1
|
Bejerman N, Dietzgen R, Debat H. Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses. Viruses 2023; 15:2402. [PMID: 38140643 PMCID: PMC10747219 DOI: 10.3390/v15122402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented viruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae, and they should be classified in a novel genus within this family for which we suggest the name "Trirhavirus". Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (family Fimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genus Cytorhabdovirus into three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of the genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.
Collapse
Affiliation(s)
- Nicolas Bejerman
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
| | - Ralf Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Humberto Debat
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
| |
Collapse
|
2
|
R N, Kh M, Hegde SN, Begum N, Kukkupuni SK, Gowda M, Narendran P. De novo genome assembly and annotation of the medicinal plant Tinospora cordifolia (Willd.) Miers ex Hook. f. & Thom's. Funct Integr Genomics 2023; 23:330. [PMID: 37935874 DOI: 10.1007/s10142-023-01262-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023]
Abstract
Indian natural climbing shrub Tinospora cordifolia, often known as "Guduchi" and "Amrita," is a highly esteemed medicinal plant in the Indian system of medicine (ISM). It is a member of the Menispermaceae family which consists of a rich source of protein, micronutrients, and rich source of bioactive components which are used in treating various systemic diseases. The current study was designed to know the biological characterization of the plant genome and biosynthesis of plant metabolites essential for its medicinal applications. Tinospora cordifolia's complete genome was sequenced using Illumina HiSeq2500 sequencing technology. The draft genome was assembled through a de novo method. An integrative genome annotation approach was used to perform functional gene prediction. The pathway analysis was carried out using the KEGG database. The total genome size obtained after genome assembly was 894 Mb with an N50 of 9148 bp. The integrative annotation approach resulted in 35,111 protein-coding genes. In addition, genes responsible for the synthesis of syringin, a secondary metabolite found in plants, were identified. In comparison to the standard drug (dopamine, rasagiline, and selegiline), syringin's molecular docking exhibited a greater binding affinity from the range of - 4.3 to - 6.6 kcal/mol for all the targets of Parkinson's disease and for Alzheimer's targets; it has shown the maximum potency from the range of - 6.5 to - 7.4 kcal/mol with respect to the standard drug (donepezil, galantamine, and rivastigmine). This study provides the genomic information of Tinospora cordifolia which is helpful in understanding genomic insights and metabolic pathways connected to the corresponding plant genome and predicts the possible useful effect for the molecular characterization of therapeutic drugs.
Collapse
Affiliation(s)
- Namitha R
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Manasa Kh
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Santhosh N Hegde
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Noorunnisa Begum
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Subrahmanya Kumar Kukkupuni
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India
| | - Malali Gowda
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India.
| | - Pavithra Narendran
- The University of Trans-Disciplinary Health Sciences and Technology (TDU), 74/2, Post Attur via Yelahanka, Jarakabande Kaval, Bengaluru, 560 064, India.
| |
Collapse
|
3
|
Krishna TA, Maharajan T, Krishna TA, Ceasar SA. Insights into Metabolic Engineering of Bioactive Molecules in Tetrastigma hemsleyanum Diels & Gilg: A Traditional Medicinal Herb. Curr Genomics 2023; 24:72-83. [PMID: 37994327 PMCID: PMC10662378 DOI: 10.2174/0113892029251472230921053135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/17/2023] [Accepted: 08/20/2023] [Indexed: 11/24/2023] Open
Abstract
Plants are a vital source of bioactive molecules for various drug development processes. Tetrastigma hemsleyanum is one of the endangered medicinal plant species well known to the world due to its wide range of therapeutic effects. Many bioactive molecules have been identified from this plant, including many classes of secondary metabolites such as flavonoids, phenols, terpenoids, steroids, alkaloids, etc. Due to its slow growth, it usually takes 3-5 years to meet commercial medicinal materials for this plant. Also, T. hemsleyanum contains low amounts of specific bioactive compounds, which are challenging to isolate easily. Currently, scientists are attempting to increase bioactive molecules' production from medicinal plants in different ways or to synthesize them chemically. The genomic tools helped to understand medicinal plants' genome organization and led to manipulating genes responsible for various biosynthesis pathways. Metabolic engineering has made it possible to enhance the production of secondary metabolites by introducing manipulated biosynthetic pathways to attain high levels of desirable bioactive molecules. Metabolic engineering is a promising approach for improving the production of secondary metabolites over a short time period. In this review, we have highlighted the scope of various biotechnological approaches for metabolic engineering to enhance the production of secondary metabolites for pharmaceutical applications in T. hemsleyanum. Also, we summarized the progress made in metabolic engineering for bioactive molecule enhancement in T. hemsleyanum. It may lead to reducing the destruction of the natural habitat of T. hemsleyanum and conserving them through the cost-effective production of bioactive molecules in the future.
Collapse
Affiliation(s)
- T.P. Ajeesh Krishna
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India
| | - T. Maharajan
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India
| | - T.P. Adarsh Krishna
- Research & Development Division, Sreedhareeyam Farmherbs India Pvt. Ltd, Ernakulam, 686-662, Kerala, India
| | - S. Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kochi, 683104, Kerala, India
| |
Collapse
|
4
|
Singh V, Singh V. Characterizing the circadian connectome of Ocimum tenuiflorum using an integrated network theoretic framework. Sci Rep 2023; 13:13108. [PMID: 37567911 PMCID: PMC10421869 DOI: 10.1038/s41598-023-40212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Across the three domains of life, circadian clock is known to regulate vital physiological processes, like, growth, development, defence etc. by anticipating environmental cues. In this work, we report an integrated network theoretic methodology comprising of random walk with restart and graphlet degree vectors to characterize genome wide core circadian clock and clock associated raw candidate proteins in a plant for which protein interaction information is available. As a case study, we have implemented this framework in Ocimum tenuiflorum (Tulsi); one of the most valuable medicinal plants that has been utilized since ancient times in the management of a large number of diseases. For that, 24 core clock (CC) proteins were mined in 56 template plant genomes to build their hidden Markov models (HMMs). These HMMs were then used to identify 24 core clock proteins in O. tenuiflorum. The local topology of the interologous Tulsi protein interaction network was explored to predict the CC associated raw candidate proteins. Statistical and biological significance of the raw candidates was determined using permutation and enrichment tests. A total of 66 putative CC associated proteins were identified and their functional annotation was performed.
Collapse
Affiliation(s)
- Vikram Singh
- Centre for Computational Biology and Bioinformatics, Central University of Himahcal Pradesh, Dharamshala, Himahcal Pradesh, 176206, India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, Central University of Himahcal Pradesh, Dharamshala, Himahcal Pradesh, 176206, India.
| |
Collapse
|
5
|
Swarna Meenakshi P, Jaiganesh R, Eswaramoorthy R. Formulation and evaluation of Ocimum sanctum Linn containing carboxymethylcellulose and sorbitol based hydrogel. Bioinformation 2023; 19:546-551. [PMID: 37886155 PMCID: PMC10599679 DOI: 10.6026/97320630019546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/31/2023] [Accepted: 05/31/2023] [Indexed: 10/28/2023] Open
Abstract
It is of interest to formulate a hydrogel consisting of Ocimum sanctum Linn, sorbitol, and carboxymethyl cellulose and to evaluate the physical properties of the hydrogel. The hydrogel was prepared by dissolving Ocimum sanctum Linn extract into the mixture containing sorbitol and carboxymethyl cellulose. The formulation was further evaluated for its swelling index, contact angle, in -vitro release properties, and surface analysis using atomic force microscopy. The swelling index showed a significant increase in weight from 1st hr to the 84th hour which is 11.1% and 15.8% respectively. The contact angle test showed a value of 72.81° and 75.99° respectively. In vitro drug release showed a burst release till the 6th day followed by a sustained release till the 20th day. Atomic force microscopy revealed smooth and consistent surface topography with a mean size of 51µm in diameter which depicts that the particles are well dispersed throughout the hydrogel matrix. Data show that hydrogel containing Ocimum sanctum Linn extract, sorbitol, and carboxymethyl cellulose could be an efficient economic primeval substitute that is non-toxic, natural, and structured for clinical application.
Collapse
Affiliation(s)
- P Swarna Meenakshi
- Department of Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS)Saveetha University, Chennai
| | - Ramamurthy Jaiganesh
- Department of Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS)Saveetha University, Chennai
| | - Rajalakshmanan Eswaramoorthy
- Department of Periodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS)Saveetha University, Chennai
| |
Collapse
|
6
|
Gossart N, Berhin A, Sergeant K, Alam I, André C, Hausman JF, Boutry M, Hachez C. Engineering Nicotiana tabacum trichomes for triterpenic acid production. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 328:111573. [PMID: 36563941 DOI: 10.1016/j.plantsci.2022.111573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
In this work, we aimed at implementing the biosynthesis of triterpenic acids in Nicotiana tabacum glandular trichomes. Although endogenous genes coding for enzymes involved in such biosynthetic pathway are found in the Nicotiana tabacum genome, implementing such pathway specifically in glandular trichomes required to boost endogenous enzymatic activities. Five transgenes coding for a farnesyl-diphosphate synthase, a squalene synthase, a squalene epoxidase, a beta-amyrin synthase and a beta-amyrin 28-monooxygenase were introduced in N.tabacum, their expression being driven by pMALD1, a trichome-specific transcriptional promoter. This study aimed at testing whether sinking isoprenoid precursors localized in plastids, by exploiting potential cross-talks allowing the exchange of terpenoid pools from the chloroplast to the cytosol, could be a way to improve overall yield. By analyzing metabolites extracted from entire leaves, a low amount of ursolic acid was detected in plants expressing the five transgenes. Our study shows that the terpene biosynthetic pathway could be, in part, redirected in N.tabacum glandular trichomes with no deleterious phenotype at the whole plant level (chlorosis, dwarfism,…). In light of our results, possible ways to improve the final yield are discussed.
Collapse
Affiliation(s)
- Nicola Gossart
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Alice Berhin
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Kjell Sergeant
- Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Iftekhar Alam
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium; Plant Biotechnology Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Christelle André
- Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg; The New Zealand Institute for Plant and Food Research Ltd (PFR), Private Bag 92169, Auckland, New Zealand
| | - Jean-François Hausman
- Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Marc Boutry
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Charles Hachez
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-Neuve, Belgium.
| |
Collapse
|
7
|
Identification of Key Aromatic Compounds in Basil ( Ocimum L.) Using Sensory Evaluation, Metabolomics and Volatilomics Analysis. Metabolites 2023; 13:metabo13010085. [PMID: 36677010 PMCID: PMC9865694 DOI: 10.3390/metabo13010085] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Basil (Ocimum L.) is widely used as a flavor ingredient, however research on basil flavor is limited. In the current study, nine basil species were selected, including Ocimum basilicum L.var. pilosum (Willd.) Benth., Ocimum sanctum, Ocimum basilicum cinnamon, Ocimum gratissimum var. suave, Ocimum tashiroi, Ocimum basilicum, Ocimum americanum, Ocimum basilicum ct linalool, and Ocimum basilicum var. basilicum, and their fragrance and flavor characteristics were assessed by sensory evaluation. The results indicated that Ocimum basilicum var. basilicum and Ocimum gratissimum var. suave have a strong clove smell and exhibited a piquant taste. Metabolomics and volatilomics analyses measured 100 nonvolatile metabolites and 134 volatiles. Differential analysis showed that eugenol, γ-terpinene, germacrene D and malic acid were among the most varied metabolites in basil species. Combined with sensory evaluation results, correlation analysis revealed that β-pinene and γ-cadinene contributed to the piquant smell, while eugenol and germacrene D contributed to the clove smell, and malic acid and L-(−)-arabitol contributed to the sweet flavor in basil. This study provided comprehensive flavor chemistry profiles of basil species and could be used as a guide for basil flavor improvement. The better understanding of objective sensory attributes and chemical composition of fresh basil could introduce the improved cultivars with preponderant traits, which is also in accordance with the various demands of breeders and growers, food producers, and consumers.
Collapse
|
8
|
March of molecular breeding techniques in the genetic enhancement of herbal medicinal plants: present and future prospects. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00406-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
9
|
Sharma T, Sharma U, Kumar S. Iridoid glycosides from Picrorhiza genus endemic to the Himalayan region: phytochemistry, biosynthesis, pharmacological potential and biotechnological intercessions to boost production. Crit Rev Biotechnol 2022; 44:1-16. [PMID: 36184806 DOI: 10.1080/07388551.2022.2117681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Iridoid glycosides are monoterpenoids synthesized in several plant species known to exhibit a diverse range of pharmacological activities. They are used as important bioactive ingredients in many commercially available drug formulations and as lead compounds in pharmaceutical research. The genus Picrorhiza comprises two medicinally important herbs endemic to the Himalayan region viz. Picrorhiza kurrooa Royle and Picrorhiza scrophulariiflora Hong. The medicinal properties of these two species are mainly due to iridoid glycosides present in their root, rhizome, and leaves. Unregulated harvesting from the wild, habitat specificity, narrow distribution range, small population size and lack of organized cultivation led to the enrolling of these species in the endangered category by the International Union for Conservation of Nature and Natural Resources (IUCN). Therefore, there is a need for immediate biotechnological and molecular interventions. Such intercessions will open up new vistas for large-scale propagation, development of genomic/transcriptomic resources for understanding the biosynthetic pathway, the possibility of genetic/metabolic manipulations, and possible commercialization of iridoid glycosides. The current review article elucidates the phytochemistry and pharmacological importance of iridoid glycosides from the genus Picrorhiza. In addition, the role of biotechnological approaches and opportunities offered by next-generation sequencing technologies in overcoming challenges associated with the genetic engineering of these species are also discussed.
Collapse
Affiliation(s)
- Tanvi Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Upendra Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource and Technology, Palampur, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
10
|
Sharma R, Patil C, Majeed J, Kumar S, Aggarwal G. Next-generation sequencing in the biodiversity conservation of endangered medicinal plants. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:73795-73808. [PMID: 36098925 DOI: 10.1007/s11356-022-22842-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Medicinal plants have been used as traditional herbal medicines in the treatment of various types of diseases. However, the increased demand for these plants highlights the importance of conservation specifically for endangered species. Significant advancements in next-generation sequencing (NGS) technologies have accelerated medicinal plant research while reducing costs and time demands. NGS systems enable high-throughput whole genome sequencing as well as direct RNA sequencing and transcriptome analysis. The sequence data sets created can be used in a variety of areas of study, including biodiversity conservation, comparative genomics, transcriptomic analysis, single cell mining, metagenomics, epigenetics, molecular marker discovery, multi genome sequencing, and so on. Commercial sequencing service providers are constantly working to improve technologies to address bioinformatics problems in NGS data analysis. Several genome sequencing projects on medicinal plants have been completed recently and a few more are in the works. In some medicinal plants, massive NGS-based data has been developed. In the present review, we have attempted to briefly discuss advancements in NGS technology on medicinally essential plants in India. The review will also provide ideas for applying NGS technologies for exploring genomes of various endangered medicinal plants whose genome sequences are not normally available and thus provides valuable insights for the conservation of these vulnerable species.
Collapse
Affiliation(s)
- Ruchika Sharma
- Centre for Precision Medicine and Pharmacy, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Chandragouda Patil
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Jaseela Majeed
- Department of Pharmaceutical Management, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Subodh Kumar
- Centre for Precision Medicine and Pharmacy, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India
| | - Geeta Aggarwal
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi, 110017, India.
| |
Collapse
|
11
|
Exploring the medicinally important secondary metabolites landscape through the lens of transcriptome data in fenugreek (Trigonella foenum graecum L.). Sci Rep 2022; 12:13534. [PMID: 35941189 PMCID: PMC9359999 DOI: 10.1038/s41598-022-17779-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/30/2022] [Indexed: 11/08/2022] Open
Abstract
Fenugreek (Trigonella foenum-graecum L.) is a self-pollinated leguminous crop belonging to the Fabaceae family. It is a multipurpose crop used as herb, spice, vegetable and forage. It is a traditional medicinal plant in India attributed with several nutritional and medicinal properties including antidiabetic and anticancer. We have performed a combined transcriptome assembly from RNA sequencing data derived from leaf, stem and root tissues. Around 209,831 transcripts were deciphered from the assembly of 92% completeness and an N50 of 1382 bases. Whilst secondary metabolites of medicinal value, such as trigonelline, diosgenin, 4-hydroxyisoleucine and quercetin, are distributed in several tissues, we report transcripts that bear sequence signatures of enzymes involved in the biosynthesis of such metabolites and are highly expressed in leaves, stem and roots. One of the antidiabetic alkaloid, trigonelline and its biosynthesising enzyme, is highly abundant in leaves. These findings are of value to nutritional and the pharmaceutical industry.
Collapse
|
12
|
Girme A, Bhoj P, Saste G, Pawar S, Mirgal A, Raut D, Chavan M, Hingorani L. Development and Validation of RP-HPLC Method for Vicenin-2, Orientin, Cynaroside, Betulinic Acid, Genistein, and Major Eight Bioactive Constituents with LC-ESI-MS/MS Profiling in Ocimum Genus. J AOAC Int 2021; 104:1634-1651. [PMID: 33930142 DOI: 10.1093/jaoacint/qsab067] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/31/2021] [Accepted: 04/12/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND Ocimum genus, known as Tulsi or Basil, is a prominent botanical class in Asian culture, especially in India. The leaves have immunomodulatory, antioxidant, stress-relieving, and adaptogenic roles in traditional and modern medicine, with prominent usage in herbal teas and nutraceuticals. OBJECTIVE An high-performance liquid chromatography-photodiode array (HPLC-PDA) method was developed and validated for quantification of vicenin-2, orientin, cynaroside, betulinic acid, genistein with syringic acid, rosmarinic acid, eugenol, carnosic acid, oleanolic acid, ursolic acid, luteolin, and apigenin and was confirmed using a novel electrospray ionisation-mass spectrometry (ESI-MS/MS) method in the Ocimum genus samples. METHOD The methodology parameters were developed on an reverse phase (RP) C18 column with a gradient elution of 1 mL/min flow rate for 0.1% o-phosphoric acid and acetonitrile at 210 and 340 nm wavelengths. RESULTS The validation data for 13 bioactive compounds showed good linearity (r2 > 0.99) with sensitive LOD (0.034-0.684 µg/mL) and LOQ (0.100-2.068 µg/mL) with recoveries (83.66-101.53%). The results of the quantification were found to be precise (RSD, <5.0%) and accurate (relative error (RE), -0.60-1.06). The method performance was verified by analyzing 10 samples of O. tenuiflorum from the 10 geographical states of India (RSD, <5.0%) and were found to be robust. This HPLC-PDA method with ESI-MS/MS confirmation was applicable to the 13 cultivars from O. thyrsiflorum, O. citriodorum, O. americanum, O. africanum, O. basilicum, O. gratissimum, and O. tenuiflorum species. CONCLUSIONS The validated HPLC-PDA and LC-ESI-MS/MS method was found to be selective and suitable for analyzing 13 compounds in O. tenuiflorum and 12 cultivars from the Ocimum genus as a quality control tool. This method can be used in routine analysis as an inexpensive alternative to advanced techniques. HIGHLIGHTS This work is the first to report for vicenin-2, orientin, cynaroside, betulinic acid, and genistein, with simultaneous analysis of eight bioactive compounds in the Ocimum genus.
Collapse
Affiliation(s)
- Aboli Girme
- Pharmanza Herbal Pvt. Ltd, Anand, Gujarat, India
| | - Prajkta Bhoj
- Pharmanza Herbal Pvt. Ltd, Anand, Gujarat, India.,Amrutvahini College of Pharmacy, Ahmednagar, Maharashtra, India
| | - Ganesh Saste
- Pharmanza Herbal Pvt. Ltd, Anand, Gujarat, India
| | | | - Amit Mirgal
- Pharmanza Herbal Pvt. Ltd, Anand, Gujarat, India
| | - Dipak Raut
- Amrutvahini College of Pharmacy, Ahmednagar, Maharashtra, India
| | | | | |
Collapse
|
13
|
Alhindi T, Al-Abdallat AM. Genome-Wide Identification and Analysis of the MADS-Box Gene Family in American Beautyberry ( Callicarpa americana). PLANTS 2021; 10:plants10091805. [PMID: 34579338 PMCID: PMC8466759 DOI: 10.3390/plants10091805] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/27/2022]
Abstract
The MADS-box gene family encodes a number of transcription factors that play key roles in various plant growth and development processes from response to environmental cues to cell differentiation and organ identity, especially the floral organogenesis, as in the prominent ABCDE model of flower development. Recently, the genome of American beautyberry (Callicarpa americana) has been sequenced. It is a shrub native to the southern region of United States with edible purple-colored berries; it is a member of the Lamiaceae family, a family of medical and agricultural importance. Seventy-eight MADS-box genes were identified from 17 chromosomes of the C. americana assembled genome. Peptide sequences blast and analysis of phylogenetic relationships with MADS-box genes of Sesame indicum, Solanum lycopersicum, Arabidopsis thaliana, and Amborella trichopoda were performed. Genes were separated into 32 type I and 46 type II MADS-box genes. C. americana MADS-box genes were clustered into four groups: MIKCC, MIKC*, Mα-type, and Mγ-type, while the Mβ-type group was absent. Analysis of the gene structure revealed that from 1 to 15 exons exist in C. americana MADS-box genes. The number of exons in type II MADS-box genes (5–15) greatly exceeded the number in type I genes (1–9). The motif distribution analysis of the two types of MADS-box genes showed that type II MADS-box genes contained more motifs than type I genes. These results suggested that C. americana MADS-box genes type II had more complex structures and might have more diverse functions. The role of MIKC-type MADS-box genes in flower and fruit development was highlighted when the expression profile was analyzed in different organs transcriptomes. This study is the first genome-wide analysis of the C. americana MADS-box gene family, and the results will further support any functional and evolutionary studies of C. americana MADS-box genes and serve as a reference for related studies of other plants in the medically important Lamiaceae family.
Collapse
Affiliation(s)
- Tareq Alhindi
- Department of Biological Sciences, School of Science, The University of Jordan, Amman 11942, Jordan
- Correspondence:
| | - Ayed M. Al-Abdallat
- Department of Horticulture and Crop Science, School of Agriculture, The University of Jordan, Amman 11942, Jordan;
| |
Collapse
|
14
|
Gurav TP, Dholakia BB, Giri AP. A glance at the chemodiversity of Ocimum species: Trends, implications, and strategies for the quality and yield improvement of essential oil. PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2021; 21:879-913. [PMID: 34366748 PMCID: PMC8326315 DOI: 10.1007/s11101-021-09767-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/08/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Ocimum species represent commercially important medicinal and aromatic plants. The essential oil biosynthesized by Ocimum species is enriched with specialized metabolites specifically, terpenoids and phenylpropanoids. Interestingly, various Ocimum species are known to exhibit diverse chemical profiles, and this chemical diversity has been at the center of many studies to identify commercially important chemotypes. Here, we present various chemotypes from the Ocimum species and emphasize trends, implications, and strategies for the quality and yield improvement of essential oil. Globally, many Ocimum species have been analyzed for their essential oil composition in over 50 countries. Asia represents the highest number of chemotypes, followed by Africa, South America, and Europe. Ocimum basilicum L. has been the most widespread and well-studied species, followed by O. gratissimum L., O. tenuiflorum L., O. canum Sims, O. americanum and O. kilimandscharicum Gürke. Moreover, various molecular reasons, benefits, adverse health effects and mechanisms behind this vast chemodiversity have been discussed. Different strategies of plant breeding, metabolic engineering, transgenic, and tissue-culture, along with anatomical modifications, are surveyed to enhance specific chemotypic profiles and essential oil yield in numerous Ocimum species. Consequently, chemical characterization of the essential oil obtained from Ocimum species has become indispensable for its proper utilization. The present chemodiversity knowledge from Ocimum species will help to exploit various applications in the industrial, agriculture, biopharmaceutical, and food sectors. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s11101-021-09767-z.
Collapse
Affiliation(s)
- Tanuja P. Gurav
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008 India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002 India
| | | | - Ashok P. Giri
- Plant Molecular Biology Unit, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008 India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002 India
| |
Collapse
|
15
|
Song Z, Li X. Recent Advances in Molecular Marker-Assisted Breeding for Quality Improvement of Traditional Chinese Medicine. Curr Pharm Biotechnol 2021; 22:867-875. [PMID: 32351179 DOI: 10.2174/1389201021666200430121013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The quality of Traditional Chinese Medicine (TCM), reflected by its bioactive compounds and associated contents, is directly linked to its clinical efficacy. Therefore, it is of great importance to improve the quality of TCM by increasing the bioactive compound content. METHODS Mapping the active component content-associated QTLs in TCM and further markerassisted breeding has enabled us to rapidly and effectively cultivate new varieties with high bioactive compound contents, which has opened the door for genetic breeding studies on medicinal plants. RESULTS In this paper, a strategy and technical molecular breeding method for TCM are discussed. The development of four methods and progress in functional marker development, as well as the applications of such markers in TCM, are reviewed. CONCLUSION The progress in, challenges of, and future of marker-assisted breeding for quality improvement of TCM are discussed, which provide valuable scientific references for future molecular breeding.
Collapse
Affiliation(s)
- Zhenqiao Song
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| |
Collapse
|
16
|
Crosstalk of Multi-Omics Platforms with Plants of Therapeutic Importance. Cells 2021; 10:cells10061296. [PMID: 34071113 PMCID: PMC8224614 DOI: 10.3390/cells10061296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/25/2021] [Accepted: 05/10/2021] [Indexed: 02/06/2023] Open
Abstract
From time immemorial, humans have exploited plants as a source of food and medicines. The World Health Organization (WHO) has recorded 21,000 plants with medicinal value out of 300,000 species available worldwide. The promising modern "multi-omics" platforms and tools have been proven as functional platforms able to endow us with comprehensive knowledge of the proteome, genome, transcriptome, and metabolome of medicinal plant systems so as to reveal the novel connected genetic (gene) pathways, proteins, regulator sequences and secondary metabolite (molecule) biosynthetic pathways of various drug and protein molecules from a variety of plants with therapeutic significance. This review paper endeavors to abridge the contemporary advancements in research areas of multi-omics and the information involved in decoding its prospective relevance to the utilization of plants with medicinal value in the present global scenario. The crosstalk of medicinal plants with genomics, transcriptomics, proteomics, and metabolomics approaches will be discussed.
Collapse
|
17
|
Genome-Wide Analysis of Terpene Synthase Gene Family in Mentha longifolia and Catalytic Activity Analysis of a Single Terpene Synthase. Genes (Basel) 2021; 12:genes12040518. [PMID: 33918244 PMCID: PMC8066702 DOI: 10.3390/genes12040518] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/17/2022] Open
Abstract
Terpenoids are a wide variety of natural products and terpene synthase (TPS) plays a key role in the biosynthesis of terpenoids. Mentha plants are rich in essential oils, whose main components are terpenoids, and their biosynthetic pathways have been basically elucidated. However, there is a lack of systematic identification and study of TPS in Mentha plants. In this work, we genome-widely identified and analyzed the TPS gene family in Mentha longifolia, a model plant for functional genomic research in the genus Mentha. A total of 63 TPS genes were identified in the M. longifolia genome sequence assembly, which could be divided into six subfamilies. The TPS-b subfamily had the largest number of genes, which might be related to the abundant monoterpenoids in Mentha plants. The TPS-e subfamily had 18 members and showed a significant species-specific expansion compared with other sequenced Lamiaceae plant species. The 63 TPS genes could be mapped to nine scaffolds of the M. longifolia genome sequence assembly and the distribution of these genes is uneven. Tandem duplicates and fragment duplicates contributed greatly to the increase in the number of TPS genes in M. longifolia. The conserved motifs (RR(X)8W, NSE/DTE, RXR, and DDXXD) were analyzed in M. longifolia TPSs, and significant differentiation was found between different subfamilies. Adaptive evolution analysis showed that M. longifolia TPSs were subjected to purifying selection after the species-specific expansion, and some amino acid residues under positive selection were identified. Furthermore, we also cloned and analyzed the catalytic activity of a single terpene synthase, MlongTPS29, which belongs to the TPS-b subfamily. MlongTPS29 could encode a limonene synthase and catalyze the biosynthesis of limonene, an important precursor of essential oils from the genus Mentha. This study provides useful information for the biosynthesis of terpenoids in the genus Mentha.
Collapse
|
18
|
Li YG, Mou FJ, Li KZ. De novo RNA sequencing and analysis reveal the putative genes involved in diterpenoid biosynthesis in Aconitum vilmorinianum roots. 3 Biotech 2021; 11:96. [PMID: 33520582 DOI: 10.1007/s13205-021-02646-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 01/06/2021] [Indexed: 12/01/2022] Open
Abstract
In this study, the putative genes involved in diterpenoid alkaloids biosynthesis in A. vilmorinianum roots were revealed by transcriptome sequencing. 59.39 GB of clean bases and 119,660 unigenes were assembled, of which 69,978 unigenes (58.48%) were annotated. We identified 27 classes of genes (139 candidate genes) involved in the synthesis of diterpenoid alkaloids, including the mevalonate (MVA) pathway, the methylerythritol 4-phosphate (MEP) pathway, the farnesyl diphosphate regulatory pathway, and the diterpenoid scaffold synthetic pathway. 12 CYP450 genes were identified. We found that hydroxymethylglutaryl-CoA reductase was the key enzyme in MVA metabolism, which was regulated by miR6300. Transcription factors, such as bHLH, AP2/EREBP, and MYB, used to synthesize the diterpenes were analyzed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02646-6.
Collapse
Affiliation(s)
- Yi-Guo Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Jingming South Road 727#, Kunming, 650500 People's Republic of China
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Jingming South Road 727#, Kunming, 650500 People's Republic of China
- Kunming Biological Resources Development and Innovation Office, Kunming Bureau of Agriculture and Rural Affairs, Kunming, 650500 People's Republic of China
| | - Feng-Juan Mou
- Faculty of Forestry, Southwest Forestry University, Bailongsi 300#, Panlong, Kunming, 650224 Yunnan People's Republic of China
| | - Kun-Zhi Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Jingming South Road 727#, Kunming, 650500 People's Republic of China
| |
Collapse
|
19
|
Kurepa J, Smalle JA. Composition of the metabolomic bio-coronas isolated from Ocimum sanctum and Rubia tinctorum. BMC Res Notes 2021; 14:6. [PMID: 33407859 PMCID: PMC7789504 DOI: 10.1186/s13104-020-05420-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Objective Nanoharvesting from intact plants, organs, and cultured cells is a method in which nanoparticles are co-incubated with the target tissue, which leads to the internalization of nanoparticles. Internalized nanoparticles are coated in situ with specific metabolites that form a dynamic surface layer called a bio-corona. Our previous study showed that metabolites that form the bio-corona around anatase TiO2 nanoparticles incubated with leaves of the model plant Arabidopsis thaliana are enriched for flavonoids and lipids. The present study focused on the identification of metabolites isolated by nanoharvesting from two medicinal plants, Ocimum sanctum (Tulsi) and Rubia tinctorum (common madder). Results To identify metabolites that form the bio-corona, Tulsi leaves and madder roots were incubated with ultra-small anatase TiO2 nanoparticles, the coated nanoparticles were collected, and the adsorbed molecules were released from the nanoparticle surface and analyzed using an untargeted metabolomics approach. Similar to the results in which Arabidopsis tissue was used as a source of metabolites, TiO2 nanoparticle bio-coronas from Tulsi and madder were enriched for flavonoids and lipids, suggesting that nanoharvesting has a wide-range application potential. The third group of metabolites enriched in bio-coronas isolated from both plants were small peptides with C-terminal arginine and lysine residues.
Collapse
Affiliation(s)
- Jasmina Kurepa
- Plant Physiology, Biochemistry, Molecular Biology Program, Department of Plant and Soil Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA
| | - Jan A Smalle
- Plant Physiology, Biochemistry, Molecular Biology Program, Department of Plant and Soil Sciences, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, 40546, USA.
| |
Collapse
|
20
|
Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
Collapse
Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
| |
Collapse
|
21
|
Gonda I, Faigenboim A, Adler C, Milavski R, Karp MJ, Shachter A, Ronen G, Baruch K, Chaimovitsh D, Dudai N. The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding. DNA Res 2020; 27:6042144. [PMID: 33340318 PMCID: PMC7758295 DOI: 10.1093/dnares/dsaa027] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Indexed: 01/02/2023] Open
Abstract
Sweet basil, Ocimum basilicum L., is a well-known culinary herb grown worldwide, but its uses go beyond the kitchen to traditional medicine, cosmetics and gardening. To date, the lack of an available reference genome has limited the utilization of advanced molecular breeding methods. We present a draft version of the sweet basil genome of the cultivar ‘Perrie’, a fresh-cut Genovese-type basil. Genome sequencing showed basil to be a tetraploid organism with a genome size of 2.13 Gbp, assembled in 12,212 scaffolds, with > 90% of the assembly being composed of 107 scaffolds. About 76% of the genome is composed of repetitive elements, with the majority being long-terminal repeats. We constructed and annotated 62,067 protein-coding genes and determined their expression in different plant tissues. We analysed the currently known phenylpropanoid volatiles biosynthesis genes. We demonstrated the necessity of the reference genome for a comprehensive understanding of this important pathway in the context of tetraploidy and gene redundancy. A complete reference genome is essential to overcome this redundancy and to avoid off-targeting when designing a CRISPR: Cas9-based genome editing research. This work bears promise for developing fast and accurate breeding tools to provide better cultivars for farmers and improved products for consumers.
Collapse
Affiliation(s)
- Itay Gonda
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Adi Faigenboim
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Chen Adler
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Renana Milavski
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Merrie-Jean Karp
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Alona Shachter
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Gil Ronen
- NRGene Ltd, Park HaMada, Ness Ziona, Israel
| | | | - David Chaimovitsh
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| | - Nativ Dudai
- Unit of Aromatic and Medicinal Plants, Newe Ya'ar Research Center, Agricultural Research Organization, Ramat Yishay, Israel
| |
Collapse
|
22
|
Son J, Lee SY. Therapeutic Potential of Ursonic Acid: Comparison with Ursolic Acid. Biomolecules 2020; 10:E1505. [PMID: 33147723 PMCID: PMC7693102 DOI: 10.3390/biom10111505] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022] Open
Abstract
Plants have been used as drugs to treat human disease for centuries. Ursonic acid (UNA) is a naturally occurring pentacyclic triterpenoid extracted from certain medicinal herbs such as Ziziphus jujuba. Since the pharmacological effects and associated mechanisms of UNA are not well-known, in this work, we attempt to introduce the therapeutic potential of UNA with a comparison to ursolic acid (ULA), a well-known secondary metabolite, for beneficial effects. UNA has a keto group at the C-3 position, which may provide a critical difference for the varied biological activities between UNA and ULA. Several studies previously showed that UNA exerts pharmaceutical effects similar to, or stronger than, ULA, with UNA significantly decreasing the survival and proliferation of various types of cancer cells. UNA has potential to exert inhibitory effects in parasitic protozoa that cause several tropical diseases. UNA also exerts other potential effects, including antihyperglycemic, anti-inflammatory, antiviral, and antioxidant activities. Of note, a recent study highlighted the suppressive potential of UNA against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Molecular modifications of UNA may enhance bioavailability, which is crucial for in vivo and clinical studies. In conclusion, UNA has promising potential to be developed in anticancer and antiprotozoan pharmaceuticals. In-depth investigations may increase the possibility of UNA being developed as a novel reagent for chemotherapy.
Collapse
Affiliation(s)
| | - Sang Yeol Lee
- Department of Life Sciences, College of BioNano Technology, Gachon University, Seongnam, Gyeonggi 13120, Korea;
| |
Collapse
|
23
|
Suthar MK, Saran PL. Anthocyanins from Ocimum sanctum L., a promising biomolecule for development of cost-effective and widely applicable pH indicator. 3 Biotech 2020; 10:388. [PMID: 32832338 DOI: 10.1007/s13205-020-02380-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/04/2020] [Indexed: 10/23/2022] Open
Abstract
A novel cost-effective and widely applicable pH indicator was developed using anthocyanins extracted from the purple subtype of Ocimum sanctum L. and common lab filter paper. This pH indicator was successfully tested to monitor the pH of a wide range of buffers, solutions, irrigation water, and soil solution. Upon testing, the indicator displayed specific colors at corresponding pH ranges. Sucrose showed a stabilizing effect for the color of the extracted anthocyanins. Further, molecular analysis indicated that the leaves from the purple subtypes showed higher transcripts abundance for chalcone synthase, chalcone isomerase, anthocyanidin synthase, and dihydroflavonol 4-reductase than that of the green subtype. Similarly, transcription factors HY5 and a bHLH putatively involved in the biosynthesis of anthocyanins showed up-regulation in the purple subtype of O. sanctum.
Collapse
|
24
|
Singh P, Kalunke RM, Shukla A, Tzfadia O, Thulasiram HV, Giri AP. Biosynthesis and tissue-specific partitioning of camphor and eugenol in Ocimum kilimandscharicum. PHYTOCHEMISTRY 2020; 177:112451. [PMID: 32619737 DOI: 10.1016/j.phytochem.2020.112451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/13/2020] [Accepted: 06/14/2020] [Indexed: 05/12/2023]
Abstract
In Ocimum kilimandscharicum, the relative volatile composition of camphor in leaves was as high as 55%, while that of eugenol in roots was 57%. These metabolites were differentially partitioned between the aerial and root tissues. Global metabolomics revealed tissue-specific biochemical specialization, evident by the differential distribution of 2588 putative metabolites across nine tissues. Next-generation sequencing analysis indicated differential expression of 51 phenylpropanoid and 55 terpenoid pathway genes in aerial and root tissues. By integrating metabolomics with transcriptomics, the camphor biosynthesis pathway in O. kilimandscharicum was elucidated. In planta bioassays revealed the role of geranyl diphosphate synthase (gpps) and borneol dehydrogenase (bdh) in camphor biosynthesis. Further, the partitioning of camphor was attributed to tissue-specific gene expression of both the pathway entry point (gpps) and terminal (bdh) enzyme. Unlike camphor, eugenol accumulated more in roots; however, absence of the eugenol synthase gene in roots indicated long distance transport from aerial tissues. In silico co-expression analysis indicated the potential involvement of ATP-binding cassette, multidrug and toxic compound extrusion, and sugar transporters in eugenol transport. Similar partitioning was evident across five other Ocimum species. Overall, our work indicates that metabolite partitioning maybe a finely regulated process, which may have implications on plant growth, development, and defense.
Collapse
Affiliation(s)
- Priyanka Singh
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India; Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India
| | - Raviraj M Kalunke
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India
| | - Anurag Shukla
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India
| | - Oren Tzfadia
- Department of Plant Systems Biology, Ghent University, Belgium
| | - Hirekodathakallu V Thulasiram
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India; CSIR- Institute of Genomics and Integrative Biology, Mall Road, New Delhi, 110007, India
| | - Ashok P Giri
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, 411008, Maharashtra, India.
| |
Collapse
|
25
|
Vajpayee M, Singh M, Ledwani L, Prakash R, Nema SK. Investigation of Antimicrobial Activity of DBD Air Plasma-Treated Banana Fabric Coated with Natural Leaf Extracts. ACS OMEGA 2020; 5:19034-19049. [PMID: 32775906 PMCID: PMC7408206 DOI: 10.1021/acsomega.0c02380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/06/2020] [Indexed: 06/02/2023]
Abstract
This paper focuses on the investigation of the antimicrobial activity of banana fabric treated with dielectric barrier discharge (DBD) plasma. The fabric was exposed to air plasma for varying treatment times of 1-5 min followed by coating with green tea (Camellia sinensis) and tulsi (Ocimum sanctum) leaf extracts at five different concentrations. The treated fabric was evaluated in terms of surface wettability by a range of tests like wet-out time analysis, hydrophilicity test, and contact angle measurements. The functional groups formed on the treated fabric were analyzed by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. The surface morphology was studied using atomic force microscopy (AFM) and scanning electron microscopy (SEM), and the surface chemistry was studied using X-ray photoelectron spectroscopy (XPS). The FTIR and XPS analysis results indicate that the plasma-treated fabric was found to have a higher concentration of polar groups (-COOH, -OH, -C=O) that has improved surface hydrophilicity and functionality. The antimicrobial activity of the treated fabric surface was determined both qualitatively and quantitatively by the agar plate method and modified Hoenstein test, against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria. An improvement in the antimicrobial property was observed in plasma-treated banana fabric coated with natural extracts even after four washing cycles. This study suggests that air DBD plasma treatment followed by the absorption of tea/tulsi leaf extracts can serve as a better tool for developing natural antimicrobial textiles, which could serve the purpose in medical and healthcare sectors concerning recent times. It has eventually led to better absorption of plant extracts, thereby increasing their antimicrobial activity.
Collapse
Affiliation(s)
- Mona Vajpayee
- Manipal
University Jaipur, Jaipur 303007, Rajasthan, India
| | - Mumal Singh
- Manipal
University Jaipur, Jaipur 303007, Rajasthan, India
| | - Lalita Ledwani
- Manipal
University Jaipur, Jaipur 303007, Rajasthan, India
| | - Ram Prakash
- Indian
Institute of Technology Jodhpur, Karwar 342037, Rajasthan, India
| | - Sudhir Kumar Nema
- FCIPT, Institute for Plasma Research, HBNI, Gandhinagar, Gujarat 382016, India
| |
Collapse
|
26
|
Lichman BR, Godden GT, Buell CR. Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:74-83. [PMID: 32344371 DOI: 10.1016/j.pbi.2020.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 02/19/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Plants are reservoirs of extreme chemical diversity, yet biosynthetic pathways remain underexplored in the majority of taxa. Access to improved, inexpensive genomic and computational technologies has recently enhanced our understanding of plant specialized metabolism at the biochemical and evolutionary levels including the elucidation of pathways leading to key metabolites. Furthermore, these approaches have provided insights into the mechanisms of chemical evolution, including neofunctionalization and subfunctionalization, structural variation, and modulation of gene expression. The broader utilization of genomic tools across the plant tree of life, and an expansion of genomic resources from multiple accessions within species or populations, will improve our overall understanding of chemodiversity. These data and knowledge will also lead to greater insight into the selective pressures contributing to and maintaining this diversity, which in turn will enable the development of more accurate predictive models of specialized metabolism in plants.
Collapse
Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Carol Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48824, USA.
| |
Collapse
|
27
|
Jiang SY, Jin J, Sarojam R, Ramachandran S. A Comprehensive Survey on the Terpene Synthase Gene Family Provides New Insight into Its Evolutionary Patterns. Genome Biol Evol 2020; 11:2078-2098. [PMID: 31304957 PMCID: PMC6681836 DOI: 10.1093/gbe/evz142] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2019] [Indexed: 12/02/2022] Open
Abstract
Terpenes are organic compounds and play important roles in plant growth and development as well as in mediating interactions of plants with the environment. Terpene synthases (TPSs) are the key enzymes responsible for the biosynthesis of terpenes. Although some species were employed for the genome-wide identification and characterization of the TPS family, limited information is available regarding the evolution, expansion, and retention mechanisms occurring in this gene family. We performed a genome-wide identification of the TPS family members in 50 sequenced genomes. Additionally, we also characterized the TPS family from aromatic spearmint and basil plants using RNA-Seq data. No TPSs were identified in algae genomes but the remaining plant species encoded various numbers of the family members ranging from 2 to 79 full-length TPSs. Some species showed lineage-specific expansion of certain subfamilies, which might have contributed toward species or ecotype divergence or environmental adaptation. A large-scale family expansion was observed mainly in dicot and monocot plants, which was accompanied by frequent domain loss. Both tandem and segmental duplication significantly contributed toward family expansion and expression divergence and played important roles in the survival of these expanded genes. Our data provide new insight into the TPS family expansion and evolution and suggest that TPSs might have originated from isoprenyl diphosphate synthase genes.
Collapse
Affiliation(s)
- Shu-Ye Jiang
- Genome Structural Biology Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
| | - Jingjing Jin
- Genome Structural Biology Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore.,School of Computing, National University of Singapore, Singapore.,China Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Rajani Sarojam
- Genome Structural Biology Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
| | - Srinivasan Ramachandran
- Genome Structural Biology Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
| |
Collapse
|
28
|
Singh V, Singh G, Singh V. TulsiPIN: An Interologous Protein Interactome of Ocimum tenuiflorum. J Proteome Res 2020; 19:884-899. [PMID: 31789043 DOI: 10.1021/acs.jproteome.9b00683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ocimum tenuiflorum, commonly known as holy basil or tulsi, is globally recognized for its multitude of medicinal properties. However, a comprehensive study revealing the complex interplay among its constituent proteins at subcellular level is still lacking. To bridge this gap, in this work, a genome-scale interologous protein-protein interaction (PPI) network, TulsiPIN, is developed using 36 template plants, which consists of 13 660 nodes and 327 409 binary interactions. A high confidence network, hc-TulsiPIN, consisting of 7719 nodes having 95 532 interactions is inferred using domain-domain interaction information along with interolog-based statistics, and its reliability is assessed using pathway enrichment, functional homogeneity, and protein colocalization of PPIs. Examination of topological features revealed that hc-TulsiPIN possesses conventional properties, like small-world, scale-free, and modular architecture. A total of 1625 vital proteins are predicted by statistically evaluating hc-TulsiPIN with two ensembles of corresponding random networks, each consisting of 10 000 realizations of Erdoős-Rényi and Barabási-Albert models. Also, numerous regulatory proteins like transcription factors, transcription regulators, and protein kinases are profiled. Using 36 guide genes participating in 9 secondary metabolite biosynthetic pathways, a subnetwork consisting of 171 proteins and 612 interactions was constructed, and 127 of these proteins could be successfully characterized. Detailed information of TulsiPIN is available at https://cuhpcbbtulsipin.shinyapps.io/tulsipin_v0/ .
Collapse
Affiliation(s)
- Vikram Singh
- Centre for Computational Biology and Bioinformatics , Central University of Himahcal Pradesh , Dharamshala 176206 , India
| | - Gagandeep Singh
- Centre for Computational Biology and Bioinformatics , Central University of Himahcal Pradesh , Dharamshala 176206 , India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics , Central University of Himahcal Pradesh , Dharamshala 176206 , India
| |
Collapse
|
29
|
Jamdade RA, Mahmoud T, Gairola S. Prospects of genomic resources available at the global databases for the flora of United Arab Emirates. 3 Biotech 2019; 9:333. [PMID: 31475085 PMCID: PMC6702620 DOI: 10.1007/s13205-019-1855-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/01/2019] [Indexed: 10/26/2022] Open
Abstract
This article emphasizes available genomic resources at the global databases National Center for Biotechnology Information (NCBI) GenBank, Gramene and Phytozome for the selected 378 plant taxa of the United Arab Emirates (UAE). Germplasm of these species was collected and banked at the Sharjah Seed Bank and Herbarium (SSBH) along with their related information on habit, habitat and occurrence. The occurrence statistics exhibits almost 19.84% species under rare-to-very rare category, the GenBank search statistics for this category indicates 17.72% species as studied and 2.11% as not studied. Overall, from the global search statistics for 378 plant species, it seems that about 40 (10.58%) species remained unstudied. Most of the unstudied species were herbaceous plants belonging to the mountainous habitat. Moreover, full genomes were recorded for 7 species at NCBI GenBank, 2 species at Phytozome and 1 species at Gramene database. The local search statistics (for UAE) exhibits about 10.58% of the flora that still remained unstudied and only 11 (2.90%) of the recorded species were having genomic information at NCBI GenBank. It is necessary to prioritize studies on such species that could provide valuable insight on their genetic composition in order to understand their adaptation to the natural environment. At present, the SSBH is cataloguing UAE's flora using core barcode and assisted markers that could provide a robust DNA barcode library for native plants of UAE. Our study appeals researchers to recognize and prioritize the species that need attention to enrich their genomic resources at the global databases by supporting nucleotide libraries with their conspecifics. At present, genomic resources for UAE plant taxa are limited, but with the advent of low-cost sequencing technologies these resources would flourish in the near future. Nevertheless, the information generated through genomic studies could be utilized for conservation and management of threatened and endangered plant species, Crop Wild Relatives and medicinal plants. We hope this article will promote interest in conducting additional studies in genomics of desert plants by encouraging researchers to participate in this emerging field.
Collapse
Affiliation(s)
- Rahul A. Jamdade
- Plant Biotechnology Laboratory, Sharjah Research Academy, P. Box 60999, Sharjah, UAE
| | - Tamer Mahmoud
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, P. Box 60999, Sharjah, UAE
| | - Sanjay Gairola
- Sharjah Seed Bank and Herbarium, Sharjah Research Academy, P. Box 60999, Sharjah, UAE
| |
Collapse
|
30
|
Monick S, Mohanty V, Khan M, Yerneni G, Kumar R, Cantu J, Ichi S, Xi G, Singh BR, Tomita T, Mayanil CS. A Phenotypic Switch of Differentiated Glial Cells to Dedifferentiated Cells Is Regulated by Folate Receptor α. Stem Cells 2019; 37:1441-1454. [PMID: 31381815 PMCID: PMC6899875 DOI: 10.1002/stem.3067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/18/2022]
Abstract
In a previous study, we showed that folate receptor‐α (FRα) translocates to the nucleus where it acts as a transcription factor and upregulates Hes1, Oct4, Sox2, and Klf4 genes responsible for pluripotency. Here, we show that acetylation and phosphorylation of FRα favor its nuclear translocation in the presence of folate and can cause a phenotypic switch from differentiated glial cells to dedifferentiated cells. shRNA‐FRα mediated knockdown of FRα was used to confirm the role of FRα in dedifferentiation. Ocimum sanctum hydrophilic fraction‐1 treatment not only blocks the folate mediated dedifferentiation of glial cells but also promotes redifferentiation of dedifferentiated glial cells, possibly by reducing the nuclear translocation of ~38 kDa FRα and subsequent interaction with chromatin assembly factor‐1. stem cells2019;37:1441–1454
Collapse
Affiliation(s)
- Sarah Monick
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Vineet Mohanty
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Mariam Khan
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Gowtham Yerneni
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Raj Kumar
- Institute of Advanced Sciences, Dartmouth, Massachusetts, USA
| | - Jorge Cantu
- Department of Biology, Northeastern Illinois University, Chicago, Illinois, USA
| | - Shunsuke Ichi
- Department of Neurosurgery, Japanese Red Cross Medical Center, Tokyo, Japan
| | - Guifa Xi
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bal Ram Singh
- Institute of Advanced Sciences, Dartmouth, Massachusetts, USA
| | - Tadanori Tomita
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chandra Shekhar Mayanil
- Developmental Biology Program, Stanley Manne Children's Research Institute, Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Institute of Advanced Sciences, Dartmouth, Massachusetts, USA
| |
Collapse
|
31
|
Shameer K, Naika MB, Shafi KM, Sowdhamini R. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:19-39. [DOI: 10.1016/j.pbiomolbio.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/23/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
|
32
|
The transcriptome enables the identification of candidate genes behind medicinal value of Drumstick tree (Moringa oleifera). Genomics 2019; 112:621-628. [PMID: 31048014 DOI: 10.1016/j.ygeno.2019.04.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/26/2019] [Accepted: 04/21/2019] [Indexed: 11/21/2022]
Abstract
Moringa oleifera is a plant well-known for its nutrition value, drought resistance and medicinal properties. cDNA libraries from five different tissues (leaf, root, stem, seed and flower) of M. oleifera cultivar Bhagya were generated and sequenced. We developed a bioinformatics pipeline to assemble transcriptome, along with the previously published M. oleifera genome, to predict 17,148 gene models. Few candidate genes related to biosynthesis of secondary metabolites, vitamins and ion transporters were identified. Expressions were further confirmed by real-time quantitative PCR experiments for few promising leads. Quantitative estimation of metabolites, as well as elemental analysis, was also carried out to support our observations. Enzymes in the biosynthesis of vitamins and metabolites like quercetin and kaempferol are highly expressed in leaves, flowers and seeds. The expression of iron transporters and calcium storage proteins were observed in root and leaves. In general, leaves retain the highest amount of small molecules of interest.
Collapse
|
33
|
Upadhyay AK, Sowdhamini R. Genome-Wide Analysis of Domain-Swap Predicted Products in the Genome of Anti-Stress Medicinal Plant: Ocimum tenuiflorum. Bioinform Biol Insights 2019; 13:1177932218821362. [PMID: 30692846 PMCID: PMC6335655 DOI: 10.1177/1177932218821362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/08/2018] [Indexed: 11/18/2022] Open
Abstract
Computational approaches to high-throughput data are gaining importance because
of explosion of sequences in the post-genomic era. This explosion of sequence
data creates a huge gap among the domains of sequence structure and function,
since the experimental techniques to determine the structure and function are
very expensive, time taking, and laborious in nature. Therefore, there is an
urgent need to emphasize on the development of computational approaches in the
field of biological systems. Engagement of proteins in quaternary arrangements,
such as domain swapping, might be relevant for higher compatibility of such
genes at stress conditions. In this study, the capacity to engage in domain
swapping was predicted from mere sequence information in the whole genome of
holy Basil (Ocimum tenuiflorum), which is well known to be an
anti-stress agent. Approximately, one-fourth of the proteins of O
tenuiflorum are predicted to undergo three-dimensional (3D)-domain
swapping. Furthermore, function annotation was carried out on all the predicted
domain-swap sequences from the O tenuiflorum and
Arabidopsis thaliana for their distribution in different
Pfam protein families and gene ontology (GO) terms. These domain-swapped protein
sequences are associated with many Pfam protein families with a wide range of GO
annotation terms. A comparative analysis of domain-swap-predicted sequences in
O tenuiflorum with gene products in A
thaliana reveals that around 26% (2522 sequences) are close
homologues across the 2 genomes. Functional annotation of predicted
domain-swapped sequences infers that predicted domain-swap sequences are
involved in diverse molecular functions, such as in gene regulation of abiotic
stress conditions and adaptation to different environmental niches. Finally, the
positively predicted sequences of A thaliana and O
tenuiflorum were also examined for their presence in stress
regulome, as recorded in our STIFDB database, to check the involvement of these
proteins in different abiotic stresses.
Collapse
Affiliation(s)
- Atul Kumar Upadhyay
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, India.,Division of Bioinformatics, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | | |
Collapse
|
34
|
Roy NS, Kim JA, Choi AY, Ban YW, Park NI, Park KC, Yang HS, Choi IY, Kim S. RNA-Seq De Novo Assembly and Differential Transcriptome Analysis of Korean Medicinal Herb Cirsium japonicum var. spinossimum. Genomics Inform 2018; 16:e34. [PMID: 30602095 PMCID: PMC6440657 DOI: 10.5808/gi.2018.16.4.e34] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 12/17/2018] [Indexed: 12/20/2022] Open
Abstract
Cirsium japonicum belongs to the Asteraceae or Compositae family and is a medicinal plant in Asia that has a variety of effects, including tumour inhibition, improved immunity with flavones, and antidiabetic and hepatoprotective effects. Silymarin is synthesized by 4-coumaroyl-CoA via both the flavonoid and phenylpropanoid pathways to produce the immediate precursors taxifolin and coniferyl alcohol. Then, the oxidative radicalization of taxifolin and coniferyl alcohol produces silymarin. We identified the expression of genes related to the synthesis of silymarin in C. japonicum in three different tissues, namely, flowers, leaves, and roots, through RNA sequencing. We obtained 51,133 unigenes from transcriptome sequencing by de novo assembly using Trinity v2.1.1, TransDecoder v2.0.1, and CD-HIT v4.6 software. The differentially expressed gene analysis revealed that the expression of genes related to the flavonoid pathway was higher in the flowers, whereas the phenylpropanoid pathway was more highly expressed in the roots. In this study, we established a global transcriptome dataset for C. japonicum. The data shall not only be useful to focus more deeply on the genes related to product medicinal metabolite including flavolignan but also to study the functional genomics for genetic engineering of C. japonicum.
Collapse
Affiliation(s)
- Neha Samir Roy
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea.,Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea
| | - Jung-A Kim
- Biological Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea
| | | | - Yong-Wook Ban
- Department of Forest Environmental System, Kangwon National University, Chuncheon 24341, Korea
| | - Nam-Il Park
- Department of Plant Science, Gangneung Wonju National University, Gangneung 25457, Korea
| | - Kyong-Cheul Park
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Hee-Sun Yang
- Biological Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea.,Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea
| | - Soonok Kim
- Biological Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea
| |
Collapse
|
35
|
Pathak RK, Baunthiyal M, Pandey D, Kumar A. Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities. 3 Biotech 2018; 8:454. [PMID: 30370195 PMCID: PMC6195494 DOI: 10.1007/s13205-018-1473-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
With the continuous increase in the population of developing countries and decline of natural resources, there is an urgent need to qualitatively and quantitatively augment crop productivity by using new tools and technologies for improvement of agriculturally important traits. The new scientific and technological omics-based approaches have enabled us to deal with several issues and challenges faced by modern agricultural system and provided us novel opportunities for ensuring food and nutritional security. Recent developments in sequencing techniques have made available huge amount of genomic and transcriptomic data on model and cultivated crop plants including Arabidopsis thaliana, Oryza sativa, Triticum aestivum etc. The sequencing data along with other data generated through several omics platforms have significantly influenced the disciplines of crop sciences. Gene discovery and expression profiling-based technologies are offering enormous opportunities to the scientific community which can now apply marker-assisted selection technology to assess and enhance diversity in their collected germplasm, introgress essential traits from new sources and investigate genes that control key traits of crop plants. Utilization of omics science and technologies for crop productivity, protection and management has recently been receiving a lot of attention; the majority of the efforts have been put into signifying the possible applications of various omics technologies in crop plant sciences. This article highlights the background of challenges and opportunities for augmentation of crop productivity through interventions of omics technologies in India.
Collapse
Affiliation(s)
- Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Mamta Baunthiyal
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Present Address: Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
| |
Collapse
|
36
|
Yasodha R, Vasudeva R, Balakrishnan S, Sakthi AR, Abel N, Binai N, Rajashekar B, Bachpai VKW, Pillai C, Dev SA. Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation. DNA Res 2018; 25:409-419. [PMID: 29800113 PMCID: PMC6105116 DOI: 10.1093/dnares/dsy013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/19/2018] [Indexed: 12/31/2022] Open
Abstract
Teak (Tectona grandis L. f.) is one of the precious bench mark tropical hardwood having qualities of durability, strength and visual pleasantries. Natural teak populations harbour a variety of characteristics that determine their economic, ecological and environmental importance. Sequencing of whole nuclear genome of teak provides a platform for functional analyses and development of genomic tools in applied tree improvement. A draft genome of 317 Mb was assembled at 151× coverage and annotated 36, 172 protein-coding genes. Approximately about 11.18% of the genome was repetitive. Microsatellites or simple sequence repeats (SSRs) are undoubtedly the most informative markers in genotyping, genetics and applied breeding applications. We generated 182,712 SSRs at the whole genome level, of which, 170,574 perfect SSRs were found; 16,252 perfect SSRs showed in silico polymorphisms across six genotypes suggesting their promising use in genetic conservation and tree improvement programmes. Genomic SSR markers developed in this study have high potential in advancing conservation and management of teak genetic resources. Phylogenetic studies confirmed the taxonomic position of the genus Tectona within the family Lamiaceae. Interestingly, estimation of divergence time inferred that the Miocene origin of the Tectona genus to be around 21.4508 million years ago.
Collapse
Affiliation(s)
- Ramasamy Yasodha
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Ramesh Vasudeva
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala, India
| | - Swathi Balakrishnan
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
| | - Ambothi Rathnasamy Sakthi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Nicodemus Abel
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Nagarajan Binai
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Balaji Rajashekar
- Genotypic Technology Private Limited, Bengaluru, Karnataka, India.,Institute of Computer Science, University of Tartu, Estonia
| | - Vijay Kumar Waman Bachpai
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Chandrasekhara Pillai
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
| | - Suma Arun Dev
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
| |
Collapse
|
37
|
Patel M, Patel S, Mangukia N, Patel S, Mankad A, Pandya H, Rawal R. Ocimum basilicum miRNOME revisited: A cross kingdom approach. Genomics 2018; 111:772-785. [PMID: 29775783 DOI: 10.1016/j.ygeno.2018.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/29/2018] [Accepted: 04/27/2018] [Indexed: 02/06/2023]
Abstract
O. basilicum is medicinally important herb having inevitable role in human health. However, the mechanism of action is largely unknown. Present study aims to understand the mechanism of regulation of key human target genes that could plausibly modulated by O. basilicum miRNAs in cross kingdom manner using computational and system biology approach. O. basilicum miRNA sequences were retrieved and their corresponding human target genes were identified using psRNA target and interaction analysis of hub nodes. Six O. basilicum derived miRNAs were found to modulate 26 human target genes which were associated `with PI3K-AKTand MAPK signaling pathways with PTPN11, EIF2S2, NOS1, IRS1 and USO1 as top 5 Hub nodes. O. basilicum miRNAs not only regulate key human target genes having a significance in various diseases but also paves the path for future studies that might explore potential of miRNA mediated cross-kingdom regulation, prevention and treatment of various human diseases including cancer.
Collapse
Affiliation(s)
- Maulikkumar Patel
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Shanaya Patel
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Naman Mangukia
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Saumya Patel
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Archana Mankad
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Himanshu Pandya
- Department of Botany, Bioinformatics and Climate change impacts management, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Rakesh Rawal
- Department of Life Sciences, Food Science and Nutrition, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India.
| |
Collapse
|
38
|
Wheeler GL, Carstens BC. Evaluating the adaptive evolutionary convergence of carnivorous plant taxa through functional genomics. PeerJ 2018; 6:e4322. [PMID: 29404217 PMCID: PMC5797450 DOI: 10.7717/peerj.4322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/13/2018] [Indexed: 12/18/2022] Open
Abstract
Carnivorous plants are striking examples of evolutionary convergence, displaying complex and often highly similar adaptations despite lack of shared ancestry. Using available carnivorous plant genomes along with non-carnivorous reference taxa, this study examines the convergence of functional overrepresentation of genes previously implicated in plant carnivory. Gene Ontology (GO) coding was used to quantitatively score functional representation in these taxa, in terms of proportion of carnivory-associated functions relative to all functional sequence. Statistical analysis revealed that, in carnivorous plants as a group, only two of the 24 functions tested showed a signal of substantial overrepresentation. However, when the four carnivorous taxa were analyzed individually, 11 functions were found to be significant in at least one taxon. Though carnivorous plants collectively may show overrepresentation in functions from the predicted set, the specific functions that are overrepresented vary substantially from taxon to taxon. While it is possible that some functions serve a similar practical purpose such that one taxon does not need to utilize both to achieve the same result, it appears that there are multiple approaches for the evolution of carnivorous function in plant genomes. Our approach could be applied to tests of functional convergence in other systems provided on the availability of genomes and annotation data for a group.
Collapse
Affiliation(s)
- Gregory L. Wheeler
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, United States of America
| | - Bryan C. Carstens
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, United States of America
| |
Collapse
|
39
|
Rastogi S, Shasany AK. Ocimum Genome Sequencing—A Futuristic Therapeutic Mine. THE OCIMUM GENOME 2018. [PMCID: PMC7124093 DOI: 10.1007/978-3-319-97430-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Next-generation sequencing (NGS) platforms from the past decade are in the continuous efforts of changing the impact of sequencing on our current knowledge about plant genes, genomes, and their regulation. Holy basil (Ocimum tenuiflorum L. or sanctum L.) genome sequencing has also paved the path for deeper exploration of the medicinal properties of this beneficial herb making it a true ‘elixir of life.’ The draft genome sequence of the holy basil has not only opened the avenues for the drug discovery but has also widened the prospects of the molecular breeding for development of new improved plant varieties.
Collapse
|
40
|
Rather GA, Sharma A, Pandith SA, Kaul V, Nandi U, Misra P, Lattoo SK. De novo transcriptome analyses reveals putative pathway genes involved in biosynthesis and regulation of camptothecin in Nothapodytes nimmoniana (Graham) Mabb. PLANT MOLECULAR BIOLOGY 2018; 96:197-215. [PMID: 29270891 DOI: 10.1007/s11103-017-0690-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 12/06/2017] [Indexed: 05/28/2023]
Abstract
Comprehensive transcriptome analysis of leaf and root tissues of Nothapodytes nimmoniana unravels several putative pathway genes, transcription factors and CYPs related to camptothecin (CPT) biosynthesis. Additionally, post-transcriptional suppression by artificial microRNA (aMIR) of NnCYP76B6 (geraniol 10-hydroxylase) suggests its role in CPT biosynthesis. Tissue-specific LC-MS/MS analysis revealed the presence of secologanin as the central intermediate of MIA pathway in N. nimmoniana. Nothapodytes nimmoniana is a rich source of potent anticancer drug camptothecin (CPT) whose biosynthetic pathway is unresolved due to the lack of genomic and transcriptomic information. Present investigation entails deep transcriptome analysis of N. nimmoniana which led to identification of putative pathway genes and regulatory components involved in CPT biosynthesis. Using Illumina HiSeq 2500 sequencing platform a total of 31,172,889 (6.23 Gb) and 31,218,626 (6.24 Gb) raw reads were generated from leaf and root wood, respectively. These were assembled de novo into 138,183 unique contigs. Additionally, 16 cytochrome P450 transcripts related to secondary metabolism were also identified. Further, transcriptome data pool presented 1683 putative transcription factors of which transcripts corresponding to WRKY TFs were the most abundant (14.14%). A total of 2741 transcripts were differentially expressed out of which 478 contigs showed downregulation in root wood and 2263 contigs were up-regulated. Further, comparative analyses of 17 genes involved in CPT biosynthetic pathway were validated by qRT-PCR. On basis of intermediates, two distinct seco-iridoid pathways are involved in the biosynthesis of monoterpene indole alkaloids either through multiple isomers of strictosidinic acid or strictosidine. Tissue-specific LC-MS/MS analysis revealed the presence of secologanin as the central intermediate of MIA pathway in N. nimmoniana. Geraniol-10 hydroxylase (NnCYP76B6) an important enzyme in CPT biosynthesis which specifically shunts geraniol into the secologanin pathway was also cloned from the trancriptome resource. In planta transient expression of NnCYP76B6 showed a significant enhancement in mRNA transcript levels coincident with enhanced CPT accumulation. Further, artificial microRNA (aMIR) mediated downregulation of NnCYP76B6 resulted in reduction of mRNA transcript levels as well as CPT content in comparison to control. These empirical results suggest a plausible regulatory role for NnCYP76B6 in CPT biosynthesis and also establish a valuable repository for deciphering various structural, rate limiting and regulatory genes of CPT biosynthetic pathway.
Collapse
Affiliation(s)
- Gulzar A Rather
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Arti Sharma
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Shahzad A Pandith
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Veenu Kaul
- Department of Botany, University of Jammu, Jammu Tawi, 180006, India
| | - Utpal Nandi
- PK-PD Toxicology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India
| | - Prashant Misra
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
| | - Surrinder K Lattoo
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu Tawi, 180001, India.
| |
Collapse
|
41
|
Goswami HK, Ram HK. Ancient Food Habits Dictate that Food Can Be Medicine but Medicine Cannot Be "Food"!! MEDICINES (BASEL, SWITZERLAND) 2017; 4:E82. [PMID: 29137206 PMCID: PMC5750606 DOI: 10.3390/medicines4040082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/07/2017] [Accepted: 11/08/2017] [Indexed: 11/16/2022]
Abstract
Background: Extensive surveys of several population settlements in different parts of India-covering plains, mountains, valleys, river banks and deeper areas of forests at different altitudes-between 1968 and 2016 demonstrated that the basic vital need of hunger is being fulfilled since antiquity by plants in the wild. Methods: Based on collections, consultations with local population personnel and literature searches, this paper presents many plants that are commonly used as food and focuses on their products, which are rich in alkaloids, polysaccharides, steroids, terpenoids, flavonoids, aminoacids, fatty acids and antibiotics etc. These complex organic compounds are suitable for the production of drugs for many ailments/diseases, including the prevention of cancers. Results: There are more than 100 families including several hundred plant taxa from various plant groups like angiosperms, bryophytes, pteridophytes, gymnosperms and even fleshy fungi, which have offered essential food items to ever-growing human populations since antiquity. Phytochemicals functioning as antioxidants are exceedingly beneficial to the human body but excess consumption of these compounds, adding higher levels of antioxidants, may even be responsible for chronic diseases including aging, cancer, cardiovascular diseases, rheumatoid arthritis, atherosclerosis, etc. These medicines can obviously be taken in small and prescribed quantities but can never be consumed as "food items."
Collapse
Affiliation(s)
- Hit Kishore Goswami
- Retired Professor of Botany & Genetics, 24, Kaushalnagar, P.O. Misrod, Bhopal (MP) 462026, India.
| | - Hitendra Kumar Ram
- Department of Biodiversity Conservation and management, ABVH University, Bhopal (MP) 462001, India.
| |
Collapse
|
42
|
Nguyen HTL, Panyoyai N, Paramita VD, Mantri N, Kasapis S. Physicochemical and viscoelastic properties of honey from medicinal plants. Food Chem 2017; 241:143-149. [PMID: 28958512 DOI: 10.1016/j.foodchem.2017.08.070] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/30/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]
Abstract
The present work investigated the physicochemical and structural properties of Tulsi, Alfalfa and two varieties of Manuka honey derived from medicinal plants. Chemical analysis yielded data on the content of reducing sugars (glucose and fructose) that dominate the honey matrix, and of the minor constituents of protein, phenols and flavonoids. Standard chemical assays were used to develop a database of water content, electrical conductivity, pH, ash content, visual appearance and colour intensity. Physicochemical characteristics were related to structural behaviour of the four honey types, as recorded by small-deformation dynamic oscillation in shear, micro- and modulated differential scanning calorimetry, wide angle X-ray diffraction and infrared spectroscopy. The preponderance of hydrogen bonds in intermolecular associations amongst monosaccharides in honey yields a semi-amorphous or semi-crystalline system. That allowed prediction of the calorimetric and mechanical glass transition temperatures that demarcate the passage from liquid-like to solid-like consistency at subzero temperatures.
Collapse
Affiliation(s)
- Huong Thi Lan Nguyen
- School of Science, RMIT University, Bundoora Campus, Bundoora, Vic 3083, Melbourne, Australia
| | - Naksit Panyoyai
- School of Science, RMIT University, Bundoora Campus, Bundoora, Vic 3083, Melbourne, Australia
| | - Vilia Darma Paramita
- School of Science, RMIT University, Bundoora Campus, Bundoora, Vic 3083, Melbourne, Australia
| | - Nitin Mantri
- School of Science, RMIT University, Bundoora Campus, Bundoora, Vic 3083, Melbourne, Australia
| | - Stefan Kasapis
- School of Science, RMIT University, Bundoora Campus, Bundoora, Vic 3083, Melbourne, Australia.
| |
Collapse
|
43
|
Huang AC, Kautsar SA, Hong YJ, Medema MH, Bond AD, Tantillo DJ, Osbourn A. Unearthing a sesterterpene biosynthetic repertoire in the Brassicaceae through genome mining reveals convergent evolution. Proc Natl Acad Sci U S A 2017; 114:E6005-E6014. [PMID: 28673978 PMCID: PMC5530694 DOI: 10.1073/pnas.1705567114] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sesterterpenoids are a rare terpene class harboring untapped chemodiversity and bioactivities. Their structural diversity originates primarily from the scaffold-generating sesterterpene synthases (STSs). In fungi, all six known STSs are bifunctional, containing C-terminal trans-prenyltransferase (PT) and N-terminal terpene synthase (TPS) domains. In plants, two colocalized PT and TPS gene pairs from Arabidopsis thaliana were recently reported to synthesize sesterterpenes. However, the landscape of PT and TPS genes in plant genomes is unclear. Here, using a customized algorithm for systematically searching plant genomes, we reveal a suite of physically colocalized pairs of PT and TPS genes for the biosynthesis of a large sesterterpene repertoire in the wider Brassicaceae. Transient expression of seven TPSs from A. thaliana, Capsella rubella, and Brassica oleracea in Nicotiana benthamiana yielded fungal-type sesterterpenes with tri-, tetra-, and pentacyclic scaffolds, and notably (-)-ent-quiannulatene, an enantiomer of the fungal metabolite (+)-quiannulatene. Protein and structural modeling analysis identified an amino acid site implicated in structural diversification. Mutation of this site in one STS (AtTPS19) resulted in premature termination of carbocation intermediates and accumulation of bi-, tri-, and tetracyclic sesterterpenes, revealing the cyclization path for the pentacyclic sesterterpene (-)-retigeranin B. These structural and mechanistic insights, together with phylogenetic analysis, suggest convergent evolution of plant and fungal STSs, and also indicate that the colocalized PT-TPS gene pairs in the Brassicaceae may have originated from a common ancestral gene pair present before speciation. Our findings further provide opportunities for rapid discovery and production of sesterterpenes through metabolic and protein engineering.
Collapse
Affiliation(s)
- Ancheng C Huang
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Satria A Kautsar
- Bioinformatics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Young J Hong
- Department of Chemistry, University of California, Davis, CA 95616
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Andrew D Bond
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, CA 95616
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom;
| |
Collapse
|
44
|
Zhuang Y, Tripp EA. The draft genome of Ruellia speciosa (Beautiful Wild Petunia: Acanthaceae). DNA Res 2017; 24:179-192. [PMID: 28431014 PMCID: PMC5397612 DOI: 10.1093/dnares/dsw054] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 11/13/2022] Open
Abstract
The genus Ruellia (Wild Petunias; Acanthaceae) is characterized by an enormous diversity of floral shapes and colours manifested among closely related species. Using Illumina platform, we reconstructed the draft genome of Ruellia speciosa, with a scaffold size of 1,021 Mb (or ∼1.02 Gb) and an N50 size of 17,908 bp, spanning ∼93% of the estimated genome (∼1.1 Gb). The draft assembly predicted 40,124 gene models and phylogenetic analyses of four key enzymes involved in anthocyanin colour production [flavanone 3-hydroxylase (F3H), flavonoid 3'-hydroxylase (F3'H), flavonoid 3',5'-hydroxylase (F3'5'H), and dihydroflavonol 4-reductase (DFR)] found that most angiosperms here sampled harboured at least one copy of F3H, F3'H, and DFR. In contrast, fewer than one-half (but including R. speciosa) harboured a copy of F3'5'H, supporting observations that blue flowers and/or fruits, which this enzyme is required for, are less common among flowering plants. Ka/Ks analyses of duplicated copies of F3'H and DFR in R. speciosa suggested purifying selection in the former but detected evidence of positive selection in the latter. The genome sequence and annotation of R. speciosa represents only one of only four families sequenced in the large and important Asterid clade of flowering plants and, as such, will facilitate extensive future research on this diverse group, particularly with respect to floral evolution.
Collapse
Affiliation(s)
- Yongbin Zhuang
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309, USA
- Museum of Natural History, University of Colorado, UCB 350, Boulder, CO 80309, USA
| | - Erin A. Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO 80309, USA
- Museum of Natural History, University of Colorado, UCB 350, Boulder, CO 80309, USA
| |
Collapse
|
45
|
Zhan X, Yang L, Wang D, Zhu JK, Lang Z. De novo assembly and analysis of the transcriptome of Ocimum americanum var. pilosum under cold stress. BMC Genomics 2016; 17:209. [PMID: 26955811 PMCID: PMC4784345 DOI: 10.1186/s12864-016-2507-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/19/2016] [Indexed: 01/21/2023] Open
Abstract
Background Ocimum americanum var. pilosum is a chilling-sensitive, widely distributed plant that is consumed as a vegetable in central and southern China. To increase our understanding of cold stress responses in this species, we performed de novo transcriptome assembly for O. americanum var. pilosum and compared the transcriptomes of plants grown under normal and low temperatures. Results A total of 115,022,842 high quality, clean reads were obtained from four libraries (two replicates of control samples and two replicates of chilling-treated samples) and were used to perform de novo transcriptome assembly. After isoforms were considered, 42,816 unigenes were generated, 30,748 of which were similar to known proteins as determined by a BLASTx search (E-value < =1.0E-05) against NCBI non-redundant, Swiss-Prot, Gene Ontology, KEGG, and Cluster of COG databases. Comparative analysis of transcriptomes revealed that 5179 unigenes were differentially expressed (with at least 2-fold changes, FDR < 0.01) in chilling-treated samples, and that 2344 and 2835 unigenes were up- and down-regulated by chilling stress, respectively. Expression of the 10 most up-regulated and the five most down-regulated unigenes was validated by qRT-PCR. To increase our understanding of these differentially expressed unigenes, we performed Gene ontology and KEGG pathway enrichment analyses. The CBF-mediated transcriptional cascade, a well-known cold tolerance pathway, was reconstructed using our de novo assembled transcriptome. Conclusion Our study has generated a genome-wide transcript profile of O. americanum var. pilosum and a de novo assembled transcriptome, which can be used to characterize genes related to diverse biological processes. This is the first study to assess the cold-responsive transcriptome in an Ocimum species. Our results suggest that cold temperature significantly affects genes related to protein translation and cellular metabolism in this chilling sensitive species. Although most of the CBF pathway genes have orthologs in O. americanum var. pilosum, none of the identified cold responsive (COR) gene orthologs was induced by cold, which is consistent with the lack of cold tolerance in this plant. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2507-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lan Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dong Wang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jian Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. .,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. .,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
| |
Collapse
|
46
|
Xavier C, Molina J. Phylogeny of medicinal plants depicts cultural convergence among immigrant groups in New York City. J Herb Med 2016. [DOI: 10.1016/j.hermed.2015.12.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
47
|
Singh P, Kalunke RM, Giri AP. Towards comprehension of complex chemical evolution and diversification of terpene and phenylpropanoid pathways in Ocimum species. RSC Adv 2015. [DOI: 10.1039/c5ra16637c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Evolution of chemical diversity and diversification of terpene and phenylpropanoid pathway inOcimumspecies.
Collapse
Affiliation(s)
- Priyanka Singh
- Plant Molecular Biology Unit
- Division of Biochemical Sciences
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Raviraj M. Kalunke
- Plant Molecular Biology Unit
- Division of Biochemical Sciences
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Ashok P. Giri
- Plant Molecular Biology Unit
- Division of Biochemical Sciences
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| |
Collapse
|