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Calvete JJ, Lomonte B, Saviola AJ, Calderón Celis F, Ruiz Encinar J. Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives. MASS SPECTROMETRY REVIEWS 2024; 43:977-997. [PMID: 37155340 DOI: 10.1002/mas.21850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/24/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.
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Affiliation(s)
- Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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Nakatani H, Yamashiro K, Uchiyama T, Motokucho S, Dao ATN, Kim HJ, Yagi M, Kyozuka Y. Effect of Copper Antifouling Paint on Marine Degradation of Polypropylene: Uneven Distribution of Microdebris between Nagasaki Port and Goto Island, Japan. Molecules 2024; 29:1173. [PMID: 38474685 DOI: 10.3390/molecules29051173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Microplastics (MP) encompass not only plastic products but also paint particles. Marine microdebris, including MP, was retrieved from five sampling stations spanning Nagasaki-Goto island and was classified into six types, primarily consisting of MP (A), Si-based (B), and Cu-based (C) paint particles. Type-A particles, i.e., MP, were exceedingly small, with 74% of them having a long diameter of 25 µm or less. The vertical distribution of type C, containing cuprous oxide, exhibited no depth dependence, with its dominant size being less than 7 μm. It was considered that the presence of type C was associated with a natural phenomenon of MP loss. To clarify this, polypropylene (PP) samples containing cuprous oxide were prepared, and their accelerated degradation behavior was studied using a novel enhanced degradation method employing a sulfate ion radical as an initiator. Infrared spectroscopy revealed the formation of a copper soap compound in seawater. Scanning electron microscopy/energy-dispersive X-ray spectroscopy analysis indicated that the chemical reactions between Cl- and cuprous oxide produced Cu+ ions. The acceleration of degradation induced by the copper soap formed was studied through the changes in the number of PP chain scissions, revealing that the presence of type-C accelerated MP degradation.
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Affiliation(s)
- Hisayuki Nakatani
- Polymeri Materials Laboratory, Chemistry and Materials Engineering Program, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
- Organization for Marine Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kaito Yamashiro
- Polymeri Materials Laboratory, Chemistry and Materials Engineering Program, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Taishi Uchiyama
- Polymeri Materials Laboratory, Chemistry and Materials Engineering Program, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Suguru Motokucho
- Polymeri Materials Laboratory, Chemistry and Materials Engineering Program, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
- Organization for Marine Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Anh Thi Ngoc Dao
- Polymeri Materials Laboratory, Chemistry and Materials Engineering Program, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Hee-Jin Kim
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Mitsuharu Yagi
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yusaku Kyozuka
- Organization for Marine Science and Technology, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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Sanniyasi E, Gopal RK, Damodharan R, Thirumurugan T, Mahendran V. Bioaccumulation of Titanium in diatom Cyclotella atomus Hust. Biometals 2024; 37:71-86. [PMID: 37566151 DOI: 10.1007/s10534-023-00528-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Diatomaceous earth or diatomite is a fossil rock deposit of diatoms made up of silica and other minerals. A distinguishing feature of diatoms that placed them in the single class of microalgae Bacillariophyceae, is the frustule, a transparent, hard-shelled cell wall. It's interesting to note that the diatom has specific proteins and enzymes for heavy metal detoxification and can intake and store more heavy metals in its frustule. Consequently, an attempt has been made in this study to determine the bioaccumulation of metals in the frustules of the diatom. Hence, a centric diatom was isolated from the freshwater sample collected from the Adyar River, Chennai, Tamil Nadu. The diameter of the cell was 5-7.5 µm and 20-23 striations with radial arrangement. A single, dark off-center fultoportula and marginal fultoportula on the striae are found in the diatom. Additionally, one rimoportula between two marginal fultoportula distributed on the striae between the costa was also seen. As a result, the isolated diatom was morphologically identified as Cyclotella atomus Hust. Simultaneously, the bioaccumulation study reveals that the Titanium (Ti) was found accumulated in the frustules of the diatom incubated in the Ti-supplemented culture medium based on the scanning electron microscope-energy-dispersive X-ray analysis (SEM-EDAX). Therefore, the biogenic accumulation and fabrication of Titanium frustules in diatom have advantages in enhancing the efficiency of solar cells.
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Affiliation(s)
- Elumalai Sanniyasi
- Department of Biotechnology, University of Madras, Guindy Campus, Chennai, 600 025, India.
| | - Rajesh Kanna Gopal
- Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, 600077, India
| | - Rajesh Damodharan
- Department of Biotechnology, University of Madras, Guindy Campus, Chennai, 600 025, India
| | - Tarani Thirumurugan
- Department of Biotechnology, Rajalakshmi Engineering College (Autonomous), Thandalam, Chennai, 602 105, India
| | - Vishali Mahendran
- Department of Biotechnology, Rajalakshmi Engineering College (Autonomous), Thandalam, Chennai, 602 105, India
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Chasapis CT, Perlepes SP, Bjørklund G, Peana M. Structural modeling of protein ensembles between E3 RING ligases and SARS-CoV-2: The role of zinc binding domains. J Trace Elem Med Biol 2023; 75:127089. [PMID: 36209710 PMCID: PMC9531365 DOI: 10.1016/j.jtemb.2022.127089] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/13/2022] [Accepted: 09/28/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND The ubiquitin system is a modification process with many different cellular functions including immune signaling and antiviral functions. E3 ubiquitin ligases are enzymes that recruit an E2 ubiquitin-conjugating enzyme bound to ubiquitin in order to catalyze the transfer of ubiquitin from the E2 to a protein substrate. The RING E3s, the most abundant type of ubiquitin ligases, are characterized by a zinc (II)-binding domain called RING (Really Interesting New Gene). Viral replication requires modifying and hijacking key cellular pathways within host cells such as cellular ubiquitination. There are well-established examples where a viral proteins bind to RING E3s, redirecting them to degrade otherwise long-lived host proteins or inhibiting E3's ubiquitination activity. Recently, three binary interactions between SARS-CoV-2 proteins and innate human immune signaling Ε3 RING ligases: NSP15-RNF41, ORF3a-TRIM59 and NSP9-MIB1 have been experimentally established. METHODS In this work, we have investigated the mode of the previous experimentally supported NSP15-RNF41, ORF3a,-TRIM59 and NSP9-MIB1 binary interactions by in silico methodologies intending to provide structural insights of E3-virus interplay that can help identify potential inhibitors that could block SARS-CoV-2 infection of immune cells. CONCLUSION In silico methodologies have shown that the above human E3 ligases interact with viral partners through their Zn(II) binding domains. This RING mediated formation of stable SARS-CoV-2-E3 complexes indicates a critical structural role of RING domains in immune system disruption by SARS-CoV-2-infection. DATA AVAILABILITY The data used to support the findings of this research are included within the article and are labeled with references.
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Affiliation(s)
- Christos T Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece.
| | | | - Geir Bjørklund
- Council for Nutritional and Environmental Medicine (CONEM), Mo i Rana, Norway
| | - Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, Italy.
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Peana M, Pelucelli A, Chasapis CT, Perlepes SP, Bekiari V, Medici S, Zoroddu MA. Biological Effects of Human Exposure to Environmental Cadmium. Biomolecules 2022; 13:biom13010036. [PMID: 36671421 PMCID: PMC9855641 DOI: 10.3390/biom13010036] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Cadmium (Cd) is a toxic metal for the human organism and for all ecosystems. Cd is naturally found at low levels; however, higher amounts of Cd in the environment result from human activities as it spreads into the air and water in the form of micropollutants as a consequence of industrial processes, pollution, waste incineration, and electronic waste recycling. The human body has a limited ability to respond to Cd exposure since the metal does not undergo metabolic degradation into less toxic species and is only poorly excreted. The extremely long biological half-life of Cd essentially makes it a cumulative toxin; chronic exposure causes harmful effects from the metal stored in the organs. The present paper considers exposure and potential health concerns due to environmental cadmium. Exposure to Cd compounds is primarily associated with an elevated risk of lung, kidney, prostate, and pancreatic cancer. Cd has also been linked to cancers of the breast, urinary system, and bladder. The multiple mechanisms of Cd-induced carcinogenesis include oxidative stress with the inhibition of antioxidant enzymes, the promotion of lipid peroxidation, and interference with DNA repair systems. Cd2+ can also replace essential metal ions, including redox-active ones. A total of 12 cancer types associated with specific genes coding for the Cd-metalloproteome were identified in this work. In addition, we summarize the proper treatments of Cd poisoning, based on the use of selected Cd detoxifying agents and chelators, and the potential for preventive approaches to counteract its chronic exposure.
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Affiliation(s)
- Massimiliano Peana
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
- Correspondence: (M.P.); (A.P.)
| | - Alessio Pelucelli
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
- Correspondence: (M.P.); (A.P.)
| | - Christos T. Chasapis
- Institute of Chemical Biology, National Hellenic Research Foundation, 11635 Athens, Greece
| | | | - Vlasoula Bekiari
- School of Agricultural Science, University of Patras, 30200 Messolonghi, Greece
| | - Serenella Medici
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
| | - Maria Antonietta Zoroddu
- Department of Chemical, Physical, Mathematical and Natural Sciences, University of Sassari, 07100 Sassari, Italy
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