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Moeller FU, Webster NS, Herbold CW, Behnam F, Domman D, Albertsen M, Mooshammer M, Markert S, Turaev D, Becher D, Rattei T, Schweder T, Richter A, Watzka M, Nielsen PH, Wagner M. Characterization of a thaumarchaeal symbiont that drives incomplete nitrification in the tropical sponge Ianthella basta. Environ Microbiol 2019; 21:3831-3854. [PMID: 31271506 PMCID: PMC6790972 DOI: 10.1111/1462-2920.14732] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 06/14/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022]
Abstract
Marine sponges represent one of the few eukaryotic groups that frequently harbour symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However, in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of ammonia-oxidizing archaea (AOA). Here, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and isotope-based functional assays. 'Candidatus Nitrosospongia ianthellae' is only distantly related to cultured AOA. It is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbour nitrite-oxidizing microbes. Furthermore, this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system, represent important adaptations of AOA to life within these ancient filter-feeding animals.
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Affiliation(s)
- Florian U. Moeller
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Nicole S. Webster
- Australian Institute of Marine ScienceTownsvilleQueenslandAustralia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesUniversity of QueenslandSt LuciaQueenslandAustralia
| | - Craig W. Herbold
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Faris Behnam
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Daryl Domman
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Mads Albertsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Maria Mooshammer
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
| | - Stephanie Markert
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Dmitrij Turaev
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Dörte Becher
- Institute of Microbiology, Microbial ProteomicsUniversity of GreifswaldGreifswaldGermany
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, Division of Computational Systems BiologyUniversity of ViennaAustria
| | - Thomas Schweder
- Institute of Marine Biotechnology e.VGreifswaldGermany
- Institute of Pharmacy, Pharmaceutical BiotechnologyUniversity of GreifswaldGreifswaldGermany
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Margarete Watzka
- Centre for Microbiology and Environmental Systems Science, Division of Terrestrial Ecosystem ResearchUniversity of ViennaAustria
| | - Per Halkjaer Nielsen
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Division of Microbial EcologyUniversity of ViennaAustria
- Center for Microbial Communities, Department of Chemistry and BioscienceAalborg University9220AalborgDenmark
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Herrera-Gamboa JG, López-Alvarado CB, Pérez-Ortega E, Damas-Buenrostro LC, Cabada-Amaya JC, Pereyra-Alférez B. Proteomic analysis of two malting barleys ( Hordeum vulgare L.) and their impact on wort quality. J Cereal Sci 2018. [DOI: 10.1016/j.jcs.2018.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
Zymography, the detection, identification, and even quantification of enzyme activity fractionated by gel electrophoresis, has received increasing attention in the last years, as revealed by the number of articles published. A number of enzymes are routinely detected by zymography, especially with clinical interest. This introductory chapter reviews the major principles behind zymography. New advances of this method are basically focused towards two-dimensional zymography and transfer zymography as will be explained in the rest of the chapters. Some general considerations when performing the experiments are outlined as well as the major troubleshooting and safety issues necessary for correct development of the electrophoresis.
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Chen S, Meng F, Chen Z, Tomlinson BN, Wesley JM, Sun GY, Whaley-Connell AT, Sowers JR, Cui J, Gu Z. Two-dimensional zymography differentiates gelatinase isoforms in stimulated microglial cells and in brain tissues of acute brain injuries. PLoS One 2015; 10:e0123852. [PMID: 25859655 PMCID: PMC4393235 DOI: 10.1371/journal.pone.0123852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 02/22/2015] [Indexed: 12/24/2022] Open
Abstract
Excessive activation of gelatinases (MMP-2/-9) is a key cause of detrimental outcomes in neurodegenerative diseases. A single-dimension zymography has been widely used to determine gelatinase expression and activity, but this method is inadequate in resolving complex enzyme isoforms, because gelatinase expression and activity could be modified at transcriptional and posttranslational levels. In this study, we investigated gelatinase isoforms under in vitro and in vivo conditions using two-dimensional (2D) gelatin zymography electrophoresis, a protocol allowing separation of proteins based on isoelectric points (pI) and molecular weights. We observed organomercuric chemical 4-aminophenylmercuric acetate-induced activation of MMP-2 isoforms with variant pI values in the conditioned medium of human fibrosarcoma HT1080 cells. Studies with murine BV-2 microglial cells indicated a series of proform MMP-9 spots separated by variant pI values due to stimulation with lipopolysaccharide (LPS). The MMP-9 pI values were shifted after treatment with alkaline phosphatase, suggesting presence of phosphorylated isoforms due to the proinflammatory stimulation. Similar MMP-9 isoforms with variant pI values in the same molecular weight were also found in mouse brains after ischemic and traumatic brain injuries. In contrast, there was no detectable pI differentiation of MMP-9 in the brains of chronic Zucker obese rats. These results demonstrated effective use of 2D zymography to separate modified MMP isoforms with variant pI values and to detect posttranslational modifications under different pathological conditions.
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Affiliation(s)
- Shanyan Chen
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Center for Translational Neuroscience, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, Missouri, United States of America
| | - Fanjun Meng
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Center for Translational Neuroscience, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Zhenzhou Chen
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Center for Translational Neuroscience, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Brittany N. Tomlinson
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Center for Translational Neuroscience, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- MS in Pathology program, University of Missouri Graduate School, Columbia, Missouri, United States of America
| | - Jennifer M. Wesley
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Center for Translational Neuroscience, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Grace Y. Sun
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Center for Translational Neuroscience, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Department of Biochemistry, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Adam T. Whaley-Connell
- Department of Internal Medicine Diabetes and Cardiovascular Center, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, United States of America
| | - James R. Sowers
- Department of Internal Medicine Diabetes and Cardiovascular Center, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, United States of America
| | - Jiankun Cui
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Center for Translational Neuroscience, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, United States of America
| | - Zezong Gu
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Center for Translational Neuroscience, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, United States of America
- * E-mail:
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Di Bari G, Gentile E, Latronico T, Corriero G, Fasano A, Marzano CN, Liuzzi GM. Comparative analysis of protein profiles of aqueous extracts from marine sponges and assessment of cytotoxicity on different mammalian cell types. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2014; 38:1007-1015. [PMID: 25461562 DOI: 10.1016/j.etap.2014.10.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/20/2014] [Accepted: 10/26/2014] [Indexed: 06/04/2023]
Abstract
Marine natural products extracted from sponges represent a new source for drug discovery. Here we describe a simple method for preparing aqueous extracts from 7 Mediterranean demosponges, which allowed the extraction of water-soluble compounds, such as proteins by homogenization of sponge tissue in phosphate buffered saline (PBS). The comparative analysis by SDS-PAGE showed differences in number of bands, bandwidth and intensity among the sponges analyzed. The PAS/silver staining revealed a substantial and different glycoprotein assortment among the demosponges studied. To further study the biological activities present in the sponge extracts, we determined the non-cytotoxic doses on four different mammalian cell types demonstrating that the optimal non-cytotoxic doses were cell type- and extract-dependent. In conclusion, the extraction method described in this paper represents a fast and efficient procedure for the extraction of water-soluble proteins from marine sponges. Furthermore, the cell viability data suggest the feasibility of this method for the direct in vitro cell-based assays.
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Affiliation(s)
- Gaetano Di Bari
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Eugenia Gentile
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Tiziana Latronico
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Giuseppe Corriero
- Department of Biology, University of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Anna Fasano
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy
| | | | - Grazia Maria Liuzzi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy.
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Bashir MEH, Ward JM, Cummings M, Karrar EE, Root M, Mohamed ABA, Naclerio RM, Preuss D. Dual function of novel pollen coat (surface) proteins: IgE-binding capacity and proteolytic activity disrupting the airway epithelial barrier. PLoS One 2013; 8:e53337. [PMID: 23308195 PMCID: PMC3538775 DOI: 10.1371/journal.pone.0053337] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 11/27/2012] [Indexed: 11/18/2022] Open
Abstract
Background The pollen coat is the first structure of the pollen to encounter the mucosal immune system upon inhalation. Prior characterizations of pollen allergens have focused on water-soluble, cytoplasmic proteins, but have overlooked much of the extracellular pollen coat. Due to washing with organic solvents when prepared, these pollen coat proteins are typically absent from commercial standardized allergenic extracts (i.e., “de-fatted”), and, as a result, their involvement in allergy has not been explored. Methodology/Principal Findings Using a unique approach to search for pollen allergenic proteins residing in the pollen coat, we employed transmission electron microscopy (TEM) to assess the impact of organic solvents on the structural integrity of the pollen coat. TEM results indicated that de-fatting of Cynodon dactylon (Bermuda grass) pollen (BGP) by use of organic solvents altered the structural integrity of the pollen coat. The novel IgE-binding proteins of the BGP coat include a cysteine protease (CP) and endoxylanase (EXY). The full-length cDNA that encodes the novel IgE-reactive CP was cloned from floral RNA. The EXY and CP were purified to homogeneity and tested for IgE reactivity. The CP from the BGP coat increased the permeability of human airway epithelial cells, caused a clear concentration-dependent detachment of cells, and damaged their barrier integrity. Conclusions/Significance Using an immunoproteomics approach, novel allergenic proteins of the BGP coat were identified. These proteins represent a class of novel dual-function proteins residing on the coat of the pollen grain that have IgE-binding capacity and proteolytic activity, which disrupts the integrity of the airway epithelial barrier. The identification of pollen coat allergens might explain the IgE-negative response to available skin-prick-testing proteins in patients who have positive symptoms. Further study of the role of these pollen coat proteins in allergic responses is warranted and could potentially lead to the development of improved diagnostic and therapeutic tools.
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Affiliation(s)
- Mohamed Elfatih H Bashir
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, The University of Chicago, Chicago, Illinois, United States of America.
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Slattery M, Ankisetty S, Corrales J, Marsh-Hunkin KE, Gochfeld DJ, Willett KL, Rimoldi JM. Marine proteomics: a critical assessment of an emerging technology. JOURNAL OF NATURAL PRODUCTS 2012; 75:1833-1877. [PMID: 23009278 DOI: 10.1021/np300366a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.
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Affiliation(s)
- Marc Slattery
- Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA.
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Analysis of pineapple [Ananas comosus (L.) Merr.] fruit proteinases by 2-D zymography and direct identification of the major zymographic spots by mass spectrometry. Food Chem 2010. [DOI: 10.1016/j.foodchem.2010.06.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Larocca M, Rossano R, Riccio P. Analysis of green kiwi fruit (Actinidia deliciosa cv. Hayward) proteinases by two-dimensional zymography and direct identification of zymographic spots by mass spectrometry. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2010; 90:2411-2418. [PMID: 20672335 DOI: 10.1002/jsfa.4100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
BACKGROUND Proteinases present in kiwi fruits are potentially allergenic enzymes belonging to the papain family of cysteine proteinases. Actinidin is a prominent kiwi enzyme. The study of kiwi proteinases is important for the follow-up of fruit maturation, a deeper insight in the allergenic properties of individual proteins, and the application of kiwi proteinases for meat tenderisation and other industrial purposes. RESULTS Kiwi crude extracts were analysed by two-dimensional zymography on gelatin-containing gels. The digestion by the reactivated proteolytic enzymes after electrophoresis resulted in insights into kiwi proteinases. A mixture of several enzyme isotypes with the same pI but different molecular mass was observed. Clear spots, corresponding to the proteolytic activities, were excised, digested with trypsin, and submitted to MALDI-ToF mass spectrometry for protein identification. The most representative enzyme was actinidin. CONCLUSIONS The innovative achievements of the present study are the: (1) two-dimensional zymographic map of kiwi gelatinases without the need for extensive purification; and (2) direct identification of proteinase isotypes by means of direct MALDI-ToF MS analysis of the zymographic spots.
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Affiliation(s)
- Marilena Larocca
- Department of Biology, Defence and Agro-Forestal Biotechnology, Center of Bioproteomics, University of Basilicata, 85100 Potenza, Italy
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Strategies to evade false positives in the in situ analysis of peptide antibiotics in SDS–PAGE gels. Anal Biochem 2008; 373:401-3. [DOI: 10.1016/j.ab.2007.09.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 09/16/2007] [Accepted: 09/17/2007] [Indexed: 11/18/2022]
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