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Obadi M, Xu B. Characteristics and applications of plant-derived antifreeze proteins in frozen dough: A review. Int J Biol Macromol 2024; 255:128202. [PMID: 37979748 DOI: 10.1016/j.ijbiomac.2023.128202] [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: 08/02/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/20/2023]
Abstract
Frozen dough technology has been widely used in the food industry at home and abroad due to its advantages of extending shelf life, preventing aging, and facilitating refrigeration and transportation. However, during the transportation and storage process of frozen dough, the growth and recrystallization of ice crystals caused by temperature fluctuations can lead to a deterioration in the quality of the dough, resulting in poor sensory characteristics of the final product and decreased consumption, which limits the large-scale application of frozen dough. In response to this issue, antifreeze proteins (AFPs) could be used as a beneficial additive to frozen dough that can combine with ice crystals, modify the ice crystal morphology, reduce the freezing point of water, and inhibit the recrystallization of ice crystals. Because of its special structure and function, it can well alleviate the quality deterioration problem caused by ice crystal recrystallization during frozen storage of dough, especially the plant-derived AFPs, which have a prominent effect on inhibiting ice crystal recrystallization. In this review, we introduce the characteristics and mechanisms of action of plant-derived AFPs. Furthermore, the application of plant-derived AFPs in frozen dough are also discussed.
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Affiliation(s)
- Mohammed Obadi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
| | - Bin Xu
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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2
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Yadav K, Arya M, Prakash S, Jha BS, Manchanda P, Kumar A, Deswal R. Brassica juncea leaf cuticle contains xylose and mannose (xylomannan) which inhibit ice recrystallization on the leaf surface. PLANTA 2023; 258:44. [PMID: 37460860 DOI: 10.1007/s00425-023-04203-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
Abstract
MAIN CONCLUSION Conjugated sugars showed antifreeze activity in the cuticle by ice recrystallization inhibition rather than thermal hysteresis, enhancing freezing capacity at the surface of B. juncea leaves. Antifreeze biomolecules play a crucial role in mitigating the physical damage from frost by controlling extracellular ice crystal growth in plants. Antifreeze proteins (AFPs) are reported from the apoplast of different plants. Interestingly, there is no report about antifreeze properties of the cuticle. Here, we report the potential antifreeze activity in the Brassica juncea (BJ) leaf cuticle. Nano LC-MS/MS analysis of a cuticle protein enriched fraction (CPE) predicted over 30 putative AFPs using CryoProtect server and literature survey. Ice crystal morphology (ICM) and ice recrystallization inhibition (IRI) analysis of ABC supernatant showed heat and pronase-resistant, non-protein antifreeze activities as well as hexagonal ice crystals with TH of 0.17 °C and IRI 46%. The ZipTip processed ABC supernatant (without peptides) had no effect on TH activity, confirming a non-protein antifreeze molecule contributing to activity. To understand the origin and to confirm the source of antifreeze activity, cuticular membranes were isolated by pectinase and cellulase hydrolysis. FTIR analysis of the intact cuticle showed xylose, mannose, cellulose, and glucose. Xylanase and cellulase treatments of the ZipTip processed ABC supernatant led to an increase in sugar content and 50% loss in antifreeze activity. UV spectroscopy and NMR analysis supported the finding of FTIR and enzyme hydrolysis suggesting the contribution of xylose and mannose to antifreeze activity. By TLC analysis, conjugated sugars were found in the cuticle. This work has opened up a new research area where the antifreeze capacity needs to be established with regard to complete characterization and mechanism of action of the antifreeze carbohydrates (conjugated sugars) on the leaf surface.
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Affiliation(s)
- Kailash Yadav
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Meenakshi Arya
- Department of Botany, Dyal Singh College, University of Delhi, Delhi, 110003, India
| | - Satya Prakash
- Department of Botany, Acharya Narendra Dev College, University of Delhi, Delhi, 110019, India
| | - Bhavana Sharma Jha
- Department of Botany, Gargi College, University of Delhi, Delhi, 110049, India
| | - Preet Manchanda
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Abhishek Kumar
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Renu Deswal
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India.
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3
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Ma Q, Niu C, Wang C, Chen C, Li Y, Wei M. Effects of differentially expressed microRNAs induced by rootstocks and silicon on improving chilling tolerance of cucumber seedlings (Cucumis sativus L.). BMC Genomics 2023; 24:250. [PMID: 37165319 PMCID: PMC10173649 DOI: 10.1186/s12864-023-09337-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 04/26/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Rootstocks can improve the chilling tolerance of grafted cucumbers, but their effectiveness varies. Rootstocks with strong de-blooming capacity may result in lower chilling tolerance of grafted cucumbers compared to those with weak de-blooming capacity, while also reducing the silicon absorption. However, it remains unclear whether this reduction in chilling tolerance is due to differences in rootstock genotypes or the reduction in silicon absorption. RESULTS The chilling tolerance of cucumber seedlings was improved by using rootstocks and silicon nutrition. Rootstocks had a more significant effect than silicon nutrition, and the weak de-blooming rootstock 'Yunnan figleaf gourd' was superior to the strong de-blooming rootstock 'Huangchenggen No. 2'. Compared to self-rooted cucumber, twelve miRNAs were regulated by two rootstocks, including seven identical miRNAs (novel-mir23, novel-mir26, novel-mir30, novel-mir37, novel-mir46, miR395a and miR398a-3p) and five different miRNAs (novel-mir32, novel-mir38, novel-mir65, novel-mir78 and miR397a). Notably, four of these miRNAs (novel-mir38, novel-mir65, novel-mir78 and miR397a) were only identified in 'Yunnan figleaf gourd'-grafted cucumbers. Furthermore, six miRNAs (miR168a-5p, miR390a-5p, novel-mir26, novel-mir55, novel-mir67 and novel-mir70) were found to be responsive to exogenous silicon. Target gene prediction for 20 miRNAs resulted in 520 genes. Functional analysis of these target genes showed that 'Yunnan figleaf gourd' improves the chilling tolerance of cucumber by regulating laccase synthesis and sulfate metabolism, while 'Huangchenggen No. 2' and exogenous silicon reduced chilling stress damage to cucumber by regulating ROS scavenging and protein protection, respectively. CONCLUSION Among the identified miRNAs, novel-mir46 and miR398a-3p were found in cucumbers in response to chilling stress and two types of rootstocks. However, no identical miRNAs were identified in response to chilling stress and silicon. In addition, the differential expression of novel-mir38, novel-mir65, novel-mir78 and miR397a may be one of the important reasons for the differences in chilling tolerance of grafted cucumbers caused by two types of rootstocks.
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Affiliation(s)
- Qiang Ma
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
| | - Chenxu Niu
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
| | - Chao Wang
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Taian, 271018, China
- State Key Laboratory of Crop Biology, Taian, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China
| | - Chunhua Chen
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
- State Key Laboratory of Crop Biology, Taian, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China
| | - Yan Li
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Taian, 271018, China
- State Key Laboratory of Crop Biology, Taian, 271018, China
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China
| | - Min Wei
- College of Horticultural Science and Engineering, Shandong Agricultural University, Taian, 271018, China.
- Scientific Observing and Experimental Station of Environment Controlled Agricultural Engineering in Huang-Huai-Hai Region, Ministry of Agriculture and Rural Affairs, Taian, 271018, China.
- State Key Laboratory of Crop Biology, Taian, 271018, China.
- Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production in Shandong, Taian, 271018, China.
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Mattoon EM, McHargue W, Bailey CE, Zhang N, Chen C, Eckhardt J, Daum CG, Zane M, Pennacchio C, Schmutz J, O'Malley RC, Cheng J, Zhang R. High-throughput identification of novel heat tolerance genes via genome-wide pooled mutant screens in the model green alga Chlamydomonas reinhardtii. PLANT, CELL & ENVIRONMENT 2023; 46:865-888. [PMID: 36479703 PMCID: PMC9898210 DOI: 10.1111/pce.14507] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 11/04/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Different high temperatures adversely affect crop and algal yields with various responses in photosynthetic cells. The list of genes required for thermotolerance remains elusive. Additionally, it is unclear how carbon source availability affects heat responses in plants and algae. We utilized the insertional, indexed, genome-saturating mutant library of the unicellular, eukaryotic green alga Chlamydomonas reinhardtii to perform genome-wide, quantitative, pooled screens under moderate (35°C) or acute (40°C) high temperatures with or without organic carbon sources. We identified heat-sensitive mutants based on quantitative growth rates and identified putative heat tolerance genes (HTGs). By triangulating HTGs with heat-induced transcripts or proteins in wildtype cultures and MapMan functional annotations, we presented a high/medium-confidence list of 933 Chlamydomonas genes with putative roles in heat tolerance. Triangulated HTGs include those with known thermotolerance roles and novel genes with little or no functional annotation. About 50% of these high-confidence HTGs in Chlamydomonas have orthologs in green lineage organisms, including crop species. Arabidopsis thaliana mutants deficient in the ortholog of a high-confidence Chlamydomonas HTG were also heat sensitive. This work expands our knowledge of heat responses in photosynthetic cells and provides engineering targets to improve thermotolerance in algae and crops.
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Affiliation(s)
- Erin M. Mattoon
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Plant and Microbial Biosciences Program, Division of Biology and Biomedical Sciences, Washington University in Saint Louis, St. Louis, Missouri 63130, USA
| | - William McHargue
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Ningning Zhang
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri 65211, USA
| | - James Eckhardt
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Chris G. Daum
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matt Zane
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christa Pennacchio
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Schmutz
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ronan C. O'Malley
- U.S. Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri 65211, USA
| | - Ru Zhang
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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de Souza Araújo DM, de Almeida AAF, Pirovani CP, Mora-Ocampo IY, Lima Silva JP, Valle Meléndez RR. Molecular, biochemical and micromorphological responses of cacao seedlings of the Parinari series, carrying the lethal gene Luteus-Pa, in the presence and absence of cotyledons. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:550-569. [PMID: 36525937 DOI: 10.1016/j.plaphy.2022.11.009] [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: 05/29/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Investigations of the compatibility between cacao genotypes of the population of the Parinari series (Pa), resulting from the reciprocal crossing of Pa 30 × Pa 169 and Pa 121 × Pa 169, allowed the verification of the occurrence of the recessive lethal single character called Luteus-Pa. These genotypes have this gene in heterozygosity, which when intercross or self-fertilize, segregate in a 3:1 ratio. Normal (NS) and mutant (MS) seedlings grow normally and, after a period of approximately 30 days of age, MS leaves begin to show a metallic yellow color, followed by necrotic spots, and death of the entire seedling, approximately 40 days after the emergency. The work evaluate the molecular, biochemical and micromorphological responses in NS and MS, with and without cotyledons, resulting from the crossing of the Pa 30 × Pa 169 cacao genotypes, aiming to elucidate the possible lethal mechanisms of the homozygous recessive Luteus-Pa. The presence of the lethal gene Luteus-Pa in the seedlings of the cacao genotypes of the population of the Parinari (Pa), with and without cotyledons, resulting from the crossing of Pa 30 × Pa 169, in addition to regulating the synthesis of proteins related to the photosynthetic and stress defense processes, promoted an increase in the synthesis of proteins involved in the glycolic pathway, induced oxidative stress, altered the mobilization of cotyledonary reserves, the integrity of cell membranes, leaf micromorphology and induced the death of seedlings, soon after depletion of protein and carbohydrate reserves, especially in the absence of cotyledons.
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Affiliation(s)
- D'avila Maria de Souza Araújo
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Alex-Alan Furtado de Almeida
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil.
| | - Carlos Priminho Pirovani
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Irma Yuliana Mora-Ocampo
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - João Paulo Lima Silva
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil
| | - Raúl René Valle Meléndez
- State University of Santa Cruz, Department of Biological Sciences, km 16 Jorge Amado Highway, 45662-900, Ilhéus, BA, Brazil; Executive Commission for the Cacao farming Plan, km 22 Jorge Amado Highway, 45650-780, Ilhéus, BA, Brazil
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Satyakam, Zinta G, Singh RK, Kumar R. Cold adaptation strategies in plants—An emerging role of epigenetics and antifreeze proteins to engineer cold resilient plants. Front Genet 2022; 13:909007. [PMID: 36092945 PMCID: PMC9459425 DOI: 10.3389/fgene.2022.909007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Cold stress adversely affects plant growth, development, and yield. Also, the spatial and geographical distribution of plant species is influenced by low temperatures. Cold stress includes chilling and/or freezing temperatures, which trigger entirely different plant responses. Freezing tolerance is acquired via the cold acclimation process, which involves prior exposure to non-lethal low temperatures followed by profound alterations in cell membrane rigidity, transcriptome, compatible solutes, pigments and cold-responsive proteins such as antifreeze proteins. Moreover, epigenetic mechanisms such as DNA methylation, histone modifications, chromatin dynamics and small non-coding RNAs play a crucial role in cold stress adaptation. Here, we provide a recent update on cold-induced signaling and regulatory mechanisms. Emphasis is given to the role of epigenetic mechanisms and antifreeze proteins in imparting cold stress tolerance in plants. Lastly, we discuss genetic manipulation strategies to improve cold tolerance and develop cold-resistant plants.
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7
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Kumar V, Kashyap P, Kumar S, Thakur V, Kumar S, Singh D. Multiple Adaptive Strategies of Himalayan Iodobacter sp. PCH194 to High-Altitude Stresses. Front Microbiol 2022; 13:881873. [PMID: 35875582 PMCID: PMC9298515 DOI: 10.3389/fmicb.2022.881873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/01/2022] [Indexed: 11/24/2022] Open
Abstract
Bacterial adaption to the multiple stressed environments of high-altitude niches in the Himalayas is intriguing and is of considerable interest to biotechnologists. Previously, we studied the culturable and unculturable metagenome microbial diversity from glacial and kettle lakes in the Western Himalayas. In this study, we explored the adaptive strategies of a unique Himalayan eurypsychrophile Iodobacter sp. PCH194, which can synthesize polyhydroxybutyrate (PHB) and violacein pigment. Whole-genome sequencing and analysis of Iodobacter sp. PCH194 (4.58 Mb chromosome and three plasmids) revealed genetic traits associated with adaptive strategies for cold/freeze, nutritional fluctuation, defense against UV, acidic pH, and the kettle lake's competitive environment. Differential proteome analysis suggested the adaptive role of chaperones, ribonucleases, secretion systems, and antifreeze proteins under cold stress. Antifreeze activity inhibiting the ice recrystallization at −9°C demonstrated the bacterium's survival at subzero temperature. The bacterium stores carbon in the form of PHB under stress conditions responding to nutritional fluctuations. However, violacein pigment protects the cells from UV radiation. Concisely, genomic, proteomic, and physiological studies revealed the multiple adaptive strategies of Himalayan Iodobacter to survive the high-altitude stresses.
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Affiliation(s)
- Vijay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Prakriti Kashyap
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Subhash Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, India
| | - Vikas Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, India
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre (CSIR-HRDC), Ghaziabad, India
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8
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Kashyap P, Kumar S. Ice structuring protein extract of Hordeum vulgare var. dolma grain reduces drip loss and loss of soluble vitamin content in peas during frozen storage. Cryobiology 2022; 104:1-7. [PMID: 34826400 DOI: 10.1016/j.cryobiol.2021.11.178] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 01/15/2023]
Abstract
The Himalayan plants face low temperature during their life cycle and are expected to possess antifreeze proteins. The present work describes screening of six plant species that grow in Himalayas, for their ice structuring properties with an aim to provide a vegetarian source of ice structuring proteins. The ice-structuring protein extract of barley [Hordeum vulgare; variety Dolma (HvISE)] and wheat [Triticum aestivum; variety Him Pratham DH 114 (TaISE) ]showed inhibition of growth of ice crystals during the process of recrystallization. This property was analyzed for its application in frozen peas by pretreatment with HvISE before freezing. The drip loss was measured in frozen peas after thawing. Further, the water-soluble vitamins; thiamine, pyridoxine, riboflavin, and ascorbic acid were quantified before and after freezing of green peas by UHPLC-PDA. The pretreatment with HvISE reduced the loss of ascorbic acid, riboflavin, and pyridoxine during their frozen storage. The present study identified barley as a remarkable source of ice structuring proteins and validated its potential for frozen peas. The work has enormous implications in frozen food industry, in general.
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Affiliation(s)
- Prakriti Kashyap
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176 061, India.
| | - Sanjay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176 061, India.
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9
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Baskaran A, Kaari M, Venugopal G, Manikkam R, Joseph J, Bhaskar PV. Anti freeze proteins (Afp): Properties, sources and applications - A review. Int J Biol Macromol 2021; 189:292-305. [PMID: 34419548 DOI: 10.1016/j.ijbiomac.2021.08.105] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022]
Abstract
Extreme cold marine and freshwater temperatures (below 4 °C) induce massive deterioration to the cell membranes of organisms resulting in the formation of ice crystals, consequently causing organelle damage or cell death. One of the adaptive mechanisms organisms have evolved to thrive in cold environments is the production of antifreeze proteins with the functional capabilities to withstand frigid temperatures. Antifreeze proteins are extensively identified in different cold-tolerant species and they facilitate the persistence of cold-adapted organisms by decreasing the freezing point of their body fluids. Various structurally diverse types of antifreeze proteins detected possess the ability to modify ice crystal growth by thermal hysteresis and ice recrystallization inhibition. The unique properties of antifreeze proteins have made them a promising resource in industry, biomedicine, food storage and cryobiology. This review collates the findings of the various studies carried out in the past and the recent developments observed in the properties, functional mechanisms, classification, distinct sources and the ever-increasing applications of antifreeze proteins. This review also summarizes the possibilities of the way forward to identify new avenues of research on anti-freeze proteins.
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Affiliation(s)
- Abirami Baskaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Manigundan Kaari
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Gopikrishnan Venugopal
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Radhakrishnan Manikkam
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India.
| | - Jerrine Joseph
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600 119, Tamil Nadu, India
| | - Parli V Bhaskar
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Vasco-da-Gama 403804, Goa, India
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10
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Hu XL, Lu H, Hassan MM, Zhang J, Yuan G, Abraham PE, Shrestha HK, Villalobos Solis MI, Chen JG, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Cheng ZMM, Yang X. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. HORTICULTURE RESEARCH 2021; 8:130. [PMID: 34059650 PMCID: PMC8167165 DOI: 10.1038/s41438-021-00570-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/26/2021] [Indexed: 05/02/2023]
Abstract
Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant-microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.
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Affiliation(s)
- Xiao-Li Hu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zong-Ming Max Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Xiaohan Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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11
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Arya M, Prakash S, Sougrakpam Y, Deswal R. Brassica juncea leaf cuticle proteome analysis shows myrosinase protein, antifreeze activity, and post-translationally modified secretory proteins. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:234-247. [PMID: 33647583 DOI: 10.1016/j.plaphy.2021.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Plant cuticle, the site of perception of stress signals, is an extracellular hydrophobic barrier that covers the epidermis of the above-ground parts. This lipidic layer has been explored for its cutin and wax composition. However, reports on the cuticle proteins are scanty. Therefore, leaf cuticle proteins of Brassica juncea isolated using organic solvents (chloroform-methanol, 2:1(v/v)) were analyzed using gel based and quantitative shotgun proteomics. Out of 615 proteins identified, 27% (169) had signal peptides supporting extracellular localization. Bioinformatics tool, QuickGO predicted the involvement of these proteins in catabolism (21%), peptidase activity (13%), oxidoreductase (12%), defense response (9%), fatty acid binding (9%), nutrient reservoir activity (8%), chitin binding (7%) and lipid transport (2%). Myrosinase-catalyzed glucosinolate hydrolysis releases bioactive compounds, which contribute to plant defense. This system is termed as "mustard oil bomb". Myrosinase and its associating protein, GDSL esterase/lipase ESM1 (involved in cuticle structuring and defense) were detected in the cuticle. GDSL-esterase/lipase ESM1 and β-glucanase (an antifreeze protein) showed in vitro activity. Analysis of cuticle extract by nanoliter osmometer-phase contrast microscopy detected antifreeze activity due to non-protein component. Post-translational modification analysis using PTM viewer predicted N-glycosylation (66%), N-terminal proteolysis (40%), and phosphorylation (32%) to be the dominant modification in the classical secretory proteins. N-glycosylation of myrosinase and GDSL esterase/lipase, ESM1 was confirmed by Con A affinoblotting. This study not only identified leaf cuticle proteins, but also laid the foundation for exploring the extracellular glucosinolate-myrosinase system, PTM crosstalk, and antifreeze activity as stress adaptive strategies in B. juncea.
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Affiliation(s)
- Meenakshi Arya
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India.
| | - Satya Prakash
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India.
| | - Yaiphabi Sougrakpam
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India.
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India.
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12
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Cheng H, Shao Z, Lu C, Duan D. Genome-wide identification of chitinase genes in Thalassiosira pseudonana and analysis of their expression under abiotic stresses. BMC PLANT BIOLOGY 2021; 21:87. [PMID: 33568068 PMCID: PMC7874618 DOI: 10.1186/s12870-021-02849-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The nitrogen-containing polysaccharide chitin is the second most abundant biopolymer on earth and is found in the cell walls of diatoms, where it serves as a scaffold for biosilica deposition. Diatom chitin is an important source of carbon and nitrogen in the marine environment, but surprisingly little is known about basic chitinase metabolism in diatoms. RESULTS Here, we identify and fully characterize 24 chitinase genes from the model centric diatom Thalassiosira pseudonana. We demonstrate that their expression is broadly upregulated under abiotic stresses, despite the fact that chitinase activity itself remains unchanged, and we discuss several explanations for this result. We also examine the potential transcriptional complexity of the intron-rich T. pseudonana chitinase genes and provide evidence for two separate tandem duplication events during their evolution. CONCLUSIONS Given the many applications of chitin and chitin derivatives in suture production, wound healing, drug delivery, and other processes, new insight into diatom chitin metabolism has both theoretical and practical value.
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Affiliation(s)
- Haomiao Cheng
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhanru Shao
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China.
| | - Chang Lu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, P. R. China.
- Laboratory for Marine Biology and Biotechnology, Pilot Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, P. R. China.
- State Key Laboratory of Bioactive Seaweed Substances, Qingdao Bright Moon Seaweed Group Co Ltd, Qingdao, 266400, P. R. China.
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13
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Kashyap P, Kumar S, Singh D. Performance of antifreeze protein HrCHI4 from Hippophae rhamnoides in improving the structure and freshness of green beans upon cryopreservation. Food Chem 2020; 320:126599. [DOI: 10.1016/j.foodchem.2020.126599] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/18/2020] [Accepted: 03/10/2020] [Indexed: 01/26/2023]
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14
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Xiang H, Yang X, Ke L, Hu Y. The properties, biotechnologies, and applications of antifreeze proteins. Int J Biol Macromol 2020; 153:661-675. [PMID: 32156540 DOI: 10.1016/j.ijbiomac.2020.03.040] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 01/30/2023]
Abstract
By natural selection, organisms evolve different solutions to cope with extremely cold weather. The emergence of an antifreeze protein gene is one of the most momentous solutions. Antifreeze proteins possess an importantly functional ability for organisms to survive in cold environments and are widely found in various cold-tolerant species. In this review, we summarize the origin of antifreeze proteins, describe the diversity of their species-specific properties and functions, and highlight the related biotechnology on the basis of both laboratory tests and bioinformatics analysis. The most recent advances in the applications of antifreeze proteins are also discussed. We expect that this systematic review will contribute to the comprehensive knowledge of antifreeze proteins to readers.
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Affiliation(s)
- Hong Xiang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Xiaohu Yang
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Lei Ke
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology
| | - Yong Hu
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China.; CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institutes of Advanced Technology.
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15
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Sharma B, Arora S, Sahoo D, Deswal R. Comparative fatty acid profiling of Indian seabuckthorn showed altitudinal gradient dependent species-specific variations. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:41-49. [PMID: 32158119 PMCID: PMC7036392 DOI: 10.1007/s12298-019-00720-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/14/2019] [Accepted: 10/10/2019] [Indexed: 05/15/2023]
Abstract
The present study provides the first comparative fatty acid profiling of the three Indian seabuckthorn species, collected from varying altitudes (2900-4300 masl) of Trans-Himalayas (Hippophae rhamnoides, H. tibetana) and Sikkim Himalayas (H. salicifolia) regions. Gas chromatography-mass spectrometry analysis showed variability in fatty acid composition of different seabuckthorn populations. Sikkim populations showed higher (1.28-1.6 folds) palmitic acid than Trans-Himalayan populations which possess higher linoleic (1.3-1.5 folds) and linolenic (1.6-1.8 folds) acids. Interestingly, a strong altitudinal gradient associated positive correlation was observed with the degree of unsaturation and PUFA content while negative correlation was observed with saturated fatty acids content of different seabuckthorn populations. H. salicifolia collected from Sikkim showed healthy ω-6:ω-3 ratio (closer to 1:1) of functional lipids exhibiting its better nutraceutical potential than other commonly used seed oils. Interestingly, H. tibetana from Losar showed higher (5.81) degree of unsaturation than Sikkim populations (3.5) suggesting its better stress tolerance trait. Chemo-taxonomic diversity analysis also formed two broad clusters of Trans-Himalayan and Sikkim populations which correlated with earlier taxonomic studies.
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Affiliation(s)
- Bhavana Sharma
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, Delhi 110007 India
| | - Shaweta Arora
- Department of Botany, University of Delhi, New Delhi, Delhi India
| | - Dinabandhu Sahoo
- Department of Biotechnology, Institute of Bioresources and Sustainable Development, Imphal, Manipur India
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, Delhi 110007 India
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16
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Sharma B, Deswal R. Ecophysiolomic analysis of stress tolerant Himalayan shrub Hipppophae rhamnoides shows multifactorial acclimation strategies induced by diverse environmental conditions. PHYSIOLOGIA PLANTARUM 2020; 168:58-76. [PMID: 30737802 DOI: 10.1111/ppl.12942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/29/2019] [Accepted: 02/04/2019] [Indexed: 05/10/2023]
Abstract
Climatic fluctuations are a major global concern, affecting the agronomic productivity of plants. Hippophae rhamnoides a naturally growing stress tolerant Himalayan shrub was chosen to understand its stress hardiness mechanism. Comparative proteomic and biochemical analysis were done for pooled berry populations (HrB13 and HrB14) growing in two different environmental conditions. HrB13, growing under sub-optimal environmental conditions exhibited differential abundance of stress responsive proteins, which were the rate limiting enzymes associated with stress-responsive metabolic pathways, including Xanthine dehydrogenase (reactive oxygen species [ROS] signaling), Farnesyl diphosphate synthase (phenylpropanoid pathway), endosomal BRO-1 domain protein (ultraviolet [UV]-light stress), Phosphofructokinase (sugar metabolism) and Ubiquitin thioesterase (protein alterations). Biochemical investigations showed a positive correlation between proteomic plasticity (HrB13) and 1.6 to 15-fold accumulation of downstream adaptive metabolic signatures like enzymes and antioxidants involved in ROS scavenging pathways (Catalase, Ascorbate peroxidase, Glutathione reductase, ascorbate and glutathione content), secondary metabolites (phenolics, flavonoids, carotenoids) and polyunsaturated fatty acids (∝ - linolenic acid and linoleic acid). Interactome and KEGG pathway analysis also supported interactions of differentially accumulated proteins with stress-responsive signaling components involved in physiological pathways associated with stress tolerance. This is the first 'ecophysiolomics' study, showing the response of seabuckthorn to multiple stress conditions via activation of multifactorial acclimation strategies leading to morphological, metabolic and physiological modifications, resulting in dark orange berries in HrB13. Higher accumulation of omega-6 fatty acids, carotenoids and ascorbate during suboptimal growth conditions, provides exciting prospects for enhancing pharmaceutical properties of seabuckthorn berries, emphasizing need to analyze diversity of plant signaling mechanisms under changing climate conditions.
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Affiliation(s)
- Bhavana Sharma
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, 110007, India
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17
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Purification of dual-functioning chitinases with hydrolytic and antifreeze activities from Hippophae rhamnoides seedlings. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42485-019-00007-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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18
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Chakraborty S, Jana B. Calcium ion implicitly modulates the adsorption ability of ion-dependent type II antifreeze proteins on an ice/water interface: a structural insight. Metallomics 2019; 11:1387-1400. [DOI: 10.1039/c9mt00100j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ca2+modulates the dynamics of ion-dependent type II AFP to efficiently adsorb on ice surface with high degree of specificity.
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Affiliation(s)
- Sandipan Chakraborty
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Jadavpur
- Kolkata-700032
- India
| | - Biman Jana
- School of Chemical Sciences
- Indian Association for the Cultivation of Science
- Jadavpur
- Kolkata-700032
- India
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19
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Single-step purification and characterization of antifreeze proteins from leaf and berry of a freeze-tolerant shrub seabuckthorn (Hippophae rhamnoides
). J Sep Sci 2018; 41:3938-3945. [DOI: 10.1002/jssc.201800553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 08/01/2018] [Accepted: 08/17/2018] [Indexed: 11/07/2022]
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20
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Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R. Proteomics survey of Solanaceae family: Current status and challenges ahead. J Proteomics 2017; 169:41-57. [PMID: 28528990 DOI: 10.1016/j.jprot.2017.05.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/19/2017] [Accepted: 05/16/2017] [Indexed: 10/25/2022]
Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 68583-0915, USA
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
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21
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Label-free quantitative secretome analysis of Xanthomonas oryzae pv. oryzae highlights the involvement of a novel cysteine protease in its pathogenicity. J Proteomics 2017; 169:202-214. [DOI: 10.1016/j.jprot.2017.02.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 01/23/2017] [Accepted: 02/14/2017] [Indexed: 11/24/2022]
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22
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Fang DA, Zhou YF, Zhang MY, Xu DP, Liu K, Duan JR. Developmental Expression of HSP60 and HSP10 in the Coilia nasus Testis during Upstream Spawning Migration. Genes (Basel) 2017; 8:genes8070189. [PMID: 28754007 PMCID: PMC5541322 DOI: 10.3390/genes8070189] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/17/2017] [Accepted: 07/19/2017] [Indexed: 01/03/2023] Open
Abstract
Heat shock protein 60 (HSP60) and heat shock protein 10 (HSP10) are important chaperones, which have been proven to have essential roles in mediating the correct folding of nuclear encoded proteins imported to mitochondria. Mitochondria are known as the power house of the cell, with which it produces energy and respires aerobically. In this regard, the obtained HSP60 and HSP10 have typical characteristics of the HSP60/10 family signature. Their mRNA transcripts detected were highest during the developmental phase (in April), while the lowest levels were found in the resting phase (after spawning in late July). Additionally, the strongest immunolabeling positive signals were found in the primary spermatocyte, with lower positive staining in secondary sperm cells, and a weak or absent level in the mature sperm. At the electron microscopic level, immunogold particles were localized in the mitochondrial matrix. Data indicated that HSP10 and HSP60 were inducible and functional in the Coilia nasus testis development and migration process, suggesting their essential roles in this process. The results also indicated that HSP60 may be one indicator of properly working mitochondrial import and refolding in the fish testis. This study also provides an expanded perspective on the role of heat shock protein families in spawning migration biology.
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Affiliation(s)
- Di-An Fang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Shanshui Road 9, Wuxi 214000, Jiangsu, China.
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Ministry of Agriculture, Xuejiali 69, Wuxi 214000, Jiangsu, China.
| | - Yan-Feng Zhou
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Shanshui Road 9, Wuxi 214000, Jiangsu, China.
| | - Min-Ying Zhang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Shanshui Road 9, Wuxi 214000, Jiangsu, China.
| | - Dong-Po Xu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Shanshui Road 9, Wuxi 214000, Jiangsu, China.
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Ministry of Agriculture, Xuejiali 69, Wuxi 214000, Jiangsu, China.
| | - Kai Liu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Shanshui Road 9, Wuxi 214000, Jiangsu, China.
| | - Jin-Rong Duan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Shanshui Road 9, Wuxi 214000, Jiangsu, China.
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23
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Kashyap P, Deswal R. A novel class I Chitinase from Hippophae rhamnoides: Indications for participating in ICE-CBF cold stress signaling pathway. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 259:62-70. [PMID: 28483054 DOI: 10.1016/j.plantsci.2017.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/07/2017] [Accepted: 03/10/2017] [Indexed: 05/23/2023]
Abstract
Plant chitinases are the members of PR (Pathogenesis related) proteins family and protect plants from biotic and abiotic stress. A novel chitinase HrCHI1 (Accession number JQ289153) of 954bp ORF encoding 317 amino acids protein was cloned, expressed and characterized from seabuckthorn, a cold/freeze tolerant shrub. The 3D structure (predicted with I-TASSER server) showed highest homology with Oryza sativa class I chitinase (PDB 2dkvA). Putative promoter region (obtained by genome walking) showed GCC box, E-boxes, the binding site for bHLH proteins and DRE elements, the CBF (C-repeat binding factor) binding site besides TATA and CAAT boxes. The gel shift assay with the nuclear extract indicated that the HrCHI1 might be participating in CBF/ERF dependent cold stress signaling pathway. The quantitative transcript profiling supported this observation as cold induced expression of HrCBF peaked earlier (at 1h) while HrCHI1 peaked latter (after 3h) indicating HrCHI1 expression might be induced by HrCBF. Further, HrCHI1 expression was methyl jasmonate (MeJa) dependent and salicylic acid (SA) independent. HrCHI1 was expressed in E. coli and purified using chitin affinity chromatography. It showed 512U/mg chitinase hydrolytic activity and resolved as a 34kDa spot with a slightly basic pI (8.5) on a 2-D gel. The E. coli cells containing recombinant chitinase showed higher rate of growth in cold in comparison with the cells containing the empty vector. In conclusion, we have isolated and characterized a cold responsive basic class I chitinase which is regulated by MeJa and seems to be functioning via CBF/ERF dependent cold stress signaling pathway.
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Affiliation(s)
- Prakriti Kashyap
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, India
| | - Renu Deswal
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, India.
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24
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Bredow M, Tomalty HE, Walker VK. Identification of Plant Ice-binding Proteins Through Assessment of Ice-recrystallization Inhibition and Isolation Using Ice-affinity Purification. J Vis Exp 2017. [PMID: 28518108 DOI: 10.3791/55302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Ice-binding proteins (IBPs) belong to a family of stress-induced proteins that are synthesized by certain organisms exposed to subzero temperatures. In plants, freeze damage occurs when extracellular ice crystals grow, resulting in the rupture of plasma membranes and possible cell death. Adsorption of IBPs to ice crystals restricts further growth by a process known as ice-recrystallization inhibition (IRI), thereby reducing cellular damage. IBPs also demonstrate the ability to depress the freezing point of a solution below the equilibrium melting point, a property known as thermal hysteresis (TH) activity. These protective properties have raised interest in the identification of novel IBPs due to their potential use in industrial, medical and agricultural applications. This paper describes the identification of plant IBPs through 1) the induction and extraction of IBPs in plant tissue, 2) the screening of extracts for IRI activity, and 3) the isolation and purification of IBPs. Following the induction of IBPs by low temperature exposure, extracts are tested for IRI activity using a 'splat assay', which allows the observation of ice crystal growth using a standard light microscope. This assay requires a low protein concentration and generates results that are quickly obtained and easily interpreted, providing an initial screen for ice binding activity. IBPs can then be isolated from contaminating proteins by utilizing the property of IBPs to adsorb to ice, through a technique called 'ice-affinity purification'. Using cell lysates collected from plant extracts, an ice hemisphere can be slowly grown on a brass probe. This incorporates IBPs into the crystalline structure of the polycrystalline ice. Requiring no a priori biochemical or structural knowledge of the IBP, this method allows for recovery of active protein. Ice-purified protein fractions can be used for downstream applications including the identification of peptide sequences by mass spectrometry and the biochemical analysis of native proteins.
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Affiliation(s)
| | | | - Virginia K Walker
- Department of Biology, Queen's University; Department of Biomedical and Molecular Sciences, Queen's University; School of Environmental Sciences, Queen's University
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25
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Qihong Z, Jie L, Xiao X, Qian X, Wei G, Jichen X. PicW orthologs from spruce with differential freezing tolerance expressed in Escherichia coli. Int J Biol Macromol 2017; 101:595-602. [PMID: 28315763 DOI: 10.1016/j.ijbiomac.2017.03.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/09/2017] [Accepted: 03/13/2017] [Indexed: 12/19/2022]
Abstract
Spruce can grow at an extra low temperature (LT), and is inferred with important antifreezing gene resources. The research here identified 4 different spruce varieties, named as PicW1, PicW2, PicM and PicK. Sequence alignment showed base-substitution and deficiency mutations among them with sequence identity between 97.61% and 99.25%. Each gene was transferred into E. coli, where protein was induced by IPTG (isopropyl-β-d-thiogalactoside). Strains cultured at -5°C showed the lethal dose 50% (LD-50) between 53h and 57h for the transgenic strains, but 35h for the control. Strains cultivated at -20°C showed the LD-50 between 38h and 44h for the transgenic strains, but 25h for the control. Further, the soluble gene proteins were extracted and purified for Differential Scanning Calorimeter (DSC) test, which showed characteristic thermal hysteresis (TH) value of 0.77°C (PicW1), 0.78°C (PicW2), 0.72°C (PicM), and 0.86°C (PicK) respectively, significantly higher than the value of 0.05°C of the control (BSA). Summarily, four homologous proteins showed good antifreeze property with the range from high to low as PicK>PicW2>PicW1>PicM. It suggested that they can be used as resources for genetic engineering of plant cold tolerance.
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Affiliation(s)
- Zhao Qihong
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China.
| | - Liu Jie
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China.
| | - Xu Xiao
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China
| | - Xu Qian
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China
| | - Gao Wei
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China
| | - Xu Jichen
- National Engineering Laboratory of Tree Breeding, Beijing Forestry University, 100083, China.
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van de Meene AML, Doblin MS, Bacic A. The plant secretory pathway seen through the lens of the cell wall. PROTOPLASMA 2017; 254:75-94. [PMID: 26993347 DOI: 10.1007/s00709-016-0952-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/27/2016] [Accepted: 02/01/2016] [Indexed: 05/18/2023]
Abstract
Secretion in plant cells is often studied by looking at well-characterised, evolutionarily conserved membrane proteins associated with particular endomembrane compartments. Studies using live cell microscopy and fluorescent proteins have illuminated the highly dynamic nature of trafficking, and electron microscopy studies have resolved the ultrastructure of many compartments. Biochemical and molecular analyses have further informed about the function of particular proteins and endomembrane compartments. In plants, there are over 40 cell types, each with highly specialised functions, and hence potential variations in cell biological processes and cell wall structure. As the primary function of secretion in plant cells is for the biosynthesis of cell wall polysaccharides and apoplastic transport complexes, it follows that utilising our knowledge of cell wall glycosyltransferases (GTs) and their polysaccharide products will inform us about secretion. Indeed, this knowledge has led to novel insights into the secretory pathway, including previously unseen post-TGN secretory compartments. Conversely, our knowledge of trafficking routes of secretion will inform us about polarised and localised deposition of cell walls and their constituent polysaccharides/glycoproteins. In this review, we look at what is known about cell wall biosynthesis and the secretory pathway and how the different approaches can be used in a complementary manner to study secretion and provide novel insights into these processes.
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Affiliation(s)
- A M L van de Meene
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - M S Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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Bredow M, Vanderbeld B, Walker VK. Ice-binding proteins confer freezing tolerance in transgenic Arabidopsis thaliana. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:68-81. [PMID: 27317906 PMCID: PMC5253476 DOI: 10.1111/pbi.12592] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/30/2016] [Accepted: 06/10/2016] [Indexed: 05/07/2023]
Abstract
Lolium perenne is a freeze-tolerant perennial ryegrass capable of withstanding temperatures below -13 °C. Ice-binding proteins (IBPs) presumably help prevent damage associated with freezing by restricting the growth of ice crystals in the apoplast. We have investigated the expression, localization and in planta freezing protection capabilities of two L. perenne IBP isoforms, LpIRI2 and LpIRI3, as well as a processed IBP (LpAFP). One of these isoforms, LpIRI2, lacks a conventional signal peptide and was assumed to be a pseudogene. Nevertheless, both LpIRI2 and LpIRI3 transcripts were up-regulated following cold acclimation. LpIRI2 also demonstrated ice-binding activity when produced recombinantly in Escherichia coli. Both the LpIRI3 and LpIRI2 isoforms appeared to accumulate in the apoplast of transgenic Arabidopsis thaliana plants. In contrast, the fully processed isoform, LpAFP, remained intracellular. Transgenic plants expressing either LpIRI2 or LpIRI3 showed reduced ion leakage (12%-39%) after low-temperature treatments, and significantly improved freezing survival, while transgenic LpAFP-expressing lines did not confer substantial subzero protection. Freeze protection was further enhanced by with the introduction of more than one IBP isoform; ion leakage was reduced 26%-35% and 10% of plants survived temperatures as low as -8 °C. Our results demonstrate that apoplastic expression of multiple L. perenne IBP isoforms shows promise for providing protection to crops susceptible to freeze-induced damage.
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Affiliation(s)
| | | | - Virginia K. Walker
- Department of BiologyQueen's UniversityKingstonONCanada
- Department of Biomedical and Molecular Sciences and School of Environmental StudiesQueen's UniversityKingstonONCanada
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Bredow M, Walker VK. Ice-Binding Proteins in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:2153. [PMID: 29312400 PMCID: PMC5744647 DOI: 10.3389/fpls.2017.02153] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 12/05/2017] [Indexed: 05/04/2023]
Abstract
Sub-zero temperatures put plants at risk of damage associated with the formation of ice crystals in the apoplast. Some freeze-tolerant plants mitigate this risk by expressing ice-binding proteins (IBPs), that adsorb to ice crystals and modify their growth. IBPs are found across several biological kingdoms, with their ice-binding activity and function uniquely suited to the lifestyle they have evolved to protect, be it in fishes, insects or plants. While IBPs from freeze-avoidant species significantly depress the freezing point, plant IBPs typically have a reduced ability to lower the freezing temperature. Nevertheless, they have a superior ability to inhibit the recrystallization of formed ice. This latter activity prevents ice crystals from growing larger at temperatures close to melting. Attempts to engineer frost-hardy plants by the controlled transfer of IBPs from freeze-avoiding fish and insects have been largely unsuccessful. In contrast, the expression of recombinant IBP sequences from freeze-tolerant plants significantly reduced electrolyte leakage and enhanced freezing survival in freeze-sensitive plants. These promising results have spurred additional investigations into plant IBP localization and post-translational modifications, as well as a re-evaluation of IBPs as part of the anti-stress and anti-pathogen axis of freeze-tolerant plants. Here we present an overview of plant freezing stress and adaptation mechanisms and discuss the potential utility of IBPs for the generation of freeze-tolerant crops.
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Affiliation(s)
- Melissa Bredow
- Department of Biology, Queen’s University, Kingston, ON, Canada
- *Correspondence: Melissa Bredow,
| | - Virginia K. Walker
- Department of Biomedical and Molecular Sciences, and School of Environmental Studies, Queen’s University, Kingston, ON, Canada
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Bredow M, Vanderbeld B, Walker VK. Knockdown of Ice-Binding Proteins in Brachypodium distachyon Demonstrates Their Role in Freeze Protection. PLoS One 2016; 11:e0167941. [PMID: 27959937 PMCID: PMC5154533 DOI: 10.1371/journal.pone.0167941] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 11/22/2016] [Indexed: 11/18/2022] Open
Abstract
Sub-zero temperatures pose a major threat to the survival of cold-climate perennials. Some of these freeze-tolerant plants produce ice-binding proteins (IBPs) that offer frost protection by restricting ice crystal growth and preventing expansion-induced lysis of the plasma membranes. Despite the extensive in vitro characterization of such proteins, the importance of IBPs in the freezing stress response has not been investigated. Using the freeze-tolerant grass and model crop, Brachypodium distachyon, we characterized putative IBPs (BdIRIs) and generated the first 'IBP-knockdowns'. Seven IBP sequences were identified and expressed in Escherichia coli, with all of the recombinant proteins demonstrating moderate to high levels of ice-recrystallization inhibition (IRI) activity, low levels of thermal hysteresis (TH) activity (0.03-0.09°C at 1 mg/mL) and apparent adsorption to ice primary prism planes. Following plant cold acclimation, IBPs purified from wild-type B. distachyon cell lysates similarly showed high levels of IRI activity, hexagonal ice-shaping, and low levels of TH activity (0.15°C at 0.5 mg/mL total protein). The transfer of a microRNA construct to wild-type plants resulted in the attenuation of IBP activity. The resulting knockdown mutant plants had reduced ability to restrict ice-crystal growth and a 63% reduction in TH activity. Additionally, all transgenic lines were significantly more vulnerable to electrolyte leakage after freezing to -10°C, showing a 13-22% increase in released ions compared to wild-type. IBP-knockdown lines also demonstrated a significant decrease in viability following freezing to -8°C, with some lines showing only two-thirds the survival seen in control lines. These results underscore the vital role IBPs play in the development of a freeze-tolerant phenotype and suggests that expression of these proteins in frost-susceptible plants could be valuable for the production of more winter-hardy crops.
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Affiliation(s)
- Melissa Bredow
- Department of Biology, Queen’s University, Kingston, ON, Canada
| | | | - Virginia K. Walker
- Department of Biology, Queen’s University, Kingston, ON, Canada
- Department of Biomedical and Molecular Sciences, and School of Environmental Studies, Queen’s University, Kingston, ON, Canada
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He C, Gao G, Zhang J, Duan A, Luo H. Proteome profiling reveals insights into cold-tolerant growth in sea buckthorn. Proteome Sci 2016; 14:14. [PMID: 27761102 PMCID: PMC5054542 DOI: 10.1186/s12953-016-0103-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/03/2016] [Indexed: 11/13/2022] Open
Abstract
Background Low temperature is one of the crucial environmental factors limiting the productivity and distribution of plants. Sea buckthorn (Hippophae rhamnoides L.), a well recognized multipurpose plant species, live successfully in in cold desert regions. But their molecular mechanisms underlying cold tolerance are not well understood. Methods Physiological and biochemical responses to low-temperature stress were studied in seedlings of sea buckthorn. Differentially expressed protein spots were analyzed using multiplexing fluorescent two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) coupled with matrix-assisted laser desorption/ionization (MALDI) time-of-flight/time-of-flight (TOF/TOF) mass spectrometry (MS), the concentration of phytohormone was measured using enzyme-linked immunosorbent assay, and a spectrophotometric assay was used to measure enzymatic reactions. Results With the increase of cold stress intensity, the photosynthesis rate, transpiration rate, stomatal conductance in leaves and contents of abscisic acid (ABA) and indole acetic acid (IAA) in roots decreased significantly; however, water-use efficiency, ABA and zeatin riboside in leaves increased significantly, while cell membrane permeability, malondialdehyde and IAA in leaves increased at 7 d and then decreased at 14 d. DIGE and MS/MS analysis identified 32 of 39 differentially expressed protein spots under low-temperature stress, and their functions were mainly involved in metabolism, photosynthesis, signal transduction, antioxidative systems and post-translational modification. Conclusion The changed protein abundance and corresponding physiological–biochemical response shed light on the molecular mechanisms related to cold tolerance in cold-tolerant plants and provide key candidate proteins for genetic improvement of plants. Electronic supplementary material The online version of this article (doi:10.1186/s12953-016-0103-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caiyun He
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
| | - Guori Gao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China ; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, People's Republic of China
| | - Aiguo Duan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, People's Republic of China
| | - Hongmei Luo
- Experimental Center of Desert Forestry, Chinese Academy of Forestry, InnerMonglia, People's Republic of China
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31
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Sougrakpam Y, Deswal R. Hippophae rhamnoides N-glycoproteome analysis: a small step towards sea buckthorn proteome mining. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:473-484. [PMID: 27924120 PMCID: PMC5120047 DOI: 10.1007/s12298-016-0390-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 05/09/2023]
Abstract
Hippophae rhamnoides is a hardy shrub capable of growing under extreme environmental conditions namely, high salt, drought and cold. Its ability to grow under extreme conditions and its wide application in pharmaceutical and nutraceutical industry calls for its in-depth analysis. N-glycoproteome mining by con A affinity chromatography from seedling was attempted. The glycoproteome was resolved on first and second dimension gel electrophoresis. A total of 48 spots were detected and 10 non-redundant proteins were identified by MALDI-TOF/TOF. Arabidopsis thaliana protein disulfide isomerase-like 1-4 (ATPDIL1-4) electron transporter, protein disulphide isomerase, calreticulin 1 (CRT1), glycosyl hydrolase family 38 (GH 38) protein, phantastica, maturase k, Arabidopsis trithorax related protein 6 (ATXR 6), cysteine protease inhibitor were identified out of which ATXR 6, phantastica and putative ATPDIL1-4 electron transporter are novel glycoproteins. Calcium binding protein CRT1 was validated for its calcium binding by stains all staining. GO analysis showed involvement of GH 38 and ATXR 6 in glycan and lysine degradation pathways. This is to our knowledge the first report of glycoproteome analysis for any Elaeagnaceae member.
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Affiliation(s)
- Yaiphabi Sougrakpam
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, India
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, India
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Kim SW, Gupta R, Lee SH, Min CW, Agrawal GK, Rakwal R, Kim JB, Jo IH, Park SY, Kim JK, Kim YC, Bang KH, Kim ST. An Integrated Biochemical, Proteomics, and Metabolomics Approach for Supporting Medicinal Value of Panax ginseng Fruits. FRONTIERS IN PLANT SCIENCE 2016; 7:994. [PMID: 27458475 PMCID: PMC4930952 DOI: 10.3389/fpls.2016.00994] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Panax ginseng roots are well known for their medicinal properties and have been used in Korean and Chinese traditional medicines for 1000s of years. However, the medicinal value of P. ginseng fruits remain poorly characterized. In this study, we used an integrated biochemical, proteomics, and metabolomics approach to look into the medicinal properties of ginseng fruits. DPPH (1,1-diphenyl-2-picrylhydrazyl) and ABTS [2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid)] assays showed higher antioxidant activities in ginseng fruits than leaves or roots. Two-dimensional gel electrophoresis (2-DE) profiling of ginseng fruit proteins (cv. Cheongsun) showed more than 400 spots wherein a total of 81 protein spots were identified by mass spectrometry using NCBInr, UniRef, and an in-house developed RNAseq (59,251 protein sequences)-based databases. Gene ontology analysis showed that most of the identified proteins were related to the hydrolase (18%), oxidoreductase (16%), and ATP binding (15%) activities. Further, a comparative proteome analysis of four cultivars of ginseng fruits (cvs. Yunpoong, Gumpoong, Chunpoong, and Cheongsun) led to the identification of 22 differentially modulated protein spots. Using gas chromatography-time of flight mass spectrometry (GC-TOF MS), 66 metabolites including amino acids, sugars, organic acids, phenolic acids, phytosterols, tocopherols, and policosanols were identified and quantified. Some of these are well known medicinal compounds and were not previously identified in ginseng. Interestingly, the concentration of almost all metabolites was higher in the Chunpoong and Gumpoong cultivars. Parallel comparison of the four cultivars also revealed higher amounts of the medicinal metabolites in Chunpoong and Gumpoong cultivars. Taken together, our results demonstrate that ginseng fruits are a rich source of medicinal compounds with potential beneficial health effects.
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Affiliation(s)
- So W. Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, MiryangSouth Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, MiryangSouth Korea
| | - Seo H. Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, MiryangSouth Korea
| | - Cheol W. Min
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, MiryangSouth Korea
| | - Ganesh K. Agrawal
- Research Laboratory for Biotechnology and Biochemistry, KathmanduNepal
- Global Research Arch for Developing Education Academy Private Limited, BirgunjNepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry, KathmanduNepal
- Global Research Arch for Developing Education Academy Private Limited, BirgunjNepal
- Faculty of Health and Sport Sciences and Tsukuba International Academy for Sport Studies, University of Tsukuba, IbarakiJapan
- Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, TokyoJapan
| | - Jong B. Kim
- Department of Biotechnology, College of Biomedical and Health Sciences, Konkuk University, Choong-JuSouth Korea
| | - Ick H. Jo
- Department of Herbal Crop Research, Rural Development Administration, EumseongSouth Korea
| | - Soo-Yun Park
- National Academy of Agricultural Science, Rural Development Administration, Jeollabuk-doSouth Korea
| | - Jae K. Kim
- Division of Life Sciences, Incheon National University, IncheonSouth Korea
| | - Young-Chang Kim
- Department of Herbal Crop Research, Rural Development Administration, EumseongSouth Korea
| | - Kyong H. Bang
- Department of Herbal Crop Research, Rural Development Administration, EumseongSouth Korea
| | - Sun T. Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, MiryangSouth Korea
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An open source cryostage and software analysis method for detection of antifreeze activity. Cryobiology 2016; 72:251-7. [PMID: 27041219 DOI: 10.1016/j.cryobiol.2016.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/26/2016] [Accepted: 03/28/2016] [Indexed: 11/23/2022]
Abstract
The aim of this study is to provide the reader with a simple setup that can detect antifreeze proteins (AFP) by inhibition of ice recrystallisation in very small sample sizes. This includes an open source cryostage, a method for preparing and loading samples as well as a software analysis method. The entire setup was tested using hyperactive AFP from the cerambycid beetle, Rhagium mordax. Samples containing AFP were compared to buffer samples, and the results are visualised as crystal radius evolution over time and in absolute change over 30 min. Statistical analysis showed that samples containing AFP could reliably be told apart from controls after only two minutes of recrystallisation. The goal of providing a fast, cheap and easy method for detecting antifreeze proteins in solution was met, and further development of the system can be followed at https://github.com/pechano/cryostage.
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Robinson DG, Ding Y, Jiang L. Unconventional protein secretion in plants: a critical assessment. PROTOPLASMA 2016; 253:31-43. [PMID: 26410830 DOI: 10.1007/s00709-015-0887-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 09/18/2015] [Indexed: 05/27/2023]
Abstract
Unconventional protein secretion (UPS) is a collective term for mechanisms by which cytosolic proteins that lack a signal peptide ("leaderless secretory proteins" (LSPs)) can gain access to the cell exterior. Numerous examples of UPS have been well documented in animal and yeast cells. In contrast, our understanding of the mechanism(s) and function of UPS in plants is very limited. This review evaluates the available literature on this subject. The apparent large numbers of LSPs in the plant secretome suggest that UPS also occurs in plants but is not a proof. Although the direct transport of LSPs across the plant plasma membrane (PM) has not yet been described, it is possible that as in other eukaryotes, exosomes may be released from plant cells through fusion of multivesicular bodies (MVBs) with the PM. In this way, LSPs, but also small RNAs (sRNAs), that are passively taken up from the cytosol into the intraluminal vesicles of MVBs, could reach the apoplast. Another possible mechanism is the recently discovered exocyst-positive organelle (EXPO), a double-membrane-bound compartment, distinct from autophagosomes, which appears to sequester LSPs.
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Affiliation(s)
- David G Robinson
- Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 230, D-69120, Heidelberg, Germany.
| | - Yu Ding
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Liwen Jiang
- Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
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35
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Liu Y, Joly V, Dorion S, Rivoal J, Matton DP. The Plant Ovule Secretome: A Different View toward Pollen-Pistil Interactions. J Proteome Res 2015; 14:4763-75. [PMID: 26387803 DOI: 10.1021/acs.jproteome.5b00618] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
During plant sexual reproduction, continuous exchange of signals between the pollen and the pistil (stigma, style, and ovary) plays important roles in pollen recognition and selection, establishing breeding barriers and, ultimately, leading to optimal seed set. After navigating through the stigma and the style, pollen tubes (PTs) reach their final destination, the ovule. This ultimate step is also regulated by numerous signals emanating from the embryo sac (ES) of the ovule. These signals encompass a wide variety of molecules, but species-specificity of the pollen-ovule interaction relies mainly on secreted proteins and their receptors. Isolation of candidate genes involved in pollen-pistil interactions has mainly relied on transcriptomic approaches, overlooking potential post-transcriptional regulation. To address this issue, ovule exudates were collected from the wild potato species Solanum chacoense using a tissue-free gravity-extraction method (tf-GEM). Combined RNA-seq and mass spectrometry-based proteomics led to the identification of 305 secreted proteins, of which 58% were ovule-specific. Comparative analyses using mature ovules (attracting PTs) and immature ovules (not attracting PTs) revealed that the last maturation step of ES development affected almost half of the ovule secretome. Of 128 upregulated proteins in anthesis stage, 106 were not regulated at the mRNA level, emphasizing the importance of post-transcriptional regulation in reproductive development.
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Affiliation(s)
- Yang Liu
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal , 4101 rue Sherbrooke est, Montréal, Québec H1X 2B2, Canada
| | - Valentin Joly
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal , 4101 rue Sherbrooke est, Montréal, Québec H1X 2B2, Canada
| | - Sonia Dorion
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal , 4101 rue Sherbrooke est, Montréal, Québec H1X 2B2, Canada
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal , 4101 rue Sherbrooke est, Montréal, Québec H1X 2B2, Canada
| | - Daniel P Matton
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal , 4101 rue Sherbrooke est, Montréal, Québec H1X 2B2, Canada
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36
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Narula K, Pandey A, Gayali S, Chakraborty N, Chakraborty S. Birth of plant proteomics in India: a new horizon. J Proteomics 2015; 127:34-43. [PMID: 25920368 DOI: 10.1016/j.jprot.2015.04.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 01/02/2023]
Abstract
UNLABELLED In the post-genomic era, proteomics is acknowledged as the next frontier for biological research. Although India has a long and distinguished tradition in protein research, the initiation of proteomics studies was a new horizon. Protein research witnessed enormous progress in protein separation, high-resolution refinements, biochemical identification of the proteins, protein-protein interaction, and structure-function analysis. Plant proteomics research, in India, began its journey on investigation of the proteome profiling, complexity analysis, protein trafficking, and biochemical modeling. The research article by Bhushan et al. in 2006 marked the birth of the plant proteomics research in India. Since then plant proteomics studies expanded progressively and are now being carried out in various institutions spread across the country. The compilation presented here seeks to trace the history of development in the area during the past decade based on publications till date. In this review, we emphasize on outcomes of the field providing prospects on proteomic pathway analyses. Finally, we discuss the connotation of strategies and the potential that would provide the framework of plant proteome research. BIOLOGICAL SIGNIFICANCE The past decades have seen rapidly growing number of sequenced plant genomes and associated genomic resources. To keep pace with this increasing body of data, India is in the provisional phase of proteomics research to develop a comparative hub for plant proteomes and protein families, but it requires a strong impetus from intellectuals, entrepreneurs, and government agencies. Here, we aim to provide an overview of past, present and future of Indian plant proteomics, which would serve as an evaluation platform for those seeking to incorporate proteomics into their research programs. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Aarti Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Gayali
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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37
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Kesari P, Patil DN, Kumar P, Tomar S, Sharma AK, Kumar P. Structural and functional evolution of chitinase-like proteins from plants. Proteomics 2015; 15:1693-705. [PMID: 25728311 DOI: 10.1002/pmic.201400421] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 01/16/2015] [Accepted: 02/24/2015] [Indexed: 02/06/2023]
Abstract
The plant genome contains a large number of sequences that encode catalytically inactive chitinases referred to as chitinase-like proteins (CLPs). Although CLPs share high sequence and structural homology with chitinases of glycosyl hydrolase 18 (TIM barrel domain) and 19 families, they may lack the binding/catalytic activity. Molecular genetic analysis revealed that gene duplication events followed by mutation in the existing chitinase gene have resulted in the loss of activity. The evidences show that adaptive functional diversification of the CLPs has been achieved through alterations in the flexible regions than in the rigid structural elements. The CLPs plays an important role in the defense response against pathogenic attack, biotic and abiotic stress. They are also involved in the growth and developmental processes of plants. Since the physiological roles of CLPs are similar to chitinase, such mutations have led to plurifunctional enzymes. The biochemical and structural characterization of the CLPs is essential for understanding their roles and to develop potential utility in biotechnological industries. This review sheds light on the structure-function evolution of CLPs from chitinases.
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Affiliation(s)
- Pooja Kesari
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Dipak Narhari Patil
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pramod Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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Ma L, Yang L, Zhao J, Wei J, Kong X, Wang C, Zhang X, Yang Y, Hu X. Comparative proteomic analysis reveals the role of hydrogen sulfide in the adaptation of the alpine plant Lamiophlomis rotata to altitude gradient in the Northern Tibetan Plateau. PLANTA 2015; 241:887-906. [PMID: 25526962 DOI: 10.1007/s00425-014-2209-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/15/2014] [Indexed: 05/20/2023]
Abstract
We found the novel role of hydrogen sulfide in the adaptation of the alpine plant to altitude gradient in the Northern Tibetan Plateau. Alpine plants have developed strategies to survive the extremely cold conditions prevailing at high altitudes; however, the mechanism underlying the evolution of these strategies remains unknown. Hydrogen sulfide (H2S) is an essential messenger that enhances plant tolerance to environmental stress; however, its role in alpine plant adaptation to environmental stress has not been reported until now. In this work, we conducted a comparative proteomics analysis to investigate the dynamic patterns of protein expression in Lamiophlomis rotata plants grown at three different altitudes. We identified and annotated 83 differentially expressed proteins. We found that the levels and enzyme activities of proteins involved in H2S biosynthesis markedly increased at higher altitudes, and that H2S accumulation increased. Exogenous H2S application increased antioxidant enzyme activity, which reduced ROS (reactive oxygen species) damage, and GSNOR (S-nitrosoglutathione reductase) activity, which reduced RNS (reactive nitrogen species) damage, and activated the downstream defense response, resulting in protein degradation and proline and sugar accumulation. However, such defense responses could be reversed by applying H2S biosynthesis inhibitors. Based on these findings, we conclude that L. rotata uses multiple strategies to adapt to the alpine stress environment and that H2S plays a central role during this process.
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Affiliation(s)
- Lan Ma
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201, Yunnan, China
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Chaudhary S, Sharma PC. DeepSAGE based differential gene expression analysis under cold and freeze stress in seabuckthorn (Hippophae rhamnoides L.). PLoS One 2015; 10:e0121982. [PMID: 25803684 PMCID: PMC4372589 DOI: 10.1371/journal.pone.0121982] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/07/2015] [Indexed: 11/19/2022] Open
Abstract
Seabuckthorn (Hippophae rhamnoides L.), an important plant species of Indian Himalayas, is well known for its immense medicinal and nutritional value. The plant has the ability to sustain growth in harsh environments of extreme temperatures, drought and salinity. We employed DeepSAGE, a tag based approach, to identify differentially expressed genes under cold and freeze stress in seabuckthorn. In total 36.2 million raw tags including 13.9 million distinct tags were generated using Illumina sequencing platform for three leaf tissue libraries including control (CON), cold stress (CS) and freeze stress (FS). After discarding low quality tags, 35.5 million clean tags including 7 million distinct clean tags were obtained. In all, 11922 differentially expressed genes (DEGs) including 6539 up regulated and 5383 down regulated genes were identified in three comparative setups i.e. CON vs CS, CON vs FS and CS vs FS. Gene ontology and KEGG pathway analysis were performed to assign gene ontology term to DEGs and ascertain their biological functions. DEGs were mapped back to our existing seabuckthorn transcriptome assembly comprising of 88,297 putative unigenes leading to the identification of 428 cold and freeze stress responsive genes. Expression of randomly selected 22 DEGs was validated using qRT-PCR that further supported our DeepSAGE results. The present study provided a comprehensive view of global gene expression profile of seabuckthorn under cold and freeze stresses. The DeepSAGE data could also serve as a valuable resource for further functional genomics studies aiming selection of candidate genes for development of abiotic stress tolerant transgenic plants.
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Affiliation(s)
- Saurabh Chaudhary
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, 110078, India
| | - Prakash C. Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, 110078, India
- * E-mail:
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Zingde SM. Has Proteomics come of age in India? J Proteomics 2015; 127:3-6. [PMID: 25748142 DOI: 10.1016/j.jprot.2015.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/25/2015] [Indexed: 12/24/2022]
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Middleton AJ, Vanderbeld B, Bredow M, Tomalty H, Davies PL, Walker VK. Isolation and characterization of ice-binding proteins from higher plants. Methods Mol Biol 2015; 1166:255-77. [PMID: 24852641 DOI: 10.1007/978-1-4939-0844-8_19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The characterization of ice-binding proteins from plants can involve many techniques, only a few of which are presented here. Chief among these methods are tests for ice recrystallization inhibition activity. Two distinct procedures are described; neither is normally used for precise quantitative assays. Thermal hysteresis assays are used for quantitative studies but are also useful for ice crystal morphologies, which are important for the understanding of ice-plane binding. Once the sequence of interest is cloned, recombinant expression, necessary to verify ice-binding protein identity can present challenges, and a strategy for recovery of soluble, active protein is described. Lastly, verification of function in planta borrows from standard protocols, but with an additional screen applicable to ice-binding proteins. Here we have attempted to assist researchers wishing to isolate and characterize ice-binding proteins from plants with a few methods critical to success.
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Affiliation(s)
- Adam J Middleton
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada, K7L 3N6
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Gupta R, Lee SE, Agrawal GK, Rakwal R, Park S, Wang Y, Kim ST. Understanding the plant-pathogen interactions in the context of proteomics-generated apoplastic proteins inventory. FRONTIERS IN PLANT SCIENCE 2015; 6:352. [PMID: 26082784 PMCID: PMC4451336 DOI: 10.3389/fpls.2015.00352] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 05/03/2015] [Indexed: 05/14/2023]
Abstract
The extracellular space between cell wall and plasma membrane acts as the first battle field between plants and pathogens. Bacteria, fungi, and oomycetes that colonize the living plant tissues are encased in this narrow region in the initial step of infection. Therefore, the apoplastic region is believed to be an interface which mediates the first crosstalk between host and pathogen. The secreted proteins and other metabolites, derived from both host and pathogen, interact in this apoplastic region and govern the final relationship between them. Hence, investigation of protein secretion and apoplastic interaction could provide a better understanding of plant-microbe interaction. Here, we are briefly discussing the methods available for the isolation and normalization of the apoplastic proteins, as well as the current state of secretome studies focused on the in-planta interaction between the host and the pathogen.
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Affiliation(s)
- Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
| | - So Eui Lee
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
| | - Ganesh K. Agrawal
- Research Laboratory for Biotechnology and BiochemistryKathmandu, Nepal
- Global Research Arch for Developing Education (GRADE), Academy Private LimitedBirgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and BiochemistryKathmandu, Nepal
- Global Research Arch for Developing Education (GRADE), Academy Private LimitedBirgunj, Nepal
- Organization for Educational Initiatives, University of TsukubaTsukuba, Japan
- Faculty of Health and Sport Sciences, Tsukuba International Academy for Sport Studies, University of TsukubaTsukuba, Japan
| | - Sangryeol Park
- Bio-crop Development Division, National Academy of Agricultural Science, Rural Development AdministrationJeonju, South Korea
| | - Yiming Wang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding ResearchCologne, Germany
- *Correspondence: Sun Tae Kim, Department of Plant Bioscience, Pusan National University, Miryang 627-706, South Korea
| | - Sun T. Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National UniversityMiryang, South Korea
- Yiming Wang, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne weg 10, Cologne 50829, Germany
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Wilson SL, Voordouw G, Walker VK. Towards the selection of a produced water enrichment for biological gas hydrate inhibitors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:10254-10261. [PMID: 24819435 DOI: 10.1007/s11356-014-2912-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 04/14/2014] [Indexed: 06/03/2023]
Abstract
Economic concerns associated with the recovery of non-conventional hydrocarbon reserves include unexpected ice as well as ice-like gas hydrate formation. Antifreeze proteins (AFPs) inhibit ice growth, and experiments with fish, plant, and insect AFPs have shown promise of effective gas hydrate inhibition in lab-scale experiments. If produced on an industrial scale, AFPs could provide a more environmentally friendly alternative to kinetic inhibitors, but a large-scale production of these AFPs is not currently feasible. We believe that these difficulties could be surmounted by the production of microbial AFPs, but to date, only a few such proteins have been identified and purified, and none of these are associated with hydrocarbon reserves. Here, we have used ice-affinity and freeze-thaw stress to select microbes derived from oil and gas formation water, or produced water, as a source of anaerobic microbial communities. Ice-affinity successfully incorporated anaerobic bacteria under aerobic conditions, and the mixed culture had ice-associating properties. Under these conditions, ice-affinity selection does not result in cultivatable isolates, but similar, cultivable microbes were obtained following freeze-thaw selection under anaerobic conditions. Since these mixed cultures inhibited the growth of ice crystals, they also have the potential to inhibit hydrate growth. Overall, freeze-thaw selection provides a promising first step towards the isolation of microbes capable of the inhibition of ice and gas hydrate growth, for possible application for energy exploration and recovery at high-latitudes and in-deep, cold waters.
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Affiliation(s)
- Sandra L Wilson
- Department of Biology, Queen's University, Kingston, Ontario, K7L 3N6, Canada,
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Sehrawat A, Deswal R. S-nitrosylation analysis in Brassica juncea apoplast highlights the importance of nitric oxide in cold-stress signaling. J Proteome Res 2014; 13:2599-619. [PMID: 24684139 DOI: 10.1021/pr500082u] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Reactive nitrogen species (RNS) including nitric oxide (NO) are important components of stress signaling. However, RNS-mediated signaling in the apoplast remains largely unknown. NO production measured in the shoot apoplast of Brassica juncea seedlings showed nonenzymatic nitrite reduction to NO. Thiol pool quantification showed cold-induced increase in the protein (including S-nitrosothiols) as well as non protein thiols. Proteins from the apoplast were resolved as 109 spots on the 2-D gel, while S-nitrosoglutathione-treated (a NO donor), neutravidin-agarose affinity chromatography-purified S-nitrosylated proteins were resolved as 52 spots. Functional categorization after MALDI-TOF/TOF identification showed 41 and 38% targets to be metabolic/cell-wall-modifying and stress-related, respectively, suggesting the potential role(s) of S-nitrosylation in regulating these responses. Additionally, identification of cold-stress-modulated putative S-nitrosylated proteins by nLC-MS/MS showed that only 38.4% targets with increased S-nitrosylation were secreted by classical pathway, while the majority (61.6%) of these were secreted by unknown/nonclassical pathways. Cold-stress-increased dehydroascorbate reductase and glutathione S-transferase activity via S-nitrosylation and promoted ROS detoxification by ascorbate regeneration and hydrogen peroxide detoxification. Taken together, cold-mediated NO production, thiol pool enrichment, and identification of the 48 putative S-nitrosylated proteins, including 25 novel targets, provided the preview of RNS-mediated cold-stress signaling in the apoplast.
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Affiliation(s)
- Ankita Sehrawat
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi , Delhi 110007, India
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Gupta R, Deswal R. Refolding of β-stranded class I chitinases of Hippophae rhamnoides enhances the antifreeze activity during cold acclimation. PLoS One 2014; 9:e91723. [PMID: 24626216 PMCID: PMC3953593 DOI: 10.1371/journal.pone.0091723] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 02/14/2014] [Indexed: 11/18/2022] Open
Abstract
Class I chitinases hydrolyse the β-1,4-linkage of chitin and also acquire antifreeze activity in some of the overwintering plants during cold stress. Two chitinases, HrCHT1a of 31 kDa and HrCHT1b of 34 kDa, were purified from cold acclimated and non-acclimated seabuckthorn seedlings using chitin affinity chromatography. 2-D gels of HrCHT1a and HrCHT1b showed single spots with pIs 7.0 and 4.6 respectively. N-terminal sequence of HrCHT1b matched with the class I chitinase of rice and antifreeze proteins while HrCHT1a could not be sequenced as it was N-terminally blocked. Unlike previous reports, where antifreeze activity of chitinase was cold inducible, our results showed that antifreeze activity is constitutive property of class I chitinase as both HrCHT1a and HrCHT1b isolated even from non-acclimated seedlings, exhibited antifreeze activity. Interestingly, HrCHT1a and HrCHT1b purified from cold acclimated seedlings, exhibited 4 and 2 times higher antifreeze activities than those purified from non-acclimated seedlings, suggesting that antifreeze activity increased during cold acclimation. HrCHT1b exhibited 23–33% higher hydrolytic activity and 2–4 times lower antifreeze activity than HrCHT1a did. HrCHT1b was found to be a glycoprotein; however, its antifreeze activity was independent of glycosylation as even deglycosylated HrCHT1b exhibited antifreeze activity. Circular dichroism (CD) analysis showed that both these chitinases were rich in unusual β-stranded conformation (36–43%) and the content of β-strand increased (∼11%) during cold acclimation. Surprisingly, calcium decreased both the activities of HrCHT1b while in case of HrCHT1a, a decrease in the hydrolytic activity and enhancement in its antifreeze activity was observed. CD results showed that addition of calcium also increased the β-stranded conformation of HrCHT1a and HrCHT1b. This is the first report, which shows that antifreeze activity is constitutive property of class I chitinase and cold acclimation and calcium regulate these activities of chitinases by changing the secondary structure.
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Affiliation(s)
- Ravi Gupta
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, India
| | - Renu Deswal
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, India
- * E-mail:
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Tanveer T, Shaheen K, Parveen S, Kazi AG, Ahmad P. Plant secretomics: identification, isolation, and biological significance under environmental stress. PLANT SIGNALING & BEHAVIOR 2014; 9:e29426. [PMID: 25763623 PMCID: PMC4203502 DOI: 10.4161/psb.29426] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/01/2014] [Accepted: 06/02/2014] [Indexed: 05/03/2023]
Abstract
Plant secretomes are the proteins secreted by the plant cells and are involved in the maintenance of cell wall structure, relationship between host and pathogen, communication between different cells in the plant, etc. Amalgamation of methodologies like bioinformatics, biochemical, and proteomics are used to separate, classify, and outline secretomes by means of harmonizing in planta systems and in vitro suspension cultured cell system (SSCs). We summed up and explained the meaning of secretome, methods used for the identification and isolation of secreted proteins from extracellular space and methods for the assessment of purity of secretome proteins in this review. Two D PAGE method and HPLC based methods for the analysis together with different bioinformatics tools used for the prediction of secretome proteins are also discussed. Biological significance of secretome proteins under different environmental stresses, i.e., salt stress, drought stress, oxidative stress, etc., defense responses and plant interactions with environment are also explained in detail.
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Affiliation(s)
- Tehreem Tanveer
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Kanwal Shaheen
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Sajida Parveen
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Alvina Gul Kazi
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Parvaiz Ahmad
- Department of Botany; S.P. College; Jammu and Kashmir, India
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Lehtonen MT, Takikawa Y, Rönnholm G, Akita M, Kalkkinen N, Ahola-Iivarinen E, Somervuo P, Varjosalo M, Valkonen JPT. Protein secretome of moss plants (Physcomitrella patens) with emphasis on changes induced by a fungal elicitor. J Proteome Res 2013; 13:447-59. [PMID: 24295333 DOI: 10.1021/pr400827a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Studies on extracellular proteins (ECPs) contribute to understanding of the multifunctional nature of apoplast. Unlike vascular plants (tracheophytes), little information about ECPs is available from nonvascular plants, such as mosses (bryophytes). In this study, moss plants (Physcomitrella patens) were grown in liquid culture and treated with chitosan, a water-soluble form of chitin that occurs in cell walls of fungi and insects and elicits pathogen defense in plants. ECPs released to the culture medium were compared between chitosan-treated and nontreated control cultures using quantitative mass spectrometry (Orbitrap) and 2-DE-LC-MS/MS. Over 400 secreted proteins were detected, of which 70% were homologous to ECPs reported in tracheophyte secretomes. Bioinformatics analyses using SignalP and SecretomeP predicted classical signal peptides for secretion (37%) or leaderless secretion (27%) for most ECPs of P. patens, but secretion of the remaining proteins (36%) could not be predicted using bioinformatics. Cultures treated with chitosan contained 72 proteins not found in untreated controls, whereas 27 proteins found in controls were not detected in chitosan-treated cultures. Pathogen defense-related proteins dominated in the secretome of P. patens, as reported in tracheophytes. These results advance knowledge on protein secretomes of plants by providing a comprehensive account of ECPs of a bryophyte.
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Affiliation(s)
- Mikko T Lehtonen
- Department of Agricultural Sciences, University of Helsinki , PO Box 27, FI-00014 Helsinki, Finland
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Deswal R, Gupta R, Dogra V, Singh R, Abat JK, Sarkar A, Mishra Y, Rai V, Sreenivasulu Y, Amalraj RS, Raorane M, Chaudhary RP, Kohli A, Giri AP, Chakraborty N, Zargar SM, Agrawal VP, Agrawal GK, Job D, Renaut J, Rakwal R. Plant proteomics in India and Nepal: current status and challenges ahead. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2013; 19:461-477. [PMID: 24431515 PMCID: PMC3781272 DOI: 10.1007/s12298-013-0198-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Plant proteomics has made tremendous contributions in understanding the complex processes of plant biology. Here, its current status in India and Nepal is discussed. Gel-based proteomics is predominantly utilized on crops and non-crops to analyze majorly abiotic (49 %) and biotic (18 %) stress, development (11 %) and post-translational modifications (7 %). Rice is the most explored system (36 %) with major focus on abiotic mainly dehydration (36 %) stress. In spite of expensive proteomics setup and scarcity of trained workforce, output in form of publications is encouraging. To boost plant proteomics in India and Nepal, researchers have discussed ground level issues among themselves and with the International Plant Proteomics Organization (INPPO) to act in priority on concerns like food security. Active collaboration may help in translating this knowledge to fruitful applications.
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Affiliation(s)
- Renu Deswal
- />Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, India
| | - Ravi Gupta
- />Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi, India
| | - Vivek Dogra
- />Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh India
| | - Raksha Singh
- />Department of Plant Molecular Biology, College of Life Science, Sejong University, Seoul, Republic of Korea
| | - Jasmeet Kaur Abat
- />Department of Botany, Gargi College, University of Delhi, New Delhi, India
| | - Abhijit Sarkar
- />Department of Botany, Banaras Hindu University, Varanasi, India
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
| | - Yogesh Mishra
- />Department of Plant Physiology, Umeå Plant Science Center, Umeå University, Umeå, Sweden
| | - Vandana Rai
- />National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
| | - Yelam Sreenivasulu
- />Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh India
| | - Ramesh Sundar Amalraj
- />Plant Pathology Section, Sugarcane Breeding Institute, Indian Council of Agricultural Research, Tamil Nadu, India
| | - Manish Raorane
- />Plant Molecular Biology Laboratory, Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Manila, Philippines
| | - Ram Prasad Chaudhary
- />Central Department of Botany, and Research Centre for Applied Science and Technology, Tribhuvan University, Kirtipur, Nepal
| | - Ajay Kohli
- />Plant Molecular Biology Laboratory, Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Manila, Philippines
| | - Ashok Prabhakar Giri
- />Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune, India
| | | | - Sajad Majeed Zargar
- />School of Biotechnology, SK University of Agricultural Sciences and Technology, Chatha, Jammu, 180009 Jammu and Kashmir India
| | | | - Ganesh Kumar Agrawal
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
| | - Dominique Job
- />CNRS/Bayer Crop Science (UMR 5240) Joint Laboratory, Lyon, France
| | - Jenny Renaut
- />Department of Environment and Agrobiotechnologies, Centre de Recherche Public-Gabriel Lippmann, Belvaux, GD Luxembourg
| | - Randeep Rakwal
- />Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal
- />Organization for Educational Initiatives, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577 Japan
- />Department of Anatomy I, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa, Tokyo 142-8555 Japan
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Nawrot R, Barylski J, Schulze WX. Incorrectly annotated keratin derived peptide sequences lead to misleading MS/MS data interpretation. J Proteomics 2013; 91:270-3. [DOI: 10.1016/j.jprot.2013.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 07/01/2013] [Accepted: 07/07/2013] [Indexed: 11/25/2022]
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