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Abstract
Mass spectrometry (MS)-based top-down proteomics (TDP) requires high-resolution separation of proteoforms before electrospray ionization (ESI)-MS and tandem mass spectrometry (MS/MS). Capillary isoelectric focusing (cIEF)-ESI-MS and MS/MS could be an ideal method for TDP because cIEF can enable separation of proteoforms based on their isoelectric points (pIs) with ultra-high resolution. cIEF-ESI-MS has been well-recognized for protein characterization since 1990s. However, the widespread adoption of cIEF-MS for the characterization of proteoforms had been impeded by several technical challenges, including the lack of highly sensitive and robust ESI interface for coupling cIEF to MS, ESI suppression of analytes from ampholytes, and the requirement of manual operations. In this mini review, we summarize the technical improvements of cIEF-ESI-MS for characterizing proteoforms and highlight some recent applications to hydrophobic proteins, urinary albumin variants, charge variants of monoclonal antibodies, and large-scale TDP of complex proteomes.
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Affiliation(s)
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, East Lansing, MI, United States
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Morozov SY, Solovyev AG. Small hydrophobic viral proteins involved in intercellular movement of diverse plant virus genomes. AIMS Microbiol 2020; 6:305-329. [PMID: 33134746 PMCID: PMC7595835 DOI: 10.3934/microbiol.2020019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/13/2020] [Indexed: 12/12/2022] Open
Abstract
Most plant viruses code for movement proteins (MPs) targeting plasmodesmata to enable cell-to-cell and systemic spread in infected plants. Small membrane-embedded MPs have been first identified in two viral transport gene modules, triple gene block (TGB) coding for an RNA-binding helicase TGB1 and two small hydrophobic proteins TGB2 and TGB3 and double gene block (DGB) encoding two small polypeptides representing an RNA-binding protein and a membrane protein. These findings indicated that movement gene modules composed of two or more cistrons may encode the nucleic acid-binding protein and at least one membrane-bound movement protein. The same rule was revealed for small DNA-containing plant viruses, namely, viruses belonging to genus Mastrevirus (family Geminiviridae) and the family Nanoviridae. In multi-component transport modules the nucleic acid-binding MP can be viral capsid protein(s), as in RNA-containing viruses of the families Closteroviridae and Potyviridae. However, membrane proteins are always found among MPs of these multicomponent viral transport systems. Moreover, it was found that small membrane MPs encoded by many viruses can be involved in coupling viral replication and cell-to-cell movement. Currently, the studies of evolutionary origin and functioning of small membrane MPs is regarded as an important pre-requisite for understanding of the evolution of the existing plant virus transport systems. This paper represents the first comprehensive review which describes the whole diversity of small membrane MPs and presents the current views on their role in plant virus movement.
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Affiliation(s)
- Sergey Y Morozov
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.,Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia
| | - Andrey G Solovyev
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.,Department of Virology, Biological Faculty, Moscow State University, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
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Zhao C, Kim Y, Zeng Y, Li M, Wang X, Hu C, Gorman C, Dai SY, Ding SY, Yuan JS. Co-Compartmentation of Terpene Biosynthesis and Storage via Synthetic Droplet. ACS Synth Biol 2018; 7:774-781. [PMID: 29439563 DOI: 10.1021/acssynbio.7b00368] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Traditional bioproduct engineering focuses on pathway optimization, yet is often complicated by product inhibition, downstream consumption, and the toxicity of certain products. Here, we present the co-compartmentation of biosynthesis and storage via a synthetic droplet as an effective new strategy to improve the bioproduct yield, with squalene as a model compound. A hydrophobic protein was designed and introduced into the tobacco chloroplast to generate a synthetic droplet for terpene storage. Simultaneously, squalene biosynthesis enzymes were introduced to chloroplasts together with the droplet-forming protein to co-compartmentalize the biosynthesis and storage of squalene. The strategy has enabled a record yield of squalene at 2.6 mg/g fresh weight without compromising plant growth. Confocal fluorescent microscopy imaging, stimulated Raman scattering microscopy, and droplet composition analysis confirmed the formation of synthetic storage droplet in chloroplast. The co-compartmentation of synthetic storage droplet with a targeted metabolic pathway engineering represents a new strategy for enhancing bioproduct yield.
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Affiliation(s)
- Cheng Zhao
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub , Texas A&M University , College Station , Texas 77843 , United States
- Department of Plant Pathology and Microbiology , Texas A&M University , College Station , Texas 77843 , United States
- Institute for Plant Genomics and Biotechnology , Texas A&M University , College Station , Texas 77843 , United States
| | - YongKyoung Kim
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub , Texas A&M University , College Station , Texas 77843 , United States
- Department of Plant Pathology and Microbiology , Texas A&M University , College Station , Texas 77843 , United States
- Institute for Plant Genomics and Biotechnology , Texas A&M University , College Station , Texas 77843 , United States
| | - Yining Zeng
- Biosciences Center , National Renewable Energy Laboratory , Golden , Colorado 80401 , United States
| | - Man Li
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub , Texas A&M University , College Station , Texas 77843 , United States
- Department of Plant Pathology and Microbiology , Texas A&M University , College Station , Texas 77843 , United States
- Institute for Plant Genomics and Biotechnology , Texas A&M University , College Station , Texas 77843 , United States
| | - Xin Wang
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub , Texas A&M University , College Station , Texas 77843 , United States
- Department of Plant Pathology and Microbiology , Texas A&M University , College Station , Texas 77843 , United States
- Institute for Plant Genomics and Biotechnology , Texas A&M University , College Station , Texas 77843 , United States
| | - Cheng Hu
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub , Texas A&M University , College Station , Texas 77843 , United States
- Department of Plant Pathology and Microbiology , Texas A&M University , College Station , Texas 77843 , United States
- Institute for Plant Genomics and Biotechnology , Texas A&M University , College Station , Texas 77843 , United States
| | - Connor Gorman
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub , Texas A&M University , College Station , Texas 77843 , United States
- Department of Plant Pathology and Microbiology , Texas A&M University , College Station , Texas 77843 , United States
- Institute for Plant Genomics and Biotechnology , Texas A&M University , College Station , Texas 77843 , United States
| | - Susie Y Dai
- State Hygienic Lab , University of Iowa , Coralville , Iowa 52241 , United States
| | - Shi-You Ding
- Department of Plant Biology , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Joshua S Yuan
- Texas A&M Agrilife Synthetic and Systems Biology Innovation Hub , Texas A&M University , College Station , Texas 77843 , United States
- Department of Plant Pathology and Microbiology , Texas A&M University , College Station , Texas 77843 , United States
- Institute for Plant Genomics and Biotechnology , Texas A&M University , College Station , Texas 77843 , United States
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Elliot MA, Karoonuthaisiri N, Huang J, Bibb MJ, Cohen SN, Kao CM, Buttner MJ. The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation in Streptomyces coelicolor. Genes Dev 2003; 17:1727-40. [PMID: 12832397 PMCID: PMC196181 DOI: 10.1101/gad.264403] [Citation(s) in RCA: 186] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The filamentous bacterium Streptomyces coelicolor differentiates by forming specialized, spore-bearing aerial hyphae that grow into the air. Using microarrays, we identified genes that are down-regulated in a mutant unable to erect aerial hyphae. Through this route, we identified a previously unknown layer of aerial mycelium surface proteins (the "chaplins"). The chaplins share a hydrophobic domain of approximately 40 residues (the "chaplin domain"), and all have a secretion signal. The five short chaplins (ChpD,E,F,G,H) have one chaplin domain, whereas the three long chaplins (ChpA,B,C) have two chaplin domains and a C-terminal "sorting signal" that targets them for covalent attachment to the cell wall by sortase enzyme. Expression of the two chaplin genes examined (chpE, chpH) depended on aerial hyphae formation but not sporulation, and egfp fusions showed their expression localized to aerial structures. Mass spectrometry of cell wall extracts confirmed that the short chaplins localized to the cell surface. Deletion of chaplin genes caused severe delays in aerial hyphae formation, a phenotype rescued by exogenous application of chaplin proteins. These observations implicate the chaplins in aerial mycelium formation, and suggest that coating of the envelope by the chaplins is required for aerial hyphae to grow out of the aqueous environment of the substrate mycelium into the air.
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Affiliation(s)
- Marie A Elliot
- Department of Molecular Microbiology, John Innes Centre, Colney, Norwich NR4 7UH, UK.
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