposed as a drug target. Results Using ab initio, fragment assembly structure modelling, we predicted the structure of GP0.4 with two programs. A structure similarity-based network was used to identify a U-shaped helix-turn-helix candidate fold as being favoured. ClusPro was used to dock this structure prediction to a homology model of E. coli FtsZ resulting in a favourable predicted interaction mode. Alternative docking methods supported the proposed mode which offered an immediate explanation for the anti-filamenting activity of GP0.4. Importantly, further strong support derived from a previously characterised insertion mutation, known to abolish GP0.4 activity, that is positioned in close proximity to the proposed GP0.4/FtsZ interface. Conclusions The mode of interaction predicted by bioinformatics techniques strongly suggests a mechanism through which GP0.4 inhibits FtsZ and further establishes the latter’s druggable intrafilament interface as a potential drug target. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-2149-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam J Simpkin
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
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128
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Ferrier GA, Kim SJ, Kaddis CS, Loo JA, Ann Zimmer C, Zimmer RK. MULTIFUNCin: A Multifunctional Protein Cue Induces Habitat Selection by, and Predation on, Barnacles. Integr Comp Biol 2016; 56:901-913. [PMID: 27371385 DOI: 10.1093/icb/icw076] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Foundation species provide critical resources to ecological community members and are major determinants of biodiversity. The barnacle Balanus glandula is one such species and dominates space among the higher reaches on wave-swept shores. Here, we show that B. glandula produces a 199.6-kDa glycoprotein (named "MULTIFUNCin"), and following secretion, a 390-kDa homodimer in its native state. MULTIFUNCin expression is localized in the epidermis, cuticle, and new shell material. Consequently, this molecule can specify upon contact the immediate presence of a live barnacle. Shared, conserved domains place MULTIFUNCin in the α2-macroglobulin (A2M) subgroup of the thioester-containing protein family. Although previously undescribed, MULTIFUNCin shares 78% nucleotide sequence homology with a settlement-inducing pheromone (SIP) of the barnacle, Amphibalanus amphitrite Based on this and further evidence, we propose that the two proteins are orthologues and evolved ancestrally in structural and immunological roles. More recently, they became exploited as chemical cues for con- and heterospecific organisms, alike. MULTIFUNCin and SIP both induce habitat selection (settlement) by conspecific barnacle larvae. In addition, MULTIFUNCin acts as a potent feeding stimulant to major barnacle predators (sea stars and several whelk species). Promoting immigration via settlement on the one hand, and death via predation on the other, MULTIFUNCin simultaneously mediates opposing demographic processes toward structuring both predator and prey populations. As a multifunctional protein cue, MULTIFUNCin provides valuable sensory information, conveys different messages to different species, and drives complex biotic interactions.
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Affiliation(s)
- Graham A Ferrier
- *Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Steven J Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Catherine S Kaddis
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.,UCLA/DOE Institute for Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA
| | - Cheryl Ann Zimmer
- *Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA.,Moreton Bay Research Station, Centre for Marine Science, and School of Biological Sciences, University of Queensland, St Lucia, Brisbane 4072, Queensland, Australia
| | - Richard K Zimmer
- *Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA .,Moreton Bay Research Station, Centre for Marine Science, and School of Biological Sciences, University of Queensland, St Lucia, Brisbane 4072, Queensland, Australia
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Enhancing production of lipase MAS1 from marine Streptomyces sp. strain in Pichia pastoris by chaperones co-expression. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.06.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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130
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Adaptive Gene Loss? Tracing Back the Pseudogenization of the Rabbit CCL8 Chemokine. J Mol Evol 2016; 83:12-25. [PMID: 27306379 DOI: 10.1007/s00239-016-9747-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 05/03/2016] [Indexed: 10/21/2022]
Abstract
Studies of the process of pseudogenization have widened our understanding of adaptive evolutionary change. In Rabbit, an alteration at the second extra-cellular loop of the CCR5 chemokine receptor was found to be associated with the pseudogenization of one of its prime ligands, the chemokine CCL8. This relationship has raised questions about the existence of a causal link between both events, which would imply adaptive gene loss. This hypothesis is evaluated here by tracing back the history of the genetic modifications underlying the chemokine pseudogenization. The obtained data indicate that mutations at receptor and ligand genes occurred after the lineage split of New World Leporids versus Old World Leporids and prior to the generic split of the of Old World species studied, which occurred an estimated 8-9 million years ago. More important, they revealed the emergence, before this zoographical split, of a "slippery" nucleotide motif (CCCCGGG) at the 3' region of CCL8-exon2. Such motives are liable of generating +1G or -1G frameshifts, which could, however, be overcome by "translesion" synthesis or somatic reversion. The CCL8 pseudogenization in the Old World lineage was apparently initiated by three synapomorphic point mutations at the exon2-intron2 boundary which provide at short range premature terminating codons, independently of the reading frame imposed by the slippery motif. The presence of this motif in New World Leporids might allow verifying this scenario. The importance of CCL8-CCR5 signaling in parasite-host interaction would suggest that the CCL8 knock-out in Old World populations might be related to changes in pathogenic environment.
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131
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Kumar RB, Priya BS, Suresh MX. In silico analysis of potential inhibitors of Ca(2+) activated K(+) channel blocker, Charybdotoxin-C from Leiurus quinquestriatus hebraeus through molecular docking and dynamics studies. Indian J Pharmacol 2016; 47:280-4. [PMID: 26069365 PMCID: PMC4450553 DOI: 10.4103/0253-7613.157123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/04/2014] [Accepted: 02/26/2015] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE Charybdotoxin-C (ChTx-C), from the scorpion Leiurus, quinquestriatus hebraeus blocks the calcium-activated potassium channels and causes hyper excitability of the nervous system. Detailed understanding the structure of ChTx-C, conformational stability, and intermolecular interactions are required to select the potential inhibitors of the toxin. MATERIALS AND METHODS The structure of ChTx-C was modeled using Modeller 9v7. The amino acid residues lining the binding site were predicted and used for toxin-ligand docking studies, further, selected toxin-inhibitor complexes were studied using molecular dynamics (MD) simulations. RESULTS The predicted structure has 91.7% of amino acids in the core and allowed regions of Ramachandran plot. A total of 133 analog compounds of existing drugs for scorpion bites were used for docking. As a result of docking, a list of compounds was shown good inhibiting properties with target protein. By analyzing the interactions, Ser 15, Lys 32 had significant interactions with selected ligand molecules and Val5, which may have hydrophobic interaction with the cyclic group of the ligand. MD simulation studies revealed that the conformation and intermolecular interactions of all selected toxin-inhibitor complexes were stable. CONCLUSION The interactions of the ligand and active site amino acids were found out for the best-docked poses in turn helpful in designing potential antitoxins which may further be exploited in toxin based therapies.
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Affiliation(s)
- R Barani Kumar
- Department of Bioinformatics, Sathyabama University, Chennai, Tamil Nadu, India
| | - B Shanmuga Priya
- Department of Bioinformatics, Sathyabama University, Chennai, Tamil Nadu, India
| | - M Xavier Suresh
- Department of Bioinformatics, Sathyabama University, Chennai, Tamil Nadu, India
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132
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Predicted 3D Model of the Rabies Virus Glycoprotein Trimer. BIOMED RESEARCH INTERNATIONAL 2016; 2016:1674580. [PMID: 27294109 PMCID: PMC4879324 DOI: 10.1155/2016/1674580] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/21/2016] [Accepted: 03/06/2016] [Indexed: 12/20/2022]
Abstract
The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained.
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133
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Christie AE. Prediction of Scylla olivacea (Crustacea; Brachyura) peptide hormones using publicly accessible transcriptome shotgun assembly (TSA) sequences. Gen Comp Endocrinol 2016; 230-231:1-16. [PMID: 26965954 DOI: 10.1016/j.ygcen.2016.03.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/06/2016] [Indexed: 12/21/2022]
Abstract
The aquaculture of crabs from the genus Scylla is of increasing economic importance for many Southeast Asian countries. Expansion of Scylla farming has led to increased efforts to understand the physiology and behavior of these crabs, and as such, there are growing molecular resources for them. Here, publicly accessible Scylla olivacea transcriptomic data were mined for putative peptide-encoding transcripts; the proteins deduced from the identified sequences were then used to predict the structures of mature peptide hormones. Forty-nine pre/preprohormone-encoding transcripts were identified, allowing for the prediction of 187 distinct mature peptides. The identified peptides included isoforms of adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, bursicon β, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/molt-inhibiting hormone, diuretic hormone 31, eclosion hormone, FMRFamide-like peptide, HIGSLYRamide, insulin-like peptide, intocin, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, pigment dispersing hormone, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, SIFamide and tachykinin-related peptide, all well-known neuropeptide families. Surprisingly, the tissue used to generate the transcriptome mined here is reported to be testis. Whether or not the testis samples had neural contamination is unknown. However, if the peptides are truly produced by this reproductive organ, it could have far reaching consequences for the study of crustacean endocrinology, particularly in the area of reproductive control. Regardless, this peptidome is the largest thus far predicted for any brachyuran (true crab) species, and will serve as a foundation for future studies of peptidergic control in members of the commercially important genus Scylla.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
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Tzean Y, Chou TH, Hsiao CC, Shu PY, Walton JD, Tzean SS. Cloning and characterization of cuticle-degrading serine protease from nematode-trapping fungus Arthrobotrys musiformis. MYCOSCIENCE 2016. [DOI: 10.1016/j.myc.2015.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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135
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Guardiani C, Leggio L, Scorciapino MA, de Pinto V, Ceccarelli M. A computational study of ion current modulation in hVDAC3 induced by disulfide bonds. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:813-23. [PMID: 26806159 DOI: 10.1016/j.bbamem.2016.01.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 12/05/2015] [Accepted: 01/19/2016] [Indexed: 11/29/2022]
Abstract
The human VDAC channel exists in three isoforms characterized by high sequence homology and structural similarity. Yet the function and mode of action of hVDAC3 are still elusive. The presence of six surface cysteines exposed to the oxidizing environment of the mitochondrial inter-membrane space suggests the possible establishment of intramolecular disulfide bonds. Two natural candidates for disulfide bridge formation are Cys2 and Cys8 that, located on the flexible N-terminal domain, can easily come in contact. A third potentially important residue is Cys122 that is close to Cys2 in the homology model of VDAC3. Here we analyzed the impact of SS bonds through molecular dynamics simulations of derivatives of hVDAC3 (dubbed SS-2-8, SS-2-122, SS-8-122) including a single disulfide bond. Simulations showed that in SS-8-122, the fragment 1-7 crosses the top part of the barrel partially occluding the pore and causing a 20% drop of conductance. In order to identify other potential channel-occluding disulfide bonds, we used a set of neural networks and structural bioinformatics algorithms, after filtering with the steric constraints imposed by the 3D-structure. We identified other three species, namely SS-8-65, SS-2-36 and SS-8-36. While the conductance of SS-8-65 and SS-2-36 is about 30% lower than that of the species without disulfide bonds, the conductance of SS-8-36 was 40-50% lower. The results show how VDAC3 is able to modulate its pore size and current by exploiting the mobility of the N-terminal and forming, upon external stimuli, disulfide bridges with cysteine residues located on the barrel and exposed to the inter-membrane space.
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Affiliation(s)
- Carlo Guardiani
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche (CNR-IOM), UOS, Cagliari, Italy
| | - Loredana Leggio
- Department of Biomedical and Biotechnological Sciences, BIOMETEC, University of Catania, Italy; National Institute for Biomembranes and Biosystems, Section of Catania, viale A. Doria 6, 95125 Catania, Italy
| | - Mariano Andrea Scorciapino
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche (CNR-IOM), UOS, Cagliari, Italy; Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari, Italy
| | - Vito de Pinto
- Department of Biomedical and Biotechnological Sciences, BIOMETEC, University of Catania, Italy; National Institute for Biomembranes and Biosystems, Section of Catania, viale A. Doria 6, 95125 Catania, Italy
| | - Matteo Ceccarelli
- Istituto Officina dei Materiali, Consiglio Nazionale delle Ricerche (CNR-IOM), UOS, Cagliari, Italy; Department of Physics, University of Cagliari, Cagliari, Italy.
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Abstract
AbstractCutin hydrolase (EC 3.1.1.74), an extracellular polyesterase found in pollens, bacteria and fungi, is an efficient catalyst that exhibits hydrolytic activity on a variety of water-soluble esters, synthetic fibers, plastics and triglycerides. Thus, cutinase can be used in various applications such as ester synthesis, bio-scouring, food and detergent industries. Ancut2 is one of five genes encoding cutinases present in the Aspergillus niger ATCC 10574 genome. The cDNA of Ancut2 comprising of an open reading frame of 816 bp encoding a protein of 271 amino acid residues, was isolated and expressed in Pichia pastoris. The partially purified recombinant cutinase exhibited a molecular mass of approximately 40 kDa. The enzyme showed highest activity at 40°C with a preference for acidic pH (5.0-6.0). AnCUT2 showed hydrolytic activity towards various p-nitrophenyl esters with preference towards shorter chain esters such as p-nitrophenyl butyrate (C4). Scanning Electron Microscopy demonstrated that AnCUT2 was capable of modifying surfaces of synthetic polycaprolactone and polyethylene terephthalate plastics. The properties of this enzyme suggest that it may be applied in synthetic fiber modification and fruit processing industries.
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Christie AE, Chi M, Lameyer TJ, Pascual MG, Shea DN, Stanhope ME, Schulz DJ, Dickinson PS. Neuropeptidergic Signaling in the American Lobster Homarus americanus: New Insights from High-Throughput Nucleotide Sequencing. PLoS One 2015; 10:e0145964. [PMID: 26716450 PMCID: PMC4696782 DOI: 10.1371/journal.pone.0145964] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/10/2015] [Indexed: 11/20/2022] Open
Abstract
Peptides are the largest and most diverse class of molecules used for neurochemical communication, playing key roles in the control of essentially all aspects of physiology and behavior. The American lobster, Homarus americanus, is a crustacean of commercial and biomedical importance; lobster growth and reproduction are under neuropeptidergic control, and portions of the lobster nervous system serve as models for understanding the general principles underlying rhythmic motor behavior (including peptidergic neuromodulation). While a number of neuropeptides have been identified from H. americanus, and the effects of some have been investigated at the cellular/systems levels, little is currently known about the molecular components of neuropeptidergic signaling in the lobster. Here, a H. americanus neural transcriptome was generated and mined for sequences encoding putative peptide precursors and receptors; 35 precursor- and 41 receptor-encoding transcripts were identified. We predicted 194 distinct neuropeptides from the deduced precursor proteins, including members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin C, bursicon, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone (CHH), CHH precursor-related peptide, diuretic hormone 31, diuretic hormone 44, eclosion hormone, FLRFamide, GSEFLamide, insulin-like peptide, intocin, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, pigment dispersing hormone, proctolin, pyrokinin, SIFamide, sulfakinin and tachykinin-related peptide families. While some of the predicted peptides are known H. americanus isoforms, most are novel identifications, more than doubling the extant lobster neuropeptidome. The deduced receptor proteins are the first descriptions of H. americanus neuropeptide receptors, and include ones for most of the peptide groups mentioned earlier, as well as those for ecdysis-triggering hormone, red pigment concentrating hormone and short neuropeptide F. Multiple receptors were identified for most peptide families. These data represent the most complete description of the molecular underpinnings of peptidergic signaling in H. americanus, and will serve as a foundation for future gene-based studies of neuropeptidergic control in the lobster.
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Affiliation(s)
- Andrew E. Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center and Technology, 6500 College Station, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, Hawaii, 96822, United States of America
- * E-mail:
| | - Megan Chi
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center and Technology, 6500 College Station, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, Hawaii, 96822, United States of America
| | - Tess J. Lameyer
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, Maine, 04672, United States of America
| | - Micah G. Pascual
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center and Technology, 6500 College Station, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, Hawaii, 96822, United States of America
| | - Devlin N. Shea
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, Maine, 04672, United States of America
| | - Meredith E. Stanhope
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, Maine, 04672, United States of America
| | - David J. Schulz
- Division of Biological Sciences, University of Missouri, 218A LeFevre Hall, Columbia, Missouri, 65211, United States of America
| | - Patsy S. Dickinson
- Department of Biology, Bowdoin College, 6500 College Station, Brunswick, Maine, 04672, United States of America
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Chinchio M, Czaplewski C, Liwo A, Ołdziej S, Scheraga HA. Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field. J Chem Theory Comput 2015; 3:1236-48. [PMID: 26633198 DOI: 10.1021/ct7000842] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many proteins contain disulfide bonds that are usually essential for maintaining function and a stable structure. Several algorithms attempt to predict the arrangement of disulfide bonds in the context of protein structure prediction, but none can simulate the entire process of oxidative folding, including dynamic formation and breaking of disulfide bonds. In this work, a potential function developed to model disulfide bonds is coupled with the united-residue (UNRES) force field, and used in both canonical and replica exchange molecular dynamics simulations to produce complete oxidative folding pathways. The potential function is obtained by introducing a transition barrier that separates the bonded and nonbonded states of the half-cystine residues. Tests on several helical proteins show that improved predictions are obtained when dynamic disulfide-bond formation and breaking are considered. The effect of the disulfide bonds on the folding kinetics is also investigated, particularly their role in stabilizing folding intermediates, resulting in slower folding.
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Affiliation(s)
- M Chinchio
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdaǹsk, Sobieskiego 18, 80-952 Gdaǹsk, Poland
| | - C Czaplewski
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdaǹsk, Sobieskiego 18, 80-952 Gdaǹsk, Poland
| | - A Liwo
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdaǹsk, Sobieskiego 18, 80-952 Gdaǹsk, Poland
| | - S Ołdziej
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdaǹsk, Sobieskiego 18, 80-952 Gdaǹsk, Poland
| | - H A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and Faculty of Chemistry, University of Gdaǹsk, Sobieskiego 18, 80-952 Gdaǹsk, Poland
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139
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Christie AE, Chi M. Identification of the first neuropeptides from the enigmatic hexapod order Protura. Gen Comp Endocrinol 2015; 224:18-37. [PMID: 26055220 DOI: 10.1016/j.ygcen.2015.05.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
Abstract
The Hexapoda consists of two classes, the Entognatha and the Insecta, with the former group considered basal to the latter. The Protura is a basal order within the Entognatha, the members of which are minute soil dwellers first identified in the early 20th century. Recently, a transcriptome shotgun assembly (TSA) was generated for the proturan Acerentomon sp., providing the first significant molecular resource for this enigmatic hexapod order. As part of an ongoing effort to predict peptidomes for little studied members of the Arthropoda, we have mined this TSA dataset for transcripts encoding putative neuropeptide precursors and predicted the structures of mature peptides from the deduced proteins. Forty-seven peptide-encoding transcripts were mined from the Acerentomon TSA dataset, with 202 distinct peptides predicted from them. The peptides identified included isoforms of adipokinetic hormone, adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, allatotropin, bursicon α, bursicon β, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/ion transport peptide, diuretic hormone 31, diuretic hormone 44, ecdysis-triggering hormone, eclosion hormone, FMRFamide-like peptide, GSEFLamide, insulin-like peptide, intocin, leucokinin, myosuppressin, neuropeptide F, orcokinin, proctolin, pyrokinin, RYamide, short neuropeptide F, SIFamide, sulfakinin and tachykinin-related peptide; these are the first neuropeptides described from any proturan. Comparison of the Acerentomon precursors and mature peptides with those from other arthropods revealed features characteristic of both the insects and the crustaceans, which is consistent with the hypothesized phylogenetic position of the Protura within the Pancrustacea, i.e. at or near the point of divergence of the hexapods from the crustaceans.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
| | - Megan Chi
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
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140
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Christie AE, Chi M. Prediction of the neuropeptidomes of members of the Astacidea (Crustacea, Decapoda) using publicly accessible transcriptome shotgun assembly (TSA) sequence data. Gen Comp Endocrinol 2015; 224:38-60. [PMID: 26070255 DOI: 10.1016/j.ygcen.2015.06.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 05/30/2015] [Accepted: 06/03/2015] [Indexed: 11/20/2022]
Abstract
The decapod infraorder Astacidea is comprised of clawed lobsters and freshwater crayfish. Due to their economic importance and their use as models for investigating neurochemical signaling, much work has focused on elucidating their neurochemistry, particularly their peptidergic systems. Interestingly, no astacidean has been the subject of large-scale peptidomic analysis via in silico transcriptome mining, this despite growing transcriptomic resources for members of this taxon. Here, the publicly accessible astacidean transcriptome shotgun assembly data were mined for putative peptide-encoding transcripts; these sequences were used to predict the structures of mature neuropeptides. One hundred seventy-six distinct peptides were predicted for Procambarus clarkii, including isoforms of adipokinetic hormone-corazonin-like peptide (ACP), allatostatin A (AST-A), allatostatin B, allatostatin C (AST-C) bursicon α, bursicon β, CCHamide, crustacean hyperglycemic hormone (CHH)/ion transport peptide (ITP), diuretic hormone 31 (DH31), eclosion hormone (EH), FMRFamide-like peptide, GSEFLamide, intocin, leucokinin, neuroparsin, neuropeptide F, pigment dispersing hormone, pyrokinin, RYamide, short neuropeptide F (sNPF), SIFamide, sulfakinin and tachykinin-related peptide (TRP). Forty-six distinct peptides, including isoforms of AST-A, AST-C, bursicon α, CCHamide, CHH/ITP, DH31, EH, intocin, myosuppressin, neuroparsin, red pigment concentrating hormone, sNPF and TRP, were predicted for Pontastacus leptodactylus, with a bursicon β and a neuroparsin predicted for Cherax quadricarinatus. The identification of ACP is the first from a decapod, while the predictions of CCHamide, EH, GSEFLamide, intocin, neuroparsin and RYamide are firsts for the Astacidea. Collectively, these data greatly expand the catalog of known astacidean neuropeptides and provide a foundation for functional studies of peptidergic signaling in members of this decapod infraorder.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
| | - Megan Chi
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
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141
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Christie AE. In silico prediction of a neuropeptidome for the eusocial insect Mastotermes darwiniensis. Gen Comp Endocrinol 2015; 224:69-83. [PMID: 26095226 DOI: 10.1016/j.ygcen.2015.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 06/09/2015] [Indexed: 12/22/2022]
Abstract
Mastotermes darwiniensis is the most basal living member of the Isoptera (termites), yet it exhibits an extremely advanced level of eusocial organization. Given the interest in, and the high levels of differential developmental and behavioral control needed for, eusociality, it is surprising that essentially nothing is known about the native peptides of M. darwiniensis, which undoubtedly represent the largest and most diverse class of hormones present in this species. The recent public deposition of a 100,000(+)-sequence transcriptome for M. darwiniensis provides a means for peptide discovery in this termite. Here, this resource was mined for putative peptide-encoding transcripts via the BLAST algorithm tblastn and known arthropod neuropeptide precursor queries; mature peptide structures were predicted from the deduced pre/preprohormones using a well-vetted bioinformatics workflow. Thirty-four M. darwiniensis peptide-encoding transcripts were identified, with 163 distinct mature peptides predicted from these sequences. These peptides included members of the adipokinetic hormone, adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin C, allatotropin, bursicon β, CCHamide, corazonin, crustacean cardioactive peptide, crustacean hyperglycemic hormone/ion transport peptide, diuretic hormone 31, diuretic hormone 44, FMRFamide-like peptide, insulin-like peptide, leucokinin, myosuppressin, neuroparsin, neuropeptide F, orcokinin, pigment dispersing hormone, pyrokinin, RYamide, short neuropeptide F, SIFamide, sulfakinin and tachykinin-related peptide families. This peptidome is the largest thus far predicted for any member of the Isoptera, and provides a foundation for initiating studies of peptidergic signaling in this and other termites, including ones directed at understanding the roles peptide hormones play in the developmental and behavioral control required for eusociality.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
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142
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Tonk M, Knorr E, Cabezas-Cruz A, Valdés JJ, Kollewe C, Vilcinskas A. Tribolium castaneum defensins are primarily active against Gram-positive bacteria. J Invertebr Pathol 2015; 132:208-215. [PMID: 26522790 DOI: 10.1016/j.jip.2015.10.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 10/27/2015] [Accepted: 10/28/2015] [Indexed: 11/16/2022]
Abstract
The red flour beetle Tribolium castaneum is a destructive insect pest of stored food and feed products, and a model organism for development, evolutionary biology and immunity. The insect innate immune system includes antimicrobial peptides (AMPs) with a wide spectrum of targets including viruses, bacteria, fungi and parasites. Defensins are an evolutionarily-conserved class of AMPs and a potential new source of antimicrobial agents. In this context, we report the antimicrobial activity, phylogenetic and structural properties of three T. castaneum defensins (Def1, Def2 and Def3) and their relevance in the immunity of T. castaneum against bacterial pathogens. All three recombinant defensins showed bactericidal activity against Micrococcus luteus and Bacillus thuringiensis serovar tolworthi, but only Def1 and Def2 showed a bacteriostatic effect against Staphylococcus epidermidis. None of the defensins showed activity against the Gram-negative bacteria Escherichia coli and Pseudomonas entomophila or against the yeast Saccharomyces cerevisiae. All three defensins were transcriptionally upregulated following a bacterial challenge, suggesting a key role in the immunity of T. castaneum against bacterial pathogens. Phylogenetic analysis showed that defensins from T. castaneum, mealworms, Udo longhorn beetle and houseflies cluster within a well-defined clade of insect defensins. We conclude that T. castaneum defensins are primarily active against Gram-positive bacteria and that other AMPs may play a more prominent role against Gram-negative species.
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Affiliation(s)
- Miray Tonk
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Strasse, D-35394 Giessen, Germany.
| | - Eileen Knorr
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Strasse, D-35394 Giessen, Germany.
| | - Alejandro Cabezas-Cruz
- Center for Infection and Immunity of Lille (CIIL), INSERM U1019 - CNRS UMR 8204, Université Lille Nord de France, Institut Pasteur de Lille, Lille, France.
| | - James J Valdés
- Biology Centre of the AS CR, Institute of Parasitology, Branišovská 31, 37005 České Budějovice, Czech Republic.
| | - Christian Kollewe
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Strasse, D-35394 Giessen, Germany.
| | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Strasse, D-35394 Giessen, Germany; Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany.
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143
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Christie AE. Neuropeptide discovery in Symphylella vulgaris (Myriapoda, Symphyla): In silico prediction of the first myriapod peptidome. Gen Comp Endocrinol 2015; 223:73-86. [PMID: 26407502 DOI: 10.1016/j.ygcen.2015.09.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 09/22/2015] [Indexed: 12/27/2022]
Abstract
Arthropods have contributed greatly to our understanding of peptidergic control of physiology and behavior, and being the largest and most diverse animal phylum, represent a model for investigating peptide hormone evolution. Surprisingly, one arthropod subphylum, the Myriapoda, is uninvestigated in terms of its peptide hormones. The public deposition of a transcriptome for Symphylella vulgaris, a pseudocentipede, provides a means for peptide discovery in myriapods. Here, in silico transcriptome mining was used to identify 47 S. vulgaris neuropeptide-encoding transcripts within this dataset. The identified transcripts allowed for the deduction of 31 unique pre/preprohormone sequences, with 97 distinct mature peptides predicted from the deduced proteins. The predicted S. vulgaris peptidome includes members of the adipokinetic hormone/red pigment concentrating hormone, adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin C (AST-C), allatotropin, CCHamide, crustacean cardioactive peptide, GSEFLamide, insulin-like peptide, intocin, proctolin, pyrokinin, short neuropeptide F, SIFamide and sulfakinin families. This is the first, and thus far only, peptidome predicted for a myriapod. Of particular note were a modified AST-C, TYWKQCAFNAVSRFamide, that lacks one of two cysteine residues (i.e. one at position 13) stereotypically present in members of this peptide family (and hence is missing the disulfide bridge that spans these residues) and a SIFamide, PPFNGSIFamide, that is truncated due to a lysine for arginine substitution in the dibasic residue pair commonly located at positions 3 and 4 of stereotypical full-length isoforms (e.g. the crustacean peptide GYRKPPFNGSIFamide). The peptides predicted here represent the only extant resource for initiating investigations of native peptidergic signaling in the Myriapoda.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
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144
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Guillier C, Gamm M, Lucchi G, Truntzer C, Pecqueur D, Ducoroy P, Adrian M, Héloir MC. Toward the Identification of Two Glycoproteins Involved in the Stomatal Deregulation of Downy Mildew-Infected Grapevine Leaves. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1227-1236. [PMID: 26106900 DOI: 10.1094/mpmi-05-15-0115-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Stomata remain abnormally opened and unresponsive to abscisic acid in grapevine leaves infected by downy mildew. This deregulation occurs from 3 days postinoculation and increases concomitantly with leaf colonization by the pathogen. Using epidermal peels, we demonstrated that the active compound involved in this deregulation is located in the apoplast. Biochemical assays showed that the active compound present in the apoplastic fluids isolated from Plasmopara viticola-infected grapevine leaves (IAF) is a CysCys bridge-independent, thermostable and glycosylated protein. Fractionation guided assays based on chromatography coupled to stomatal response and proteomic analysis allowed the identification of both plant and pathogen proteins in the active fraction obtained from IAF. Further in silico analysis and discriminant filtrations based on the comparison between predictions and experimental indications lead to the identification of two Vitis vinifera proteins as candidates for the observed stomatal deregulation.
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Affiliation(s)
- Christelle Guillier
- 1 CNRS, UMR1347 Agroécologie, ERL CNRS 6300, BP 86510, F-21000 Dijon, France
| | - Magdalena Gamm
- 2 Université de Bourgogne, UMR1347 Agroécologie, ERL CNRS 6300, BP 86510, F-21000 Dijon, France
| | - Géraldine Lucchi
- 3 Clinical Innovation Proteomic Platform - CLIPP, 15 Boulevard Maréchal de Lattre de Tassigny, BP37013, F-21070 Dijon cedex, France
| | - Caroline Truntzer
- 3 Clinical Innovation Proteomic Platform - CLIPP, 15 Boulevard Maréchal de Lattre de Tassigny, BP37013, F-21070 Dijon cedex, France
| | - Delphine Pecqueur
- 3 Clinical Innovation Proteomic Platform - CLIPP, 15 Boulevard Maréchal de Lattre de Tassigny, BP37013, F-21070 Dijon cedex, France
| | - Patrick Ducoroy
- 3 Clinical Innovation Proteomic Platform - CLIPP, 15 Boulevard Maréchal de Lattre de Tassigny, BP37013, F-21070 Dijon cedex, France
| | - Marielle Adrian
- 2 Université de Bourgogne, UMR1347 Agroécologie, ERL CNRS 6300, BP 86510, F-21000 Dijon, France
| | - Marie-Claire Héloir
- 2 Université de Bourgogne, UMR1347 Agroécologie, ERL CNRS 6300, BP 86510, F-21000 Dijon, France
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145
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Ghanbarnia K, Fudal I, Larkan NJ, Links MG, Balesdent MH, Profotova B, Fernando WGD, Rouxel T, Borhan MH. Rapid identification of the Leptosphaeria maculans avirulence gene AvrLm2 using an intraspecific comparative genomics approach. MOLECULAR PLANT PATHOLOGY 2015; 16:699-709. [PMID: 25492575 PMCID: PMC6638346 DOI: 10.1111/mpp.12228] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Five avirulence genes from Leptosphaeria maculans, the causal agent of blackleg of canola (Brassica napus), have been identified previously through map-based cloning. In this study, a comparative genomic approach was used to clone the previously mapped AvrLm2. Given the lack of a presence-absence gene polymorphism coincident with the AvrLm2 phenotype, 36 L. maculans isolates were resequenced and analysed for single-nucleotide polymorphisms (SNPs) in predicted small secreted protein-encoding genes present within the map interval. Three SNPs coincident with the AvrLm2 phenotype were identified within LmCys1, previously identified as a putative effector-coding gene. Complementation of a virulent isolate with LmCys1, as the candidate AvrLm2 allele, restored the avirulent phenotype on Rlm2-containing B. napus lines. AvrLm2 encodes a small cysteine-rich protein with low similarity to other proteins in the public databases. Unlike other avirulence genes, AvrLm2 resides in a small GC island within an AT-rich isochore of the genome, and was never found to be deleted completely in virulent isolates.
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Affiliation(s)
- Kaveh Ghanbarnia
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada, R3T 2N2
| | | | - Nicholas J Larkan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
| | - Matthew G Links
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
- Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5C9
| | | | | | | | | | - M Hossein Borhan
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada, S7N 0X2
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146
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Gerdol M, Puillandre N, De Moro G, Guarnaccia C, Lucafò M, Benincasa M, Zlatev V, Manfrin C, Torboli V, Giulianini PG, Sava G, Venier P, Pallavicini A. Identification and Characterization of a Novel Family of Cysteine-Rich Peptides (MgCRP-I) from Mytilus galloprovincialis. Genome Biol Evol 2015. [PMID: 26201648 PMCID: PMC4558851 DOI: 10.1093/gbe/evv133] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We report the identification of a novel gene family (named MgCRP-I) encoding short secreted cysteine-rich peptides in the Mediterranean mussel Mytilus galloprovincialis. These peptides display a highly conserved pre-pro region and a hypervariable mature peptide comprising six invariant cysteine residues arranged in three intramolecular disulfide bridges. Although their cysteine pattern is similar to cysteines-rich neurotoxic peptides of distantly related protostomes such as cone snails and arachnids, the different organization of the disulfide bridges observed in synthetic peptides and phylogenetic analyses revealed MgCRP-I as a novel protein family. Genome- and transcriptome-wide searches for orthologous sequences in other bivalve species indicated the unique presence of this gene family in Mytilus spp. Like many antimicrobial peptides and neurotoxins, MgCRP-I peptides are produced as pre-propeptides, usually have a net positive charge and likely derive from similar evolutionary mechanisms, that is, gene duplication and positive selection within the mature peptide region; however, synthetic MgCRP-I peptides did not display significant toxicity in cultured mammalian cells, insecticidal, antimicrobial, or antifungal activities. The functional role of MgCRP-I peptides in mussel physiology still remains puzzling.
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Affiliation(s)
- Marco Gerdol
- Department of Life Sciences, University of Trieste, Italy
| | - Nicolas Puillandre
- Muséum National d'Histoire Naturelle, Département Systématique et Evolution, ISyEB Institut (UMR 7205 CNRS/UPMC/MNHN/EPHE), Paris, France
| | | | - Corrado Guarnaccia
- Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | | | | | - Ventislav Zlatev
- Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Chiara Manfrin
- Department of Life Sciences, University of Trieste, Italy
| | | | | | - Gianni Sava
- Department of Life Sciences, University of Trieste, Italy
| | - Paola Venier
- Department of Biology, University of Padova, Italy
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147
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Raimondi D, Orlando G, Vranken WF. An Evolutionary View on Disulfide Bond Connectivities Prediction Using Phylogenetic Trees and a Simple Cysteine Mutation Model. PLoS One 2015; 10:e0131792. [PMID: 26161671 PMCID: PMC4498770 DOI: 10.1371/journal.pone.0131792] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/07/2015] [Indexed: 01/09/2023] Open
Abstract
Disulfide bonds are crucial for many structural and functional aspects of proteins. They have a stabilizing role during folding, can regulate enzymatic activity and can trigger allosteric changes in the protein structure. Moreover, knowledge of the topology of the disulfide connectivity can be relevant in genomic annotation tasks and can provide long range constraints for ab-initio protein structure predictors. In this paper we describe PhyloCys, a novel unsupervised predictor of disulfide bond connectivity from known cysteine oxidation states. For each query protein, PhyloCys retrieves and aligns homologs with HHblits and builds a phylogenetic tree using ClustalW. A simplified model of cysteine co-evolution is then applied to the tree in order to hypothesize the presence of oxidized cysteines in the inner nodes of the tree, which represent ancestral protein sequences. The tree is then traversed from the leaves to the root and the putative disulfide connectivity is inferred by observing repeated patterns of tandem mutations between a sequence and its ancestors. A final correction is applied using the Edmonds-Gabow maximum weight perfect matching algorithm. The evolutionary approach applied in PhyloCys results in disulfide bond predictions equivalent to Sephiroth, another approach that takes whole sequence information into account, and is 26-29% better than state of the art methods based on cysteine covariance patterns in multiple sequence alignments, while requiring one order of magnitude fewer homologous sequences (10(3) instead of 10(4)), thus extending its range of applicability. The software described in this article and the datasets used are available at http://ibsquare.be/phylocys.
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Affiliation(s)
- Daniele Raimondi
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Department of Structural Biology, VIB, Brussels, Belgium
- Machine Learning Group, ULB, Brussels, Belgium
| | - Gabriele Orlando
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Department of Structural Biology, VIB, Brussels, Belgium
- Machine Learning Group, ULB, Brussels, Belgium
| | - Wim F. Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
- Department of Structural Biology, VIB, Brussels, Belgium
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148
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Pereiro P, Varela M, Diaz-Rosales P, Romero A, Dios S, Figueras A, Novoa B. Zebrafish Nk-lysins: First insights about their cellular and functional diversification. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 51:148-159. [PMID: 25813149 DOI: 10.1016/j.dci.2015.03.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 03/19/2015] [Accepted: 03/19/2015] [Indexed: 06/04/2023]
Abstract
Nk-lysins are antimicrobial proteins produced by cytotoxic T lymphocytes and natural killer cells with a broad antimicrobial spectrum (including bacteria, fungi and parasites). Nevertheless, the implication of these proteins in the protection against viral infections is still poorly understood. In this work, four different Nk-lysin genes (nkla, nklb, nklc and nkld) were identified in the zebrafish genome. That means that zebrafish is the species with the higher repertoire of Nk-lysin genes described so far. The differential expression pattern of the Nk-lysins in several tissues, during ontogeny, among the different kidney cell populations, as well as between Rag1(-/-) and Rag1(+/+) individuals, could suggest a certain specialization of different cell types in the production of different Nk-lysin. Moreover, only two of these genes (nkla and nkld) were significantly up-regulated after viral infection, and this observation could be also a consequence of a functional diversification of the zebrafish Nk-lysins.
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Affiliation(s)
- P Pereiro
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | - M Varela
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | - P Diaz-Rosales
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | - A Romero
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | - S Dios
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | - A Figueras
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain
| | - B Novoa
- Instituto de Investigaciones Marinas (IIM), CSIC, Vigo, Spain.
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149
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Baranowska Körberg I, Hofmeister W, Markljung E, Cao J, Nilsson D, Ludwig M, Draaken M, Holmdahl G, Barker G, Reutter H, Vukojević V, Clementson Kockum C, Lundin J, Lindstrand A, Nordenskjöld A. WNT3 involvement in human bladder exstrophy and cloaca development in zebrafish. Hum Mol Genet 2015; 24:5069-78. [DOI: 10.1093/hmg/ddv225] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/12/2015] [Indexed: 01/16/2023] Open
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150
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Bocian-Ostrzycka KM, Grzeszczuk MJ, Dziewit L, Jagusztyn-Krynicka EK. Diversity of the Epsilonproteobacteria Dsb (disulfide bond) systems. Front Microbiol 2015; 6:570. [PMID: 26106374 PMCID: PMC4460558 DOI: 10.3389/fmicb.2015.00570] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/24/2015] [Indexed: 12/20/2022] Open
Abstract
The bacterial proteins of the Dsb family-important components of the post-translational protein modification system-catalyze the formation of disulfide bridges, a process that is crucial for protein structure stabilization and activity. Dsb systems play an essential role in the assembly of many virulence factors. Recent rapid advances in global analysis of bacteria have thrown light on the enormous diversity among bacterial Dsb systems. While the Escherichia coli disulfide bond-forming system is quite well understood, the mechanisms of action of Dsb systems in other bacteria, including members of class Epsilonproteobacteria that contain pathogenic and non-pathogenic bacteria colonizing extremely diverse ecological niches, are poorly characterized. Here we present a review of current knowledge on Epsilonproteobacteria Dsb systems. We have focused on the Dsb systems of Campylobacter spp. and Helicobacter spp. because our knowledge about Dsb proteins of Wolinella and Arcobacter spp. is still scarce and comes mainly from bioinformatic studies. Helicobacter pylori is a common human pathogen that colonizes the gastric epithelium of humans with severe consequences. Campylobacter spp. is a leading cause of zoonotic enteric bacterial infections in most developed and developing nations. We focus on various aspects of the diversity of the Dsb systems and their influence on pathogenicity, particularly because Dsb proteins are considered as potential targets for a new class of anti-virulence drugs to treat human infections by Campylobacter or Helicobacter spp.
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