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Chen S, Ding G, Wang Z, Cai H, Xu F. Proteomic and comparative genomic analysis reveals adaptability of Brassica napus to phosphorus-deficient stress. J Proteomics 2015; 117:106-19. [PMID: 25644742 DOI: 10.1016/j.jprot.2015.01.012] [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: 09/11/2014] [Revised: 01/11/2015] [Accepted: 01/20/2015] [Indexed: 10/24/2022]
Abstract
UNLABELLED Given low solubility and immobility in many soils of the world, phosphorus (P) may be the most widely studied macronutrient for plants. In an attempt to gain an insight into the adaptability of Brassica napus to P deficiency, proteome alterations of roots and leaves in two B. napus contrasting genotypes, P-efficient 'Eyou Changjia' and P-inefficient 'B104-2', under long-term low P stress and short-term P-free starvation conditions were investigated, and proteomic combined with comparative genomic analyses were conducted to interpret the interrelation of differential abundance protein species (DAPs) responding to P deficiency with quantitative trait loci (QTLs) for P deficiency tolerance. P-efficient 'Eyou Changjia' had higher dry weight and P content, and showed high tolerance to low P stress compared with P-inefficient 'B104-2'. A total of 146 DAPs were successfully identified by MALDI TOF/TOF MS, which were categorized into several groups including defense and stress response, carbohydrate and energy metabolism, signaling and regulation, amino acid and fatty acid metabolism, protein process, biogenesis and cellular component, and function unknown. 94 of 146 DAPs were mapped to a linkage map constructed by a B. napus population derived from a cross between the two genotypes, and 72 DAPs were located in the confidence intervals of QTLs for P efficiency related traits. We conclude that the identification of these DAPs and the co-location of DAPs with QTLs in the B. napus linkage genetic map provide us novel information in understanding the adaptability of B. napus to P deficiency, and helpful to isolate P-efficient genes in B. napus. BIOLOGICAL SIGNIFICANCE Low P seriously limits the production and quality of B. napus. Proteomics and genetic linkage map were widely used to study the adaptive strategies of B. napus response to P deficiency, proteomic combined with comparative genetic analysis to investigate the correlations between DAPs and QTLs are scarce. Thus, we herein investigated proteome alteration of the roots and leaves in two B. napus genotypes, with different P-deficient tolerances, in response to long-term low P stress and short-term P-free starvation by 2-DE. And comparative genomic was conducted to map the DAPs to the linkage map of B. napus by sequence alignment. The present study offers new insights into adaptability mechanism of B. napus to P deficiency and provides novel information in map-based cloning to isolate the genes in B. napus and scientific improvement of P-efficient in practice.
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Affiliation(s)
- Shuisen Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenhua Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongmei Cai
- Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Center, Huazhong Agricultural University, Wuhan 430070, China.
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Bazhulina NP, Surovaya AN, Gursky YG, Andronova VL, Moiseeva ED, Nikitin CACM, Golovkin MV, Galegov GА, Grokhovsky SL, Gursky GV. Complex of the herpes simplex virus type 1 origin binding protein UL9 with DNA as a platform for the design of a new type of antiviral drugs. J Biomol Struct Dyn 2013; 32:1456-73. [PMID: 23879454 PMCID: PMC4066892 DOI: 10.1080/07391102.2013.820110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The herpes simplex virus type 1 origin-binding protein, OBP, is a DNA helicase encoded by the UL9 gene. The protein binds in a sequence-specific manner to the viral origins of replication, two OriS sites and one OriL site. In order to search for efficient inhibitors of the OBP activity, we have obtained a recombinant origin-binding protein expressed in Escherichia coli cells. The UL9 gene has been amplified by PCR and inserted into a modified plasmid pET14 between NdeI and KpnI sites. The recombinant protein binds to Box I and Box II sequences and possesses helicase and ATPase activities. In the presence of ATP and viral protein ICP8 (single-strand DNA-binding protein), the initiator protein induces unwinding of the minimal OriS duplex (≈80 bp). The protein also binds to a single-stranded DNA (OriS*) containing a stable Box I-Box III hairpin and an unstable AT-rich hairpin at the 3'-end. In the present work, new minor groove binding ligands have been synthesized which are capable to inhibit the development of virus-induced cytopathic effect in cultured Vero cells. Studies on binding of these compounds to DNA and synthetic oligonucleotides have been performed by fluorescence methods, gel mobility shift analysis and footprinting assays. Footprinting studies have revealed that Pt-bis-netropsin and related molecules exhibit preferences for binding to the AT-spacer in OriS. The drugs stabilize structure of the AT-rich region and inhibit the fluctuation opening of AT-base pairs which is a prerequisite to unwinding of DNA by OBP. Kinetics of ATP-dependent unwinding of OriS in the presence and absence of netropsin derivatives have been studied by measuring the efficiency of Forster resonance energy transfer (FRET) between fluorophores attached to 5'- and 3'- ends of an oligonucleotide in the minimal OriS duplex. The results are consistent with the suggestion that OBP is the DNA Holiday junction (HJ) binding helicase. The protein induces conformation changes (bending and partial melting) of OriS duplexes and stimulates HJ formation in the absence of ATP. The antiviral activity of bis-netropsins is coupled with their ability to inhibit the fluctuation opening of АТ base pairs in the А + Т cluster and their capacity to stabilize the structure of the АТ-rich hairpin in the single-stranded oligonucleotide corresponding to the upper chain in the minimal duplex OriS. The antiviral activities of bis-netropsins in cell culture and their therapeutic effects on HSV1-infected laboratory animals have been studied.
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Affiliation(s)
- N P Bazhulina
- a V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , ul. Vavilova 32, 119991 , Moscow , Russia
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Li D, Zhu H, Liu K, Liu X, Leggewie G, Udvardi M, Wang D. Purple acid phosphatases of Arabidopsis thaliana. Comparative analysis and differential regulation by phosphate deprivation. J Biol Chem 2002; 277:27772-81. [PMID: 12021284 DOI: 10.1074/jbc.m204183200] [Citation(s) in RCA: 170] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Purple acid phosphatases (PAPs) are members of the metallo-phosphoesterase family. They are characterized by the presence of seven conserved amino acid residues involved in coordinating the dimetal nuclear center in their reactive site. We compared the 29 PAPs predicted for Arabidopsis thaliana in their varieties of potential metal-ligating residues. Although 24 members possessed sets of metal-ligating residues typical of known PAPs, 1 member lacked four of the seven residues. For the remaining four members, potential metal-ligating residues were generally more similar to those in metal-dependent exonucleases and related proteins. Evidence was obtained for the expression of the majority of the 29 PAPs. To facilitate future investigations, a scheme for naming Arabidopsis PAPs and a system for classifying the 29 PAPs are proposed. The cDNA sequences and the responses to phosphate deprivation of seven Arabidopsis PAPs (AtPAP7-AtPAP13) were characterized. For some AtPAPs analyzed, there were fully processed transcripts as well as splice variants. The splice variants of AtPAP10 were found to associate with polyribosomes and may be translated into a NH(2)-terminal truncated protein. Phylogenetic investigations showed that AtPAPs 7 and 8, together with similar enzymes from other plant species, formed the low molecular weight plant PAP group. Members of this group were more closely related to PAPs from mammalian cells. AtPAPs 9-13, together with kidney bean PAP, formed the high molecular weight PAP group. In phosphate deprivation experiments, gene transcription of AtPAP11 and AtPAP12 was induced and increased, respectively, whereas that of the remaining five AtPAPs was not affected by phosphate deprivation. The present work demonstrates that structure variation and expression regulation of plant PAPs are more complex than previously described and provides a framework for comprehensive molecular genetic and biochemical studies of all Arabidopsis PAPs in the future.
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Affiliation(s)
- Dongping Li
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Poirier Y, Bucher M. Phosphate transport and homeostasis in Arabidopsis. THE ARABIDOPSIS BOOK 2002; 1:e0024. [PMID: 22303200 PMCID: PMC3243343 DOI: 10.1199/tab.0024] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Affiliation(s)
- Yves Poirier
- Institute of Ecology, Laboratory of Plant Biotechnology, University of Lausanne, CH-1015 Lausanne, Switzerland, Fax, 41 21 692 4195;
| | - Marcel Bucher
- Federal Institute of Technology (ETH) Zurich, Biology Department, Institute of Plant Sciences, Plant Biochemistry & Physiology Group, Experimental Station Eschikon 33, CH-8315 Lindau, Switzerland, Fax, 41 52 354 9219;
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Miller SS, Liu J, Allan DL, Menzhuber CJ, Fedorova M, Vance CP. Molecular control of acid phosphatase secretion into the rhizosphere of proteoid roots from phosphorus-stressed white lupin. PLANT PHYSIOLOGY 2001; 127:594-606. [PMID: 11598233 DOI: 10.1104/pp.010097] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
White lupin (Lupinus albus) grown under P deficiency displays a suite of highly coordinated adaptive responses. Included among these is secretion of copious amounts of acid phosphatase (APase). Although numerous reports document that plants secrete APases in response to P deficiency, little is known of the biochemical and molecular events involved in this process. Here we characterize the secreted APase protein, cDNA, and gene from white lupin. The secreted APase enzyme is a glycoprotein with broad substrate specificity. It is synthesized as a preprotein with a deduced M(r) of 52,000 containing a 31-amino acid presequence. Analysis of the presequence predicts that the protein is targeted to outside the cell. The processed protein has a predicted M(r) of 49,000 but migrates as a protein with M(r) of 70,000 on sodium dodecyl sulfate gels. This is likely due to glycosylation. Enhanced expression is fairly specific to proteoid roots of P-stressed plants and involves enhanced synthesis of both enzyme protein and mRNA. Secreted APase appears to be encoded by a single gene containing seven exons interrupted by six introns. The 5'-upstream putative promoter of the white lupin-secreted APase contains a 50-base pair region having 72% identity to an Arabidopsis APase promoter that is responsive to P deficiency. The white lupin-secreted APase promoter and targeting sequence may be useful tools for genetically engineering important proteins from plant roots.
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Affiliation(s)
- S S Miller
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, 55108, USA.
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Abstract
We introduce the use of Arabidopsis thaliana callus culture as a system for proteomic analysis of plant organelles using liquid-grown callus. This callus is relatively homogeneous, reproducible and cytoplasmically rich, and provides organelles in sufficient quantities for proteomic studies. A database was generated of mitochondrial, endoplasmic reticulum (ER), Golgi/prevacuolar compartment and plasma membrane (PM) markers using two-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis (2-D SDS-PAGE) and peptide sequencing or mass spectrometric methods. The major callus membrane-associated proteins were characterised as being integral or peripheral by Triton X-114 phase partitioning. The database was used to define specific proteins at the Arabidopsis callus plasma membrane. This database of organelle proteins provides the basis for future characterisation of the expression and localisation of novel plant proteins.
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Affiliation(s)
- T A Prime
- Department of Biochemistry, Cambridge, UK
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Abstract
Phosphorus is one of the major plant nutrients that is least available in the soil. Consequently, plants have developed numerous morphological, physiological, biochemical, and molecular adaptations to acquire phosphate (Pi). Enhanced ability to acquire Pi and altered gene expression are the hallmarks of plant adaptation to Pi deficiency. The intricate mechanisms involved in maintaining Pi homeostasis reflect the complexity of Pi acquisition and translocation in plants. Recent discoveries of multiple Pi transporters have opened up opportunities to study the molecular basis of Pi acquisition by plants. An increasing number of genes are now known to be activated under Pi starvation. Some of these genes may be involved in Pi acquisition, transfer, and signal transduction during Pi stress. This review provides an overview of plant adaptations leading to enhanced Pi acquisition, with special emphasis on recent developments in the molecular biology of Pi acquisition.
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Affiliation(s)
- K. G. Raghothama
- Department of Horticulture, Purdue University, West Lafayette, Indiana 47907; e-mail:
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Du X, Mullins JT. Glucan 1,3-β-glucosidase activities of Achlya bisexualis:synthesis and properties. Mycologia 1999. [DOI: 10.1080/00275514.1999.12061026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Xin Du
- Department of Botany, P.O. Box 118526, University of Florida, Gainesville, Florida 32611-8526
| | - J. Thomas Mullins
- Department of Botany, P.O. Box 118526, University of Florida, Gainesville, Florida 32611-8526
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Abstract
Previously we identified Mt4, a phosphate starvation inducible cDNA from Medicago truncatula which is down-regulated in roots in response to phosphate fertilization as well as colonization by arbuscular mycorrhizal (AM) fungi (AM). Here we present further studies of Mt4. Expression was highly sensitive to exogenous applications of phosphate fertilizer; transcripts were abundant in roots fertilized with nutrient solution lacking phosphate, reduced when fertilized with 0.02 or 0.1 mM phosphate and undetectable when fertilized with 1 or 5 mM phosphate. A time course experiment, to study the expression of Mt4 following colonization by AM fungi, revealed that Mt4 transcripts increased in uncolonized roots during the first three weeks of growth and then plateaued, while transcript levels in roots colonized with the AM fungus, Glomas versiforme, increased transiently and then decreased. Although the Mt4 gene is expressed exclusively in roots, transcripts were also detected in M. truncatula cell suspension cultures following phosphate starvation. A genomic clone containing the Mt4 gene and 1133 bp of the 5' flanking sequence was identified from a M. truncatula genomic library. The promoter region contains a conserved cis-element found in the promoters of phosphate starvation inducible genes of yeast and tomato. As Mt4 is the first cDNA reported to show independent regulation by both phosphate and mycorrhizal fungi, the genomic clone may provide a starting point from which to analyze the signal transduction pathways involved in these two processes.
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Affiliation(s)
- S M Burleigh
- The Samuel Roberts Noble Foundation, Plant Biology Division, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, USA
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