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Zhu M, Zang Y, Zhang X, Shang S, Xue S, Chen J, Tang X. Insights into the regulation of energy metabolism during the seed-to-seedling transition in marine angiosperm Zostera marina L.: Integrated metabolomic and transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1130292. [PMID: 36968358 PMCID: PMC10036900 DOI: 10.3389/fpls.2023.1130292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Seed development is a crucial phase in the life cycle of seed-propagated plants. As the only group of angiosperms that evolved from terrestrial plants to complete their life cycle submerged in marine environments, the mechanisms underlying seed development in seagrasses are still largely unknown. In the present study, we attempted to combine transcriptomic, metabolomic, and physiological data to comprehensively analyze the molecular mechanism that regulates energy metabolism in Zostera marina seeds at the four major developmental stages. Our results demonstrated that seed metabolism was reprogrammed with significant alteration of starch and sucrose metabolism, glycolysis, the tricarboxylic acid cycle (TCA cycle), and the pentose phosphate pathway during the transition from seed formation to seedling establishment. The interconversion of starch and sugar provided energy storage substances in mature seeds and further acted as energy sources to support seed germination and seedling growth. The glycolysis pathway was active during Z. marina germination and seedling establishment, which provided pyruvate for TCA cycle by decomposing soluble sugar. Notably, the biological processes of glycolysis were severely inhibited during Z. marina seed maturation may have a positive effect on seed germination, maintaining a low level of metabolic activity during seed maturation to preserve seed viability. Increased acetyl-CoA and ATP contents were accompanied with the higher TCA cycle activity during seed germination and seedling establishment, indicating that the accumulations of precursor and intermediates metabolite that can strengthen the TCA cycle and facilitate energy supply for Z. marina seed germination and seedling growth. The large amount of oxidatively generated sugar phosphate promotes fructose 1,6-bisphosphate synthesis to feed back to glycolysis during seed germination, indicating that the pentose phosphate pathway not only provides energy for germination, but also complements the glycolytic pathway. Collectively, our findings suggest these energy metabolism pathways cooperate with each other in the process of seed transformation from maturity to seedling establishment, transforming seed from storage tissue to highly active metabolic tissue to meet the energy requirement seed development. These findings provide insights into the roles of the energy metabolism pathway in the complete developmental process of Z. marina seeds from different perspectives, which could facilitate habitat restoration of Z. marina meadows via seeds.
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Affiliation(s)
- Meiling Zhu
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Yu Zang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, Shandong, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, Shandong, China
| | - Shuai Shang
- College of Biological and Environmental Engineering, Binzhou University, Binzhou, Shandong, China
| | - Song Xue
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Jun Chen
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
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2
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Dai D, Ma Z, Song R. Maize endosperm development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:613-627. [PMID: 33448626 DOI: 10.1111/jipb.13069] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/12/2021] [Indexed: 05/22/2023]
Abstract
Recent breakthroughs in transcriptome analysis and gene characterization have provided valuable resources and information about the maize endosperm developmental program. The high temporal-resolution transcriptome analysis has yielded unprecedented access to information about the genetic control of seed development. Detailed spatial transcriptome analysis using laser-capture microdissection has revealed the expression patterns of specific populations of genes in the four major endosperm compartments: the basal endosperm transfer layer (BETL), aleurone layer (AL), starchy endosperm (SE), and embryo-surrounding region (ESR). Although the overall picture of the transcriptional regulatory network of endosperm development remains fragmentary, there have been some exciting advances, such as the identification of OPAQUE11 (O11) as a central hub of the maize endosperm regulatory network connecting endosperm development, nutrient metabolism, and stress responses, and the discovery that the endosperm adjacent to scutellum (EAS) serves as a dynamic interface for endosperm-embryo crosstalk. In addition, several genes that function in BETL development, AL differentiation, and the endosperm cell cycle have been identified, such as ZmSWEET4c, Thk1, and Dek15, respectively. Here, we focus on current advances in understanding the molecular factors involved in BETL, AL, SE, ESR, and EAS development, including the specific transcriptional regulatory networks that function in each compartment during endosperm development.
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Affiliation(s)
- Dawei Dai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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Investigating an increase in Florida manatee mortalities using a proteomic approach. Sci Rep 2021; 11:4282. [PMID: 33608577 PMCID: PMC7895937 DOI: 10.1038/s41598-021-83687-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 02/05/2021] [Indexed: 12/28/2022] Open
Abstract
Two large-scale Florida manatee (Trichechus manatus latirostris) mortality episodes were reported on separate coasts of Florida in 2013. The east coast mortality episode was associated with an unknown etiology in the Indian River Lagoon (IRL). The west coast mortality episode was attributed to a persistent Karenia brevis algal bloom or 'red tide' centered in Southwest Florida. Manatees from the IRL also had signs of cold stress. To investigate these two mortality episodes, two proteomic experiments were performed, using two-dimensional difference in gel electrophoresis (2D-DIGE) and isobaric tags for relative and absolute quantification (iTRAQ) LC-MS/MS. Manatees from the IRL displayed increased levels of several proteins in their serum samples compared to controls, including kininogen-1 isoform 1, alpha-1-microglobulin/bikunen precursor, histidine-rich glycoprotein, properdin, and complement C4-A isoform 1. In the red tide group, the following proteins were increased: ceruloplasmin, pyruvate kinase isozymes M1/M2 isoform 3, angiotensinogen, complement C4-A isoform 1, and complement C3. These proteins are associated with acute-phase response, amyloid formation and accumulation, copper and iron homeostasis, the complement cascade pathway, and other important cellular functions. The increased level of complement C4 protein observed in the red tide group was confirmed through the use of Western Blot.
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Chen Q, Huang R, Xu Z, Zhang Y, Li L, Fu J, Wang G, Wang J, Du X, Gu R. Label-Free Comparative Proteomic Analysis Combined with Laser-Capture Microdissection Suggests Important Roles of Stress Responses in the Black Layer of Maize Kernels. Int J Mol Sci 2020; 21:ijms21041369. [PMID: 32085613 PMCID: PMC7072901 DOI: 10.3390/ijms21041369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/14/2020] [Accepted: 02/16/2020] [Indexed: 12/20/2022] Open
Abstract
The black layer (BL) is traditionally used as an indicator for kernel harvesting in maize, as it turns visibly dark when the kernel reaches physiological maturity. However, the molecular roles of BL in kernel development have not been fully elucidated. In this work, microscopy images showed that BL began to appear at a growth stage earlier than 10 days after pollination (DAP), and its color gradually deepened to become dark as the development period progressed. Scanning electron microscopy observations revealed that BL is a tissue structure composed of several layers of cells that are gradually squeezed and compressed during kernel development. Laser-capture microdissection (LCM) was used to sample BL and its neighboring inner tissue, basal endosperm transfer layer (BETL), and outer tissue, inner epidermis (IEP), from 20 DAP of kernels. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling (MALDI-TOF MS profiling) detected 41, 104, and 120 proteins from LCM-sampled BL, BETL, and IEP, respectively. Gene ontology (GO) analysis indicated that the 41 BL proteins were primarily involved in the response to stress and stimuli. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that the BL proteins were enriched in several defense pathways, such as the ascorbate and aldarate metabolic pathways. Among the 41 BL proteins, six were BL-specific proteins that were only detected from BL. Annotations of five BL-specific proteins were related to stress responses. During kernel development, transcriptional expression of most BL proteins showed an increase, followed by a decrease, and reached a maximum zero to 20 DAP. These results suggest a role for BL in stress responses for protecting filial tissue against threats from maternal sides, which helps to elucidate the biological functions of BL.
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Affiliation(s)
- Quanquan Chen
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Ran Huang
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Zhenxiang Xu
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Yaxin Zhang
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Li Li
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.F.); (G.W.)
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.F.); (G.W.)
| | - Jianhua Wang
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
| | - Xuemei Du
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
- Correspondence: (X.D.); (R.G.)
| | - Riliang Gu
- Center for Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Key Laboratory of Crop Heterosis Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; (Q.C.); (R.H.); (Z.X.); (Y.Z.); (L.L.); (J.W.)
- Correspondence: (X.D.); (R.G.)
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5
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An Effective Method of Isolating Honey Proteins. Molecules 2019; 24:molecules24132399. [PMID: 31261846 PMCID: PMC6651845 DOI: 10.3390/molecules24132399] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 12/21/2022] Open
Abstract
Honey is a natural sweetener composed mostly of sugars, but it contains also pollen grains, proteins, free amino acids, and minerals. The amounts and proportions of these components depend on the honey type and bee species. Despite the low content of honey protein, they are becoming a popular study object, and have recently been used as markers of the authenticity and quality of honey. Currently, the most popular methods of protein isolation from honey are dialysis against distilled water, lyophilization of dialysate, or various precipitation protocols. In this work, we propose a new method based on saturated phenol. We tested it on three popular polish honey types and we proved its compatibility with both 1D and 2D polyacrylamide gel electrophoresis (PAGE) and MS (mass spectrometry) techniques. The elaborated technique is also potentially less expensive and less time-consuming than other previously described methods, while being equally effective.
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Cao S, Engilberge S, Girard E, Gabel F, Franzetti B, Maupin-Furlow JA. Structural Insight into Ubiquitin-Like Protein Recognition and Oligomeric States of JAMM/MPN + Proteases. Structure 2017; 25:823-833.e6. [PMID: 28479062 DOI: 10.1016/j.str.2017.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/26/2017] [Accepted: 04/10/2017] [Indexed: 11/25/2022]
Abstract
JAMM/MPN+ metalloproteases cleave (iso)peptide bonds C-terminal to ubiquitin (Ub) and ubiquitin-like protein (Ubl) domains and typically require association with protein partners for activity, which has limited a molecular understanding of enzyme function. To provide an insight, we solved the X-ray crystal structures of a catalytically active Pyrococcus furiosus JAMM/MPN+ metalloprotease (PfJAMM1) alone and in complex with a Ubl (PfSAMP2) to 1.7- to 1.9-Å resolution. PfJAMM1 was found to have a redox sensitive dimer interface. In the PfJAMM1-bound state of the SAMP2, a Ubl-to-Ub conformational change was detected. Surprisingly, distant homologs of PfJAMM1 were found to be closely related in 3D structure, including the interface for Ubl/Ub binding. From this work, we infer the molecular basis of how JAMM/MPN+ proteases recognize and cleave Ubl/Ub tags from diverse proteins and highlight an α2-helix structural element that is conserved and crucial for binding and removing the Ubl SAMP2 tag.
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Affiliation(s)
- Shiyun Cao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Sylvain Engilberge
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Eric Girard
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Frank Gabel
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Bruno Franzetti
- Institut de Biologie Structurale (IBS), University Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France.
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
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Mostafa I, Yoo MJ, Zhu N, Geng S, Dufresne C, Abou-Hashem M, El-Domiaty M, Chen S. Membrane Proteomics of Arabidopsis Glucosinolate Mutants cyp79B2/B3 and myb28/29. FRONTIERS IN PLANT SCIENCE 2017; 8:534. [PMID: 28443122 PMCID: PMC5387099 DOI: 10.3389/fpls.2017.00534] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/24/2017] [Indexed: 05/09/2023]
Abstract
Glucosinolates (Gls) constitute a major group of natural metabolites represented by three major classes (aliphatic, indolic and aromatic) of more than 120 chemical structures. In our previous work, soluble proteins and metabolites in Arabidopsis mutants deficient of aliphatic (myb28/29) and indolic Gls (cyp79B2B3) were analyzed. Here we focus on investigating the changes at the level of membrane proteins in these mutants. Our LC/MS-MS analyses of tandem mass tag (TMT) labeled peptides derived from the cyp79B2/B3 and myb28/29 relative to wild type resulted in the identification of 4,673 proteins, from which 2,171 are membrane proteins. Fold changes and statistical analysis showed 64 increased and 74 decreased in cyp79B2/B3, while 28 increased and 17 decreased in myb28/29. As to the shared protein changes between the mutants, one protein was increased and eight were decreased. Bioinformatics analysis of the changed proteins led to the discovery of three cytochromes in glucosinolate molecular network (GMN): cytochrome P450 86A7 (At1g63710), cytochrome P450 71B26 (At3g26290), and probable cytochrome c (At1g22840). CYP86A7 and CYP71B26 may play a role in hydroxyl-indolic Gls production. In addition, flavone 3'-O-methyltransferase 1 represents an interesting finding as it is likely to participate in the methylation process of the hydroxyl-indolic Gls to form methoxy-indolic Gls. The analysis also revealed additional new nodes in the GMN related to stress and defense activity, transport, photosynthesis, and translation processes. Gene expression and protein levels were found to be correlated in the cyp79B2/B3, but not in the myb28/29.
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Affiliation(s)
- Islam Mostafa
- Department of Biology, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig UniversityZagazig, Egypt
| | - Mi-Jeong Yoo
- Department of Biology, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
| | - Ning Zhu
- Department of Biology, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
| | - Sisi Geng
- Department of Biology, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
| | | | - Maged Abou-Hashem
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig UniversityZagazig, Egypt
| | - Maher El-Domiaty
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig UniversityZagazig, Egypt
| | - Sixue Chen
- Department of Biology, University of FloridaGainesville, FL, USA
- Genetics Institute, University of FloridaGainesville, FL, USA
- Plant Molecular and Cellular Biology Program, University of FloridaGainesville, FL, USA
- Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
- *Correspondence: Sixue Chen
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Mostafa I, Zhu N, Yoo MJ, Balmant KM, Misra BB, Dufresne C, Abou-Hashem M, Chen S, El-Domiaty M. New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3 glucosinolate mutants. J Proteomics 2016; 138:1-19. [PMID: 26915584 DOI: 10.1016/j.jprot.2016.02.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/07/2016] [Accepted: 02/17/2016] [Indexed: 12/24/2022]
Abstract
UNLABELLED Glucosinolates present in Brassicales are important for human health and plant defense against insects and pathogens. Here we investigate the proteomes and metabolomes of Arabidopsis myb28/29 and cyp79B2/B3 mutants deficient in aliphatic glucosinolates and indolic glucosinolates, respectively. Quantitative proteomics of the myb28/29 and cyp79B2/B3 mutants led to the identification of 2785 proteins, of which 142 proteins showed significant changes in the two mutants compared to wild type (WT). By mapping the differential proteins using STRING, we detected 59 new edges in the glucosinolate metabolic network. These connections can be classified as primary with direct roles in glucosinolate metabolism, secondary related to plant stress responses, and tertiary involved in other biological processes. Gene Ontology analysis of the differential proteins showed high level of enrichment in the nodes belonging to metabolic process including glucosinolate biosynthesis and response to stimulus. Using metabolomics, we quantified 292 metabolites covering a broad spectrum of metabolic pathways, and 89 exhibited differential accumulation patterns between the mutants and WT. The changing metabolites (e.g., γ-glutamyl amino acids, auxins and glucosinolate hydrolysis products) complement our proteomics findings. This study contributes toward engineering and breeding of glucosinolate profiles in plants in efforts to improve human health, crop quality and productivity. BIOLOGICAL SIGNIFICANCE Glucosinolates in Brassicales constitute an important group of natural metabolites important for plant defense and human health. Its biosynthetic pathways and transcriptional regulation have been well-studied. Using Arabidopsis mutants of important genes in glucosinolate biosynthesis, quantitative proteomics and metabolomics led to identification of many proteins and metabolites that are potentially related to glucosinolate metabolism. This study provides a comprehensive insight into the molecular networks of glucosinolate metabolism, and will facilitate efforts toward engineering and breeding of glucosinolate profiles for enhanced crop defense, and nutritional value.
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Affiliation(s)
- Islam Mostafa
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Ning Zhu
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Mi-Jeong Yoo
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Kelly M Balmant
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA
| | - Biswapriya B Misra
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Craig Dufresne
- Thermo Fisher Scientific, West Palm Beach, FL 33407, USA
| | - Maged Abou-Hashem
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Sixue Chen
- Department of Biology, University of Florida, Gainesville, FL 32610, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32610, USA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32610, USA.
| | - Maher El-Domiaty
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
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Alvarez S, Naldrett MJ. Plant Structure and Specificity - Challenges and Sample Preparation Considerations for Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:63-81. [PMID: 27975213 DOI: 10.1007/978-3-319-41448-5_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Plants are considered as a simple structured organism when compared to humans and other vertebrates. The number of organs and tissue types is very limited. Instead the origin of the complexity comes from the high number and variety of plant species that exist, with >300,000 compared to 5000 in mammals. Proteomics, defined as the large-scale study of the proteins present in a tissue, cell or cellular compartment at a defined time point, was introduced in 1994. However, the first publications reported in the plant proteomics field only appeared at the beginning of the twenty-first century. Since these early years, the increase of proteomic studies in plants has only followed a linear trend. The main reason for this stems from the challenges specific to studying plants, those of protein extraction from cells with variously strengthened cellulosic cell walls, and a high abundance of interfering compounds, such as phenolic compounds and pigments located in plastids throughout the plant. Indeed, the heterogeneity between different organs and tissue types, between species and different developmental stages, requires the use of optimized plant protein extraction methods as described in this section. The second bottleneck of plant proteomics, which will not be discussed or reviewed here, is the lack of genomic information. Without sequence databases of the >300,000 species, proteomic studies of plants, especially of those that are not considered economically relevant, are impossible to accomplish.
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Affiliation(s)
- Sophie Alvarez
- Center for Biotechnology, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE, 68588, USA.
| | - Michael J Naldrett
- Center for Biotechnology, University of Nebraska-Lincoln, Beadle Center, 1901 Vine St, Lincoln, NE, 68588, USA
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Dong Y, Wang Q, Zhang L, Du C, Xiong W, Chen X, Deng F, Ma Z, Qiao D, Hu C, Ren Y, Li Y. Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn. PLoS One 2015; 10:e0143181. [PMID: 26587848 PMCID: PMC4654522 DOI: 10.1371/journal.pone.0143181] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 11/02/2015] [Indexed: 12/31/2022] Open
Abstract
The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.
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Affiliation(s)
- Yongbin Dong
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Qilei Wang
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Long Zhang
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Chunguang Du
- Deptment of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, United States of America
| | - Wenwei Xiong
- Deptment of Biology and Molecular Biology, Montclair State University, Montclair, NJ 07043, United States of America
| | - Xinjian Chen
- College of Life Sciences, Henan Agricultural University, 63 Nongye Rd, Zhengzhou, China
| | - Fei Deng
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Zhiyan Ma
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Dahe Qiao
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Chunhui Hu
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Yangliu Ren
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
| | - Yuling Li
- College of Agronomy, Henan Agricultural University, Collaborative Innovation Center of Henan Grain Crops, National Key Laboratory of Wheat and Maize Crop Science, 63 Nongye Rd, Zhengzhou, China
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Zhang HM, Wheeler S, Xia X, Radchuk R, Weber H, Offler CE, Patrick JW. Differential transcriptional networks associated with key phases of ingrowth wall construction in trans-differentiating epidermal transfer cells of Vicia faba cotyledons. BMC PLANT BIOLOGY 2015; 15:103. [PMID: 25887034 PMCID: PMC4437447 DOI: 10.1186/s12870-015-0486-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/01/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Transfer cells are characterized by intricate ingrowth walls, comprising an uniform wall upon which wall ingrowths are deposited. The ingrowth wall forms a scaffold to support an amplified plasma membrane surface area enriched in membrane transporters that collectively confers transfer cells with an enhanced capacity for membrane transport at bottlenecks for apo-/symplasmic exchange of nutrients. However, the underlying molecular mechanisms regulating polarized construction of the ingrowth wall and membrane transporter profile are poorly understood. RESULTS An RNAseq study of an inducible epidermal transfer cell system in cultured Vicia faba cotyledons identified transfer cell specific transcriptomes associated with uniform wall and wall ingrowth deposition. All functional groups of genes examined were expressed before and following transition to a transfer cell fate. What changed were the isoform profiles of expressed genes within functional groups. Genes encoding ethylene and Ca(2+) signal generation and transduction pathways were enriched during uniform wall construction. Auxin-and reactive oxygen species-related genes dominated during wall ingrowth formation and ABA genes were evenly expressed across ingrowth wall construction. Expression of genes encoding kinesins, formins and villins was consistent with reorganization of cytoskeletal components. Uniform wall and wall ingrowth specific expression of exocyst complex components and SNAREs suggested specific patterns of exocytosis while dynamin mediated endocytotic activity was consistent with establishing wall ingrowth loci. Key regulatory genes of biosynthetic pathways for sphingolipids and sterols were expressed across ingrowth wall construction. Transfer cell specific expression of cellulose synthases was absent. Rather xyloglucan, xylan and pectin biosynthetic genes were selectively expressed during uniform wall construction. More striking was expression of genes encoding enzymes for re-modelling/degradation of cellulose, xyloglucans, pectins and callose. Extensins dominated the cohort of expressed wall structural proteins and particularly so across wall ingrowth development. Ion transporters were selectively expressed throughout ingrowth wall development along with organic nitrogen transporters and a large group of ABC transporters. Sugar transporters were less represented. CONCLUSIONS Pathways regulating signalling and intracellular organization were fine tuned whilst cell wall construction and membrane transporter profiles were altered substantially upon transiting to a transfer cell fate. Each phase of ingrowth wall construction was linked with unique cohorts of expressed genes.
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Affiliation(s)
- Hui-Ming Zhang
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Simon Wheeler
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Xue Xia
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Ruslana Radchuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466, Gatersleben, Germany.
| | - Hans Weber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466, Gatersleben, Germany.
| | - Christina E Offler
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.
| | - John W Patrick
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia.
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Romero J, Zarate M, Arriola K, Gonzalez C, Silva-Sanchez C, Staples C, Adesogan A. Screening exogenous fibrolytic enzyme preparations for improved in vitro digestibility of bermudagrass haylage. J Dairy Sci 2015; 98:2555-67. [DOI: 10.3168/jds.2014-8059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 12/27/2014] [Indexed: 01/22/2023]
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Silva-Sanchez C, Chen S, Li J, Chourey PS. A comparative glycoproteome study of developing endosperm in the hexose-deficient miniature1 (mn1) seed mutant and its wild type Mn1 in maize. FRONTIERS IN PLANT SCIENCE 2014; 5:63. [PMID: 24616729 PMCID: PMC3935489 DOI: 10.3389/fpls.2014.00063] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 02/07/2014] [Indexed: 05/04/2023]
Abstract
In maize developing seeds, transfer cells are prominently located at the basal endosperm transfer layer (BETL). As the first filial cell layer, BETL is a gateway to sugars, nutrients and water from mother plant; and anchor of numerous functions such as sucrose turnover, auxin and cytokinin biosynthesis/accumulation, energy metabolism, defense response, and signaling between maternal and filial generations. Previous studies showed that basal developing endosperms of miniature1 (mn1) mutant seeds lacking the Mn1-encoded cell wall invertase II, are also deficient for hexose. Given the role of glucose as one of the key sugars in protein glycosylation and proper protein folding; we performed a comparative large scale glycoproteome profiling of total proteins of these two genotypes (mn1 mutant vs. Mn1 wild type) using 2D gel electrophoresis and glycosylation/total protein staining, followed by image analysis. Protein identification was done by LC-MS/MS. A total of 413 spots were detected; from which, 113 spots matched between the two genotypes. Of these, 45 showed >20% decrease/increase in glycosylation level and were selected for protein identification. A large number of identified proteins showed decreased glycosylation levels in mn1 developing endosperms as compared to the Mn1. Functional classification of proteins, showed mainly of post-translational modification, protein turnover, chaperone activities, carbohydrate and amino acid biosynthesis/transport, and cell wall biosynthesis. These proteins and activities were related to endoplasmic reticulum (ER) stress and unfolded protein response (UPR) as a result of the low glycolsylation levels of the mutant proteins. Overall, these results provide for the first time a global glycoproteome profile of maize BETL-enriched basal endosperm to better understand their role in seed development in maize.
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Affiliation(s)
- Cecilia Silva-Sanchez
- Proteomics, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
| | - Sixue Chen
- Proteomics, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
- Department of Biology, UF Genetics Institute, University of FloridaGainesville, FL, USA
| | - Jinxi Li
- Proteomics, Interdisciplinary Center for Biotechnology Research, University of FloridaGainesville, FL, USA
| | - Prem S. Chourey
- United States Department of Agriculture, Agricultural Research Service, Center for Medical, Agricultural and Veterinary EntomologyGainesville, FL, USA
- Department of Agronomy, University of FloridaGainesville, FL, USA
- *Correspondence: Prem S. Chourey, United States Department of Agriculture, Agricultural Research Service, 1600 SW 23rd Drive, Gainesville, FL 32608, USA e-mail:
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Lopato S, Borisjuk N, Langridge P, Hrmova M. Endosperm transfer cell-specific genes and proteins: structure, function and applications in biotechnology. FRONTIERS IN PLANT SCIENCE 2014; 5:64. [PMID: 24578704 PMCID: PMC3936200 DOI: 10.3389/fpls.2014.00064] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/07/2014] [Indexed: 05/21/2023]
Abstract
Endosperm transfer cells (ETC) are one of four main types of cells in endosperm. A characteristic feature of ETC is the presence of cell wall in-growths that create an enlarged plasma membrane surface area. This specialized cell structure is important for the specific function of ETC, which is to transfer nutrients from maternal vascular tissue to endosperm. ETC-specific genes are of particular interest to plant biotechnologists, who use genetic engineering to improve grain quality and yield characteristics of important field crops. The success of molecular biology-based approaches to manipulating ETC function is dependent on a thorough understanding of the functions of ETC-specific genes and ETC-specific promoters. The aim of this review is to summarize the existing data on structure and function of ETC-specific genes and their products. Potential applications of ETC-specific genes, and in particular their promoters for biotechnology will be discussed.
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Affiliation(s)
- Sergiy Lopato
- *Correspondence: Sergiy Lopato, Australian Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia e-mail:
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Ruan YL, Patrick JW, Shabala S, Slewinski TL. Uptake and regulation of resource allocation for optimal plant performance and adaptation to stress. FRONTIERS IN PLANT SCIENCE 2013; 4:455. [PMID: 24294215 PMCID: PMC3827556 DOI: 10.3389/fpls.2013.00455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 10/23/2013] [Indexed: 05/12/2023]
Affiliation(s)
- Yong-Ling Ruan
- School of Environmental and Life Sciences, The University of NewcastleCallaghan, NSW, Australia
- Australia-China Research Centre for Crop Improvement, The University of NewcastleCallaghan, NSW, Australia
| | - John W. Patrick
- School of Environmental and Life Sciences, The University of NewcastleCallaghan, NSW, Australia
- Australia-China Research Centre for Crop Improvement, The University of NewcastleCallaghan, NSW, Australia
| | - Sergey Shabala
- School of Agricultural Science, University of TasmaniaHobart, TAS, Australia
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