1
|
Joshi AG, Harini K, Meenakshi I, Shafi KM, Pasha SN, Mahita J, Sajeevan RS, Karpe SD, Ghosh P, Nitish S, Gandhimathi A, Mathew OK, Prasanna SH, Malini M, Mutt E, Naika M, Ravooru N, Rao RM, Shingate PN, Sukhwal A, Sunitha MS, Upadhyay AK, Vinekar RS, Sowdhamini R. A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways. MethodsX 2020; 7:101053. [PMID: 33024710 PMCID: PMC7528181 DOI: 10.1016/j.mex.2020.101053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/29/2020] [Indexed: 11/28/2022] Open
Abstract
This protocol describes a stepwise process to identify proteins of interest from a query proteome derived from NGS data. We implemented this protocol on Moringa oleifera transcriptome to identify proteins involved in secondary metabolite and vitamin biosynthesis and ion transport. This knowledge-driven protocol identifies proteins using an integrated approach involving sensitive sequence search and evolutionary relationships. We make use of functionally important residues (FIR) specific for the query protein family identified through its homologous sequences and literature. We screen protein hits based on the clustering with true homologues through phylogenetic tree reconstruction complemented with the FIR mapping. The protocol was validated for the protein hits through qRT-PCR and transcriptome quantification. Our protocol demonstrated a higher specificity as compared to other methods, particularly in distinguishing cross-family hits. This protocol was effective in transcriptome data analysis of M. oleifera as described in Pasha et al.Knowledge-driven protocol to identify secondary metabolite synthesizing protein in a highly specific manner. Use of functionally important residues for screening of true hits. Beneficial for metabolite pathway reconstruction in any (species, metagenomics) NGS data.
Collapse
Affiliation(s)
- Adwait G Joshi
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - K Harini
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Iyer Meenakshi
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - K Mohamed Shafi
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Yelahanka, Bangalore 560064, Karnataka, India
| | - Shaik Naseer Pasha
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Jarjapu Mahita
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Radha Sivarajan Sajeevan
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Snehal D Karpe
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Pritha Ghosh
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Sathyanarayanan Nitish
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Yelahanka, Bangalore 560064, Karnataka, India
| | - A Gandhimathi
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Oommen K Mathew
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Subramanian Hari Prasanna
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Manoharan Malini
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Eshita Mutt
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Mahantesha Naika
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Nithin Ravooru
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Rajas M Rao
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Prashant N Shingate
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Anshul Sukhwal
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Margaret S Sunitha
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Atul K Upadhyay
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India.,Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147004, Punjab, India
| | - Rithvik S Vinekar
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (NCBS-TIFR), GKVK campus, Bellary road, Bangalor 560065, Karnataka, India
| |
Collapse
|
2
|
Upadhyay AK, Chacko AR, Gandhimathi A, Ghosh P, Harini K, Joseph AP, Joshi AG, Karpe SD, Kaushik S, Kuravadi N, Lingu CS, Mahita J, Malarini R, Malhotra S, Malini M, Mathew OK, Mutt E, Naika M, Nitish S, Pasha SN, Raghavender US, Rajamani A, Shilpa S, Shingate PN, Singh HR, Sukhwal A, Sunitha MS, Sumathi M, Ramaswamy S, Gowda M, Sowdhamini R. Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties. BMC Plant Biol 2015; 15:212. [PMID: 26315624 PMCID: PMC4552454 DOI: 10.1186/s12870-015-0562-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/24/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Krishna Tulsi, a member of Lamiaceae family, is a herb well known for its spiritual, religious and medicinal importance in India. The common name of this plant is 'Tulsi' (or 'Tulasi' or 'Thulasi') and is considered sacred by Hindus. We present the draft genome of Ocimum tenuiflurum L (subtype Krishna Tulsi) in this report. The paired-end and mate-pair sequence libraries were generated for the whole genome sequenced with the Illumina Hiseq 1000, resulting in an assembled genome of 374 Mb, with a genome coverage of 61 % (612 Mb estimated genome size). We have also studied transcriptomes (RNA-Seq) of two subtypes of O. tenuiflorum, Krishna and Rama Tulsi and report the relative expression of genes in both the varieties. RESULTS The pathways leading to the production of medicinally-important specialized metabolites have been studied in detail, in relation to similar pathways in Arabidopsis thaliana and other plants. Expression levels of anthocyanin biosynthesis-related genes in leaf samples of Krishna Tulsi were observed to be relatively high, explaining the purple colouration of Krishna Tulsi leaves. The expression of six important genes identified from genome data were validated by performing q-RT-PCR in different tissues of five different species, which shows the high extent of urosolic acid-producing genes in young leaves of the Rama subtype. In addition, the presence of eugenol and ursolic acid, implied as potential drugs in the cure of many diseases including cancer was confirmed using mass spectrometry. CONCLUSIONS The availability of the whole genome of O.tenuiflorum and our sequence analysis suggests that small amino acid changes at the functional sites of genes involved in metabolite synthesis pathways confer special medicinal properties to this herb.
Collapse
Affiliation(s)
- Atul K Upadhyay
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Anita R Chacko
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - A Gandhimathi
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Pritha Ghosh
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - K Harini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Agnel P Joseph
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Adwait G Joshi
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
- Manipal University, Madhav Nagar, 576104, Manipal, Karnataka, India.
| | - Snehal D Karpe
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Swati Kaushik
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Nagesh Kuravadi
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Chandana S Lingu
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - J Mahita
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Ramya Malarini
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Sony Malhotra
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Manoharan Malini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Oommen K Mathew
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
- School of Chemical and Biotechnology, SASTRA (A University), 613401, Thanjavur, TamilNadu, India.
| | - Eshita Mutt
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Mahantesha Naika
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Sathyanarayanan Nitish
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Shaik Naseer Pasha
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
- Manipal University, Madhav Nagar, 576104, Manipal, Karnataka, India.
| | - Upadhyayula S Raghavender
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Anantharamanan Rajamani
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - S Shilpa
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Prashant N Shingate
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
- Manipal University, Madhav Nagar, 576104, Manipal, Karnataka, India.
| | | | - Anshul Sukhwal
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
- School of Chemical and Biotechnology, SASTRA (A University), 613401, Thanjavur, TamilNadu, India.
| | - Margaret S Sunitha
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Manojkumar Sumathi
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - S Ramaswamy
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Malali Gowda
- Centre for Cellular and Molecular Platforms, GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, 560 065, Bangalore, India.
| |
Collapse
|
3
|
Naika M, Shameer K, Sowdhamini R. Comparative analyses of stress-responsive genes in Arabidopsis thaliana: insight from genomic data mining, functional enrichment, pathway analysis and phenomics. Mol Biosyst 2013; 9:1888-908. [PMID: 23645342 DOI: 10.1039/c3mb70072k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biotic and abiotic stresses adversely affect agriculture by reducing crop growth and productivity worldwide. To investigate the abiotic stress-responsive genes in Arabidopsis thaliana, we compiled a dataset of stress signals and differentially upregulated genes (>= 2.5 fold change) from Stress-responsive transcription Factors DataBase (STIFDB) with additional set of stress signals and genes curated from PubMed and Gene Expression Omnibus. A dataset of 3091 genes differentially upregulated due to 14 different stress signals (abscisic acid, aluminum, cold, cold-drought-salt, dehydration, drought, heat, iron, light, NaCl, osmotic stress, oxidative stress, UV-B and wounding) were curated and used for the analysis. Details about stress-responsive enriched genes and their association with stress signals can be obtained from STIFDB2 database . The gene-stress-signal data were analyzed using an enrichment-based meta-analysis framework consisting of two different ontologies (Gene Ontology and Plant Ontology), biological pathway and functional domain annotations. We found several shared and distinct biological processes, cellular components and molecular functions associated with stress-responsive genes. Pathway analysis revealed that stress-responsive genes perturbed the pathways under the "Metabolic pathways" category. We also found several shared and stress-signal specific protein domains, suggesting functional mechanisms regulating stress-response. Phenomic characteristics of abiotic stress-responsive genes were ascertained for several stresses and found to be shared by multiple stresses in both anatomy and temporal categories of Plant Ontology. We found several constitutive stress-responsive genes that are differentially upregulated due to perturbation of different stress signals, for example a gene (AT1G68440) involved in phenylpropanoid metabolism and polyamine catabolism as responsive to seven different stress signals. We also performed structure-function prediction of five genes associated responsive to multiple abiotic stress signals. We envisage that results from our analysis that provide insight into functional repertoire, metabolic pathways and phenomic characteristics common and specifically associated with stress signals would help to understand abiotic stress regulome in Arabidopsis thaliana and may also help to develop an improved plant variety using molecular breeding and genetic engineering techniques that are rapidly stress-responsive and tolerant.
Collapse
Affiliation(s)
- Mahantesha Naika
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bangalore, 560065, India.
| | | | | |
Collapse
|
4
|
Naika M, Shameer K, Mathew OK, Gowda R, Sowdhamini R. STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice. Plant Cell Physiol 2013; 54:e8. [PMID: 23314754 PMCID: PMC3583027 DOI: 10.1093/pcp/pcs185] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 12/18/2012] [Indexed: 05/21/2023]
Abstract
Understanding the principles of abiotic and biotic stress responses, tolerance and adaptation remains important in plant physiology research to develop better varieties of crop plants. Better understanding of plant stress response mechanisms and application of knowledge derived from integrated experimental and bioinformatics approaches are gaining importance. Earlier, we showed that compiling a database of stress-responsive transcription factors and their corresponding target binding sites in the form of Hidden Markov models at promoter, untranslated and upstream regions of stress-up-regulated genes from expression analysis can help in elucidating various aspects of the stress response in Arabidopsis. In addition to the extensive content in the first version, STIFDB2 is now updated with 15 stress signals, 31 transcription factors and 5,984 stress-responsive genes from three species (Arabidopsis thaliana, Oryza sativa subsp. japonica and Oryza sativa subsp. indica). We have employed an integrated biocuration and genomic data mining approach to characterize the data set of transcription factors and consensus binding sites from literature mining and stress-responsive genes from the Gene Expression Omnibus. STIFDB2 currently has 38,798 associations of stress signals, stress-responsive genes and transcription factor binding sites predicted using the Stress-responsive Transcription Factor (STIF) algorithm, along with various functional annotation data. As a unique plant stress regulatory genomics data platform, STIFDB2 can be utilized for targeted as well as high-throughput experimental and computational studies to unravel principles of the stress regulome in dicots and gramineae. STIFDB2 is available from the URL: http://caps.ncbs.res.in/stifdb2.
Collapse
Affiliation(s)
- Mahantesha Naika
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560 065, India
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK Campus, Bellary Road, Bangalore 560 065, India
| | - Khader Shameer
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560 065, India
- Present address: Division of Biomedical Statistics and Informatics, Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Oommen K. Mathew
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560 065, India
| | - Ramanjini Gowda
- Department of Plant Biotechnology, University of Agricultural Sciences, GKVK Campus, Bellary Road, Bangalore 560 065, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560 065, India
- *Corresponding author: Email,
| |
Collapse
|