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Lee SG, Woo SM, Seo SU, Lee CH, Baek MC, Jang SH, Park ZY, Yook S, Nam JO, Kwon TK. Cathepsin D promotes polarization of tumor-associated macrophages and metastasis through TGFBI-CCL20 signaling. Exp Mol Med 2024; 56:383-394. [PMID: 38297161 PMCID: PMC10907383 DOI: 10.1038/s12276-024-01163-9] [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: 02/11/2023] [Revised: 10/23/2023] [Accepted: 11/23/2023] [Indexed: 02/02/2024] Open
Abstract
M2-like tumor-associated macrophages (TAMs) are risk factors for cancer progression and metastasis. However, the mechanisms underlying their polarization are still not fully understood. Although cathepsin D (Cat D) has been reported as a procarcinogenic factor, little is known about the functional role of Cat D in the tumor microenvironment (TME). This study aimed to explore the effect and molecular mechanisms of Cat D in the TME. Cat D knockout (KO) altered the cytokine secretion pattern and induced TAM reprogramming from the M2 to M1 subtype, thereby preventing epithelial-mesenchymal transition and tumor metastasis. Mechanistically, we identified transforming growth factor beta-induced protein (TGFBI) as a Cat D target protein that is specifically associated with TAM polarization. Elevated TGFBI expression in Cat D KO cancer cells resulted in a decline in M2-like TAM polarization. Our RNA-sequencing results indicated that the cancer cell-secreted chemokine CCL20 is a major secretory chemokine for Cat D-TGFBI-mediated TAM polarization. In contrast, Cat D overexpression accelerated TAM polarization into M2-like cells by suppressing TGFBI expression. In addition, the double Cat D and TGFBI KO rescued the inhibitory effects of Cat D KO on tumor metastasis by controlling TAM and T-cell activation. These findings indicated that Cat D contributes to cancer metastasis through TGFBI-mediated TAM reprogramming. Cat D deletion inhibits M2-like TAM polarization through TGFBI-mediated CCL20 expression, reprogramming the immunosuppressive TME. Our results open a potential new avenue for therapy focused on eliminating tumor metastasis.
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Affiliation(s)
- Seul Gi Lee
- Department of Immunology, School of Medicine, Keimyung University, Daegu, Republic of Korea
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA
| | - Seon Min Woo
- Department of Immunology, School of Medicine, Keimyung University, Daegu, Republic of Korea
| | - Seung Un Seo
- Department of Immunology, School of Medicine, Keimyung University, Daegu, Republic of Korea
| | - Chan-Hyeong Lee
- Department of Molecular Medicine, CMRI, Exosome Convergence Research Center (ECRC), School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Moon-Chang Baek
- Department of Molecular Medicine, CMRI, Exosome Convergence Research Center (ECRC), School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Se Hwan Jang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Zee Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, Korea
| | - Simmyung Yook
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ju-Ock Nam
- Department of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Taeg Kyu Kwon
- Department of Immunology, School of Medicine, Keimyung University, Daegu, Republic of Korea.
- Center for Forensic Pharmaceutical Science, Keimyung University, Daegu, Republic of Korea.
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Zhu C, Box MS, Thiruppathi D, Hu H, Yu Y, Martin C, Doust AN, McSteen P, Kellogg EA. Pleiotropic and nonredundant effects of an auxin importer in Setaria and maize. PLANT PHYSIOLOGY 2022; 189:715-734. [PMID: 35285930 DOI: 10.1101/2021.10.14.464408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/16/2022] [Indexed: 05/26/2023]
Abstract
Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in green millet (Setaria viridis) and maize (Zea mays), we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A green fluorescent protein (GFP)-tagged construct of the Setaria AUX1 protein Sparse Panicle1 (SPP1) under its native promoter showed that SPP1 localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis indicated that most gene expression modules are conserved between mutant and wild-type plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, and leaf and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.
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Affiliation(s)
- Chuanmei Zhu
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Mathew S Box
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | | | - Hao Hu
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Oklahoma 74078, USA
| | - Yunqing Yu
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Callista Martin
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Andrew N Doust
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Oklahoma 74078, USA
| | - Paula McSteen
- Division of Biological Sciences, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
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Zhu C, Box MS, Thiruppathi D, Hu H, Yu Y, Martin C, Doust AN, McSteen P, Kellogg EA. Pleiotropic and nonredundant effects of an auxin importer in Setaria and maize. PLANT PHYSIOLOGY 2022; 189:715-734. [PMID: 35285930 PMCID: PMC9157071 DOI: 10.1093/plphys/kiac115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in green millet (Setaria viridis) and maize (Zea mays), we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A green fluorescent protein (GFP)-tagged construct of the Setaria AUX1 protein Sparse Panicle1 (SPP1) under its native promoter showed that SPP1 localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis indicated that most gene expression modules are conserved between mutant and wild-type plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, and leaf and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.
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Affiliation(s)
- Chuanmei Zhu
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Mathew S Box
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | | | - Hao Hu
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Oklahoma 74078, USA
| | - Yunqing Yu
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Callista Martin
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Andrew N Doust
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Oklahoma 74078, USA
| | - Paula McSteen
- Division of Biological Sciences, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA
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Shim SH, Mahong B, Lee SK, Kongdin M, Lee C, Kim YJ, Qu G, Zhang D, Ketudat Cairns JR, Jeon JS. Rice β-glucosidase Os12BGlu38 is required for synthesis of intine cell wall and pollen fertility. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:784-800. [PMID: 34570888 DOI: 10.1093/jxb/erab439] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Glycoside hydrolase family1 β-glucosidases play a variety of roles in plants, but their in planta functions are largely unknown in rice (Oryza sativa). In this study, the biological function of Os12BGlu38, a rice β-glucosidase, expressed in bicellular to mature pollen, was examined. Genotype analysis of progeny of the self-fertilized heterozygous Os12BGlu38 T-DNA mutant, os12bglu38-1, found no homozygotes and a 1:1 ratio of wild type to heterozygotes. Reciprocal cross analysis demonstrated that Os12BGlu38 deficiency cannot be inherited through the male gamete. In cytological analysis, the mature mutant pollen appeared shrunken and empty. Histochemical staining and TEM showed that mutant pollen lacked intine cell wall, which was rescued by introduction of wild-type Os12BGlu38 genomic DNA. Metabolite profiling analysis revealed that cutin monomers and waxes, the components of the pollen exine layer, were increased in anthers carrying pollen of os12bglu38-1 compared with wild type and complemented lines. Os12BGlu38 fused with green fluorescent protein was localized to the plasma membrane in rice and tobacco. Recombinant Os12BGlu38 exhibited β-glucosidase activity on the universal substrate p-nitrophenyl β-d-glucoside and some oligosaccharides and glycosides. These findings provide evidence that function of a plasma membrane-associated β-glucosidase is necessary for proper intine development.
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Affiliation(s)
- Su-Hyeon Shim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Bancha Mahong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Sang-Kyu Lee
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Korea
| | - Manatchanok Kongdin
- School of Chemistry, Institute of Science, and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Chanhui Lee
- Department of Plant and Environmental New Resources, Kyung Hee University, Yongin, Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Korea
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Department of Life Science and Environmental Biochemistry, Pusan National University, Miryang, Korea
| | - Guorun Qu
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dabing Zhang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University and University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - James R Ketudat Cairns
- School of Chemistry, Institute of Science, and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Korea
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Liu Y, Ma L, Cao D, Gong Z, Fan J, Hu H, Jin X. Investigation of cell wall proteins of C. sinensis leaves by combining cell wall proteomics and N-glycoproteomics. BMC PLANT BIOLOGY 2021; 21:384. [PMID: 34416854 PMCID: PMC8377857 DOI: 10.1186/s12870-021-03166-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 08/10/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND C. sinensis is an important economic crop with fluoride over-accumulation in its leaves, which poses a serious threat to human health due to its leaf consumption as tea. Recently, our study has indicated that cell wall proteins (CWPs) probably play a vital role in fluoride accumulation/detoxification in C. sinensis. However, there has been a lack in CWP identification and characterization up to now. This study is aimed to characterize cell wall proteome of C. sinensis leaves and to develop more CWPs related to stress response. A strategy of combined cell wall proteomics and N-glycoproteomics was employed to investigate CWPs. CWPs were extracted by sequential salt buffers, while N-glycoproteins were enriched by hydrophilic interaction chromatography method using C. sinensis leaves as a material. Afterwards all the proteins were subjected to UPLC-MS/MS analysis. RESULTS A total of 501 CWPs and 195 CWPs were identified respectively by cell wall proteomics and N-glycoproteomics profiling with 118 CWPs in common. Notably, N-glycoproteomics is a feasible method for CWP identification, and it can enhance CWP coverage. Among identified CWPs, proteins acting on cell wall polysaccharides constitute the largest functional class, most of which might be involved in cell wall structure remodeling. The second largest functional class mainly encompass various proteases related to CWP turnover and maturation. Oxidoreductases represent the third largest functional class, most of which (especially Class III peroxidases) participate in defense response. As expected, identified CWPs are mainly related to plant cell wall formation and defense response. CONCLUSION This was the first large-scale investigation of CWPs in C. sinensis through cell wall proteomics and N-glycoproteomics. Our results not only provide a database for further research on CWPs, but also an insight into cell wall formation and defense response in C. sinensis.
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Affiliation(s)
- Yanli Liu
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, No. 10 Nanhu Road, Wuhan, 430064, Hubei, People's Republic of China
| | - Linlong Ma
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, No. 10 Nanhu Road, Wuhan, 430064, Hubei, People's Republic of China
| | - Dan Cao
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, No. 10 Nanhu Road, Wuhan, 430064, Hubei, People's Republic of China
| | - Ziming Gong
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, No. 10 Nanhu Road, Wuhan, 430064, Hubei, People's Republic of China
| | - Jing Fan
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, No. 10 Nanhu Road, Wuhan, 430064, Hubei, People's Republic of China
| | - Hongju Hu
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, No. 10 Nanhu Road, Wuhan, 430064, Hubei, People's Republic of China
| | - Xiaofang Jin
- Fruit and Tea Research Institute, Hubei Academy of Agricultural Sciences, No. 10 Nanhu Road, Wuhan, 430064, Hubei, People's Republic of China.
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Liu E, MacMillan CP, Shafee T, Ma Y, Ratcliffe J, van de Meene A, Bacic A, Humphries J, Johnson KL. Fasciclin-Like Arabinogalactan-Protein 16 (FLA16) Is Required for Stem Development in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:615392. [PMID: 33362841 PMCID: PMC7758453 DOI: 10.3389/fpls.2020.615392] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/23/2020] [Indexed: 05/19/2023]
Abstract
The predominant Fascilin 1 (FAS1)-containing proteins in plants belong to the Fasciclin-Like Arabinogalactan-protein (FLA) family of extracellular glycoproteins. In addition to FAS1 domains, these multi-domain FLA proteins contain glycomotif regions predicted to direct addition of large arabinogalactan (AG) glycans and many contain signal sequences for addition of a glycosylphosphatidylinositol (GPI)-anchor to tether them to the plasma membrane. FLAs are proposed to play both structural and signaling functions by forming a range of interactions in the plant extracellular matrix, similar to FAS1-containing proteins in animals. FLA group B members contain two FAS1 domains and are not predicted to be GPI-anchored. None of the group B members have been functionally characterized or their sub-cellular location resolved, limiting understanding of their function. We investigated the group B FLA16 in Arabidopsis that is predominantly expressed in inflorescence tissues. FLA16 is the most highly expressed FLA in the stem after Group A members FLA11 and FLA12 that are stem specific. A FLA16-YFP fusion protein driven by the endogenous putative FLA16 promoter in wild type background showed expression in cells with secondary cell walls, and FLA16 displayed characteristics of cell wall glycoproteins with moderate glycosylation. Investigation of a fla16 mutant showed loss of FLA16 leads to reduced stem length and altered biomechanical properties, likely as a result of reduced levels of cellulose. Immuno-labeling indicated support for FLA16 location to the plasma-membrane and (apoplastic) cell wall of interfascicular stem fiber cells. Together these results indicate FLA16, a two-FAS1 domain FLAs, plays a role in plant secondary cell wall synthesis and function.
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Affiliation(s)
- Edgar Liu
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Colleen P. MacMillan
- CSIRO, Agriculture and Food, CSIRO Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Thomas Shafee
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Yingxuan Ma
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Julian Ratcliffe
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | | | - Antony Bacic
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
| | - John Humphries
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Kim L. Johnson
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Sino-Australia Plant Cell Wall Research Centre, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, China
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Boschetti E, Righetti PG. Detection of Plant Low-Abundance Proteins by Means of Combinatorial Peptide Ligand Library Methods. Methods Mol Biol 2020; 2139:381-404. [PMID: 32462601 DOI: 10.1007/978-1-0716-0528-8_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The detection and identification of low-abundance proteins from plant tissues is still a major challenge. Among the reasons are the low protein content, the presence of few very high-abundance proteins, and the presence of massive amounts of other biochemical compounds. In the last decade numerous technologies have been devised to resolve the situation, in particular with methods based on solid-phase combinatorial peptide ligand libraries. This methodology, allowing for an enhancement of low-abundance proteins, has been extensively applied with the advantage of deciphering the proteome composition of various plant organs. This general methodology is here described extensively along with a number of possible variations. Specific guidelines are suggested to cover peculiar situations or to comply with other associated analytical methods.
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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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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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10
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Di Silvestre D, Bergamaschi A, Bellini E, Mauri P. Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World. Proteomes 2018; 6:proteomes6020027. [PMID: 29865292 PMCID: PMC6027444 DOI: 10.3390/proteomes6020027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/26/2022] Open
Abstract
The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.
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Affiliation(s)
- Dario Di Silvestre
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Andrea Bergamaschi
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Edoardo Bellini
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - PierLuigi Mauri
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
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11
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Kumar D, Kumar R, Baek D, Hyun TK, Chung WS, Yun DJ, Kim JY. Arabidopsis thaliana RECEPTOR DEAD KINASE1 Functions as a Positive Regulator in Plant Responses to ABA. MOLECULAR PLANT 2017; 10:223-243. [PMID: 27923613 DOI: 10.1016/j.molp.2016.11.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 11/18/2016] [Accepted: 11/23/2016] [Indexed: 05/18/2023]
Abstract
Abscisic acid (ABA) is a major phytohormone involved in important stress-related and developmental plant processes. Membrane-delimited ABA signal transduction plays an important role in early ABA signaling, but the molecular mechanisms connecting core signaling components to the plasma membrane remain unclear. Plants have evolved a large number of receptor-like kinases (RLKs) to modulate diverse biological processes by perceiving extracellular stimuli and activating downstream signaling responses. In this study, a putative leucine-rich repeat-RLK gene named RECEPTOR DEAD KINASE1 (AtRDK1) was identified and characterized in Arabidopsis thaliana. RDK1 promoter-GUS analysis revealed that RDK1 is expressed ubiquitously in the various tissues in Arabidopsis, and its expression is mainly induced by ABA. In the presence of ABA, RDK1-deficient rdk1-1 and rdk1-2 lines showed significant resistance in cotyledon greening and root growth, whereas RDK1-overexpressing lines showed enhanced sensitivity. Consistently, the expression of ABA-responsive genes was significantly downregulated in rdk1 mutant seedlings, which were also hypersensitive to drought stress with increased water loss. Interestingly, RDK1 was found to be an atypical kinase localized to the plasma membrane and did not require its kinase activity during ABA-mediated inhibition of seedling development. Accordingly, RDK1 interacted in the plasma membrane with type 2C protein phosphatase ABSCISIC ACID INSENSITIVE1 (ABI1); this interaction was further enhanced by exogenous application of ABA, suggesting that RDK1-mediated recruitment of ABI1 onto the plasma membrane is important for ABA signaling. Taken together, these results reveal an important role for RDK1 in plant responses to abiotic stress conditions in an ABA-dependent manner.
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Affiliation(s)
- Dhinesh Kumar
- Division of Applied Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Ritesh Kumar
- Division of Applied Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Dongwon Baek
- Division of Applied Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Tae-Kyung Hyun
- Department of Industrial Plant Science and Technology, College of Agricultural, Life and Environmental Sciences, Chungbuk National University, Cheongju 28644, Korea
| | - Woo Sik Chung
- Division of Applied Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea
| | - Dae-Jin Yun
- Division of Applied Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea.
| | - Jae-Yean Kim
- Division of Applied Life Sciences, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Korea.
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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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13
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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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