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Shao M, Feng Y, Yang S, Feng T, Zeng F, Lu S, Ma Z, Chen B, Mao J. Molecular evolution of Phytocyanin gene and analysis of expression at different coloring periods in apple (Malus domestica). BMC PLANT BIOLOGY 2024; 24:374. [PMID: 38714922 PMCID: PMC11077699 DOI: 10.1186/s12870-024-05069-6] [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: 01/27/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND PC (phytocyanin) is a class of copper-containing electron transfer proteins closely related to plant photosynthesis, abiotic stress responses growth and development in plants, and regulation of the expression of some flavonoids and phenylpropanoids, etc., however, compared with other plants, the PC gene family has not been systematically characterized in apple. RESULTS A total of 59 MdPC gene members unevenly distributed across 12 chromosomes were identified at the genome-wide level. The proteins of the MdPC family were classified into four subfamilies based on differences in copper binding sites and glycosylation sites: Apple Early nodulin-like proteins (MdENODLs), Apple Uclacyanin-like proteins (MdUCLs), Apple Stellacyanin-like proteins (MdSCLs), and Apple Plantacyanin-like proteins (MdPLCLs). Some MdPC members with similar gene structures and conserved motifs belong to the same group or subfamily. The internal collinearity analysis revealed 14 collinearity gene pairs among members of the apple MdPC gene. Interspecific collinearity analysis showed that apple had 31 and 35 homologous gene pairs with strawberry and grape, respectively. Selection pressure analysis indicated that the MdPC gene was under purifying selection. Prediction of protein interactions showed that MdPC family members interacted strongly with the Nad3 protein. GO annotation results indicated that the MdPC gene also regulated the biosynthesis of phenylpropanoids. Chip data analysis showed that (MdSCL3, MdSCL7 and MdENODL27) were highly expressed in mature fruits and peels. Many cis-regulatory elements related to light response, phytohormones, abiotic stresses and flavonoid biosynthetic genes regulation were identified 2000 bp upstream of the promoter of the MdPC gene, and qRT-PCR results showed that gene members in Group IV (MdSCL1/3, MdENODL27) were up-regulated at all five stages of apple coloring, but the highest expression was observed at the DAF13 (day after fruit bag removal) stage. The gene members in Group II (MdUCL9, MdPLCL3) showed down-regulated or lower expression in the first four stages of apple coloring but up-regulated and highest expression in the DAF 21 stage. CONCLUSION Herein, one objective of these findings is to provide valuable information for understanding the structure, molecular evolution, and expression pattern of the MdPC gene, another major objective in this study was designed to lay the groundwork for further research on the molecular mechanism of PC gene regulation of apple fruit coloration.
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Affiliation(s)
- Miao Shao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Yongqing Feng
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Shangwen Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Tong Feng
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Fanwei Zeng
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Shixiong Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070, PR China.
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Aza P, Camarero S. Fungal Laccases: Fundamentals, Engineering and Classification Update. Biomolecules 2023; 13:1716. [PMID: 38136587 PMCID: PMC10741624 DOI: 10.3390/biom13121716] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Multicopper oxidases (MCOs) share a common catalytic mechanism of activation by oxygen and cupredoxin-like folding, along with some common structural determinants. Laccases constitute the largest group of MCOs, with fungal laccases having the greatest biotechnological applicability due to their superior ability to oxidize a wide range of aromatic compounds and lignin, which is enhanced in the presence of redox mediators. The adaptation of these versatile enzymes to specific application processes can be achieved through the directed evolution of the recombinant enzymes. On the other hand, their substrate versatility and the low sequence homology among laccases make their exact classification difficult. Many of the ever-increasing amounts of MCO entries from fungal genomes are automatically (and often wrongly) annotated as laccases. In a recent comparative genomic study of 52 basidiomycete fungi, MCO classification was revised based on their phylogeny. The enzymes clustered according to common structural motifs and theoretical activities, revealing three novel groups of laccase-like enzymes. This review provides an overview of the structure, catalytic activity, and oxidative mechanism of fungal laccases and how their biotechnological potential as biocatalysts in industry can be greatly enhanced by protein engineering. Finally, recent information on newly identified MCOs with laccase-like activity is included.
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Affiliation(s)
| | - Susana Camarero
- Margarita Salas Center for Biological Research, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain;
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Dong Y, Zhang L, Chang X, Wang X, Li G, Chen S, Jin S. Overexpression of LpCPC from Lilium pumilum confers saline-alkali stress (NaHCO 3) resistance. PLANT SIGNALING & BEHAVIOR 2022; 17:2057723. [PMID: 35403568 PMCID: PMC9009912 DOI: 10.1080/15592324.2022.2057723] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
Lilium Pumilum with wide distribution is highly tolerant to salinity. The blue copper protein LpCPC (Lilium pumilum Cucumber Peeling Cupredoxin) gene was cloned from Lilium pumilum, which has the conserved regions of type I copper protein. Moreover, LpCPC has the closest relation to CPC from Actinidia chinensis using DNAMAN software and MEGA7 software. qRT-PCR indicated that LpCPC expression was higher in root and bulb of Lilium pumilum, and the expression of the LpCPC gene increased and reached the highest level at 12 h in bulbs under 20 mM NaHCO3. The transgenic yeast was more tolerant compared with the control under NaHCO3 stress. Compared with the wild type, overexpressing plants indicated a relatively lower degree of wilting. In addition, the chlorophyll content, soluble phenol content, and lignin content of overexpressing lines were higher than that of wild-type, whereas the relative conductivity of overexpressing plants was significantly lower than that of wild-type plants. Expression of essential genes including NHX1 and SOS1 in salt stress response pathways are steadily higher in overexpression tobacco than that in wild-types. Transgenic lines had much higher levels of CCR1 and CAD, which are involved in lignin production, compared with wild-type lines. The yeast two-hybrid technique was applied to screen probable interacting proteins interacting with LpCPC. Eight proteins interacted with LpCPC were screened, and five of which were demonstrated to be associated with plant salinity resistance. Overall, the role of gene LpCPC is mediating molecule responses in increasing saline-alkali stress resistance, indicating that it is an essential gene to enhance salt tolerance in Lilium pumilum.
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Affiliation(s)
- Yi Dong
- Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry UniversityKey Laboratory of Saline-alkali, Harbin, Heilongjiang, China
- Aulin College, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Ling Zhang
- Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry UniversityKey Laboratory of Saline-alkali, Harbin, Heilongjiang, China
| | - Xu Chang
- Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry UniversityKey Laboratory of Saline-alkali, Harbin, Heilongjiang, China
| | - Xiaolu Wang
- Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry UniversityKey Laboratory of Saline-alkali, Harbin, Heilongjiang, China
| | - Guanrong Li
- Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry UniversityKey Laboratory of Saline-alkali, Harbin, Heilongjiang, China
| | - Shiya Chen
- Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry UniversityKey Laboratory of Saline-alkali, Harbin, Heilongjiang, China
| | - Shumei Jin
- Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry UniversityKey Laboratory of Saline-alkali, Harbin, Heilongjiang, China
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4
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Jin S, Wang X, Dong Y, Li G, Chang X, Zhang L, Jin S. The gene LpBCP increased NaHCO 3 resistance by enhancing lignin or ROS scavenging in the Nicotiana benthamiana. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:1057-1065. [PMID: 35976073 DOI: 10.1111/plb.13462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Lilium pumilum is an excellent wildflower germplasm resource with high resistance to salinity stress. The gene LpBCP plays an important role in salinity tolerance of L. pumilum. Studying the molecular mechanism of salinity resistance in L. pumilum will provide insights into multiple aspects, including breeding better varieties, environmental protection, improving soil conditions, etc. Conventional methods were used to determine different physiological indicators of Nicotiana benthamiana after NaHCO3 treatment, i.e. chlorophyll content, soluble phenol content and lignin content. RT-qPCR was carried out to find expression of LpBCP in different organs and under abiotic stresses. DAB was used to detect H2 O2 in leaves in situ. A yeast two-hybrid system was used to screen for LpBCP interacting proteins. LpBCP was cloned from bulbs of L. pumilum. The highest expression of LpBCP was in roots and bulbs of transgenic plants. LpBCP-overexpressed plants showed less wilting, compared to WT plants. LpBCP transgenic plants have higher chlorophyll, soluble phenol and lignin content, and lower relative conductivity under 500 mM NaHCO3 stress. In addition, H2 O2 scavenging in transgenic plants was much improved, indicating increased resistance to NaHCO3 stress. Thirteen LpBCP-interacting proteins were screened using the yeast two-hybrid method and five were associated with salt stress. Based on our findings, LPBCP could be a key gene that can be used to improve L. pumilum salt tolerance.
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Affiliation(s)
- S Jin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
- Forestry College, Northeast Forestry University, Harbin, China
| | - X Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Y Dong
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
- Aulin College, Northeast Forestry University, Harbin, China
| | - G Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - X Chang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - L Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - S Jin
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
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5
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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6
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Reyt G, Chao Z, Flis P, Salas-González I, Castrillo G, Chao DY, Salt DE. Uclacyanin Proteins Are Required for Lignified Nanodomain Formation within Casparian Strips. Curr Biol 2020; 30:4103-4111.e6. [PMID: 32857976 PMCID: PMC7575197 DOI: 10.1016/j.cub.2020.07.095] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/14/2020] [Accepted: 07/28/2020] [Indexed: 01/09/2023]
Abstract
Casparian strips (CSs) are cell wall modifications of vascular plants restricting extracellular free diffusion into and out of the vascular system [1]. This barrier plays a critical role in controlling the acquisition of nutrients and water necessary for normal plant development [2-5]. CSs are formed by the precise deposition of a band of lignin approximately 2 μm wide and 150 nm thick spanning the apoplastic space between adjacent endodermal cells [6, 7]. Here, we identified a copper-containing protein, Uclacyanin1 (UCC1), that is sub-compartmentalized within the CS. UCC1 forms a central CS nanodomain in comparison with other CS-located proteins that are found to be mainly accumulated at the periphery of the CS. We found that loss-of-function of two uclacyanins (UCC1 and UCC2) reduces lignification specifically in this central CS nanodomain, revealing a nano-compartmentalized machinery for lignin polymerization. This loss of lignification leads to increased endodermal permeability and, consequently, to a loss of mineral nutrient homeostasis.
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Affiliation(s)
- Guilhem Reyt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Zhenfei Chao
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Paulina Flis
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Isai Salas-González
- Curriculum in Bioinformatics and Computational Biology, Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gabriel Castrillo
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - David E Salt
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK.
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7
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Sun Y, Wu Z, Wang Y, Yang J, Wei G, Chou M. Identification of Phytocyanin Gene Family in Legume Plants and their Involvement in Nodulation of Medicago truncatula. PLANT & CELL PHYSIOLOGY 2019; 60:900-915. [PMID: 30649463 DOI: 10.1093/pcp/pcz007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
The establishment of symbiosis between legume and rhizobium results in the formation of nodule. Phytocyanins (PCs) are a class of plant-specific blue copper proteins, playing critical roles in plant development including nodule formation. Although a few PC genes have been isolated from nodules, their functions are still unclear. Here, we performed a genome-wide identification of PC family in seven sequenced legume species (Medicago truncatula, Glycine max, Cicer arietinum, Cajanus cajan, Lotus japonicus, Vigna angularis and Phaseolus vulgaris) and found PCs experienced a remarkable expansion in M. truncatula and G. max. Further, we conducted an in-depth analysis of PC family in the model legume M. truncatula. Briefly, 82 MtPCs were divided into four subfamilies and clustered into seven clades, with a large proportion of tandem duplications and various cross-tissues expression patterns. Importantly, some PCs, such as MtPLC1, MtENODL27 and MtENODL28 were preferentially expressed in nodules. Further, RNA interference (RNAi) experiment revealed the knockdown of MtENDOL27 and MtENDOL28 impaired rhizobia infection, nodule numbers and nitrogenase activity. Moreover, in the MtENODL27-RNAi nodules, the infected cells were reduced and the symbiosomes did not reach the elongated stage, indicating MtENDOL27 is required for rhizobia infection and nodule development. In addition, co-expression analysis showed MtPLC1, MtENODL27 and MtENODL28 were grouped into two different functional modules and co-expressed with the known symbiotic nitrogen fixation-related genes, suggesting that they might participate in nodulation via different ways. In summary, this study provides a useful resource for future researches on the structure and function of PCs in nodulation.
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Affiliation(s)
- Yali Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Zefeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Yujie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Jieyu Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
| | - Minxia Chou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest Agriculture and Forestry University, Yangling, China
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Liu Y, Cao D, Ma L, Jin X, Yang P, Ye F, Liu P, Gong Z, Wei C. TMT-based quantitative proteomics analysis reveals the response of tea plant (Camellia sinensis) to fluoride. J Proteomics 2018; 176:71-81. [PMID: 29408313 DOI: 10.1016/j.jprot.2018.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 01/29/2018] [Accepted: 02/01/2018] [Indexed: 01/19/2023]
Abstract
The tea plant is a fluoride hyperaccumulator, and fluoride accumulation in its leaves is closely related to human health. To dissect molecular mechanisms underlying fluoride accumulation/detoxification, the leaves of tea seedlings exposed to different fluoride treatments for 30 days were sampled for physiological and proteomics analyses. The results showed that fluoride had no adverse effects on the growth of tea seedlings in spite of high content fluoride accumulation in their leaves. Through TMT coupled with UPLC MS/MS, 189 differentially accumulated proteins were quantified, of which 41 and 148 were localized in the cell wall and cellular compartments respectively. 41 cell wall proteins were mainly conductive to cell wall structure rearrangement, signaling modulation and the protection cells from damages; 148 cellular compartments proteins mainly contributed to diverse metabolisms reprogramming, energy reallocation and plant defense. Notably, upregulation of several proteins including GHs, smHSPs, DRT100, YLS2-like, primary amine oxidase, GDSL esterase/lipases and citrate synthase probably enhanced the defense of tea seedlings against fluoride. Collectively, our results presented a comprehensive proteomics analysis on the leaves of tea seedlings in response to fluoride, which would contribute to further deciphering of molecular mechanisms underlying fluoride accumulation/detoxification in tea plant. SIGNIFICANCE The tea plant (Camellia sinensis) is an important economic crop with its made tea occupying up the third non-alcohol beverage in the world. Tea plant is also a fluoride hyperaccumulator with up to 98% fluoride accumulation in the leaves by initiative absorption. Due to the fact that about 40% to 90% of fluoride could be readily released into tea infusion and then absorbed by human body, overaccumulation of fluoride in tea leaves is closely related to human health. Therefore, it is very necessary to deeply dissect the mechanisms underlying fluoride accumulation/detoxification in tea plant. Previously, numerous studies were conducted to investigate fluoride specification and fluoride localization of tea plant at morphological, physiological and biochemical levels, which documented that fluoride was majorly immobilized in the cell walls and stored in the vacuoles in the form of fluoride-ligands complexes. However, the molecular mechanisms governing cell wall immobilization and vacuolar compartmentation of fluoride were still remaining unknown. Thus, a quantitative proteomics study into the leaves of tea seedlings upon exposure to fluoride was performed in current study. Our results showed that 41 and 148 of 189 differentially accumulated proteins were targeted into the cell wall and cellular compartments respectively, revealing that cell wall proteins and cellular compartments proteins played crucial roles in the response of tea seedlings to fluoride. Our results were also in good agreement with the idea that the cell wall was involved in fluoride accumulation/detoxification in tea plant. However, the functions of key interested differentially accumulated proteins need be further analyzed in follow-up work.
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Affiliation(s)
- Yanli Liu
- Institute of Fruit and tea, Hubei Academy of Agricultural sciences, Wuhan 430209, China
| | - Dan Cao
- Institute of Fruit and tea, Hubei Academy of Agricultural sciences, Wuhan 430209, China
| | - Linlong Ma
- Institute of Fruit and tea, Hubei Academy of Agricultural sciences, Wuhan 430209, China
| | - Xiaofang Jin
- Institute of Fruit and tea, Hubei Academy of Agricultural sciences, Wuhan 430209, China.
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Moshan, 430074, China
| | - Fei Ye
- Institute of Fruit and tea, Hubei Academy of Agricultural sciences, Wuhan 430209, China
| | - Panpan Liu
- Institute of Fruit and tea, Hubei Academy of Agricultural sciences, Wuhan 430209, China
| | - Ziming Gong
- Institute of Fruit and tea, Hubei Academy of Agricultural sciences, Wuhan 430209, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China.
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9
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Roger M, Sciara G, Biaso F, Lojou E, Wang X, Bauzan M, Giudici-Orticoni MT, Vila AJ, Ilbert M. Impact of copper ligand mutations on a cupredoxin with a green copper center. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:351-359. [DOI: 10.1016/j.bbabio.2017.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 11/26/2022]
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10
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Calderan-Rodrigues MJ, Jamet E, Douché T, Bonassi MBR, Cataldi TR, Fonseca JG, San Clemente H, Pont-Lezica R, Labate CA. Cell wall proteome of sugarcane stems: comparison of a destructive and a non-destructive extraction method showed differences in glycoside hydrolases and peroxidases. BMC PLANT BIOLOGY 2016; 16:14. [PMID: 26754199 PMCID: PMC4709929 DOI: 10.1186/s12870-015-0677-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/05/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND Sugarcane has been used as the main crop for ethanol production for more than 40 years in Brazil. Recently, the production of bioethanol from bagasse and straw, also called second generation (2G) ethanol, became a reality with the first commercial plants started in the USA and Brazil. However, the industrial processes still need to be improved to generate a low cost fuel. One possibility is the remodeling of cell walls, by means of genetic improvement or transgenesis, in order to make the bagasse more accessible to hydrolytic enzymes. We aimed at characterizing the cell wall proteome of young sugarcane culms, to identify proteins involved in cell wall biogenesis. Proteins were extracted from the cell walls of 2-month-old culms using two protocols, non-destructive by vacuum infiltration vs destructive. The proteins were identified by mass spectrometry and bioinformatics. RESULTS A predicted signal peptide was found in 84 different proteins, called cell wall proteins (CWPs). As expected, the non-destructive method showed a lower percentage of proteins predicted to be intracellular than the destructive one (33% vs 44%). About 19% of CWPs were identified with both methods, whilst the infiltration protocol could lead to the identification of 75% more CWPs. In both cases, the most populated protein functional classes were those of proteins related to lipid metabolism and oxido-reductases. Curiously, a single glycoside hydrolase (GH) was identified using the non-destructive method whereas 10 GHs were found with the destructive one. Quantitative data analysis allowed the identification of the most abundant proteins. CONCLUSIONS The results highlighted the importance of using different protocols to extract proteins from cell walls to expand the coverage of the cell wall proteome. Ten GHs were indicated as possible targets for further studies in order to obtain cell walls less recalcitrant to deconstruction. Therefore, this work contributed to two goals: enlarge the coverage of the sugarcane cell wall proteome, and provide target proteins that could be used in future research to facilitate 2G ethanol production.
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Affiliation(s)
- Maria Juliana Calderan-Rodrigues
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Elisabeth Jamet
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France.
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France.
| | - Thibaut Douché
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France.
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France.
| | - Maria Beatriz Rodrigues Bonassi
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Thaís Regiani Cataldi
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Juliana Guimarães Fonseca
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
| | - Hélène San Clemente
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France.
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France.
| | - Rafael Pont-Lezica
- Université de Toulouse; UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, BP 42617, F-31326, Castanet-Tolosan, France
- CNRS; UMR 5546, BP 42617, F-31326, Castanet-Tolosan, France
| | - Carlos Alberto Labate
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Av. Pádua Dias 11, CP 83, 13400-970, Piracicaba, SP, Brazil.
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11
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Pérez-Henarejos SA, Alcaraz LA, Donaire A. Blue Copper Proteins: A rigid machine for efficient electron transfer, a flexible device for metal uptake. Arch Biochem Biophys 2015; 584:134-48. [DOI: 10.1016/j.abb.2015.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/24/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
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12
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Moshkov KA, Zaitsev VN, Grishina TV, Stefanov VE. Multinuclear blue copper-proteins: the evolutionary design. J EVOL BIOCHEM PHYS+ 2014. [DOI: 10.1134/s0022093014030016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Liu Y, Cusano AM, Wallace EC, Mekmouche Y, Ullah S, Robert V, Tron T. Characterization of C-terminally engineered laccases. Int J Biol Macromol 2014; 69:435-41. [DOI: 10.1016/j.ijbiomac.2014.05.053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 05/16/2014] [Accepted: 05/20/2014] [Indexed: 10/25/2022]
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14
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Isomorphic deactivation of a Pseudomonas aeruginosa oxidoreductase: The crystal structure of Ag(I) metallated azurin at 1.7 Å. J Inorg Biochem 2013; 128:11-6. [PMID: 23911566 DOI: 10.1016/j.jinorgbio.2013.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 11/21/2022]
Abstract
Multiple biophysical methods demonstrate that silver effectively metallates Pseudomonas aeruginosa apo-azurin in solution. X-ray crystallography of the silver-modified protein reveals that silver binds to azurin at the traditional copper mediated active site with nearly identical geometry. Cyclic voltammetry indicates that the silver adduct is redox inert. Our results suggest that a potential mechanism for the microbial toxicity of silver is the deactivation of copper oxidoreductases by the effective binding and structural mimicry by silver without the corresponding function.
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15
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Kaas Q, Craik DJ. NMR of plant proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:1-34. [PMID: 23611313 DOI: 10.1016/j.pnmrs.2013.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
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16
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Abstract
Multicopper blue proteins, composed of several repetitive copper-binding domains similar to one-domain cupredoxin-like proteins, were found in almost all organisms. They are classified into the three different groups, based on their two-, three- or six-domain organization. We found orthologs of chordate six-domain copper-binding proteins in animals, plants, bacteria and archea. The phylogenetic analysis of 183 multicopper blue proteins and their copper-binding sites comparison make us think that all the modern six-domain blue proteins have originated from the common ancestral six-domain protein in the process of gene duplication and copper-binding sites loss as a result of amino acid substitutions.
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17
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Lazarides T, Sazanovich IV, Simaan AJ, Kafentzi MC, Delor M, Mekmouche Y, Faure B, Réglier M, Weinstein JA, Coutsolelos AG, Tron T. Visible Light-Driven O2 Reduction by a Porphyrin–Laccase System. J Am Chem Soc 2013; 135:3095-103. [DOI: 10.1021/ja309969s] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Theodore Lazarides
- Chemistry
Department, University of Crete, Voutes
Campus, 71003 Heraklion,
Crete, Greece
| | - Igor V. Sazanovich
- Department
of Chemistry, University of Sheffield,
Sheffield S3 7HF, United Kingdom
| | - A. Jalila Simaan
- Aix-Marseille Université, CNRS
UMR 7313, case 342, 13397 Marseille Cedex 20, France
| | - Maria Chrisanthi Kafentzi
- Chemistry
Department, University of Crete, Voutes
Campus, 71003 Heraklion,
Crete, Greece
- Aix-Marseille Université, CNRS
UMR 7313, case 342, 13397 Marseille Cedex 20, France
| | - Milan Delor
- Department
of Chemistry, University of Sheffield,
Sheffield S3 7HF, United Kingdom
| | - Yasmina Mekmouche
- Aix-Marseille Université, CNRS
UMR 7313, case 342, 13397 Marseille Cedex 20, France
| | - Bruno Faure
- Aix-Marseille Université, CNRS
UMR 7313, case 342, 13397 Marseille Cedex 20, France
| | - Marius Réglier
- Aix-Marseille Université, CNRS
UMR 7313, case 342, 13397 Marseille Cedex 20, France
| | - Julia A. Weinstein
- Department
of Chemistry, University of Sheffield,
Sheffield S3 7HF, United Kingdom
| | | | - Thierry Tron
- Aix-Marseille Université, CNRS
UMR 7313, case 342, 13397 Marseille Cedex 20, France
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18
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Abstract
Biological trace metals are needed in small quantities, but used by all living organisms. They are employed in key cellular functions in a variety of biological processes, resulting in the various degree of dependence of organisms on metals. Most effort in the field has been placed on experimental studies of metal utilization pathways and metal-dependent proteins. On the other hand, systemic level analyses of metalloproteomes (or metallomes) have been limited for most metals. In this chapter, we focus on the recent advances in comparative genomics, which provides many insights into evolution and function of metal utilization. These studies suggested that iron and zinc are widely used in biology (presumably by all organisms), whereas some other metals such as copper, molybdenum, nickel, and cobalt, show scattered occurrence in various groups of organisms. For these metals, most user proteins are well characterized and their dependence on a specific element is evolutionarily conserved. We also discuss evolutionary dynamics of the dependence of user proteins on different metals. Overall, comparative genomics analysis of metallomes provides a foundation for the systemic level understanding of metal utilization as well as for investigating the general features, functions, and evolutionary dynamics of metal use in the three domains of life.
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19
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The putative phytocyanin genes in Chinese cabbage (Brassica rapa L.): genome-wide identification, classification and expression analysis. Mol Genet Genomics 2012; 288:1-20. [DOI: 10.1007/s00438-012-0726-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 11/07/2012] [Indexed: 02/07/2023]
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20
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Poon S, Heath RL, Clarke AE. A chimeric arabinogalactan protein promotes somatic embryogenesis in cotton cell culture. PLANT PHYSIOLOGY 2012; 160:684-95. [PMID: 22858635 PMCID: PMC3461548 DOI: 10.1104/pp.112.203075] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 07/30/2012] [Indexed: 05/05/2023]
Abstract
Arabinogalactan proteins (AGPs) are a family of extracellular plant proteoglycans implicated in many aspects of plant growth and development, including in vitro somatic embryogenesis (SE). We found that specific AGPs were produced by cotton (Gossypium hirsutum) calli undergoing SE and that when these AGPs were isolated and incorporated into tissue culture medium, cotton SE was promoted. When the AGPs were partly or fully deglycosylated, SE-promoting activity was not diminished. Testing of AGPs separated by reverse-phase high-performance liquid chromatography revealed that the SE-promoting activity resided in a hydrophobic fraction. We cloned a full-length complementary DNA (cotton PHYTOCYANIN-LIKE ARABINOGALACTAN-PROTEIN1 [GhPLA1]) that encoded the protein backbone of an AGP in the active fraction. It has a chimeric structure comprising an amino-terminal signal sequence, a phytocyanin-like domain, an AGP-like domain, and a hydrophobic carboxyl-terminal domain. Recombinant production of GhPLA1 in tobacco (Nicotiana tabacum) cells enabled us to purify and analyze a single glycosylated AGP and to demonstrate that this chimeric AGP promotes cotton SE. Furthermore, the nonglycosylated phytocyanin-like domain from GhPLA1, which was bacterially produced, also promoted SE, indicating that the glycosylated AGP domain was unnecessary for in vitro activity.
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Affiliation(s)
- Simon Poon
- School of Botany, University of Melbourne, Victoria 3010, Australia.
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21
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Guzzi R, Sportelli L, Yanagisawa S, Li C, Kostrz D, Dennison C. The influence of active site loop mutations on the thermal stability of azurin from Pseudomonas aeruginosa. Arch Biochem Biophys 2012; 521:18-23. [PMID: 22446157 DOI: 10.1016/j.abb.2012.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 03/05/2012] [Accepted: 03/06/2012] [Indexed: 10/28/2022]
Abstract
The copper site and overall structures of azurin (AZ) variants in which the amicyanin (AMI) and plastocyanin (PC) metal binding loops have been introduced, AZAMI and AZPC, respectively, are similar to that of AZ, whereas the loop conformations resemble those in the native proteins. To assess the influence of these loop mutations on stability, the thermal unfolding of AZAMI and AZPC has been investigated by differential scanning calorimetry, absorption and fluorescence spectroscopy. The calorimetric profiles of both variants exhibit a complex shape consisting of two endothermic peaks and an exothermic peak. The temperature of the maximum heat of absorption for the single endothermic peak is 82.7°C for AZ, whereas for AZAMI and AZPC the most intense endothermic peaks are at 74.9 and 68.1°C comparable to values for AMI and PC, respectively. Denaturation investigated using the temperature dependence of the absorbance at ∼600nm and Trp emission, also demonstrates decreased stability for both loop mutants. The thermal transition between the native and the denaturated states is irreversible, scan rate dependent and consistent with the two-state irreversible model. The structure of the active-site loop has a dramatic effect on the kinetic stability and the unfolding pathway of cupredoxins.
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Affiliation(s)
- Rita Guzzi
- Molecular Biophysics Laboratory and CNISM Unit, Department of Physics, University of Calabria, Ponte P. Bucci, Cubo 31C, 87036 Rende (CS), Italy.
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22
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Robert V, Mekmouche Y, Pailley PR, Tron T. Engineering laccases: in search for novel catalysts. Curr Genomics 2011; 12:123-9. [PMID: 21966250 PMCID: PMC3129046 DOI: 10.2174/138920211795564340] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/07/2011] [Accepted: 03/11/2011] [Indexed: 11/28/2022] Open
Abstract
Laccases (p-diphenol oxidase, EC 1.10.3.2) are blue multicopper oxidases that catalyze the reduction of dioxygen to water, with a concomitant oxidation of small organic substrates. Since the description at the end of the nineteenth century of a factor catalyzing the rapid hardening of the latex of the Japanese lacquer trees (Rhus sp.) exposed to air laccases from different origins (plants, fungi bacteria) have been continuously discovered and extensively studied. Nowadays, molecular evolution and other powerful protein modification techniques offer possibilities to develop tailored laccases for a wide array of applications including drug synthesis, biosensors or biofuel cells. Here, we give an overview on strategies and results of our laboratory in the design of new biocatalysts based on laccases.
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Affiliation(s)
- Viviane Robert
- Laboratoire Biosciences, Institut des Sciences Moléculaires de Marseille, Université Aix-Marseille, ISM2 CNRS UMR 6263, Marseille Cedex 20, France
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23
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Folding and unfolding in the blue copper protein rusticyanin: role of the oxidation state. Bioinorg Chem Appl 2011:54232. [PMID: 18354738 PMCID: PMC2267886 DOI: 10.1155/2007/54232] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 05/02/2007] [Accepted: 06/27/2007] [Indexed: 11/17/2022] Open
Abstract
The unfolding process of the blue copper protein rusticyanin has been studied from the structural and the thermodynamic points of view at two pH values (pH 2.5 and 7.0). When Rc unfolds, copper ion remains bound to the polypeptide chain. Nuclear magnetic resonance data suggest that three of the copper ligands in the folded state are bound to the metal ion in the unfolded form, while the other native ligand is detached. These structural changes are reflected in the redox potentials of the protein in both folded and unfolded forms. The affinities of the copper ion in both redox states have been also determined at the two specified pH values. The results indicate that the presence of two histidine ligands in the folded protein can compensate the change in the net charge that the copper ion receives from their ligands, while, in the unfolded protein, charges of aminoacids are completely transferred to the copper ion, altering decisively the relative stability of its two-redox states.
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24
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Ligat L, Lauber E, Albenne C, San Clemente H, Valot B, Zivy M, Pont-Lezica R, Arlat M, Jamet E. Analysis of the xylem sap proteome of Brassica oleracea reveals a high content in secreted proteins. Proteomics 2011; 11:1798-813. [PMID: 21413152 DOI: 10.1002/pmic.201000781] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/01/2011] [Accepted: 02/01/2011] [Indexed: 01/03/2023]
Abstract
Xylem plays a major role in plant development and is considered part of the apoplast. Here, we studied the proteome of Brassica oleracea cv Bartolo and compared it to the plant cell wall proteome of another Brassicaceae, the model plant Arabidopsis thaliana. B. oleracea was chosen because it is technically difficult to harvest enough A. thaliana xylem sap for proteomic analysis. We studied the whole proteome and an N-glycoproteome obtained after Concanavalin A affinity chromatography. Altogether, 189 proteins were identified by LC-MS/MS using Brassica EST and cDNA sequences. A predicted signal peptide was found in 164 proteins suggesting that most proteins of the xylem sap are secreted. Eighty-one proteins were identified in the N-glycoproteome, with 25 of them specific of this fraction, suggesting that they were concentrated during the chromatography step. All the protein families identified in this study were found in the cell wall proteomes. However, proteases and oxido-reductases were more numerous in the xylem sap proteome, whereas enzyme inhibitors were rare. The origin of xylem sap proteins is discussed. All the experimental data including the MS/MS data were made available in the WallProtDB cell wall proteomic database.
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Affiliation(s)
- Laetitia Ligat
- Université de Toulouse, UPS, UMR, Surfaces Cellulaires et Signalisation chez les Végétaux, Castanet-Tolosan, France
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25
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Incorporation of the red copper nitrosocyanin binding loop into blue copper azurin. J Biol Inorg Chem 2010; 16:473-80. [DOI: 10.1007/s00775-010-0746-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 11/24/2010] [Indexed: 10/18/2022]
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26
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Sakurai H. Overview and Frontier for the Development of Metallopharmaceutics. ACTA ACUST UNITED AC 2010. [DOI: 10.1248/jhs.56.129] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Hiromu Sakurai
- Laboratory of Pharmacoanalytical Chemistry, Department of Physical Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science
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27
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Choi M, Sukumar N, Liu A, Davidson VL. Defining the role of the axial ligand of the type 1 copper site in amicyanin by replacement of methionine with leucine. Biochemistry 2009; 48:9174-84. [PMID: 19715303 DOI: 10.1021/bi900836h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of replacing the axial methionine ligand of the type 1 copper site with leucine on the structure and function of amicyanin have been characterized. The crystal structures of the oxidized and reduced forms of the protein reveal that the copper site is now tricoordinate with no axial ligand, and that the copper coordination distances for the two ligands provided by histidines are significantly increased. Despite these structural changes, the absorption and EPR spectra of M98L amicyanin are only slightly altered and still consistent with that of a typical type 1 site. The oxidation-reduction midpoint potential (E(m)) value becomes 127 mV more positive as a consequence of the M98L mutation, most likely because of the increased hydrophobicity of the copper site. The most dramatic effect of the mutation was on the electron transfer (ET) reaction from reduced M98L amicyanin to cytochrome c(551i) within the protein ET complex. The rate decreased 435-fold, which was much more than expected from the change in E(m). Examination of the temperature dependence of the ET rate (k(ET)) revealed that the mutation caused a 13.6-fold decrease in the electronic coupling (H(AB)) for the reaction. A similar decrease was predicted from a comparative analysis of the crystal structures of reduced M98L and native amicyanins. The most direct route of ET for this reaction is through the Met98 ligand. Inspection of the structures suggests that the major determinant of the large decrease in the experimentally determined values of H(AB) and k(ET) is the increased distance from the copper to the protein within the type 1 site of M98L amicyanin.
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Affiliation(s)
- Moonsung Choi
- Department of Biochemistry, The University of Mississippi Medical Center, Jackson, Mississippi 39216-4505, USA
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28
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Jamet E, Roujol D, San-Clemente H, Irshad M, Soubigou-Taconnat L, Renou JP, Pont-Lezica R. Cell wall biogenesis of Arabidopsis thaliana elongating cells: transcriptomics complements proteomics. BMC Genomics 2009; 10:505. [PMID: 19878582 PMCID: PMC2774874 DOI: 10.1186/1471-2164-10-505] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 10/31/2009] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Plant growth is a complex process involving cell division and elongation. Arabidopsis thaliana hypocotyls undergo a 100-fold length increase mainly by cell elongation. Cell enlargement implicates significant changes in the composition and structure of the cell wall. In order to understand cell wall biogenesis during cell elongation, mRNA profiling was made on half- (active elongation) and fully-grown (after growth arrest) etiolated hypocotyls. RESULTS Transcriptomic analysis was focused on two sets of genes. The first set of 856 genes named cell wall genes (CWGs) included genes known to be involved in cell wall biogenesis. A significant proportion of them has detectable levels of transcripts (55.5%), suggesting that these processes are important throughout hypocotyl elongation and after growth arrest. Genes encoding proteins involved in substrate generation or in synthesis of polysaccharides, and extracellular proteins were found to have high transcript levels. A second set of 2927 genes labeled secretory pathway genes (SPGs) was studied to search for new genes encoding secreted proteins possibly involved in wall expansion. Based on transcript level, 433 genes were selected. Genes not known to be involved in cell elongation were found to have high levels of transcripts. Encoded proteins were proteases, protease inhibitors, proteins with interacting domains, and proteins involved in lipid metabolism. In addition, 125 of them encoded proteins with yet unknown function. Finally, comparison with results of a cell wall proteomic study on the same material revealed that 48 out of the 137 identified proteins were products of the genes having high or moderate level of transcripts. About 15% of the genes encoding proteins identified by proteomics showed levels of transcripts below background. CONCLUSION Members of known multigenic families involved in cell wall biogenesis, and new genes that might participate in cell elongation were identified. Significant differences were shown in the expression of such genes in half- and fully-grown hypocotyls. No clear correlation was found between the abundance of transcripts (transcriptomic data) and the presence of the proteins (proteomic data) demonstrating (i) the importance of post-transcriptional events for the regulation of genes during cell elongation and (ii) that transcriptomic and proteomic data are complementary.
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Affiliation(s)
- Elisabeth Jamet
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS - UPS -Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
| | - David Roujol
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS - UPS -Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
| | - Hélène San-Clemente
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS - UPS -Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
| | - Muhammad Irshad
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS - UPS -Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
- Department of Botany, Govt. Post-Graduate College, 23200 Mardan, Pakistan
| | | | - Jean-Pierre Renou
- UMR INRA 1165 - CNRS 8114 - UEVE, 2 rue Gaston Crémieux, CP 5708, 91057 Evry, France
| | - Rafael Pont-Lezica
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS - UPS -Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
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Cusano AM, Mekmouche Y, Meglecz E, Tron T. Plasticity of laccase generated by homeologous recombination in yeast. FEBS J 2009; 276:5471-80. [PMID: 19694803 DOI: 10.1111/j.1742-4658.2009.07231.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Laccase-encoding sequences sharing 65-71% identity were shuffledin vivo by homeologous recombination. Yeast efficiently repaired linearized plasmids containing clac1, clac2 or clac5 Trametes sp. C30 cDNAs using a clac3 PCR fragment. From transformants secreting active variants, three chimeric laccases (LAC131, LAC232 and LAC535), each resulting from double crossovers, were purified, and their apparent kinetic parameters were determined using 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) and syringaldazine (SGZ) as substrates. At acidic pH, the apparent kinetic parameters of the chimera were not distinguishable from each other or from those obtained for the LAC3 enzyme used as reference. On the other hand, the pH tolerance of the variants was visibly extended towards alkaline pH values. Compared to the parental LAC3, a 31-fold increase in apparent k(cat) was observed for LAC131 at pH 8. This factor is one of the highest ever observed for laccase in a single mutagenesis step.
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Affiliation(s)
- Angela M Cusano
- Laboratoire Biosciences, Institut des Sciences Moléculaires de Marseille, Université Aix-Marseille, ISM2 CNRS UMR 6263, Marseille Cedex 20, France
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30
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Zhang Y, Gladyshev VN. Comparative Genomics of Trace Elements: Emerging Dynamic View of Trace Element Utilization and Function. Chem Rev 2009; 109:4828-61. [DOI: 10.1021/cr800557s] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yan Zhang
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
| | - Vadim N. Gladyshev
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0664
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31
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Rizzuti B, Sportelli L, Guzzi R. Molecular dynamics of amicyanin reveals a conserved dynamical core for blue copper proteins. Proteins 2009; 74:961-71. [PMID: 18767164 DOI: 10.1002/prot.22204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Molecular dynamics simulation has been carried out for the blue copper protein amicyanin from two different sources, Paracoccus denitrificans and Paraccocus versutus, to investigate the structural and dynamical properties common to the two molecules and to identify prominent features shared with proteins of the same family, the monomeric cupredoxins. The two amicyanins have almost identical secondary and tertiary structure. In the simulation, they differ for the number of hydrogen bonds in the main chain and the conformation of some beta-strands. However, they strictly maintain the arrangement of the portions of the beta-barrel that are conserved in the folding architecture of the blue copper proteins. Paracoccus versutus amicyanin equilibrates more rapidly, shows lower atomic deviation values, and is less rigid with respect to Paracoccus denitrificans amicyanin. Principal component analysis reveals that the conformational subspaces corresponding to eigenvectors with the same index for each of the two molecules are not necessarily equivalent. Nevertheless, a core scaffold with constrained dynamics exist for both amicyanins. In addition, two fairly flexible regions that are located on the opposite side with respect to the interaction sites with the partner molecules in the redox process have been evidenced in the protein structure. This description of amicyanin, with a few mobile regions remote from the active site and a rigid scaffold including most of the protein beta-barrel, has a close similarity with that of azurin and plastocyanin, two other cupredoxins previously investigated in simulation. Furthermore, similarities in the distribution of the atomic fluctuations indicate that amicyanin, azurin, and plastocyanin possess common dynamical features, in spite of differences in their structure. On the basis of these findings, we suggest that topological constraints imposed by the folding in correspondence of protein regions that are the most conserved determine the protein dynamics of the cupredoxin family. The dynamical properties of the cupredoxins might be controlled for functional advantages that include the binding mechanism with the biological partners and the collective inner motions of the protein matrix required for the electron transfer, whereas long-range conformational changes in the redox reaction should be excluded.
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Affiliation(s)
- Bruno Rizzuti
- Laboratorio Licryl CNR-INFM, Dipartimento di Fisica, Università della Calabria, Rende, Italy
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Clemente HS, Pont-Lezica R, Jamet E. Bioinformatics as a tool for assessing the quality of sub-cellular proteomic strategies and inferring functions of proteins: plant cell wall proteomics as a test case. Bioinform Biol Insights 2009; 3:15-28. [PMID: 20140071 PMCID: PMC2808182 DOI: 10.4137/bbi.s2065] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identification from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identified proteins in order to answer biological questions. The aim of the work was to get a new tool for improving the quality of proteomics of sub-cellular compartments. Starting from the analysis of problems found in databases, we designed a new Arabidopsis database named ProtAnnDB (http://www.polebio.scsv.ups-tlse.fr/ProtAnnDB/). It collects in one page predictions of sub-cellular localization and of functional domains made by available software. Using this database allows not only improvement of interpretation of proteomic data (top-down analysis), but also of procedures to isolate sub-cellular compartments (bottom-up quality control).
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Affiliation(s)
- Hélène San Clemente
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS-UPS-Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
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Guzzi R, Sportelli L, Sato K, Cannistraro S, Dennison C. Thermal unfolding studies of a phytocyanin. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1997-2003. [DOI: 10.1016/j.bbapap.2008.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 07/03/2008] [Accepted: 07/03/2008] [Indexed: 10/21/2022]
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Yanagisawa S, Crowley PB, Firbank SJ, Lawler AT, Hunter DM, McFarlane W, Li C, Kohzuma T, Banfield MJ, Dennison C. π-Interaction Tuning of the Active Site Properties of Metalloproteins. J Am Chem Soc 2008; 130:15420-8. [DOI: 10.1021/ja8038135] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sachiko Yanagisawa
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Peter B. Crowley
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Susan J. Firbank
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Anne T. Lawler
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - David M. Hunter
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - William McFarlane
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Chan Li
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Takamitsu Kohzuma
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Mark J. Banfield
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
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Irshad M, Canut H, Borderies G, Pont-Lezica R, Jamet E. A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana: confirmed actors and newcomers. BMC PLANT BIOLOGY 2008; 8:94. [PMID: 18796151 PMCID: PMC2551616 DOI: 10.1186/1471-2229-8-94] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 09/16/2008] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cell elongation in plants requires addition and re-arrangements of cell wall components. Even if some protein families have been shown to play roles in these events, a global picture of proteins present in cell walls of elongating cells is still missing. A proteomic study was performed on etiolated hypocotyls of Arabidopsis used as model of cells undergoing elongation followed by growth arrest within a short time. RESULTS Two developmental stages (active growth and after growth arrest) were compared. A new strategy consisting of high performance cation exchange chromatography and mono-dimensional electrophoresis was established for separation of cell wall proteins. This work allowed identification of 137 predicted secreted proteins, among which 51 had not been identified previously. Apart from expected proteins known to be involved in cell wall extension such as xyloglucan endotransglucosylase-hydrolases, expansins, polygalacturonases, pectin methylesterases and peroxidases, new proteins were identified such as proteases, proteins related to lipid metabolism and proteins of unknown function. CONCLUSION This work highlights the CWP dynamics that takes place between the two developmental stages. The presence of proteins known to be related to cell wall extension after growth arrest showed that these proteins may play other roles in cell walls. Finally, putative regulatory mechanisms of protein biological activity are discussed from this global view of cell wall proteins.
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Affiliation(s)
- Muhammad Irshad
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS – UPS-Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
| | - Hervé Canut
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS – UPS-Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
| | - Gisèle Borderies
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS – UPS-Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
| | - Rafael Pont-Lezica
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS – UPS-Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
| | - Elisabeth Jamet
- Surfaces cellulaires et Signalisation chez les Végétaux, UMR 5546 CNRS – UPS-Université de Toulouse, Pôle de Biotechnologie Végétale, 24 chemin de Borde-Rouge, BP 42617 Auzeville, 31326 Castanet-Tolosan, France
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Gschwind RM. Organocuprates and Diamagnetic Copper Complexes: Structures and NMR Spectroscopic Structure Elucidation in Solution. Chem Rev 2008; 108:3029-53. [DOI: 10.1021/cr800286r] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruth M. Gschwind
- Institut für Organische Chemie, Universität Regensburg, Universitätsstrasse 31, D-93040 Regensburg, Germany
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Abstract
Many approaches are being used to engineer metalloproteins, with most of these informed by, and aiming to further elucidate, the basic structural requirements for biological metal centers. Cupredoxins are type 1 (T1) copper-containing electron transfer (ET) proteins with a -barrel fold that is thought to constrain metal site structure. The T1 copper ion is bound by ligands mainly originating from a single active site loop whose length and structure varies. This Highlight article will focus on protein engineering studies which have investigated the role of the metal-binding loop for active site integrity and functionality. Scaffold differences are present within the cupredoxin family and their influence has also been assessed. Given the widespread occurrence of -barrel domains in nature, and the array of metal sites in proteins composed of loop regions, the studies described on this model system have implications for a variety of metalloproteins.
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Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK.
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Tang JA, Ellis BD, Warren TH, Hanna JV, Macdonald CLB, Schurko RW. Solid-State 63Cu and 65Cu NMR Spectroscopy of Inorganic and Organometallic Copper(I) Complexes. J Am Chem Soc 2007; 129:13049-65. [DOI: 10.1021/ja073238x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joel A. Tang
- Contribution from the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4, Department of Chemistry, Georgetown University, P.O Box 571227, Washington, D.C. 20057-1227, and ANSTO NMR Facility, Materials Division, Australian Nuclear Science and Technology Organisation, Sydney, Australia, NSW, 2234
| | - Bobby D. Ellis
- Contribution from the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4, Department of Chemistry, Georgetown University, P.O Box 571227, Washington, D.C. 20057-1227, and ANSTO NMR Facility, Materials Division, Australian Nuclear Science and Technology Organisation, Sydney, Australia, NSW, 2234
| | - Timothy H. Warren
- Contribution from the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4, Department of Chemistry, Georgetown University, P.O Box 571227, Washington, D.C. 20057-1227, and ANSTO NMR Facility, Materials Division, Australian Nuclear Science and Technology Organisation, Sydney, Australia, NSW, 2234
| | - John V. Hanna
- Contribution from the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4, Department of Chemistry, Georgetown University, P.O Box 571227, Washington, D.C. 20057-1227, and ANSTO NMR Facility, Materials Division, Australian Nuclear Science and Technology Organisation, Sydney, Australia, NSW, 2234
| | - Charles L. B. Macdonald
- Contribution from the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4, Department of Chemistry, Georgetown University, P.O Box 571227, Washington, D.C. 20057-1227, and ANSTO NMR Facility, Materials Division, Australian Nuclear Science and Technology Organisation, Sydney, Australia, NSW, 2234
| | - Robert W. Schurko
- Contribution from the Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada N9B 3P4, Department of Chemistry, Georgetown University, P.O Box 571227, Washington, D.C. 20057-1227, and ANSTO NMR Facility, Materials Division, Australian Nuclear Science and Technology Organisation, Sydney, Australia, NSW, 2234
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Kataoka K, Komori H, Ueki Y, Konno Y, Kamitaka Y, Kurose S, Tsujimura S, Higuchi Y, Kano K, Seo D, Sakurai T. Structure and function of the engineered multicopper oxidase CueO from Escherichia coli--deletion of the methionine-rich helical region covering the substrate-binding site. J Mol Biol 2007; 373:141-52. [PMID: 17804014 DOI: 10.1016/j.jmb.2007.07.041] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Revised: 07/16/2007] [Accepted: 07/17/2007] [Indexed: 10/23/2022]
Abstract
CueO is a multicopper oxidase (MCO) that is involved in the homeostasis of Cu in Escherichia coli and is the sole cuprous oxidase to have ever been found. Differing from other MCOs, the substrate-binding site of CueO is deeply buried under a methionine-rich helical region including alpha-helices 5, 6, and 7 that interfere with the access of organic substrates. We deleted the region Pro357-His406 and replaced it with a Gly-Gly linker. The crystal structures of a truncated mutant in the presence and in the absence of excess Cu(II) indicated that the scaffold of the CueO molecule and metal-binding sites were reserved in comparison with those of CueO. In addition, the high thermostability of the protein molecule and its spectroscopic and magnetic properties due to four Cu centers were also conserved after truncation. As for functions, the cuprous oxidase activity of the mutant was reduced to ca 10% that of recombinant CueO owing to the decrease in the affinity of the labile Cu site for Cu(I) ions, although activities for laccase substrates such as 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid), p-phenylenediamine, and 2,6-dimethoxyphenol increased due to changes in the access of these organic substrates to the type I Cu site. The present engineering of CueO indicates that the methionine-rich alpha-helices function as a barrier to the access of bulky organic substrates, which provides CueO with specificity as a cuprous oxidase.
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Affiliation(s)
- Kunishige Kataoka
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa 920-1192, Japan
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Abstract
A quantitative measure of the degree of folding of azurins and pseudoazurins has been made. We have found that the reduction potential of azurins and pseudoazurins is a function of the contribution to the degree of folding of His117, a key amino acid in electron transfer which is directly bonded to copper in these proteins. The folding degree of His117 explains 95% of the variance in the experimental values of the reduction potential of azurins and pseudoazurins. The change in the folding degree of this amino acid influences several geometric parameters of the main backbones of these proteins. Among them, the angle formed between N(His117)...Cu...S(Cys112), which plays an important role in electron transport, but not the N(His117)...Cu distance, shows some non-linear correlation with the reduction potential of azurins and pseudoazurins. However, it is only able to explain less than 75% in the variance of the reduction potential of these proteins instead of the 95% explained by the folding degree of His117.
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Affiliation(s)
- Ernesto Estrada
- Complex Systems Research Group, X-Ray Unit, Edificio CACTUS, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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Dennison C. Ligand and loop variations at type 1 copper sites: influence on structure and reactivity. Dalton Trans 2005:3436-42. [PMID: 16234922 DOI: 10.1039/b507440c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Type 1 (T1) copper sites promote biological electron transfer and are found in the cupredoxins and a number of copper-containing enzymes including the multi-copper oxidases. A T1 copper site usually has a distorted tetrahedral geometry with strong ligands provided by the thiolate sulfur of a Cys and the imidazole nitrogens of two His residues. The active site structure is typically completed by a weak axial Met ligand (a second weak axial interaction is found in azurin resulting in a trigonal bipyramidal geometry). The axial Met is not conserved and Gln, Phe, Leu and Val are also found in this position. Three of the four ligands at a T1 copper site are situated on a single C-terminal loop whose length and structure varies. Studies are discussed which investigate both the influence of physiologically relevant axial ligand alterations, and also of mutations to the length and structure of the ligand-containing loop, on the properties of T1 copper sites.
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Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne, UK NE2 4HH.
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Sato K, Crowley PB, Dennison C. Transient homodimer interactions studied using the electron self-exchange reaction. J Biol Chem 2005; 280:19281-8. [PMID: 15743773 DOI: 10.1074/jbc.m500842200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transient homodimer protein interactions have been investigated by analyzing the influence of ionic strength (NaCl) on the electron self-exchange (the bimolecular reaction whereby the two oxidation states of a redox protein interconvert) rate constant (k(ese)) of four plastocyanins. The k(ese) values for the plastocyanins from spinach, Dryopteris crassirhizoma (a fern), and the green alga Ulva pertusa, which possess acidic patches of varying size and locations, increase 190-, 29-, and 21-fold, respectively, at elevated ionic strength (I = 2.03 M). In contrast, the k(ese) for the almost neutral cyanobacterial plastocyanin from Anabaena variabilis exhibits very little dependence on ionic strength. The temperature dependence of the k(ese) for spinach plastocyanin (I = 0.28 M) provides evidence for poor packing at the homodimer interface. Representative structures of the transient homodimers involved in electron self-exchange, which are consistent with fits of the ionic strength dependence of k(ese) to van Leeuwen theory, have been obtained from protein modeling and docking simulations. The Coulombic energy of the docked homodimers follows the order spinach > D. crassirhizoma > U. pertusa > A. variabilis, which matches that of the overall influence of ionic strength on k(ese). Analysis of the homodimer structures indicates that poor packing and high planarity are features of the interface that favor transient interactions. The physiologically relevant Mg2+ ion has a much more pronounced influence on the k(ese) of spinach plastocyanin, which along with the known properties of the thylakoid lumen suggests a biological role for electron self-exchange.
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Affiliation(s)
- Katsuko Sato
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, United Kingdom
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Harrison MD, Dennison C. Characterization of Arabidopsis thaliana stellacyanin: A comparison with umecyanin. Proteins 2004; 55:426-35. [PMID: 15048833 DOI: 10.1002/prot.20017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cupredoxin domain of a putative type 1 blue copper protein (BCB) from Arabidopsis thaliana was overexpressed and purified. A recursive polymerase chain reaction method was used to synthesize an artificial coding region for the cupredoxin domain of horseradish stellacyanin (commonly known as umecyanin), prior to overexpression and purification. The recombinant proteins were refolded from inclusion bodies and reconstituted with copper, and their in vitro characteristics were studied. Recombinant umecyanin, which is nonglycosylated, has identical spectroscopic and redox properties to the native protein. The UV/Vis and EPR spectra of recombinant BCB and umecyanin demonstrate that they have comparable axial type 1 copper binding sites. Paramagnetic (1)H NMR spectroscopy highlights the similarity between the active site architectures of BCB and umecyanin. The reduction potential of recombinant BCB is 252 mV, compared to 293 mV for recombinant umecyanin. Identical pK(a) values of 9.7 are obtained for the alkaline transitions in both proteins. This study demonstrates that BCB is the A. thaliana stellacyanin and the results form the biochemical basis for a discussion of BCB function in the model vascular plant.
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Affiliation(s)
- Mark D Harrison
- School of Natural Sciences, University of Newcastle upon Tyne, Newcastle upon Tyne, United Kingdom
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Nakamura K, Kawabata T, Yura K, Go N. Novel types of two-domain multi-copper oxidases: possible missing links in the evolution. FEBS Lett 2003; 553:239-44. [PMID: 14572631 DOI: 10.1016/s0014-5793(03)01000-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
An analysis of the genome sequence database revealed novel types of two-domain multi-copper oxidases. The two-domain proteins have the conspicuous combination of blue-copper and inter-domain trinuclear copper binding residues, which is common in ceruloplasmin and ascorbate oxidase but not in nitrite reductase, and therefore are considered to retain the characteristics of the plausible ancestral form of ceruloplasmin and ascorbate oxidase. A possible evolutionary relationship of these proteins is proposed.
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Affiliation(s)
- Kensuke Nakamura
- Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, 630-0101 Nara, Japan.
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