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Guo Q, Li D, Zhai Y, Gu Z. CCPRD: A Novel Analytical Framework for the Comprehensive Proteomic Reference Database Construction of NonModel Organisms. ACS OMEGA 2020; 5:15370-15384. [PMID: 32637811 PMCID: PMC7331046 DOI: 10.1021/acsomega.0c01278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Protein reference databases are a critical part of producing efficient proteomic analyses. However, the method for constructing clean, efficient, and comprehensive protein reference databases of nonmodel organisms is lacking. Existing methods either do not have contamination control procedures, or these methods rely on a three-frame and/or six-frame translation that sharply increases the search space and the need for computational resources. Herein, we propose a framework for constructing a customized comprehensive proteomic reference database (CCPRD) from draft genomes and deep sequencing transcriptomes. Its effectiveness is demonstrated by incorporating the proteomes of nematocysts from endoparasitic cnidarian: myxozoans. By applying customized contamination removal procedures, contaminations in omic data were successfully identified and removed. This is an effective method that does not result in overdecontamination. This can be shown by comparing the CCPRD MS results with an artificially contaminated database and another database with removed contaminations in genomes and transcriptomes added back. CCPRD outperformed traditional frame-based methods by identifying 35.2-50.7% more peptides and 35.8-43.8% more proteins, with a maximum of 84.6% in size reduction. A BUSCO analysis showed that the CCPRD maintained a relatively high level of completeness compared to traditional methods. These results confirm the superiority of the CCPRD over existing methods in peptide and protein identification numbers, database size, and completeness. By providing a general framework for generating the reference database, the CCPRD, which does not need a high-quality genome, can potentially be applied to nonmodel organisms and significantly contribute to proteomic research.
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Affiliation(s)
- Qingxiang Guo
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Dan Li
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Yanhua Zhai
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
| | - Zemao Gu
- Department of Aquatic
Animal Medicine, College of Fisheries, Huazhong
Agricultural University, Wuhan, Hubei Province 430070, PR China
- Hubei Engineering Technology Research
Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, PR China
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Liu X, Huan Z, Zhang Q, Zhong M, Chen W, Aslam M, Du H. Glutamine Synthetase (GS): A Key Enzyme for Nitrogen Assimilation in The Macroalga Gracilariopsis lemaneiformis (Rhodophyta). JOURNAL OF PHYCOLOGY 2019; 55:1059-1070. [PMID: 31206671 DOI: 10.1111/jpy.12891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/17/2019] [Indexed: 05/21/2023]
Abstract
This study aimed to address the importance of glutamine synthetase II (GSII) during nitrogen assimilation in macroalga Gracilariopsis lemaneiformis. The cDNA full-length sequence of the three glGSII genes was revealed to have the 5' m7 G cap, 5'-untranslated region, open reading frame (ORF), 3'-untranslated region, and a 3' poly (A) tail. The three glGSIIs were classified into plastid glGS2 and cytosolic glGS1-1 and glGS1-2, having conserved GSII domains but different cDNA sequences. The complicated 5' end flanking region indicates complex function of glGS genes. glGS1 genes were significantly up-regulated under the different NH4+ : NO3- ratio (i.e., 40:10, 25:25, 10:40, and 0:50) except glGS2 which dramatically up-regulated under the low NH4+ : NO3- ratio (i.e., 10:40 and 0:50) during different cultivation times. These different expression patterns perhaps are due to the different biological roles of GS1 and GS2 in the gene family. Furthermore, hypothetical working model of nitrogen assimilation pathway exhibiting the role of glGS1 and glGS2 is proposed. Finally, glGS2 was expressed in Escherichia coli BL21 (DE3), and the optimal conditions for culture (15°C, overnight), purification (500 mM imidazole washing), and activity (pH 7.4, 37°C) were established. This study lays a very important foundation for exploring the role of GS in nitrogen assimilation in algae and plants.
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Affiliation(s)
- Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, 515063, China
| | - Zhongyan Huan
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, 515063, China
| | - Qingfang Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, 515063, China
| | - Mingqi Zhong
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, 515063, China
| | - Weizhou Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, 515063, China
| | - Muhammad Aslam
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, 515063, China
| | - Hong Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology and STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou, 515063, China
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Calegario G, Freitas L, Santos E, Silva B, Oliveira L, Garcia G, Omachi C, Pereira R, Thompson C, Thompson F. Environmental modulation of the proteomic profiles from closely phylogenetically related populations of the red seaweed Plocamium brasiliense. PeerJ 2019; 7:e6469. [PMID: 30972241 PMCID: PMC6450377 DOI: 10.7717/peerj.6469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/17/2019] [Indexed: 11/30/2022] Open
Abstract
The genus Plocamium encompasses seaweeds that are widely distributed throughout the world’s oceans, with Plocamium brasiliense found along the tropical and subtropical coasts of the Western Atlantic. This wide distribution can lead to structured populations due to environmental differences (e.g., light levels or temperature), restricted gene flow, and the presence of cryptic species. Abiotic variation can also affect gene expression, which consequently leads to differences in the seaweeds protein profile. This study aimed to analyze the genetic and proteomic profiles of P. brasiliense sampled in two geographically distinct sites on the coastline of Rio de Janeiro state, Brazil: Arraial do Cabo (P1) and Búzios (P2). The genetic profiles of macroalgal specimens from these two sites were indistinguishable as assessed by the markers UPA/23S, rbcL, and COI-5P; however, the protein profiles varied significantly between populations from the two sites. At both sites the ribulose-1,5-biphosphate carboxylase/oxygenase was the most abundant protein found in P. brasiliense specimens. The number of phycobiliproteins differed between both sites with the highest numbers being found at P1, possibly due to water depth. The differences in proteomic profiles of the two nearly identical populations of P. brasiliense suggest that environmental parameters such as light availability and desiccation might induce distinct protein expression, probably as a result of the phenotypic plasticity within this population of seaweed.
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Affiliation(s)
- Gabriela Calegario
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucas Freitas
- Department of Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Genetics, Evolution, Microbiology and Immunology, State University of Campinas, Campinas, São Paulo, Brazil
| | - Eidy Santos
- Unit of Biology, State University of the West Zone, Rio de Janeiro, Brazil
| | - Bruno Silva
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Louisi Oliveira
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gizele Garcia
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Undergraduate Education, Federal University of Rio de Janeiro, Macaé, Brazil
| | - Cláudia Omachi
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renato Pereira
- Department of Marine Biology, Fluminense Federal University, Niterói, Brazil.,Rio de Janeiro Botanical Garden, Rio de Janeiro, Brazil
| | - Cristiane Thompson
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabiano Thompson
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,SAGE-COPPE, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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