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Almeida AM, Ali SA, Ceciliani F, Eckersall PD, Hernández-Castellano LE, Han R, Hodnik JJ, Jaswal S, Lippolis JD, McLaughlin M, Miller I, Mohanty AK, Mrljak V, Nally JE, Nanni P, Plowman JE, Poleti MD, Ribeiro DM, Rodrigues P, Roschitzki B, Schlapbach R, Starič J, Yang Y, Zachut M. Domestic animal proteomics in the 21st century: A global retrospective and viewpoint analysis. J Proteomics 2021; 241:104220. [PMID: 33838350 DOI: 10.1016/j.jprot.2021.104220] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/01/2021] [Accepted: 04/02/2021] [Indexed: 12/12/2022]
Abstract
Animal production and health are of significant economic importance, particularly regarding the world food supply. Animal and veterinary sciences have evolved immensely in the past six decades, particularly in genetics, nutrition, housing, management and health. To address major challenges such as those posed by climate change or metabolic disorders, it is of utmost importance to use state-of-the-art research tools. Proteomics and the other post-genomic tools (transcriptomics or metabolomics) are among them. Proteomics has experienced a considerable development over the last decades. This brought developments to different scientific fields. The use and adoption of proteomics tools in animal and veterinary sciences has some limitations (database availability or access to proteomics platforms and funding). As a result, proteomics' use by animal science researchers varies across the globe. In this viewpoint article, we focus on the developments of domestic animal proteomics over the last decade in different regions of the globe and how the researchers have coped with such challenges. In the second part of the article, we provide examples of funding, educational and laboratory establishment initiatives designed to foster the development of (animal-based) proteomics. International scientific collaboration is a definitive and key feature in the development and advancement of domestic animal proteomics. SIGNIFICANCE: Animal production and health are very important for food supply worldwide particularly as a source of proteinaceous foods. Animal and veterinary sciences have evolved immensely in the last decades. In order to address the major contemporary challenges facing animal and veterinary sciences, it is of utmost importance to use state-of-the-art research tools such as Proteomics and other Omics. Herein, we focus on the major developments in domestic animal proteomics worldwide during the last decade and how different regions of the world have used the technology in this specific research field. We address also major international efforts aiming to increase the research output in this area and highlight the importance of international cooperation to address specific problems inherent to domestic animal proteomics.
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Affiliation(s)
- André M Almeida
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal.
| | - Syed Azmal Ali
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Fabrizio Ceciliani
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, 20133 Milano, Italy
| | - P David Eckersall
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Lorenzo E Hernández-Castellano
- Department of Animal Science, AU-Foulum, Aarhus University, 8830 Tjele, Denmark; Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413 Arucas, Spain
| | - Rongwei Han
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Jaka J Hodnik
- Veterinary Faculty, Clinic for Reproduction and Large Animals - Section for Ruminants, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Shalini Jaswal
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - John D Lippolis
- Ruminant Diseases and Immunology Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa 50010, United States
| | - Mark McLaughlin
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Ingrid Miller
- Institute of Medical Biochemistry, University of Veterinary Medicine, Veterinaerplatz 1, A-1210 Vienna, Austria
| | - Ashok Kumar Mohanty
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Vladimir Mrljak
- ERA Chair FP7, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Jarlath E Nally
- Ruminant Diseases and Immunology Research Unit, USDA, Agricultural Research Service, National Animal Disease Center, Ames, Iowa 50010, United States
| | - Paolo Nanni
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology ETH Zurich / University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | | | - Mirele D Poleti
- FZEA - Faculty of Animal Science and Food Engineering, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | - David M Ribeiro
- LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisboa, Portugal
| | - Pedro Rodrigues
- CCMAR - Centre of Marine Sciences of Algarve, University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology ETH Zurich / University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology ETH Zurich / University of Zurich, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Jože Starič
- Veterinary Faculty, Clinic for Reproduction and Large Animals - Section for Ruminants, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Yongxin Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China
| | - Maya Zachut
- Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization/Volcani Center, Rishon Lezion 7505101, Israel
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In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins. Sci Rep 2018; 8:17246. [PMID: 30467398 PMCID: PMC6250715 DOI: 10.1038/s41598-018-35589-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/07/2018] [Indexed: 01/05/2023] Open
Abstract
Bacillus subtilis is a sporulating Gram-positive bacterium widely used in basic research and biotechnology. Despite being one of the best-characterized bacterial model organism, recent proteomics studies identified only about 50% of its theoretical protein count. Here we combined several hundred MS measurements to obtain a comprehensive map of the proteome, phosphoproteome and acetylome of B. subtilis grown at 37 °C in minimal medium. We covered 75% of the theoretical proteome (3,159 proteins), detected 1,085 phosphorylation and 4,893 lysine acetylation sites and performed a systematic bioinformatic characterization of the obtained data. A subset of analyzed MS files allowed us to reconstruct a network of Hanks-type protein kinases, Ser/Thr/Tyr phosphatases and their substrates. We applied genomic phylostratigraphy to gauge the evolutionary age of B. subtilis protein classes and revealed that protein modifications were present on the oldest bacterial proteins. Finally, we performed a proteogenomic analysis by mapping all MS spectra onto a six-frame translation of B. subtilis genome and found evidence for 19 novel ORFs. We provide the most extensive overview of the proteome and post-translational modifications for B. subtilis to date, with insights into functional annotation and evolutionary aspects of the B. subtilis genome.
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