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Li Y, Zhan G, Tu M, Wang Y, Cao J, Sun S. A chromosome-scale genome and proteome draft of Tremella fuciformis. Int J Biol Macromol 2023; 247:125749. [PMID: 37429350 DOI: 10.1016/j.ijbiomac.2023.125749] [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: 03/28/2023] [Revised: 06/09/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
In this study, we first reported a high-quality chromosome-scale genome of Tremella fuciformis using Pacbio HiFi sequencing combining Hi-C technology. According to 21.6 Gb PacBio HiFi reads and 18.1 Gb Hi-C valid reads, we drafted a T. fuciformis genome of 27.38 Mb assigned to 10 chromosomes, with the contig N50 of 2.28 Mb, GC content of 56.51 %, BUSCOs completeness of 93.1 % and consensus quality value of 33.7. The following annotation of genomic components predicted 5,171 repeat sequences, 283 RNAs, and 10,150 protein-coding genes. Next, the intracellular proteins at three differential life stages of T. fuciformis (conidium, hyphal and fruiting body) were identified by the shot-gun proteomics. 6,823 canonical proteins (68.1 % of predicted proteome) have been identified with protein FDR cut-off of 0.01, establishing the first proteome draft of predicted protein-coding genes of T. fuciformis. Finally, 24 T. fuciformis polysaccharides (TPS) biosynthesis-related genes in mycelia were identified by comparative transcriptomics and proteomics, which may be more active than in conidium and revealed the TPS biosynthesis process in mycelia. This present study elucidated T. fuciformis genome composition and organization, drafted its associated proteome, and provided a genome-view of TPS biosynthesis, which will be a powerful platform for biological and genetic studies in T. fuciformis.
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Affiliation(s)
- Yaxing Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Basic Forestry and Proteomics Research Center, Fujian Agriculture and forestry university, China
| | - Guanping Zhan
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Min Tu
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and forestry university, China
| | - Yuhua Wang
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and forestry university, China
| | - Jixuan Cao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shujing Sun
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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2
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Iwai M, Kajino T, Nakatochi M, Yanagisawa K, Hosono Y, Isomura H, Shimada Y, Suzuki M, Taguchi A, Takahashi T. Long non-coding RNA TILR constitutively represses TP53 and apoptosis in lung cancer. Oncogene 2023; 42:364-373. [PMID: 36522487 DOI: 10.1038/s41388-022-02546-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 12/16/2022]
Abstract
Non-coding RNAs have an integral regulatory role in numerous functions related to lung cancer development. Here, we report identification of a novel lncRNA, termed TP53-inhibiting lncRNA (TILR), which was found to function as a constitutive negative regulator of p53 expression, including activation of downstream genes such as p21 and MDM2, and induction of apoptosis. A proteomic search for TILR-associated proteins revealed an association with PCBP2, while the mid-portion of TILR was found to be required for both PCBP2 and p53 mRNA binding. In addition, depletion of PCBP2 resulted in phenocopied effects of TILR silencing. TILR was also shown to suppress p53 expression in a post-transcriptional manner, as well as via a positive feedback loop involving p53 and Fanconi anemia pathway genes. Taken together, the present findings clearly demonstrate that TILR constitutively inhibits p53 expression in cooperation with PCBP2, thus maintaining p53 transcriptional activity at a level sufficiently low for avoidance of spurious apoptosis induction.
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Affiliation(s)
- Mika Iwai
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Taisuke Kajino
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, 461-8673, Japan
| | - Kiyoshi Yanagisawa
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.,Department of Molecular and Cancer Medicine, Faculty of Pharmacy, Meijo University, Nagoya, 468-8502, Japan
| | - Yasuyuki Hosono
- Division of Molecular Therapeutics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan.,Department of Pharmacology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, 700-8558, Japan
| | - Hisanori Isomura
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan
| | - Yukako Shimada
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.,Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan
| | - Motoshi Suzuki
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan.,Department of Molecular Oncology, School of Medicine, Fujita Health University, Toyoake, 470-1192, Japan
| | - Ayumu Taguchi
- Division of Molecular Diagnostics, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan.,Division of Advanced Cancer Diagnostics, Department of Cancer Diagnostics and Therapeutics, Nagoya University Graduate School of Medicine, Nagoya, 464-8681, Japan
| | - Takashi Takahashi
- Division of Molecular Carcinogenesis, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan. .,Aichi Cancer Center, Nagoya, 464-8681, Japan.
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3
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Bu F, Cheng Q, Zhang Y, Zhang X, Yan K, Liu F, Li Z, Lu X, Ren Y, Liu S. Discovery of Missing Proteins from an Aneuploidy Cell Line Using a Proteogenomic Approach. J Proteome Res 2021; 20:5329-5339. [PMID: 34748338 DOI: 10.1021/acs.jproteome.1c00772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the steadfast development of proteomic technology, the number of missing proteins (MPs) has been continuously shrinking, with approximately 1470 MPs that have not been explored yet. Due to this phenomenon, the discovery of MPs has been increasingly more difficult and elusive. In order to face this challenge, we have hypothesized that a stable aneuploid cell line with increased chromosomes serves as a useful material for assisting MP exploration. Ker-CT cell line with trisomy at chromosome 5 and 20 was selected for this purpose. With a combination strategy of RNA-Seq and LC-MS/MS, a total of 22 178 transcripts and 8846 proteins were identified in Ker-CT. Although the transcripts corresponding to 15 and 15 MP genes located at chromosome 5 and 20 were detected, none of the MPs were found in Ker-CT. Surprisingly, 3 MPs containing at least two unique non-nest peptides of length ≥9 amino acids were identified in Ker-CT, whose genes are located on chromosome 3 and 10, respectively. Furthermore, the 3 MPs were verified using the method of parallel reaction monitoring (PRM). These results suggest that the abnormal status of chromosomes may not only impact the expression of the corresponding genes in trisomy chromosomes, but also influence that of other chromosomes, which benefits MP discovery. The data obtained in this study are available via ProteomeXchange (PXD028647) and PeptideAtlas (PASS01700), respectively.
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Affiliation(s)
- Fanyu Bu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Qingqiu Cheng
- Clinical Laboratory Center of Dongguan Eighth People's Hospital, Dongguan 523325, China
| | - Yuxing Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Xia Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Keqiang Yan
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Frank Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Zelong Li
- Biological Resource Center of Plants, Animals and Microorganisms, China National Gene Bank, BGI-Shenzhen, Guangdong 518120, China
| | - Xiaomei Lu
- Clinical Laboratory Center of Dongguan Eighth People's Hospital, Dongguan 523325, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
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4
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Ye M, Zhang J, Wei M, Liu B, Dong K. Emerging role of long noncoding RNA-encoded micropeptides in cancer. Cancer Cell Int 2020; 20:506. [PMID: 33088214 PMCID: PMC7565808 DOI: 10.1186/s12935-020-01589-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/19/2020] [Accepted: 10/01/2020] [Indexed: 12/19/2022] Open
Abstract
Increasing evidence has indicated that long noncoding RNAs (lncRNAs) play various important roles in the development of cancers. The widespread applications of ribosome profiling and ribosome nascent chain complex sequencing revealed that some short open reading frames of lncRNAs have micropeptide-coding potential. The resulting micropeptides have been shown to participate in N6-methyladenosine modification, tumor angiogenesis, cancer metabolism, and signal transduction. This review summarizes current information regarding the reported roles of lncRNA-encoded micropeptides in cancer, and explores the potential clinical value of these micropeptides in the development of anti-cancer drugs and prognostic tumor biomarkers.
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Affiliation(s)
- Mujie Ye
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
| | - Jingjing Zhang
- Department of Medical Imaging, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210001 China
| | - Meng Wei
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
| | - Baihui Liu
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, No.399 Wanyuan Road, Minhang District, Shanghai, 201102 China.,Key Laboratory of Neonatal Disease, Ministry of Health, Shanghai, 201102 China
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5
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Ma J, Chen T, Wu S, Yang C, Bai M, Shu K, Li K, Zhang G, Jin Z, He F, Hermjakob H, Zhu Y. iProX: an integrated proteome resource. Nucleic Acids Res 2020; 47:D1211-D1217. [PMID: 30252093 PMCID: PMC6323926 DOI: 10.1093/nar/gky869] [Citation(s) in RCA: 912] [Impact Index Per Article: 228.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/14/2018] [Indexed: 11/13/2022] Open
Abstract
Sharing of research data in public repositories has become best practice in academia. With the accumulation of massive data, network bandwidth and storage requirements are rapidly increasing. The ProteomeXchange (PX) consortium implements a mode of centralized metadata and distributed raw data management, which promotes effective data sharing. To facilitate open access of proteome data worldwide, we have developed the integrated proteome resource iProX (http://www.iprox.org) as a public platform for collecting and sharing raw data, analysis results and metadata obtained from proteomics experiments. The iProX repository employs a web-based proteome data submission process and open sharing of mass spectrometry-based proteomics datasets. Also, it deploys extensive controlled vocabularies and ontologies to annotate proteomics datasets. Users can use a GUI to provide and access data through a fast Aspera-based transfer tool. iProX is a full member of the PX consortium; all released datasets are freely accessible to the public. iProX is based on a high availability architecture and has been deployed as part of the proteomics infrastructure of China, ensuring long-term and stable resource support. iProX will facilitate worldwide data analysis and sharing of proteomics experiments.
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Affiliation(s)
- Jie Ma
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Tao Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Songfeng Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Chunyuan Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Mingze Bai
- Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Kunxian Shu
- Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Kenli Li
- National Supercomputing Center in Changsha, Hunan University, Changsha 410082, China
| | - Guoqing Zhang
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai 200235, China
| | - Zhong Jin
- Computer Network Information Center, Chinese Academy of Sciences, Beijing 100190, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Henning Hermjakob
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China.,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
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6
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Lu S, Zhang J, Lian X, Sun L, Meng K, Chen Y, Sun Z, Yin X, Li Y, Zhao J, Wang T, Zhang G, He QY. A hidden human proteome encoded by 'non-coding' genes. Nucleic Acids Res 2019; 47:8111-8125. [PMID: 31340039 PMCID: PMC6735797 DOI: 10.1093/nar/gkz646] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/07/2019] [Accepted: 07/15/2019] [Indexed: 01/27/2023] Open
Abstract
It has been a long debate whether the 98% ‘non-coding’ fraction of human genome can encode functional proteins besides short peptides. With full-length translating mRNA sequencing and ribosome profiling, we found that up to 3330 long non-coding RNAs (lncRNAs) were bound to ribosomes with active translation elongation. With shotgun proteomics, 308 lncRNA-encoded new proteins were detected. A total of 207 unique peptides of these new proteins were verified by multiple reaction monitoring (MRM) and/or parallel reaction monitoring (PRM); and 10 new proteins were verified by immunoblotting. We found that these new proteins deviated from the canonical proteins with various physical and chemical properties, and emerged mostly in primates during evolution. We further deduced the protein functions by the assays of translation efficiency, RNA folding and intracellular localizations. As the new protein UBAP1-AST6 is localized in the nucleoli and is preferentially expressed by lung cancer cell lines, we biologically verified that it has a function associated with cell proliferation. In sum, we experimentally evidenced a hidden human functional proteome encoded by purported lncRNAs, suggesting a resource for annotating new human proteins.
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Affiliation(s)
- Shaohua Lu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jing Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xinlei Lian
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.,Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Li Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Kun Meng
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yang Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhenghua Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xingfeng Yin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yaxing Li
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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7
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Shi T, Wei Q, Wang Z, Zhang G, Sun X, He QY. Photocatalytic Protein Damage by Silver Nanoparticles Circumvents Bacterial Stress Response and Multidrug Resistance. mSphere 2019; 4:e00175-19. [PMID: 31043515 PMCID: PMC6495337 DOI: 10.1128/msphere.00175-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 04/16/2019] [Indexed: 01/24/2023] Open
Abstract
Silver nanoparticles (AgNPs) are known for their broad-spectrum antibacterial properties, especially against antibiotic-resistant bacteria. However, the bactericidal mechanism of AgNPs remains unclear. In this study, we found that the bactericidal ability of AgNPs is induced by light. In contrast to previous postulates, visible light is unable to trigger silver ion release from AgNPs or to promote AgNPs to induce reactive oxygen species (ROS) in Escherichia coli In fact, we revealed that light excited AgNPs to induce protein aggregation in a concentration-dependent manner in E. coli, indicating that the bactericidal ability of AgNPs relies on the light-catalyzed oxidation of cellular proteins via direct binding to proteins, which was verified by fluorescence spectra. AgNPs likely absorb the light energy and transfer it to the proteins, leading to the oxidation of proteins and thus promoting the death of the bacteria. Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics revealed that the bacteria failed to develop effective resistance to the light-excited AgNPs. This direct physical mechanism is unlikely to be counteracted by any known drug resistance mechanisms of bacteria and therefore may serve as a last resort against drug resistance. This mechanism also provides a practical hint regarding the antimicrobial application of AgNPs-light exposure improves the efficacy of AgNPs.IMPORTANCE Although silver nanoparticles (AgNPs) are well known for their antibacterial properties, the mechanism by which they kill bacterial cells remains a topic of debate. In this study, we uncovered the bactericidal mechanism of AgNPs, which is induced by light. We tested the efficacy of AgNPs against a panel of antimicrobial-resistant pathogens as well as Escherichia coli under conditions of light and darkness and revealed that light excited the AgNPs to promote protein aggregation within the bacterial cells. Our report makes a significant contribution to the literature because this mechanism bypasses microbial drug resistance mechanisms, thus presenting a viable option for the treatment of multidrug-resistant bacteria.
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Affiliation(s)
- Tianyuan Shi
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qiuxia Wei
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Zhen Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xuesong Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
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8
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Liao X, Zhao J, Liang S, Jin J, Li C, Xiao R, Li L, Guo M, Zhang G, Lin Y. Enhancing co-translational folding of heterologous protein by deleting non-essential ribosomal proteins in Pichia pastoris. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:38. [PMID: 30828383 PMCID: PMC6383220 DOI: 10.1186/s13068-019-1377-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 02/12/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Translational regulation played an important role in the correct folding of heterologous proteins to form bioactive conformations during biogenesis. Translational pausing coordinates protein translation and co-translational folding. Decelerating translation elongation speed has been shown to improve the soluble protein yield when expressing heterologous proteins in industrial expression hosts. However, rational redesign of translational pausing via synonymous mutations may not be feasible in many cases. Our goal was to develop a general and convenient strategy to improve heterologous protein synthesis in Pichia pastoris without mutating the expressed genes. RESULTS Here, a large-scale deletion library of ribosomal protein (RP) genes was constructed for heterologous protein expression in Pichia pastoris, and 59% (16/27) RP deletants have significantly increased heterologous protein yield. This is due to the delay of 60S subunit assembly by deleting non-essential ribosomal protein genes or 60S subunit processing factors, thus globally decreased the translation elongation speed and improved the co-translational folding, without perturbing the relative transcription level and translation initiation. CONCLUSION Global decrease in the translation elongation speed by RP deletion enhanced co-translational folding efficiency of nascent chains and decreased protein aggregates to improve heterologous protein yield. A potential expression platform for efficient pharmaceutical proteins and industrial enzymes production was provided without synonymous mutation.
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Affiliation(s)
- Xihao Liao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632 China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Jingjie Jin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632 China
| | - Cheng Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Ruiming Xiao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Lu Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Institute of Biomanufacturing Technology & Collaborative Innovation Center, Shanghai, 200237 China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632 China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006 China
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9
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Zhao J, Qin B, Nikolay R, Spahn CMT, Zhang G. Translatomics: The Global View of Translation. Int J Mol Sci 2019; 20:ijms20010212. [PMID: 30626072 PMCID: PMC6337585 DOI: 10.3390/ijms20010212] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 01/01/2023] Open
Abstract
In all kingdoms of life, proteins are synthesized by ribosomes in a process referred to as translation. The amplitude of translational regulation exceeds the sum of transcription, mRNA degradation and protein degradation. Therefore, it is essential to investigate translation in a global scale. Like the other “omics”-methods, translatomics investigates the totality of the components in the translation process, including but not limited to translating mRNAs, ribosomes, tRNAs, regulatory RNAs and nascent polypeptide chains. Technical advances in recent years have brought breakthroughs in the investigation of these components at global scale, both for their composition and dynamics. These methods have been applied in a rapidly increasing number of studies to reveal multifaceted aspects of translation control. The process of translation is not restricted to the conversion of mRNA coding sequences into polypeptide chains, it also controls the composition of the proteome in a delicate and responsive way. Therefore, translatomics has extended its unique and innovative power to many fields including proteomics, cancer research, bacterial stress response, biological rhythmicity and plant biology. Rational design in translation can enhance recombinant protein production for thousands of times. This brief review summarizes the main state-of-the-art methods of translatomics, highlights recent discoveries made in this field and introduces applications of translatomics on basic biological and biomedical research.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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10
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Weldemariam MM, Han CL, Shekari F, Kitata RB, Chuang CY, Hsu WT, Kuo HC, Choong WK, Sung TY, He FC, Chung MCM, Salekdeh GH, Chen YJ. Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins. J Proteome Res 2018; 17:4138-4151. [DOI: 10.1021/acs.jproteome.8b00407] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mehari Muuz Weldemariam
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 112, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
| | - Faezeh Shekari
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Ching-Yu Chuang
- Genomics Research Center, Academia Sinica, Taiepei 115, Taiwan
| | | | | | | | | | - Fu-Chu He
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206 China
| | - Maxey Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, 14 Science Drive 4, singapore, 117543 Singpore
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 112, Taiwan
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11
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Ma F, Liu F, Xu W, Li L. Surfactant and Chaotropic Agent Assisted Sequential Extraction/On-Pellet Digestion (SCAD) for Enhanced Proteomics. J Proteome Res 2018; 17:2744-2754. [PMID: 29923408 PMCID: PMC6171104 DOI: 10.1021/acs.jproteome.8b00197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
As a popular sample preparation approach, filter-aided sample preparation (FASP) has been widely used in proteomic analysis. However, several limitations have been noted, including sample loss during filtration, repetitive centrifugation steps, and the possibility of breakage of filtration membrane. Extraction bias among different sample preparation strategies presents another challenge. To overcome these limitations and address remaining challenges, we developed a novel surfactant and chaotropic agent assisted sequential extraction/on-pellet digestion (SCAD) protocol. The new strategy resulted in higher protein yield and improved peptide recovery and protein coverage compared to two conventional sample preparation methods (FASP and urea). In combination of three strategies, more than 10,000 distinct protein groups were identified with 1% FDR from MDA-MB-231 cells without any prefractionation. This in-depth proteome analysis was accomplished by optimization of protein extraction, enzymatic digestion, LC gradient, and peptide sequencing method. Ingenuity Pathways Analysis (IPA) of proteins exclusively identified in SCAD revealed several crucial signaling pathways that regulate breast cancer progression. SCAD also enabled an unbiased extraction of different categories of proteins (membrane, intracellular, nuclear) associated with tumorigenesis, which integrates the advantages of FASP and urea extraction. This novel strategy expedites comprehensive protein identification, which is applicable for biomarker discovery in various types of cancers.
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Affiliation(s)
- Fengfei Ma
- School of Pharmacy, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
| | - Fabao Liu
- McArdle Laboratory for Cancer Research, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin‒Madison, Madison, Wisconsin 53705, United States
- Department of Chemistry, University of Wisconsin‒Madison, Madison, Wisconsin 53706, United States
- School of Life Sciences, Tianjin University, Tianjin 300072, P. R. China
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12
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Sun X, Cui Y, Wang Q, Tang S, Cao X, Luo H, He Z, Hu X, Nie X, Yang Y, Wang T. Proteogenomic Analyses Revealed Favorable Metabolism Pattern Alterations in Rotifer Brachionus plicatilis Fed with Selenium-rich Chlorella. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:6699-6707. [PMID: 29874910 DOI: 10.1021/acs.jafc.8b00139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Organoselenium have garnered attention because of their potential to be used as ingredients in new anti-aging and antioxidation medicines and food. Rotifers are frequently used as a model organism for aging research. In this study, we used Se-enriched Chlorella (Se- Chlorella), a novel organoselenium compound, to feed Brachionus plicatilis to establish a rotifer model with a prolonged lifespan. The results showed that the antioxidative effect in Se-enriched rotifer was associated with an increase in guaiacol peroxidase (GPX) and catalase (CAT). The authors then performed the first proteogenomic analysis of rotifers to understand their possible metabolic mechanisms. With the de novo assembly of RNA-Seq reads as the reference, we mapped the proteomic output generated by iTRAQ-based mass spectrometry. We found that the differentially expressed proteins were primarily involved in antireactive oxygen species (ROS) and antilipid peroxidation (LPO), selenocompound metabolism, glycolysis, and amino acid metabolisms. Furthermore, the ROS level of rotifers was diminished after Se- Chlorella feeding, indicating that Se- Chlorella could help rotifers to enhance their amino acid metabolism and shift the energy generating metabolism from tricarboxylic acid cycle to glycolysis, which leads to reduced ROS production. This is the first report to demonstrate the anti-aging effect of Se- Chlorella on rotifers and to provide a possible mechanism for this activity. Thus, Se- Chlorella is a promising novel organoselenium compound with the potential to prolong human lifespans.
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Affiliation(s)
- Xian Sun
- Institute of Hydrobiology and Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms , Guangdong Higher Education Institutes , Guangzhou 510006 , China
| | - Yizhi Cui
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Institute of Life and Health Engineering , Jinan University , Guangzhou 510632 , China
| | - Qing Wang
- Institute of Hydrobiology and Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms , Guangdong Higher Education Institutes , Guangzhou 510006 , China
| | - Shengquan Tang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Institute of Life and Health Engineering , Jinan University , Guangzhou 510632 , China
| | - Xin Cao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Institute of Life and Health Engineering , Jinan University , Guangzhou 510632 , China
| | - Hongtian Luo
- Institute of Hydrobiology and Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms , Guangdong Higher Education Institutes , Guangzhou 510006 , China
| | - Zhili He
- School of Environmental Science and Engineering , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Xiaonong Hu
- Institute of Hydrobiology and Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms , Guangdong Higher Education Institutes , Guangzhou 510006 , China
| | - Xiangping Nie
- Institute of Hydrobiology and Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms , Guangdong Higher Education Institutes , Guangzhou 510006 , China
| | - Yufeng Yang
- Institute of Hydrobiology and Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms , Guangdong Higher Education Institutes , Guangzhou 510006 , China
| | - Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and Institute of Life and Health Engineering , Jinan University , Guangzhou 510632 , China
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13
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Cao K, Lai F, Zhao XL, Wei QX, Miao XY, Ge R, He QY, Sun X. The mechanism of iron-compensation for manganese deficiency of Streptococcus pneumoniae. J Proteomics 2018; 184:62-70. [DOI: 10.1016/j.jprot.2018.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/17/2018] [Accepted: 06/07/2018] [Indexed: 12/18/2022]
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14
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Stein CS, Jadiya P, Zhang X, McLendon JM, Abouassaly GM, Witmer NH, Anderson EJ, Elrod JW, Boudreau RL. Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency. Cell Rep 2018; 23:3710-3720.e8. [PMID: 29949756 PMCID: PMC6091870 DOI: 10.1016/j.celrep.2018.06.002] [Citation(s) in RCA: 155] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/16/2018] [Accepted: 05/30/2018] [Indexed: 01/07/2023] Open
Abstract
Mitochondria are composed of many small proteins that control protein synthesis, complex assembly, metabolism, and ion and reactive oxygen species (ROS) handling. We show that a skeletal muscle- and heart-enriched long non-coding RNA, LINC00116, encodes a highly conserved 56-amino-acid microprotein that we named mitoregulin (Mtln). Mtln localizes to the inner mitochondrial membrane, where it binds cardiolipin and influences protein complex assembly. In cultured cells, Mtln overexpression increases mitochondrial membrane potential, respiration rates, and Ca2+ retention capacity while decreasing mitochondrial ROS and matrix-free Ca2+. Mtln-knockout mice display perturbations in mitochondrial respiratory (super)complex formation and activity, fatty acid oxidation, tricarboxylic acid (TCA) cycle enzymes, and Ca2+ retention capacity. Blue-native gel electrophoresis revealed that Mtln co-migrates alongside several complexes, including the complex I assembly module, complex V, and supercomplexes. Under denaturing conditions, Mtln remains in high-molecular-weight complexes, supporting its role as a sticky molecular tether that enhances respiratory efficiency by bolstering protein complex assembly and/or stability.
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Affiliation(s)
- Colleen S Stein
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Pooja Jadiya
- Center of Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Xiaoming Zhang
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jared M McLendon
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Gabrielle M Abouassaly
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nathan H Witmer
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ethan J Anderson
- Department of Pharmaceutical Sciences and Experimental Therapeutics, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, College of Pharmacy, University of Iowa, Iowa City, IA, USA
| | - John W Elrod
- Center of Translational Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Ryan L Boudreau
- Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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15
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Chen Z, Yang L, Cui Y, Zhou Y, Yin X, Guo J, Zhang G, Wang T, He QY. Cytoskeleton-centric protein transportation by exosomes transforms tumor-favorable macrophages. Oncotarget 2018; 7:67387-67402. [PMID: 27602764 PMCID: PMC5341883 DOI: 10.18632/oncotarget.11794] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/21/2016] [Indexed: 12/21/2022] Open
Abstract
The exosome is a key initiator of pre-metastatic niche in numerous cancers, where macrophages serve as primary inducers of tumor microenvironment. However, the proteome that can be exosomally transported from cancer cells to macrophages has not been sufficiently characterized so far. Here, we used colorectal cancer (CRC) exosomes to educate tumor-favorable macrophages. With a SILAC-based mass spectrometry strategy, we successfully traced the proteome transported from CRC exosomes to macrophages. Such a proteome primarily focused on promoting cytoskeleton rearrangement, which was biologically validated with multiple cell lines. We reproduced the exosomal transportation of functional vimentin as a proof-of-concept example. In addition, we found that some CRC exosomes could be recognized by macrophages via Fc receptors. Therefore, we revealed the active and necessary role of exosomes secreted from CRC cells to transform cancer-favorable macrophages, with the cytoskeleton-centric proteins serving as the top functional unit.
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Affiliation(s)
- Zhipeng Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lijuan Yang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yizhi Cui
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yanlong Zhou
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xingfeng Yin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jiahui Guo
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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16
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Tang S, Deng S, Guo J, Chen X, Zhang W, Cui Y, Luo Y, Yan Z, He QY, Shen S, Wang T. Deep Coverage Tissue and Cellular Proteomics Revealed IL-1β Can Independently Induce the Secretion of TNF-Associated Proteins from Human Synoviocytes. THE JOURNAL OF IMMUNOLOGY 2017; 200:821-833. [DOI: 10.4049/jimmunol.1700480] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 10/31/2017] [Indexed: 01/15/2023]
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17
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Paik YK, Omenn GS, Hancock WS, Lane L, Overall CM. Advances in the Chromosome-Centric Human Proteome Project: looking to the future. Expert Rev Proteomics 2017; 14:1059-1071. [PMID: 29039980 DOI: 10.1080/14789450.2017.1394189] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION The mission of the Chromosome-Centric Human Proteome Project (C-HPP), is to map and annotate the entire predicted human protein set (~20,000 proteins) encoded by each chromosome. The initial steps of the project are focused on 'missing proteins (MPs)', which lacked documented evidence for existence at protein level. In addition to remaining 2,579 MPs, we also target those annotated proteins having unknown functions, uPE1 proteins, alternative splice isoforms and post-translational modifications. We also consider how to investigate various protein functions involved in cis-regulatory phenomena, amplicons lncRNAs and smORFs. Areas covered: We will cover the scope, historic background, progress, challenges and future prospects of C-HPP. This review also addresses the question of how we can best improve the methodological approaches, select the optimal biological samples, and recommend stringent protocols for the identification and characterization of MPs. A new strategy for functional analysis of some of those annotated proteins having unknown function will also be discussed. Expert commentary: If the project moves well by reshaping the original goals, the current working modules and team work in the proposed extended planning period, it is anticipated that a progressively more detailed draft of an accurate chromosome-based proteome map will become available with functional information.
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Affiliation(s)
- Young-Ki Paik
- a Yonsei Proteome Research Center and Department of Biochemistry , Yonsei University , Seoul , Korea
| | - Gilbert S Omenn
- b Department of Computational Medicine & Bioinformatics , University of Michigan , Ann Arbor , MI , USA
| | - William S Hancock
- c Department of Chemical Biology , Northeastern University , Boston , Massachusetts 02115 , USA
| | - Lydie Lane
- d Department of Human Protein Sciences, Faculty of Medicine , University of Geneva , Geneva , Switzerland.,e Swiss Institute of Bioinformatics , Geneva , Switzerland
| | - Christopher M Overall
- f Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry , University of British Columbia , Vancouver , Canada
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18
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Zhang W, Chen X, Yan Z, Chen Y, Cui Y, Chen B, Huang C, Zhang W, Yin X, He QY, He F, Wang T. Detergent-Insoluble Proteome Analysis Revealed Aberrantly Aggregated Proteins in Human Preeclampsia Placentas. J Proteome Res 2017; 16:4468-4480. [PMID: 28965414 DOI: 10.1021/acs.jproteome.7b00352] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Preeclampsia (PE) is a placenta disease, featured by hypertension, proteinuria, and other multiorgan dysfunctions, and its etiology is unclear. We and others have shown that intensive endoplasmic reticulum (ER) stress and unfolded protein response (UPR) occur in the PE placenta. In this study, we isolated detergent-insoluble proteins (DIPs) from human placenta tissues, which were enriched with protein aggregates, to characterize the placenta UPR in PE. With data-independent acquisition (DIA) mass spectrometry, we identified 2066 DIPs across all normal (n = 10) and PE (n = 10) placenta samples, among which 110 and 108 DIPs were significantly up- and down-regulated in PE, respectively. Per clustering analysis, differential DIPs could generally distinguish PE from normal placentas. We verified the MS quantitation of endoglin and vimentin by immunoblotting. In addition, we observed that PE placenta tissues have remarkably more endoglin in the cytoplasm. Furthermore, we found that DIPs were evenly distributed across different chromosomes and could be enriched in diversified gene ontology terms, while differential DIPs avoided to distribute on X-chromosome. Significantly up-regulated DIPs in PE were focused on the top functions of lipid metabolism, while 23 of these DIPs could form the top network regulating cellular movement, development, growth, and proliferation. Our results implicate that human PE placentas have disease-relevant differential DIPs, which reflect aberrantly aggregated proteins of placental tissues. The mass spectrometry proteomics data have been deposited to ProteomeXchange consortium with the data set identifier PXD006654, and iProX database (accession number: IPX0000948000).
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Affiliation(s)
- Wanling Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Xing Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Ziqi Yan
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Yang Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Yizhi Cui
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | | | | | | | - Xingfeng Yin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
| | | | - Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University , 601 Huangpu Avenue West, Guangzhou, Guangdong 510632, China
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19
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Wang Y, Chen Y, Zhang Y, Wei W, Li Y, Zhang T, He F, Gao Y, Xu P. Multi-Protease Strategy Identifies Three PE2 Missing Proteins in Human Testis Tissue. J Proteome Res 2017; 16:4352-4363. [PMID: 28959888 DOI: 10.1021/acs.jproteome.7b00340] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although 5 years of the missing proteins (MPs) study have been completed, searching for MPs remains one of the core missions of the Chromosome-Centric Human Proteome Project (C-HPP). Following the next-50-MPs challenge of the C-HPP, we have focused on the testis-enriched MPs by various strategies since 2015. On the basis of the theoretical analysis of MPs (2017-01, neXtProt) using multiprotease digestion, we found that nonconventional proteases (e.g. LysargiNase, GluC) could improve the peptide diversity and sequence coverage compared with Trypsin. Therefore, a multiprotease strategy was used for searching more MPs in the same human testis tissues separated by 10% SDS-PAGE, followed by high resolution LC-MS/MS system (Q Exactive HF). A total of 7838 proteins were identified. Among them, three PE2 MPs in neXtProt 2017-01 have been identified: beta-defensin 123 ( Q8N688 , chr 20q), cancer/testis antigen family 45 member A10 ( P0DMU9 , chr Xq), and Histone H2A-Bbd type 2/3 ( P0C5Z0 , chr Xq). However, because only one unique peptide of ≥9 AA was identified in beta-defensin 123 and Histone H2A-Bbd type 2/3, respectively, further analysis indicates that each falls under the exceptions clause of the HPP Guidelines v2.1. After a spectrum quality check, isobaric PTM and single amino acid variant (SAAV) filtering, and verification with a synthesized peptide, and based on overlapping peptides from different proteases, these three MPs should be considered as exemplary examples of MPs found by exceptional criteria. Other MPs were considered as candidates but need further validation. All MS data sets have been deposited to the ProteomeXchange with identifier PXD006465.
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Affiliation(s)
- Yihao Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine , Beijing 100850, China
| | - Yang Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University , Guangzhou 510275, China
| | - Wei Wei
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Tao Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yue Gao
- Department of Pharmacology and Toxicology, Beijing Institute of Radiation Medicine , Beijing 100850, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University , Wuhan 430072, China.,Graduate School, Anhui Medical University , Hefei 230032, China.,Tianjin Baodi Hospital , Tianjin 301800, China
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20
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Zhang J, Lu S, Zhou Y, Meng K, Chen Z, Cui Y, Shi Y, Wang T, He QY. Motile hepatocellular carcinoma cells preferentially secret sugar metabolism regulatory proteins via exosomes. Proteomics 2017; 17. [PMID: 28590090 DOI: 10.1002/pmic.201700103] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/14/2017] [Accepted: 05/29/2017] [Indexed: 01/29/2023]
Abstract
Exosomes are deliverers of critically functional proteins, capable of transforming target cells in numerous cancers, including hepatocellular carcinoma (HCC). We hypothesize that the motility of HCC cells can be featured by comparative proteome of exosomes. Hence, we performed the super-SILAC-based MS analysis on the exosomes secreted by three human HCC cell lines, including the non-motile Hep3B cell, and the motile 97H and LM3 cells. More than 1400 exosomal proteins were confidently quantified in each MS analysis with highly biological reproducibility. We justified that 469 and 443 exosomal proteins represented differentially expressed proteins (DEPs) in the 97H/Hep3B and LM3/Hep3B comparisons, respectively. These DEPs focused on sugar metabolism-centric canonical pathways per ingenuity pathway analysis, which was consistent with the gene ontology analysis on biological process enrichment. These pathways included glycolysis I, gluconeogenesis I and pentose phosphate pathways; and the DEPs enriched in these pathways could form a tightly connected network. By analyzing the relative abundance of proteins and translating mRNAs, we found significantly positive correlation between exosomes and cells. The involved exosomal proteins were again focusing on sugar metabolism. In conclusion, motile HCC cells tend to preferentially export more sugar metabolism-associated proteins via exosomes that differentiate them from non-motile HCC cells.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, P. R. China
| | - Shaohua Lu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, P. R. China
| | - Ye Zhou
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, P. R. China
| | - Kun Meng
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, P. R. China
| | - Zhipeng Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, P. R. China
| | - Yizhi Cui
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, P. R. China
| | - Yunfeng Shi
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, P. R. China
| | - Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, P. R. China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, P. R. China
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21
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Luo Y, Mok TS, Lin X, Zhang W, Cui Y, Guo J, Chen X, Zhang T, Wang T. SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma. Sci Rep 2017; 7:41191. [PMID: 28117408 PMCID: PMC5259699 DOI: 10.1038/srep41191] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/15/2016] [Indexed: 02/08/2023] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a serious threat to public health, and the biomarker discovery is of urgent needs. The data-independent mode (DIA) based sequential window acquisition of all theoretical fragment-ion spectra (SWATH) mass spectrometry (MS) has been proved to be precise in protein quantitation and efficient for cancer biomarker researches. In this study, we performed the first SWATH-MS analysis comparing the NPC and normal tissues. Spike-in stable isotope labeling by amino acids in cell culture (super-SILAC) MS was used as a shotgun reference. We identified and quantified 1414 proteins across all SWATH-MS analyses. We found that SWATH-MS had a unique feature to preferentially detect proteins with smaller molecular weights than either super-SILAC MS or human proteome background. With SWATH-MS, 29 significant differentially express proteins (DEPs) were identified. Among them, carbonic anhydrase 2 (CA2) was selected for further validation per novelty, MS quality and other supporting rationale. With the tissue microarray analysis, we found that CA2 had an AUC of 0.94 in differentiating NPC from normal tissue samples. In conclusion, SWATH-MS has unique features in proteome analysis, and it leads to the identification of CA2 as a potentially new diagnostic biomarker for NPC.
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Affiliation(s)
- Yanzhang Luo
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China
| | - Tin Seak Mok
- Department of Otorhinolaryngology, The First Affiliated Hospital, Jinan University, Guangzhou 510632, P. R. China
| | - Xiuxian Lin
- Department of Otorhinolaryngology, The First Affiliated Hospital, Jinan University, Guangzhou 510632, P. R. China
| | - Wanling Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China
| | - Yizhi Cui
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China
| | - Jiahui Guo
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China
| | - Xing Chen
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China
| | - Tao Zhang
- Department of Otorhinolaryngology, The First Affiliated Hospital, Jinan University, Guangzhou 510632, P. R. China
| | - Tong Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, P. R. China
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22
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Wang Y, Yu RY, Zhang J, Zhang WX, Huang ZH, Hu HF, Li YL, Li B, He QY. Inhibition of Nrf2 enhances the anticancer effect of 6-O-angeloylenolin in lung adenocarcinoma. Biochem Pharmacol 2017; 129:43-53. [PMID: 28104435 DOI: 10.1016/j.bcp.2017.01.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 01/10/2017] [Indexed: 12/13/2022]
Abstract
6-O-Angeloylenolin (6-OA), a sesquiterpene lactone isolated from Centipeda minima (L.) A. Br. (Compositae), has been used to treat respiratory diseases for centuries. However, whether and how 6-OA exerts anticancer effects against lung cancer remains to be elucidated. In this study, we showed that 6-OA markedly suppressed the cell viability and colony formation of lung cancer cells H1299 and A549, with no significant toxic effect on non-cancer cells HBE. Annexin V/7-AAD assay revealed that 6-OA induced cell apoptosis in dose- and time-dependent manners, which was further confirmed by the increased expression of cleaved caspase-3. To uncover the molecular mechanism how 6-OA exerts its anticancer effects, SILAC quantitative proteomics was performed to identify 6-OA-regulated proteins in lung cancer cells. Ingenuity Pathway Analysis revealed that these 6-OA-regulated proteins were mainly involved in Nrf2-mediated oxidative stress response, which was confirmed by the nuclear translocation of Nrf2 upon 6-OA treatment. Moreover, we found that 6-OA stimulated the accumulation of reactive oxygen species (ROS), whereas inhibition of ROS generation with N-acetyl l-cysteine could block the 6-OA-induced anticancer effects. Furthermore, blockade of cellular anti-oxidative system by Nrf2 knockdown significantly augmented the 6-OA-induced apoptosis. Taken together, we demonstrated that 6-OA exerts its anticancer effects by generating ROS, and inhibition of Nrf2 anti-oxidative system potentiated these effects. These results suggest that 6-OA may be used to treat lung cancer, with better outcome by combining with Nrf2 inhibitor to block Nrf2 pathway.
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Affiliation(s)
- Yang Wang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Ru-Yuan Yu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jing Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Wei-Xia Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhi-Hao Huang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Hui-Fang Hu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yao-Lan Li
- College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Bin Li
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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23
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Segura V, Garin-Muga A, Guruceaga E, Corrales FJ. Progress and pitfalls in finding the 'missing proteins' from the human proteome map. Expert Rev Proteomics 2016; 14:9-14. [PMID: 27885863 DOI: 10.1080/14789450.2017.1265450] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION The Human Proteome Project was launched with two main goals: the comprehensive and systematic definition of the human proteome map and the development of ready to use analytical tools to measure relevant proteins in their biological context in health and disease. Despite the great progress in this endeavour, there is still a group of reluctant proteins with no, or scarce, experimental evidence supporting their existence. These are called the 'missing proteins' and represent one of the biggest challenges to complete the human proteome map. Areas covered: This review focuses on the description of the missing proteome based on the HUPO standards, the analysis of the reasons explaining the difficulty of detecting missing proteins and the strategies currently used in the search for missing proteins. The present and future of the quest for the missing proteins is critically revised hereafter. Expert commentary: An overarching multidisciplinary effort is currently being done under the HUPO umbrella to allow completion of the human proteome map. It is expected that the detection of missing proteins will grow in the coming years since the methods and the best tissue/cell type sample for their search are already on the table.
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Affiliation(s)
- Victor Segura
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Alba Garin-Muga
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Elizabeth Guruceaga
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
| | - Fernando J Corrales
- a Proteomics and Bioinformatics Laboratory, CIMA , University of Navarra , Pamplona , Spain
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24
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Zhang X. Detergents: Friends not foes for high-performance membrane proteomics toward precision medicine. Proteomics 2016; 17. [PMID: 27633951 DOI: 10.1002/pmic.201600209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/31/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023]
Abstract
Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic, and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples. Frequently, expected membrane proteins and peptides are not identified by shotgun bottom-up proteomics, let alone robust quantitation. This review argues the cause of this proteomic crisis is not detergents per se, but the choice of detergents. Recently, inclusion of compatible detergents for membrane protein extraction and digestion has revealed stark improvements in both quantitative and structural proteomics. This review analyzes detergent properties behind recent proteomic advances, and proposes that rational use of detergents may reconcile outstanding membrane proteomics dilemmas, enabling ultradeep coverage and minimal artifacts for robust protein and endogenous PTM measurements. The simplicity of detergent tools confers bottom-up membrane proteomics the sophistication toward precision medicine.
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Affiliation(s)
- Xi Zhang
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
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25
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Guo J, Cui Y, Yan Z, Luo Y, Zhang W, Deng S, Tang S, Zhang G, He QY, Wang T. Phosphoproteome Characterization of Human Colorectal Cancer SW620 Cell-Derived Exosomes and New Phosphosite Discovery for C-HPP. J Proteome Res 2016; 15:4060-4072. [PMID: 27470641 DOI: 10.1021/acs.jproteome.6b00391] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jiahui Guo
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yizhi Cui
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Ziqi Yan
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yanzhang Luo
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Wanling Zhang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Suyuan Deng
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Shengquan Tang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Tong Wang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
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26
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Paik YK, Omenn GS, Overall CM, Deutsch EW, Hancock WS. Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light. J Proteome Res 2016; 14:3409-14. [PMID: 26337862 DOI: 10.1021/acs.jproteome.5b00785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Gilbert S Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan 48109, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle, Washington 98109, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - William S Hancock
- Department of Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
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27
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Lian X, Guo J, Gu W, Cui Y, Zhong J, Jin J, He QY, Wang T, Zhang G. Genome-Wide and Experimental Resolution of Relative Translation Elongation Speed at Individual Gene Level in Human Cells. PLoS Genet 2016; 12:e1005901. [PMID: 26926465 PMCID: PMC4771717 DOI: 10.1371/journal.pgen.1005901] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 02/05/2016] [Indexed: 11/18/2022] Open
Abstract
In the process of translation, ribosomes first assemble on mRNAs (translation initiation) and then translate along the mRNA (elongation) to synthesize proteins. Elongation pausing is deemed highly relevant to co-translational folding of nascent peptides and the functionality of protein products, which positioned the evaluation of elongation speed as one of the central questions in the field of translational control. By integrating three types of RNA-seq methods, we experimentally and computationally resolved elongation speed, with our proposed elongation velocity index (EVI), a relative measure at individual gene level and under physiological condition in human cells. We successfully distinguished slow-translating genes from the background translatome. We demonstrated that low-EVI genes encoded more stable proteins. We further identified cell-specific slow-translating codons, which might serve as a causal factor of elongation deceleration. As an example for the biological relevance, we showed that the relatively slow-translating genes tended to be associated with the maintenance of malignant phenotypes per pathway analyses. In conclusion, EVI opens a new view to understand why human cells tend to avoid simultaneously speeding up translation initiation and decelerating elongation, and the possible cancer relevance of translating low-EVI genes to gain better protein quality. In protein synthesis, ribosome assembles to mRNA to initiate translation, followed by the process of elongation to read the codons along the mRNA molecule for polypeptide chain production. It is known that slowing down the elongation speed at certain regions of mRNA is critical for the correct folding of numerous proteins—the so-called “pause-to-fold”. However, it has been an open question to evaluate elongation speed under cellular physiological conditions in genome-wide scale. Here, we used three types of next-generation sequencing approaches to experimentally and computationally address this question. With a new relative measure of elongation velocity index (EVI), we successfully distinguished slow-translating genes. Their protein products are more stable than the background genes. We found that different cell types tended to have distinct slow-translating codons, which might be relevant to the cell/tissue specific tRNA composition. Such elongation deceleration is potentially disease-relevant: cancer cells tend to slow down numerous cancer-favorable genes, and vice versa. Furthermore, we justified that translation initiation and elongation are evolutionarily synergistic as no gene with both high initiation efficiency and low elongation speed was observed: that would cause a traffic jam of ribosomes that should be maximally avoided per evolution.
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Affiliation(s)
- Xinlei Lian
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jiahui Guo
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Wei Gu
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Yizhi Cui
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jiayong Zhong
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Jingjie Jin
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
| | - Qing-Yu He
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
- * E-mail: (GZ); (TW); (QYH)
| | - Tong Wang
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
- * E-mail: (GZ); (TW); (QYH)
| | - Gong Zhang
- Institute of Life and Health Engineering, Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China
- * E-mail: (GZ); (TW); (QYH)
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28
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Yang L, Lian X, Zhang W, Guo J, Wang Q, Li Y, Chen Y, Yin X, Yang P, Lan F, He QY, Zhang G, Wang T. Finding Missing Proteins from the Epigenetically Manipulated Human Cell with Stringent Quality Criteria. J Proteome Res 2015. [DOI: 10.1021/acs.jproteome.5b00480] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Lijuan Yang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xinlei Lian
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Wanling Zhang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jie Guo
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing Wang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yaxing Li
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yang Chen
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xingfeng Yin
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | | | | | - Qing-Yu He
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Wang
- Key
Laboratory of Functional Protein Research of Guangdong Higher Education
Institutes, Institute of Life and Health Engineering, College of Life
Science and Technology, Jinan University, Guangzhou 510632, China
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