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Spät P, Krauspe V, Hess WR, Maček B, Nalpas N. Deep Proteogenomics of a Photosynthetic Cyanobacterium. J Proteome Res 2023; 22:1969-1983. [PMID: 37146978 PMCID: PMC10243305 DOI: 10.1021/acs.jproteome.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Indexed: 05/07/2023]
Abstract
Cyanobacteria, the evolutionary ancestors of plant chloroplasts, contribute substantially to the Earth's biogeochemical cycles and are of great interest for a sustainable economy. Knowledge of protein expression is the key to understanding cyanobacterial metabolism; however, proteome studies in cyanobacteria are limited and cover only a fraction of the theoretical proteome. Here, we performed a comprehensive proteogenomic analysis of the model cyanobacterium Synechocystis sp. PCC 6803 to characterize the expressed (phospho)proteome, re-annotate known and discover novel open reading frames (ORFs). By mapping extensive shotgun mass spectrometry proteomics data onto a six-frame translation of the Synechocystis genome, we refined the genomic annotation of 64 ORFs, including eight completely novel ORFs. Our study presents the largest reported (phospho)proteome dataset for a unicellular cyanobacterium, covering the expression of about 80% of the theoretical proteome under various cultivation conditions, such as nitrogen or carbon limitation. We report 568 phosphorylated S/T/Y sites that are present on numerous regulatory proteins, including the transcriptional regulators cyAbrB1 and cyAbrB2. We also catalogue the proteins that have never been detected under laboratory conditions and found that a large portion of them is plasmid-encoded. This dataset will serve as a resource, providing dedicated information on growth condition-dependent protein expression and phosphorylation.
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Affiliation(s)
- Philipp Spät
- Quantitative
Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Vanessa Krauspe
- Genetics
& Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany
| | - Wolfgang R. Hess
- Genetics
& Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Schänzlestraße 1, 79104 Freiburg im Breisgau, Germany
| | - Boris Maček
- Quantitative
Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
| | - Nicolas Nalpas
- Quantitative
Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Auf der Morgenstelle 15, 72076 Tübingen, Germany
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Zhang J, Qin W, Hu C, Gu S, Chai X, Yang M, Zhou F, Wang X, Chen K, Yan G, Wang G, Jiang C, Warren A, Xiong J, Miao W. Giant proteins in a giant cell: Molecular basis of ultrafast Ca 2+-dependent cell contraction. SCIENCE ADVANCES 2023; 9:eadd6550. [PMID: 36812318 PMCID: PMC9946354 DOI: 10.1126/sciadv.add6550] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The giant single-celled eukaryote, Spirostomum, exhibits one of the fastest movements in the biological world. This ultrafast contraction is dependent on Ca2+ rather than ATP and therefore differs to the actin-myosin system in muscle. We obtained the high-quality genome of Spirostomum minus from which we identified the key molecular components of its contractile apparatus, including two major Ca2+ binding proteins (Spasmin 1 and 2) and two giant proteins (GSBP1 and GSBP2), which act as the backbone and allow for the binding of hundreds of spasmins. The evidence suggests that the GSBP-spasmin protein complex is the functional unit of the mesh-like contractile fibrillar system, which, coupled with various other subcellular structures, provides the mechanism for repetitive ultrafast cell contraction and extension. These findings improve our understanding of the Ca2+-dependent ultrafast movement and provide a blueprint for future biomimicry, design, and construction of this kind of micromachine.
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Affiliation(s)
- Jing Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Weiwei Qin
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Che Hu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Harbin Normal University, Harbin 150025, China
| | - Siyu Gu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaocui Chai
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Mingkun Yang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fang Zhou
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xueyan Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Chen
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guanxiong Yan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guangying Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Chuanqi Jiang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Jie Xiong
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Miao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Freshwater Ecology and Biotechnology of China, Wuhan 430072, China
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming 650223, China
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The increasing role of structural proteomics in cyanobacteria. Essays Biochem 2022; 67:269-282. [PMID: 36503929 PMCID: PMC10070481 DOI: 10.1042/ebc20220095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
Abstract
Cyanobacteria, also known as blue–green algae, are ubiquitous organisms on the planet. They contain tremendous protein machineries that are of interest to the biotechnology industry and beyond. Recently, the number of annotated cyanobacterial genomes has expanded, enabling structural studies on known gene-coded proteins to accelerate. This review focuses on the advances in mass spectrometry (MS) that have enabled structural proteomics studies to be performed on the proteins and protein complexes within cyanobacteria. The review also showcases examples whereby MS has revealed critical mechanistic information behind how these remarkable machines within cyanobacteria function.
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Jiang S, Shi J, Li Y, Zhang Z, Chang L, Wang G, Wu W, Yu L, Dai E, Zhang L, Lyu Z, Xu P, Zhang Y. Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC2 155 by proteogenomic analysis. Front Microbiol 2022; 13:1015140. [PMID: 36312923 PMCID: PMC9597629 DOI: 10.3389/fmicb.2022.1015140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/12/2022] [Indexed: 11/22/2022] Open
Abstract
Accurate identification of novel peptides remains challenging because of the lack of evaluation criteria in large-scale proteogenomic studies. Mirror proteases of trypsin and lysargiNase can generate complementary b/y ion series, providing the opportunity to efficiently assess authentic novel peptides in experiments other than filter potential targets by different false discovery rates (FDRs) ranking. In this study, a pair of in-house developed acetylated mirror proteases, Ac-Trypsin and Ac-LysargiNase, were used in Mycolicibacterium smegmatis MC2 155 for proteogenomic analysis. The mirror proteases accurately identified 368 novel peptides, exhibiting 75–80% b and y ion coverages against 65–68% y or b ion coverages of Ac-Trypsin (38.9% b and 68.3% y) or Ac-LysargiNase (65.5% b and 39.6% y) as annotated peptides from M. smegmatis MC2 155. The complementary b and y ion series largely increased the reliability of overlapped sequences derived from novel peptides. Among these novel peptides, 311 peptides were annotated in other public M. smegmatis strains, and 57 novel peptides with more continuous b and y pairs were obtained for further analysis after spectral quality assessment. This enabled mirror proteases to successfully correct six annotated proteins' N-termini and detect 17 new coding open reading frames (ORFs). We believe that mirror proteases will be an effective strategy for novel peptide detection in both prokaryotic and eukaryotic proteogenomics.
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Affiliation(s)
- Songhao Jiang
- Key Laboratory of Microbial Diversity Research and Application of Hebei, School of Life Sciences, Hebei University, Baoding, China
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Jiahui Shi
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Yanchang Li
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Zhenpeng Zhang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Lei Chang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Guibin Wang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
| | - Wenhui Wu
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
- Guangzhou University of Chinese Medicine, Second Clinical Medicine College, Guangzhou Higher Education Mega Center, Guangzhou, China
| | - Liyan Yu
- Research Unit of Proteomics and Research and Development of New Drug, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Erhei Dai
- The Fifth Hospital of Shijiazhuang, School of Public Health, Shijiazhuang, China
| | - Lixia Zhang
- Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese Medicine, Tianjin Institute of Respiratory Diseases, Haihe Hospital, Tianjin University, Tianjin, China
| | - Zhitang Lyu
- Key Laboratory of Microbial Diversity Research and Application of Hebei, School of Life Sciences, Hebei University, Baoding, China
- Zhitang Lyu
| | - Ping Xu
- Key Laboratory of Microbial Diversity Research and Application of Hebei, School of Life Sciences, Hebei University, Baoding, China
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
- Guangzhou University of Chinese Medicine, Second Clinical Medicine College, Guangzhou Higher Education Mega Center, Guangzhou, China
- Research Unit of Proteomics and Research and Development of New Drug, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Ping Xu
| | - Yao Zhang
- Beijing Proteome Research Center, National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing, China
- Yao Zhang
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Zhu H, Jiang S, Zhou W, Chi H, Sun J, Shi J, Zhang Z, Chang L, Yu L, Zhang L, Lyu Z, Xu P, Zhang Y. Ac-LysargiNase efficiently helps genome reannotation of Mycolicibacterium smegmatis MC2 155. J Proteomics 2022; 264:104622. [DOI: 10.1016/j.jprot.2022.104622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
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