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Nayak SN, Aravind B, Malavalli SS, Sukanth BS, Poornima R, Bharati P, Hefferon K, Kole C, Puppala N. Omics Technologies to Enhance Plant Based Functional Foods: An Overview. Front Genet 2021; 12:742095. [PMID: 34858472 PMCID: PMC8631721 DOI: 10.3389/fgene.2021.742095] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Functional foods are natural products of plants that have health benefits beyond necessary nutrition. Functional foods are abundant in fruits, vegetables, spices, beverages and some are found in cereals, millets, pulses and oilseeds. Efforts to identify functional foods in our diet and their beneficial aspects are limited to few crops. Advances in sequencing and availability of different omics technologies have given opportunity to utilize these tools to enhance the functional components of the foods, thus ensuring the nutritional security. Integrated omics approaches including genomics, transcriptomics, proteomics, metabolomics coupled with artificial intelligence and machine learning approaches can be used to improve the crops. This review provides insights into omics studies that are carried out to find the active components and crop improvement by enhancing the functional compounds in different plants including cereals, millets, pulses, oilseeds, fruits, vegetables, spices, beverages and medicinal plants. There is a need to characterize functional foods that are being used in traditional medicines, as well as utilization of this knowledge to improve the staple foods in order to tackle malnutrition and hunger more effectively.
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Affiliation(s)
- Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. Aravind
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Sachin S. Malavalli
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. S. Sukanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - R. Poornima
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Pushpa Bharati
- Department of Food Science and Nutrition, University of Agricultural Sciences, Dharwad, India
| | - Kathleen Hefferon
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - Chittaranjan Kole
- President, International Phytomedomics and Nutriomics Consortium (ipnc.info), Daejeon, South Korea
| | - Naveen Puppala
- New Mexico State University-Agricultural Science Center at Clovis, New Mexico, NM, United States
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Recent applications of bio-engineering principles to modulate the functionality of proteins in food systems. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.04.055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Thery T, Lynch KM, Arendt EK. Natural Antifungal Peptides/Proteins as Model for Novel Food Preservatives. Compr Rev Food Sci Food Saf 2019; 18:1327-1360. [DOI: 10.1111/1541-4337.12480] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 05/17/2019] [Accepted: 07/04/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Thibaut Thery
- School of Food and Nutritional SciencesUniv. College Cork Ireland
| | - Kieran M. Lynch
- School of Food and Nutritional SciencesUniv. College Cork Ireland
| | - Elke K. Arendt
- School of Food and Nutritional SciencesUniv. College Cork Ireland
- Microbiome IrelandUniv. College Cork Ireland
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ZENG XH, WEI YM, JIANG QT, QI PF, ZHENG YL. SNP Analysis and Haplotype Identification in Chymotrypsin Inhibitor-2 (CI-2) Gene of Barley. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1671-2927(09)60003-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Porcelli F, Verardi R, Shi L, Henzler-Wildman KA, Ramamoorthy A, Veglia G. NMR structure of the cathelicidin-derived human antimicrobial peptide LL-37 in dodecylphosphocholine micelles. Biochemistry 2008; 47:5565-72. [PMID: 18439024 PMCID: PMC5873590 DOI: 10.1021/bi702036s] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
LL-37 is the only cathelicidin-derived polypeptide found in humans. Its eclectic function makes this peptide one of the most intriguing chemical defense agents, with crucial roles in moderating inflammation, promoting wound healing, and boosting the human immune system. LL-37 kills both prokaryotic and eukaryotic cells through physical interaction with cell membranes. In order to study its active conformation in membranes, we have reconstituted LL-37 into dodecylphosphocholine (DPC) micelles and determined its three-dimensional structure. We found that, under our experimental conditions, this peptide adopts a helix-break-helix conformation. Both the N- and C-termini are unstructured and solvent exposed. The N-terminal helical domain is more dynamic, while the C-terminal helix is more solvent protected and structured (high density of NOEs, slow H/D exchange). When it interacts with DPC, LL-37 is adsorbed on the surface of the micelle with the hydrophilic face exposed to the water phase and the hydrophobic face buried in the micelle hydrocarbon region. The break between the helices is positioned at K12 and is probably stabilized by a hydrophobic cluster formed by I13, F17, and I20 in addition to a salt bridge between K12 and E16. These results support the proposed nonpore carpet-like mechanism of action, in agreement with the solid-state NMR studies, and pave the way for understanding the function of the mature LL-37 at the atomic level.
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Affiliation(s)
| | | | | | | | - Ayyalusamy Ramamoorthy
- To whom correspondence should be addressed. G.V.: tel, (612) 625-0758; fax, (612) 625-2163, . A.R.: tel, (734) 647-6572;
| | - Gianluigi Veglia
- To whom correspondence should be addressed. G.V.: tel, (612) 625-0758; fax, (612) 625-2163, . A.R.: tel, (734) 647-6572;
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Beauregard M, Hefford MA. Enhancement of essential amino acid contents in crops by genetic engineering and protein design. PLANT BIOTECHNOLOGY JOURNAL 2006; 4:561-74. [PMID: 17309730 DOI: 10.1111/j.1467-7652.2006.00204.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The importance and urgency of providing humans and animals with quality proteins are reflected in the growing scientific and industrial interest in augmenting the nutritive value of the world's protein sources. Such nutritive value is determined by the protein content in 'essential amino acids', those that cannot be synthesized de novo and that must be supplied from the diet. It is the object of this review to discuss recent advances in the genetic modification of crops that aim to provide enhanced quantities of essential amino acids.
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Affiliation(s)
- Marc Beauregard
- Plant Biology Group, Département de Chimie-Biologie, Université du Québec à Trois-Rivières, Trois-Rivières, QC, Canada, G9A 5H7.
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Roesler KR, Rao AG. Conformation and stability of barley chymotrypsin inhibitor-2 (CI-2) mutants containing multiple lysine substitutions. PROTEIN ENGINEERING 1999; 12:967-73. [PMID: 10585502 DOI: 10.1093/protein/12.11.967] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A major goal of agricultural biotechnology is to increase the nutritional value of maize seed through the expression of heterologous proteins enriched in lysine. One promising candidate is barley chymotrypsin inhibitor-2 (CI-2), a plant protein that has been extensively characterized with respect to structure and function. Based on the tertiary structure of wild-type (WT) CI-2, five mutants with lysine contents ranging from 20 to 25 mol percent were designed, expressed in Escherichia coli and purified by ion exchange and gel permeation chromatography. Inasmuch as previous transgenic experiments suggested that proper folding and stability may be essential for in vivo accumulation of the engineered proteins in plant cells, we first undertook an in vitro study of the conformation and thermodynamic stability of the CI-2 mutants in order to select an ideal candidate for plant expression. Mutant and WT CI-2 proteins had similar circular dichroism spectra, suggesting similar secondary structures. However, differences in the accessibility of the sole tryptophan residue, Trp24, indicated that the local conformation differed among the mutants. The thermodynamic stability of the mutants ranged from <2 to 4.9 kcal/mol compared with approximately 7 kcal/mol for the wild-type protein. In conjunction with proteolytic stability studies, we have identified one mutant that has the potential to be expressed in a stable manner in plant cells.
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Affiliation(s)
- K R Roesler
- Pioneer Hi-Bred International, Inc., 7300 NW 62nd Avenue, PO Box 1004, Johnston, IA 50131-1004, USA
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Munger RG, Cerhan JR, Chiu BC. Prospective study of dietary protein intake and risk of hip fracture in postmenopausal women. Am J Clin Nutr 1999; 69:147-52. [PMID: 9925137 DOI: 10.1093/ajcn/69.1.147] [Citation(s) in RCA: 215] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The role of dietary protein intake in osteoporosis remains controversial. Protein is an important structural component of bone and protein supplementation improves the medical outcome of hip fracture patients, but it is unknown whether protein intake can reduce the incidence risk of hip fracture. OBJECTIVE The relation between intake of protein and other nutrients and subsequent incidence of hip fracture was evaluated. DESIGN Nutrient intake was assessed with a food-frequency questionnaire in a cohort of Iowa women aged 55-69 y at baseline in 1986. Incident hip fractures were ascertained through follow-up questionnaires mailed to participants in 1987 and 1989 and verified by physician reports. RESULTS Forty-four cases of incident hip fractures were included in the analyses of 104338 person-years (the number of subjects studied times the number of years of follow-up) of follow-up data. The risk of hip fracture was not related to intake of calcium or vitamin D, but was negatively associated with total protein intake. Animal rather than vegetable sources of protein appeared to account for this association. In a multivariate model with inclusion of age, body size, parity, smoking, alcohol intake, estrogen use, and physical activity, the relative risks of hip fracture decreased across increasing quartiles of intake of animal protein as follows: 1.00 (reference), 0.59 (95% CI: 0.26, 1.34), 0.63 (0.28, 1.42), and 0.31 (0.10, 0.93); P for trend = 0.037. CONCLUSION Intake of dietary protein, especially from animal sources, may be associated with a reduced incidence of hip fractures in postmenopausal women.
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Affiliation(s)
- R G Munger
- Department of Nutrition and Food Sciences, Utah State University, Logan 84322-8700, USA.
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Barthe P, Yang YS, Chiche L, Hoh F, Strub MP, Guignard L, Soulier J, Stern MH, van Tilbeurgh H, Lhoste JM, Roumestand C. Solution structure of human p8MTCP1, a cysteine-rich protein encoded by the MTCP1 oncogene, reveals a new alpha-helical assembly motif. J Mol Biol 1997; 274:801-15. [PMID: 9405159 DOI: 10.1006/jmbi.1997.1438] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
MTCP1 (for Mature-T-Cell Proliferation) is the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype. The three-dimensional solution structure of the human p8(MTCP1) protein encoded by the MTCP1 oncogene was determined by homonuclear proton two-dimensional NMR methods at 600 MHz. After sequence specific assignments, a total of 931 distance restraints and 57 dihedral restraints were collected. The location of the three previously unassigned disulfide bridges was determined from preliminary DIANA structures, using a statistical analysis of intercystinyl distances. The solution structure of p8(MTCP1) is presented as a set of 30 DIANA structures, further refined by restrained molecular dynamics using a simulated annealing protocol with the AMBER force field. The r.m.s.d. values with respect to the mean structure for the backbone and all heavy atoms for a family of 30 structures are 0.73(+/-0.28) and 1.17(+/-0.23) A, when the structured core of the protein (residues 5 to 63) is considered. The solution structure of p8(MTCP1) reveals an original scaffold consisting of three alpha helices, associated with a new cysteine motif. Two of the helices are covalently paired by two disulfide bridges, forming an alpha-hairpin which resembles an antiparallel coiled-coil. The third helix is oriented roughly parallel to the plane defined by the alpha-antiparallel motif and its axis forms an angle of approximately 60 degrees with respect to the main axis of this motif.
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Affiliation(s)
- P Barthe
- CNRS-UMR 9955, INSERM-U414, Faculté de Pharmacie, Université de Montpellier I, 15 Avenue Charles Flahault, Montpellier Cedex, 34060, France
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Orrù S, Scaloni A, Giannattasio M, Urech K, Pucci P, Schaller G. Amino acid sequence, S-S bridge arrangement and distribution in plant tissues of thionins from Viscum album. Biol Chem 1997; 378:989-96. [PMID: 9348108 DOI: 10.1515/bchm.1997.378.9.989] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The complete primary structure of a cytotoxic 5 kDa polypeptide, viscotoxin A1, isolated from Viscum album L., has been determined by combining classical Edman degradation methodology with advanced mass spectrometric procedures. The same integrated approach allowed correction of the sequence of viscotoxin A2 and definition of the pattern of the disulfide bridges. The arrangement of the cysteine pairing was determined as Cys3-Cys40, Cys4-Cys32 and Cys16-Cys26. The primary structure of viscotoxin A1 shares a high degree of similarity with the known viscotoxins and more generally with the plant alpha- and beta-thionins. The pattern of S-S bridges determined for viscotoxin A2 and A1 is similar to that inferred by X-ray and NMR analysis in crambin and related to that present in alpha-purothionin and beta-hordothionin, thus indicating a highly conserved organization of the S-S pairings within the entire family. This arrangement of S-S bridges describes a peculiar structural motif, indicated as 'concentric motif', which is suggested to stabilize a common structure occurring in various small proteins able to interact with cell membranes. The distribution of the new variant toxin in different mistletoe subspecies was investigated. Viscotoxin A1 is abundant in the seeds of the three European subspecies of V. album whereas it represents a minor component in the shoots.
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Affiliation(s)
- S Orrù
- Centro Internazionale di Servizi di Spettrometria di Massa del CNR, Napoli, Italy
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Han KH, Park KH, Yoo HJ, Cha H, Suh SW, Thomas F, Moon TS, Kim SM. Determination of the three-dimensional structure of hordothionin-alpha by nuclear magnetic resonance. Biochem J 1996; 313 ( Pt 3):885-92. [PMID: 8611171 PMCID: PMC1216994 DOI: 10.1042/bj3130885] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The high-resolution three-dimensional solution structure of the plant toxin hordothionin-alpha obtained from korean barley was determined by using two-dimensional NMR techniques combined with distance geometry and restrained molecular dynamics. Experimentally derived restraints including 292 interproton distances from nuclear Overhauser effect measurements, 16 hydrogen bond restraints together with four disulphide bridge restraints were used as input to calculations of distance geometry and restrained molecular dynamics. Also included in the calculations were 36 phi and 17 chi 1 torsion angles obtained from 33JHN alpha and 3J alpha beta coupling constants in double quantum filtered COSY and primitive exclusive COSY experiments, respectively. The overall protein fold is similar to crambin and purothionin-alpha 1. Two alpha-helices running in opposite directions are found on the basis of 3JHN alpha and 3J alpha beta and deuterium exchange rates for backbone NH protons, and encompass residues 7-18 and 22-28. These two helices are connected by a turn and form a 'helix-turn-helix' motif. A short stretch of an anti-parallel beta-sheet exists between residues 1-4 and 31-34. the two protein termini of hordothionin-alpha are 'well-anchored'; the N-terminus of the protein is immobilized by this short beta-sheet whereas the C-terminus is 'pasted' to the carbonyl group of Cys-4 by a very stable hydrogen bond. The average root-mean-square differences for the backbone and heavy atoms after the restrained molecular dynamics calculations are 0.62 and 1.16 A respectively. These numbers represent a significant improvement over the corresponding values for the previous NMR structures of other thionins. The distance violation from the experimental interproton distances for the final structures is 0.14 for all atoms.
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Affiliation(s)
- K H Han
- Korea Research Institute of Bioscience and Biotechnology, KIST, Taejon, Korea
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