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Antonaru LA, Selinger VM, Jung P, Di Stefano G, Sanderson ND, Barker L, Wilson DJ, Büdel B, Canniffe DP, Billi D, Nürnberg DJ. Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales. ISME COMMUNICATIONS 2023; 3:113. [PMID: 37857858 PMCID: PMC10587186 DOI: 10.1038/s43705-023-00319-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 10/21/2023]
Abstract
Deserts represent an extreme challenge for photosynthetic life. Despite their aridity, they are often inhabited by diverse microscopic communities of cyanobacteria. These organisms are commonly found in lithic habitats, where they are partially sheltered from extremes of temperature and UV radiation. However, living under the rock surface imposes additional constraints, such as limited light availability, and enrichment of longer wavelengths than are typically usable for oxygenic photosynthesis. Some cyanobacteria from the genus Chroococcidiopsis can use this light to photosynthesize, in a process known as far-red light photoacclimation, or FaRLiP. This genus has commonly been reported from both hot and cold deserts. However, not all Chroococcidiopsis strains carry FaRLiP genes, thus motivating our study into the interplay between FaRLiP and extreme lithic environments. The abundance of sequence data and strains provided the necessary material for an in-depth phylogenetic study, involving spectroscopy, microscopy, and determination of pigment composition, as well as gene and genome analyses. Pigment analyses revealed the presence of red-shifted chlorophylls d and f in all FaRLiP strains tested. In addition, eight genus-level taxa were defined within the encompassing Chroococcidiopsidales, clarifying the phylogeny of this long-standing polyphyletic order. FaRLiP is near universally present in a generalist genus identified in a wide variety of environments, Chroococcidiopsis sensu stricto, while it is rare or absent in closely related, extremophile taxa, including those preferentially inhabiting deserts. This likely reflects the evolutionary process of gene loss in specialist lineages.
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Affiliation(s)
- Laura A Antonaru
- Institute for Experimental Physics, Freie Universität Berlin, Berlin, Germany.
- Department of Life Sciences, Imperial College London, London, UK.
| | - Vera M Selinger
- Institute for Experimental Physics, Freie Universität Berlin, Berlin, Germany
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany
| | - Patrick Jung
- Department of Integrative Biotechnology, University of Applied Sciences Kaiserslautern, Pirmasens, Germany
| | - Giorgia Di Stefano
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Nicholas D Sanderson
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel J Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Burkhard Büdel
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Daniel P Canniffe
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Dennis J Nürnberg
- Institute for Experimental Physics, Freie Universität Berlin, Berlin, Germany.
- Dahlem Centre of Plant Sciences, Freie Universität Berlin, Berlin, Germany.
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2
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Sound JK, Peters A, Bellamy-Carter J, Rad-Menéndez C, MacKechnie K, Green DH, Leney AC. Rapid Cyanobacteria Species Identification with High Sensitivity Using Native Mass Spectrometry. Anal Chem 2021; 93:14293-14299. [PMID: 34657414 PMCID: PMC8552214 DOI: 10.1021/acs.analchem.1c03412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacteria have evolved over billions of years to adapt and survive in diverse climates. Environmentally, this presents a huge challenge because cyanobacteria can now rapidly form algae blooms that are detrimental to aquatic life. In addition, many cyanobacteria produce toxins, making them hazardous to animals and humans that they encounter. Rapid identification of cyanobacteria is essential to monitor and prevent toxic algae blooms. Here, we show for the first time how native mass spectrometry can quickly and precisely identify cyanobacteria from diverse aquatic environments. By monitoring phycobiliproteins, abundant protein complexes within cyanobacteria, simple, easy-to-understand mass spectral "fingerprints" were created that were unique to each species. Moreover, our method is 10-fold more sensitive than the current MALDI-TOF mass spectrometric methods, meaning that cyanobacteria can be monitored using this technology prior to bloom formation. Together, the data show great promise for the simultaneous detection and identification of co-existing cyanobacteria in situ.
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Affiliation(s)
- Jaspreet K Sound
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Anna Peters
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | | | - Cecilia Rad-Menéndez
- Scottish Association for Marine Science, Argyll PA37 1QA, U.K.,Culture Collection of Algae and Protozoa (CCAP), Scottish Marine Institute, Oban PA37 1QA, U.K
| | - Karen MacKechnie
- Scottish Association for Marine Science, Argyll PA37 1QA, U.K.,Culture Collection of Algae and Protozoa (CCAP), Scottish Marine Institute, Oban PA37 1QA, U.K
| | - David H Green
- Scottish Association for Marine Science, Argyll PA37 1QA, U.K
| | - Aneika C Leney
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
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3
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Krupka M, Raskova Kafkova L, Barkocziova L, Sloupenska K, Brokesova D, Sebela M, Raska M. Preparation and properties of recombinant Clostridium ramosum IgA proteinase. Isolation of Fc-SC and Fab fragments of human secretory IgA. Protein Expr Purif 2021; 184:105891. [PMID: 33895263 DOI: 10.1016/j.pep.2021.105891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/23/2021] [Accepted: 04/17/2021] [Indexed: 11/17/2022]
Abstract
Immunoglobulin A (IgA) proteinase from Clostridium ramosum is the enzyme which cleaves IgA of both subclasses; in contrast, the other bacterial proteinases cleave only IgA1 proteins. Previous reports characterized the activity of proteinase naturally secreted by C. ramosum specific for the normal human serum IgA of IgA1 and IgA2m(1) subclasses and also for secretory IgA (SIgA). Its amino acid sequence was determined, and the recombinant proteinase which cleaved IgA of both subclasses was prepared. Here we report the optimized expression, purification, storage conditions and activity testing against purified human milk SIgA. The recombinant C. ramosum IgA proteinase isolated in the high degree of purity exhibited almost complete cleavage of SIgA of both subclasses. The proteinase remained active upon storage for more than 10 month at -20 °C without substantial loss of enzymatic activity. Purified SIgA fragments are suitable for studies of all antigen-binding and Fc-dependent functions of SIgA involved in the protection against infections with mucosal pathogens.
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Affiliation(s)
- Michal Krupka
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Leona Raskova Kafkova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic.
| | - Lucia Barkocziova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Kristyna Sloupenska
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Diana Brokesova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic
| | - Marek Sebela
- Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University Olomouc, Olomouc, Czech Republic
| | - Milan Raska
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University Olomouc, Olomouc, Czech Republic.
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4
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Šebela M, Raus M, Ondřej V, Hašler P. The Influence of Metabolic Inhibitors, Antibiotics, and Microgravity on Intact Cell MALDI-TOF Mass Spectra of the Cyanobacterium Synechococcus Sp. UPOC S4. Molecules 2021; 26:molecules26061683. [PMID: 33802864 PMCID: PMC8002600 DOI: 10.3390/molecules26061683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/02/2021] [Accepted: 03/11/2021] [Indexed: 11/28/2022] Open
Abstract
The aim and novelty of this paper are found in assessing the influence of inhibitors and antibiotics on intact cell MALDI-TOF mass spectra of the cyanobacterium Synechococcus sp. UPOC S4 and to check the impact on reliability of identification. Defining the limits of this method is important for its use in biology and applied science. The compounds included inhibitors of respiration, glycolysis, citrate cycle, and proteosynthesis. They were used at 1–10 μM concentrations and different periods of up to 3 weeks. Cells were also grown without inhibitors in a microgravity because of expected strong effects. Mass spectra were evaluated using controls and interpreted in terms of differential peaks and their assignment to protein sequences by mass. Antibiotics, azide, and bromopyruvate had the greatest impact. The spectral patterns were markedly altered after a prolonged incubation at higher concentrations, which precluded identification in the database of reference spectra. The incubation in microgravity showed a similar effect. These differences were evident in dendrograms constructed from the spectral data. Enzyme inhibitors affected the spectra to a smaller extent. This study shows that only a long-term presence of antibiotics and strong metabolic inhibitors in the medium at 10−5 M concentrations hinders the correct identification of cyanobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF).
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Affiliation(s)
- Marek Šebela
- Department of Biochemistry and Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic;
- Correspondence: (M.Š.); (P.H.)
| | - Martin Raus
- Department of Biochemistry and Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic;
| | - Vladan Ondřej
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic;
| | - Petr Hašler
- Department of Botany, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic;
- Correspondence: (M.Š.); (P.H.)
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Jayathirtha M, Dupree EJ, Manzoor Z, Larose B, Sechrist Z, Neagu AN, Petre BA, Darie CC. Mass Spectrometric (MS) Analysis of Proteins and Peptides. Curr Protein Pept Sci 2020; 22:92-120. [PMID: 32713333 DOI: 10.2174/1389203721666200726223336] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 05/12/2020] [Accepted: 05/28/2020] [Indexed: 01/09/2023]
Abstract
The human genome is sequenced and comprised of ~30,000 genes, making humans just a little bit more complicated than worms or flies. However, complexity of humans is given by proteins that these genes code for because one gene can produce many proteins mostly through alternative splicing and tissue-dependent expression of particular proteins. In addition, post-translational modifications (PTMs) in proteins greatly increase the number of gene products or protein isoforms. Furthermore, stable and transient interactions between proteins, protein isoforms/proteoforms and PTM-ed proteins (protein-protein interactions, PPI) add yet another level of complexity in humans and other organisms. In the past, all of these proteins were analyzed one at the time. Currently, they are analyzed by a less tedious method: mass spectrometry (MS) for two reasons: 1) because of the complexity of proteins, protein PTMs and PPIs and 2) because MS is the only method that can keep up with such a complex array of features. Here, we discuss the applications of mass spectrometry in protein analysis.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Emmalyn J Dupree
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zaen Manzoor
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Brianna Larose
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Zach Sechrist
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Iasi, Romania
| | - Brindusa Alina Petre
- Laboratory of Biochemistry, Department of Chemistry, Al. I. Cuza University of Iasi, Iasi, Romania, Center for Fundamental Research and Experimental Development in Translation Medicine - TRANSCEND, Regional Institute of Oncology, Iasi, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY, United States
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Asukabe H, Akahori S, Ueno E, Nakayama T, Yamashita R, Arii S, Harada KI, Imanishi SY. Cyanobacterial Classification with the Toxicity Using MALDI Biotyper. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1572-1578. [PMID: 32501712 DOI: 10.1021/jasms.0c00148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
An abnormal growth of cyanobacteria in eutrophicated freshwaters can cause various environmental problems. In particular, Microcystis producing hepatotoxic cyclic heptapeptides microcystins (MCs) has been globally observed. Recent studies have demonstrated that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) offers a rapid classification of cyanobacteria; however, they have not fully considered the toxicity yet. In this study, we have performed MALDI-TOF MS for intact cyanobacterial cells using Biotyper software and optimized their conditions to achieve cyanobacterial classification with the toxicity. The detection mass range used for Biotyper was extended to cover small molecules, but their intense ions were suppressed as a function of the used instrument Autoflex Speed, which enabled simultaneous observations of large molecular fingerprints and small MCs with comparable ion intensity. Hierarchical clustering of mass spectra obtained under the optimized conditions differentiated toxic and non-toxic clusters of Microcystis strains and furthermore formed a tight cluster of non-toxic strains possessing the MC biosynthesis gene mcyG. Spectral libraries were expanded to >30 genera (>80 strains) under the default and optimized conditions to improve the confidence of cyanobacterial classification. Consequently, spectral library searching allowed for characterization of cyanobacteria from a field sample as mixed toxic and non-toxic Microcystis cells, without isolating those cells.
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Affiliation(s)
- Hirohiko Asukabe
- Faculty of Pharmacy, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
| | - Satoko Akahori
- Faculty of Pharmacy, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
| | - Ema Ueno
- Faculty of Pharmacy, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
| | - Takuma Nakayama
- Faculty of Pharmacy, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
| | - Ryuji Yamashita
- Graduate School of Environmental and Human Sciences, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
| | - Suzue Arii
- Faculty of Pharmacy, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
| | - Ken-Ichi Harada
- Faculty of Pharmacy, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
- Graduate School of Environmental and Human Sciences, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
| | - Susumu Y Imanishi
- Faculty of Pharmacy, Meijo University, Yagotoyama 150, Tempaku, Nagoya 468-8503, Japan
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Maghembe R, Damian D, Makaranga A, Nyandoro SS, Lyantagaye SL, Kusari S, Hatti-Kaul R. Omics for Bioprospecting and Drug Discovery from Bacteria and Microalgae. Antibiotics (Basel) 2020; 9:antibiotics9050229. [PMID: 32375367 PMCID: PMC7277505 DOI: 10.3390/antibiotics9050229] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/10/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022] Open
Abstract
"Omics" represent a combinatorial approach to high-throughput analysis of biological entities for various purposes. It broadly encompasses genomics, transcriptomics, proteomics, lipidomics, and metabolomics. Bacteria and microalgae exhibit a wide range of genetic, biochemical and concomitantly, physiological variations owing to their exposure to biotic and abiotic dynamics in their ecosystem conditions. Consequently, optimal conditions for adequate growth and production of useful bacterial or microalgal metabolites are critically unpredictable. Traditional methods employ microbe isolation and 'blind'-culture optimization with numerous chemical analyses making the bioprospecting process laborious, strenuous, and costly. Advances in the next generation sequencing (NGS) technologies have offered a platform for the pan-genomic analysis of microbes from community and strain downstream to the gene level. Changing conditions in nature or laboratory accompany epigenetic modulation, variation in gene expression, and subsequent biochemical profiles defining an organism's inherent metabolic repertoire. Proteome and metabolome analysis could further our understanding of the molecular and biochemical attributes of the microbes under research. This review provides an overview of recent studies that have employed omics as a robust, broad-spectrum approach for screening bacteria and microalgae to exploit their potential as sources of drug leads by focusing on their genomes, secondary metabolite biosynthetic pathway genes, transcriptomes, and metabolomes. We also highlight how recent studies have combined molecular biology with analytical chemistry methods, which further underscore the need for advances in bioinformatics and chemoinformatics as vital instruments in the discovery of novel bacterial and microalgal strains as well as new drug leads.
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Affiliation(s)
- Reuben Maghembe
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
- Department of Biological and Marine Sciences, Marian University College, P.O. Box 47, Bagamoyo, Tanzania;
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, 22100 Lund, Sweden
| | - Donath Damian
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
| | - Abdalah Makaranga
- Department of Biological and Marine Sciences, Marian University College, P.O. Box 47, Bagamoyo, Tanzania;
- International Center for Genetic Engineering and Biotechnology (ICGEB), Omics of Algae Group, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Stephen Samwel Nyandoro
- Chemistry Department, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35061, Dar es Salaam, Tanzania;
| | - Sylvester Leonard Lyantagaye
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 25179, Dar es Salaam, Tanzania; (R.M.); (D.D.); (S.L.L.)
- Department of Biochemistry, Mbeya College of Health and Allied Sciences, University of Dar es Salaam, P.O. Box 608, Mbeya, Tanzania
| | - Souvik Kusari
- Institute of Environmental Research (INFU), Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
- Correspondence: (S.K.); (R.H.-K.); Tel.: +49-2317554086 (S.K.); +46-462224840 (R.H.-K.)
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Box 124, 22100 Lund, Sweden
- Correspondence: (S.K.); (R.H.-K.); Tel.: +49-2317554086 (S.K.); +46-462224840 (R.H.-K.)
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