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Safaeizadeh M, Boller T, Becker C. Comparative RNA-seq analysis of Arabidopsis thaliana response to AtPep1 and flg22, reveals the identification of PP2-B13 and ACLP1 as new members in pattern-triggered immunity. PLoS One 2024; 19:e0297124. [PMID: 38833485 PMCID: PMC11149889 DOI: 10.1371/journal.pone.0297124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 12/28/2023] [Indexed: 06/06/2024] Open
Abstract
In this research, a high-throughput RNA sequencing-based transcriptome analysis technique (RNA-Seq) was used to evaluate differentially expressed genes (DEGs) in the wild type Arabidopsis seedlings in response to AtPep1, a well-known peptide representing an endogenous damage-associated molecular pattern (DAMP), and flg22, a well-known microbe-associated molecular pattern (MAMP). We compared and dissected the global transcriptional landscape of Arabidopsis thaliana in response to AtPep1 and flg22 and could identify shared and unique DEGs in response to these elicitors. We found that while a remarkable number of flg22 up-regulated genes were also induced by AtPep1, 256 genes were exclusively up-regulated in response to flg22, and 328 were exclusively up-regulated in response to AtPep1. Furthermore, among down-regulated DEGs upon flg22 treatment, 107 genes were exclusively down-regulated by flg22 treatment, while 411 genes were exclusively down-regulated by AtPep1. We found a number of hitherto overlooked genes to be induced upon treatment with either flg22 or with AtPep1, indicating their possible involvement general pathways in innate immunity. Here, we characterized two of them, namely PP2-B13 and ACLP1. pp2-b13 and aclp1 mutants showed increased susceptibility to infection by the virulent pathogen Pseudomonas syringae DC3000 and its mutant Pst DC3000 hrcC (lacking the type III secretion system), as evidenced by increased proliferation of the two pathogens in planta. Further, we present evidence that the aclp1 mutant is deficient in ethylene production upon flg22 treatment, while the pp2-b13 mutant is deficient in the production of reactive oxygen species (ROS). The results from this research provide new information for a better understanding of the immune system in Arabidopsis.
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Affiliation(s)
- Mehdi Safaeizadeh
- Department of Cellular and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
- Zürich-Basel Plant Science Center, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Thomas Boller
- Zürich-Basel Plant Science Center, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Claude Becker
- LMU Biocentre, Faculty of Biology, Ludwig-Maximilian-University Munich, Martinsried, Germany
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Sun Y, Zhao N, Sun H, Xu S, Lu Y, Xi H, Guo Z, Shi H. Transcriptome Profiling Reveals Molecular Responses to Salt Stress in Common Vetch ( Vicia sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:714. [PMID: 38475559 DOI: 10.3390/plants13050714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Common vetch (Vicia sativa L.) is an important annual diploid leguminous forage. In the present study, transcriptomic profiling in common vetch in response to salt stress was conducted using a salt-tolerant line (460) and a salt-sensitive line (429). The common responses in common vetch and the specific responses associated with salt tolerance in 460 were analyzed. Several KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, including plant hormone and MAPK (mitogen-activated protein kinase) signaling, galactose metabolism, and phenylpropanoid phenylpropane biosynthesis, were enriched in both lines, though some differentially expressed genes (DEGs) showed distinct expression patterns. The roots in 460 showed higher levels of lignin than in 429. α-linolenic acid metabolism, carotenoid biosynthesis, the photosynthesis-antenna pathway, and starch and sucrose metabolism pathways were specifically enriched in salt-tolerant line 460, with higher levels of accumulated soluble sugars in the leaves. In addition, higher transcript levels of genes involved in ion homeostasis and reactive oxygen species (ROS) scavenging were observed in 460 than in 429 in response to salt stress. The transcriptomic analysis in common vetch in response to salt stress provides useful clues for further investigations on salt tolerance mechanism in the future.
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Affiliation(s)
- Yanmei Sun
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Na Zhao
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongjian Sun
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Shan Xu
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiwen Lu
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Haojie Xi
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenfei Guo
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Haifan Shi
- Key Laboratory of State Forestry and Grassland Administration on Grass Germplasm Resources Innovation and Utilization in the Middle and Lower Reaches of the Yangtze River, College of Grassland Science, Nanjing Agricultural University, Nanjing 210095, China
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Geng L, Li M, Xie S, Wang H, He X, Sun N, Zhang G, Ye L. HvBGlu3, a GH1 β-glucosidase enzyme gene, negatively influences β-glucan content in barley grains. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:14. [PMID: 38165440 DOI: 10.1007/s00122-023-04517-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
KEY MESSAGE HvBGlu3, a β-glucosidase enzyme gene, negatively influences β-glucan content in barley grains by mediating starch and sucrose metabolism in developing grains. Barley grains are rich in β-glucan, an important factor affecting end-use quality. Previously, we identified several stable marker-trait associations (MTAs) and novel candidate genes associated with β-glucan content in barley grains using GWAS (Genome Wide Association Study) analysis. The gene HORVU3Hr1G096910, encoding β-glucosidase 3, named HvBGlu3, is found to be associated with β-glucan content in barley grains. In this study, conserved domain analysis suggested that HvBGlu3 belongs to glycoside hydrolase family 1 (GH1). Gene knockout assay revealed that HvBGlu3 negatively influenced β-glucan content in barley grains. Transcriptome analysis of developing grains of hvbglu3 mutant and the wild type indicated that the knockout of the gene led to the increased expression level of genes involved in starch and sucrose metabolism. Glucose metabolism analysis showed that the contents of many sugars in developing grains were significantly changed in hvbglu3 mutants. In conclusion, HvBGlu3 modulates β-glucan content in barley grains by mediating starch and sucrose metabolism in developing grains. The obtained results may be useful for breeders to breed elite barley cultivars for food use by screening barley lines with loss of function of HvBGlu3 in barley breeding.
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Affiliation(s)
- La Geng
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Mengdi Li
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Shanggeng Xie
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Han Wang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Xinyi He
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Nannan Sun
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000, China
| | - Guoping Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000, China
| | - Lingzhen Ye
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
- Shandong (Linyi) Institute of Modern Agriculture, Zhejiang University, Linyi, 276000, China.
- New Rural Development Institute, Zhejiang University, Hangzhou, 310058, China.
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Pan Y, Li Y, Liu Z, Zou J, Li Q. Computational genomics insights into cold acclimation in wheat. Front Genet 2022; 13:1015673. [PMID: 36338961 PMCID: PMC9632429 DOI: 10.3389/fgene.2022.1015673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Development of cold acclimation in crops involves transcriptomic reprograming, metabolic shift, and physiological changes. Cold responses in transcriptome and lipid metabolism has been examined in separate studies for various crops. In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in four wheat genotypes of distinct cold tolerance. Differential expression was investigated between cold treated and control samples and between the winter-habit and spring-habit wheat genotypes. Collectively, 12,676 differentially expressed genes (DEGs) were identified. Principal component analysis of these DEGs indicated that the first, second, and third principal components (PC1, PC2, and PC3) explained the variance in cold treatment, vernalization and cold hardiness, respectively. Differential expression feature extraction (DEFE) analysis revealed that the winter-habit wheat genotype Norstar had high number of unique DEGs (1884 up and 672 down) and 63 winter-habit genes, which were clearly distinctive from the 64 spring-habit genes based on PC1, PC2 and PC3. Correlation analysis revealed 64 cold hardy genes and 39 anti-hardy genes. Cold acclimation encompasses a wide spectrum of biological processes and the involved genes work cohesively as revealed through network propagation and collective association strength of local subnetworks. Integration of transcriptomics and lipidomics data revealed that the winter-habit genes, such as COR413-TM1, CIPKs and MYB20, together with the phosphatidylglycerol lipids, PG(34:3) and PG(36:6), played a pivotal role in cold acclimation and coordinated cohesively associated subnetworks to confer cold tolerance.
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Affiliation(s)
- Youlian Pan
- Digital Technologies, National Research Council Canada, Ottawa, ON, Canada
- *Correspondence: Youlian Pan, ; Qiang Li,
| | - Yifeng Li
- Digital Technologies, National Research Council Canada, Ottawa, ON, Canada
- Department of Computer Science, Department of Biological Science, Brock University, St. Catharines, ON, Canada
| | - Ziying Liu
- Digital Technologies, National Research Council Canada, Ottawa, ON, Canada
| | - Jitao Zou
- Aquatic and Crop Research and Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Qiang Li
- Aquatic and Crop Research and Development, National Research Council Canada, Saskatoon, SK, Canada
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- *Correspondence: Youlian Pan, ; Qiang Li,
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Manzoor M, Zargar SM, Akhter P, Urwat U, Mahajan R, Bhat SA, Dar TA, Khan I. Morphological, Biochemical, and Proteomic Studies Revealed Impact of Fe and P Crosstalk on Root Development in Phaseolus vulgaris L. Appl Biochem Biotechnol 2021; 193:3898-3914. [PMID: 34524636 DOI: 10.1007/s12010-021-03662-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
Mineral stress is one of the major abiotic stresses faced by crop plants. The present study was undertaken to investigate the impact of mineral stress (iron (Fe) and phosphorus (P)) on various morphological and biochemical responses of the shoot and root tissues and root architecture of common bean (Phaseolus vulgaris L.). This study also leads us to the identification of P stress responsive proteins. The study was conducted under in vitro conditions, in which seeds of Shalimar French Bean-1 (SFB-1) variety were cultured on four different MGRL medium (control (P1Fe1), iron deficient (P1Fe0), phosphorus deficient (P0Fe1), and phosphorus and iron deficient (P0Fe0)). Chlorophyll content of leaves, Fe/P content of root tissues, total sugars, proline, length, and weight of shoot and root tissues were assessed and compared within and between the treatments. The analyzed data revealed significant difference between control and other three treatments. Chlorophyll content of shoots was found significantly decreased under mineral stress treatments P0Fe1, P1Fe0, and P0Fe0 than control. Length and weight of shoot and root were also observed significantly decreased under P0Fe1, P1Fe0, and P0Fe0 as compared to control. Total sugar was significantly higher in P0Fe1 of roots in comparison to control. Proline content was significantly higher in both tissues of shoots and roots of plants grown under P1Fe0, P0Fe1, and P0Fe0 than control condition. Furthermore, we unexpectedly observed the recovery of roots (mainly primary roots) under P0Fe0 as compared to P1Fe0 and P0Fe1. Interestingly higher concentration of Fe was also observed in P0Fe1 compared to other treatments and also higher concentration of P was observed in P1Fe1. These findings suggested that there is a crosstalk between Fe and P and also revealed that there is a disruption in the ability of PR (primary root) to sense local P deficiency in the absence of Fe. Furthermore, proteomics analysis (SDS-PAGE followed by MALDI MS) helped in identification of defensive proteins in P stress condition compared to control.
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Affiliation(s)
- Madhiya Manzoor
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-E-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India, 190025
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-E-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India, 190025.
| | - Parveen Akhter
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-E-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India, 190025
| | - Uneeb Urwat
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-E-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India, 190025
| | - Reetika Mahajan
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-E-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India, 190025
| | - Sajad Ahmad Bhat
- Division of Basic Science, Sher-E-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India
| | - Tanveer Ali Dar
- Department of Clinical Biochemistry, University of Kashmir, Hazratbal, Srinagar, Jammu & Kashmir, India
| | - Imran Khan
- Division of Agricultural Statistics, Sher-E-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India
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Sun S, Lin M, Qi X, Chen J, Gu H, Zhong Y, Sun L, Muhammad A, Bai D, Hu C, Fang J. Full-length transcriptome profiling reveals insight into the cold response of two kiwifruit genotypes (A. arguta) with contrasting freezing tolerances. BMC PLANT BIOLOGY 2021; 21:365. [PMID: 34380415 PMCID: PMC8356467 DOI: 10.1186/s12870-021-03152-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/02/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Kiwifruit (Actinidia Lindl.) is considered an important fruit species worldwide. Due to its temperate origin, this species is highly vulnerable to freezing injury while under low-temperature stress. To obtain further knowledge of the mechanism underlying freezing tolerance, we carried out a hybrid transcriptome analysis of two A. arguta (Actinidi arguta) genotypes, KL and RB, whose freezing tolerance is high and low, respectively. Both genotypes were subjected to - 25 °C for 0 h, 1 h, and 4 h. RESULTS SMRT (single-molecule real-time) RNA-seq data were assembled using the de novo method, producing 24,306 unigenes with an N50 value of 1834 bp. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs showed that they were involved in the 'starch and sucrose metabolism', the 'mitogen-activated protein kinase (MAPK) signaling pathway', the 'phosphatidylinositol signaling system', the 'inositol phosphate metabolism', and the 'plant hormone signal transduction'. In particular, for 'starch and sucrose metabolism', we identified 3 key genes involved in cellulose degradation, trehalose synthesis, and starch degradation processes. Moreover, the activities of beta-GC (beta-glucosidase), TPS (trehalose-6-phosphate synthase), and BAM (beta-amylase), encoded by the abovementioned 3 key genes, were enhanced by cold stress. Three transcription factors (TFs) belonging to the AP2/ERF, bHLH (basic helix-loop-helix), and MYB families were involved in the low-temperature response. Furthermore, weighted gene coexpression network analysis (WGCNA) indicated that beta-GC, TPS5, and BAM3.1 were the key genes involved in the cold response and were highly coexpressed together with the CBF3, MYC2, and MYB44 genes. CONCLUSIONS Cold stress led various changes in kiwifruit, the 'phosphatidylinositol signaling system', 'inositol phosphate metabolism', 'MAPK signaling pathway', 'plant hormone signal transduction', and 'starch and sucrose metabolism' processes were significantly affected by low temperature. Moreover, starch and sucrose metabolism may be the key pathway for tolerant kiwifruit to resist low temperature damages. These results increase our understanding of the complex mechanisms involved in the freezing tolerance of kiwifruit under cold stress and reveal a series of candidate genes for use in breeding new cultivars with enhanced freezing tolerance.
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Affiliation(s)
- Shihang Sun
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China
| | - Miaomiao Lin
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Xiujuan Qi
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Jinyong Chen
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Hong Gu
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yunpeng Zhong
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Leiming Sun
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Abid Muhammad
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Danfeng Bai
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Chungen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jinbao Fang
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
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Bian Z, Wang D, Liu Y, Xi Y, Wang X, Meng S. Analysis of Populus glycosyl hydrolase family I members and their potential role in the ABA treatment and drought stress response. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 163:178-188. [PMID: 33848930 DOI: 10.1016/j.plaphy.2021.03.057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Glycoside hydrolase family 1 (GH1) β-glucosidases (BGLUs) are encoded by a large number of genes and are involved in many developmental processes and stress responses in plants. Due to their importance in plant growth and development, genome-wide analyses have been conducted in the model plant species Arabidopsis thaliana, rice and maize but not in woody plant species, which have important economic and ecological value. In this study, we systematically analyzed Populus BGLUs (PtBGLUs) and demonstrated the involvement of several genes under stress conditions. Forty-four PtBGLUs were identified in Populus databases; these genes were located on 11 chromosomes, and the proteins of several PtBGLU genes were highly similar. More than 90% of PtBGLUs contain three conserved motifs. Collinearity results showed that 44 PtBGLU genes resulted from 12 tandem and 5 segmental duplication events. Phylogenetic analysis revealed that 128 BGLU genes from Populus trichocarpa, A. thaliana and Oryza sativa could be classified into 4 subgroups and subgroup Ⅱ and Ⅳ were differently having PtBGLUs and AtBGLUs. We further investigated whether several PtBGLUs responded to drought stress and ABA treatment, and the results showed that most of the selected BGLU genes were expressed in response to stress, which is consistent with previous studies involving rice and Arabidopsis homologous genes. Large numbers of stress-, hormone-, and development-related elements in the PtBGLU promoters suggest that BGLU genes may be involved in complex networks. Taken together, our results provide valuable information for an improved understanding of β-glucosidase function in woody plants.
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Affiliation(s)
- Zhan Bian
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China.
| | - Dongli Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China.
| | - Yunshan Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China; College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, Chongqing, 404100, China
| | - Yimin Xi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China
| | - Xiaoling Wang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, Jiangxi, 330096, China.
| | - Sen Meng
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, Guangdong, 510520, China.
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Zhang X, Su E, Li S, Chen X, Fan Z, Liu M, Ma B, Li H. Molecular analyses of the diversity and function of the family 1 β-glucosidase-producing microbial community in compost. Can J Microbiol 2021; 67:713-723. [PMID: 33905664 DOI: 10.1139/cjm-2020-0576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The diversity and transcription efficiency of GH1 family β-glucosidase genes were investigated in natural and inoculated composts using a DNA clone library and real-time qPCR. Compositional differences were observed in the functional community between both composting processes. Proteobacteria, Actinobacteria, Firmicutes, and Chloroflexi were the dominant phyla. Twenty representative β-glucosidase genes were quantitatively analyzed from DNA and RNA pools. Principal component analysis and Pearson's correlation analysis showed that cellulose degradation is correlated with the composition and succession of functional microbial communities, and this correlation was mainly observed in Proteobacteria and Actinobacteria. Compared with inoculated compost, the functional microbial communities in natural compost with a low diversity index exhibited weak buffering capacity for function in response to environmental changes. This may explain the consistency and dysfunction of cellulose degradation and transcriptional regulation by dominant β-glucosidase genes. Except for the β-glucosidase genes encoding constitutive enzymes, individual β-glucosidase genes responded to environmental changes more drastically than the group β-glucosidase genes. Correlation results suggested that β-glucosidase genes belonging to Micrococcales played an important role in the regulation of intracellular β-glucosidase. These results indicated that the responses of functional microorganisms were different during both composting processes, and were reflected at both the individual and group levels.
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Affiliation(s)
- Xinyue Zhang
- Northeast Agricultural University, 12430, Harbin, China;
| | - Erlie Su
- Northeast Agricultural University, 12430, Harbin, China;
| | - Shanshan Li
- Northeast Agricultural University, 12430, Harbin, China;
| | - Xiehui Chen
- Northeast Agricultural University, 12430, Harbin, China;
| | - Zhihua Fan
- Northeast Agricultural University, 12430, Harbin, China;
| | - Meiting Liu
- Northeast Agricultural University, 12430, Harbin, Harbin, China;
| | - Bo Ma
- Northeast Agricultural University, 12430, Harbin, China, 150030;
| | - Hongtao Li
- Northeast Agricultural University, 12430, Harbin, China, 150030;
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Nath P, Goyal A. Structure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans. J Mol Model 2021; 27:106. [PMID: 33694107 PMCID: PMC7945971 DOI: 10.1007/s00894-021-04721-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/01/2021] [Indexed: 11/30/2022]
Abstract
Structure and conformational behaviour of a putative β-1,4-glucosidase of glycoside hydrolase family 3 (PsGH3) from Pseudopedobacter saltans was predicted by using in-silico tools. PsGH3 modeled structure constructed using Phyre2 displayed multidomain architecture comprising an N-terminal (β/α)8-fold domain followed by (α/β)6-sandwich domain, PA14 domain, and a C-terminal domain resembling an immunoglobulin fold. Ramachandran plot displayed 99.3% of amino acids in the allowed region and 0.7% residues in the disallowed region. Multiple sequence alignment (MSA) and structure superposition of PsGH3 with other homologues from GH3 family revealed the conserved residues, Asp274 and Glu624 present in loops LA and LB, respectively originating from N-terminal domain act as catalytic residues. The volume and area calculated for PsGH3 displayed a deep active-site conformation comparable with its homologues, β-1,4-glucosidases (GH3) of Kluyveromyces marxianus and Streptomyces venezuelae. Molecular dynamic (MD) simulation of PsGH3 structure for 80 ns suggested stable and compact structure. Molecular docking studies revealed deeper active site conformation of PsGH3 that could house larger cellooligosaccharides up to 7° of polymerization (DP7). The amino acid residues, Ala86, Leu88, Cys275, Pro483, Phe493, Asn417, Asn491, Pro492, and Leu495 created a binding pocket near the catalytic cleft, crucial for ligand binding. MD simulation of PsGH3 in the presence of cellooligosaccharides, viz., cellobiose and celloheptaose showed stability in terms of RMSD, Rg, and SASA values till 80 ns. The calculation of average number of hydrogen bond (H-bond), interaction energy, and binding free energy confirmed the stronger binding affinity of the larger cellooligosaccharides such as celloheptaose in the binding cavity of PsGH3.
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Affiliation(s)
- Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.
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Raza A, Su W, Hussain MA, Mehmood SS, Zhang X, Cheng Y, Zou X, Lv Y. Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Cold Tolerance in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2021; 12:721681. [PMID: 34691103 PMCID: PMC8532563 DOI: 10.3389/fpls.2021.721681] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/30/2021] [Indexed: 05/18/2023]
Abstract
Rapeseed (Brassica napus L.) is an important oilseed crop in the world. Its productivity is significantly influenced by numerous abiotic stresses, including cold stress (CS). Consequently, enhancement in CS tolerance is becoming an important area for agricultural investigation and crop improvement. Therefore, the current study aimed to identify the stress-responsive genes, metabolites, and metabolic pathways based on a combined transcriptome and metabolome analysis to understand the CS responses and tolerance mechanisms in the cold-tolerant (C18) and cold-sensitive (C6) rapeseed varieties. Based on the metabolome analysis, 31 differentially accumulated metabolites (DAMs) were identified between different comparisons of both varieties at the same time points. From the transcriptome analysis, 2,845, 3,358, and 2,819 differentially expressed genes (DEGs) were detected from the comparison of C6-0 vs. C18-0, C6-1 vs. C18-1, and C6-7 vs. C18-7. By combining the transcriptome and metabolome data sets, we found that numerous DAMs were strongly correlated with several differentially expressed genes (DEGs). A functional enrichment analysis of the DAMs and the correlated DEGs specified that most DEGs and DAMs were mainly enriched in diverse carbohydrates and amino acid metabolisms. Among them, starch and sucrose metabolism and phenylalanine metabolism were significantly enriched and played a vital role in the CS adaption of rapeseed. Six candidate genes were selected from the two pathways for controlling the adaption to low temperature. In a further validation, the T-DNA insertion mutants of their Arabidopsis homologous, including 4cl3, cel5, fruct4, ugp1, axs1, and bam2/9, were characterized and six lines differed significantly in levels of freezing tolerance. The outcome of the current study provided new prospects for the understanding of the molecular basis of CS responses and tolerance mechanisms in rapeseed and present a set of candidate genes for use in improving CS adaptability in the same plant.
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Affiliation(s)
- Ali Raza
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Wei Su
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Muhammad Azhar Hussain
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Sundas Saher Mehmood
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xuekun Zhang
- College of Agriculture, Engineering Research Center of Ecology and Agricultural Use of Wetland of Ministry of Education, Yangtze University, Jingzhou, China
| | - Yong Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiling Zou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yan Lv
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
- *Correspondence: Yan Lv
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11
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Rajkumar MS, Shankar R, Garg R, Jain M. Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars. Genomics 2020; 112:3537-3548. [PMID: 32278023 DOI: 10.1016/j.ygeno.2020.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/13/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022]
Abstract
DNA methylation governs gene regulation in plants in response to environmental conditions. Here, we analyzed role of DNA methylation under desiccation and salinity stresses in three (IR64, stress-sensitive; Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) rice cultivars via bisulphite sequencing. Methylation in CG context within gene body and methylation in CHH context in distal promoter regions were positively correlated with gene expression. Hypomethylation in Nagina 22 and hypermethylation in Pokkali in response to desiccation and salinity stresses, respectively, were correlated with higher expression of few abiotic stress response related genes. Most of the differentially methylated and differentially expressed genes (DMR-DEGs) were cultivar-specific, suggesting an important role of DNA methylation in abiotic stress responses in rice in cultivar-specific manner. DMR-DEGs harboring differentially methylated cytosines due to DNA polymorphisms between the sensitive and tolerant cultivars in their promoter regions and/or coding regions were identified, suggesting the role of epialleles in abiotic stress responses.
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Affiliation(s)
- Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rama Shankar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India.
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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12
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Xiang X, Zhang P, Yu P, Zhang Y, Yang Z, Sun L, Wu W, Khan RM, Abbas A, Cheng S, Cao L. LSSR1 facilitates seed setting rate by promoting fertilization in rice. RICE (NEW YORK, N.Y.) 2019; 12:31. [PMID: 31073866 PMCID: PMC6509318 DOI: 10.1186/s12284-019-0280-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/25/2019] [Indexed: 05/03/2023]
Abstract
Seed setting rate is one of the major components that determine rice (Oryza sativa L.) yield. Successful fertilization is necessary for normal seed setting. However, little is known about the molecular mechanisms governing this process. In this study, we report a novel rice gene, LOW SEED SETTING RATE1 (LSSR1), which regulates the seed setting rate by facilitating rice fertilization. LSSR1 encodes a putative GH5 cellulase, which is highly conserved in plants. LSSR1 is predominantly expressed in anthers during the microsporogenesis stage, and its encoded protein contains a signal peptide at the N-terminal, which may be a secretory protein that stores in pollen grains and functions during rice fertilization. To explore the physiological function of LSSR1 in rice, loss-of-function mutants of LSSR1 were created through the CRISPR-Cas9 system, which showed a significant decrease in rice seed setting rate. However, the morphology of the vegetative and reproductive organs appears normal in lssr1 mutant lines. In addition, lssr1 pollen grains could be normally stained by I2-KI solution. Cytological results demonstrate that the blockage of fertilization mostly accounted for the low seed setting rate in lssr1 mutant lines, which was most likely caused by abnormal pollen grain germination, failed pollen tube penetration, and retarded pollen tube elongation. Together, our results suggest that LSSR1 plays an important role in rice fertilization, which in turn is vital for maintaining rice seed setting rate.
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Affiliation(s)
- Xiaojiao Xiang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Peipei Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Ping Yu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Yingxin Zhang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Zhengfu Yang
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lianping Sun
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Weixun Wu
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Riaz Muhammad Khan
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Adil Abbas
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Shihua Cheng
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
| | - Liyong Cao
- Key Laboratory for Zhejiang Super Rice Research and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006 China
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13
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Dilnur T, Peng Z, Pan Z, Palanga KK, Jia Y, Gong W, Du X. Association Analysis of Salt Tolerance in Asiatic cotton ( Gossypium arboretum) with SNP Markers. Int J Mol Sci 2019; 20:ijms20092168. [PMID: 31052464 PMCID: PMC6540053 DOI: 10.3390/ijms20092168] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022] Open
Abstract
Salinity is not only a major environmental factor which limits plant growth and productivity, but it has also become a worldwide problem. However, little is known about the genetic basis underlying salt tolerance in cotton. This study was carried out to identify marker-trait association signals of seven salt-tolerance-related traits and one salt tolerance index using association analysis for 215 accessions of Asiatic cotton. According to a comprehensive index of salt tolerance (CIST), 215 accessions were mainly categorized into four groups, and 11 accessions with high salinity tolerance were selected for breeding. Genome-wide association studies (GWAS) revealed nine SNP rich regions significantly associated with relative fresh weight (RFW), relative stem length (RSL), relative water content (RWC) and CIST. The nine SNP rich regions analysis revealed 143 polymorphisms that distributed 40 candidate genes and significantly associated with salt tolerance. Notably, two SNP rich regions on chromosome 7 were found to be significantly associated with two salinity related traits, RFW and RSL, by the threshold of −log10P ≥ 6.0, and two candidate genes (Cotton_A_37775 and Cotton_A_35901) related to two key SNPs (Ca7_33607751 and Ca7_77004962) were possibly associated with salt tolerance in G. arboreum. These can provide fundamental information which will be useful for future molecular breeding of cotton, in order to release novel salt tolerant cultivars.
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Affiliation(s)
- Tussipkan Dilnur
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhen Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Koffi Kibalou Palanga
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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14
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Identification of charcoal rot resistance QTLs in sorghum using association and in silico analyses. J Appl Genet 2018; 59:243-251. [PMID: 29876718 DOI: 10.1007/s13353-018-0446-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/30/2018] [Accepted: 05/20/2018] [Indexed: 01/01/2023]
Abstract
Charcoal rot disease, a root and stem disease caused by the soil-borne fungus Macrophomina phaseolina (Tassi) Goid., is a major biotic stress that limits sorghum productivity worldwide. Charcoal rot resistance-related parameters, e.g., pre-emergence damping-off%, post-emergence damping-off%, charcoal rot disease severity, and plant survival rates, were measured in a structured sorghum population consisting of 107 landraces. Analysis of variance of charcoal rot resistance-related parameters revealed significant variations in the response to M. phaseolina infection within evaluated accessions. Continuous phenotypic variations for resistance-related parameters were observed indicating a quantitative inheritance of resistance. The population was genotyped using 181 simple sequence repeat (SSR) markers. Association analysis identified 13 markers significantly associated with quantitative trait genes (QTLs) conferring resistance to charcoal rot disease with an R2 value ranging between 9.47 to 18.87%, nine of which are environment-specific loci. Several QTL-linked markers are significantly associated with more than one resistance-related parameter, suggesting that those QTLs might contain genes involved in the plant defense response. In silico analysis of four novel major QTLs identified 11 putative gene homologs that could be considered as candidate genes for resistance against charcoal rot disease. Cluster analysis using the genotypic data of 181 SSR markers from 107 sorghum accessions identified 12 main clusters. The results provide a basis for further functional characterization of charcoal rot disease resistance or defense genes in sorghum and for further dissection of their molecular mechanisms.
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15
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Zang X, Liu M, Fan Y, Xu J, Xu X, Li H. The structural and functional contributions of β-glucosidase-producing microbial communities to cellulose degradation in composting. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:51. [PMID: 29492106 PMCID: PMC5828080 DOI: 10.1186/s13068-018-1045-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 02/06/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Compost habitats sustain a vast ensemble of microbes that engender the degradation of cellulose, which is an important part of global carbon cycle. β-Glucosidase is the rate-limiting enzyme of degradation of cellulose. Thus, analysis of regulation of β-glucosidase gene expression in composting is beneficial to a better understanding of cellulose degradation mechanism. Genetic diversity and expression of β-glucosidase-producing microbial communities, and relationships of cellulose degradation, metabolic products and the relative enzyme activity during natural composting and inoculated composting were evaluated. RESULTS Compared with natural composting, adding inoculation agent effectively improved the degradation of cellulose, and maintained high level of the carboxymethyl cellulose (CMCase) and β-glucosidase activities in thermophilic phase. Gene expression analysis showed that glycoside hydrolase family 1 (GH1) family of β-glucosidase genes contributed more to β-glucosidase activity in the later thermophilic phase in inoculated compost. In the cooling phase of natural compost, glycoside hydrolase family 3 (GH3) family of β-glucosidase genes contributed more to β-glucosidase activity. Intracellular β-glucosidase activity played a crucial role in the regulation of β-glucosidase gene expression, and upregulation or downregulation was also determined by extracellular concentration of glucose. At sufficiently high glucose concentrations, the functional microbial community in compost was altered, which may contribute to maintaining β-glucosidase activity despite the high glucose content. CONCLUSION This research provides an ecological functional map of microorganisms involved in carbon metabolism in cattle manure-rice straw composting. The performance of the functional microbial groups in the two composting treatments is different, which is related to the cellulase activity and cellulose degradation, respectively.
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Affiliation(s)
- Xiangyun Zang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Meiting Liu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Yihong Fan
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Jie Xu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Xiuhong Xu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
| | - Hongtao Li
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin, 150030 China
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16
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Zang X, Liu M, Wang H, Fan Y, Zhang H, Liu J, Xing E, Xu X, Li H. The distribution of active β-glucosidase-producing microbial communities in composting. Can J Microbiol 2017; 63:998-1008. [PMID: 28892642 DOI: 10.1139/cjm-2017-0368] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. Cellulose degradation is an important part of the global carbon cycle, and β-glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. This work analyzes the succession of β-glucosidase-producing microbial communities that persist throughout cattle manure - rice straw composting, and evaluates their metabolic activities and community advantage during the various phases of composting. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families 1 and 3 (GH1 and GH3) amplified from DNA were classified and gene abundance levels were analyzed. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Deinococcus-Thermus. This indicates that a diverse microbial community utilizes cellobiose. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting; there was a shift to Actinomycetes in the maturing stage. Proteobacteria accounted for the highest proportions during the heating and thermophilic phases of composting. By contrast, the fungal phylum Ascomycota was a minor microbial community constituent in thermophilic phase of composting. Combined with the analysis of the temperature, cellulose degradation rate and the carboxymethyl cellulase and β-glucosidase activities showed that the bacterial GH1 family β-glucosidase genes make greater contribution in cellulose degradation at the later thermophilic stage of composting. In summary, even GH1 bacteria families β-glucosidase genes showing low abundance in DNA may be functionally important in the later thermophilic phase of composting. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in compost. Several β-glucosidase-producing bacteria and fungi identified in this study may represent potential indicators of composting in cellulose degradation.
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Affiliation(s)
- Xiangyun Zang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Meiting Liu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Han Wang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Yihong Fan
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Haichang Zhang
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Jiawen Liu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Enlu Xing
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Xiuhong Xu
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Hongtao Li
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.,College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
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17
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Functional Analysis of a Novel β-(1,3)-Glucanase from Corallococcus sp. Strain EGB Containing a Fascin-Like Module. Appl Environ Microbiol 2017. [PMID: 28625980 DOI: 10.1128/aem.01016-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
A novel β-(1,3)-glucanase gene designated lamC, cloned from Corallococcus sp. strain EGB, contains a fascin-like module and a glycoside hydrolase family 16 (GH16) catalytic module. LamC displays broad hydrolytic activity toward various polysaccharides. Analysis of the hydrolytic products revealed that LamC is an exo-acting enzyme on β-(1,3)(1,3)- and β-(1,6)-linked glucan substrates and an endo-acting enzyme on β-(1,4)-linked glucan and xylan substrates. Site-directed mutagenesis of conserved catalytic Glu residues (E304A and E309A) demonstrated that these activities were derived from the same active site. Excision of the fascin-like module resulted in decreased activity toward β-(1,3)(1,3)-linked glucans. The carbohydrate-binding assay showed that the fascin-like module was a novel β-(1,3)-linked glucan-binding module. The functional characterization of the fascin-like module and catalytic module will help us better understand these enzymes and modules.IMPORTANCE In this report of a bacterial β-(1,3)(1,3)-glucanase containing a fascin-like module, we reveal the β-(1,3)(1,3)-glucan-binding function of the fascin-like module present in the N terminus of LamC. LamC displays exo-β-(1,3)/(1,6)-glucanase and endo-β-(1,4)-glucanase/xylanase activities with a single catalytic domain. Thus, LamC was identified as a novel member of the GH16 family.
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18
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Zhou Y, Zeng L, Gui J, Liao Y, Li J, Tang J, Meng Q, Dong F, Yang Z. Functional characterizations of β-glucosidases involved in aroma compound formation in tea ( Camellia sinensis ). Food Res Int 2017; 96:206-214. [DOI: 10.1016/j.foodres.2017.03.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/01/2017] [Accepted: 03/30/2017] [Indexed: 01/18/2023]
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19
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Parveda M, Kiran B, Punita DL, Kavi Kishor PB. Overexpression of SbAP37 in rice alleviates concurrent imposition of combination stresses and modulates different sets of leaf protein profiles. PLANT CELL REPORTS 2017; 36:773-786. [PMID: 28393269 DOI: 10.1007/s00299-017-2134-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/15/2017] [Indexed: 06/07/2023]
Abstract
SbAP37 transcription factor contributes to a combination of abiotic stresses when applied simultaneously in rice. It modulates a plethora of proteins that might regulate the downstream pathways to impart salt stress tolerance. APETALA type of transcription factor was isolated from Sorghum bicolor (SbAP37), overexpressed in rice using a salt inducible abscisic acid 2 (ABA2) promoter through Agrobacterium tumefaciens following in planta method. Transgenics were confirmed by PCR amplification of SbAP37, hygromycin phosphotransferase (hptII) marker and ABA2 promoter and DNA blot analysis. Plants were exposed to 150 mM NaCl coupled with high day/night 36 ± 2/25 ± 2 °C temperatures and also drought stress by withholding water for 1-week separately at the booting stage. SbAP37 expression was 2.8- to 4.7-folds higher in transgenic leaf under salt, but 1.8- to 3.3-folds higher in roots under drought stress. Native gene expression analysis showed that it is expressed more in stem than in roots and leaves under 150 mM NaCl and 6% PEG stress. In the present study, proteomic analysis of transgenics exposed to 150 mM NaCl coupled with elevated temperatures was taken up using quadrupole time-of-flight (Q-TOF) mass spectrometry (MS). The leaf proteome revealed 11 down regulated, 26 upregulated, 101 common (shared), 193 newly synthesized proteins in transgenics besides 368 proteins in untransformed plants. Some of these protein sets appeared different and unique to combined stresses. Our results suggest that the SbAP37 has the potential to improve combined stress tolerance without causing undesirable phenotypic characters when used under the influence of ABA2 promoter.
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Affiliation(s)
| | - B Kiran
- Bayer BioScience Pvt. Ltd., Madhapur, Hyderabad, 500 081, India
| | - D L Punita
- Department of Genetics, Osmania University, Hyderabad, 500 007, India
| | - P B Kavi Kishor
- Department of Genetics, Osmania University, Hyderabad, 500 007, India.
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20
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Pei X, Zhao J, Cai P, Sun W, Ren J, Wu Q, Zhang S, Tian C. Heterologous expression of a GH3 β-glucosidase from Neurospora crassa in Pichia pastoris with high purity and its application in the hydrolysis of soybean isoflavone glycosides. Protein Expr Purif 2016; 119:75-84. [PMID: 26596358 DOI: 10.1016/j.pep.2015.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/30/2015] [Accepted: 11/10/2015] [Indexed: 01/30/2023]
Abstract
Previous studies have shown isoflavone aglycones to have more biological effects than their counterparts, isoflavone glycones. Some β-glucosidases can hydrolyze isoflavone glucosides to release aglycones, and discovery of these has attracted great interest. A glycoside hydrolase (GH) family 3 β-glucosidase (bgl2) gene from Neurospora crassa was heterologously expressed in Pichia pastoris with high purity. The recombinant BGL2 enzyme displayed its highest activity at pH 5.0 and 60 °C, and had its maximum activity against p-nitrophenyl-β-d-glucopyranoside (pNPG) (143.27 ± 4.79 U/mg), followed by cellobiose (74.99 ± 0.78 U/mg), gentiobiose (47.55 ± 0.15 U/mg), p-nitrophenyl-β-d-cellobioside (pNPC) (40.07 ± 0.87 U/mg), cellotriose (12.31 ± 0.36 U/mg) and cellotetraose (9.04 ± 0.14 U/mg). The kinetic parameters of Km and Vmax were 0.21 ± 0.01 mM and 147.93 ± 2.77 μM/mg/min for pNPG. The purified enzyme showed a heightened ability to convert the major soybean isoflavone glycosides (daidzin, genistin and glycitin) into their corresponding aglycone forms (daidzien, genistein and glycitein). With this activity against soybean isoflavone glycosides, BGL2 shows great potential for applications in the food, animal feed, and pharmaceutical industries.
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Affiliation(s)
- Xue Pei
- College of Plant Sciences, Jilin University, Changchun 130062, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Junqi Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Pengli Cai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wenliang Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jie Ren
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qiaqing Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Shihong Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Chaoguang Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
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21
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Paul S, Gayen D, Datta SK, Datta K. Dissecting root proteome of transgenic rice cultivars unravels metabolic alterations and accumulation of novel stress responsive proteins under drought stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:133-43. [PMID: 25804816 DOI: 10.1016/j.plantsci.2015.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/05/2015] [Accepted: 02/11/2015] [Indexed: 05/24/2023]
Abstract
Generation of drought tolerant rice plants by overexpressing Arabidopsis DREB1A is a significant development for abiotic stress research. However, the metabolic network regulated in the drought tolerant transgenic rice plants is poorly understood. In this research study, we have demonstrated the comparative proteome analysis between the roots of wild type and transgenic DREB1A overexpressing homozygous plants under drought stress condition. After 7d of dehydration stress at reproductive stage, the plants were re-watered for 24h. The roots were collected separately from wild type and transgenic plants grown under water, drought stress and re-watering conditions and total proteins were analyzed by two-dimensional gel electrophoresis (2-DE) coupled with mass spectrometry (MS). Among the large number of differentially accumulated spots, 30, 27 and 20 spots were successfully identified as differentially expressed proteins in three different conditions respectively. The major class of identified proteins belongs to carbohydrate and energy metabolism category while stress and defense related proteins are especially up-accumulated under drought stress in both the plants. A novel protein, R40C1 was reported to be up-accumulated in roots of transgenic plants which may play an important role in generation of drought tolerant plants. Protein-protein interaction helps to identify the network of drought stress signaling pathways.
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Affiliation(s)
- Soumitra Paul
- Laboratory of Translational Research on Transgenic Crops, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Dipak Gayen
- Laboratory of Translational Research on Transgenic Crops, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Swapan K Datta
- Laboratory of Translational Research on Transgenic Crops, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Karabi Datta
- Laboratory of Translational Research on Transgenic Crops, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata 700019, West Bengal, India.
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Rouyi C, Baiya S, Lee SK, Mahong B, Jeon JS, Ketudat-Cairns JR, Ketudat-Cairns M. Recombinant Expression and Characterization of the Cytoplasmic Rice β-Glucosidase Os1BGlu4. PLoS One 2014; 9:e96712. [PMID: 24802508 PMCID: PMC4011751 DOI: 10.1371/journal.pone.0096712] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/10/2014] [Indexed: 12/23/2022] Open
Abstract
The Os1BGlu4 β-glucosidase is the only glycoside hydrolase family 1 member in rice that is predicted to be localized in the cytoplasm. To characterize the biochemical function of rice Os1BGlu4, the Os1bglu4 cDNA was cloned and used to express a thioredoxin fusion protein in Escherichia coli. After removal of the tag, the purified recombinant Os1BGlu4 (rOs1BGlu4) exhibited an optimum pH of 6.5, which is consistent with Os1BGlu4's cytoplasmic localization. Fluorescence microscopy of maize protoplasts and tobacco leaf cells expressing green fluorescent protein-tagged Os1BGlu4 confirmed the cytoplasmic localization. Purified rOs1BGlu4 can hydrolyze p-nitrophenyl (pNP)-β-d-glucoside (pNPGlc) efficiently (kcat/Km = 17.9 mM−1·s−1), and hydrolyzes pNP-β-d-fucopyranoside with about 50% the efficiency of the pNPGlc. Among natural substrates tested, rOs1BGlu4 efficiently hydrolyzed β-(1,3)-linked oligosaccharides of degree of polymerization (DP) 2–3, and β-(1,4)-linked oligosaccharide of DP 3–4, and hydrolysis of salicin, esculin and p-coumaryl alcohol was also detected. Analysis of the hydrolysis of pNP-β-cellobioside showed that the initial hydrolysis was between the two glucose molecules, and suggested rOs1BGlu4 transglucosylates this substrate. At 10 mM pNPGlc concentration, rOs1BGlu4 can transfer the glucosyl group of pNPGlc to ethanol and pNPGlc. This transglycosylation activity suggests the potential use of Os1BGlu4 for pNP-oligosaccharide and alkyl glycosides synthesis.
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Affiliation(s)
- Chen Rouyi
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang District, Nakhon Ratchasima, Thailand
- Guizhou Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Supaporn Baiya
- School of Biochemistry, Institute of Science, Suranaree University of Technology, Muang District, Nakhon Ratchasima, Thailand
| | - Sang-Kyu Lee
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi, Korea
| | - Bancha Mahong
- Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin, Gyeonggi, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi, Korea
- Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin, Gyeonggi, Korea
| | - James R. Ketudat-Cairns
- School of Biochemistry, Institute of Science, Suranaree University of Technology, Muang District, Nakhon Ratchasima, Thailand
| | - Mariena Ketudat-Cairns
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang District, Nakhon Ratchasima, Thailand
- * E-mail:
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Mustafa G, Komatsu S. Quantitative proteomics reveals the effect of protein glycosylation in soybean root under flooding stress. FRONTIERS IN PLANT SCIENCE 2014; 5:627. [PMID: 25477889 PMCID: PMC4235293 DOI: 10.3389/fpls.2014.00627] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/22/2014] [Indexed: 05/22/2023]
Abstract
Flooding stress has a negative impact on soybean cultivation because it severely impairs growth and development. To understand the flooding responsive mechanism in early stage soybeans, a glycoproteomic technique was used. Two-day-old soybeans were treated with flooding for 2 days and roots were collected. Globally, the accumulation level of glycoproteins, as revealed by cross-reaction with concanavalin A decreased by 2 days of flooding stress. Glycoproteins were enriched from total protein extracts using concanavalin A lectin resin and analyzed using a gel-free proteomic technique. One-hundred eleven and 69 glycoproteins were identified without and with 2 days of flooding stress, respectively. Functional categorization of these identified glycoproteins indicated that the accumulation level of proteins related to protein degradation, cell wall, and glycolysis increased, while stress-related proteins decreased under flooding stress. Also the accumulation level of glycoproteins localized in the secretory pathway decreased under flooding stress. Out of 23 common glycoproteins between control and flooding conditions, peroxidases and glycosyl hydrolases were decreased by 2 days of flooding stress. mRNA expression levels of proteins in the endoplasmic reticulum and N-glycosylation related proteins were downregulated by flooding stress. These results suggest that flooding might negatively affect the process of N-glycosylation of proteins related to stress and protein degradation; however glycoproteins involved in glycolysis are activated.
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Affiliation(s)
- Ghazala Mustafa
- Graduate School of Life and Environmental Science, University of TsukubaTsukuba, Japan
- National Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Science, University of TsukubaTsukuba, Japan
- National Institute of Crop Science, National Agriculture and Food Research OrganizationTsukuba, Japan
- *Correspondence: Setsuko Komatsu, National Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-18, Tsukuba 305-8518, Japan e-mail:
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Li H, Xu X, Chen H, Zhang Y, Xu J, Wang J, Lu X. Molecular analyses of the functional microbial community in composting by PCR-DGGE targeting the genes of the β-glucosidase. BIORESOURCE TECHNOLOGY 2013; 134:51-8. [PMID: 23500559 DOI: 10.1016/j.biortech.2013.01.077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/12/2013] [Accepted: 01/16/2013] [Indexed: 05/06/2023]
Abstract
The study investigated the β-glucosidase-producing microbial communities and the enzymatic dynamics of CMCase and β-glucosidase during the process of cattle manure-rice straw composting. In order to analyze the succession of functional community by PCR-denaturing gradient gel electrophoresis (DGGEs), three sets of PCR primers were designed to amplify the family 1 and 3 β-glucosidase genes from both bacteria and fungi. The results showed in general that the stable functional community composition as well as for the high level enzymatic activities of both cellulase and β-glucosidase occurred during the last phase (days 14-31) of composting. In the process of composting, that functional groups were determined by the stable bands (GH1-F, GH1-H, GH1-G, GH3E-D and GH3E-E) may significantly contribute to the increase of β-glucosidase activities in the later phase. Especially, the bands from the family 1 β-glucosidase genes were appeared before that from the family 3 β-glucosidase genes from fungi, then the former was substituted for the latter gradually in the cooling phase. We found significant correlations between the β-glucosidase activity and the communities of the functional bacteria and fungi. The results indicated that different β-glucosidase-producing microbe release different amounts or activities of β-glucosidase, and that the composition of microbial communities may play a major role in determining overall β-glucosidase activity during the composting process.
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Affiliation(s)
- Hongtao Li
- College of Resources and Environmental Sciences, Northeast Agricultural University, Harbin 150030, China
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Singhania RR, Patel AK, Sukumaran RK, Larroche C, Pandey A. Role and significance of beta-glucosidases in the hydrolysis of cellulose for bioethanol production. BIORESOURCE TECHNOLOGY 2013; 127:500-7. [PMID: 23069613 DOI: 10.1016/j.biortech.2012.09.012] [Citation(s) in RCA: 321] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 09/05/2012] [Accepted: 09/05/2012] [Indexed: 05/02/2023]
Abstract
One of the major challenges in the bioconversion of lignocellulosic biomass into liquid biofuels includes the search for a glucose tolerant beta-gulucosidase. Beta-glucosidase is the key enzyme component present in cellulase and completes the final step during cellulose hydrolysis by converting the cellobiose to glucose. This reaction is always under control as it gets inhibited by its product glucose. It is a major bottleneck in the efficient biomass conversion by cellulase. To circumvent this problem several strategies have been adopted which we have discussed in the article along with its production strategies and general properties. It plays a very significant role in bioethanol production from biomass through enzymatic route. Hence several amendments took place in the commercial preparation of cellulase for biomass hydrolysis, which contains higher and improved beta-glucosidase for efficient biomass conversion. This article presents beta-glucosidase as the key component for bioethanol from biomass through enzymatic route.
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Affiliation(s)
- Reeta Rani Singhania
- Laboratoire de Génie Chimique et Biochimique, Université Blaise Pascal, Polytech Clermont-Ferrand, Aubiere cedex, France.
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Abdeljalil S, Trigui-Lahiani H, Lazzez H, Gargouri A. Cloning, molecular characterization, and mRNA expression of the thermostable family 3 β-glucosidase from the rare fungus Stachybotrys microspora. Mol Biotechnol 2012; 54:842-52. [PMID: 23242634 DOI: 10.1007/s12033-012-9633-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The filamentous fungus Stachybotrys microspora possess a rich β-glucosidase system composed of five β-glucosidases. Three of them were already purified to homogeneity and characterized. In order to isolate the β-glucosidase genes from S. microspora and study their regulation, a PCR strategy using consensus primers was used as a first step. This approach enabled the isolation of three different fragments of family 3 β-glucosidase gene. A representative genomic library was constructed and probed with one amplified fragment gene belonging to family 3 of β-glucosidase. After two rounds of hybridization, seven clones were obtained and the analysis of DNA plasmids leads to the isolation of one clone (CF3) with the largest insert of 7 kb. The regulatory region shows multiple TC-rich elements characteristic of constitutive promoter, explaining the expression of this gene under glucose condition, as shown by zymogram and RT-PCR analysis. The tertiary structure of the deduced amino acid sequence of Smbgl3 was predicted and has shown three conserved domains: an (α/β)8 triose phosphate isomerase (TIM) barrel, (α/β)5 sandwich, and fibronectin type III domain involved in protein thermostability. Zymogram analysis highlighted such thermostable character of this novel β-glucosidase.
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Affiliation(s)
- Salma Abdeljalil
- Laboratoire de Valorisation de la Biomasse et Production de Protéines chez les Eucaryotes, Centre de Biotechnologie de Sfax, University of Sfax, Route Sidi Mansour, BP 1177, 3018 Sfax, Tunisia.
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Aspeborg H, Coutinho PM, Wang Y, Brumer H, Henrissat B. Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5). BMC Evol Biol 2012; 12:186. [PMID: 22992189 PMCID: PMC3526467 DOI: 10.1186/1471-2148-12-186] [Citation(s) in RCA: 325] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 09/13/2012] [Indexed: 12/02/2022] Open
Abstract
Background The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on β-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5. Results About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data. Examination of subfamilies with catalytically-active members revealed that one third are monospecific (containing a single enzyme activity), although new functions may be discovered with biochemical characterization in the future. Furthermore, twenty subfamilies presently have no characterization whatsoever and many others have only limited structural and biochemical data. Mapping of functional knowledge onto the GH5 phylogenetic tree revealed that the sequence space of this historical and industrially important family is far from well dispersed, highlighting targets in need of further study. The analysis also uncovered a number of GH5 proteins which have lost their catalytic machinery, indicating evolution towards novel functions. Conclusion Overall, the subfamily division of GH5 provides an actively curated resource for large-scale protein sequence annotation for glycogenomics; the subfamily assignments are openly accessible via the Carbohydrate-Active Enzyme database at
http://www.cazy.org/GH5.html.
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Affiliation(s)
- Henrik Aspeborg
- Division of Glycoscience, School of Biotechnology, KTH - Royal Institute of Technology, AlbaNova University Center, Stockholm SE-106 91, Sweden
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Liu J, Li ZR, Mao XH. Clinical significance of expression of fascin and MMP-9 in hilar cholangiocarcinoma. Shijie Huaren Xiaohua Zazhi 2012; 20:795-799. [DOI: 10.11569/wcjd.v20.i9.795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To detect the expression of fascin and matrix metalloproteinase-9 (MMP-9) in hilar cholangiocarcinoma and to analyze their clinical significance.
METHODS: The expression of fascin and MMP-9 was examined by immunohistochemistry in 56 cases of hilar cholangiocarcinoma and 14 cases of normal tissue of the bile duct.
RESULTS: The positive rates of fascin and MMP-9 expression in hilar cholangiocarcinoma were obviously higher than those in normal tissue of the bile duct (58.9% vs 0%, 73.2% vs 14.3%, both P < 0.05). Both fascin and MMP-9 expression were associated with histological grade, lymph node metastasis, and portal vein invasion (all P < 0.05). In hair cholangiocarcinoma, the expression of fascin was positively correlative with that of MMP-9 (P < 0.05).
CONCLUSION: The expression of fascin and MMP-9 in hilar cholangiocarcinoma plays important roles in tumor progression and metastasis.
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Tyler L, Bragg JN, Wu J, Yang X, Tuskan GA, Vogel JP. Annotation and comparative analysis of the glycoside hydrolase genes in Brachypodium distachyon. BMC Genomics 2010; 11:600. [PMID: 20973991 PMCID: PMC3091745 DOI: 10.1186/1471-2164-11-600] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 10/25/2010] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Glycoside hydrolases cleave the bond between a carbohydrate and another carbohydrate, a protein, lipid or other moiety. Genes encoding glycoside hydrolases are found in a wide range of organisms, from archea to animals, and are relatively abundant in plant genomes. In plants, these enzymes are involved in diverse processes, including starch metabolism, defense, and cell-wall remodeling. Glycoside hydrolase genes have been previously cataloged for Oryza sativa (rice), the model dicotyledonous plant Arabidopsis thaliana, and the fast-growing tree Populus trichocarpa (poplar). To improve our understanding of glycoside hydrolases in plants generally and in grasses specifically, we annotated the glycoside hydrolase genes in the grasses Brachypodium distachyon (an emerging monocotyledonous model) and Sorghum bicolor (sorghum). We then compared the glycoside hydrolases across species, at the levels of the whole genome and individual glycoside hydrolase families. RESULTS We identified 356 glycoside hydrolase genes in Brachypodium and 404 in sorghum. The corresponding proteins fell into the same 34 families that are represented in rice, Arabidopsis, and poplar, helping to define a glycoside hydrolase family profile which may be common to flowering plants. For several glycoside hydrolase familes (GH5, GH13, GH18, GH19, GH28, and GH51), we present a detailed literature review together with an examination of the family structures. This analysis of individual families revealed both similarities and distinctions between monocots and eudicots, as well as between species. Shared evolutionary histories appear to be modified by lineage-specific expansions or deletions. Within GH families, the Brachypodium and sorghum proteins generally cluster with those from other monocots. CONCLUSIONS This work provides the foundation for further comparative and functional analyses of plant glycoside hydrolases. Defining the Brachypodium glycoside hydrolases sets the stage for Brachypodium to be a grass model for investigations of these enzymes and their diverse roles in planta. Insights gained from Brachypodium will inform translational research studies, with applications for the improvement of cereal crops and bioenergy grasses.
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Affiliation(s)
- Ludmila Tyler
- USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Jennifer N Bragg
- USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
| | - Jiajie Wu
- USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Xiaohan Yang
- Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John P Vogel
- USDA-ARS Western Regional Research Center, Albany, CA 94710, USA
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Ketudat Cairns JR, Esen A. β-Glucosidases. Cell Mol Life Sci 2010; 67:3389-405. [PMID: 20490603 PMCID: PMC11115901 DOI: 10.1007/s00018-010-0399-2] [Citation(s) in RCA: 359] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 04/13/2010] [Accepted: 04/30/2010] [Indexed: 10/19/2022]
Abstract
β-Glucosidases (3.2.1.21) are found in all domains of living organisms, where they play essential roles in the removal of nonreducing terminal glucosyl residues from saccharides and glycosides. β-Glucosidases function in glycolipid and exogenous glycoside metabolism in animals, defense, cell wall lignification, cell wall β-glucan turnover, phytohormone activation, and release of aromatic compounds in plants, and biomass conversion in microorganisms. These functions lead to many agricultural and industrial applications. β-Glucosidases have been classified into glycoside hydrolase (GH) families GH1, GH3, GH5, GH9, and GH30, based on their amino acid sequences, while other β-glucosidases remain to be classified. The GH1, GH5, and GH30 β-glucosidases fall in GH Clan A, which consists of proteins with (β/α)(8)-barrel structures. In contrast, the active site of GH3 enzymes comprises two domains, while GH9 enzymes have (α/α)(6) barrel structures. The mechanism by which GH1 enzymes recognize and hydrolyze substrates with different specificities remains an area of intense study.
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Affiliation(s)
- James R Ketudat Cairns
- Schools of Biochemistry and Chemistry, Institute of Science, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, Thailand.
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Sansenya S, Ketudat Cairns JR, Opassiri R. Expression, purification, crystallization and preliminary X-ray analysis of rice (Oryza sativa L.) Os4BGlu12 beta-glucosidase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:320-3. [PMID: 20208171 PMCID: PMC2833047 DOI: 10.1107/s174430911000103x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 01/08/2010] [Indexed: 11/10/2022]
Abstract
Rice (Oryza sativa L.) Os4BGlu12, a glycoside hydrolase family 1 beta-glucosidase (EC 3.2.1.21), was expressed as a fusion protein with an N-terminal thioredoxin/His(6) tag in Escherichia coli strain Origami B (DE3) and purified with subsequent removal of the N-terminal tag. Native Os4BGlu12 and its complex with 2,4-dinitrophenyl-2-deoxy-2-fluoro-beta-D-glucopyranoside (DNP2FG) were crystallized using 19% polyethylene glycol (3350 or 2000, respectively) in 0.1 M Tris-HCl pH 8.5, 0.16 M NaCl at 288 K. Diffraction data sets for the apo and inhibitor-bound forms were collected to 2.50 and 2.45 A resolution, respectively. The space group and the unit-cell parameters of the crystal indicated the presence of two molecules per asymmetric unit, with a solvent content of 50%. The structure of Os4BGlu12 was successfully solved in space group P4(3)2(1)2 by molecular replacement using the white clover cyanogenic beta-glucosidase structure (PDB code 1cbg) as a search model.
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Affiliation(s)
- Sompong Sansenya
- Schools of Biochemistry and Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - James R. Ketudat Cairns
- Schools of Biochemistry and Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Rodjana Opassiri
- Schools of Biochemistry and Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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Kawaura K, Mochida K, Enju A, Totoki Y, Toyoda A, Sakaki Y, Kai C, Kawai J, Hayashizaki Y, Seki M, Shinozaki K, Ogihara Y. Assessment of adaptive evolution between wheat and rice as deduced from full-length common wheat cDNA sequence data and expression patterns. BMC Genomics 2009; 10:271. [PMID: 19534823 PMCID: PMC2703658 DOI: 10.1186/1471-2164-10-271] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 06/18/2009] [Indexed: 01/08/2023] Open
Abstract
Background Wheat is an allopolyploid plant that harbors a huge, complex genome. Therefore, accumulation of expressed sequence tags (ESTs) for wheat is becoming particularly important for functional genomics and molecular breeding. We prepared a comprehensive collection of ESTs from the various tissues that develop during the wheat life cycle and from tissues subjected to stress. We also examined their expression profiles in silico. As full-length cDNAs are indispensable to certify the collected ESTs and annotate the genes in the wheat genome, we performed a systematic survey and sequencing of the full-length cDNA clones. This sequence information is a valuable genetic resource for functional genomics and will enable carrying out comparative genomics in cereals. Results As part of the functional genomics and development of genomic wheat resources, we have generated a collection of full-length cDNAs from common wheat. By grouping the ESTs of recombinant clones randomly selected from the full-length cDNA library, we were able to sequence 6,162 independent clones with high accuracy. About 10% of the clones were wheat-unique genes, without any counterparts within the DNA database. Wheat clones that showed high homology to those of rice were selected in order to investigate their expression patterns in various tissues throughout the wheat life cycle and in response to abiotic-stress treatments. To assess the variability of genes that have evolved differently in wheat and rice, we calculated the substitution rate (Ka/Ks) of the counterparts in wheat and rice. Genes that were preferentially expressed in certain tissues or treatments had higher Ka/Ks values than those in other tissues and treatments, which suggests that the genes with the higher variability expressed in these tissues is under adaptive selection. Conclusion We have generated a high-quality full-length cDNA resource for common wheat, which is essential for continuation of the ongoing curation and annotation of the wheat genome. The data for each clone's expression in various tissues and stress treatments and its variability in wheat and rice as a result of their diversification are valuable tools for functional genomics in wheat and for comparative genomics in cereals.
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Affiliation(s)
- Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, Maioka-cho 641-12, Yokohama 244-0813, Japan.
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Porter BW, Paidi M, Ming R, Alam M, Nishijima WT, Zhu YJ. Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family. Mol Genet Genomics 2009; 281:609-26. [PMID: 19263082 DOI: 10.1007/s00438-009-0434-x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 02/04/2009] [Indexed: 12/11/2022]
Abstract
The majority of plant disease resistance proteins identified to date belong to a limited number of structural classes, of which those containing nucleotide-binding site (NBS) motifs are the most common. This study provides a detailed analysis of the NBS-encoding genes of the fifth sequenced angiosperm, Carica papaya. Despite having a significantly larger genome than Arabidopsis thaliana, papaya has fewer NBS genes. Nevertheless, papaya maintains genes belonging to both Toll/interleukin-1 receptor (TIR) and non-TIR subclasses. Papaya's NBS gene family shares most similarity with Vitis vinifera homologs, but seven non-TIR members with distinct motif sequence represent a novel subgroup. Transcript splice variants and adjacent genes encoding resistance-associated proteins may provide functional compensation for the apparent scarcity of NBS class resistance genes. Looking forward, the papaya NBS gene family is uniquely small in size but structurally diverse, making it suitable for functional studies aimed at a broader understanding of plant resistance genes.
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Affiliation(s)
- Brad W Porter
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Mānoa, Honolulu, HI 96822, USA.
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