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Pick LM, Oehme V, Hartmann J, Wenzlaff J, Tang Q, Grogan G, Ansorge-Schumacher MB. SilE-R and SilE-S-DABB Proteins Catalying Enantiospecific Hydrolysis of Organosilyl Ethers. Angew Chem Int Ed Engl 2024; 63:e202404105. [PMID: 38630059 DOI: 10.1002/anie.202404105] [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: 02/28/2024] [Indexed: 06/11/2024]
Abstract
Silyl ethers fulfil a fundamental role in synthetic organic chemistry as protecting groups and their selective cleavage is an important factor in their application. We present here for the first time two enzymes, SilE-R and SilE-S, which are able to hydrolyse silyl ethers. They belong to the stress-response dimeric A/B barrel domain (DABB) family and are able to cleave the Si-O bond with opposite enantiopreference. Silyl ethers containing aromatic, cyclic or aliphatic alcohols and, depending on the alcohol moiety, silyl functions as large as TBDMS are accepted. The X-ray crystal structure of SilE-R, determined to a resolution of 1.98 Å, in combination with mutational studies, revealed an active site featuring two histidine residues, H8 and H79, which likely act synergistically as nucleophile and Brønsted base in the hydrolytic mechanism, which has not previously been described for enzymes. Although the natural function of SilE-R and SilE-S is unknown, we propose that these 'silyl etherases' may have significant potential for synthetic applications.
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Affiliation(s)
- Lisa M Pick
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Viviane Oehme
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Julia Hartmann
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Jessica Wenzlaff
- Professur für Molekulare Biotechnologie, Technische Universität Dresden, 01062, Dresden, Germany
| | - Qingyun Tang
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Gideon Grogan
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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2
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Wang S, Wang K, Xia Q, Xia S. Genome-Wide Identification and Multi-Stress Response Analysis of the DABB-Type Protein-Encoding Genes in Brassica napus. Int J Mol Sci 2024; 25:5721. [PMID: 38891905 PMCID: PMC11171964 DOI: 10.3390/ijms25115721] [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: 04/16/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
The DABB proteins, which are characterized by stress-responsive dimeric A/B barrel domains, have multiple functions in plant biology. In Arabidopsis thaliana, these proteins play a crucial role in defending against various pathogenic fungi. However, the specific roles of DABB proteins in Brassica napus remain elusive. In this study, 16 DABB encoding genes were identified, distributed across 10 chromosomes of the B. napus genome, which were classified into 5 branches based on phylogenetic analysis. Genes within the same branch exhibited similar structural domains, conserved motifs, and three-dimensional structures, indicative of the conservation of BnaDABB genes (BnaDABBs). Furthermore, the enrichment of numerous cis-acting elements in hormone induction and light response were revealed in the promoters of BnaDABBs. Expression pattern analysis demonstrated the involvement of BnaDABBs, not only in the organ development of B. napus but also in response to abiotic stresses and Sclerotinia sclerotiorum infection. Altogether, these findings imply the significant impacts of BnaDABBs on plant growth and development, as well as stress responses.
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Affiliation(s)
| | | | | | - Shitou Xia
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China; (S.W.); (K.W.); (Q.X.)
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3
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Mohanan MV, Pushpanathan A, Jayanarayanan AN, Selvarajan D, Ramalingam S, Govind H, Chinnaswamy A. Isolation of 5' regulatory region of COLD1 gene and its functional characterization through transient expression analysis in tobacco and sugarcane. 3 Biotech 2023; 13:228. [PMID: 37304407 PMCID: PMC10256666 DOI: 10.1007/s13205-023-03650-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023] Open
Abstract
Chilling Tolerant Divergence 1 (COLD1) gene consists of Golgi pH Receptor (GPHR) as well as Abscisic Acid-linked G Protein-Coupled Receptor (ABA_GPCR), which are the major transmembrane proteins in plants. This gene expression has been found to be differentially regulated, under various stress conditions, in wild Saccharum-related genera, Erianthus arundinaceus, compared to commercial sugarcane variety. In this study, Rapid Amplification of Genomic Ends (RAGE) technique was employed to isolate the 5' upstream region of COLD1 gene to gain knowledge about the underlying stress regulatory mechanism. The current study established the cis-acting elements, main promoter regions, and Transcriptional Start Site (TSS) present within the isolated 5' upstream region (Cold1P) of COLD1, with the help of specific bioinformatics techniques. Phylogenetic analysis results revealed that the isolated Cold1P promoter is closely related to the species, Sorghum bicolor. Cold1P promoter-GUS gene construct was generated in pCAMBIA 1305.1 vector that displayed a constitutive expression of the GUS reporter gene in both monocot as well as dicot plants. The histochemical GUS assay outcomes confirmed that Cold1P can drive expression in both monocot as well as dicot plants. Cold1P's activities under several abiotic stresses such as cold, heat, salt, and drought, revealed its differential expression profile in commercial sugarcane variety. The highest activity of the GUS gene was found after 24 h of cold stress, driven by the isolated Cold1P promoter. The outcomes from GUS fluorimetric assay correlated with that of the GUS expression findings. This is the first report on Cold1P isolated from the species, E. arundinaceus. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03650-8.
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Affiliation(s)
| | | | | | - Dharshini Selvarajan
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | | | - Hemaprabha Govind
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
| | - Appunu Chinnaswamy
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India
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Fu S, Pang A, Guo X, He Y, Song S, Ge J, Li J, Li W, Xiong Y, Wang L, Wang D, Tang BZ. Bioinspired Supramolecular Nanotoroids with Aggregation-Induced Emission Characteristics. ACS NANO 2022; 16:12720-12726. [PMID: 35959972 DOI: 10.1021/acsnano.2c04480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Supramolecular toroids have attracted continuous attention because of their fascinating topological structure and important role in biological systems. However, it still remains a great challenge to construct supramolecular functional toroids and clarify the formation mechanism. Herein, we develop a strategy to prepare supramolecular helical fluorescent nanotoroids by cooperative self-assembly of an amino acid and a dendritic amphiphile (AIE-den-1) with aggregation-induced emission characteristics. Mechanistic investigation on the basis of fluorescence and circular dichroism analyses suggests that the toroid formation can be driven by the interactions of AIE-den-1 with amino acid and goes through a topological morphology transformation from nanofibers to left-handed nanotoroids by means of a twist-fused-loop process.
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Affiliation(s)
- Shuang Fu
- Center for AIE Research, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China
- Science and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, China
| | - Aimin Pang
- Science and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, China
| | - Xiang Guo
- Science and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, China
| | - Youling He
- Center for AIE Research, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China
| | - Shanliang Song
- Center for AIE Research, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jinyin Ge
- Center for AIE Research, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jiangao Li
- Center for AIE Research, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wei Li
- Science and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace Chemotechnology, Xiangyang 441003, China
| | - Yu Xiong
- Center for AIE Research, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China
| | - Lei Wang
- Center for AIE Research, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China
| | - Dong Wang
- Center for AIE Research, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Key Laboratory of Functional Aggregate Materials, The Chinese University of Hong Kong-Shenzhen, Shenzhen 518172, China
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5
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Leonardi C, Toscano V, Genovese C, Mosselmans JFW, Ngwenya BT, Raccuia SA. Evaluation of cadmium and arsenic effects on wild and cultivated cardoon genotypes selected for metal phytoremediation and bioenergy purposes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:55102-55115. [PMID: 34128170 PMCID: PMC8494702 DOI: 10.1007/s11356-021-14705-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Cynara cardunculus L. is a multipurpose crop, characterized by high production of biomass suitable for energy purposes and green chemistry. Taking advantage of its already demonstrated ability to grow in polluted environments that characterize many world marginal lands, the aim of this work was to investigate the response of different cardoon genotypes to exposure to cadmium (Cd) and arsenic (As) pollution, in order to use this crop for rehabilitation of contaminated sites and its biomass for energy production. In this study, seeds of two wild cardoon accessions harvested in rural and industrial Sicilian areas and of a selected line of domestic cardoon were used, and the grown plants were spiked with As and Cd, alone or in combination, at two different concentrations (500 and 2000 μM) and monitored for 45 days. The growth parameters showed that all the plants survived until the end of experiment, with growth stimulation in the presence of low concentrations of As and Cd, relative to metal-free controls. Biomass production was mostly allocated in the roots in As treatment and in the shoots in Cd treatment. Cd EXAFS analysis showed that tolerance to high concentrations of both metals was likely linked to complexation of Cd with oxygen-containing ligands, possibly organic acids, in both root and leaf biomass with differences in behaviour among genotypes. Under As+Cd contamination, the ability of the plants to translocate As to aboveground system increased also showing that, for both metal(loid)s, there were significant differences between genotypes studied. Moreover, the results showed that Cynara cardunculus var. sylvestris collected in an industrial area is the genotype that, among those studied, had the best phytoextraction capability for each metal(loid).
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Affiliation(s)
- Chiara Leonardi
- Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne, 81, 95124, Catania, Italy.
- National Research Council, Institute for Agricultural and Forest Systems in the Mediterranean, Via Empedocle, 58, 95128, Catania, Italy.
| | - Valeria Toscano
- National Research Council, Institute for Agricultural and Forest Systems in the Mediterranean, Via Empedocle, 58, 95128, Catania, Italy
| | - Claudia Genovese
- National Research Council, Institute for Agricultural and Forest Systems in the Mediterranean, Via Empedocle, 58, 95128, Catania, Italy
| | | | | | - Salvatore Antonino Raccuia
- National Research Council, Institute for Agricultural and Forest Systems in the Mediterranean, Via Empedocle, 58, 95128, Catania, Italy
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6
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Bachar O, Meirovich MM, Kurzion R, Yehezkeli O. In vivo and in vitro protein mediated synthesis of palladium nanoparticles for hydrogenation reactions. Chem Commun (Camb) 2020; 56:11211-11214. [PMID: 32815936 DOI: 10.1039/d0cc04812g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report the biosynthesis of size confined palladium nanoparticles (Pd-NPs). The 2-3 nm size Pd-NPs were grown in 12-mer protein stable protein 1 (SP1), which serves as a template for the NP formation. We further show that by controlling the protein expression levels in the cells we can alter the cells' catalytic activity. The in vivo grown Pd-NPs were utilized in a hydrogenation reaction, converting acetylene feedstock into ethylene and ethane. The presented concept can be further used for a wide range of applications by exploiting the synergetic effect of the biotic elements with the abiotic ones.
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Affiliation(s)
- Oren Bachar
- Faculty of Biotechnology & Food Engineering, Israel Institute of Technology, Haifa 3200003, Israel
| | - Matan Moshe Meirovich
- Faculty of Biotechnology & Food Engineering, Israel Institute of Technology, Haifa 3200003, Israel
| | - Ronni Kurzion
- Faculty of Biotechnology & Food Engineering, Israel Institute of Technology, Haifa 3200003, Israel
| | - Omer Yehezkeli
- Faculty of Biotechnology & Food Engineering, Israel Institute of Technology, Haifa 3200003, Israel and Russell Berrie Nanotechnology Institute, Technion, Israel Institute of Technology, Haifa 3200003, Israel. and The Nancy and Stephen Grand Technion Energy Program, Israel Institute of Technology, Haifa 3200003, Israel
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7
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Babar U, Nawaz MA, Arshad U, Azhar MT, Atif RM, Golokhvast KS, Tsatsakis AM, Shcerbakova K, Chung G, Rana IA. Transgenic crops for the agricultural improvement in Pakistan: a perspective of environmental stresses and the current status of genetically modified crops. GM CROPS & FOOD 2019; 11:1-29. [PMID: 31679447 DOI: 10.1080/21645698.2019.1680078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transgenic technologies have emerged as a powerful tool for crop improvement in terms of yield, quality, and quantity in many countries of the world. However, concerns also exist about the possible risks involved in transgenic crop cultivation. In this review, literature is analyzed to gauge the real intensity of the issues caused by environmental stresses in Pakistan. In addition, the research work on genetically modified organisms (GMOs) development and their performance is analyzed to serve as a guide for the scientists to help them select useful genes for crop transformation in Pakistan. The funding of GMOs research in Pakistan shows that it does not follow the global trend. We also present socio-economic impact of GM crops and political dimensions in the seed sector and the policies of the government. We envisage that this review provides guidelines for public and private sectors as well as the policy makers in Pakistan and in other countries that face similar environmental threats posed by the changing climate.
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Affiliation(s)
- Usman Babar
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Amjad Nawaz
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Usama Arshad
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.,Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
| | - Kirill S Golokhvast
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Aristides M Tsatsakis
- Department of Toxicology and Forensics, School of Medicine, University of Crete, Heraklion, Greece
| | - Kseniia Shcerbakova
- Education and Scientific Center of Nanotechnology, Far Eastern Federal University, Vladivostok, Russian Federation
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Republic of Korea
| | - Iqrar Ahmad Rana
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.,Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
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8
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Rohilla P, Yadav JP. Acute salt stress differentially modulates nitrate reductase expression in contrasting salt responsive rice cultivars. PROTOPLASMA 2019; 256:1267-1278. [PMID: 31041536 DOI: 10.1007/s00709-019-01378-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
Salt stress response includes alteration in the activity of various important enzymes in plants. Nitrate reductase (NR) is one of the known enzyme affected by salt stress. In this study, contrasting salt responsive cultivars (CVS) (IR64-sensitive and CSR 36-tolerant) were considered to study the regulation of NR genes under salt stress conditions. Using Arabidopsis genes Nia1 and Nia2, three different NR genes were identified in rice and their expression study was conducted. Under stress condition, salt-sensitive CVS (IR64) showed a decrease in NR activity under in vitro and in vivo conditions, whereas tolerant CVS showed an increase in NR activity. Different trends for NR activity in contrasting genotype are explained by the variable number of GATA element in the upstream region of the NR gene. This variation of NR activity in contrasting CVS further co-relates with the transcript level of NR genes. The transcript level of three different NR genes also evidenced the effect of CREs in gene regulation. Promoter (1-kb upstream region) of different NR genes contained different abiotic stress-responsive CREs, which explain the differential behavior of these genes towards the abiotic stress. Overall, this study concludes the role of CREs in the regulation of NR gene and indicates the importance of transcriptional control of NR activity under stress condition. This is the first type of report that highlights the role of the regulatory mechanism of NR genes under salt stress condition.
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Affiliation(s)
- Pooja Rohilla
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Jaya Parkash Yadav
- Department of Genetics, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
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9
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Zhou J, Zhang J, Gao G, Wang H, He X, Chen T, Ke L, Rao P, Wang Q. Boiling Licorice Produces Self-Assembled Protein Nanoparticles: A Novel Source of Bioactive Nanomaterials. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:9354-9361. [PMID: 31339706 DOI: 10.1021/acs.jafc.9b03208] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
As a popular ingredient for western and traditional Chinese medicine, the root and rhizome of Chinese licorice (Glycyrrhiza uralensis Fisch.) is often administered in the form of a decoction. The protein nanoparticles (NPs) self-assembled during the process of decoction. A major constitutive protein (GLP) was purified and determined to have a molecular weight of 28 kDa with an N-terminal sequence of NPDGL IACYC GQYCW. Over 80% of the purified GLP self-assembled into spherical NPs with diameters of 74.1 ± 0.7 nm and ζ-potential of -24.3 ± 1.7 mV when boiled in Tris-HCl buffer (pH = 7.9, 20 mM) at 100 °C for 60 min. Each nanoparticle was estimated by the SEC-MALLS approach to be composed of approximately 23 protein molecules. The NPs and GLP showed low cellular toxicity upon four types of cells including MDCK, L-02, HepG2, and Caco2 cells, while the NPs promoted proliferation of normal hepatocytes by 67%. The NPs solubilized the insoluble astragaloside IV by encapsulation. The results suggest a great potential for GLP-NPs as a promising prototype of a type of drug vehicle, a novel source of bioactive nanomaterials from herbal proteins, as well as a new mode of function with herbal components.
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Affiliation(s)
- Jianwu Zhou
- Food Nutrition Sciences Centre, School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310012 , China
| | - Jian Zhang
- Food Nutrition Sciences Centre, School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310012 , China
| | - Guanzhen Gao
- Food Nutrition Sciences Centre, School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310012 , China
| | - Huiqin Wang
- Food Nutrition Sciences Centre, School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310012 , China
| | - Xiaoyan He
- Institute of Biotechnology , Fuzhou University , Fuzhou 350000 , China
| | - Tianbao Chen
- School of Pharmacy , Queen's University Belfast , Belfast BT9 7BL , United Kingdom
| | - Lijing Ke
- Food Nutrition Sciences Centre, School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310012 , China
| | - Pingfan Rao
- Food Nutrition Sciences Centre, School of Food Science and Biotechnology , Zhejiang Gongshang University , Hangzhou 310012 , China
| | - Qiang Wang
- Institute of Food Science and Technology , Chinese Academy of Agricultural Sciences , Beijing 100193 , China
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Korpi A, Anaya-Plaza E, Välimäki S, Kostiainen M. Highly ordered protein cage assemblies: A toolkit for new materials. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 12:e1578. [PMID: 31414574 DOI: 10.1002/wnan.1578] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/19/2019] [Accepted: 06/28/2019] [Indexed: 12/16/2022]
Abstract
Protein capsids are specialized and versatile natural macromolecules with exceptional properties. Their homogenous, spherical, rod-like or toroidal geometry, and spatially directed functionalities make them intriguing building blocks for self-assembled nanostructures. High degrees of functionality and modifiability allow for their assembly via non-covalent interactions, such as electrostatic and coordination bonding, enabling controlled self-assembly into higher-order structures. These assembly processes are sensitive to the molecules used and the surrounding conditions, making it possible to tune the chemical and physical properties of the resultant material and generate multifunctional and environmentally sensitive systems. These materials have numerous potential applications, including catalysis and drug delivery. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.
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Affiliation(s)
- Antti Korpi
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Eduardo Anaya-Plaza
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Salla Välimäki
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
| | - Mauri Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, Aalto, Finland
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11
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Gdor E, Levy D, Aharon L, Shoseyov O, Mandler D. SP1 based self-assembled selective molecular nanochannels. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2017.10.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Yang G, Wu L, Chen G, Jiang M. Precise protein assembly of array structures. Chem Commun (Camb) 2018; 52:10595-605. [PMID: 27384233 DOI: 10.1039/c6cc04190f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The assembly of proteins into various nano-objects with regular and periodic microstructures, i.e. protein arrays, is a fast-growing field in materials science. Due to the structural complexity of proteins, reports in this field are still quite limited. In this review, we summarize the recent developments in protein array construction by different driving forces, including electrostatic interactions, metal-ligand interactions, molecular recognition and protein-protein interactions. In line with our particular interest, assemblies driven by molecular recognition are particularly explored. Finally, functionalities of the obtained protein arrays are briefly discussed.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Libin Wu
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Guosong Chen
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
| | - Ming Jiang
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.
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13
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Liu G, Liu K, Gao Y, Zheng Y. Involvement of C-Terminal Histidines in Soybean PM1 Protein Oligomerization and Cu2+ Binding. PLANT & CELL PHYSIOLOGY 2017; 58:1018-1029. [PMID: 28387856 DOI: 10.1093/pcp/pcx046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/20/2017] [Indexed: 05/06/2023]
Abstract
Late embryogenesis abundant (LEA) proteins are widely distributed among plant species, where they contribute to abiotic stress tolerance. LEA proteins can be classified into seven groups according to conserved sequence motifs. The PM1 protein from soybean, which belongs to the Pfam LEA_1 group, has been shown previously to be at least partially natively unfolded, to bind metal ions and potentially to stabilize proteins and membranes. Here, we investigated the role of the PM1 C-terminal domain and in particular the multiple histidine residues in this half of the protein. We constructed recombinant plasmids expressing full-length PM1 and two truncated forms, PM1-N and PM1-C, which represent the N- and C-terminal halves of the protein, respectively. Immunoblotting and cross-linking experiments showed that full-length PM1 forms oligomers and high molecular weight (HMW) complexes in vitro and in vivo, while PM1-C, but not PM1-N, also formed oligomers and HMW complexes in vitro. When the histidine residues in PM1 and PM1-C were chemically modified, oligomerization was abolished, suggesting that histidines play a key role in this process. Furthermore, we demonstrated that high Cu2+ concentrations promote oligomerization and induce PM1 and PM1-C to form HMW complexes. Therefore, we speculate that PM1 proteins not only maintain ion homeostasis in the cytoplasm, but also potentially stabilize and protect other proteins during abiotic stress by forming a large, oligomeric molecular shield around biological targets.
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Affiliation(s)
- Guobao Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, PR China
| | - Ke Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, PR China
| | - Yang Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, PR China
| | - Yizhi Zheng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, PR China
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14
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Zhou J, Liu J, Lin D, Gao G, Wang H, Guo J, Rao P, Ke L. Boiling-induced nanoparticles and their constitutive proteins from Isatis indigotica Fort. root decoction: Purification and identification. J Tradit Complement Med 2016; 7:178-187. [PMID: 28417088 PMCID: PMC5388084 DOI: 10.1016/j.jtcme.2016.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 06/27/2016] [Accepted: 08/15/2016] [Indexed: 02/04/2023] Open
Abstract
Colloidal particles are essential components of sun-dried Isatis indigotica Fort. roots (Ban-Lan-Gen in Chinese, BLG) decoction. Nanoparticles (NPs) were isolated from BLG decoction with size exclusion chromatography and characterized. Their average diameter is ∼120 nm, reversibly responding to pH and temperature changes. They promoted the growth of normal cells but suppressed that of cancerogenic cells and macrophages. Two constitutive glycated proteins were identified from the NPs, namely BLGP1 and BLGP2. Their N-terminal amino acid sequences were V-X-R-E-V-V-K-D-I and V-V-R-E-V-V-K-D-I-A-G-A-V-Q-T-N-E-Q-Y. Their full-length cDNA sequences were cloned to obtain the highly homological amino acid sequences of non-glycated proteins, whose theoretical molecular weights are 21831.64 Da and 21841.67 Da. Using pepsin hydrolysis and mass spectrometry, four possible glycation adducts were identified in BLGP1, whereas one in BLGP2. To conclude, bioactive nanoparticles isolated from the herbal decoction are intelligent nanoassemblies composed of a new boiling-stable protein. Glycation plays a critical role in heat-induced formation of these nanoassemblies. The novel, intelligent, safe and stable nano-carriers for drug delivery may be developed using BLG NPs as prototype.
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Affiliation(s)
- Jianwu Zhou
- SIBS, CAS-ZJGSU Joint Centre for Food and Nutrition Research, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Jie Liu
- SIBS, CAS-ZJGSU Joint Centre for Food and Nutrition Research, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Dai Lin
- SIBS, CAS-ZJGSU Joint Centre for Food and Nutrition Research, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Guanzhen Gao
- SIBS, CAS-ZJGSU Joint Centre for Food and Nutrition Research, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Huiqin Wang
- SIBS, CAS-ZJGSU Joint Centre for Food and Nutrition Research, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Jingke Guo
- SIBS, CAS-ZJGSU Joint Centre for Food and Nutrition Research, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Pingfan Rao
- SIBS, CAS-ZJGSU Joint Centre for Food and Nutrition Research, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Lijing Ke
- SIBS, CAS-ZJGSU Joint Centre for Food and Nutrition Research, Zhejiang Gongshang University, Hangzhou 310012, China
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15
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Miao L, Fan Q, Zhao L, Qiao Q, Zhang X, Hou C, Xu J, Luo Q, Liu J. The construction of functional protein nanotubes by small molecule-induced self-assembly of cricoid proteins. Chem Commun (Camb) 2016; 52:4092-5. [DOI: 10.1039/c6cc00632a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Induced by small molecular ethylenediamine and “zero-length” covalent crosslinking, covalently crosslinked SeSP1 protein nanotubes with great GPx activity was fabricated.
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Affiliation(s)
- Lu Miao
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
| | - Qiusheng Fan
- School of Life Sciences
- Jilin University
- Changchun 130012
- China
| | - Linlu Zhao
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
| | - Qinglong Qiao
- Key Laboratory of Separation Science for Analytical Chemistry
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Xiyu Zhang
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
| | - Chunxi Hou
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
| | - Jiayun Xu
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
| | - Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular Structure and Materials
- College of Chemistry
- Jilin University
- Changchun 130012
- China
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16
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Angelucci F, Bellelli A, Ardini M, Ippoliti R, Saccoccia F, Morea V. One ring (or two) to hold them all – on the structure and function of protein nanotubes. FEBS J 2015; 282:2827-45. [PMID: 26059483 DOI: 10.1111/febs.13336] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 03/31/2015] [Accepted: 06/04/2015] [Indexed: 01/07/2023]
Abstract
Understanding the structural determinants relevant to the formation of supramolecular assemblies of homo-oligomeric proteins is a traditional and central scope of structural biology. The knowledge thus gained is crucial both to infer their physiological function and to exploit their architecture for bionanomaterials design. Protein nanotubes made by one-dimensional arrays of homo-oligomers can be generated by either a commutative mechanism, yielding an 'open' structure (e.g. actin), or a noncommutative mechanism, whereby the final structure is formed by hierarchical self-assembly of intermediate 'closed' structures. Examples of the latter process are poorly described and the rules by which they assemble have not been unequivocally defined. We have collected and investigated examples of homo-oligomeric circular arrangements that form one-dimensional filaments of stacked rings by the noncommutative mechanism in vivo and in vitro. Based on their quaternary structure, circular arrangements of protein subunits can be subdivided into two groups that we term Rings of Dimers (e.g. peroxiredoxin and stable protein 1) and Dimers of Rings (e.g. thermosome/rosettasome), depending on the sub-structures that can be identified within the assembly (and, in some cases, populated in solution under selected experimental conditions). Structural analysis allowed us to identify the determinants by which ring-like molecular chaperones form filamentous-like assemblies and to formulate a novel hypothesis by which nanotube assembly, molecular chaperone activity and macromolecular crowding may be interconnected.
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Affiliation(s)
- Francesco Angelucci
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Italy
| | - Andrea Bellelli
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
| | - Matteo Ardini
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Health, Life and Environmental Sciences, University of L'Aquila, Italy
| | - Fulvio Saccoccia
- Department of Biochemical Sciences 'A. Rossi Fanelli', Sapienza University of Rome and Istituto Pasteur-Fondazione Cenci Bolognetti, Rome, Italy
| | - Veronica Morea
- CNR - National Research Council of Italy, Institute of Molecular Biology and Pathology, Rome, Italy
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17
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Sun H, Miao L, Li J, Fu S, An G, Si C, Dong Z, Luo Q, Yu S, Xu J, Liu J. Self-assembly of cricoid proteins induced by "soft nanoparticles": an approach to design multienzyme-cooperative antioxidative systems. ACS NANO 2015; 9:5461-9. [PMID: 25952366 DOI: 10.1021/acsnano.5b01311] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
A strategy to construct high-ordered protein nanowires by electrostatic assembly of cricoid proteins and "soft nanoparticles" was developed. Poly(amido amine) (PAMAM) dendrimers on high generation that have been shown to be near-globular macromolecules with all of the amino groups distributing throughout the surface were ideal electropositive "soft nanoparticles" to induce electrostatic assembly of electronegative cricoid proteins. Atomic force microscopy and transmission electron microscopy all showed that one "soft nanoparticle" (generation 5 PAMAM, PD5) could electrostatically interact with two cricoid proteins (stable protein one, SP1) in an opposite orientation to form sandwich structure, further leading to self-assembled protein nanowires. The designed nanostructures could act as versatile scaffolds to develop multienzyme-cooperative antioxidative systems. By means of inducing catalytic selenocysteine and manganese porphyrin to SP1 and PD5, respectively, we successfully designed antioxidative protein nanowires with both excellent glutathione peroxidase and superoxide dismutase activities. Also, the introduction of selenocysteine and manganese porphyrin did not affect the assembly morphologies. Moreover, this multienzyme-cooperative antioxidative system exhibited excellent biological effect and low cell cytotoxicity.
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Affiliation(s)
- Hongcheng Sun
- †State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Lu Miao
- †State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Jiaxi Li
- †State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shuang Fu
- †State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Guo An
- †State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Chengye Si
- †State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Zeyuan Dong
- †State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Quan Luo
- †State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shuangjiang Yu
- ‡Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun 130021, China
| | - Jiayun Xu
- †State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Junqiu Liu
- †State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
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18
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Dufoo-Hurtado MD, Huerta-Ocampo JÁ, Barrera-Pacheco A, Barba de la Rosa AP, Mercado-Silva EM. Low temperature conditioning of garlic (Allium sativum L.) "seed" cloves induces alterations in sprouts proteome. FRONTIERS IN PLANT SCIENCE 2015; 6:332. [PMID: 26029231 PMCID: PMC4429546 DOI: 10.3389/fpls.2015.00332] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Low-temperature conditioning of garlic "seed" cloves substitutes the initial climatic requirements of the crop and accelerates the cycle. We have reported that "seed" bulbs from "Coreano" variety conditioned at 5°C for 5 weeks reduces growth and plant weight as well as the crop yields and increases the synthesis of phenolic compounds and anthocyanins. Therefore, this treatment suggests a cold stress. Plant acclimation to stress is associated with deep changes in proteome composition. Since proteins are directly involved in plant stress response, proteomics studies can significantly contribute to unravel the possible relationships between protein abundance and plant stress acclimation. The aim of this work was to study the changes in the protein profiles of garlic "seed" cloves subjected to conditioning at low-temperature using proteomics approach. Two sets of garlic bulbs were used, one set was stored at room temperature (23°C), and the other was conditioned at low temperature (5°C) for 5 weeks. Total soluble proteins were extracted from sprouts of cloves and separated by two-dimensional gel electrophoresis. Protein spots showing statistically significant changes in abundance were analyzed by LC-ESI-MS/MS and identified by database search analysis using the Mascot search engine. The results revealed that low-temperature conditioning of garlic "seed" cloves causes alterations in the accumulation of proteins involved in different physiological processes such as cellular growth, antioxidative/oxidative state, macromolecules transport, protein folding and transcription regulation process. The metabolic pathways affected include protein biosynthesis and quality control system, photosynthesis, photorespiration, energy production, and carbohydrate and nucleotide metabolism. These processes can work cooperatively to establish a new cellular homeostasis that might be related with the physiological and biochemical changes observed in previous studies.
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Affiliation(s)
- Miguel D. Dufoo-Hurtado
- Laboratorio de Fisiología y Bioquímica Poscosecha de Frutas y Hortalizas, Departamento de Investigación y Posgrado, Facultad de Química, Universidad Autónoma de QuerétaroQuerétaro, Mexico
| | - José Á. Huerta-Ocampo
- Laboratorio de Proteómica y Biomedicina Molecular, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C.San Luis Potosí, Mexico
| | - Alberto Barrera-Pacheco
- Laboratorio de Proteómica y Biomedicina Molecular, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C.San Luis Potosí, Mexico
| | - Ana P. Barba de la Rosa
- Laboratorio de Proteómica y Biomedicina Molecular, División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C.San Luis Potosí, Mexico
| | - Edmundo M. Mercado-Silva
- Laboratorio de Fisiología y Bioquímica Poscosecha de Frutas y Hortalizas, Departamento de Investigación y Posgrado, Facultad de Química, Universidad Autónoma de QuerétaroQuerétaro, Mexico
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19
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Giarola V, Krey S, Frerichs A, Bartels D. Taxonomically restricted genes of Craterostigma plantagineum are modulated in their expression during dehydration and rehydration. PLANTA 2015; 241:193-208. [PMID: 25262421 DOI: 10.1007/s00425-014-2175-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/13/2014] [Indexed: 05/24/2023]
Abstract
Taxonomically restricted genes are known to contribute to the evolution of new traits. In Craterostigma plantagineum two of such genes are modulated during dehydration and rehydration and seem to contribute to a successful recovery after desiccation. The resurrection plant Craterostigma plantagineum can tolerate extreme water loss. Protective molecules linked to desiccation tolerance were identified in C. plantagineum but underlying mechanisms are far from being completely understood. A transcriptome analysis revealed several genes which could not be annotated and are, therefore, interesting candidates for understanding desiccation tolerance. Genes which occur only in some species are defined as orphan or taxonomically restricted genes (TRGs) and may be important for the evolution of new traits. Several of these TRGs are modulated in expression during dehydration/rehydration in C. plantagineum. Here we report the characterisation of two of these TRGs encoding a cysteine-rich rehydration-responsive protein 1 (CpCRP1) and an early dehydration-responsive protein 1 (CpEDR1). The involvement of CpCRP1 and CpEDR1 in different phases of the dehydration/rehydration cycle is shown by transcript and protein expression analysis. In silico sequence analyses predicted that both genes are likely to interact with other cellular components and are localised in two different cellular compartments. GFP fusion proteins demonstrated that CpCRP1 is secreted into the apoplasm, whereas CpEDR1 is imported into chloroplasts. Putative homologs of CpCRP1 and CpEDR1 were identified in Lindernia brevidens and Lindernia subracemosa which belong to the same family as C. plantagineum thus suggesting a recent evolution of the genes in this family. According to expression profiles, CpCRP1 may play a role in normal conditions and during rehydration, whereas CpEDR1 may be required for the acquisition of desiccation tolerance and protect photosynthetic structures during dehydration and rehydration.
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Affiliation(s)
- Valentino Giarola
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
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20
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Ying YL, Cao C, Long YT. Single molecule analysis by biological nanopore sensors. Analyst 2014; 139:3826-35. [PMID: 24991734 DOI: 10.1039/c4an00706a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nanopore sensors provide a highly innovative technique for a rapid and label-free single molecule analysis, which holds a great potential in routing applications. Biological nanopores have been used as ultra-sensitive sensors over a wide range of single molecule analysis including DNA sequencing, disease diagnosis, drug screening, environment monitoring and the construction of molecule machines. This mini review will focus on the current strategies for the identification and characterization of an individual analyte, especially based on our recent achievements in biological nanopore biosensors.
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Affiliation(s)
- Yi-Lun Ying
- Key Laboratory for Advanced Materials & Department of Chemistry, East China University of Science and Technology, P. R. China.
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21
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Trupiano D, Rocco M, Renzone G, Scaloni A, Rossi M, Viscosi V, Chiatante D, Scippa GS. Temporal analysis of poplar woody root response to bending stress. PHYSIOLOGIA PLANTARUM 2014; 150:174-193. [PMID: 23683290 DOI: 10.1111/ppl.12072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 03/27/2013] [Accepted: 05/03/2013] [Indexed: 06/02/2023]
Abstract
Temperate perennial woody plants use different environmental signals to coordinate their growth and development in relation to seasonal changes. Preliminary evidences suggest that, even during dormancy, plants maintain effective metabolic activities and molecular mechanisms ensuring them an eventual recording of mechanical loads during winter times. Despite their great importance for productivity and survival, plant biology investigations have poorly characterized the root growth cycle and its response to environmental stresses. In this study, we describe the proteomic changes occurring over the time in poplar root either in the absence or in response to a bending stress; corresponding expression of cell cycle regulator and auxin transporter genes was also evaluated by reverse transcription polymerase chain reaction analysis. Our results confirm previous evidences on the effect of the bending stress on the anticipation of root growth resumption, providing additional insights on a temporal modulation of various plant metabolic processes involved in dormancy break, growth resumption and stress response in the bent root; these events seem related to the differential compression and tension force distribution occurring over the plant taproot.
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Affiliation(s)
- Dalila Trupiano
- Dipartimento di Bioscienze e Territorio, University of Molise, 86090 , Pesche, IS, Italy
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22
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Schreiber A, Schiller SM. Nanobiotechnology of protein-based compartments: steps toward nanofactories. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2013. [DOI: 10.1680/bbn.13.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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23
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Wang HY, Li Y, Qin LX, Heyman A, Shoseyov O, Willner I, Long YT, Tian H. Single-molecule DNA detection using a novel SP1 protein nanopore. Chem Commun (Camb) 2013; 49:1741-3. [DOI: 10.1039/c3cc38939a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Abstract
Proteins are the work-horses of life and excute the essential processes involved in the growth and repair of cells. These roles include all aspects of cell signalling, metabolism and repair that allow living things to exist. They are not only chemical catalysts and machine components, they are also structural components of the cell or organism, capable of self-organisation into strong supramolecular cages, fibres and meshes. How proteins are encoded genetically and how they are sythesised in vivo is now well understood, and for an increasing number of proteins, the relationship between structure and function is known in exquisite detail. The next challenge in bionanoscience is to adapt useful protein systems to build new functional structures. Well-defined natural structures with potential useful shapes are a good starting point. With this in mind, in this chapter we discuss the properties of natural and artificial protein channels, nanotubes and cages with regard to recent progress and potential future applications. Chemistries for attaching together different proteins to form superstructures are considered as well as the difficulties associated with designing complex protein structures ab initio.
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Affiliation(s)
- Jonathan G. Heddle
- Heddle Initiative Research Unit RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
| | - Jeremy R. H. Tame
- Protein Design Laboratory Yokohama City University 1-7—29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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25
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26
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Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides. Proc Natl Acad Sci U S A 2012; 109:12811-6. [PMID: 22802619 DOI: 10.1073/pnas.1200330109] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Δ(9)-Tetrahydrocannabinol (THC) and other cannabinoids are responsible for the psychoactive and medicinal properties of Cannabis sativa L. (marijuana). The first intermediate in the cannabinoid biosynthetic pathway is proposed to be olivetolic acid (OA), an alkylresorcinolic acid that forms the polyketide nucleus of the cannabinoids. OA has been postulated to be synthesized by a type III polyketide synthase (PKS) enzyme, but so far type III PKSs from cannabis have been shown to produce catalytic byproducts instead of OA. We analyzed the transcriptome of glandular trichomes from female cannabis flowers, which are the primary site of cannabinoid biosynthesis, and searched for polyketide cyclase-like enzymes that could assist in OA cyclization. Here, we show that a type III PKS (tetraketide synthase) from cannabis trichomes requires the presence of a polyketide cyclase enzyme, olivetolic acid cyclase (OAC), which catalyzes a C2-C7 intramolecular aldol condensation with carboxylate retention to form OA. OAC is a dimeric α+β barrel (DABB) protein that is structurally similar to polyketide cyclases from Streptomyces species. OAC transcript is present at high levels in glandular trichomes, an expression profile that parallels other cannabinoid pathway enzymes. Our identification of OAC both clarifies the cannabinoid pathway and demonstrates unexpected evolutionary parallels between polyketide biosynthesis in plants and bacteria. In addition, the widespread occurrence of DABB proteins in plants suggests that polyketide cyclases may play an overlooked role in generating plant chemical diversity.
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27
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Wang W, Wu X, Xiong E, Tai F. Improving gel-based proteome analysis of soluble protein extracts by heat prefractionation. Proteomics 2012; 12:938-43. [DOI: 10.1002/pmic.201100475] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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28
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Qin LX, Li Y, Li DW, Jing C, Chen BQ, Ma W, Heyman A, Shoseyov O, Willner I, Tian H, Long YT. Electrodeposition of Single-Metal Nanoparticles on Stable Protein 1 Membranes: Application of Plasmonic Sensing by Single Nanoparticles. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201106482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Qin LX, Li Y, Li DW, Jing C, Chen BQ, Ma W, Heyman A, Shoseyov O, Willner I, Tian H, Long YT. Electrodeposition of Single-Metal Nanoparticles on Stable Protein 1 Membranes: Application of Plasmonic Sensing by Single Nanoparticles. Angew Chem Int Ed Engl 2011; 51:140-4. [DOI: 10.1002/anie.201106482] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 10/31/2011] [Indexed: 11/09/2022]
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30
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Frasconi M, Heyman A, Medalsy I, Porath D, Mazzei F, Shoseyov O. Wiring of redox enzymes on three dimensional self-assembled molecular scaffold. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12606-13. [PMID: 21895003 DOI: 10.1021/la2020435] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The integration of biological molecules and nanoscale components provides a fertile basis for the construction of hybrid materials of synergic properties and functions. Stable protein 1 (SP1), a highly stable ring shaped protein, was recently used to display different functional domains, to bind nanoparticles (NPs), and to spontaneously form two and three-dimensional structures. Here we show an approach to wire redox enzymes on this self-assembled protein-nanoparticle hybrid. Those hybrids are genetically engineered SP1s, displaying glucose oxidase (GOx) enzymes tethered to the protein inner pore. Moreover, the Au-NP-protein hybrids self-assembled to multiple enzymatic layers on the surface. By wiring the redox enzymes to the electrode, we present an active structure for the bioelectrocatalytic oxidation of glucose. This system demonstrates for the first time a three-dimensional assembly of multiple catalytic modules on a protein scaffold with an efficient electrical wiring of the enzyme units on an electrode surface, thus implementing a hybrid electrically active unit for nanobioelectronic applications.
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Affiliation(s)
- Marco Frasconi
- Department of Chemistry and Drug Technology, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
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31
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Khoutorsky A, Heyman A, Shoseyov O, Spira ME. Formation of hydrophilic nanochannels in the membrane of living cells by the ringlike stable protein-SP1. NANO LETTERS 2011; 11:2901-4. [PMID: 21651305 DOI: 10.1021/nl201368w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The assembly of functional junction between nerve cells and electronic sensing pads is a critical problem in the construction of effective neuroelectronic hybrid systems. Here, we demonstrate for the first time that the ringlike Stable Protein 1 (Sp1) and its derivatives can be used to generate hydrophilic nanochannels in the plasma membrane of living cells. Since SP1-derivatives can be linked to both the plasma membrane, gold or silicon surfaces, they may serve to ohmically link between cells interior and electronic sensing devices.
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Affiliation(s)
- Arkady Khoutorsky
- Department of Neurobiology, The Life Sciences Institute, Faculty of Science, Hebrew University of Jerusalem, Israel
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32
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Cell-free antigens from Paracoccidioides brasiliensis drive IL-4 production and increase the severity of paracoccidioidomycosis. PLoS One 2011; 6:e21423. [PMID: 21731741 PMCID: PMC3120880 DOI: 10.1371/journal.pone.0021423] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 05/30/2011] [Indexed: 11/19/2022] Open
Abstract
The thermally dimorphic fungus Paracoccidioides brasiliensis (Pb) is the causative agent of paracoccidioidomycosis (PCM), one of the most frequent systemic mycosis that affects the rural population in Latin America. PCM is characterized by a chronic inflammatory granulomatous reaction, which is consequence of a Th1-mediated adaptive immune response. In the present study we investigated the mechanisms involved in the immunoregulation triggered after a prior contact with cell-free antigens (CFA) during a murine model of PCM. The results showed that the inoculation of CFA prior to the infection resulted in disorganized granulomatous lesions and increased fungal replication in the lungs, liver and spleen, that paralleled with the higher levels of IL-4 when compared with the control group. The role of IL-4 in facilitating the fungal growth was demonstrated in IL-4-deficient- and neutralizing anti-IL-4 mAb-treated mice. The injection of CFA did not affect the fungal growth in these mice, which, in fact, exhibited a significant diminished amount of fungus in the tissues and smaller granulomas. Considering that in vivo anti-IL-4-application started one week after the CFA-inoculum, it implicates that IL-4-CFA-induced is responsible by the mediation of the observed unresponsiveness. Further, the characterization of CFA indicated that a proteic fraction is required for triggering the immunosuppressive mechanisms, while glycosylation or glycosphingolipids moieties are not. Taken together, our data suggest that the prior contact with soluble Pb antigens leads to severe PCM in an IL-4 dependent manner.
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Cohen D, Bogeat-Triboulot MB, Tisserant E, Balzergue S, Martin-Magniette ML, Lelandais G, Ningre N, Renou JP, Tamby JP, Le Thiec D, Hummel I. Comparative transcriptomics of drought responses in Populus: a meta-analysis of genome-wide expression profiling in mature leaves and root apices across two genotypes. BMC Genomics 2010; 11:630. [PMID: 21073700 PMCID: PMC3091765 DOI: 10.1186/1471-2164-11-630] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 11/12/2010] [Indexed: 12/18/2022] Open
Abstract
Background Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induced responses were analysed in leaves and root apices and were compared with available transcriptome data from other Populus species. Results Using a multi-species designed microarray, a genomic DNA-based selection of probesets provided an unambiguous between-genotype comparison. Analyses of functional group enrichment enabled the extraction of processes physiologically relevant to drought response. The drought-driven changes in gene expression occurring in root apices were consistent across treatments and genotypes. For mature leaves, the transcriptome response varied weakly but in accordance with the duration of water deficit. A differential clustering algorithm revealed similar and divergent gene co-expression patterns among the two genotypes. Since moderate stress levels induced similar physiological responses in both genotypes, the genotype-dependent transcriptional responses could be considered as intrinsic divergences in genome functioning. Our meta-analysis detected several candidate genes and processes that are differentially regulated in root and leaf, potentially under developmental control, and preferentially involved in early and long-term responses to drought. Conclusions In poplar, the well-known drought-induced activation of sensing and signalling cascades was specific to the early response in leaves but was found to be general in root apices. Comparing our results to what is known in arabidopsis, we found that transcriptional remodelling included signalling and a response to energy deficit in roots in parallel with transcriptional indices of hampered assimilation in leaves, particularly in the drought-sensitive poplar genotype.
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Affiliation(s)
- David Cohen
- INRA, Nancy Université, UMR1137 Ecologie et Ecophysiologie Forestières, IFR 110 EFABA, F-54280 Champenoux, France
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Erba EB, Ruotolo BT, Barsky D, Robinson CV. Ion Mobility-Mass Spectrometry Reveals the Influence of Subunit Packing and Charge on the Dissociation of Multiprotein Complexes. Anal Chem 2010; 82:9702-10. [DOI: 10.1021/ac101778e] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elisabetta Boeri Erba
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Brandon T. Ruotolo
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Daniel Barsky
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Carol V. Robinson
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
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Medalsy I, Klein M, Heyman A, Shoseyov O, Remacle F, Levine RD, Porath D. Logic implementations using a single nanoparticle-protein hybrid. NATURE NANOTECHNOLOGY 2010; 5:451-457. [PMID: 20400968 DOI: 10.1038/nnano.2010.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 03/04/2010] [Indexed: 05/29/2023]
Abstract
A Set-Reset machine is the simplest logic circuit with a built-in memory. Its output is a (nonlinear) function of the input and of the state stored in the machine's memory. Here, we report a nanoscale Set-Reset machine operating at room temperature that is based on a 5-nm silicon nanoparticle attached to the inner pore of a stable circular protein. The nanoparticle-protein hybrid can also function as a balanced ternary multiplier. Conductive atomic force microscopy is used to implement the logic input and output operations, and the processing of the logic Set and Reset operations relies on the finite capacitance of the nanoparticle provided by the good electrical isolation given by the protein, thus enabling stability of the logic device states. We show that the machine can be cycled, such that in every successive cycle, the previous state in the memory is retained as the present state. The energy cost of one cycle of computation is minimized to the cost of charging this state.
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Affiliation(s)
- Izhar Medalsy
- Department of Physical Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Moraïs S, Heyman A, Barak Y, Caspi J, Wilson DB, Lamed R, Shoseyov O, Bayer EA. Enhanced cellulose degradation by nano-complexed enzymes: Synergism between a scaffold-linked exoglucanase and a free endoglucanase. J Biotechnol 2010; 147:205-11. [PMID: 20438772 DOI: 10.1016/j.jbiotec.2010.04.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 04/13/2010] [Accepted: 04/23/2010] [Indexed: 11/19/2022]
Abstract
Protein molecular scaffolds are attracting interest as natural candidates for the presentation of enzymes and acceleration of catalytic reactions. We have previously reported evidence that the stable protein 1 (SP1) from Populustremula can be employed as a molecular scaffold for the presentation of either catalytic or structural binding (cellulosomal cohesin) modules. In the present work, we have displayed a potent exoglucanase (Cel6B) from the aerobic cellulolytic bacterium, Thermobifida fusca, on a cohesin-bearing SP1 scaffold. For this purpose, a chimaeric form of the enzyme, fused to a cellulosomal dockerin module, was prepared. Full incorporation of 12 dockerin-bearing exoglucanase molecules onto the cohesin-bearing scaffold was achieved. Cellulase activity was tested on two cellulosic substrates with different levels of crystallinity, and the activity of the scaffold-linked exoglucanase was significantly reduced, compared to the free dockerin-containing enzyme. However, addition of relatively low concentrations of a free wild-type endoglucanase (T. fusca Cel5A) that bears a cellulose-binding module, in combination with the complexed exoglucanase resulted in a marked rise in activity on both cellulosic substrates. The endoglucanase cleaves internal sites of the cellulose chains, and the new chain ends of the substrate were now readily accessible to the scaffold-borne exoglucanase, thereby resulting in highly effective, synergistic degradation of cellulosic substrates.
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Affiliation(s)
- Sarah Moraïs
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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37
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Carrier-free immobilized enzymes for biocatalysis. Biotechnol Lett 2009; 32:341-50. [PMID: 19943180 DOI: 10.1007/s10529-009-0173-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Revised: 11/03/2009] [Accepted: 11/03/2009] [Indexed: 10/20/2022]
Abstract
Methods for the preparation of carrier-free insoluble enzymes are reviewed. The technology of cross-linked enzyme aggregates has now been applied to a range of synthetically useful activities. Fusion proteins are also gaining momentum because they allow a relatively selective aggregation or even a specific self-assembly of the desired enzyme activity into insoluble particles in the absence of potentially denaturing chemicals required for precipitation and cross-linking. Recycling of insoluble protein particles for multiple rounds of batchwise reaction has been demonstrated in selected biotransformations. However, for application in a fully continuous biocatalytic process, low resistance to mechanical stress and high compressibility are issues for consideration on carrier-free enzyme particles.
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Heyman A, Medalsy I, Betâ
Or O, Dgany O, Gottlieb M, Porath D, Shoseyov O. Protein Scaffold Engineering Towards Tunable Surface Attachment. Angew Chem Int Ed Engl 2009; 48:9290-4. [DOI: 10.1002/anie.200903075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Heyman A, Medalsy I, Betâ
Or O, Dgany O, Gottlieb M, Porath D, Shoseyov O. Protein Scaffold Engineering Towards Tunable Surface Attachment. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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40
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Dafoe NJ, Zamani A, Ekramoddoullah AKM, Lippert D, Bohlmann J, Constabel CP. Analysis of the poplar phloem proteome and its response to leaf wounding. J Proteome Res 2009; 8:2341-50. [PMID: 19245218 DOI: 10.1021/pr800968r] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Phloem exudate collected from hybrid poplar (Populus trichocarpa x Populus deltoides) was estimated to have more than 100 proteins, of which 48 were identified using LC-MS/MS. Comparative two-dimensional gel electrophoresis demonstrated that two phloem exudate proteins were significantly (P<0.05) upregulated 24 h after leaf wounding. These were identified as pop3/SP1 and a thaumatin-like protein. This is the first characterization of a phloem proteome from a tree species.
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Affiliation(s)
- Nicole J Dafoe
- Centre for Forest Biology and Department of Biology, University of Victoria, Victoria, BC, Canada
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41
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Heyman A, Medalsy I, Dgany O, Porath D, Markovich G, Shoseyov O. Float and compress: honeycomb-like array of a highly stable protein scaffold. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:5226-5229. [PMID: 19397358 DOI: 10.1021/la804132z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Organizing nano-objects, proteins in particular, on surfaces is one of the primary goals of bio/chemical nanotechnology. A highly stable protein scaffold (6His-SP1) was organized into a hexagonal 2D array by a new, versatile method. The protein was expelled from solution into the air/water interface and compressed in a Langmuir trough into a closely packed monolayer without the use of phospholipids or other surfactants at the interface. The 2D arrays formed at the air/water interface were characterized by transmission electron microscopy (TEM) and atomic force microscopy (AFM).
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Affiliation(s)
- Arnon Heyman
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and the Otto Warburg Minerva Center for Agricultural Biotechnology, The Hebrew University of Jerusalem, Rehovot, Israel
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Kolodyazhnaya YS, Kutsokon NK, Levenko BA, Syutikova OS, Rakhmetov DB, Kochetov AV. Transgenic plants tolerant to abiotic stresses. CYTOL GENET+ 2009. [DOI: 10.3103/s0095452709020108] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Nordon RE, Craig SJ, Foong FC. Molecular engineering of the cellulosome complex for affinity and bioenergy applications. Biotechnol Lett 2009; 31:465-76. [PMID: 19116695 DOI: 10.1007/s10529-008-9899-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Revised: 11/26/2008] [Accepted: 12/04/2008] [Indexed: 11/24/2022]
Abstract
The cellulosome complex has evolved to degrade plant cell walls and, as such, combines tenacious binding to cellulose with diverse catalytic activities against amorphous and crystalline cellulose. Cellulolytic microorganisms provide an extensive selection of domains; those with affinity for cellulose, cohesins and their dockerin binding partners that define cellulosome stoichiometry and architecture, and a range of catalytic activities against carbohydrates. These robust domains provide the building blocks for molecular design. This review examines how protein modules derived from the cellulosome have been incorporated into chimaeric proteins to provide biosynthetic tools for research and industry. These applications include affinity tags for protein purification, and non-chemical methods for immobilisation and presentation of recombinant protein domains on cellulosic substrates. Cellulosomal architecture provides a paradigm for design of enzymatic complexes that synergistically combine multiple catalytic subunits to achieve higher specific activity than would be obtained using free enzymes. Multimeric enzymatic complexes may have industrial applications of relevance for an emerging carbon economy. Biocatalysis will lead to more efficient utilisation of renewable carbon-fixing energy sources with the added benefits of reducing chemical waste streams and reliance on petroleum.
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Affiliation(s)
- Robert E Nordon
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, 2052 NSW, Australia.
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Heddle JG. Protein cages, rings and tubes: useful components of future nanodevices? Nanotechnol Sci Appl 2008; 1:67-78. [PMID: 24198461 PMCID: PMC3781744 DOI: 10.2147/nsa.s4092] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
There is a great deal of interest in the possibility that complex nanoscale devices can be designed and engineered. Such devices will lead to the development of new materials, electronics and smart drugs. Producing complex nanoscale devices, however will present many challenges and the components of such devices will require a number of special features. Devices will be engineered to incorporate desired functionalities but, because of the difficulties of controlling matter precisely at the nanoscale with current technology, the nanodevice components must self-assemble. In addition, nanocomponents that are to have wide applicability in various devices must have enough flexibility to integrate into a large number of potentially very different environments. These challenges are daunting and complex, and artificial nanodevices have not yet been constructed. However, the existence of nanomachines in nature in the form of proteins (eg, enzymes) suggests that they will be possible to produce. As the material from which nature's nanomachines are made, proteins seem ideal to form the basis of engineered components of such nanodevices. Initially, engineering projects may focus on building blocks such as rings, cages and tubes, examples of which exist in nature and may act as a useful start point for modification and further development. This review focuses on the recent research and possible future development of such protein building blocks.
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Affiliation(s)
- Jonathan G Heddle
- Global Edge Institute, Tokyo Institute of Technology, Nagatsuda, Midori-ku, Yokohama Kanagawa, Japan
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45
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Zhu B, Xiong AS, Peng RH, Xu J, Zhou J, Xu JT, Jin XF, Zhang Y, Hou XL, Yao QH. Heat stress protection in Aspen sp1 transgenic Arabidopsis thaliana. BMB Rep 2008; 41:382-7. [DOI: 10.5483/bmbrep.2008.41.5.382] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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46
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Park SC, Lee JR, Shin SO, Park Y, Lee SY, Hahm KS. Characterization of a heat-stable protein with antimicrobial activity from Arabidopsis thaliana. Biochem Biophys Res Commun 2007; 362:562-7. [PMID: 17720140 DOI: 10.1016/j.bbrc.2007.07.188] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Accepted: 07/19/2007] [Indexed: 10/23/2022]
Abstract
A heat-stable protein with antimicrobial activity was isolated from Arabidopsis thaliana plants by buffer-soluble extraction and two chromatographic procedures. The results of MALDI-TOF analysis revealed that the isolated protein shares high sequence identity with aspen SP1. To determine the exact antimicrobial properties of this protein, a cDNA encoding the protein was isolated from an A. thaliana leaf cDNA library and named AtHS1. AtHS1 mRNA was induced by exposure to external stresses, such as salicylic acid and jasmonic acid. We also analyzed the antimicrobial activity of recombinant AtHS1 expressed in Escherichia coli. This protein inhibited pathogenic fungal strains, except for Phytophthora infestans and Phytophthora nicotianae, and it exhibited antibacterial activity against E. coli and Staphylococcus aureus. These results suggest that AtHS1 shows good potential for use as a natural material in the study of antimicrobial agents.
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Affiliation(s)
- Seong-Cheol Park
- Research Center for Proteineous Materials (RCPM), Chosun University, Kwangju 501-759, Republic of Korea
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Heyman A, Barak Y, Caspi J, Wilson DB, Altman A, Bayer EA, Shoseyov O. Multiple display of catalytic modules on a protein scaffold: nano-fabrication of enzyme particles. J Biotechnol 2007; 131:433-9. [PMID: 17826857 DOI: 10.1016/j.jbiotec.2007.07.940] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Revised: 03/30/2007] [Accepted: 07/20/2007] [Indexed: 10/23/2022]
Abstract
Self assembly is a prerequisite for fabricating nanoscale structures. Here we present a new fusion protein based on the stress-responsive homo-oligomeric protein, SP1. This ring-shaped protein is a highly stable homododecamer, which can be potentially utilized to self-assemble different modules and enzymes in a predicted and oriented manner. For that purpose, a cohesin module (a component of the bacterial cellulosome) was selected, its gene fused in-frame to SP1, and the fusion protein was expressed in Escherichia coli. The cohesin module, specialized to incorporate different enzymes through specific recognition of a dockerin modular counterpart, is used to display new moieties on the SP1 scaffold. The SP1 scaffold displayed 12 active cohesin modules and specific binding to a dockerin-fused cellulase enzyme from Thermobifida fusca. Moreover, we found a significant increase in specific activity of the scaffold-displayed enzymes.
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Affiliation(s)
- Arnon Heyman
- The Robert H Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agricultural, Food and Environmental Quality Sciences, The Hebrew University of Jerusalem, Rehovot, Israel
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Nakayama K, Okawa K, Kakizaki T, Honma T, Itoh H, Inaba T. Arabidopsis Cor15am is a chloroplast stromal protein that has cryoprotective activity and forms oligomers. PLANT PHYSIOLOGY 2007; 144:513-23. [PMID: 17384167 PMCID: PMC1913801 DOI: 10.1104/pp.106.094581] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Many plants acquire increased freezing tolerance when they are exposed to nonfreezing temperatures of a certain duration. This process is known as cold acclimation and allows plants to protect themselves from freezing injury. A wide variety of polypeptides are induced during cold acclimation, among which is one encoded by COR15A in Arabidopsis (Arabidopsis thaliana). Previous studies showed that the COR15A gene encodes a small, plastid-targeted polypeptide that is processed to a mature form called Cor15am. In this study, we examined the biochemical properties and activities of Cor15am in more detail. We provide evidence that Cor15am localizes almost exclusively to the chloroplast stroma. In addition, the cold-regulated accumulation of Cor15am is affected by chloroplast functionality. Both gel-filtration chromatography and protein cross-linking reveal that Cor15am forms oligomers in the stroma of chloroplasts. Although Cor15am accumulates in response to low temperature, cold acclimation is not a prerequisite for oligomerization of Cor15am. Structural analysis suggests that Cor15am is composed of both ordered and random structures, and can stay soluble with small structural change after boiling and freeze-thaw treatments. Recombinant Cor15am exhibits in vitro cryoprotection of a freeze-labile enzyme, l-lactate dehydrogenase. Furthermore, Cor15am is capable of associating with l-lactate dehydrogenase in vitro and with potential stromal substrates in vivo. On the basis of these results, we propose that Arabidopsis Cor15am is a cryoprotective protein that forms oligomers in the chloroplast stroma, and that direct association of Cor15am with its substrates is part of its cryoprotective mechanism.
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Affiliation(s)
- Katsuhiro Nakayama
- The 21st Century Centers of Excellence Program, Cryobiosystem Research Center, Iwate University, Morioka 020-8550, Japan
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Bogeat-Triboulot MB, Brosché M, Renaut J, Jouve L, Le Thiec D, Fayyaz P, Vinocur B, Witters E, Laukens K, Teichmann T, Altman A, Hausman JF, Polle A, Kangasjärvi J, Dreyer E. Gradual soil water depletion results in reversible changes of gene expression, protein profiles, ecophysiology, and growth performance in Populus euphratica, a poplar growing in arid regions. PLANT PHYSIOLOGY 2007; 143:876-92. [PMID: 17158588 PMCID: PMC1803728 DOI: 10.1104/pp.106.088708] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2006] [Accepted: 11/21/2006] [Indexed: 05/06/2023]
Abstract
The responses of Populus euphratica Oliv. plants to soil water deficit were assessed by analyzing gene expression, protein profiles, and several plant performance criteria to understand the acclimation of plants to soil water deficit. Young, vegetatively propagated plants originating from an arid, saline field site were submitted to a gradually increasing water deficit for 4 weeks in a greenhouse and were allowed to recover for 10 d after full reirrigation. Time-dependent changes and intensity of the perturbations induced in shoot and root growth, xylem anatomy, gas exchange, and water status were recorded. The expression profiles of approximately 6,340 genes and of proteins and metabolites (pigments, soluble carbohydrates, and oxidative compounds) were also recorded in mature leaves and in roots (gene expression only) at four stress levels and after recovery. Drought successively induced shoot growth cessation, stomatal closure, moderate increases in oxidative stress-related compounds, loss of CO2 assimilation, and root growth reduction. These effects were almost fully reversible, indicating that acclimation was dominant over injury. The physiological responses were paralleled by fully reversible transcriptional changes, including only 1.5% of the genes on the array. Protein profiles displayed greater changes than transcript levels. Among the identified proteins for which expressed sequence tags were present on the array, no correlation was found between transcript and protein abundance. Acclimation to water deficit involves the regulation of different networks of genes in roots and shoots. Such diverse requirements for protecting and maintaining the function of different plant organs may render plant engineering or breeding toward improved drought tolerance more complex than previously anticipated.
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Affiliation(s)
- Marie-Béatrice Bogeat-Triboulot
- Institut National de la Recherche Agronomique Nancy, Unité Mixte de Recherche 1137 Institut National de la Recherche Agronomique-Université Henri Poincaré Ecologie et Ecophysiologie Forestières, F-54280 Champenoux, France.
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Torres GA, Gimenes MA, Rosa Jr. VED, Quecini V. Identifying water stress-response mechanisms in citrus by in silico transcriptome analysis. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000500018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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