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Priyanka P, Gopalakrishnan AP, Nisar M, Shivamurthy PB, George M, John L, Sanjeev D, Yandigeri T, Thomas SD, Rafi A, Dagamajalu S, Velikkakath AKG, Abhinand CS, Kanekar S, Prasad TSK, Balaya RDA, Raju R. A global phosphosite-correlated network map of Thousand And One Kinase 1 (TAOK1). Int J Biochem Cell Biol 2024; 170:106558. [PMID: 38479581 DOI: 10.1016/j.biocel.2024.106558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/19/2024] [Accepted: 03/09/2024] [Indexed: 03/25/2024]
Abstract
Thousand and one amino acid kinase 1 (TAOK1) is a sterile 20 family Serine/Threonine kinase linked to microtubule dynamics, checkpoint signaling, DNA damage response, and neurological functions. Molecular-level alterations of TAOK1 have been associated with neurodevelopment disorders and cancers. Despite their known involvement in physiological and pathophysiological processes, and as a core member of the hippo signaling pathway, the phosphoregulatory network of TAOK1 has not been visualized. Aimed to explore this network, we first analyzed the predominantly detected and differentially regulated TAOK1 phosphosites in global phosphoproteome datasets across diverse experimental conditions. Based on 709 qualitative and 210 quantitative differential cellular phosphoproteome datasets that were systematically assembled, we identified that phosphorylation at Ser421, Ser9, Ser965, and Ser445 predominantly represented TAOK1 in almost 75% of these datasets. Surprisingly, the functional role of all these phosphosites in TAOK1 remains unexplored. Hence, we employed a robust strategy to extract the phosphosites in proteins that significantly correlated in expression with predominant TAOK1 phosphosites. This led to the first categorization of the phosphosites including those in the currently known and predicted interactors, kinases, and substrates, that positively/negatively correlated with the expression status of each predominant TAOK1 phosphosites. Subsequently, we also analyzed the phosphosites in core proteins of the hippo signaling pathway. Based on the TAOK1 phosphoregulatory network analysis, we inferred the potential role of the predominant TAOK1 phosphosites. Especially, we propose pSer9 as an autophosphorylation and TAOK1 kinase activity-associated phosphosite and pS421, the most frequently detected phosphosite in TAOK1, as a significant regulatory phosphosite involved in the maintenance of genome integrity. Considering that the impact of all phosphosites that predominantly represent each kinase is essential for the efficient interpretation of global phosphoproteome datasets, we believe that the approach undertaken in this study is suitable to be extended to other kinases for accelerated research.
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Affiliation(s)
- Pahal Priyanka
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Athira Perunelly Gopalakrishnan
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Mahammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | - Mejo George
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Diya Sanjeev
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Tanuja Yandigeri
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Sonet D Thomas
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Ahmad Rafi
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Shobha Dagamajalu
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Anoop Kumar G Velikkakath
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Chandran S Abhinand
- Center for Systems Biology and Molecular Medicine (CSBMM), Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India.
| | - Saptami Kanekar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
| | | | | | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to be University), Mangalore 575018, India.
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Bo Z, Li X, Zhang C, Guo M, Cao Y, Zhang X, Wu Y. Phosphoproteomic landscape of pseudorabies virus infection reveals multiple potential antiviral targets. Microbiol Spectr 2024; 12:e0301023. [PMID: 37991362 PMCID: PMC10783065 DOI: 10.1128/spectrum.03010-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/16/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE Pseudorabies virus (PRV) is a kind of alpha herpesvirus that infects a wide range of animals and even human beings. Therefore, it is important to explore the mechanisms behind PRV replication and pathogenesis. By conducting a tandem mass tag-based phosphoproteome, this study revealed the phosphorylated proteins and cellular response pathways involved in PRV infection. Findings from this study shed light on the relationship between the phosphorylated cellular proteins and PRV infection, as well as guiding the discovery of targets for the development of antiviral compounds against PRV.
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Affiliation(s)
- Zongyi Bo
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaojuan Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Chengcheng Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Mengjiao Guo
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yongzhong Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaorong Zhang
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yantao Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
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Batie M, Fasanya T, Kenneth NS, Rocha S. Oxygen-regulated post-translation modifications as master signalling pathway in cells. EMBO Rep 2023; 24:e57849. [PMID: 37877678 DOI: 10.15252/embr.202357849] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 10/26/2023] Open
Abstract
Oxygen is essential for viability in mammalian organisms. However, cells are often exposed to changes in oxygen availability, due to either increased demand or reduced oxygen supply, herein called hypoxia. To be able to survive and/or adapt to hypoxia, cells activate a variety of signalling cascades resulting in changes to chromatin, gene expression, metabolism and viability. Cellular signalling is often mediated via post-translational modifications (PTMs), and this is no different in response to hypoxia. Many enzymes require oxygen for their activity and oxygen can directly influence several PTMS. Here, we review the direct impact of changes in oxygen availability on PTMs such as proline, asparagine, histidine and lysine hydroxylation, lysine and arginine methylation and cysteine dioxygenation, with a focus on mammalian systems. In addition, indirect hypoxia-dependent effects on phosphorylation, ubiquitination and sumoylation will also be discussed. Direct and indirect oxygen-regulated changes to PTMs are coordinated to achieve the cell's ultimate response to hypoxia. However, specific oxygen sensitivity and the functional relevance of some of the identified PTMs still require significant research.
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Affiliation(s)
- Michael Batie
- Department of Biochemistry, Cell and Systems Biology, Institute of Molecular Systems and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Temitope Fasanya
- Department of Biochemistry, Cell and Systems Biology, Institute of Molecular Systems and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Niall S Kenneth
- Department of Biochemistry, Cell and Systems Biology, Institute of Molecular Systems and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sonia Rocha
- Department of Biochemistry, Cell and Systems Biology, Institute of Molecular Systems and Integrative Biology, University of Liverpool, Liverpool, UK
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Batie M, Kenneth NS, Rocha S. Systems approaches to understand oxygen sensing: how multi-omics has driven advances in understanding oxygen-based signalling. Biochem J 2022; 479:245-257. [PMID: 35119457 PMCID: PMC8883490 DOI: 10.1042/bcj20210554] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 12/11/2022]
Abstract
Hypoxia is a common denominator in the pathophysiology of a variety of human disease states. Insight into how cells detect, and respond to low oxygen is crucial to understanding the role of hypoxia in disease. Central to the hypoxic response is rapid changes in the expression of genes essential to carry out a wide range of functions to adapt the cell/tissue to decreased oxygen availability. These changes in gene expression are co-ordinated by specialised transcription factors, changes to chromatin architecture and intricate balances between protein synthesis and destruction that together establish changes to the cellular proteome. In this article, we will discuss the advances of our understanding of the cellular oxygen sensing machinery achieved through the application of 'omics-based experimental approaches.
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Affiliation(s)
- Michael Batie
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L697ZB, U.K
| | - Niall S. Kenneth
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L697ZB, U.K
| | - Sonia Rocha
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L697ZB, U.K
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