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Chen J, Gao G, Chen P, Chen K, Wang X, Bai L, Yu C, Zhu A. Integrative Transcriptome and Proteome Analysis Identifies Major Molecular Regulation Pathways Involved in Ramie ( Boehmeria nivea (L.) Gaudich) under Nitrogen and Water Co-Limitation. PLANTS 2020; 9:plants9101267. [PMID: 32992865 PMCID: PMC7650756 DOI: 10.3390/plants9101267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 11/21/2022]
Abstract
Water and N are the most important factors affecting ramie (Boehmeria nivea (L.) Gaudich) growth. In this study, de novo transcriptome assembly and Tandem Mass Tags (TMT) based quantitative proteome analysis of ramie under nitrogen and water co-limitation conditions were performed, and exposed to treatments, including drought and N-deficit (WdNd), proper water but N-deficit (WNd), proper N but drought (WdN), and proper N and water (CK), respectively. A total of 64,848 unigenes (41.92% of total unigenes) were annotated in at least one database, including NCBI non-redundant protein sequences (Nr), Swiss-Prot, Protein family (Pfam), Gene Ontology (GO) and KEGG Orthology (KO), and 4268 protein groups were identified. Most significant changes in transcript levels happened under water-limited conditions, but most significant changes in protein level happened under water-limited conditions only with proper N. Poor correlation between differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) was observed in ramie responding to the treatments. DEG/DEP regulation patterns related to major metabolic processes responding to water and N deficiency were analyzed, including photosynthesis, ethylene responding, glycolysis, and nitrogen metabolism. Moreover, 41 DEGs and 61 DEPs involved in regulating adaptation of ramie under water and N stresses were provided in the study, including DEGs/DEPs related to UDP—glucuronosyhransferase (UGT), ATP synthase, and carbonate dehydratase. The strong dependency of N-response of ramie on water conditions at the gene and protein levels was highlighted. Advices for simultaneously improving water and N efficiency in ramie were also provided, especially in breeding N efficient varieties with drought resistance. This study provided extensive new information on the transcriptome, proteome, their correlation, and diversification in ramie responding to water and N co-limitation.
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Affiliation(s)
- Jikang Chen
- Longping Branch, Graduate School of Hunan University, Changsha 410082, China;
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
| | - Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
| | - Xiaofei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
| | - Lianyang Bai
- Longping Branch, Graduate School of Hunan University, Changsha 410082, China;
- Hunan Academy of Agricultural Sciences, Changsha 410125, China
- Correspondence: (L.B.); (C.Y.); (A.Z.); Tel.: +86-0731-84692799 (L.B.); +86-0731-88998511 (C.Y.); +86-0731-88998586 (A.Z.)
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
- Correspondence: (L.B.); (C.Y.); (A.Z.); Tel.: +86-0731-84692799 (L.B.); +86-0731-88998511 (C.Y.); +86-0731-88998586 (A.Z.)
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, China; (G.G.); (P.C.); (K.C.); (X.W.)
- National Breeding Center for Bast Fiber Crops, Changsha 410125, China
- Correspondence: (L.B.); (C.Y.); (A.Z.); Tel.: +86-0731-84692799 (L.B.); +86-0731-88998511 (C.Y.); +86-0731-88998586 (A.Z.)
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Wang G, Li M, Zhang C, Cheng H, Gao Y, Deng W, Li T. Transcriptome and proteome analyses reveal the regulatory networks and metabolite biosynthesis pathways during the development of Tolypocladium guangdongense. Comput Struct Biotechnol J 2020; 18:2081-2094. [PMID: 32802280 PMCID: PMC7419252 DOI: 10.1016/j.csbj.2020.07.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 12/17/2022] Open
Abstract
Tolypocladium guangdongense has a similar metabolite profile to Ophiocordyceps sinensis, a highly regarded fungus used for traditional Chinese medicine with high nutritional and medicinal value. Although the genome sequence of T. guangdongense has been reported, relatively little is known about the regulatory networks for fruiting body development and about the metabolite biosynthesis pathways. In order to address this, an analysis of transcriptome and proteome at differential developmental stages of T. guangdongense was performed. In total, 9076 genes were found to be expressed and 2040 proteins were identified. There were a large number of genes that were significantly differentially expressed between the mycelial stage and the stages. Interestingly, the correlation between the transcriptomic and proteomic data was low, suggesting the importance of the post-transcriptional processes in the growth and development of T. guangdongense. Among the genes/proteins that were both differentially expressed during the developmental process, there were numerous heat shock proteins and transcription factors. In addition, there were numerous proteins involved in terpenoid, ergosterol, adenosine and polysaccharide biosynthesis that also showed significant downregulation in their expression levels during the developmental process. Furthermore, both tryptophan and tryptamine were present at higher levels in the primordium stage. However, indole-3-acetic acid (IAA) levels continuously decreased as development proceeded, and the enzymes involved in IAA biosynthesis were also clearly differentially downregulated. These data could be meaningful in studying the molecular mechanisms of fungal development, and for the industrial and medicinal application of macro-fungi.
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Affiliation(s)
- Gangzheng Wang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Min Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.,College of Agriculture and Animal Husbandry, Tibet University, Nyingchi, 860000 Tibet, China
| | - Chenghua Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Huijiao Cheng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.,South China Agricultural University, Guangzhou 510642, China
| | - Yu Gao
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Wangqiu Deng
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Taihui Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China
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Kanyal A, Rawat M, Gurung P, Choubey D, Anamika K, Karmodiya K. Genome‐wide survey and phylogenetic analysis of histone acetyltransferases and histone deacetylases of
Plasmodium falciparum. FEBS J 2018; 285:1767-1782. [DOI: 10.1111/febs.14376] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/20/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Abhishek Kanyal
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
| | - Mukul Rawat
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
| | - Pratima Gurung
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
| | | | | | - Krishanpal Karmodiya
- Department of Biology Indian Institute of Science Education and Research Pashan, Pune India
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Peng X, Qin Z, Zhang G, Guo Y, Huang J. Integration of the proteome and transcriptome reveals multiple levels of gene regulation in the rice dl2 mutant. FRONTIERS IN PLANT SCIENCE 2015; 6:351. [PMID: 26136752 PMCID: PMC4469824 DOI: 10.3389/fpls.2015.00351] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 05/03/2015] [Indexed: 05/24/2023]
Abstract
Leaf vascular system differentiation and venation patterns play a key role in transporting nutrients and maintaining the plant shape, which is an important agronomic trait for improving photosynthetic efficiency. However, there is little knowledge about the regulation of leaf vascular specification and development. Here we utilized the rice midribless mutant (dl2) to investigate the molecular changes in transcriptome and proteome profiles during leaf vascular specification and differentiation. Using isobaric tags for relative and absolute quantification (iTRAQ) with digital gene expression (DGE) techniques, a nearly complete catalog of expressed protein and mRNA was acquired. From the catalog, we reliably identified 3172 proteins and 9,865,230 tags mapped to genes, and subsets of 141 proteins and 98 mRNAs, which were differentially expressed between the dl2 mutant and wild type. The correlation analysis between the abundance of differentially expressed mRNA and DEPs (differentially expressed proteins) revealed numerous discordant changes in mRNA/protein pairs and only a modest correlation was observed, indicative of divergent regulation of transcription and translational processes. The DEPs were analyzed for their involvement in biological processes and metabolic pathways. Up- or down- regulation of some key proteins confirmed that the physiological process of vascular differentiation is an active process. These key proteins included those not previously reported to be associated with vascular differentiation processes, and included proteins that are involved in the spliceosome pathway. Together, our results show that the developmental and physiological process of the leaf vascular system is a thoroughly regulated and complicated process and this work has identified potential targets for genetic modification that could be used to regulate the development of the leaf vasculature.
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Affiliation(s)
| | | | | | | | - Junli Huang
- *Correspondence: Junli Huang, Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Shazheng Street, Chongqing 400030, China ;
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Perrin AJ, Bartholdson SJ, Wright GJ. P-selectin is a host receptor for Plasmodium MSP7 ligands. Malar J 2015; 14:238. [PMID: 26045295 PMCID: PMC4478713 DOI: 10.1186/s12936-015-0750-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/26/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodium parasites typically elicit a non-sterile but protective immune response in human host populations, suggesting that the parasites actively modulate normal immunological mechanisms. P-selectin is a cell surface receptor expressed in mammals, that is a known component of the inflammatory response against pathogens and has been previously identified as a host factor that influences malaria-associated pathology both in human patients and rodent infection models. METHODS To better understand the molecular mechanisms underlying the involvement of P-selectin in the pathogenesis of malaria, a systematic extracellular protein interaction screen was used to identify Plasmodium falciparum merozoite surface protein 7 (MSP7) as a binding partner of human P-selectin. This interaction, and those occurring between P-selectin and Plasmodium MSP7 homologues, was characterized biochemically. RESULTS Plasmodium falciparum MSP7 and P-selectin were shown to bind each other directly via the N-terminus of PfMSP7 and the P-selectin C-type lectin and EGF-like domains. Orthologous proteins in the murine parasite Plasmodium berghei (PbMSRP1 and PbMSRP2) and mouse P-selectin also interacted. Finally, P-selectin, when complexed with MSP7, could no longer bind to its endogenous carbohydrate ligand, Sialyl-Lewis(X). CONCLUSIONS Novel interactions were identified between Plasmodium MSP7 protein family members and host P-selectin receptors. Since PfMSP7 could prevent interactions between P-selectin and its leukocyte ligands, these results provide a possible mechanism for the known immunomodulatory effects of both MSP7 and P-selectin in malaria infection models.
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Affiliation(s)
- Abigail J Perrin
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - S Josefin Bartholdson
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - Gavin J Wright
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
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Almelli T, Nuel G, Bischoff E, Aubouy A, Elati M, Wang CW, Dillies MA, Coppée JY, Ayissi GN, Basco LK, Rogier C, Ndam NT, Deloron P, Tahar R. Differences in gene transcriptomic pattern of Plasmodium falciparum in children with cerebral malaria and asymptomatic carriers. PLoS One 2014; 9:e114401. [PMID: 25479608 PMCID: PMC4257676 DOI: 10.1371/journal.pone.0114401] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 11/10/2014] [Indexed: 11/24/2022] Open
Abstract
The mechanisms underlying the heterogeneity of clinical malaria remain largely unknown. We hypothesized that differential gene expression contributes to phenotypic variation of parasites which results in a specific interaction with the host, leading to different clinical features of malaria. In this study, we analyzed the transcriptomes of isolates obtained from asymptomatic carriers and patients with uncomplicated or cerebral malaria. We also investigated the transcriptomes of 3D7 clone and 3D7-Lib that expresses severe malaria associated-variant surface antigen. Our findings revealed a specific up-regulation of genes involved in pathogenesis, adhesion to host cell, and erythrocyte aggregation in parasites from patients with cerebral malaria and 3D7-Lib, compared to parasites from asymptomatic carriers and 3D7, respectively. However, we did not find any significant difference between the transcriptomes of parasites from cerebral malaria and uncomplicated malaria, suggesting similar transcriptomic pattern in these two parasite populations. The difference between isolates from asymptomatic children and cerebral malaria concerned genes coding for exported proteins, Maurer's cleft proteins, transcriptional factor proteins, proteins implicated in protein transport, as well as Plasmodium conserved and hypothetical proteins. Interestingly, UPs A1, A2, A3 and UPs B1 of var genes were predominantly found in cerebral malaria-associated isolates and those containing architectural domains of DC4, DC5, DC13 and their neighboring rif genes in 3D7-lib. Therefore, more investigations are needed to analyze the effective role of these genes during malaria infection to provide with new knowledge on malaria pathology. In addition, concomitant regulation of genes within the chromosomal neighborhood suggests a common mechanism of gene regulation in P. falciparum.
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Affiliation(s)
- Talleh Almelli
- Institut de Recherche pour le Développement (IRD), UMR 216 Mère et Enfant Face aux Infections Tropicales, Université Paris-Descartes, Près Sorbonne Paris-Cité, Paris, France
- PRES Sorbone Paris Cité, Université Paris Descartes, Faculté de Pharmacie, Paris, France
| | - Grégory Nuel
- PRES Sorbone Paris Cité, Université Paris Descartes, Faculté de Pharmacie, Paris, France
| | - Emmanuel Bischoff
- Institut Pasteur, Unit of Molecular Immunology of Parasites, Unit of Insect Vector Genetics and Genomics, Department of Parasitology and Mycology, Paris, France
- Centre National de la Recherche Scientifique (CNRS), URA 3012, Paris, France
| | - Agnès Aubouy
- Institut de Recherche pour le Développement (IRD), UMR 152 Pharmacochimie et pharmacologie pour le développement - (PHARMA-DEV), Université Paul Sabatier, Toulouse, France
| | - Mohamed Elati
- Institute of Systems and Synthetic Biology, CNRS, University of Evry, Genopole, Evry, France
| | - Christian William Wang
- Centre for Medical Parasitology at Department of International Health, Immunology, and Microbiology, University of Copenhagen and at Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark
| | - Marie-Agnès Dillies
- Plate-forme Transcriptome et Epigénome, Departement Génomes et Génétique, Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Plate-forme Transcriptome et Epigénome, Departement Génomes et Génétique, Institut Pasteur, Paris, France
| | | | - Leonardo Kishi Basco
- Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), Laboratoire de Recherche sur le Paludisme, B. P. 288, Yaoundé, Cameroon
- Institut de Recherche pour le Développement (IRD), UMR 198 Unité de Recherche des Maladies Infectieuses et Tropicales Emergentes, Faculté de Médecine La Timone, Aix-Marseille Université, Marseille, France
| | - Christophe Rogier
- Institut Pasteur de Madagascar, B.P. 1274, Ambatofotsikely, Antananarivo, Madagascar
| | - Nicaise Tuikue Ndam
- Institut de Recherche pour le Développement (IRD), UMR 216 Mère et Enfant Face aux Infections Tropicales, Université Paris-Descartes, Près Sorbonne Paris-Cité, Paris, France
- PRES Sorbone Paris Cité, Université Paris Descartes, Faculté de Pharmacie, Paris, France
| | - Philippe Deloron
- Institut de Recherche pour le Développement (IRD), UMR 216 Mère et Enfant Face aux Infections Tropicales, Université Paris-Descartes, Près Sorbonne Paris-Cité, Paris, France
- PRES Sorbone Paris Cité, Université Paris Descartes, Faculté de Pharmacie, Paris, France
| | - Rachida Tahar
- Institut de Recherche pour le Développement (IRD), UMR 216 Mère et Enfant Face aux Infections Tropicales, Université Paris-Descartes, Près Sorbonne Paris-Cité, Paris, France
- PRES Sorbone Paris Cité, Université Paris Descartes, Faculté de Pharmacie, Paris, France
- Organisation de Coordination pour la lutte contre les Endémies en Afrique Centrale (OCEAC), Laboratoire de Recherche sur le Paludisme, B. P. 288, Yaoundé, Cameroon
- * E-mail:
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Triggers of key calcium signals during erythrocyte invasion by Plasmodium falciparum. Nat Commun 2014; 4:2862. [PMID: 24280897 PMCID: PMC3868333 DOI: 10.1038/ncomms3862] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 11/04/2013] [Indexed: 01/28/2023] Open
Abstract
Invasion of erythrocytes by Plasmodium falciparum merozoites is a complex multi-step process mediated by specific interactions between host receptors and parasite ligands. Reticulocyte-binding protein homologues (RHs) and erythrocyte-binding-like (EBL) proteins are discharged from specialized organelles and used in early steps of invasion. Here we show that monoclonal antibodies against PfRH1 (an RH) block merozoite invasion by specifically inhibiting calcium signalling in the parasite, whereas invasion-inhibiting monoclonal antibodies targeting EBA175 (an EBL protein) have no effect on signalling. We further show that inhibition of this calcium signalling prevents EBA175 discharge and thereby formation of the junction between parasite and host cell. Our results indicate that PfRH1 has an initial sensing as well as signal transduction role that leads to the subsequent release of EBA175. They also provide new insights on how RH-host cell interactions lead to essential downstream signalling events in the parasite, suggesting new targets for malaria intervention.
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Lin X, Kang L, Li H, Peng X. Fluctuation of multiple metabolic pathways is required for Escherichia coli in response to chlortetracycline stress. ACTA ACUST UNITED AC 2014; 10:901-8. [DOI: 10.1039/c3mb70522f] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bacterial antibiotic resistance has become a worldwide challenge with the overuse and misuse of drugs.
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Affiliation(s)
- Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring (School of Life Sciences, Fujian Agriculture and Forestry University)
- Fuzhou 35002, People's Republic of China
- Center for Proteomics and Metabolomics
- State Key Laboratory of Bio-Control
- School of Life Sciences
| | - Liqun Kang
- Center for Proteomics and Metabolomics
- State Key Laboratory of Bio-Control
- School of Life Sciences
- Sun Yat-Sen University
- University City
| | - Hui Li
- Center for Proteomics and Metabolomics
- State Key Laboratory of Bio-Control
- School of Life Sciences
- Sun Yat-Sen University
- University City
| | - Xuanxian Peng
- Center for Proteomics and Metabolomics
- State Key Laboratory of Bio-Control
- School of Life Sciences
- Sun Yat-Sen University
- University City
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Malaria proteomics: insights into the parasite-host interactions in the pathogenic space. J Proteomics 2013; 97:107-25. [PMID: 24140976 DOI: 10.1016/j.jprot.2013.10.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 06/23/2013] [Accepted: 10/08/2013] [Indexed: 11/23/2022]
Abstract
Proteomics is improving malaria research by providing global information on relevant protein sets from the parasite and the host in connection with its cellular structures and specific functions. In the last decade, reports have described biologically significant elements in the proteome of Plasmodium, which are selectively targeted and quantified, allowing for sensitive and high-throughput comparisons. The identification of molecules by which the parasite and the host react during the malaria infection is crucial to the understanding of the underlying pathogenic mechanisms. Hence, proteomics is playing a major role by defining the elements within the pathogenic space between both organisms that change across the parasite life cycle in association with the host transformation and response. Proteomics has identified post-translational modifications in the parasite and the host that are discussed in terms of functional interactions in malaria parasitism. Furthermore, the contribution of proteomics to the investigation of immunogens for potential vaccine candidates is summarized. The malaria-specific technological advances in proteomics are particularly suited now for identifying host-parasite interactions that could lead to promising targets for therapy, diagnosis or prevention. In this review, we examine the knowledge gained on the biology, pathogenesis, immunity and diagnosis of Plasmodium infection from recent proteomic studies. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Pease BN, Huttlin EL, Jedrychowski MP, Talevich E, Harmon J, Dillman T, Kannan N, Doerig C, Chakrabarti R, Gygi SP, Chakrabarti D. Global analysis of protein expression and phosphorylation of three stages of Plasmodium falciparum intraerythrocytic development. J Proteome Res 2013; 12:4028-45. [PMID: 23914800 DOI: 10.1021/pr400394g] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
During asexual intraerythrocytic development, Plasmodium falciparum diverges from the paradigm of the eukaryotic cell cycles by undergoing multiple rounds of DNA replication and nuclear division without cytokinesis. A better understanding of the molecular switches that coordinate a myriad of events for the progression of the parasite through the intraerythrocytic developmental stages will be of fundamental importance for rational design of intervention strategies. To achieve this goal, we performed isobaric tag-based quantitative proteomics and phosphoproteomics analyses of three developmental stages in the Plasmodium asexual cycle and identified 2767 proteins, 1337 phosphoproteins, and 6293 phosphorylation sites. Approximately 34% of identified proteins and 75% of phosphorylation sites exhibit changes in abundance as the intraerythrocytic cycle progresses. Our study identified 43 distinct phosphorylation motifs and a range of potential MAPK/CDK substrates. Further analysis of phosphorylated kinases identified 30 protein kinases with 126 phosphorylation sites within the kinase domain or in N- or C-terminal tails. Many of these phosphorylations are likely CK2-mediated. We define the constitutive and regulated expression of the Plasmodium proteome during the intraerythrocytic developmental cycle, offering an insight into the dynamics of phosphorylation during asexual cycle progression. Our system-wide comprehensive analysis is a major step toward defining kinase-substrate pairs operative in various signaling networks in the parasite.
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Affiliation(s)
- Brittany N Pease
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida 32826, United States
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Food vacuole associated enolase in plasmodium undergoes multiple post-translational modifications: evidence for atypical ubiquitination. PLoS One 2013; 8:e72687. [PMID: 24009698 PMCID: PMC3751847 DOI: 10.1371/journal.pone.0072687] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 07/18/2013] [Indexed: 01/05/2023] Open
Abstract
Plasmodium enolase localizes to several sub-cellular compartments viz. cytosol, nucleus, cell membrane, food vacuole (FV) and cytoskeleton, without having any organelle targeting signal sequences. This enzyme has been shown to undergo multiple post-translational modifications (PTMs) giving rise to several variants that show organelle specific localization. It is likely that these PTMs may be responsible for its diverse distribution and moonlighting functions. While most variants have a MW of ~50 kDa and are likely to arise due to changes in pI, food vacuole (FV) associated enolase showed three forms with MW~50, 65 and 75 kDa. Evidence from immuno-precipitation and western analysis indicates that the 65 and 75 kDa forms of FV associated enolase are ubiquitinated. Using mass spectrometry (MS), definitive evidence is obtained for the nature of PTMs in FV associated variants of enolase. Results showed several modifications, viz. ubiquitination at K147, phosphorylation at Y148 and acetylation at K142 and K384. MS data also revealed the conjugation of three ubiquitin (Ub) molecules to enolase through K147. Trimeric ubiquitin has a linear peptide linkage between the NH2-terminal methionine of the first ubiquitin (Ub1) and the C-terminal G76 of the second (Ub2). Ub2 and third ubiquitin (Ub3) were linked through an atypical isopeptide linkage between K6 of Ub2 and G76 of Ub3, respectively. Further, the tri-ubiquitinated form was found to be largely associated with hemozoin while the 50 and 65 kDa forms were present in the NP-40 soluble fraction of FV. Mass spectrometry results also showed phosphorylation of S42 in the cytosolic enolase from P. falciparum and T337 in the cytoskeleton associated enolase from P. yoelii. The composition of food vacuolar proteome and likely interactors of enolase are also being reported.
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Goodman SR, Daescu O, Kakhniashvili DG, Zivanic M. The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 2013; 238:509-18. [DOI: 10.1177/1535370213488474] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this minireview, we focus on advances in our knowledge of the human erythrocyte proteome and interactome that have occurred since our seminal review on the topic published in 2007. As will be explained, the number of unique proteins has grown from 751 in 2007 to 2289 as of today. We describe how proteomics and interactomics tools have been used to probe critical protein changes in disorders impacting the blood. The primary example used is the work done on sickle cell disease where biomarkers of severity have been identified, protein changes in the erythrocyte membranes identified, pharmacoproteomic impact of hydroxyurea studied and interactomics used to identify erythrocyte protein changes that are predicted to have the greatest impact on protein interaction networks.
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Affiliation(s)
- Steven R Goodman
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Ovidiu Daescu
- Department of Computer Science, University of Texas at Dallas, Richardson, TX 75080, USA
| | - David G Kakhniashvili
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Marko Zivanic
- Department of Computer Science, University of Texas at Dallas, Richardson, TX 75080, USA
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Galinski MR, Meyer EVS, Barnwell JW. Plasmodium vivax: modern strategies to study a persistent parasite's life cycle. ADVANCES IN PARASITOLOGY 2013; 81:1-26. [PMID: 23384620 DOI: 10.1016/b978-0-12-407826-0.00001-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Plasmodium vivax has unique attributes to support its survival in varying ecologies and climates. These include hypnozoite forms in the liver, an invasion preference for reticulocytes, caveola-vesicle complex structures in the infected erythrocyte membrane and rapidly forming and circulating gametocytes. These characteristics make this species very different from P. falciparum. Plasmodium cynomolgi and other related simian species have identical biology and can serve as informative models of P. vivax infections. Plasmodium vivax and its model parasites can be grown in non-human primates (NHP), and in short-term ex vivo cultures. For P. vivax, in the absence of in vitro culture systems, these models remain highly relevant side by side with human clinical studies. While post-genomic technologies allow for greater exploration of P. vivax-infected blood samples from humans, these come with restrictions. Two advantages of NHP models are that infections can be experimentally tailored to address hypotheses, including genetic manipulation. Also, systems biology approaches can capitalise on computational biology combined with set experimental infection periods and protocols, which may include multiple sampling times, different types of samples, and the broad use of "omics" technologies. Opportunities for research on vivax malaria are increasing with the use of existing and new methodological strategies in combination with modern technologies.
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Affiliation(s)
- Mary R Galinski
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, Georgia, USA.
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Zhang L, Selão TT, Pisareva T, Qian J, Sze SK, Carlberg I, Norling B. Deletion of Synechocystis sp. PCC 6803 leader peptidase LepB1 affects photosynthetic complexes and respiration. Mol Cell Proteomics 2013; 12:1192-203. [PMID: 23358502 DOI: 10.1074/mcp.m112.022145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The cyanobacterium Synechocystis sp. PCC 6803 possesses two leader peptidases, LepB1 (Sll0716) and LepB2 (Slr1377), responsible for the processing of signal peptide-containing proteins. Deletion of the gene for LepB1 results in an inability to grow photoautotrophically and an extreme light sensitivity. Here we show, using a combination of Blue Native/SDS-PAGE, Western blotting and iTRAQ analysis, that lack of LepB1 strongly affects the cell's ability to accumulate wild-type levels of both photosystem I (PSI) and cytochrome (Cyt) b6f complexes. The impaired assembly of PSI and Cyt b6f is considered to be caused by the no or slow processing of the integral subunits PsaF and Cyt f respectively. In particular, PsaF, one of the PSI subunits, was found incorporated into PSI in its unprocessed form, which could influence the assembly and/or stability of PSI. In contrast to these results, we found the amount of assembled photosystem II (PSII) unchanged, despite a slower processing of PsbO. Thus, imbalance in the ratios of PSI and Cyt b6f to photosystem II leads to an imbalanced photosynthetic electron flow up- and down-stream of the plastoquinone pool, resulting in the observed light sensitivity of the mutant. We conclude that LepB1 is the natural leader peptidase for PsaF, PsbO, and Cyt f. The maturation of PsbO and Cyt f can be partially performed by LepB2, whereas PsaF processing is completely dependent on LepB1. iTRAQ analysis also revealed a number of indirect effects accompanying the mutation, primarily a strong induction of the CydAB oxidase as well as a significant decrease in phycobiliproteins and chlorophyll/heme biosynthesis enzymes.
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Affiliation(s)
- Lifang Zhang
- Nanyang Technological University, School of Biological Sciences, 637551 Singapore
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Insights into the Plasmodium falciparum schizont phospho-proteome. Microbes Infect 2012; 14:811-9. [DOI: 10.1016/j.micinf.2012.04.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 04/11/2012] [Accepted: 04/12/2012] [Indexed: 12/27/2022]
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16
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Abstract
Systems biology aims to integrate multiple biological data types such as genomics, transcriptomics and proteomics across different levels of structure and scale; it represents an emerging paradigm in the scientific process which challenges the reductionism that has dominated biomedical research for hundreds of years. Systems biology will nevertheless only be successful if the technologies on which it is based are able to deliver the required type and quality of data. In this review we discuss how well positioned is proteomics to deliver the data necessary to support meaningful systems modelling in parasite biology. We summarise the current state of identification proteomics in parasites, but argue that a new generation of quantitative proteomics data is now needed to underpin effective systems modelling. We discuss the challenges faced to acquire more complete knowledge of protein post-translational modifications, protein turnover and protein-protein interactions in parasites. Finally we highlight the central role of proteome-informatics in ensuring that proteomics data is readily accessible to the user-community and can be translated and integrated with other relevant data types.
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