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Sreeharsha RV, Mudalkar S, Reddy AR. Genome sequencing and analysis uncover the regulatory elements involved in the development and oil biosynthesis of Pongamia pinnata (L.) - A potential biodiesel feedstock. Front Plant Sci 2022; 13:747783. [PMID: 36092428 PMCID: PMC9454018 DOI: 10.3389/fpls.2022.747783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Due to rapid industrialization, the consumption of petro-products has increased, while fossil fuel resources have been gradually depleted. There has been a resurgence of interest in plant-derived biofuels as a sustainable alternative to fossil fuels for the purpose of reducing greenhouse gas emissions. Pongamia pinnata L., which is also known as Millettia pinnata is an oil-yielding, leguminous tree with a large and complex genome. Despite its multiple industrial applications, this orphan tree species has inconsistent yields and a limited understanding of its functional genomics. We assessed physiological and morphological characteristics of five high-yielding pongamia accessions and deduced important yield descriptors. Furthermore, we sequenced the genome of this potential biofuel feedstock using Illumina HiSeq, NextSeq, and MiSeq platforms to generate paired-end reads. Around 173 million processed reads amounting to 65.2 Gb were assembled into a 685 Mb genome, with a gap rate of 0.02%. The sequenced scaffolds were used to identify 30,000 gene models, 406,385 Simple-Sequence-Repeat (SSR) markers, and 43.6% of repetitive sequences. We further analyzed the structural information of genes belonging to certain key metabolic pathways, including lipid metabolism, photosynthesis, circadian rhythms, plant-pathogen interactions, and karanjin biosynthesis, all of which are commercially significant for pongamia. A total of 2,219 scaffolds corresponding to 29 transcription factor families provided valuable information about gene regulation in pongamia. Similarity studies and phylogenetic analysis revealed a monophyletic group of Fabaceae members wherein pongamia out-grouped from Glycine max and Cajanus cajan, revealing its unique ability to synthesize oil for biodiesel. This study is the first step toward completing the genome sequence of this imminent biofuel tree species. Further attempts at re-sequencing with different read chemistry will certainly improve the genetic resources at the chromosome level and accelerate the molecular breeding programs.
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Affiliation(s)
- Rachapudi Venkata Sreeharsha
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- Department of Life Sciences, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | - Shalini Mudalkar
- Department of Tree Breeding and Improvement, Forest College and Research Institute (FCRI), Hyderabad, India
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Sreeharsha RV, Venkata Mohan S. Symbiotic integration of bioprocesses to design a self-sustainable life supporting ecosystem in a circular economy framework. Bioresour Technol 2021; 326:124712. [PMID: 33517050 DOI: 10.1016/j.biortech.2021.124712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 10/31/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Climate change, resource depletion and unsustainable crop productivity are major challenges that mankind is currently facing. Natural ecosystems of earth's biosphere are becoming vulnerable and there is a need to design Bioregenerative Life Support Systems (BLSS) which are ecologically engineered microcosms that could effectively deal with problems associated with urbanization and industrialization in a sustainable manner. The principles of BLSS could be integrated with waste fed biorefineries and solar energy to create a self-sustainable bioregenerative ecosystem (SSBE). Such engineered ecosystems will have potential to fulfil urban life essentials and climate change mitigation thus generating ecologically smart and resilient communities which can strengthen the global economy. This article provides a detailed overview on SSBE framework and its improvement in the contemporary era to achieve circular bioeconomy by means of effective resource recycling.
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Affiliation(s)
- Rachapudi Venkata Sreeharsha
- Bioengineering and Environmental Science Laboratory, Department of Energy and Environmental, Engineering, CSIR- Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India
| | - S Venkata Mohan
- Bioengineering and Environmental Science Laboratory, Department of Energy and Environmental, Engineering, CSIR- Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India.
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Sreeharsha RV, Mohan SV. Obscure yet Promising Oleaginous Yeasts for Fuel and Chemical Production. Trends Biotechnol 2020; 38:873-887. [DOI: 10.1016/j.tibtech.2020.02.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 02/08/2023]
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Ranadheer P, Kona R, Sreeharsha RV, Venkata Mohan S. Non-lethal nitrate supplementation enhances photosystem II efficiency in mixotrophic microalgae towards the synthesis of proteins and lipids. Bioresour Technol 2019; 283:373-377. [PMID: 30929825 DOI: 10.1016/j.biortech.2019.03.089] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [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: 01/18/2019] [Revised: 03/15/2019] [Accepted: 03/16/2019] [Indexed: 06/09/2023]
Abstract
The current study is aimed at understanding the effect of two different concentrations of nitrate (NaNO3) i.e., 2.94 mM (1X) and 8.82 mM (3X) on the productivity of Scenedesmus sp. in terms photosynthetic efficiency, growth, biomass and protein/lipid synthesis. The experiments were conducted by growing the microalgae in mixotrophic mode with a fixed dissolved organic carbon (110 mM). Chlorophyll a fluorescence fast kinetics parameter such as FV/FM, FM/FO, Pi_Abs, TRo/RC and ABS/RC depicted an improved PSII efficiency in 3X conditions. Higher nitrate concentration in BBM medium favored better assimilation of chlorophyll pigments, carbohydrates (160 mg/g), proteins (524 mg/g) and total lipids along with higher biomass (11.4 g/L). The microalgae cell growth, biomass and biochemical composition are significantly influenced by excess nitrates supplementation in the growth medium.
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Affiliation(s)
- Palle Ranadheer
- Bioengineering and Environmental Sciences Lab, CEEFF, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India
| | - Rajesh Kona
- Bioengineering and Environmental Sciences Lab, CEEFF, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India; Academy of Scientific and Innovative Research (AcSIR), India
| | - Rachapudi Venkata Sreeharsha
- Bioengineering and Environmental Sciences Lab, CEEFF, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India
| | - S Venkata Mohan
- Bioengineering and Environmental Sciences Lab, CEEFF, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India; Academy of Scientific and Innovative Research (AcSIR), India.
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Sreeharsha RV, Mudalkar S, Sengupta D, Unnikrishnan DK, Reddy AR. Mitigation of drought-induced oxidative damage by enhanced carbon assimilation and an efficient antioxidative metabolism under high CO 2 environment in pigeonpea (Cajanus cajan L.). Photosynth Res 2019; 139:425-439. [PMID: 30244353 DOI: 10.1007/s11120-018-0586-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 06/20/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
In the current study, pigeonpea (Cajanus cajan L.), a promising legume food crop was assessed for its photosynthetic physiology, antioxidative system as well as C and N metabolism under elevated CO2 and combined drought stress (DS). Pigeonpea was grown in open top chambers under elevated CO2 (600 µmol mol-1) and ambient CO2 (390 ± 20 µmol mol-1) concentrations, later subjected to DS by complete water withholding. The DS plants were re-watered and recovered (R) to gain normal physiological growth and assessed the recoverable capacity in both elevated and ambient CO2 concentrations. The elevated CO2 grown pigeonpea showed greater gas exchange physiology, nodule mass and total dry biomass over ambient CO2 grown plants under well-watered (WW) and DS conditions albeit a decrease in leaf relative water content (LRWC). Glucose, fructose and sucrose levels were measured to understand the role of hexose to sucrose ratios (H:S) in mediating the drought responses. Free amino acid levels as indicative of N assimilation provided insights into C and N balance under DS and CO2 interactions. The enzymatic and non-enzymatic antioxidants showed significant upregulation in elevated CO2 grown plants under DS thereby protecting the plant from oxidative damage caused by the reactive oxygen species. Our results clearly demonstrated the protective role of elevated CO2 under DS at lower LRWC and gained comparative advantage of mitigating the DS-induced damage over ambient CO2 grown pigeonpea.
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Affiliation(s)
- Rachapudi Venkata Sreeharsha
- Photosynthesis and Climate Change Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Shalini Mudalkar
- Photosynthesis and Climate Change Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Debashree Sengupta
- Photosynthesis and Climate Change Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Divya K Unnikrishnan
- Photosynthesis and Climate Change Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Attipalli Ramachandra Reddy
- Photosynthesis and Climate Change Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India.
- Yogi Vemana University, Kadapa, Andhra Pradesh, 516003, India.
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Kumar S, Sreeharsha RV, Mudalkar S, Sarashetti PM, Reddy AR. Molecular insights into photosynthesis and carbohydrate metabolism in Jatropha curcas grown under elevated CO 2 using transcriptome sequencing and assembly. Sci Rep 2017; 7:11066. [PMID: 28894153 PMCID: PMC5593950 DOI: 10.1038/s41598-017-11312-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 08/21/2017] [Indexed: 12/14/2022] Open
Abstract
Jatropha curcas L. (Family - Euphorbiaceae) is a perennial tree of special interest due to its potential as a biofuel plant with high carbon sequestration. In this study, physiological investigations coupled with transcriptomics in relation to photosynthesis were evaluated in Jatropha grown under ambient (395 ppm) and elevated (550 ppm) CO2 atmosphere. Morphophysiological analysis revealed that Jatropha sustained enhanced photosynthesis during its growth under elevated CO2 for one year which might be linked to improved CO2 assimilation physiology and enhanced sink activity. We sequenced and analyzed the leaf transcriptome of Jatropha after one year of growth in both conditions using Illumina HiSeq platform. After optimized assembly, a total of 69,581 unigenes were generated. The differential gene expression (DGE) analysis revealed 3013 transcripts differentially regulated in elevated CO2 conditions. The photosynthesis regulatory genes were analysed for temporal expression patterns at four different growth phases which highlighted probable events contributing to enhanced growth and photosynthetic capacity including increased reducing power, starch synthesis and sucrose mobilization under elevated CO2. Overall, our data on physiological and transcriptomic analyses suggest an optimal resource allocation to the available and developing sink organs thereby sustaining improved photosynthetic rates during long-term growth of Jatropha under CO2 enriched environment.
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Affiliation(s)
- Sumit Kumar
- Photosynthesis and Stress Biology Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rachapudi Venkata Sreeharsha
- Photosynthesis and Stress Biology Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Shalini Mudalkar
- Photosynthesis and Stress Biology Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | | | - Attipalli Ramachandra Reddy
- Photosynthesis and Stress Biology Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad, India.
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Mudalkar S, Sreeharsha RV, Reddy AR. A novel aldo-keto reductase from Jatropha curcas L. (JcAKR) plays a crucial role in the detoxification of methylglyoxal, a potent electrophile. J Plant Physiol 2016; 195:39-49. [PMID: 26995646 DOI: 10.1016/j.jplph.2016.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 10/30/2015] [Revised: 03/09/2016] [Accepted: 03/09/2016] [Indexed: 06/05/2023]
Abstract
Abiotic stress leads to the generation of reactive oxygen species (ROS) which further results in the production of reactive carbonyls (RCs) including methylglyoxal (MG). MG, an α, β-dicarbonyl aldehyde, is highly toxic to plants and the mechanism behind its detoxification is not well understood. Aldo-keto reductases (AKRs) play a role in detoxification of reactive aldehydes and ketones. In the present study, we cloned and characterised a putative AKR from Jatropha curcas (JcAKR). Phylogenetically, it forms a small clade with AKRs of Glycine max and Rauwolfia serpentina. JcAKR was heterologously expressed in Escherichia coli BL-21(DE3) cells and the identity of the purified protein was confirmed through MALDI-TOF analysis. The recombinant protein had high enzyme activity and catalytic efficiency in assays containing MG as the substrate. Protein modelling and docking studies revealed MG was efficiently bound to JcAKR. Under progressive drought and salinity stress, the enzyme and transcript levels of JcAKR were higher in leaves compared to roots. Further, the bacterial and yeast cells expressing JcAKR showed more tolerance towards PEG (5%), NaCl (200mM) and MG (5mM) treatments compared to controls. In conclusion, our results project JcAKR as a possible and potential target in crop improvement for abiotic stress tolerance.
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Affiliation(s)
- Shalini Mudalkar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
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Sreeharsha RV, Sekhar KM, Reddy AR. Delayed flowering is associated with lack of photosynthetic acclimation in Pigeon pea (Cajanus cajan L.) grown under elevated CO₂. Plant Sci 2015; 231:82-93. [PMID: 25575994 DOI: 10.1016/j.plantsci.2014.11.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 09/01/2014] [Revised: 11/21/2014] [Accepted: 11/26/2014] [Indexed: 05/19/2023]
Abstract
In the present study, we investigated the likely consequences of future atmospheric CO2 concentrations [CO2] on growth, physiology and reproductive phenology of Pigeonpea. A short duration Pigeonpea cultivar (ICPL 15011) was grown without N fertilizer from emergence to final harvest in CO2 enriched atmosphere (open top chambers; 550μmolmol(-1)) for two seasons. CO2 enrichment improved both net photosynthetic rates (Asat) and foliar carbohydrate content by 36 and 43%, respectively, which further reflected in dry biomass after harvest, showing an increment of 29% over the control plants. Greater carboxylation rates of Rubisco (Vcmax) and photosynthetic electron transport rates (Jmax) in elevated CO2 grown plants measured during different growth periods, clearly demonstrated lack of photosynthetic acclimation. Further, chlorophyll a fluorescence measurements as indicated by Fv/Fm and ΔF/Fm' ratios justified enhanced photosystem II efficiency. Mass and number of root nodules were significantly high in elevated CO2 grown plants showing 58% increase in nodule mass ratio (NMR) which directly correlated with Pn. Growth under high CO2 showed significant ontogenic changes including delayed flowering. In conclusion, our data demonstrate that the lack of photosynthetic acclimation and increased carbohydrate-nitrogen reserves modulate the vegetative and reproductive growth patterns in Pigeonpea grown under elevated CO2.
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Affiliation(s)
- Rachapudi Venkata Sreeharsha
- Photosynthesis and Climate Change Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, AP, India
| | - Kalva Madhana Sekhar
- Photosynthesis and Climate Change Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, AP, India
| | - Attipalli Ramachandra Reddy
- Photosynthesis and Climate Change Laboratory, Department of Plant Sciences, University of Hyderabad, Hyderabad 500046, AP, India.
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