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Huang Y, Mao Z, Zhang Y, Zhao J, Luan X, Wu K, Yun L, Yu J, Shi Z, Liao X, Ma H. Omics data analysis reveals the system-level constraint on cellular amino acid composition. Synth Syst Biotechnol 2024; 9:304-311. [PMID: 38510205 PMCID: PMC10951587 DOI: 10.1016/j.synbio.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
Proteins play a pivotal role in coordinating the functions of organisms, essentially governing their traits, as the dynamic arrangement of diverse amino acids leads to a multitude of folded configurations within peptide chains. Despite dynamic changes in amino acid composition of an individual protein (referred to as AAP) and great variance in protein expression levels under different conditions, our study, utilizing transcriptomics data from four model organisms uncovers surprising stability in the overall amino acid composition of the total cellular proteins (referred to as AACell). Although this value may vary between different species, we observed no significant differences among distinct strains of the same species. This indicates that organisms enforce system-level constraints to maintain a consistent AACell, even amid fluctuations in AAP and protein expression. Further exploration of this phenomenon promises insights into the intricate mechanisms orchestrating cellular protein expression and adaptation to varying environmental challenges.
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Affiliation(s)
- Yuanyuan Huang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Zhitao Mao
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Yue Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Jianxiao Zhao
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Xiaodi Luan
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Ke Wu
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Lili Yun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Jing Yu
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Zhenkun Shi
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Xiaoping Liao
- Haihe Laboratory of Synthetic Biology, Tianjin, 300308, China
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Hongwu Ma
- Biodesign Center, Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
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Zhang YJ, Luo Z, Sun Y, Liu J, Chen Z. From beasts to bytes: Revolutionizing zoological research with artificial intelligence. Zool Res 2023; 44:1115-1131. [PMID: 37933101 PMCID: PMC10802096 DOI: 10.24272/j.issn.2095-8137.2023.263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/30/2023] [Indexed: 11/08/2023] Open
Abstract
Since the late 2010s, Artificial Intelligence (AI) including machine learning, boosted through deep learning, has boomed as a vital tool to leverage computer vision, natural language processing and speech recognition in revolutionizing zoological research. This review provides an overview of the primary tasks, core models, datasets, and applications of AI in zoological research, including animal classification, resource conservation, behavior, development, genetics and evolution, breeding and health, disease models, and paleontology. Additionally, we explore the challenges and future directions of integrating AI into this field. Based on numerous case studies, this review outlines various avenues for incorporating AI into zoological research and underscores its potential to enhance our understanding of the intricate relationships that exist within the animal kingdom. As we build a bridge between beast and byte realms, this review serves as a resource for envisioning novel AI applications in zoological research that have not yet been explored.
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Affiliation(s)
- Yu-Juan Zhang
- Chongqing Key Laboratory of Vector Insects
- Chongqing Key Laboratory of Animal Biology
- College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Zeyu Luo
- Chongqing Key Laboratory of Vector Insects
- Chongqing Key Laboratory of Animal Biology
- College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Yawen Sun
- Chongqing Key Laboratory of Vector Insects
- Chongqing Key Laboratory of Animal Biology
- College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Junhao Liu
- Chongqing Key Laboratory of Vector Insects
- Chongqing Key Laboratory of Animal Biology
- College of Life Science, Chongqing Normal University, Chongqing 401331, China
| | - Zongqing Chen
- School of Mathematical Sciences
- National Center for Applied Mathematics in Chongqing, Chongqing Normal University, Chongqing 401331, China. E-mail:
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Qin W, Wan Q, Yan J, Han X, Lu W, Ma Z, Ye T, Li Y, Li C, Wang C, Tay FR, Niu L, Jiao K. Effect of Extracellular Ribonucleic Acids on Neurovascularization in Osteoarthritis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301763. [PMID: 37395388 PMCID: PMC10502862 DOI: 10.1002/advs.202301763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/14/2023] [Indexed: 07/04/2023]
Abstract
Osteoarthritis is a degenerative disease characterized by abnormal neurovascularization at the osteochondral junctions, the regulatory mechanisms of which remain poorly understood. In the present study, a murine osteoarthritic model with augmented neurovascularization at the osteochondral junction is used to examine this under-evaluated facet of degenerative joint dysfunction. Increased extracellular RNA (exRNA) content is identified in neurovascularized osteoarthritic joints. It is found that the amount of exRNA is positively correlated with the extent of neurovascularization and the expression of vascular endothelial growth factor (VEGF). In vitro binding assay and molecular docking demonstrate that synthetic RNAs bind to VEGF via electrostatic interactions. The RNA-VEGF complex promotes the migration and function of endothelial progenitor cells and trigeminal ganglion cells. The use of VEGF and VEGFR2 inhibitors significantly inhibits the amplification of the RNA-VEGF complex. Disruption of the RNA-VEGF complex by RNase and polyethyleneimine reduces its in vitro activities, as well as prevents excessive neurovascularization and osteochondral deterioration in vivo. The results of the present study suggest that exRNAs may be potential targets for regulating nerve and blood vessel ingrowth under physiological and pathological joint conditions.
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Affiliation(s)
- Wen‐pin Qin
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Qian‐Qian Wan
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Jian‐Fei Yan
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Xiao‐Xiao Han
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Wei‐Cheng Lu
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Zhang‐Yu Ma
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Tao Ye
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Yu‐Tao Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Chang‐Jun Li
- Department of EndocrinologyEndocrinology Research CenterThe Xiangya Hospital of Central South UniversityChangshaHunan410008P. R. China
| | - Chen Wang
- Department of StomatologyThe Eighth Medical Center of PLA General HospitalHaidian DistrictBeijingP. R. China100091
| | - Franklin R. Tay
- Dental College of GeorgiaAugusta UniversityAugustaGA30912USA
| | - Li‐Na Niu
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
| | - Kai Jiao
- Department of StomatologyTangdu hospitalThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of StomatologySchool of StomatologyThe Fourth Military Medical UniversityXi'anShaanxi710032P. R. China
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Lan Y, Liang Y, Xiao X, Shi Y, Zhu M, Meng C, Yang S, Khan MT, Zhang YJ. Stoichioproteomics study of differentially expressed proteins and pathways in head and neck cancer. BRAZ J BIOL 2021; 83:e249424. [PMID: 34730606 DOI: 10.1590/1519-6984.249424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/20/2021] [Indexed: 01/16/2023] Open
Abstract
Hypoxia is a prominent feature of head and neck cancer. However, the oxygen element characteristics of proteins and how they adapt to hypoxia microenvironments of head and neck cancer are still unknown. Human genome sequences and proteins expressed data of head and neck cancer were retrieved from pathology atlas of Human Protein Atlas project. Then compared the oxygen and carbon element contents between proteomes of head and neck cancer and normal oral mucosa-squamous epithelial cells, genome locations, pathways, and functional dissection associated with head and neck cancer were also studied. A total of 902 differentially expressed proteins were observed where the average oxygen content is higher than that of the lowly expressed proteins in head and neck cancer proteins. Further, the average oxygen content of the up regulated proteins was 2.54% higher than other. None of their coding genes were distributed on the Y chromosome. The up regulated proteins were enriched in endocytosis, apoptosis and regulation of actin cytoskeleton. The increased oxygen contents of the highly expressed and the up regulated proteins might be caused by frequent activity of cytoskeleton and adapted to the rapid growth and fast division of the head and neck cancer cells. The oxygen usage bias and key proteins may help us to understand the mechanisms behind head and neck cancer in targeted therapy, which lays a foundation for the application of stoichioproteomics in targeted therapy and provides promise for potential treatments for head and neck cancer.
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Affiliation(s)
- Y Lan
- Chongqing Normal University, College of Life Sciences, Shapingba, Chongqing, P.R. China
| | - Y Liang
- Chongqing Normal University, College of Life Sciences, Shapingba, Chongqing, P.R. China
| | - X Xiao
- Chongqing Normal University, College of Life Sciences, Shapingba, Chongqing, P.R. China
| | - Y Shi
- Chongqing Normal University, College of Life Sciences, Shapingba, Chongqing, P.R. China
| | - M Zhu
- Chongqing Normal University, College of Life Sciences, Shapingba, Chongqing, P.R. China
| | - C Meng
- Chongqing Normal University, College of Life Sciences, Shapingba, Chongqing, P.R. China
| | - S Yang
- Ningxia University, School of Life Sciences, Xixia, Yinchuan, Ningxia, P.R. China
| | - M T Khan
- The University of Lahore-Pakistan, Institute of Molecular Biology and Biotechnology, Lahore, Pakistan
| | - Y J Zhang
- Chongqing Normal University, College of Life Sciences, Shapingba, Chongqing, P.R. China
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Yin Y, Li B, Mou K, Khan MT, Kaushik AC, Wei D, Zhang YJ. Stoichioproteomics reveal oxygen usage bias, key proteins and pathways in glioma. BMC Med Genomics 2019; 12:125. [PMID: 31464612 PMCID: PMC6716898 DOI: 10.1186/s12920-019-0571-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/12/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The five-year survival rate and therapeutic effect of malignant glioma is low. Identification of key/associated proteins and pathways in glioma is necessary for developing effective diagnosis and targeted therapy of glioma. In addition, Glioma involves hypoxia-specific microenvironment, whether hypoxia restriction influences the stoichioproteomic characteristics of expressed proteins is unknown. METHODS In this study, we analyzed the most comprehensive immunohistochemical data from 12 human glioma samples and 4 normal cell types of cerebral cortex, identified differentially expressed proteins (DEPs), and researched the oxygen contents of DEPs, highly and lowly expressed proteins. Further we located key genes on human genome to determine their locations and enriched them for key functional pathways. RESULTS Our results showed that although no difference was detected on whole proteome, the average oxygen content of highly expressed proteins is 6.65% higher than that of lowly expressed proteins in glioma. A total of 1480 differentially expressed proteins were identified in glioma, including 226 up regulated proteins and 1254 down regulated proteins. The average oxygen content of up regulated proteins is 2.56% higher than that of down regulated proteins in glioma. The localization of differentially expressed genes on human genome showed that most genes were on chromosome 1 and least on Y. The up regulated proteins were significantly enriched in pathways including cell cycle, pathways in cancer, oocyte meiosis, DNA replication etc. Functional dissection of the up regulated proteins with high oxygen contents showed that 51.28% of the proteins were involved in cell cycle and cyclins. CONCLUSIONS Element signature of oxygen limitation could not be detected in glioma, just as what happened in plants and microbes. Unsaved use of oxygen by the highly expressed proteins and DEPs were adapted to the fast division of glioma cells. This study can help to reveal the molecular mechanism of glioma, and provide a new approach for studies of cancer-related biomacromolecules. In addition, this study lays a foundation for application of stoichioproteomics in precision medicine.
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Affiliation(s)
- Yongqin Yin
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, University City, Chongqing, 401331 People’s Republic of China
| | - Bo Li
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, University City, Chongqing, 401331 People’s Republic of China
| | - Kejie Mou
- Department of Neurosurgery, Bishan Hospital, Bishan, Chongqing, 402760 China
| | - Muhammad T. Khan
- Shanghai Jiao Tong University, Shanghai, China
- Capital University of Science & Technology, Islamabad, Pakistan
| | | | - Dongqing Wei
- Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055 China
| | - Yu-Juan Zhang
- Chongqing Key Laboratory of Vector Insects, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, University City, Chongqing, 401331 People’s Republic of China
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Zuo X, Li B, Zhu C, Yan ZW, Li M, Wang X, Zhang YJ. Stoichiogenomics reveal oxygen usage bias, key proteins and pathways associated with stomach cancer. Sci Rep 2019; 9:11344. [PMID: 31383879 PMCID: PMC6683168 DOI: 10.1038/s41598-019-47533-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/08/2019] [Indexed: 01/07/2023] Open
Abstract
Stomach cancer involves hypoxia-specific microenvironments. Stoichiogenomics explores environmental resource limitation on biological macromolecules in terms of element usages. However, the patterns of oxygen usage by proteins and the ways that proteins adapt to a cancer hypoxia microenvironment are still unknown. Here we compared the oxygen and carbon contents ([C]) between proteomes of stomach cancer (hypoxia) and two stomach glandular cells (normal). Key proteins, genome locations, pathways, and functional dissection associated with stomach cancer were also studied. An association of oxygen content ([O]) and protein expression level was revealed in stomach cancer and stomach glandular cells. For differentially expressed proteins (DEPs), oxygen contents in the up regulated proteins were3.2%higherthan that in the down regulated proteins in stomach cancer. A total of 1,062 DEPs were identified; interestingly none of these proteins were coded on Y chromosome. The up regulated proteins were significantly enriched in pathways including regulation of actin cytoskeleton, cardiac muscle contraction, pathway of progesterone-mediated oocyte maturation, etc. Functional dissection of the up regulated proteins with high oxygen contents showed that most of them were cytoskeleton, cytoskeleton associated proteins, cyclins and signaling proteins in cell cycle progression. Element signature of resource limitation could not be detected in stomach cancer for oxygen, just as what happened in plants and microbes. Unsaved use of oxygen by the highly expressed proteins was adapted to the rapid growth and fast division of the stomach cancer cells. In addition, oxygen usage bias, key proteins and pathways identified in this paper laid a foundation for application of stoichiogenomics in precision medicine.
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Affiliation(s)
- Xiaoyan Zuo
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, P.R. China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, P.R. China
| | - Chengxu Zhu
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, P.R. China
| | - Zheng-Wen Yan
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, P.R. China
| | - Miao Li
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, P.R. China
| | - Xinyi Wang
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, P.R. China
| | - Yu-Juan Zhang
- College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, P.R. China.
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