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Chinmayee C, Martin A, Gnanesh Kumar B, Singh SA. A new thermostable rhizopuspepsin: Purification and biochemical characterisation. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Maren N, Zhao F, Aryal R, Touchell D, Liu W, Ranney T, Ashrafi H. Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae). BMC Genomics 2021; 22:483. [PMID: 34182921 PMCID: PMC8237498 DOI: 10.1186/s12864-021-07641-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/20/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Tripidium ravennae is a cold-hardy, diploid species in the sugarcane complex (Poaceae subtribe Saccharinae) with considerable potential as a genetic resource for developing improved bioenergy and ornamental grasses. An improved understanding of the genetic regulation of reproductive processes (e.g., floral induction, inflorescence development, and seed development) will enable future applications of precision breeding and gene editing of floral and seed development. In particular, the ability to silence reproductive processes would allow for developing seedless forms of valuable but potentially invasive plants. The objective of this research was to characterize the gene expression environment of reproductive development in T. ravennae. RESULTS During the early phases of inflorescence development, multiple key canonical floral integrators and pathways were identified. Annotations of type II subfamily of MADS-box transcription factors, in particular, were over-represented in the GO enrichment analyses and tests for differential expression (FDR p-value < 0.05). The differential expression of floral integrators observed in the early phases of inflorescence development diminished prior to inflorescence determinacy regulation. Differential expression analysis did not identify many unique genes at mid-inflorescence development stages, though typical biological processes involved in plant growth and development expressed abundantly. The increase in inflorescence determinacy regulatory elements and putative homeotic floral development unigenes at mid-inflorescence development coincided with the expression of multiple meiosis annotations and multicellular organism developmental processes. Analysis of seed development identified multiple unigenes involved in oxidative-reductive processes. CONCLUSION Reproduction in grasses is a dynamic system involving the sequential coordination of complex gene regulatory networks and developmental processes. This research identified differentially expressed transcripts associated with floral induction, inflorescence development, and seed development in T. ravennae. These results provide insights into the molecular regulation of reproductive development and provide a foundation for future investigations and analyses, including genome annotation, functional genomics characterization, gene family evolutionary studies, comparative genomics, and precision breeding.
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Affiliation(s)
- Nathan Maren
- Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC, 27695-7609, USA.
| | - Fangzhou Zhao
- Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC, 27695-7609, USA
- College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rishi Aryal
- Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC, 27695-7609, USA
| | - Darren Touchell
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, 455 Research Drive, Mills River, NC, 28759-3423, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC, 27695-7609, USA
| | - Thomas Ranney
- Mountain Crop Improvement Lab, Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, 455 Research Drive, Mills River, NC, 28759-3423, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Campus Box 7609, Raleigh, NC, 27695-7609, USA.
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Osama SK, Kerr ED, Yousif AM, Phung TK, Kelly AM, Fox GP, Schulz BL. Proteomics reveals commitment to germination in barley seeds is marked by loss of stress response proteins and mobilisation of nutrient reservoirs. J Proteomics 2021; 242:104221. [PMID: 33866056 DOI: 10.1016/j.jprot.2021.104221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023]
Abstract
Germination is a critical process in the reproduction and propagation of flowering plants, and is also the key stage of industrial grain malting. Germination commences when seeds are steeped in water, followed by degradation of the endosperm cell walls, enzymatic digestion of starch and proteins to provide nutrients for the growing plant, and emergence of the radicle from the seed. Dormancy is a state where seeds fail to germinate upon steeping, but which prevents inappropriate premature germination of the seeds before harvest from the field. This can result in inefficiencies in industrial malting. We used Sequential Window Acquisition of all THeoretical ions Mass Spectrometry (SWATH-MS) proteomics to measure changes in the barley seed proteome throughout germination. We found a large number of proteins involved in desiccation tolerance and germination inhibition rapidly decreased in abundance after imbibition. This was followed by a decrease in proteins involved in lipid, protein and nutrient reservoir storage, consistent with induction and activation of systems for nutrient mobilisation to provide nutrients to the growing embryo. Dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, with differences in sulfur metabolic enzymes, endogenous alpha-amylase/trypsin inhibitors, and histone proteins. We verified our findings with analysis of germinating barley seeds from two commercial malting facilities, demonstrating that key features of the dynamic proteome of germinating barley seeds were conserved between laboratory and industrial scales. The results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy. SIGNIFICANCE: Germination is critical to the reproduction and propagation of flowering plants, and in industrial malting. Dormancy, where seeds fail to germinate upon steeping, can result in inefficiencies in industrial malting. Our DIA/SWATH-MS proteomics analyses identified key changes during germination, including an initial loss of proteins involved in desiccation tolerance and germination inhibition, followed by decreases in lipid, protein and nutrient reservoir storage. These changes were consistent between laboratory and industrial malting scales, and therefore demonstrate the utility of laboratory-scale barley germination as a model system for industrial malt house processes. We also showed that dormant seeds that failed to germinate showed substantial biochemical activity distinct from that of seeds undergoing germination, consistent with dormancy being an actively regulated state. Our results provide a more detailed understanding of the changes in the barley proteome during germination and give possible target proteins for testing or to inform selective breeding to enhance germination or control dormancy.
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Affiliation(s)
- Sarah K Osama
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Adel M Yousif
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Sandy Bay Campus, TAS, 7005, Australia
| | - Toan K Phung
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia
| | - Alison M Kelly
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia; Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, Qld 4350, Australia
| | - Glen P Fox
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, Qld 4350, Australia; Department of Food Science and Technology, University of California Davis, CA 95616, USA.
| | - Benjamin L Schulz
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia 4072, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane 4072, Australia.
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The Modulatory Effect of Cholesterol Synthesis by Oryza sativa Derived Bioactive Peptide Fractions: An In Vitro Investigation. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-020-10079-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kumar V, Tiku PK. A Cholesterol Homeostasis by Bioactive Peptide Fraction from Pigeon Pea By-Product: An In-Vitro Study. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-020-10143-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Dolui AK, Vijayakumar AK, Rajasekharan R, Vijayaraj P. Activity-based protein profiling of rice (Oryza sativa L.) bran serine hydrolases. Sci Rep 2020; 10:15191. [PMID: 32938958 PMCID: PMC7494864 DOI: 10.1038/s41598-020-72002-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/29/2020] [Indexed: 11/25/2022] Open
Abstract
Rice bran is an underutilized agricultural by-product with economic importance. The unique phytochemicals and fatty acid compositions of bran have been targeted for nutraceutical development. The endogenous lipases and hydrolases are responsible for the rapid deterioration of rice bran. Hence, we attempted to provide the first comprehensive profiling of active serine hydrolases (SHs) present in rice bran proteome by activity-based protein profiling (ABPP) strategy. The active site-directed fluorophosphonate probe (rhodamine and biotin-conjugated) was used for the detection and identification of active SHs. ABPP revealed 55 uncharacterized active-SHs and are representing five different known enzyme families. Based on motif and domain analyses, one of the uncharacterized and miss annotated SHs (Os12Ssp, storage protein) was selected for biochemical characterization by overexpressing in yeast. The purified recombinant protein authenticated the serine protease activity in time and protein-dependent studies. Os12Ssp exhibited the maximum activity at a pH between 7.0 and 8.0. The protease activity was inhibited by the covalent serine protease inhibitor, which suggests that the ABPP approach is indeed reliable than the sequence-based annotations. Collectively, the comprehensive knowledge generated from this study would be useful in expanding the current understanding of rice bran SHs and paves the way for better utilization/stabilization of rice bran.
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Affiliation(s)
- Achintya Kumar Dolui
- Lipid and Nutrition Laboratory, Department of Lipid Science, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Arun Kumar Vijayakumar
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.,CSIR-Central Food Technological Research Institute, Resource Centre Lucknow, Lucknow, 226018, India
| | - Ram Rajasekharan
- Lipid and Nutrition Laboratory, Department of Lipid Science, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India.,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.,School of Life Sciences, Central University of Tamil Nadu, Tamil Nadu, Neelakudi, Thiruvarur, 610 005, India
| | - Panneerselvam Vijayaraj
- Lipid and Nutrition Laboratory, Department of Lipid Science, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570020, India. .,Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.
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Purushothaman K, Bhat SK, Singh SA, Marathe GK, Appu Rao ARG. Aspartic protease from Aspergillus niger: Molecular characterization and interaction with pepstatin A. Int J Biol Macromol 2019; 139:199-212. [DOI: 10.1016/j.ijbiomac.2019.07.133] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/12/2019] [Accepted: 07/22/2019] [Indexed: 01/19/2023]
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Chinmayee CV, Vidya C, Rani A, Singh SA. Production of highly active fungal milk-clotting enzyme by solid-state fermentation. Prep Biochem Biotechnol 2019; 49:858-867. [PMID: 31219401 DOI: 10.1080/10826068.2019.1630647] [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] [Indexed: 10/26/2022]
Abstract
Cheese production is projected to reach 20 million metric tons by 2020, of which 33% is being produced using calf rennet (EC 3.4.23.4). There is shortage of calf rennet, and use of plant and microbial rennets, hydrolyze milk proteins non-specifically resulting in low curd yields. This study reports fungal enzymes obtained from cost effective medium, with minimal down streaming, whose activity is comparable with calf and Mucor rennet. Of the fifteen fungi that were screened, Mucor thermohyalospora (MTCC 1384) and Rhizopus azygosporus (MTCC 10195) exhibited the highest milk-clotting activity (MCA) of 18,383 ± 486 U/ml and 16,373 ± 558 U/ml, respectively. Optimization exhibited a 33% increase in enzyme production (30 g wheat bran containing 6% defatted soy meal at 30 °C, pH 7) for M. thermohyalospora. The enzyme was active from pH 5-10 and temperature 45-55 °C. Rhizopus azygosporus exhibited 31% increase in enzyme production (30 g wheat bran containing 4% defatted soy meal at 30 °C, pH 6) and the enzyme was active from pH 6-9 at 50 °C. Curd yields prepared from fungal enzyme extract decreased (5-9%), when compared with calf rennet and Mucor rennet. This study describes the potential of fungal enzymes, hitherto unreported, as a viable alternative to calf rennet.
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Affiliation(s)
- Cirium V Chinmayee
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute , Mysuru , India.,Currently working in AcSIR , Ghaziabad
| | - Cheral Vidya
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute , Mysuru , India.,Currently working in AcSIR , Ghaziabad
| | - Amsaraj Rani
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute , Mysuru , India
| | - Sridevi Annapurna Singh
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute , Mysuru , India
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Sreedhar R, Tiku PK. Cupincin: A Novel Cupin Domain Containing Protease from Rice ( Oryza sativa L.) Bran Comprising of Procoagulant and Fibrinogenolytic Activity. Indian J Hematol Blood Transfus 2018; 34:314-321. [PMID: 29622876 DOI: 10.1007/s12288-017-0856-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 08/01/2017] [Indexed: 11/25/2022] Open
Abstract
The current study was carried out to evaluate the pharmacological properties of cupincin- A novel cupin domain containing metalloprotease with limited proteolysis from rice bran on blood coagulation and hydrolysis of human fibrinogen. Cupincin preferentially hydrolyzed the Aα chain of fibrinogen and then the Bβ-chain, but not the γ-chain. Cupincin reduced the re-calcification time of citrated human plasma dose dependently. Analysis of citrated whole blood in the presence of cupincin by rotem showed a decrease in coagulation time and clot formation time. Sonoclot analysis indicated that cupincin cleaved fibrinogen of whole citrated blood. SDS-PAGE and sonoclot analysis (LI-30) indicated that cupincin lacked plasmin-like activity. Global hemostasis tests like rotem and sonoclot analysis determined cupincin as a procoagulant enzyme. Cupincin did not show any effect on prothrombin time and activated partial thromboplastin time tests suggesting its action on the common pathway of coagulation. The involvement of proteases from rice (Oryza sativa L.) in haemostasis has never been exploited before. This study could provide the basis for the development of new procoagulant agents from a nontoxic source like rice.
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Affiliation(s)
- Roopesh Sreedhar
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka 570020 India
| | - Purnima Kaul Tiku
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka 570020 India
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