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Cho WK, Choi H, Kim SY, Kim E, Paek SH, Kim J, Song J, Heo K, Min J, Jo Y, Lee JH, Moh SH. Transcriptional Changes in Damask Rose Suspension Cell Culture Revealed by RNA Sequencing. PLANTS (BASEL, SWITZERLAND) 2024; 13:602. [PMID: 38475449 DOI: 10.3390/plants13050602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Damask roses (Rosa x damascena) are widely used in cosmetics and pharmaceutics. Here, we established an in vitro suspension cell culture for calli derived from damask rose petals. We analyzed rose suspension cell transcriptomes obtained at two different time points by RNA sequencing to reveal transcriptional changes during rose suspension cell culture. Of the 580 coding RNAs (1.3%) highly expressed in the suspension rose cells, 68 encoded cell wall-associated proteins. However, most RNAs encoded by the chloroplasts and mitochondria are not expressed. Many highly expressed coding RNAs are involved in translation, catalyzing peptide synthesis in ribosomes. Moreover, the amide metabolic process producing naturally occurring alkaloids was the most abundant metabolic process during the propagation of rose suspension cells. During rose cell propagation, coding RNAs involved in the stress response were upregulated at an early stage, while coding RNAs associated with detoxification and transmembrane transport were upregulated at the late stage. We used transcriptome analyses to reveal important biological processes and molecular mechanisms during rose suspension cell culture. Most non-coding (nc) RNAs were not expressed in the rose suspension cells, but a few ncRNAs with unknown functions were highly expressed. The expression of ncRNAs and their target coding RNAs was highly correlated. Taken together, we revealed significant biological processes and molecular mechanisms occurring during rose suspension cell culture using transcriptome analyses.
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Affiliation(s)
- Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hoseong Choi
- Plant Health Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Soo-Yun Kim
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Euihyun Kim
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Seung Hye Paek
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Jiyeon Kim
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Jihyeok Song
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Kyoungyeon Heo
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Jiae Min
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Yeonhwa Jo
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jeong Hun Lee
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
| | - Sang Hyun Moh
- Plant Cell Research Institute of BIO-FD&C Co., Ltd., Incheon 21990, Republic of Korea
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Poulhazan A, Arnold AA, Mentink-Vigier F, Muszyński A, Azadi P, Halim A, Vakhrushev SY, Joshi HJ, Wang T, Warschawski DE, Marcotte I. Molecular-level architecture of Chlamydomonas reinhardtii's glycoprotein-rich cell wall. Nat Commun 2024; 15:986. [PMID: 38307857 PMCID: PMC10837150 DOI: 10.1038/s41467-024-45246-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/19/2024] [Indexed: 02/04/2024] Open
Abstract
Microalgae are a renewable and promising biomass for large-scale biofuel, food and nutrient production. However, their efficient exploitation depends on our knowledge of the cell wall composition and organization as it can limit access to high-value molecules. Here we provide an atomic-level model of the non-crystalline and water-insoluble glycoprotein-rich cell wall of Chlamydomonas reinhardtii. Using in situ solid-state and sensitivity-enhanced nuclear magnetic resonance, we reveal unprecedented details on the protein and carbohydrate composition and their nanoscale heterogeneity, as well as the presence of spatially segregated protein- and glycan-rich regions with different dynamics and hydration levels. We show that mannose-rich lower-molecular-weight proteins likely contribute to the cell wall cohesion by binding to high-molecular weight protein components, and that water provides plasticity to the cell-wall architecture. The structural insight exemplifies strategies used by nature to form cell walls devoid of cellulose or other glycan polymers.
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Affiliation(s)
- Alexandre Poulhazan
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, H2X 2J6, Canada
| | - Alexandre A Arnold
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, H2X 2J6, Canada
| | - Frederic Mentink-Vigier
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL, 32310, USA
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Adnan Halim
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, University of Copenhagen, Copenhagen, Denmark
| | | | - Tuo Wang
- Department of Chemistry, Michigan State University, East Lansing, MI, 48824, USA.
| | - Dror E Warschawski
- Laboratoire des Biomolécules, LBM, CNRS UMR 7203, Sorbonne Université, École Normale Supérieure, PSL University, 75005, Paris, France.
| | - Isabelle Marcotte
- Department of Chemistry, Université du Québec à Montréal, Montreal, QC, H2X 2J6, Canada.
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Ma R, Zhang M, Yang X, Guo J, Fan Y. Transcriptome analysis reveals genes related to the synthesis and metabolism of cell wall polysaccharides in goji berry (Lycium barbarum L.) from various regions. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:7050-7060. [PMID: 37340801 DOI: 10.1002/jsfa.12791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/06/2023] [Accepted: 06/14/2023] [Indexed: 06/22/2023]
Abstract
BACKGROUND In goji berries (Lycium barbarum L.), the cell wall properties and ripening environment affect fruit quality and their economic benefits. However, the mechanism underlying the cell wall remains to be fully elucidated. RESULTS The results showed that total sugar content was higher in Qinghai berries (13.87%, P < 0.01), whereas cellulose content peaked in Zhongning berries (28%, P < 0.05). Arabinose, galactose, and galacturonic acid were the principal components of the cell wall polysaccharides in goji berries. Among them, the content of galactose in Zhongning was significantly the highest (P < 0.05). Interestingly, we found that highly expressed β-glucosidase and lowly expressed endoglucanase led to cellulose accumulation by RNA-sequencing analysis. The expression analysis results suggested that pectate lyase and pectinesterase enzymes could be major factors related to higher galactose and galacturonic acid contents in Zhongning compared to in Qinghai and Gansu. The starch and sucrose metabolism pathway, pentose and glucuronate interconversions pathway, and galactose metabolism pathway played a significant role in cell wall polysaccharide synthesis and metabolism. CONCLUSION In the present study, we aimed to provide some insights into the cell wall on polysaccharide composition, structural features, and gene analysis in goji berries from Zhongning, Qinghai, and Gansu in China. These results might help to clarify the molecular function of the major genes in the cell wall polysaccharides of goji berries and provide a solid foundation for further study. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Ruixue Ma
- School of Food Science and Engineering, Ningxia University, Yinchuan, China
| | - Meng Zhang
- School of Food Science and Engineering, Ningxia University, Yinchuan, China
| | - Xiaohua Yang
- School of Food Science and Engineering, Ningxia University, Yinchuan, China
| | - Jia Guo
- School of Food Science and Engineering, Ningxia University, Yinchuan, China
| | - Yanli Fan
- School of Food Science and Engineering, Ningxia University, Yinchuan, China
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Zhou Y, Fan W, Zhang H, Zhang J, Zhang G, Wang D, Xiang G, Zhao C, Li L, He S, Lu Y, Zhao J, Meng Z, Zhang X, Meng H, Yin X, Yang S, Long G. Marsdenia tenacissima genome reveals calcium adaptation and tenacissoside biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1146-1159. [PMID: 36575579 DOI: 10.1111/tpj.16081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Marsdenia tenacissima is a medicinal plant widely distributed in the calcium-rich karst regions of southwest China. However, the lack of a reference genome has hampered the implementation of molecular techniques in its breeding, pharmacology and domestication. We generated the chromosome-level genome assembly in Apocynaceae using combined SMRT sequencing and Hi-C. The genome length was 381.76 Mb, with 98.9% of it found on 11 chromosomes. The genome contained 222.63 Mb of repetitive sequences and 21 899 predicted gene models, with a contig N50 of 6.57 Mb. Phylogenetic analysis revealed that M. tenacissima diverged from Calotropis gigantea at least 13.43 million years ago. Comparative genomics showed that M. tenacissima underwent ancient shared whole-genome duplication. This event, together with tandem duplication, contributed to 70.71% of gene-family expansion. Both pseudogene analysis and selective pressure calculations suggested calcium-related adaptive evolution in the M. tenacissima genome. Calcium-induced differentially expressed genes (DEGs) were mainly enriched in cell-wall-related processes. Domains (e.g. Fasciclin and Amb_all) and cis-elements (e.g. MYB and MYC) frequently occurred in the coding and promoter regions of cell-wall DEGs, respectively, and the expression levels of these genes correlated significantly with those of calcium-signal-related transcription factors. Moreover, calcium addition increased tenacissoside I, G and H contents. The availability of this high-quality genome provides valuable genomic information for genetic breeding and molecular design, and lends insights into the calcium adaptation of M. tenacissima in karst areas.
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Affiliation(s)
- Yanli Zhou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Wei Fan
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan, 650201, China
| | - Haoyue Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Jingling Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Guanghui Zhang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan, 650201, China
| | - Ding Wang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan, 650201, China
| | - Guisheng Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan, 650201, China
| | - Changhong Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Lianhua Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Simei He
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan, 650201, China
| | - Yingchun Lu
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan, 650201, China
| | - Jiuxia Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
| | - Zhengui Meng
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan, 650201, China
| | - Xianmin Zhang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan, 650201, China
| | - Hengling Meng
- The Life Science and Technology College, Honghe University, Mengzi, Yunnan, 661199, China
| | - Xinhua Yin
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Shengchao Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan, 650201, China
| | - Guangqiang Long
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
- National & Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwestern China, Kunming, Yunnan, 650201, China
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San Clemente H, Kolkas H, Canut H, Jamet E. Plant Cell Wall Proteomes: The Core of Conserved Protein Families and the Case of Non-Canonical Proteins. Int J Mol Sci 2022; 23:ijms23084273. [PMID: 35457091 PMCID: PMC9029284 DOI: 10.3390/ijms23084273] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 12/25/2022] Open
Abstract
Plant cell wall proteins (CWPs) play critical roles during plant development and in response to stresses. Proteomics has revealed their great diversity. With nearly 1000 identified CWPs, the Arabidopsis thaliana cell wall proteome is the best described to date and it covers the main plant organs and cell suspension cultures. Other monocot and dicot plants have been studied as well as bryophytes, such as Physcomitrella patens and Marchantia polymorpha. Although these proteomes were obtained using various flowcharts, they can be searched for the presence of members of a given protein family. Thereby, a core cell wall proteome which does not pretend to be exhaustive, yet could be defined. It comprises: (i) glycoside hydrolases and pectin methyl esterases, (ii) class III peroxidases, (iii) Asp, Ser and Cys proteases, (iv) non-specific lipid transfer proteins, (v) fasciclin arabinogalactan proteins, (vi) purple acid phosphatases and (vii) thaumatins. All the conserved CWP families could represent a set of house-keeping CWPs critical for either the maintenance of the basic cell wall functions, allowing immediate response to environmental stresses or both. Besides, the presence of non-canonical proteins devoid of a predicted signal peptide in cell wall proteomes is discussed in relation to the possible existence of alternative secretion pathways.
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Kolkas H, Balliau T, Chourré J, Zivy M, Canut H, Jamet E. The Cell Wall Proteome of Marchantia polymorpha Reveals Specificities Compared to Those of Flowering Plants. FRONTIERS IN PLANT SCIENCE 2022; 12:765846. [PMID: 35095945 PMCID: PMC8792609 DOI: 10.3389/fpls.2021.765846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/16/2021] [Indexed: 05/30/2023]
Abstract
Primary plant cell walls are composite extracellular structures composed of three major classes of polysaccharides (pectins, hemicelluloses, and cellulose) and of proteins. The cell wall proteins (CWPs) play multiple roles during plant development and in response to environmental stresses by remodeling the polysaccharide and protein networks and acting in signaling processes. To date, the cell wall proteome has been mostly described in flowering plants and has revealed the diversity of the CWP families. In this article, we describe the cell wall proteome of an early divergent plant, Marchantia polymorpha, a Bryophyte which belong to one of the first plant species colonizing lands. It has been possible to identify 410 different CWPs from three development stages of the haploid gametophyte and they could be classified in the same functional classes as the CWPs of flowering plants. This result underlied the ability of M. polymorpha to sustain cell wall dynamics. However, some specificities of the M. polymorpha cell wall proteome could be highlighted, in particular the importance of oxido-reductases such as class III peroxidases and polyphenol oxidases, D-mannose binding lectins, and dirigent-like proteins. These proteins families could be related to the presence of specific compounds in the M. polymorpha cell walls, like mannans or phenolics. This work paves the way for functional studies to unravel the role of CWPs during M. polymorpha development and in response to environmental cues.
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Affiliation(s)
- Hasan Kolkas
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
| | - Thierry Balliau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, PAPPSO, Gif-sur-Yvette, France
| | - Josiane Chourré
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
| | - Michel Zivy
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE-Le Moulon, PAPPSO, Gif-sur-Yvette, France
| | - Hervé Canut
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
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Liu W, Liu Z, Mo Z, Guo S, Liu Y, Xie Q. ATG8-Interacting Motif: Evolution and Function in Selective Autophagy of Targeting Biological Processes. FRONTIERS IN PLANT SCIENCE 2021; 12:783881. [PMID: 34912364 PMCID: PMC8666691 DOI: 10.3389/fpls.2021.783881] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/28/2021] [Indexed: 05/26/2023]
Abstract
Autophagy is an evolutionarily conserved vacuolar process functioning in the degradation of cellular components for reuse. In plants, autophagy is generally activated upon stress and its regulation is executed by numbers of AuTophaGy-related genes (ATGs), of which the ATG8 plays a dual role in both biogenesis of autophagosomes and recruitment of ATG8-interacting motif (AIM) anchored selective autophagy receptors (SARs). Such motif is either termed as AIM or ubiquitin-interacting motif (UIM), corresponding to the LC3-interacting region (LIR)/AIM docking site (LDS) or the UIM docking site (UDS) of ATG8, respectively. To date, dozens of AIM or UIM containing SARs have been characterized. However, the knowledge of these motifs is still obscured. In this review, we intend to summarize the current understanding of SAR proteins and discuss the conservation and diversification of the AIMs/UIMs, expectantly providing new insights into the evolution of them in various biological processes in plants.
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Affiliation(s)
- Wanqing Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zinan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Zulong Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Shaoying Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Qingjun Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
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Villa-Rivera MG, Cano-Camacho H, López-Romero E, Zavala-Páramo MG. The Role of Arabinogalactan Type II Degradation in Plant-Microbe Interactions. Front Microbiol 2021; 12:730543. [PMID: 34512607 PMCID: PMC8424115 DOI: 10.3389/fmicb.2021.730543] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Arabinogalactans (AGs) are structural polysaccharides of the plant cell wall. A small proportion of the AGs are associated with hemicellulose and pectin. Furthermore, AGs are associated with proteins forming the so-called arabinogalactan proteins (AGPs), which can be found in the plant cell wall or attached through a glycosylphosphatidylinositol (GPI) anchor to the plasma membrane. AGPs are a family of highly glycosylated proteins grouped with cell wall proteins rich in hydroxyproline. These glycoproteins have important and diverse functions in plants, such as growth, cellular differentiation, signaling, and microbe-plant interactions, and several reports suggest that carbohydrate components are crucial for AGP functions. In beneficial plant-microbe interactions, AGPs attract symbiotic species of fungi or bacteria, promote the development of infectious structures and the colonization of root tips, and furthermore, these interactions can activate plant defense mechanisms. On the other hand, plants secrete and accumulate AGPs at infection sites, creating cross-links with pectin. As part of the plant cell wall degradation machinery, beneficial and pathogenic fungi and bacteria can produce the enzymes necessary for the complete depolymerization of AGs including endo-β-(1,3), β-(1,4) and β-(1,6)-galactanases, β-(1,3/1,6) galactanases, α-L-arabinofuranosidases, β-L-arabinopyranosidases, and β-D-glucuronidases. These hydrolytic enzymes are secreted during plant-pathogen interactions and could have implications for the function of AGPs. It has been proposed that AGPs could prevent infection by pathogenic microorganisms because their degradation products generated by hydrolytic enzymes of pathogens function as damage-associated molecular patterns (DAMPs) eliciting the plant defense response. In this review, we describe the structure and function of AGs and AGPs as components of the plant cell wall. Additionally, we describe the set of enzymes secreted by microorganisms to degrade AGs from AGPs and its possible implication for plant-microbe interactions.
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Affiliation(s)
- Maria Guadalupe Villa-Rivera
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Mexico
| | - Everardo López-Romero
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Guanajuato, Mexico
| | - María Guadalupe Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Mexico
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Pinski A, Roujol D, Pouzet C, Bordes L, San Clemente H, Hoffmann L, Jamet E. Comparison of mass spectrometry data and bioinformatics predictions to assess the bona fide localization of proteins identified in cell wall proteomics studies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110979. [PMID: 34315595 DOI: 10.1016/j.plantsci.2021.110979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/18/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Plant cell walls have complex architectures made of polysaccharides among which cellulose, hemicelluloses, pectins and cell wall proteins (CWPs). Some CWPs are anchored in the plasma membrane through a glycosylphosphatidylinositol (GPI)-anchor. The secretion pathway is the classical route to reach the extracellular space. Based on experimental data, a canonical signal peptide (SP) has been defined, and bioinformatics tools allowing the prediction of the sub-cellular localization of proteins have been designed. In the same way, the presence of GPI-anchor attachment sites can be predicted using bioinformatics programs. This article aims at comparing the bioinformatics predictions of the sub-cellular localization of proteins assumed to be CWPs to mass spectrometry (MS) data. The sub-cellular localization of a few CWPs exhibiting particular features has been checked by cell biology approaches. Although the prediction of SP length is confirmed in most cases, it is less conclusive for GPI-anchors. Three main observations were done: (i) the variability observed at the N-terminus of a few mature CWPs could play a role in the regulation of their biological activity; (ii) one protein was shown to have a double sub-cellular localization in the cell wall and the chloroplasts; and (iii) peptides were found to be located at the C-terminus of several CWPs previously identified in GPI-anchored proteomes, thus raising the issue of their actual anchoring to the plasma membrane.
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Affiliation(s)
- Artur Pinski
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville Tolosane, France; Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032, Katowice, Poland
| | - David Roujol
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville Tolosane, France
| | - Cécile Pouzet
- FR AIB-TRI Imaging Platform Facilities, Université de Toulouse, CNRS, Auzeville Tolosane, France
| | - Luc Bordes
- FR AIB-TRI Imaging Platform Facilities, Université de Toulouse, CNRS, Auzeville Tolosane, France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville Tolosane, France
| | - Laurent Hoffmann
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville Tolosane, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville Tolosane, France.
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10
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Leschevin M, Ismael M, Quero A, San Clemente H, Roulard R, Bassard S, Marcelo P, Pageau K, Jamet E, Rayon C. Physiological and Biochemical Traits of Two Major Arabidopsis Accessions, Col-0 and Ws, Under Salinity. FRONTIERS IN PLANT SCIENCE 2021; 12:639154. [PMID: 34234793 PMCID: PMC8256802 DOI: 10.3389/fpls.2021.639154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/20/2021] [Indexed: 06/01/2023]
Abstract
Salinity affects plant growth and development as shown with the glycophyte model plant, Arabidopsis thaliana (Arabidopsis). Two Arabidopsis accessions, Wassilewskija (Ws) and Columbia (Col-0), are widely used to generate mutants available from various Arabidopsis seed resources. However, these two ecotypes are known to be salt-sensitive with different degrees of tolerance. In our study, 3-week-old Col-0 and Ws plants were treated with and without 150 mM NaCl for 48, 72, or 96 h, and several physiological and biochemical traits were characterized on shoots to identify any specific traits in their tolerance to salinity. Before salt treatment was carried out, a different phenotype was observed between Col-0 and Ws, whose main inflorescence stem became elongated in contrast to Col-0, which only displayed rosette leaves. Our results showed that Col-0 and Ws were both affected by salt stress with limited growth associated with a reduction in nutrient uptake, a degradation of photosynthetic pigments, an increase in protein degradation, as well as showing changes in carbohydrate metabolism and cell wall composition. These traits were often more pronounced in Col-0 and occurred usually earlier than in Ws. Tandem Mass Tags quantitative proteomics data correlated well with the physiological and biochemical results. The Col-0 response to salt stress was specifically characterized by a greater accumulation of osmoprotectants such as anthocyanin, galactinol, and raffinose; a lower reactive oxygen detoxification capacity; and a transient reduction in galacturonic acid content. Pectin degradation was associated with an overaccumulation of the wall-associated kinase 1, WAK1, which plays a role in cell wall integrity (CWI) upon salt stress exposure. Under control conditions, Ws produced more antioxidant enzymes than Col-0. Fewer specific changes occurred in Ws in response to salt stress apart from a higher number of different fascilin-like arabinogalactan proteins and a greater abundance of expansin-like proteins, which could participate in CWI. Altogether, these data indicate that Col-0 and Ws trigger similar mechanisms to cope with salt stress, and specific changes are more likely related to the developmental stage than to their respective genetic background.
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Affiliation(s)
- Maïté Leschevin
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Marwa Ismael
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Anthony Quero
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | | | - Romain Roulard
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Solène Bassard
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Paulo Marcelo
- Plateforme d’Ingénierie Cellulaire & Analyses des Protéines ICAP Université de Picardie Jules Verne, Amiens, France
| | - Karine Pageau
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
| | - Elisabeth Jamet
- LRSV, Université de Toulouse, CNRS, UPS, Auzeville-Tolosane, France
| | - Catherine Rayon
- UMR INRAE 1158 BioEcoAgro, BIOlogie des Plantes et Innovation, Université de Picardie Jules Verne, Amiens, France
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11
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Ves-Urai P, Krobthong S, Thongsuk K, Roytrakul S, Yokthongwattana C. Comparative secretome analysis between salinity-tolerant and control Chlamydomonas reinhardtii strains. PLANTA 2021; 253:68. [PMID: 33594587 DOI: 10.1007/s00425-021-03583-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/30/2021] [Indexed: 06/12/2023]
Abstract
Secretome analysis of a salt-tolerant and control Chlamydomonas reinhardtii revealed 514 differentially expressed proteins. Membrane transport and trafficking, signal transduction and channel proteins were up-regulated in the ST secretome. Salinity is a major abiotic stress that limits crop production worldwide. Multiple adverse effects have been reported in many living organisms exposed to high-saline concentrations. Chlamydomonas reinhardtii is known for secreting proteins in response to many environmental stresses. A salinity-tolerant (ST) strain of Chlamydomonas has been developed, whose cells were able to grow at 300 mM NaCl. The current study analyzed the secretomes of ST grown in TAP medium supplemented with 300 mM NaCl and the laboratory strain CC-503 grown in TAP medium without NaCl supplement. In total, 514 secreted proteins were identified of which 203 were up-regulated and 110 were down-regulated. Bioinformatic analysis predicted 168 proteins to be secreted or in the conventional secretory pathway. Out of these, 70 were up-regulated, while 51 proteins were down-regulated. Proteins involved in membrane transport and trafficking, signal transduction and channel proteins were altered in their expression in the ST secretome, suggesting the response of saline stress acts toward not only the intracellular pool of proteins but also the extracellular proteins. This also suggested that the secreted proteins might have roles in the extracellular space. Signal peptide (SP) prediction revealed that almost 40% of the predicted secreted proteins contained a signal peptide; however, a high proportion of proteins lacked an SP, suggesting that these proteins might be secreted through an unconventional protein secretion pathway.
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Affiliation(s)
- Parthompong Ves-Urai
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Bangkok, Thailand
| | - Sucheewin Krobthong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Rd., Pathumthani, 12120, Thailand
| | - Karnpitcha Thongsuk
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngamwongwan Rd., Bangkok, 10900, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Rd., Pathumthani, 12120, Thailand
| | - Chotika Yokthongwattana
- Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngamwongwan Rd., Bangkok, 10900, Thailand.
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900, Thailand.
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12
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Petrova N, Nazipova A, Gorshkov O, Mokshina N, Patova O, Gorshkova T. Gene Expression Patterns for Proteins With Lectin Domains in Flax Stem Tissues Are Related to Deposition of Distinct Cell Wall Types. FRONTIERS IN PLANT SCIENCE 2021; 12:634594. [PMID: 33995436 PMCID: PMC8121149 DOI: 10.3389/fpls.2021.634594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/16/2021] [Indexed: 05/10/2023]
Abstract
The genomes of higher plants encode a variety of proteins with lectin domains that are able to specifically recognize certain carbohydrates. Plants are enriched in a variety of potentially complementary glycans, many of which are located in the cell wall. We performed a genome-wide search for flax proteins with lectin domains and compared the expression of the encoding genes in different stem tissues that have distinct cell wall types with different sets of major polysaccharides. Over 400 genes encoding proteins with lectin domains that belong to different families were revealed in the flax genome; three quarters of these genes were expressed in stem tissues. Hierarchical clustering of the data for all expressed lectins grouped the analyzed samples according to their characteristic cell wall type. Most lectins differentially expressed in tissues with primary, secondary, and tertiary cell walls were predicted to localize at the plasma membrane or cell wall. These lectins were from different families and had various architectural types. Three out of four flax genes for proteins with jacalin-like domains were highly upregulated in bast fibers at the stage of tertiary cell wall deposition. The dynamic changes in transcript level of many genes for lectins from various families were detected in stem tissue over the course of gravitropic response induced by plant gravistimulation. The data obtained in this study indicate a large number of lectin-mediated events in plants and provide insight into the proteins that take part in tissue specialization and reaction to abiotic stress.
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Affiliation(s)
- Natalia Petrova
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Alsu Nazipova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Oleg Gorshkov
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Natalia Mokshina
- Laboratory of Plant Glycobiology, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
| | - Olga Patova
- Institute of Physiology, FRC Komi Science Centre of Ural Branch of Russian Academy of Sciences, Syktyvkar, Russia
| | - Tatyana Gorshkova
- Laboratory of Plant Cell Growth Mechanisms, Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Kazan, Russia
- *Correspondence: Tatyana Gorshkova,
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13
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Haeger W, Wielsch N, Shin NR, Gebauer-Jung S, Pauchet Y, Kirsch R. New Players in the Interaction Between Beetle Polygalacturonases and Plant Polygalacturonase-Inhibiting Proteins: Insights From Proteomics and Gene Expression Analyses. FRONTIERS IN PLANT SCIENCE 2021; 12:660430. [PMID: 34149758 PMCID: PMC8213348 DOI: 10.3389/fpls.2021.660430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/26/2021] [Indexed: 05/12/2023]
Abstract
Plants possess various defense strategies to counter attacks from microorganisms or herbivores. For example, plants reduce the cell-wall-macerating activity of pathogen- or insect-derived polygalacturonases (PGs) by expressing PG-inhibiting proteins (PGIPs). PGs and PGIPs belong to multi-gene families believed to have been shaped by an evolutionary arms race. The mustard leaf beetle Phaedon cochleariae expresses both active PGs and catalytically inactive PG pseudoenzymes. Previous studies demonstrated that (i) PGIPs target beetle PGs and (ii) the role of PG pseudoenzymes remains elusive, despite having been linked to the pectin degradation pathway. For further insight into the interaction between plant PGIPs and beetle PG family members, we combined affinity purification with proteomics and gene expression analyses, and identified novel inhibitors of beetle PGs from Chinese cabbage (Brassica rapa ssp. pekinensis). A beetle PG pseudoenzyme was not targeted by PGIPs, but instead interacted with PGIP-like proteins. Phylogenetic analysis revealed that PGIP-like proteins clustered apart from "classical" PGIPs but together with proteins, which have been involved in developmental processes. Our results indicate that PGIP-like proteins represent not only interesting novel PG inhibitor candidates in addition to "classical" PGIPs, but also fascinating new players in the arms race between herbivorous beetles and plant defenses.
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Affiliation(s)
- Wiebke Haeger
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Natalie Wielsch
- Mass Spectrometry Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Na Ra Shin
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Steffi Gebauer-Jung
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yannick Pauchet
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
- *Correspondence: Roy Kirsch,
| | - Roy Kirsch
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
- Yannick Pauchet,
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14
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Silva J, Ferraz R, Dupree P, Showalter AM, Coimbra S. Three Decades of Advances in Arabinogalactan-Protein Biosynthesis. FRONTIERS IN PLANT SCIENCE 2020; 11:610377. [PMID: 33384708 PMCID: PMC7769824 DOI: 10.3389/fpls.2020.610377] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/23/2020] [Indexed: 05/18/2023]
Abstract
Arabinogalactan-proteins (AGPs) are a large, complex, and highly diverse class of heavily glycosylated proteins that belong to the family of cell wall hydroxyproline-rich glycoproteins. Approximately 90% of the molecules consist of arabinogalactan polysaccharides, which are composed of arabinose and galactose as major sugars and minor sugars such as glucuronic acid, fucose, and rhamnose. About half of the AGP family members contain a glycosylphosphatidylinositol (GPI) lipid anchor, which allows for an association with the outer leaflet of the plasma membrane. The mysterious AGP family has captivated the attention of plant biologists for several decades. This diverse family of glycoproteins is widely distributed in the plant kingdom, including many algae, where they play fundamental roles in growth and development processes. The journey of AGP biosynthesis begins with the assembly of amino acids into peptide chains of proteins. An N-terminal signal peptide directs AGPs toward the endoplasmic reticulum, where proline hydroxylation occurs and a GPI anchor may be added. GPI-anchored AGPs, as well as unanchored AGPs, are then transferred to the Golgi apparatus, where extensive glycosylation occurs by the action of a variety glycosyltransferase enzymes. Following glycosylation, AGPs are transported by secretory vesicles to the cell wall or to the extracellular face of the plasma membrane (in the case of GPI-anchored AGPs). GPI-anchored proteins can be released from the plasma membrane into the cell wall by phospholipases. In this review, we present an overview of the accumulated knowledge on AGP biosynthesis over the past three decades. Particular emphasis is placed on the glycosylation of AGPs as the sugar moiety is essential to their function. Recent genetics and genomics approaches have significantly contributed to a broader knowledge of AGP biosynthesis. However, many questions remain to be elucidated in the decades ahead.
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Affiliation(s)
- Jessy Silva
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Ricardo Ferraz
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Allan M. Showalter
- Department of Environmental and Plant Biology, Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
| | - Sílvia Coimbra
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
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15
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Niu L, Liu L, Wang W. Digging for Stress-Responsive Cell Wall Proteins for Developing Stress-Resistant Maize. FRONTIERS IN PLANT SCIENCE 2020; 11:576385. [PMID: 33101346 PMCID: PMC7546335 DOI: 10.3389/fpls.2020.576385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/07/2020] [Indexed: 06/09/2023]
Abstract
As a vital component of plant cell walls, proteins play important roles in stress response by modifying the structure of cell walls and involving in the wall integrity signaling pathway. Recently, we have critically reviewed the predictors, databases, and cross-referencing of the subcellular locations of possible cell wall proteins (CWPs) in plants (Briefings in Bioinformatics 2018;19:1130-1140). Here, we briefly introduce strategies for isolating CWPs during proteomic analysis. Taking maize (Zea mays) as an example, we retrieved 1873 probable maize CWPs recorded in the UniProt KnowledgeBase (UniProtKB). After curation, 863 maize CWPs were identified and classified into 59 kinds of protein families. By referring to gene ontology (GO) annotations and gene differential expression in the Expression Atlas, we have highlighted the potential of CWPs acting in the front line of defense against biotic and abiotic stresses. Moreover, the analysis results of cis-acting elements revealed the responsiveness of the genes encoding CWPs toward phytohormones and various stresses. We suggest that the stress-responsive CWPs could be promising candidates for applications in developing varieties of stress-resistant maize.
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16
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Plant Cell Wall Proteomes: Bioinformatics and Cell Biology Tools to Assess the Bona Fide Cell Wall Localization of Proteins. Methods Mol Biol 2020. [PMID: 32617950 DOI: 10.1007/978-1-0716-0621-6_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The purification of plant cell walls is challenging because they constitute an open compartment which is not limited by a membrane like the cell organelles. Different strategies have been established to limit the contamination by proteins of other compartments in cell wall proteomics studies. Non-destructive methods rely on washing intact cells with various types of solutions without disrupting the plasma membrane in order to elute cell wall proteins. In contrast, destructive protocols involve the purification of cell walls prior to the extraction of proteins with salt solutions. In both cases, proteins known to be intracellular have been identified by mass spectrometry in cell wall proteomes. The aim of this chapter is to provide tools to assess the subcellular localization of the proteins identified in cell wall proteomics studies, including: (1) bioinformatic predictions, (2) immunocytolocalization of proteins of interest on tissue sections and (3) in muro observation of proteins of interest fused to reporter fluorescent proteins by confocal microscopy. Finally, a qualitative assessment of the work can be performed and the strategy used to prepare the samples can be optimized if necessary.
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17
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Plant Cell Wall Proteins and Development. Int J Mol Sci 2020; 21:ijms21082731. [PMID: 32326416 PMCID: PMC7215729 DOI: 10.3390/ijms21082731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 11/24/2022] Open
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18
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The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage. Int J Mol Sci 2020; 21:ijms21072488. [PMID: 32260156 PMCID: PMC7177597 DOI: 10.3390/ijms21072488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/25/2020] [Accepted: 04/01/2020] [Indexed: 12/29/2022] Open
Abstract
Plant cell wall proteins play major roles during plant development and in response to environmental cues. A bioinformatic search for functional domains has allowed identifying the PAC domain (Proline-rich, Arabinogalactan proteins, conserved Cysteines) in several proteins (PDPs) identified in cell wall proteomes. This domain is assumed to interact with pectic polysaccharides and O-glycans and to contribute to non-covalent molecular scaffolds facilitating the remodeling of polysaccharidic networks during rapid cell expansion. In this work, the characteristics of the PAC domain are described in detail, including six conserved Cys residues, their spacing, and the predicted secondary structures. Modeling has been performed based on the crystal structure of a Plantago lanceolata PAC domain. The presence of β-sheets is assumed to ensure the correct folding of the PAC domain as a β-barrel with loop regions. We show that PDPs are present in early divergent organisms from the green lineage and in all land plants. PAC domains are associated with other types of domains: Histidine-rich, extensin, Proline-rich, or yet uncharacterized. The earliest divergent organisms having PDPs are Bryophytes. Like the complexity of the cell walls, the number and complexity of PDPs steadily increase during the evolution of the green lineage. The association of PAC domains with other domains suggests a neo-functionalization and different types of interactions with cell wall polymers
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19
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Dubiel M, De Coninck T, Osterne VJS, Verbeke I, Van Damme D, Smagghe G, Van Damme EJM. The ArathEULS3 Lectin Ends up in Stress Granules and Can Follow an Unconventional Route for Secretion. Int J Mol Sci 2020; 21:E1659. [PMID: 32121292 PMCID: PMC7084908 DOI: 10.3390/ijms21051659] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/26/2022] Open
Abstract
Stress granules are cytoplasmic compartments, which serve as mRNA storage units during stress, therefore regulating translation. The Arabidopsis thaliana lectin ArathEULS3 has been widely described as a stress inducible gene. This study aimed to examine in detail the localization of ArathEULS3 lectin in normal and stressed cells. Colocalization experiments revealed that the nucleo-cytoplasmic lectin ArathEULS3 relocates to stress granules after stress. The ArathEULS3 sequence encodes a protein with a EUL lectin domain and an N-terminal domain with unknown structure and function. Bioinformatics analyses showed that the N-terminal domain sequence contains intrinsically disordered regions and likely does not exhibit a stable protein fold. Plasmolysis experiments indicated that ArathEULS3 also localizes to the apoplast, suggesting that this protein might follow an unconventional route for secretion. As part of our efforts we also investigated the interactome of ArathEULS3 and identified several putative interaction partners important for the protein translation process.
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Affiliation(s)
- Malgorzata Dubiel
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Tibo De Coninck
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Vinicius Jose Silva Osterne
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
- Laboratório de Moléculas Biologicamente Ativas, Universidade Federal do Ceará, José Aurelio Camara, S/N, 61440-970, Fortaleza 60440-970, Brazil
| | - Isabel Verbeke
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
- Center for Advanced Light Microscopy, Ghent University, 9000 Ghent, Belgium
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20
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Righetti PG, Boschetti E. Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110302. [PMID: 31779915 DOI: 10.1016/j.plantsci.2019.110302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/15/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
In plant tissues proteins are present in low amounts but in a very large number. To this peculiar situation many complex foreign components render protein extraction and purification very difficult. In the last several years interesting technologies have been described to improve the technical situation to the point that some methodologies allow reaching very low-abundance proteins and minor allergens. Among enrichment methods the one documented in this report is based on combinatorial peptide ligand libraries (CPLLs) that emerged in the last decade by contributing to largely improve the knowledge in plant proteomics. It is the aim of this review to describe how this technology allows detecting low-abundance proteins from various plant tissues and to report the dynamics of the proteome components in response to environmental changes and biotic attacks. Typical documented examples with the description of their scientific interest are reported. The described technical approach and selected applications are considered as one of the most advanced approaches for plant proteomics investigations with possibilities not only to enlarge the knowledge of plant proteomes but also to discover novel allergens as well as plant biomarkers subsequent to stressful situations.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131, Milan, Italy.
| | - Egisto Boschetti
- Scientific Consultant, JAM Conseil, 92200, Neuilly-sur-Seine, France
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21
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Wu W, Zhu S, Chen Q, Lin Y, Tian J, Liang C. Cell Wall Proteins Play Critical Roles in Plant Adaptation to Phosphorus Deficiency. Int J Mol Sci 2019; 20:E5259. [PMID: 31652783 PMCID: PMC6862644 DOI: 10.3390/ijms20215259] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 02/07/2023] Open
Abstract
Phosphorus is one of the mineral nutrient elements essential for plant growth and development. Low phosphate (Pi) availability in soils adversely affects crop production. To cope with low P stress, remodeling of root morphology and architecture is generally observed in plants, which must be accompanied by root cell wall modifications. It has been documented that cell wall proteins (CWPs) play critical roles in shaping cell walls, transmitting signals, and protecting cells against environmental stresses. However, understanding of the functions of CWPs involved in plant adaptation to P deficiency remains fragmentary. The aim of this review was to summarize advances in identification and functional characterization of CWPs in responses to P deficiency, and to highlight the critical roles of CWPs in mediating root growth, P reutilization, and mobilization in plants.
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Affiliation(s)
- Weiwei Wu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Shengnan Zhu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Qianqian Chen
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Yan Lin
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.
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22
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Elagamey E, Narula K, Chakraborty N, Chakraborty S. Extracellular Matrix Proteome: Isolation of ECM Proteins for Proteomics Studies. Methods Mol Biol 2019; 2057:155-172. [PMID: 31595478 DOI: 10.1007/978-1-4939-9790-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Understanding molecular mechanisms and cellular metabolism in varied plant processes necessitates knowledge of the expressed proteins and their subcellular distribution. Spatial partitioning of organelles generates an enclosed milieu for physiochemical reactions designed and tightly linked to a specific organelle function. Of which, extracellular matrix (ECM)/cell wall (CW) is a dynamic and chemically active compartment. The ECM proteins are organized into complex structural and functional networks involved in several metabolic processes, including carbon and nitrogen metabolism. Organellar proteomics aim for comprehensive identification of resident proteins that rely on the isolation of highly purified organelle free from contamination by other intracellular components. Extraction and isolation of plant ECM proteins features key caveats due to the lack of adjoining membrane, the presence of a polysaccharide-protein network that traps contaminants, and the existence of high phenolic content. Furthermore, due to diverse biochemical forces, including labile, weakly bound and strongly bound protein in the protein-polysaccharide matrix different elution procedures are required to enrich ECM proteins. Here, we describe a method that allows efficient fractionation of plant ECM, extraction of ECM proteins and protein profiling from variety of crop plants, including rice, chickpea and potato. This method can easily be adapted to other plant species for varied experimental conditions.
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Affiliation(s)
- Eman Elagamey
- National Institute of Plant Genome Research, New Delhi, India
- Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Kanika Narula
- National Institute of Plant Genome Research, New Delhi, India
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Sergeant K, Printz B, Guerriero G, Renaut J, Lutts S, Hausman JF. The Dynamics of the Cell Wall Proteome of Developing Alfalfa Stems. BIOLOGY 2019; 8:E60. [PMID: 31430995 PMCID: PMC6784106 DOI: 10.3390/biology8030060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/06/2019] [Accepted: 08/14/2019] [Indexed: 12/24/2022]
Abstract
In this study, the cell-wall-enriched subproteomes at three different heights of alfalfa stems were compared. Since these three heights correspond to different states in stem development, a view on the dynamics of the cell wall proteome during cell maturation is obtained. This study of cell wall protein-enriched fractions forms the basis for a description of the development process of the cell wall and the linking cell wall localized proteins with the evolution of cell wall composition and structure. The sequential extraction of cell wall proteins with CaCl2, EGTA, and LiCl-complemented buffers was combined with a gel-based proteome approach and multivariate analysis. Although the highest similarities were observed between the apical and intermediate stem regions, the proteome patterns are characteristic for each region. Proteins that bind carbohydrates and have proteolytic activity, as well as enzymes involved in glycan remobilization, accumulate in the basal stem region. Beta-amylase and ferritin likewise accumulate more in the basal stem segment. Therefore, remobilization of nutrients appears to be an important process in the oldest stem segment. The intermediate and apical regions are sites of cell wall polymer remodeling, as suggested by the high abundance of proteins involved in the remodeling of the cell wall, such as xyloglucan endoglucosylase, beta-galactosidase, or the BURP-domain containing polygalacturonase non-catalytic subunit. However, the most striking change between the different stem parts is the strong accumulation of a DUF642-conserved domain containing protein in the apical region of the stem, which suggests a particular role of this protein during the early development of stem tissues.
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Affiliation(s)
- Kjell Sergeant
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg.
| | - Bruno Printz
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
- Groupe de Recherche en Physiologie végétale (GRPV), Université catholique de Louvain, Earth and Life Institute Agronomy (ELI-A), 1348 Louvain-la-Neuve, Belgium
| | - Gea Guerriero
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
| | - Jenny Renaut
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
| | - Stanley Lutts
- Groupe de Recherche en Physiologie végétale (GRPV), Université catholique de Louvain, Earth and Life Institute Agronomy (ELI-A), 1348 Louvain-la-Neuve, Belgium
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 4362 Esch/Alzette, Luxembourg
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Fruleux A, Verger S, Boudaoud A. Feeling Stressed or Strained? A Biophysical Model for Cell Wall Mechanosensing in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:757. [PMID: 31244875 PMCID: PMC6581727 DOI: 10.3389/fpls.2019.00757] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/24/2019] [Indexed: 05/21/2023]
Abstract
Mechanical signals have recently emerged as a major cue in plant morphogenesis, notably influencing cytoskeleton organization, gene expression, protein polarity, or cell division. Although many putative mechanosensing proteins have been identified, it is unclear what mechanical cue they might sense and how this would occur. Here we briefly explain the notions of mechanical stress and strain. We present the challenges to understand their sensing by plants, focusing on the cell wall and the plasma membrane, and we review putative mechanosensing structures. We propose minimal biophysical models of mechanosensing, revealing the modes of mechanosensing according to mechanosensor lifetime, threshold force for mechanosensor dissociation, and type of association between the mechanosensor and the cell wall, as the sensor may be associated to a major load-bearing structure such as cellulose or to a minor load-bearing structure such as pectins or the plasma membrane. Permanent strain, permanent expansion, and relatively slow variations thereof are sensed in all cases; variations of stress are sensed in all cases; permanent stress is sensed only in the following specific cases: sensors associated to minor load-bearing structures slowly relaxing in a growing wall, long-lived sensors with high dissociation force and associated to major-load-bearing structures, and sensors with low dissociation force associated to major-load-baring structures behaving elastically. We also find that all sensors respond to variations in the composition or the mechanical properties of the cell wall. The level of sensing is modulated by the properties of all of mechanosensor, cell wall components, and plasma membrane. Although our models are minimal and not fully realistic, our results yield a framework to start investigating the possible functions of putative mechanosensors.
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Affiliation(s)
- Antoine Fruleux
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRA, CNRS, Lyon, France
| | - Stéphane Verger
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Arezki Boudaoud
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRA, CNRS, Lyon, France
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25
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Calderan-Rodrigues MJ, Guimarães Fonseca J, de Moraes FE, Vaz Setem L, Carmanhanis Begossi A, Labate CA. Plant Cell Wall Proteomics: A Focus on Monocot Species, Brachypodium distachyon, Saccharum spp. and Oryza sativa. Int J Mol Sci 2019; 20:E1975. [PMID: 31018495 PMCID: PMC6514655 DOI: 10.3390/ijms20081975] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 12/13/2022] Open
Abstract
Plant cell walls mostly comprise polysaccharides and proteins. The composition of monocots' primary cell walls differs from that of dicots walls with respect to the type of hemicelluloses, the reduction of pectin abundance and the presence of aromatic molecules. Cell wall proteins (CWPs) differ among plant species, and their distribution within functional classes varies according to cell types, organs, developmental stages and/or environmental conditions. In this review, we go deeper into the findings of cell wall proteomics in monocot species and make a comparative analysis of the CWPs identified, considering their predicted functions, the organs analyzed, the plant developmental stage and their possible use as targets for biofuel production. Arabidopsis thaliana CWPs were considered as a reference to allow comparisons among different monocots, i.e., Brachypodium distachyon, Saccharum spp. and Oryza sativa. Altogether, 1159 CWPs have been acknowledged, and specificities and similarities are discussed. In particular, a search for A. thaliana homologs of CWPs identified so far in monocots allows the definition of monocot CWPs characteristics. Finally, the analysis of monocot CWPs appears to be a powerful tool for identifying candidate proteins of interest for tailoring cell walls to increase biomass yield of transformation for second-generation biofuels production.
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Affiliation(s)
- Maria Juliana Calderan-Rodrigues
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Juliana Guimarães Fonseca
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Fabrício Edgar de Moraes
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Laís Vaz Setem
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Amanda Carmanhanis Begossi
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
| | - Carlos Alberto Labate
- Department of Genetics, Max Feffer Laboratory of Plant Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, CP 83, 13400-970 Piracicaba, SP, Brazil.
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26
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He J, Zhao H, Cheng Z, Ke Y, Liu J, Ma H. Evolution Analysis of the Fasciclin-Like Arabinogalactan Proteins in Plants Shows Variable Fasciclin-AGP Domain Constitutions. Int J Mol Sci 2019; 20:E1945. [PMID: 31010036 PMCID: PMC6514703 DOI: 10.3390/ijms20081945] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 01/03/2023] Open
Abstract
The fasciclin-like arabinogalactan proteins (FLAs) play important roles in plant development and adaptation to the environment. FLAs contain both fasciclin domains and arabinogalactan protein (AGP) regions, which have been identified in several plants. The evolutionary history of this gene family in plants is still undiscovered. In this study, we identified the FLA gene family in 13 plant species covering major lineages of plants using bioinformatics methods. A total of 246 FLA genes are identified with gene copy numbers ranging from one (Chondrus crispus) to 49 (Populus trichocarpa). These FLAs are classified into seven groups, mainly based on the phylogenetic analysis of plant FLAs. All FLAs in land plants contain one or two fasciclin domains, while in algae, several FLAs contain four or six fasciclin domains. It has been proposed that there was a divergence event, represented by the reduced number of fasciclin domains from algae to land plants in evolutionary history. Furthermore, introns in FLA genes are lost during plant evolution, especially from green algae to land plants. Moreover, it is found that gene duplication events, including segmental and tandem duplications are essential for the expansion of FLA gene families. The duplicated gene pairs in FLA gene family mainly evolve under purifying selection. Our findings give insight into the origin and expansion of the FLA gene family and help us understand their functions during the process of evolution.
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Affiliation(s)
- Jiadai He
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Hua Zhao
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Zhilu Cheng
- College of Landscape Architecture and Arts, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Yuwei Ke
- College of Life Sciences, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Jiaxi Liu
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
| | - Haoli Ma
- College of Agronomy, Northwest A&F University, Xianyang 712100, Shaanxi, China.
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Fonseca JG, Calderan-Rodrigues MJ, de Moraes FE, Cataldi TR, Jamet E, Labate CA. Cell Wall Proteome of Sugarcane Young and Mature Leaves and Stems. Proteomics 2019; 18. [PMID: 29274249 DOI: 10.1002/pmic.201700129] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 10/25/2017] [Indexed: 11/07/2022]
Abstract
By characterizing the cell wall proteomes of different sugarcane organs (leaves and stems) at two developmental stages (young vs mature/apical vs basal), it is possible to address unique characteristics in each of them. Four-month-old leaves show a higher proportion of oxido-reductases and proteins related to lipid metabolism (LM), besides a lower proportion of proteins acting on polysaccharides, in comparison to 4-month-old internodes. It is possible to note that sugarcane leaves and young stems have the highest LM rate than all species, which is assumed to be linked to cuticle formation. The data generated enrich the number of cell wall proteins (CWPs) identified in sugarcane, reaching 277. To our knowledge, sugarcane has now the second higher coverage of monocot CWP in plants.
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Affiliation(s)
- Juliana G Fonseca
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Maria J Calderan-Rodrigues
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Fabrício E de Moraes
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Thaís R Cataldi
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Auzeville, Castanet Tolosan, France
| | - Carlos A Labate
- Departamento de Genética, Laboratório Max Feffer de Genética de Plantas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, São Paulo, Brazil
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28
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de la Canal L, Pinedo M. Extracellular vesicles: a missing component in plant cell wall remodeling. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4655-4658. [PMID: 30007361 PMCID: PMC6137967 DOI: 10.1093/jxb/ery255] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Laura de la Canal
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata – CONICET, Funes, Mar del Plata, Argentina
| | - Marcela Pinedo
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata – CONICET, Funes, Mar del Plata, Argentina
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29
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Martínez-Rubio R, Acebes JL, Encina A, Kärkönen A. Class III peroxidases in cellulose deficient cultured maize cells during cell wall remodeling. PHYSIOLOGIA PLANTARUM 2018; 164:45-55. [PMID: 29464727 DOI: 10.1111/ppl.12710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/15/2018] [Accepted: 02/16/2018] [Indexed: 06/08/2023]
Abstract
Maize (Zea mays L.) suspension-cultured cells habituated to a cellulose biosynthesis inhibitor 2,6-dichlorobenzonitrile (DCB) have a modified cell wall, in which the reduction in the cellulose content is compensated by a network of highly cross-linked feruloylated arabinoxylans and the deposition of lignin-like polymers. For both arabinoxylan cross-linking and lignin polymerization, class III peroxidases (POXs) have been demonstrated to have a prominent role. For the first time, a comparative study of POX activity and isoforms in control and cellulose-impaired cells has been addressed, also taking into account their cellular distribution in different compartments. Proteins from the spent medium (SM), soluble cellular (SC), ionically (ICW) and covalently bound cell wall protein fractions were assayed for total and specific peroxidase activity by using coniferyl and sinapyl alcohol and ferulic acid as substrates. The isoPOX profile was obtained by isoelectric focusing. POX activity was higher in DCB-habituated than in non-habituated cells in all protein fractions at all cell culture stages. For all substrates assayed, SC and ICW fractions showed higher activity at the early log growth phase than at the late log phase. However, the highest POX activity in the spent medium was found at the late log phase. According to the isoPOX profiles, the highest diversity of isoPOXs was detected in the ICW and SM protein fractions. The latter fraction contained isoPOXs with higher activity in DCB-habituated cells. Some of the isoPOXs detected could be involved in cross-linking of arabinoxylans and in the lignin-like polymer formation in DCB-habituated cells.
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Affiliation(s)
- Romina Martínez-Rubio
- Department of Engineering and Agricultural Sciences, Universidad de León, León, 24071, Spain
| | - José Luis Acebes
- Department of Engineering and Agricultural Sciences, Universidad de León, León, 24071, Spain
| | - Antonio Encina
- Department of Engineering and Agricultural Sciences, Universidad de León, León, 24071, Spain
| | - Anna Kärkönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
- Natural Resources Institute Finland (Luke), Production Systems, Plant Genetics, Helsinki, 00790, Finland
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30
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Niu L, Yuan H, Gong F, Wu X, Wang W. Protein Extraction Methods Shape Much of the Extracted Proteomes. FRONTIERS IN PLANT SCIENCE 2018; 9:802. [PMID: 29946336 PMCID: PMC6005817 DOI: 10.3389/fpls.2018.00802] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/25/2018] [Indexed: 05/05/2023]
Affiliation(s)
| | | | | | | | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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31
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Yang D, Pan L, Chen Z, Du H, Luo B, Luo J, Pan G. The roles of microsporidia spore wall proteins in the spore wall formation and polar tube anchorage to spore wall during development and infection processes. Exp Parasitol 2018. [PMID: 29522765 DOI: 10.1016/j.exppara.2018.03.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microsporidia are highly specialized obligate intracellular, spore forming divergent fungi with a wide variety host range that includes most vertebrates and invertebrates. The resistant spores are surrounded by a rigid cell wall which consists of three layers: the electron-lucent chitin and protein inner endospore, the outer-electron-dense and mainly proteinaceous exospore and plasma membrane. Interestingly, microsporidia owns a special invasion organelle, called polar tube, coiled within the interior of the spore wall and attached to anchoring disk at the anterior end of spore. Spore wall and polar tube are the major apparatuses for mature spores adhering and infecting to the host cells. In this review, we summarize the research advances in spore wall proteins (SWPs) related to spore adherence and infection, and SWPs and deproteinated chitin spore coats (DCSCs) interaction associated with SWPs deposit processes and spore wall assembly. Furthermore, we highlight the SWPs-polar tube proteins (PTPs) interaction correlated to polar tube orderly orientation, arrangement and anchorage to anchoring disk. Based on results obtained, it is helpful to improve understanding of the spore wall assembly and polar tube orderly arrangement mechanisms and molecular pathogenesis of microsporidia infection. Also, such information will provide a basis for developing effective control strategies against microporidia.
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Affiliation(s)
- Donglin Yang
- International Academy of Targeted Therapeutics and Innovation, Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, Chongqing University of Arts and Sciences, Chongqing, China.
| | - Lixia Pan
- Chongqing Water Resources and Electric Engineering College, Chongqing, China
| | - Zhongzhu Chen
- International Academy of Targeted Therapeutics and Innovation, Chongqing Key Laboratory of Kinase Modulators as Innovative Medicine, Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, Chongqing University of Arts and Sciences, Chongqing, China
| | - Huihui Du
- Chongqing Three Gorges University, Chongqing, China
| | - Bo Luo
- Zunyi Medical University, Zunyi, Guizhou province, China
| | - Jie Luo
- College of Forestry and Life Sciences, Chongqing University of Arts and Sciences, Chongqing, China
| | - Guoqing Pan
- The State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
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32
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Wu W, Lin Y, Liu P, Chen Q, Tian J, Liang C. Association of extracellular dNTP utilization with a GmPAP1-like protein identified in cell wall proteomic analysis of soybean roots. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:603-617. [PMID: 29329437 PMCID: PMC5853315 DOI: 10.1093/jxb/erx441] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 12/13/2017] [Indexed: 05/20/2023]
Abstract
Plant root cell walls are dynamic systems that serve as the first plant compartment responsive to soil conditions, such as phosphorus (P) deficiency. To date, evidence for the regulation of root cell wall proteins (CWPs) by P deficiency remains sparse. In order to gain a better understanding of the roles played by CWPs in the roots of soybean (Glycine max) in adaptation to P deficiency, we conducted an iTRAQ (isobaric tag for relative and absolute quantitation) proteomic analysis. A total of 53 CWPs with differential accumulation in response to P deficiency were identified. Subsequent qRT-PCR analysis correlated the accumulation of 21 of the 27 up-regulated proteins, and eight of the 26 down-regulated proteins with corresponding gene expression patterns in response to P deficiency. One up-regulated CWP, purple acid phosphatase 1-like (GmPAP1-like), was functionally characterized. Phaseolus vulgaris transgenic hairy roots overexpressing GmPAP1-like displayed an increase in root-associated acid phosphatase activity. In addition, relative growth and P content were significantly enhanced in GmPAP1-like overexpressing lines compared to control lines when deoxy-ribonucleotide triphosphate (dNTP) was applied as the sole external P source. Taken together, the results suggest that the modulation of CWPs may regulate complex changes in the root system in response to P deficiency, and that the cell wall-localized GmPAP1-like protein is involved in extracellular dNTP utilization in soybean.
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Affiliation(s)
- Weiwei Wu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P. R. China
| | - Yan Lin
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P. R. China
| | - Pandao Liu
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P. R. China
- Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agriculture Sciences, Hainan, P. R. China
| | - Qianqian Chen
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P. R. China
| | - Jiang Tian
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P. R. China
| | - Cuiyue Liang
- Root Biology Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, P. R. China
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33
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Elagamey E, Sinha A, Narula K, Abdellatef MA, Chakraborty N, Chakraborty S. Molecular Dissection of Extracellular Matrix Proteome Reveals Discrete Mechanism RegulatingVerticillium DahliaeTriggered Vascular Wilt Disease in Potato. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 08/07/2017] [Indexed: 01/05/2023]
Affiliation(s)
- Eman Elagamey
- National Institute of Plant Genome Research; New Delhi India
- Plant Pathology Research Institute; Agricultural Research Center (ARC); Giza Egypt
| | - Arunima Sinha
- National Institute of Plant Genome Research; New Delhi India
| | - Kanika Narula
- National Institute of Plant Genome Research; New Delhi India
| | - Magdi A.E. Abdellatef
- National Institute of Plant Genome Research; New Delhi India
- Plant Pathology Research Institute; Agricultural Research Center (ARC); Giza Egypt
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34
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Integrating cell biology and proteomic approaches in plants. J Proteomics 2017; 169:165-175. [DOI: 10.1016/j.jprot.2017.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/29/2017] [Accepted: 04/18/2017] [Indexed: 11/22/2022]
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35
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Balagué C, Gouget A, Bouchez O, Souriac C, Haget N, Boutet‐Mercey S, Govers F, Roby D, Canut H. The Arabidopsis thaliana lectin receptor kinase LecRK-I.9 is required for full resistance to Pseudomonas syringae and affects jasmonate signalling. MOLECULAR PLANT PATHOLOGY 2017; 18:937-948. [PMID: 27399963 PMCID: PMC6638305 DOI: 10.1111/mpp.12457] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/15/2016] [Accepted: 06/22/2016] [Indexed: 05/20/2023]
Abstract
On microbial attack, plants can detect invaders and activate plant innate immunity. For the detection of pathogen molecules or cell wall damage, plants employ receptors that trigger the activation of defence responses. Cell surface proteins that belong to large families of lectin receptor kinases are candidates to function as immune receptors. Here, the function of LecRK-I.9 (At5g60300), a legume-type lectin receptor kinase involved in cell wall-plasma membrane contacts and in extracellular ATP (eATP) perception, was studied through biochemical, gene expression and reverse genetics approaches. In Arabidopsis thaliana, LecRK-I.9 expression is rapidly, highly and locally induced on inoculation with avirulent strains of Pseudomonas syringae pv. tomato (Pst). Two allelic lecrk-I.9 knock-out mutants showed decreased resistance to Pst. Conversely, over-expression of LecRK-I.9 led to increased resistance to Pst. The analysis of defence gene expression suggests an alteration of both the salicylic acid (SA) and jasmonic acid (JA) signalling pathways. In particular, LecRK-I.9 expression during plant-pathogen interaction was dependent on COI1 (CORONATINE INSENSITIVE 1) and JAR1 (JASMONATE RESISTANT 1) components, and JA-responsive transcription factors (TFs) showed altered levels of expression in plants over-expressing LecRK-I.9. A similar misregulation of these TFs was obtained by JA treatment. This study identified LecRK-I.9 as necessary for full resistance to Pst and demonstrated its involvement in the control of defence against pathogens through a regulation of JA signalling components. The role of LecRK-I.9 is discussed with regard to the potential molecular mechanisms linking JA signalling to cell wall damage and/or eATP perception.
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Affiliation(s)
- Claudine Balagué
- CNRSLaboratoire des Interactions Plantes Microorganismes (LIPM), UMR2594Castanet‐Tolosan31326France
- INRA, Laboratoire des Interactions Plantes Microorganismes (LIPM), UMR441Castanet‐Tolosan31326France
| | - Anne Gouget
- CNRSLaboratoire des Interactions Plantes Microorganismes (LIPM), UMR2594Castanet‐Tolosan31326France
- INRA, Laboratoire des Interactions Plantes Microorganismes (LIPM), UMR441Castanet‐Tolosan31326France
- Laboratoire de Recherche en Sciences VégétalesUniversité de Toulouse, CNRS, UPS; BP 42617 AuzevilleCastanet‐Tolosan31326France
| | - Olivier Bouchez
- CNRSLaboratoire des Interactions Plantes Microorganismes (LIPM), UMR2594Castanet‐Tolosan31326France
- INRA, Laboratoire des Interactions Plantes Microorganismes (LIPM), UMR441Castanet‐Tolosan31326France
| | - Camille Souriac
- CNRSLaboratoire des Interactions Plantes Microorganismes (LIPM), UMR2594Castanet‐Tolosan31326France
- INRA, Laboratoire des Interactions Plantes Microorganismes (LIPM), UMR441Castanet‐Tolosan31326France
- Laboratoire de Recherche en Sciences VégétalesUniversité de Toulouse, CNRS, UPS; BP 42617 AuzevilleCastanet‐Tolosan31326France
| | - Nathalie Haget
- Laboratoire de Recherche en Sciences VégétalesUniversité de Toulouse, CNRS, UPS; BP 42617 AuzevilleCastanet‐Tolosan31326France
| | - Stéphanie Boutet‐Mercey
- AgroParisTechInstitut Jean‐Pierre Bourgin, Unité Mixte de Recherche 1318, Saclay Plant ScienceVersailles78000France
| | - Francine Govers
- Laboratory of PhytopathologyPlant Sciences Group, Wageningen UniversityDroevendaalsesteeg 1WageningenPB6708the Netherlands
| | - Dominique Roby
- CNRSLaboratoire des Interactions Plantes Microorganismes (LIPM), UMR2594Castanet‐Tolosan31326France
- INRA, Laboratoire des Interactions Plantes Microorganismes (LIPM), UMR441Castanet‐Tolosan31326France
| | - Hervé Canut
- Laboratoire de Recherche en Sciences VégétalesUniversité de Toulouse, CNRS, UPS; BP 42617 AuzevilleCastanet‐Tolosan31326France
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Kinnaert C, Daugaard M, Nami F, Clausen MH. Chemical Synthesis of Oligosaccharides Related to the Cell Walls of Plants and Algae. Chem Rev 2017; 117:11337-11405. [DOI: 10.1021/acs.chemrev.7b00162] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Christine Kinnaert
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kongens Lyngby, Denmark
| | - Mathilde Daugaard
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kongens Lyngby, Denmark
| | - Faranak Nami
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kongens Lyngby, Denmark
| | - Mads H. Clausen
- Center for Nanomedicine and
Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kongens Lyngby, Denmark
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Duruflé H, Clemente HS, Balliau T, Zivy M, Dunand C, Jamet E. Cell wall proteome analysis of Arabidopsis thaliana
mature stems. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600449] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/18/2017] [Accepted: 01/31/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Harold Duruflé
- Laboratoire de Recherche en Sciences Végétales; CNRS, UPS; Université de Toulouse; Auzeville, Castanet Tolosan France
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales; CNRS, UPS; Université de Toulouse; Auzeville, Castanet Tolosan France
| | - Thierry Balliau
- PAPPSO; GQE - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay; Gif-sur-Yvette France
| | - Michel Zivy
- PAPPSO; GQE - Le Moulon; INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay; Gif-sur-Yvette France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales; CNRS, UPS; Université de Toulouse; Auzeville, Castanet Tolosan France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales; CNRS, UPS; Université de Toulouse; Auzeville, Castanet Tolosan France
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Ihsan MZ, Ahmad SJN, Shah ZH, Rehman HM, Aslam Z, Ahuja I, Bones AM, Ahmad JN. Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2017; 8:233. [PMID: 28289422 PMCID: PMC5326801 DOI: 10.3389/fpls.2017.00233] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 02/07/2017] [Indexed: 05/29/2023]
Abstract
The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plant's sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.
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Affiliation(s)
- Muhammad Z. Ihsan
- Cholistan Institute of Desert Studies, The Islamia University BahawalpurBahawalpur, Pakistan
| | - Samina J. N. Ahmad
- Plant Stress Physiology and Molecular Biology Lab, Department of Botany, University of Agriculture FaisalabadFaisalabad, Pakistan
- Integrated Genomics Cellular Developmental and Biotechnology Lab, Department of Entomology, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Zahid Hussain Shah
- Department of Arid Land Agriculture, Faculty of Meteorology, King Abdulaziz UniversityJeddah, Saudi Arabia
| | - Hafiz M. Rehman
- Department of Electronic and Biomedical Engineering, Chonnam National UniversityGwangju, South Korea
| | - Zubair Aslam
- Department of Agronomy, University of Agriculture FaisalabadFaisalabad, Pakistan
| | - Ishita Ahuja
- Department of Biology, Norwegian University of Science and TechnologyTrondheim, Norway
| | - Atle M. Bones
- Department of Biology, Norwegian University of Science and TechnologyTrondheim, Norway
| | - Jam N. Ahmad
- Plant Stress Physiology and Molecular Biology Lab, Department of Botany, University of Agriculture FaisalabadFaisalabad, Pakistan
- Integrated Genomics Cellular Developmental and Biotechnology Lab, Department of Entomology, University of Agriculture FaisalabadFaisalabad, Pakistan
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Abstract
This chapter describes a method allowing the purification of the cell wall for studying both polysaccharides and proteins. The plant primary cell wall is mainly composed of polysaccharides (90-95 % in mass) and of proteins (5-10 %). At the end of growth, specialized cells may synthesize a lignified secondary wall composed of polysaccharides (about 65 %) and lignin (about 35 %). Due to its composition, the cell wall is the cellular compartment having the highest density and this property is used for its purification. It plays critical roles during plant development and in response to environmental constraints. It is largely used in the food and textile industries as well as for the production of bioenergy. All these characteristics and uses explain why its study as a true cell compartment is of high interest. The proposed method of purification can be used for large amount of material but can also be downscaled to 500 mg of fresh material. Tools for checking the quality of the cell wall preparation, such as protein analysis and microscopy observation, are also provided.
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Affiliation(s)
- Hervé Canut
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP 42617, 31326 Castanet, Tolosan, France
| | - Cécile Albenne
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP 42617, 31326 Castanet, Tolosan, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP 42617, 31326 Castanet, Tolosan, France.
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Abstract
The translationally controlled tumor protein (TCTP) is a small, multifunctional protein found in most, if not all, eukaryotic lineages, involved in a myriad of key regulatory processes. Among these, the control of proliferation and inhibition of cell death, as well as differentiation, are the most important, and it is probable that other responses are derived from the ability of TCTP to influence them in both unicellular and multicellular organisms. In the latter, an additional function for TCTP stems from its capacity to be secreted via a nonclassical pathway and function in a non-cell autonomous (paracrine) manner, thus affecting the responses of neighboring or distant cells to developmental or environmental stimuli (as in the case of serum TCTP/histamine-releasing factor in mammals and phloem TCTP in Arabidopsis). The additional ability to traverse membranes without a requirement for transmembrane receptors adds to its functional flexibility. The long-distance transport of TCTP mRNA and protein in plants via the vascular system supports the notion that an important aspect of TCTP function is its ability to influence the response of neighboring and distant cells to endogenous and exogenous signals in a supracellular manner. The predicted tridimensional structure of TCTPs indicates a high degree of conservation, more than its amino acid sequence similarity could suggest. However, subtle differences in structure could lead to different activities, as evidenced by TCTPs secreted by Plasmodium spp. Similar structural variations in animal and plant TCTPs, likely the result of convergent evolution, could lead to deviations from the canonical function of this group of proteins, which could have an impact from a biomedical and agricultural perspectives.
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Affiliation(s)
| | - Roberto Ruiz-Medrano
- Department of Biotechnology and Bioengineering, Center for Research and Advanced Studies of the National Polytechnic Institute, Avenida IPN 2508, Colonia San Pedro Zacatenco, México City, 07360, México.
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Arabidopsis Regenerating Protoplast: A Powerful Model System for Combining the Proteomics of Cell Wall Proteins and the Visualization of Cell Wall Dynamics. Proteomes 2016; 4:proteomes4040034. [PMID: 28248244 PMCID: PMC5260967 DOI: 10.3390/proteomes4040034] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/04/2016] [Accepted: 11/04/2016] [Indexed: 11/17/2022] Open
Abstract
The development of a range of sub-proteomic approaches to the plant cell wall has identified many of the cell wall proteins. However, it remains difficult to elucidate the precise biological role of each protein and the cell wall dynamics driven by their actions. The plant protoplast provides an excellent means not only for characterizing cell wall proteins, but also for visualizing the dynamics of cell wall regeneration, during which cell wall proteins are secreted. It therefore offers a unique opportunity to investigate the de novo construction process of the cell wall. This review deals with sub-proteomic approaches to the plant cell wall through the use of protoplasts, a methodology that will provide the basis for further exploration of cell wall proteins and cell wall dynamics.
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Xie X, Wang Y. VqDUF642, a gene isolated from the Chinese grape Vitis quinquangularis, is involved in berry development and pathogen resistance. PLANTA 2016; 244:1075-1094. [PMID: 27424038 DOI: 10.1007/s00425-016-2569-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/08/2016] [Indexed: 06/06/2023]
Abstract
The DUF642 gene VqDUF642 , isolated from the Chinese grape species V. quinquangularis accession Danfeng-2, participates in berry development and defense responses against Erysiphe necator and Botrytis cinerea. The proteins with domains of unknown function 642 (DUF642) comprise a large protein family according to cell wall proteomic analyses in plants. However, the works about functional characterization of DUF642s in plant development and resistance to pathogens are scarce. In this study, a gene encoding a DUF642 protein was isolated from Chinese grape V. quinquangularis accession Danfeng-2, and designated as VqDUF642. Its full-length cDNA contains a 1107-bp open reading frame corresponding to a deduced 368-amino acid protein. Multiple sequence alignments and phylogenetic analysis showed that VqDUF642 is highly homologous to one of the DUF642 proteins (VvDUF642) in V. vinifera. The VqDUF642 was localized to the cell wall of tobacco epidermal cells. Accumulation of VqDUF642 protein and VqDUF642 transcript abundance increased at the later stage of grape berry development in Danfeng-2. Overexpression of VqDUF642 in transgenic tomato plants accelerated plant growth and reduced susceptibility to Botrytis cinerea. Transgenic Thompson Seedless grapevine plants overexpressing VqDUF642 exhibited enhanced resistance to Erysiphe necator and B. cinerea. Moreover, VqDUF642 overexpression affected the expression of a couple of pathogenesis-related (PR) genes in transgenic tomato and grapevine upon pathogen inoculation. Taken together, these results suggest that VqDUF642 is involved in plant development and defense against pathogenic infections.
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Affiliation(s)
- Xiaoqing Xie
- College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Yuejin Wang
- College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China.
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China.
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A & F University, No. 3, Taicheng Road, Yangling, Shaanxi, 712100, China.
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Protein Dynamics in the Plant Extracellular Space. Proteomes 2016; 4:proteomes4030022. [PMID: 28248232 PMCID: PMC5217353 DOI: 10.3390/proteomes4030022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 07/07/2016] [Accepted: 07/07/2016] [Indexed: 12/15/2022] Open
Abstract
The extracellular space (ECS or apoplast) is the plant cell compartment external to the plasma membrane, which includes the cell walls, the intercellular space and the apoplastic fluid (APF). The present review is focused on APF proteomics papers and intends to draw information on the metabolic processes occurring in the ECS under abiotic and biotic stresses, as well as under non-challenged conditions. The large majority of the proteins detected are involved in "cell wall organization and biogenesis", "response to stimulus" and "protein metabolism". It becomes apparent that some proteins are always detected, irrespective of the experimental conditions, although with different relative contribution. This fact suggests that non-challenged plants have intrinsic constitutive metabolic processes of stress/defense in the ECS. In addition to the multiple functions ascribed to the ECS proteins, should be considered the interactions established between themselves and with the plasma membrane and its components. These interactions are crucial in connecting exterior and interior of the cell, and even simple protein actions in the ECS can have profound effects on plant performance. The proteins of the ECS are permanently contributing to the high dynamic nature of this plant compartment, which seems fundamental to plant development and adaptation to the environmental conditions.
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Elagamey E, Narula K, Sinha A, Aggarwal PR, Ghosh S, Chakraborty N, Chakraborty S. Extracellular Matrix Proteome and Phosphoproteome of Potato Reveals Functionally Distinct and Diverse Canonical and Non-Canonical Proteoforms. Proteomes 2016; 4:E20. [PMID: 28248230 PMCID: PMC5217357 DOI: 10.3390/proteomes4030020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 06/06/2016] [Accepted: 06/13/2016] [Indexed: 12/26/2022] Open
Abstract
The extracellular matrix (ECM) has a molecular machinery composed of diverse proteins and proteoforms that combine properties of tensile strength with extensibility exhibiting growth-regulatory functions and self- and non-self-recognition. The identification of ECM proteoforms is the prerequisite towards a comprehensive understanding of biological functions accomplished by the outermost layer of the cell. Regulatory mechanisms of protein functions rely on post-translational modifications, phosphorylation in particular, affecting enzymatic activity, interaction, localization and stability. To investigate the ECM proteoforms, we have isolated the cell wall proteome and phosphoproteome of a tuberous crop, potato (Solanum tuberosum). LC-MS/MS analysis led to the identification of 38 proteins and 35 phosphoproteins of known and unknown functions. The findings may provide a better understanding of biochemical machinery and the integrated protein and phosphoprotein network of ECM for future functional studies of different developmental pathways and guidance cues in mechanosensing and integrity signaling.
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Affiliation(s)
- Eman Elagamey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Arunima Sinha
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Pooja Rani Aggarwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Sudip Ghosh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Francin-Allami M, Lollier V, Pavlovic M, San Clemente H, Rogniaux H, Jamet E, Guillon F, Larré C. Understanding the Remodelling of Cell Walls during Brachypodium distachyon Grain Development through a Sub-Cellular Quantitative Proteomic Approach. Proteomes 2016; 4:E21. [PMID: 28248231 PMCID: PMC5217356 DOI: 10.3390/proteomes4030021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 12/18/2022] Open
Abstract
Brachypodiumdistachyon is a suitable plant model for studying temperate cereal crops, such as wheat, barley or rice, and helpful in the study of the grain cell wall. Indeed, the most abundant hemicelluloses that are in the B. distachyon cell wall of grain are (1-3)(1-4)-β-glucans and arabinoxylans, in a ratio similar to those of cereals such as barley or oat. Conversely, these cell walls contain few pectins and xyloglucans. Cell walls play an important role in grain physiology. The modifications of cell wall polysaccharides that occur during grain development and filling are key in the determination of the size and weight of the cereal grains. The mechanisms required for cell wall assembly and remodelling are poorly understood, especially in cereals. To provide a better understanding of these processes, we purified the cell wall at three developmental stages of the B. distachyon grain. The proteins were then extracted, and a quantitative and comparative LC-MS/MS analysis was performed to investigate the protein profile changes during grain development. Over 466 cell wall proteins (CWPs) were identified and classified according to their predicted functions. This work highlights the different proteome profiles that we could relate to the main phases of grain development and to the reorganization of cell wall polysaccharides that occurs during these different developmental stages. These results provide a good springboard to pursue functional validation to better understand the role of CWPs in the assembly and remodelling of the grain cell wall of cereals.
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Affiliation(s)
| | - Virginie Lollier
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Marija Pavlovic
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Hélène San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 Chemin de Borderouge-Auzeville, BP42617, Castanet-Tolosan 31326, France.
| | - Hélène Rogniaux
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, 24 Chemin de Borderouge-Auzeville, BP42617, Castanet-Tolosan 31326, France.
| | - Fabienne Guillon
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
| | - Colette Larré
- UR1268 BIA (Biopolymères Interactions Assemblages), INRA, Nantes 44300, France.
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46
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Global proteome analysis in plants by means of peptide libraries and applications. J Proteomics 2016; 143:3-14. [DOI: 10.1016/j.jprot.2016.02.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/20/2016] [Accepted: 02/26/2016] [Indexed: 01/07/2023]
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Duan W, Huang Z, Song X, Liu T, Liu H, Hou X, Li Y. Comprehensive analysis of the polygalacturonase and pectin methylesterase genes in Brassica rapa shed light on their different evolutionary patterns. Sci Rep 2016; 6:25107. [PMID: 27112365 PMCID: PMC4844994 DOI: 10.1038/srep25107] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 04/08/2016] [Indexed: 02/03/2023] Open
Abstract
Pectins are fundamental polysaccharides in the plant primary cell wall. Polygalacturonases (PGs) and pectin methylesterases (PMEs), major components of the pectin remodeling and disassembly network, are involved in cell separation processes during many stages of plant development. A comprehensive study of these genes in plants could shed light on the evolution patterns of their structural development. In this study, we conducted whole-genome annotation, molecular evolution and gene expression analyses of PGs and PMEs in Brassica rapa and 8 other plant species. A total of 100 PGs and 110 PMEs were identified in B. rapa; they primarily diverged from 12–18 MYA and PMEs were retained more than PGs. Along with another 305 PGs and 348 PMEs in the 8 species, two different expansion or evolution types were discovered: a new branch of class A PGs appeared after the split of gymnosperms and angiosperms, which led to the rapid expansion of PGs; the pro domain was obtained or lost in the proPMEs through comprehensive analyses among PME genes. In addition, the PGs and PMEs exhibit diverged expression patterns. These findings will lead to novel insight regarding functional divergence and conservation in the gene families and provide more support for molecular evolution analyses.
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Affiliation(s)
- Weike Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhinan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.,Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hailong Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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48
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Wang J, Zhao Y, Ray I, Song M. Transcriptome responses in alfalfa associated with tolerance to intensive animal grazing. Sci Rep 2016; 6:19438. [PMID: 26763747 PMCID: PMC4725929 DOI: 10.1038/srep19438] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/02/2015] [Indexed: 01/15/2023] Open
Abstract
Tolerance of alfalfa (Medicago sativa L.) to animal grazing varies widely within the species. However, the molecular mechanisms influencing the grazing tolerant phenotype remain uncharacterized. The objective of this study was to identify genes and pathways that control grazing response in alfalfa. We analyzed whole-plant de novo transcriptomes from grazing tolerant and intolerant populations of M. sativa ssp. falcata subjected to grazing by sheep. Among the Gene Ontology terms which were identified as grazing responsive in the tolerant plants and differentially enriched between the tolerant and intolerant populations (both grazed), most were associated with the ribosome and translation-related activities, cell wall processes, and response to oxygen levels. Twenty-one grazing responsive pathways were identified that also exhibited differential expression between the tolerant and intolerant populations. These pathways were associated with secondary metabolite production, primary carbohydrate metabolic pathways, shikimate derivative dependent pathways, ribosomal subunit composition, hormone signaling, wound response, cell wall formation, and anti-oxidant defense. Sequence polymorphisms were detected among several differentially expressed homologous transcripts between the tolerant and intolerant populations. These differentially responsive genes and pathways constitute potential response mechanisms for grazing tolerance in alfalfa. They also provide potential targets for molecular breeding efforts to develop grazing-tolerant cultivars of alfalfa.
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Affiliation(s)
- Junjie Wang
- College of Ecology and Environmental Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Zhao
- College of Ecology and Environmental Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ian Ray
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, USA
| | - Mingzhou Song
- Department of Computer Science, New Mexico State University, Las Cruces, NM, USA
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Basu D, Tian L, Debrosse T, Poirier E, Emch K, Herock H, Travers A, Showalter AM. Glycosylation of a Fasciclin-Like Arabinogalactan-Protein (SOS5) Mediates Root Growth and Seed Mucilage Adherence via a Cell Wall Receptor-Like Kinase (FEI1/FEI2) Pathway in Arabidopsis. PLoS One 2016; 11:e0145092. [PMID: 26731606 PMCID: PMC4701510 DOI: 10.1371/journal.pone.0145092] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/26/2015] [Indexed: 11/29/2022] Open
Abstract
Fundamental processes that underpin plant growth and development depend crucially on the action and assembly of the cell wall, a dynamic structure that changes in response to both developmental and environmental cues. While much is known about cell wall structure and biosynthesis, much less is known about the functions of the individual wall components, particularly with respect to their potential roles in cellular signaling. Loss-of-function mutants of two arabinogalactan-protein (AGP)-specific galactosyltransferases namely, GALT2 and GALT5, confer pleiotropic growth and development phenotypes indicating the important contributions of carbohydrate moieties towards AGP function. Notably, galt2galt5 double mutants displayed impaired root growth and root tip swelling in response to salt, likely as a result of decreased cellulose synthesis. These mutants phenocopy a salt-overly sensitive mutant called sos5, which lacks a fasciclin-like AGP (SOS5/FLA4) as well as a fei1fei2 double mutant, which lacks two cell wall-associated leucine-rich repeat receptor-like kinases. Additionally, galt2gal5 as well as sos5 and fei2 showed reduced seed mucilage adherence. Quintuple galt2galt5sos5fei1fei2 mutants were produced and provided evidence that these genes act in a single, linear genetic pathway. Further genetic and biochemical analysis of the quintuple mutant demonstrated involvement of these genes with the interplay between cellulose biosynthesis and two plant growth regulators, ethylene and ABA, in modulating root cell wall integrity.
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Affiliation(s)
- Debarati Basu
- Molecular and Cellular Biology Program, Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701–2979, United States of America
| | - Lu Tian
- Molecular and Cellular Biology Program, Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701–2979, United States of America
| | - Tayler Debrosse
- Molecular and Cellular Biology Program, Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701–2979, United States of America
| | - Emily Poirier
- Molecular and Cellular Biology Program, Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701–2979, United States of America
| | - Kirk Emch
- Molecular and Cellular Biology Program, Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701–2979, United States of America
| | - Hayley Herock
- Molecular and Cellular Biology Program, Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701–2979, United States of America
| | - Andrew Travers
- Molecular and Cellular Biology Program, Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701–2979, United States of America
| | - Allan M. Showalter
- Molecular and Cellular Biology Program, Department of Environmental and Plant Biology, Ohio University, Athens, Ohio 45701–2979, United States of America
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Lonsdale A, Davis MJ, Doblin MS, Bacic A. Better Than Nothing? Limitations of the Prediction Tool SecretomeP in the Search for Leaderless Secretory Proteins (LSPs) in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1451. [PMID: 27729919 PMCID: PMC5037178 DOI: 10.3389/fpls.2016.01451] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/12/2016] [Indexed: 05/14/2023]
Abstract
In proteomic analyses of the plant secretome, the presence of putative leaderless secretory proteins (LSPs) is difficult to confirm due to the possibility of contamination from other sub-cellular compartments. In the absence of a plant-specific tool for predicting LSPs, the mammalian-trained SecretomeP has been applied to plant proteins in multiple studies to identify the most likely LSPs. This study investigates the effectiveness of using SecretomeP on plant proteins, identifies its limitations and provides a benchmark for its use. In the absence of experimentally verified LSPs we exploit the common-feature hypothesis behind SecretomeP and use known classically secreted proteins (CSPs) of plants as a proxy to evaluate its accuracy. We show that, contrary to the common-feature hypothesis, plant CSPs are a poor proxy for evaluating LSP detection due to variation in the SecretomeP prediction scores when the signal peptide (SP) is modified. Removing the SP region from CSPs and comparing the predictive performance against non-secretory proteins indicates that commonly used threshold scores of 0.5 and 0.6 result in false-positive rates in excess of 0.3 when applied to plants proteins. Setting the false-positive rate to 0.05, consistent with the original mammalian performance of SecretomeP, yields only a marginally higher true positive rate compared to false positives. Therefore the use of SecretomeP on plant proteins is not recommended. This study investigates the trade-offs of using SecretomeP on plant proteins and provides insights into predictive features for future development of plant-specific common-feature tools.
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Affiliation(s)
- Andrew Lonsdale
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of MelbourneParkville, VIC, Australia
| | - Melissa J. Davis
- The Walter and Eliza Hall Institute of Medical ResearchParkville, VIC, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of MelbourneParkville, VIC, Australia
| | - Monika S. Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of MelbourneParkville, VIC, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of MelbourneParkville, VIC, Australia
- *Correspondence: Antony Bacic,
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