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Santamaria L, Pajak A, House JD, Marsolais F. Identification and Characterization of a Pepsin- and Chymotrypsin-Resistant Peptide in the α Subunit of the 11S Globulin Legumin from Common Bean ( Phaseolus vulgaris L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14844-14850. [PMID: 38885440 PMCID: PMC11228969 DOI: 10.1021/acs.jafc.3c08744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/01/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024]
Abstract
The 11S globulin legumin typically accounts for approximately 3% of the total protein in common beans (Phaseolus vulgaris). It was previously reported that a legumin peptide of approximately 20 kDa is resistant to pepsin digestion. Sequence prediction suggested that the pepsin-resistant peptide is located at the C-terminal end of the α-subunit, within a glutamic acid-rich domain, overlapping with a chymotrypsin-resistant peptide. Using purified legumin, the peptide of approximately 20 kDa was found to be resistant to pepsin digestion in a pH-dependent manner, and its location was determined by two-dimensional gel electrophoresis and LC-MS-MS. The location of the chymotrypsin-resistant peptide was confirmed by immunoblotting with peptide-specific polyclonal antibodies. The presence of a consensus site for proline hydroxylation and arabinosylation, the detection of hydroxyproline residues, purification by lectin affinity chromatography, and a difference in electrophoretic migration between the chymotrypsin- and pepsin-resistant peptides suggest the presence of a large O-glycan within these peptides.
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Affiliation(s)
- Liliana Santamaria
- Genomics
and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3, Canada
| | - Aga Pajak
- Genomics
and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3, Canada
| | - James D. House
- Department
of Food and Human Nutritional Sciences, Faculty of Agricultural and
Food Sciences, University of Manitoba, 204 Richardson Centre, 196 Innovation
Drive, Winnipeg, Manitoba R3T 2N2, Canada
| | - Frédéric Marsolais
- Genomics
and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3, Canada
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Devi V, Bhushan B, Gupta M, Sethi M, Kaur C, Singh A, Singh V, Kumar R, Rakshit S, Chaudhary DP. Genetic and molecular understanding for the development of methionine-rich maize: a holistic approach. FRONTIERS IN PLANT SCIENCE 2023; 14:1249230. [PMID: 37794928 PMCID: PMC10546030 DOI: 10.3389/fpls.2023.1249230] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/01/2023] [Indexed: 10/06/2023]
Abstract
Maize (Zea mays) is the most important coarse cereal utilized as a major energy source for animal feed and humans. However, maize grains are deficient in methionine, an essential amino acid required for proper growth and development. Synthetic methionine has been used in animal feed, which is costlier and leads to adverse health effects on end-users. Bio-fortification of maize for methionine is, therefore, the most sustainable and environmental friendly approach. The zein proteins are responsible for methionine deposition in the form of δ-zein, which are major seed storage proteins of maize kernel. The present review summarizes various aspects of methionine including its importance and requirement for different subjects, its role in animal growth and performance, regulation of methionine content in maize and its utilization in human food. This review gives insight into improvement strategies including the selection of natural high-methionine mutants, molecular modulation of maize seed storage proteins and target key enzymes for sulphur metabolism and its flux towards the methionine synthesis, expression of synthetic genes, modifying gene codon and promoters employing genetic engineering approaches to enhance its expression. The compiled information on methionine and essential amino acids linked Quantitative Trait Loci in maize and orthologs cereals will give insight into the hotspot-linked genomic regions across the diverse range of maize germplasm through meta-QTL studies. The detailed information about candidate genes will provide the opportunity to target specific regions for gene editing to enhance methionine content in maize. Overall, this review will be helpful for researchers to design appropriate strategies to develop high-methionine maize.
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Affiliation(s)
- Veena Devi
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Bharat Bhushan
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Mamta Gupta
- Division of Biotechnology, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Mehak Sethi
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Charanjeet Kaur
- Department of Biochemistry, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Alla Singh
- Division of Biotechnology, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Vishal Singh
- Division of Plant Breeding, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Ramesh Kumar
- Division of Plant Breeding, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Sujay Rakshit
- Division of Plant Breeding, Indian Institute of Maize Research, Ludhiana, Punjab, India
| | - Dharam P. Chaudhary
- Division of Biochemistry, Indian Institute of Maize Research, Ludhiana, Punjab, India
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Zhang Y, Wang Q, Liu Y, Dong S, Zhang Y, Zhu Y, Tian Y, Li J, Wang Z, Wang Y, Yan F. Overexpressing GmCGS2 Improves Total Amino Acid and Protein Content in Soybean Seed. Int J Mol Sci 2023; 24:14125. [PMID: 37762432 PMCID: PMC10532240 DOI: 10.3390/ijms241814125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Soybean (Glycine max (L.) Merr.) is an important source of plant protein, the nutritional quality of which is considerably affected by the content of the sulfur-containing amino acid, methionine (Met). To improve the quality of soybean protein and increase the Met content in seeds, soybean cystathionine γ-synthase 2 (GmCGS2), the first unique enzyme in Met biosynthesis, was overexpressed in the soybean cultivar "Jack", producing three transgenic lines (OE3, OE4, and OE10). We detected a considerable increase in the content of free Met and other free amino acids in the developing seeds of the three transgenic lines at the 15th and 75th days after flowering (15D and 75D). In addition, transcriptome analysis showed that the expression of genes related to Met biosynthesis from the aspartate-family pathway and S-methyl Met cycle was promoted in developing green seeds of OE10. Ultimately, the accumulation of total amino acids and soluble proteins in transgenic mature seeds was promoted. Altogether, these results indicated that GmCGS2 plays an important role in Met biosynthesis, by providing a basis for improving the nutritional quality of soybean seeds.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Fan Yan
- Correspondence: (Y.W.); (F.Y.)
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Joshi J, Renaud JB, Sumarah MW, Marsolais F. Deciphering S-methylcysteine biosynthesis in common bean by isotopic tracking with mass spectrometry. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:176-186. [PMID: 31215701 DOI: 10.1111/tpj.14438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/22/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
The suboptimal content of sulfur-containing amino acids methionine and cysteine prevents common bean (Phaseolus vulgaris) from being an excellent source of protein. Nutritional improvements to this significant crop require a better understanding of the biosynthesis of sulfur-containing compounds including the nonproteogenic amino acid S-methylcysteine and the dipeptide γ-glutamyl-S-methylcysteine, which accumulate in seed. In this study, seeds were incubated with isotopically labelled serine, cysteine or methionine and analyzed by reverse phase chromatography-high resolution mass spectrometry to track stable isotopes as they progressed through the sulfur metabolome. We determined that serine and methionine are the sole precursors of free S-methylcysteine in developing seeds, indicating that this compound is likely to be synthesized through the condensation of O-acetylserine and methanethiol. BSAS4;1, a cytosolic β-substituted alanine synthase preferentially expressed in developing seeds, catalyzed the formation of S-methylcysteine in vitro. A higher flux of labelled serine or cysteine was observed in a sequential pathway involving γ-glutamyl-cysteine, homoglutathione and S-methylhomoglutathione, a likely precursor to γ-glutamyl-S-methylcysteine. Preferential incorporation of serine over cysteine supports a subcellular compartmentation of this pathway, likely to be in the chloroplast. The origin of the methyl group in S-methylhomoglutathione was traced to methionine. There was substantial incorporation of carbons from methionine into the β-alanine portion of homoglutathione and S-methylhomoglutathione, suggesting the breakdown of methionine by methionine γ-lyase and conversion of α-ketobutyrate to β-alanine via propanoate metabolism. These findings delineate the biosynthetic pathways of the sulfur metabolome of common bean and provide an insight that will aid future efforts to improve nutritional quality.
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Affiliation(s)
- Jaya Joshi
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario, N6A 3K7, Canada
| | - Justin B Renaud
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Mark W Sumarah
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
| | - Frédéric Marsolais
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario, N6A 3K7, Canada
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Joshi J, Saboori-Robat E, Solouki M, Mohsenpour M, Marsolais F. Distribution and possible biosynthetic pathway of non-protein sulfur amino acids in legumes. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4115-4121. [PMID: 31231767 DOI: 10.1093/jxb/erz291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/12/2019] [Indexed: 06/09/2023]
Abstract
Some grain legumes store sulfur in the form of non-protein amino acids in seed. γ-Glutamyl-S-methylcysteine is found in Phaseolus and several Vigna species. γ-Glutamyl-S-ethenylcysteine, an antinutritional compound, is present in Vicia narbonensis. In P. vulgaris, free S-methylcysteine levels are higher at early stages of seed development followed by a decline. γ-Glutamyl-S-methylcysteine accumulates later, in two phases, with a lag during reserve accumulation. The concentration of total S-methylcysteine, quantified after acid hydrolysis, is positively regulated by sulfate nutrition. The levels of both γ-glutamyl-S-methylcysteine and γ-glutamyl-S-ethenylcysteine are modulated in response to changes in seed protein composition. A model is proposed whereby the majority of γ-glutamyl-S-methylcysteine in P. vulgaris is synthesized via the intermediate S-methylhomoglutathione. Knowledge of the biosynthesis of non-protein sulfur amino acids is required for metabolic engineering approaches, in conjunction with manipulation of the protein sink, to increase the concentration of nutritionally essential methionine and cysteine. This would improve protein quality of some important legume crops.
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Affiliation(s)
- Jaya Joshi
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Elham Saboori-Robat
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mahmood Solouki
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Motahhareh Mohsenpour
- Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREO), Karaj, Iran
| | - Frédéric Marsolais
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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Amir R, Cohen H, Hacham Y. Revisiting the attempts to fortify methionine content in plant seeds. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4105-4114. [PMID: 30911752 DOI: 10.1093/jxb/erz134] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
The sulfur-containing amino acid methionine belongs to the group of essential amino acids, meaning that humans and animals must consume it in their diets. However, plant seeds have low levels of methionine, limiting their nutritional potential. For this reason, efforts have been made over the years to increase methionine levels in seeds. Here, we summarize these efforts and focus particularly on those utilizing diverse genetic and molecular tools. Four main approaches are described: (i) expression of methionine-rich storage proteins in a seed-specific manner to incorporate more soluble methionine into the protein fraction; (ii) reduction of methionine-poor storage proteins inside the seeds to reinforce the accumulation of methionine-rich proteins; (iii) silencing methionine catabolic enzymes; and (iv) up-regulation of key biosynthetic enzymes participating in methionine synthesis. We focus on the biosynthetic genes that operate de novo in seeds and that belong to the sulfur assimilation and aspartate family pathways, as well as genes from the methionine-specific pathway. We also include those enzymes that operate in non-seed tissues that contribute to the accumulation of methionine in seeds, such as S-methylmethionine enzymes. Finally, we discuss the biotechnological potential of these manipulations to increase methionine content in plant seeds and their effect on seed germination.
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Affiliation(s)
- Rachel Amir
- Laboratory of Plant Science, Migal - Galilee Technology Center, Kiryat Shmona, Israel
- Tel-Hai College, Upper Galilee, Israel
| | - Hagai Cohen
- Department of Plant & Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Hacham
- Laboratory of Plant Science, Migal - Galilee Technology Center, Kiryat Shmona, Israel
- Tel-Hai College, Upper Galilee, Israel
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Common Bean ( Phaseolus vulgaris L.) Accumulates Most S-Methylcysteine as Its γ-Glutamyl Dipeptide. PLANTS 2019; 8:plants8050126. [PMID: 31091711 PMCID: PMC6572574 DOI: 10.3390/plants8050126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/01/2019] [Accepted: 05/12/2019] [Indexed: 02/07/2023]
Abstract
The common bean (Phaseolus vulgaris) constitutes an excellent source of vegetable dietary protein. However, there are sub-optimal levels of the essential amino acids, methionine and cysteine. On the other hand, P. vulgaris accumulates large amounts of the γ-glutamyl dipeptide of S-methylcysteine, and lower levels of free S-methylcysteine and S-methylhomoglutathione. Past results suggest two distinct metabolite pools. Free S-methylcysteine levels are high at the beginning of seed development and decline at mid-maturation, while there is a biphasic accumulation of γ-glutamyl-S-methylcysteine, at early cotyledon and maturation stages. A possible model involves the formation of S-methylcysteine by cysteine synthase from O-acetylserine and methanethiol, whereas the majority of γ-glutamyl-S-methylcysteine may arise from S-methylhomoglutathione. Metabolite profiling during development and in genotypes differing in total S-methylcysteine accumulation showed that γ-glutamyl-S-methylcysteine accounts for most of the total S-methylcysteine in mature seed. Profiling of transcripts for candidate biosynthetic genes indicated that BSAS4;1 expression is correlated with both the developmental timing and levels of free S-methylcysteine accumulated, while homoglutathione synthetase (hGS) expression was correlated with the levels of γ-glutamyl-S-methylcysteine. Analysis of S-methylated phytochelatins by liquid chromatography and high resolution tandem mass spectrometry revealed only small amounts of homophytochelatin-2 with a single S-methylcysteine. The mitochondrial localization of phytochelatin synthase 2—predominant in seed, determined by confocal microscopy of a fusion with the yellow fluorescent protein—and its spatial separation from S-methylhomoglutathione may explain the lack of significant accumulation of S-methylated phytochelatins.
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8
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Duwadi K, Austin RS, Mainali HR, Bett K, Marsolais F, Dhaubhadel S. Slow darkening of pinto bean seed coat is associated with significant metabolite and transcript differences related to proanthocyanidin biosynthesis. BMC Genomics 2018; 19:260. [PMID: 29661146 PMCID: PMC5903001 DOI: 10.1186/s12864-018-4550-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/14/2018] [Indexed: 11/29/2022] Open
Abstract
Background Postharvest seed coat darkening in pinto bean is an undesirable trait resulting in a loss in the economic value of the crop. The extent of darkening varies between the bean cultivars and their storage conditions. Results Metabolite analysis revealed that the majority of flavonoids including proanthocyanidin monomer catechin accumulated at higher level in a regular darkening (RD) pinto line CDC Pintium than in a slow darkening (SD) line 1533–15. A transcriptome analysis was conducted to compare gene expression between CDC Pintium and 1533–15 and identify the gene (s) that may play a role in slow darkening processes in 1533–15 pinto. RNAseq against total RNA from RD and SD cultivars found several phenylpropanoid genes, metabolite transporter genes and genes involved in gene regulation or modification to be differentially expressed between CDC Pintium and 1533–15. Conclusion RNAseq analysis and metabolite data of seed coat tissue from CDC Pintium and 1533–15 revealed that the whole proanthocyanidin biosynthetic pathway was downregulated in 1533–15. Additionally, genes that encode for putative transporter proteins were also downregulated in 1533–15 suggesting both synthesis and accumulation of proanthocyanidin is reduced in SD pintos. Electronic supplementary material The online version of this article (10.1186/s12864-018-4550-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kishor Duwadi
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Ryan S Austin
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.,Department of Biology, University of Western Ontario, London, ON, Canada
| | - Hemanta R Mainali
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kirstin Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada.,Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON, N5V 4T3, Canada. .,Department of Biology, University of Western Ontario, London, ON, Canada.
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Rossi GB, Valentim-Neto PA, Blank M, Faria JCD, Arisi ACM. Comparison of Grain Proteome Profiles of Four Brazilian Common Bean (Phaseolus vulgaris L.) Cultivars. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:7588-7597. [PMID: 28777559 DOI: 10.1021/acs.jafc.7b03220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is a source of proteins for about one billion people worldwide. In Brazil, 'BRS Sublime', 'BRS Vereda', 'BRS Esteio', and 'BRS Estilo' cultivars were developed by Embrapa to offer high yield to farmers and excellent quality to final consumers. In this work, grain proteomes of these common bean cultivars were compared based on two-dimensional gel electrophoresis (2-DE) and tandem mass spectrometry (MS/MS). Principal component analysis (PCA) was applied to compare 349 matched spots in these cultivars proteomes, and all cultivars were clearly separated in PCA plot. Thirty-two differentially accumulated proteins were identified by MS. Storage proteins such as phaseolins, legumins, and lectins were the most abundant, and novel proteins were also identified. We have built a useful platform that could be used to analyze other Brazilian cultivars and genotypes of common beans.
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Affiliation(s)
| | | | | | - Josias Correa de Faria
- Embrapa Arroz e Feijão, Caixa Postal 179, 75375-000 Santo Antônio de Goiás, Goiás, Brazil
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Combining Isotope Labelling with High Resolution Liquid Chromatography-Tandem Mass Spectrometry to Study Sulfur Amino Acid Metabolism in Seeds of Common Bean (Phaseolus vulgaris). ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-56526-2_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Joshi J, Pandurangan S, Diapari M, Marsolais F. Comparison of Gene Families: Seed Storage and Other Seed Proteins. THE COMMON BEAN GENOME 2017. [DOI: 10.1007/978-3-319-63526-2_10] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Galdino Alves NE, Gonzalez de Mejía E, Mileib Vasconcelos C, Zaczuk Bassinello P, Duarte Martino HS. Postharvest storage of Carioca bean ( Phaseolus vulgaris L.) did not impair inhibition of inflammation in lipopolysaccharide-induced human THP-1 macrophage-like cells. J Funct Foods 2016. [DOI: 10.1016/j.jff.2016.02.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Karaki L, Da Silva P, Rizk F, Chouabe C, Chantret N, Eyraud V, Gressent F, Sivignon C, Rahioui I, Kahn D, Brochier-Armanet C, Rahbé Y, Royer C. Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. BMC PLANT BIOLOGY 2016; 16:63. [PMID: 26964738 PMCID: PMC4785745 DOI: 10.1186/s12870-016-0745-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/25/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Albumin 1b peptides (A1b) are small disulfide-knotted insecticidal peptides produced by Fabaceae (also called Leguminosae). To date, their diversity among this plant family has been essentially investigated through biochemical and PCR-based approaches. The availability of high-quality genomic resources for several fabaceae species, among which the model species Medicago truncatula (Mtr), allowed for a genomic analysis of this protein family aimed at i) deciphering the evolutionary history of A1b proteins and their links with A1b-nodulins that are short non-insecticidal disulfide-bonded peptides involved in root nodule signaling and ii) exploring the functional diversity of A1b for novel bioactive molecules. RESULTS Investigating the Mtr genome revealed a remarkable expansion, mainly through tandem duplications, of albumin1 (A1) genes, retaining nearly all of the same canonical structure at both gene and protein levels. Phylogenetic analysis revealed that the ancestral molecule was most probably insecticidal giving rise to, among others, A1b-nodulins. Expression meta-analysis revealed that many A1b coding genes are silent and a wide tissue distribution of the A1 transcripts/peptides within plant organs. Evolutionary rate analyses highlighted branches and sites with positive selection signatures, including two sites shown to be critical for insecticidal activity. Seven peptides were chemically synthesized and folded in vitro, then assayed for their biological activity. Among these, AG41 (aka MtrA1013 isoform, encoded by the orphan TA24778 contig.), showed an unexpectedly high insecticidal activity. The study highlights the unique burst of diversity of A1 peptides within the Medicago genus compared to the other taxa for which full-genomes are available: no A1 member in Lotus, or in red clover to date, while only a few are present in chick pea, soybean or pigeon pea genomes. CONCLUSION The expansion of the A1 family in the Medicago genus is reminiscent of the situation described for another disulfide-rich peptide family, the "Nodule-specific Cysteine-Rich" (NCR), discovered within the same species. The oldest insecticidal A1b toxin was described from the Sophorae, dating the birth of this seed-defense function to more than 58 million years, and making this model of plant/insect toxin/receptor (A1b/insect v-ATPase) one of the oldest known.
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Affiliation(s)
- L. Karaki
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />ER030-EDST; Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
- />Université de Lyon, F-69000 Lyon, France
| | - P. Da Silva
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - F. Rizk
- />ER030-EDST; Department of Life and Earth Sciences, Faculty of Sciences II, Lebanese University, Beirut, Lebanon
| | - C. Chouabe
- />Université de Lyon, F-69000 Lyon, France
- />UCBL, CarMeN Laboratory, INSERM UMR-1060, Cardioprotection Team, Faculté de Médecine, Univ Lyon-1, Université Claude Bernard Lyon1, 8 Avenue Rockefeller, 69373 Lyon Cedex 08, France
| | - N. Chantret
- />INRA, UMR1334 AGAP, 2 Place Pierre Viala, 34060 Montpellier, France
- />Supagro Montpellier, 2 Place Pierre Viala, 34060 Montpellier, France
| | - V. Eyraud
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - F. Gressent
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - C. Sivignon
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - I. Rahioui
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - D. Kahn
- />Université de Lyon, F-69000 Lyon, France
- />Université Claude Bernard Lyon 1; CNRS; INRA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - C. Brochier-Armanet
- />Université de Lyon, F-69000 Lyon, France
- />Université Claude Bernard Lyon 1; CNRS; INRA; UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, 43 boulevard du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Y. Rahbé
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
| | - C. Royer
- />INRA, UMR0203 BF2I, Biologie Fonctionnelle Insectes et Interactions, F-69621 Villeurbanne, France
- />Insa-Lyon, UMR0203 BF2I, F-69621 Villeurbanne, France
- />Université de Lyon, F-69000 Lyon, France
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14
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Pandurangan S, Diapari M, Yin F, Munholland S, Perry GE, Chapman BP, Huang S, Sparvoli F, Bollini R, Crosby WL, Pauls KP, Marsolais F. Genomic Analysis of Storage Protein Deficiency in Genetically Related Lines of Common Bean (Phaseolus vulgaris). FRONTIERS IN PLANT SCIENCE 2016; 7:389. [PMID: 27066039 PMCID: PMC4814446 DOI: 10.3389/fpls.2016.00389] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/14/2016] [Indexed: 05/06/2023]
Abstract
A series of genetically related lines of common bean (Phaseolus vulgaris L.) integrate a progressive deficiency in major storage proteins, the 7S globulin phaseolin and lectins. SARC1 integrates a lectin-like protein, arcelin-1 from a wild common bean accession. SMARC1N-PN1 is deficient in major lectins, including erythroagglutinating phytohemagglutinin (PHA-E) but not α-amylase inhibitor, and incorporates also a deficiency in phaseolin. SMARC1-PN1 is intermediate and shares the phaseolin deficiency. Sanilac is the parental background. To understand the genomic basis for variations in protein profiles previously determined by proteomics, the genotypes were submitted to short-fragment genome sequencing using an Illumina HiSeq 2000/2500 platform. Reads were aligned to reference sequences and subjected to de novo assembly. The results of the analyses identified polymorphisms responsible for the lack of specific storage proteins, as well as those associated with large differences in storage protein expression. SMARC1N-PN1 lacks the lectin genes pha-E and lec4-B17, and has the pseudogene pdlec1 in place of the functional pha-L gene. While the α-phaseolin gene appears absent, an approximately 20-fold decrease in β-phaseolin accumulation is associated with a single nucleotide polymorphism converting a G-box to an ACGT motif in the proximal promoter. Among residual lectins compensating for storage protein deficiency, mannose lectin FRIL and α-amylase inhibitor 1 genes are uniquely present in SMARC1N-PN1. An approximately 50-fold increase in α-amylase inhibitor like protein accumulation is associated with multiple polymorphisms introducing up to eight potential positive cis-regulatory elements in the proximal promoter specific to SMARC1N-PN1. An approximately 7-fold increase in accumulation of 11S globulin legumin is not associated with variation in proximal promoter sequence, suggesting that the identity of individual proteins involved in proteome rebalancing might also be determined at the translational level.
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Affiliation(s)
- Sudhakar Pandurangan
- Department of Biology, University of Western Ontario, LondonON, Canada
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
| | - Marwan Diapari
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
| | - Fuqiang Yin
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
- Department of Bioscience and Biotechnology, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Seth Munholland
- Department of Biological Sciences, University of Windsor, WindsorON, Canada
| | - Gregory E. Perry
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | - B. Patrick Chapman
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
| | - Shangzhi Huang
- Department of Bioscience and Biotechnology, School of Life Sciences, Sun Yat-sen UniversityGuangzhou, China
| | - Francesca Sparvoli
- Institute of Agricultural Biology and Biotechnology, National Research CouncilMilan, Italy
| | - Roberto Bollini
- Institute of Agricultural Biology and Biotechnology, National Research CouncilMilan, Italy
| | - William L. Crosby
- Department of Biological Sciences, University of Windsor, WindsorON, Canada
| | - Karl P. Pauls
- Department of Plant Agriculture, University of Guelph, GuelphON, Canada
| | - Frédéric Marsolais
- Department of Biology, University of Western Ontario, LondonON, Canada
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, LondonON, Canada
- *Correspondence: Frédéric Marsolais,
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15
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Pandurangan S, Sandercock M, Beyaert R, Conn KL, Hou A, Marsolais F. Differential response to sulfur nutrition of two common bean genotypes differing in storage protein composition. FRONTIERS IN PLANT SCIENCE 2015; 6:92. [PMID: 25750649 PMCID: PMC4335288 DOI: 10.3389/fpls.2015.00092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/04/2015] [Indexed: 05/28/2023]
Abstract
It has been hypothesized that the relatively low concentration of sulfur amino acids in legume seeds might be an ecological adaptation to nutrient poor, marginal soils. SARC1 and SMARC1N-PN1 are genetically related lines of common bean (dry bean, Phaseolus vulgaris) differing in seed storage protein composition. In SMARC1N-PN1, the lack of phaseolin and major lectins is compensated by increased levels of sulfur-rich proteins, resulting in an enhanced concentration of cysteine and methionine, mostly at the expense of the abundant non-protein amino acid, S-methylcysteine. To identify potential effects associated with an increased concentration of sulfur amino acids in the protein pool, the response of the two genotypes to low and high sulfur nutrition was evaluated under controlled conditions. Seed yield was increased by the high sulfate treatment in SMARC1N-PN1. The seed concentrations of sulfur, sulfate, and S-methylcysteine were altered by the sulfur treatment in both genotypes. The concentration of total cysteine and extractible globulins was increased specifically in SMARC1N-PN1. Proteomic analysis identified arcelin-like protein 4, lipoxygenase-3, albumin-2, and alpha amylase inhibitor beta chain as having increased levels under high sulfur conditions. Lipoxygenase-3 accumulation was sensitive to sulfur nutrition only in SMARC1N-PN1. Under field conditions, both SARC1 and SMARC1N-PN1 exhibited a slight increase in yield in response to sulfur treatment, typical for common bean.
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Affiliation(s)
- Sudhakar Pandurangan
- Department of Biology, University of Western OntarioLondon, ON, Canada
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Mark Sandercock
- Cereal Research Centre Morden, Agriculture and Agri-Food CanadaCanada, Morden, MB, Canada
| | - Ronald Beyaert
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Kenneth L. Conn
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Anfu Hou
- Cereal Research Centre Morden, Agriculture and Agri-Food CanadaCanada, Morden, MB, Canada
| | - Frédéric Marsolais
- Department of Biology, University of Western OntarioLondon, ON, Canada
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada
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16
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17
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Parmar N, Virdi AS, Singh N, Kaur A, Bajaj R, Rana JC, Agrawal L, Nautiyal CS. Evaluation of physicochemical, textural, mineral and protein characteristics of kidney bean grown at Himalayan region. Food Res Int 2014. [DOI: 10.1016/j.foodres.2014.08.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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18
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Chan YS, Ng TB. Northeast red beans produce a thermostable and pH-stable defensin-like peptide with potent antifungal activity. Cell Biochem Biophys 2014; 66:637-48. [PMID: 23292358 DOI: 10.1007/s12013-012-9508-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A 5.4-kDa antifungal peptide was purified from Phaseolus vulgaris L. cv. "northeast red bean" using a protocol that entailed affinity chromatography, ion exchange chromatography, and gel filtration. The molecular mass was determined by matrix-assisted laser desorption ionization time-of-flight. The N-terminal amino acid sequence of the peptide was highly homologous to defensins and defensin-like peptides from several plant species. The peptide impeded the growth of a number of pathogenic fungi, including Mycosphaerella arachidicola Khokhr. (IC50 = 1.7 μM), Setosphaeria turcica Luttr., Fusarium oxysporum Schltdl., and Valsa mali Miyabe & G. Yamada. Antifungal activity of the peptide was fully preserved at temperatures up to 100 °C and pH values from 0 to 12. Congo red deposition at the hyphal tip of M. arachidicola was detected after exposure to the peptide, signifying that the peptide had suppressed hyphal growth. The antifungal peptide did not manifest antiproliferative activity toward human breast cancer MCF7 cells and hepatoma HepG2 cells, in contradiction to the bulk of previously reported plant defensins. The data suggest distinct structural requirements for antifungal and antiproliferative activities.
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Affiliation(s)
- Yau Sang Chan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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19
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Liao D, Cram D, Sharpe AG, Marsolais F. Transcriptome Profiling Identifies Candidate Genes Associated with the Accumulation of Distinct Sulfur γ-Glutamyl Dipeptides in Phaseolus vulgaris and Vigna mungo Seeds. FRONTIERS IN PLANT SCIENCE 2013; 4:60. [PMID: 23532826 PMCID: PMC3606967 DOI: 10.3389/fpls.2013.00060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Accepted: 03/04/2013] [Indexed: 05/29/2023]
Abstract
Common bean (Phaseolus vulgaris) and black gram (Vigna mungo) accumulate γ-Glutamyl-S-methylcysteine and γ-Glutamyl-methionine in seed, respectively. Transcripts were profiled by 454 pyrosequencing data at a similar developmental stage coinciding with the beginning of the accumulation of these metabolites. Expressed sequence tags were assembled into Unigenes, which were assigned to specific genes in the early release chromosomal assembly of the P. vulgaris genome. Genes involved in multiple sulfur metabolic processes were expressed in both species. Expression of Sultr3 members was predominant in P. vulgaris, whereas expression of Sultr5 members predominated in V. mungo. Expression of the cytosolic SERAT1;1 and -1;2 was approximately fourfold higher in P. vulgaris while expression of the plastidic SERAT2;1 was twofold higher in V. mungo. Among BSAS family members, BSAS4;1, encoding a cytosolic cysteine desulfhydrase, and BSAS1;1, encoding a cytosolic O-acetylserine sulphydrylase were most highly expressed in both species. This was followed by BSAS3;1 encoding a plastidic β-cyanoalanine synthase which was more highly expressed by 10-fold in P. vulgaris. The data identify BSAS3;1 as a candidate enzyme for the biosynthesis of S-methylcysteine through the use of methanethiol as substrate instead of cyanide. Expression of GLC1 would provide a complete sequence leading to the biosynthesis of γ-Glutamyl-S-methylcysteine in plastids. The detection of S-methylhomoglutathione in P. vulgaris suggested that homoglutathione synthetase may accept, to some extent, γ-Glutamyl-S-methylcysteine as substrate, which might lead to the formation of S-methylated phytochelatins. In conclusion, 454 sequencing was effective at revealing differences in the expression of sulfur metabolic genes, providing information on candidate genes for the biosynthesis of distinct sulfur amino acid γ-Glutamyl dipeptides between P. vulgaris and V. mungo.
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Affiliation(s)
- Dengqun Liao
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food CanadaLondon, ON, Canada
| | - Dustin Cram
- National Research Council CanadaSaskatoon, SK, Canada
| | | | - Frédéric Marsolais
- Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food CanadaLondon, ON, Canada
- Department of Biology, University of Western OntarioLondon, ON, Canada
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20
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Galili G, Amir R. Fortifying plants with the essential amino acids lysine and methionine to improve nutritional quality. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:211-22. [PMID: 23279001 DOI: 10.1111/pbi.12025] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/27/2012] [Accepted: 10/12/2012] [Indexed: 05/03/2023]
Abstract
Humans, as well as farm animals, cannot synthesize a number of essential amino acids, which are critical for their survival. Hence, these organisms must obtain these essential amino acids from their diets. Cereal and legume crops, which represent the major food and feed sources for humans and livestock worldwide, possess limiting levels of some of these essential amino acids, particularly Lys and Met. Extensive efforts were made to fortify crop plants with these essential amino acids using traditional breeding and mutagenesis. However, aside from some results obtained with maize, none of these approaches was successful. Therefore, additional efforts using genetic engineering approaches concentrated on increasing the synthesis and reducing the catabolism of these essential amino acids and also on the expression of recombinant proteins enriched in them. In the present review, we discuss the basic biological aspects associated with the synthesis and accumulation of these amino acids in plants and also describe recent developments associated with the fortification of crop plants with essential amino acids by genetic engineering approaches.
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Affiliation(s)
- Gad Galili
- Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel.
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21
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CHONG KETFAH, LEONG HONWAI. TUTORIAL ON DE NOVO PEPTIDE SEQUENCING USING MS/MS MASS SPECTROMETRY. J Bioinform Comput Biol 2012; 10:1231002. [DOI: 10.1142/s0219720012310026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This paper is a self-contained introductory tutorial on the problem in proteomics known as peptide sequencing using tandem mass spectrometry. This tutorial deals specifically with de novo sequencing methods (as opposed to database search methods). We first give an introduction to peptide sequencing, its importance and history and some background on proteins. Next we show the relationship between a peptide and the final spectrum produced from a tandem mass spectrometer, together with a description of the various sources of complications that arise during the process of generating the mass spectrum. From there we model the computational problem of de novo peptide sequencing, which is basically the reverse problem of identifying the peptide which produced the spectrum. We then present several major approaches to solve it (including reviewing some of the current algorithms in each approach), and also discuss related problems and post-processing approaches.
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Affiliation(s)
- KET FAH CHONG
- Department of Computer Science, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
| | - HON WAI LEONG
- Department of Computer Science, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
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22
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Liao D, Pajak A, Karcz SR, Chapman BP, Sharpe AG, Austin RS, Datla R, Dhaubhadel S, Marsolais F. Transcripts of sulphur metabolic genes are co-ordinately regulated in developing seeds of common bean lacking phaseolin and major lectins. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:6283-95. [PMID: 23066144 PMCID: PMC3481216 DOI: 10.1093/jxb/ers280] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The lack of phaseolin and phytohaemagglutinin in common bean (dry bean, Phaseolus vulgaris) is associated with an increase in total cysteine and methionine concentrations by 70% and 10%, respectively, mainly at the expense of an abundant non-protein amino acid, S-methyl-cysteine. Transcripts were profiled between two genetically related lines differing for this trait at four stages of seed development using a high density microarray designed for common bean. Transcripts of multiple sulphur-rich proteins were elevated, several previously identified by proteomics, including legumin, basic 7S globulin, albumin-2, defensin, albumin-1, the Bowman-Birk type proteinase inhibitor, the double-headed trypsin inhibitor, and the Kunitz trypsin inhibitor. A co-ordinated regulation of transcripts coding for sulphate transporters, sulphate assimilatory enzymes, serine acetyltransferases, cystathionine β-lyase, homocysteine S-methyltransferase and methionine gamma-lyase was associated with changes in cysteine and methionine concentrations. Differential gene expression of sulphur-rich proteins preceded that of sulphur metabolic enzymes, suggesting a regulation by demand from the protein sink. Up-regulation of SERAT1;1 and -1;2 expression revealed an activation of cytosolic O-acetylserine biosynthesis. Down-regulation of SERAT2;1 suggested that cysteine and S-methyl-cysteine biosynthesis may be spatially separated in different subcellular compartments. Analysis of free amino acid profiles indicated that enhanced cysteine biosynthesis was correlated with a depletion of O-acetylserine. These results contribute to our understanding of the regulation of sulphur metabolism in developing seed in response to a change in the composition of endogenous proteins.
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Affiliation(s)
- Dengqun Liao
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Agnieszka Pajak
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Steven R. Karcz
- Agriculture and Agri-Food Canada, Bioproducts and Bioprocesses, Saskatoon Research Centre, 107 Science Place, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - B. Patrick Chapman
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Andrew G. Sharpe
- National Research Council Canada, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Ryan S. Austin
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
| | - Raju Datla
- National Research Council Canada, Plant Biotechnology Institute, 110 Gymnasium Place, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Frédéric Marsolais
- Agriculture and Agri-Food Canada, Genomics and Biotechnology, Southern Crop Protection and Food Research Centre, 1391 Sandford St., London, Ontario N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, Ontario N6A 5B7, Canada
- * To whom correspondence should be addressed. E-mail:
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23
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Chan YS, Wong JH, Fang EF, Pan WL, Ng TB. An antifungal peptide from Phaseolus vulgaris cv. brown kidney bean. Acta Biochim Biophys Sin (Shanghai) 2012; 44:307-15. [PMID: 22321825 DOI: 10.1093/abbs/gms003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A 5.4-kDa antifungal peptide, with an N-terminal sequence highly homologous to defensins and inhibitory activity against Mycosphaerella arachidicola (IC(50)= 3 μM), Setospaeria turcica and Bipolaris maydis, was isolated from the seeds of Phaseolus vulgaris cv. brown kidney bean. The peptide was purified by employing a protocol that entailed adsorption on Affi-gel blue gel and Mono S and finally gel filtration on Superdex 75. The antifungal activity of the peptide against M. arachidicola was stable in the pH range 3-12 and in the temperature range 0°C to 80°C. There was a slight reduction of the antifungal activity at pH 2 and 13, and the activity was indiscernible at pH 0, 1, and 14. The activity at 90°C and 100°C was slightly diminished. Deposition of Congo red at the hyphal tips of M. arachidicola was induced by the peptide indicating inhibition of hyphal growth. The lack of antiproliferative activity of brown kidney bean antifungal peptide toward tumor cells, in contrast to the presence of such activity of other antifungal peptides, indicates that different domains are responsible for the antifungal and antiproliferative activities.
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Affiliation(s)
- Yau Sang Chan
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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24
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Ma B, Johnson R. De novo sequencing and homology searching. Mol Cell Proteomics 2012; 11:O111.014902. [PMID: 22090170 PMCID: PMC3277775 DOI: 10.1074/mcp.o111.014902] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 11/08/2011] [Indexed: 11/06/2022] Open
Abstract
In proteomics, de novo sequencing is the process of deriving peptide sequences from tandem mass spectra without the assistance of a sequence database. Such analyses have traditionally been performed manually by human experts, and more recently by computer programs that have been developed because of the need for higher throughput. Although powerful, de novo sequencing often can only determine partially correct sequence tags because of imperfect tandem mass spectra. However, these sequence tags can then be searched in a sequence database to identify the exact or a homologous peptide. Homology searches are particularly useful for the study of organisms whose genomes have not been sequenced. This tutorial will present background important to understanding de novo sequencing, suggestions on how to do this manually, plus descriptions of computer algorithms used to automate this process and to subsequently carryout homology-based database searches. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 1).
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Affiliation(s)
- Bin Ma
- From the ‡School of Computer Science, University of Waterloo, 200 University Ave. W, Waterloo, ON, Canada N2L 3G1
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