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Yuan K, He Q, Hu Y, Feng C, Wang X, Liu H, Wang Z. Integrated physiology, transcriptome and proteome analyses highlight the potential roles of multiple hormone-mediated signaling pathways involved in tapping panel dryness in rubber tree. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112011. [PMID: 38311252 DOI: 10.1016/j.plantsci.2024.112011] [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: 10/23/2023] [Revised: 01/08/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
Currently, one of the most serious threats to rubber tree is the tapping panel dryness (TPD) that greatly restricts natural rubber production. Over-tapping or excessive ethephon stimulation is regarded as the main cause of TPD occurrence. Although extensive studies have been carried out, the molecular mechanism underlying TPD remains puzzled. An attempt was made to compare the levels of endogenous hormones and the profiles of transcriptome and proteome between healthy and TPD trees. Results showed that most of endogenous hormones such as jasmonic acid (JA), 1-aminocyclopropanecarboxylic acid (ACC), indole-3-acetic acid (IAA), trans-zeatin (tZ) and salicylic acid (SA) in the barks were significantly altered in TPD-affected rubber trees. Accordingly, multiple hormone-mediated signaling pathways were changed. In total, 731 differentially expressed genes (DEGs) and 671 differentially expressed proteins (DEPs) were identified, of which 80 DEGs were identified as putative transcription factors (TFs). Further analysis revealed that 12 DEGs and five DEPs regulated plant hormone synthesis, and that 16 DEGs and six DEPs were involved in plant hormone signal transduction pathway. Nine DEGs and four DEPs participated in rubber biosynthesis and most DEGs and all the four DEPs were repressed in TPD trees. All these results highlight the potential roles of endogenous hormones, signaling pathways mediated by these hormones and rubber biosynthesis pathway in the defense response of rubber trees to TPD. The present study extends our understanding of the nature and mechanism underlying TPD and provides some candidate genes and proteins related to TPD for further research in the future.
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Affiliation(s)
- Kun Yuan
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Qiguang He
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yiyu Hu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Chengtian Feng
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Xihao Wang
- College of Life Sciences, Hainan Normal University, Haikou, Hainan 571158, China
| | - Hui Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
| | - Zhenhui Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Genetic Resources of Rubber Tree/State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.
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Bautista-Valle MV, Camacho-Vazquez C, Elizalde-Contreras JM, Monribot-Villanueva JL, Limón AMV, Bojórquez-Velázquez E, Zamora-Briseño JA, Jorrin-Novo JV, Ruiz-May E. Comparing and integrating TMT-SPS-MS3 and label-free quantitative approaches for proteomics scrutiny in recalcitrant Mango (Mangifera indica L.) peel tissue during postharvest period. Proteomics 2024; 24:e2300239. [PMID: 37681534 DOI: 10.1002/pmic.202300239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/09/2023]
Abstract
Despite substantial advances in the use of proteomic technologies, their widespread application in fruit tissues of non-model and recalcitrant species remains limited. This hampers the understanding of critical molecular events during the postharvest period of fleshy tropical fruits. Therefore, we evaluated label-free quantitation (LFQ) and TMT-SPS-MS3 (TMT) approaches to analyse changes in the protein profile of mango peels during postharvest period. We compared two extraction methods (phenol and chloroform/methanol) and two peptide fractionation schemes (SCX and HPRP). We accurately identified 3065 proteins, of which, 1492 were differentially accumulated over at 6 days after harvesting (DAH). Both LFQ and TMT approaches share 210 differential proteins including cell wall proteins associated with fruit softening, as well as aroma and flavour-related proteins, which were increased during postharvest period. The phenolic protein extraction and the high-pH reverse-phase peptide fractionation was the most effective pipeline for relative quantification. Nevertheless, the information provided by the other tested strategies was significantly complementary. Besides, LFQ spectra allowed us to track down intact N-glycopeptides corroborating N-glycosylations on the surface of a desiccation-related protein. This work represents the largest proteomic comparison of mango peels during postharvest period made so far, shedding light on the molecular foundation of edible fruit during ripening.
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Affiliation(s)
- Mirna V Bautista-Valle
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Carolina Camacho-Vazquez
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - José M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Juan Luis Monribot-Villanueva
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Abraham M Vidal Limón
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Esaú Bojórquez-Velázquez
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Jesús Alejandro Zamora-Briseño
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
| | - Jesús V Jorrin-Novo
- Department of Biochemistry and Molecular Biology, ETSIAM, University of Cordoba, Cordoba, Spain
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec No. 351, Xalapa, Veracruz, México
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Omar SA, Ashokhan S, Abdul Majid N, Karsani SA, Lau BYC, Yaacob JS. Enhanced azadirachtin production in neem (Azadirachta indica) callus through NaCl elicitation: Insights into differential protein regulation via shotgun proteomics. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2024; 199:105778. [PMID: 38458685 DOI: 10.1016/j.pestbp.2024.105778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/19/2023] [Accepted: 01/09/2024] [Indexed: 03/10/2024]
Abstract
With their remarkable bioactivity and evolving commercial importance, plant secondary metabolites (PSMs) have gained significant research interest in recent years. Plant tissue culture serves as a credible tool to examine how abiotic stresses modulate the production of PSMs, enabling clear insights into plant stress responses and the prospects for controlled synthesis of bioactive compounds. Azadirachta indica, or neem has been recognized as a repository of secondary metabolites for centuries, particularly for the compound named azadirachtin, due to its bio-pesticidal and high antioxidant properties. Introducing salt stress as an elicitor makes it possible to enhance the synthesis of secondary metabolites, specifically azadirachtin. Thus, in this research, in vitro callus cultures of neem were micro-propagated and induced with salinity stress to explore their effects on the production of azadirachtin and identify potential proteins associated with salinity stress through comparative shotgun proteomics (LCMS/MS). To induce salinity stress, 2-month-old calli were subjected to various concentrations of NaCl (0.05-1.5%) for 4 weeks. The results showed that the callus cultures were able to adapt and survive in the salinity treatments, but displayed a reduction in fresh weight as the NaCl concentration increased. Notably, azadirachtin production was significantly enhanced in the salinity treatment compared to control, where 1.5% NaCl-treated calli produced the highest azadirachtin amount (10.847 ± 0.037 mg/g DW). The proteomics analysis showed that key proteins related to primary metabolism, such as defence, energy, cell structure, redox, transcriptional and photosynthesis, were predominantly differentially regulated (36 upregulated and 93 downregulated). While a few proteins were identified as being regulated in secondary metabolism, they were not directly involved in the synthesis of azadirachtin. In conjunction with azadirachtin elicitation, salinity stress treatment could therefore be successfully applied in commercial settings for the controlled synthesis of azadirachtin and other plant-based compounds. Further complementary omics approaches can be employed to enhance molecular-level modifications, to facilitate large-scale production of bioactive compounds in the future.
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Affiliation(s)
- Siti Ainnsyah Omar
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sharmilla Ashokhan
- School of Biotechnology, MILA University, Putra Nilai, 71800 Nilai, Negeri Sembilan, Malaysia
| | - Nazia Abdul Majid
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Saiful Anuar Karsani
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia
| | - Benjamin Yii Chung Lau
- Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Jamilah Syafawati Yaacob
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
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Taha M, Elazab ST, Abdelbagi O, Saati AA, Babateen O, Baokbah TAS, Qusty NF, Mahmoud ME, Ibrahim MM, Badawy AM. Phytochemical analysis of Origanum majorana L. extract and investigation of its antioxidant, anti-inflammatory and immunomodulatory effects against experimentally induced colitis downregulating Th17 cells. JOURNAL OF ETHNOPHARMACOLOGY 2023; 317:116826. [PMID: 37348796 DOI: 10.1016/j.jep.2023.116826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 06/24/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Origanum majorana L. is a member of the Lamiaceae family and is commonly used in Egyptian cuisine as a seasoning and flavor enhancer. It is also recognized as a well-known traditional medicine in Egypt and is widely used for treating abdominal colic due to its antispasmodic properties. However, the protective effects of Origanum majorana L. against ulcerative colitis and its underlying mechanisms remain unclear. AIM OF THE STUDY This study aimed to identify the biologically active components present in methanol extracts of Origanum majorana L. using gas chromatography/mass spectrometry (GC/MS). Additionally, it aimed to investigate the therapeutic effects of these extracts on acetic acid-induced ulcerative colitis and elucidate the potential mechanisms involved. MATERIALS AND METHODS We conducted a GC-MS analysis of the methanolic extract obtained from Origanum majorana L. Thirty-two male rats were included in the study and divided into four experimental groups, with eight rats in each group: sham, UC, UC + O. majorana, and UC sulfasalazine. After euthanizing the rats, colon tissue samples were collected for gross and microscopic examinations, assessment of oxidative stress, and molecular evaluation. GC-MS analysis identified 15 components in the extracts. Pretreatment with O. majorana L. extract and sulfasalazine significantly improved the disease activity index (DAI) and resulted in notable improvements in macroscopic and microscopic colon findings. Additionally, both treatments demonstrated preventive effects against colonic oxidative damage by reducing the levels of malondialdehyde (MDA) and increasing the levels of the antioxidant systems superoxide dismutase (SOD), catalase (CAT), and glutathione (GSH), which operate through the Nrf2/HO-1 signaling pathway. Moreover, these treatments downregulated the colonic inflammatory cascade by inhibiting NFκB, TNFα, IL-1β, IL6, IL23, IL17, COX-2, and iNOS, subsequently leading to downregulation of the JAK2/STAT3 signaling pathway and a decrease in the Th17 cell response. Furthermore, a reduction in the number of apoptotic epithelial cells that expressed caspase-3 was observed. CONCLUSION pretreatment with O. majorana L. extract significantly ameliorated acetic acid-induced ulcerative colitis. This effect could be attributed to the protective, antioxidant, anti-inflammatory, and anti-apoptotic properties of the extract.
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Affiliation(s)
- Medhat Taha
- Department of Anatomy and Embryology, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt; Department of Anatomy, Al- Qunfudah Medical College, Umm Al-Qura University, Al-Qunfudhah, 28814, Saudi Arabia.
| | - Sara T Elazab
- Department of Pharmacology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Omer Abdelbagi
- Department of Pathology, Qunfudah Faculty of Medicine, Umm-Al-Qura University, Kingdom of Saudi Arabia, Makka, 24382, Saudi Arabia
| | - Abdullah A Saati
- Department of Community Medicine and Pilgrims Healthcare, Faculty of Medicine, Umm Al-Qura University, Makkah, 24382, Saudi Arabia
| | - Omar Babateen
- Department of Physiology, Faculty of Medicine, Umm Al-Qura University, Makkah, 24382, Saudi Arabia
| | - Tourki A S Baokbah
- Department of Medical Emergency Services, College of Health Sciences-AlQunfudah, Umm Al-Qura University, Al-Qunfudah, 28814, Saudi Arabia
| | - Naeem F Qusty
- Medical Laboratories Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, 24382, Saudi Arabia
| | - Mohamed Ezzat Mahmoud
- Histology Department, Damietta Faculty of Medicine, Al-Azhar University, Damietta, 34711, Egypt
| | - Mohie Mahmoud Ibrahim
- Department of Anatomy and Embryology, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Alaa M Badawy
- Department of Anatomy and Embryology, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
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Bhattacharya S, Rathore AS. A novel filter-assisted protein precipitation (FAPP) based sample pre-treatment method for LC-MS peptide mapping for biosimilar characterization. J Pharm Biomed Anal 2023; 234:115527. [PMID: 37364451 DOI: 10.1016/j.jpba.2023.115527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 06/28/2023]
Abstract
Establishing analytical and functional comparability serves as the foundation of biosimilar development. A critical part of this exercise is sequence similarity search and categorization of post-translational modifications (PTMs), often by peptide mapping using liquid chromatography-mass spectrometry (LC-MS). When performing bottom-up proteomic sample preparation, efficient digestion of the protein and extraction of peptides for subsequent mass spectrometric analysis can be a challenge. Conventional sample preparation strategies face the risk of allowing interference of chemicals which are essential for extraction but are likely to interfere with digestion, resulting in complex chromatographic profiles due to semi-cleavages, insufficient peptide cleavages, and other unwanted reactions. Further, peptide cleanup through commonly used immobilized C-18 pipette tips can cause significant peptide loss as well as variability in individual peptide yields, thereby causing artifacts of various product-related modifications. In this study, we proposed a simple enzymatic digestion technique by incorporating different molecular weight filters and protein precipitation, with the objective to minimize interference of denaturing, reducing, and alkylating agents throughout overnight digestion. As a result, the need for peptide cleanup is significantly reduced and results in higher peptide yield. The proposed FAPP approach outperformed the conventional method across multiple metrics including, 30% more peptides, 8.19% more fully digested peptides, 14% higher sequence coverage rate, and 11.82% more site-specific alterations. Quantitative and qualitative repeatability of the proposed approach have been demonstrated. It can be concluded that the filter-assisted protein precipitation (FAPP) protocol proposed in this study offers an effective substitute for the traditional approach.
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Affiliation(s)
| | - Anurag S Rathore
- Chemical Engineering Department, Indian Institute of Technology Delhi, India.
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Piechowiak T, Skóra B, Balawejder M. Effect of postharvest nicotinamide treatment on NAD + metabolism and redox status in strawberry fruit during storage. PHYTOCHEMISTRY 2023; 213:113766. [PMID: 37343736 DOI: 10.1016/j.phytochem.2023.113766] [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: 03/31/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023]
Abstract
The increased activity of PARP enzymes is associated with a deficiency of NAD+, as well as with a loss of NADPH and ATP, and consequent deterioration of the redox state in fruits. In this study, we checked whether treatment with nicotinamide (NAM) would affect PARP-1 expression and NAD+ metabolism in strawberry fruit during storage. For this purpose, strawberry fruits were treated with 10 mM NAM and co-treated with NAM and UV-C, and then stored for 5 days at 4 °C. Research showed that nicotinamide contributes to reducing oxidative stress level by reducing PARP-1 mRNA gene expression and the protein level resulting in higher NAD+ availability, as well as improving energy metabolism and NADPH levels in fruits, regardless of whether they are exposed to UV-C. The above effects cause fruits treated with nicotinamide to be characterised by higher anti-radical activity, and a lower level of reactive oxygen species in the tissue.
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Affiliation(s)
- Tomasz Piechowiak
- Department of Chemistry and Food Toxicology, Institute of Food Technology and Nutrition, University of Rzeszow, St. Cwiklinskiej 1a, 35-601, Rzeszow, Poland.
| | - Bartosz Skóra
- Department of Biotechnology and Cell Biology, Medical College, University of Information Technology and Management in Rzeszow, St. Sucharskiego 2, 35-225, Rzeszow, Poland
| | - Maciej Balawejder
- Department of Chemistry and Food Toxicology, Institute of Food Technology and Nutrition, University of Rzeszow, St. Cwiklinskiej 1a, 35-601, Rzeszow, Poland
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Luo D, Ding Q, Ma X, Zhu J, Zou K, Hong W, Wang J, Mao C, Xie Z, Wu B, Khan I, Wang X, Feng G, Huang L. Proteomic and physiological responses of contrasting two different heat-resistant orchardgrass genotypes to heat stress. Int J Biol Macromol 2023:125463. [PMID: 37348590 DOI: 10.1016/j.ijbiomac.2023.125463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/20/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
As an important forage crop worldwide, the growth and productivity of orchardgrass are greatly impacted by high temperatures. However, little information is known about how orchardgrass proteomic changes under heat conditions. Therefore, the present study investigated the proteomics and physiological changes in 667 [AKZ-NRGR667 (heat-tolerant)] and 7602 [PI237602 (heat-sensitive)] under heat stress (40/35 °C). In addition, the responses of translational regulating of heat stress in orchardgrass were analyzed through proteomic changes using the tandem mass tags (TMT) technique. Together, 410 differentially expressed proteins (DEPs) were identified from two orchardgrass genotypes under heat at 24 h. Proteomics analyses indicated that proteins related to substance metabolism, photosynthesis, and heat shock proteins (HSPs) were differentially expressed under heat stress and control conditions. Moreover, a large proportion of HSPs were expressed in the heat-tolerant genotype as compared to the heat-sensitive genotype. In conclusion, genotype 667 has higher adaptability and repairing capability due to stronger heat tolerance capacity that can make it more suited to sustaining its survival and growth than genotype 7602. These findings can provide the basis for genetic improvements in orchardgrass and other crops facing high-temperature stress or heat environment that may lead to heat resistance or tolerance.
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Affiliation(s)
- Dan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiong Ding
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xixi Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Zhu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Kun Zou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenkai Hong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jin Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunli Mao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zheni Xie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Bingchao Wu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Imran Khan
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, 730020 Lanzhou, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Saher U, Ovais Omer M, Javeed A, Ahmad Anjum A, Rehman K, Awan T. Soluble laticifer proteins from Calotropis procera as an effective candidates for antimicrobial therapeutics. Saudi J Biol Sci 2023; 30:103659. [PMID: 37181638 PMCID: PMC10172833 DOI: 10.1016/j.sjbs.2023.103659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/24/2023] [Accepted: 04/16/2023] [Indexed: 05/16/2023] Open
Abstract
Calotropis procera is a latex-producing plant with plenty of pharmacologically active compounds. The principal motivation behind this study was to separate and characterize laticifer proteins to check their antimicrobial potential. Laticifer proteins were separated by gel filtration chromatography (GFC) and investigated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The SDS-PAGE assay detected proteins of molecular weights of 10 to 30 kDa but most of them were in the range of 25 to 30 kDa. The soluble laticifer proteins (SLPs) were tested against Gram-positive bacteria i.e., Streptococcus pyogenes and Staphylococcus aureus whereas Escherichia coli and Pseudomonas aeruginosa were tested as Gram-negative bacteria, we determined a profound anti-bacterial activity of these proteins. In addition, SLPs were also investigated against Candida albicans via the agar disc diffusion method which also showed significant anti-fungal activity. SLP exhibited antibacterial activity against P. aeruginosa, E. coli, and S. aureus with a minimum inhibitory concentration (MIC) of 2.5 mg/mL for each, while MIC was found at 0.625 mg/mL for S. pyogenes and 1.25 mg/mL for C. albicans. Moreover, enzymatic activity evaluation of SLP showed the proteolytic nature of these proteins, and this proteolytic activity was greatly enhanced after reduction which might be due to the presence of cysteine residues in the protein structure. The activity of the SLPs obtained from the latex of C. procera can be associated with the involvement of enzymes either proteases or, protease inhibitors and/or peptides.
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Affiliation(s)
- Uzma Saher
- Department of Pharmacy, The Women University, Multan 60000, Pakistan Department of Pharmacology and Toxicology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Muhammad Ovais Omer
- Department of Pharmacology and Toxicology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
- Corresponding author at: Department of Pharmacology and Toxicology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan.
| | - Aqeel Javeed
- Department of Pharmacology and Toxicology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Aftab Ahmad Anjum
- Department of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - Kanwal Rehman
- Department of Pharmacy, The Women University, Multan 60000, Pakistan
| | - Tanzeela Awan
- Department of Pharmacy, The Women University, Multan 60000, Pakistan
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Abstract
Proteins are workhorses in the cell; they form stable and more often dynamic, transient protein-protein interactions, assemblies, and networks and have an intimate interplay with DNA and RNA. These network interactions underlie fundamental biological processes and play essential roles in cellular function. The proximity-dependent biotinylation labeling approach combined with mass spectrometry (PL-MS) has recently emerged as a powerful technique to dissect the complex cellular network at the molecular level. In PL-MS, by fusing a genetically encoded proximity-labeling (PL) enzyme to a protein or a localization signal peptide, the enzyme is targeted to a protein complex of interest or to an organelle, allowing labeling of proximity proteins within a zoom radius. These biotinylated proteins can then be captured by streptavidin beads and identified and quantified by mass spectrometry. Recently engineered PL enzymes such as TurboID have a much-improved enzymatic activity, enabling spatiotemporal mapping with a dramatically increased signal-to-noise ratio. PL-MS has revolutionized the way we perform proteomics by overcoming several hurdles imposed by traditional technology, such as biochemical fractionation and affinity purification mass spectrometry. In this review, we focus on biotin ligase-based PL-MS applications that have been, or are likely to be, adopted by the plant field. We discuss the experimental designs and review the different choices for engineered biotin ligases, enrichment, and quantification strategies. Lastly, we review the validation and discuss future perspectives.
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Affiliation(s)
- Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Carnegie Mass Spectrometry Facility, Carnegie Institution for Science, Stanford, California, USA
| | - Ruben Shrestha
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Sumudu S Karunadasa
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
| | - Pei-Qiao Xie
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA;
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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Shabbir S, Wang W, Nawaz M, Boruah P, Kulyar MFEA, Chen M, Wu B, Liu P, Dai Y, Sun L, Gou Q, Liu R, Hu G, Younis T, He M. Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress. Microb Cell Fact 2023; 22:88. [PMID: 37127628 PMCID: PMC10152622 DOI: 10.1186/s12934-023-02095-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023] Open
Abstract
Acetic acid and furfural (AF) are two major inhibitors of microorganisms during lignocellulosic ethanol production. In our previous study, we successfully engineered Zymomonas mobilis 532 (ZM532) strain by genome shuffling, but the molecular mechanisms of tolerance to inhibitors were still unknown. Therefore, this study investigated the responses of ZM532 and its wild-type Z. mobilis (ZM4) to AF using multi-omics approaches (transcriptomics, genomics, and label free quantitative proteomics). Based on RNA-Seq data, two differentially expressed genes, ZMO_RS02740 (up-regulated) and ZMO_RS06525 (down-regulated) were knocked out and over-expressed through CRISPR-Cas technology to investigate their roles in AF tolerance. Overall, we identified 1865 and 14 novel DEGs in ZM532 and wild-type ZM4. In contrast, 1532 proteins were identified in ZM532 and wild-type ZM4. Among these, we found 96 important genes in ZM532 involving acid resistance mechanisms and survival rates against stressors. Furthermore, our knockout results demonstrated that growth activity and glucose consumption of mutant strains ZM532∆ZMO_RS02740 and ZM4∆ZMO_RS02740 decreased with increased fermentation time from 42 to 55 h and ethanol production up to 58% in ZM532 than that in ZM532∆ZMO_RS02740. Hence, these findings suggest ZMO_RS02740 as a protective strategy for ZM ethanol production under stressful conditions.
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Affiliation(s)
- Samina Shabbir
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Department of Chemistry, The Women University Multan, Multan, Pakistan
| | - Weiting Wang
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Mohsin Nawaz
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, China
| | - Prerona Boruah
- School of Biotechnology and Bioinformatics, DY PATIL Deemed to Be University, Navi Mumbai, India
| | | | - Mao Chen
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Panting Liu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Yonghua Dai
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Lingling Sun
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Qiyu Gou
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Renbin Liu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Guoquan Hu
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041, People's Republic of China
| | - Tahira Younis
- Department of Biochemistry and Biotechnology, The Women University Multan, Multan, Pakistan
| | - Mingxiong He
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China.
- Chengdu National Agricultural Science and Technology Center, Chengdu, People's Republic of China.
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11
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Zheng L, Liu Q, Wu R, Zhu M, Dorjee T, Zhou Y, Gao F. The alteration of proteins and metabolites in leaf apoplast and the related gene expression associated with the adaptation of Ammopiptanthus mongolicus to winter freezing stress. Int J Biol Macromol 2023; 240:124479. [PMID: 37072058 DOI: 10.1016/j.ijbiomac.2023.124479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 04/20/2023]
Abstract
Ammopiptanthus mongolicus, an evergreen broad-leaved plant, can tolerate severe freezing stress (temperatures as low as -20 °C in winter). The apoplast is the space outside the plasma membrane that plays an important role in plant responses to environmental stress. Here, we investigated, using a multi-omics approach, the dynamic alterations in the levels of proteins and metabolites in the apoplast and related gene expression changes involved in the adaptation of A. mongolicus to winter freezing stress. Of the 962 proteins identified in the apoplast, the abundance of several PR proteins, including PR3 and PR5, increased significantly in winter, which may contribute to winter freezing-stress tolerance by functioning as antifreeze proteins. The increased abundance of the cell-wall polysaccharides and cell wall-modifying proteins, including PMEI, XTH32, and EXLA1, may enhance the mechanical properties of the cell wall in A. mongolicus. Accumulation of flavonoids and free amino acids in the apoplast may be beneficial for ROS scavenging and the maintenance of osmotic homeostasis. Integrated analyses revealed gene expression changes associated with alterations in the levels of apoplast proteins and metabolites. Our study improved the current understanding of the roles of apoplast proteins and metabolites in plant adaptation to winter freezing stress.
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Affiliation(s)
- Lamei Zheng
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Qi Liu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Rongqi Wu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Ming Zhu
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Tashi Dorjee
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yijun Zhou
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
| | - Fei Gao
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; Key Laboratory of Ecology and Environment in Minority Areas, Minzu University of China, National Ethnic Affairs Commission, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China.
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12
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Dwivedi S, Ahmad IZ. Evaluation of the effect of UV-B radiation on growth, photosynthetic pigment, and antioxidant enzymes of some cyanobacteria. ENVIRONMENTAL RESEARCH 2023; 218:114943. [PMID: 36463991 DOI: 10.1016/j.envres.2022.114943] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/17/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
The current study is focused on the effects of artificial UV-B radiation on growth, proteins, and pigments, as well as the activities of several enzymatic and non-enzymatic antioxidant enzymes in some cyanobacterial strains. Cultures were maintained at 25 °C ± 1 °C under a white fluorescent tube of intensity 30-40 μE m -2s-1 with a 14:10 light and dark cycle in the laboratory and analyzed at an interval of 25, 32, 39, 46, and 53 days. The test cultures were exposed to UV-B stress for 24 h at the same intervals. We found that exposure to UV-B showed increased production of phycocyanin and carotenoids in four strains, namely, Scytonema javanicum, Nostoc muscorum, Aphanothece naegeli, and Synechococcus elongates. We also look into the effects of UV-B radiation on the proline content, non-protein thiols, radical scavenging activity, ascorbic acid, and tocopherol, total flavonoid content (TFC), total phenolic content (TPC) on these strains. Variation in the non-enzymatic antioxidants and expression levels of enzymatic enzymes and reducing power activity as compared to the non-irradiated control was found. Our study showed that cyanobacteria impart prominent antioxidant and radical scavenging properties which facilitate the defence mechanism against UV-B induced cell damage.
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Affiliation(s)
- Sonam Dwivedi
- Natural Products Laboratory, Department of Bioengineering and Biosciences, Integral University, Dasauli, Kursi Road,Lucknow, 226026, Uttar Pradesh, India
| | - Iffat Zareen Ahmad
- Natural Products Laboratory, Department of Bioengineering and Biosciences, Integral University, Dasauli, Kursi Road,Lucknow, 226026, Uttar Pradesh, India.
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13
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Wilder SM, Barnes CL. Comparing the accuracy of protein measures for arthropods. JOURNAL OF INSECT PHYSIOLOGY 2023; 144:104470. [PMID: 36525989 DOI: 10.1016/j.jinsphys.2022.104470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Data on the protein content of arthropods can be useful for addressing a variety of ecological, behavioral, and physiological hypotheses. Yet, the most accurate method for measuring protein content (i.e., amino acid analysis) is expensive and the accuracy of less expensive measures of protein is unclear. We analyzed a diversity of arthropods to test for relationships between digestible protein content as measured by amino acid analysis and several common protein measures: crude protein, Bradford assay, BCA assay, and Lowry assay. In the full dataset, the closest relationship to the amino acid data was found for the Lowry assay and the average of the Bradford and Lowry assays. However, one species, Blattella germanica, appeared to be an outlier in some analyses. When the data were analyzed without B. germanica, the closest relationships to the amino acid data were found for the Lowry assay. Our results suggest that not all protein measures are equal in their ability to estimate amino acid content. Some arthropod species can also contain chemicals that interfere with the accuracy of protein assays. Given that it is unclear how often interfering compounds are found in invertebrates, it may be best to conduct multiple assays when analyzing the protein content of arthropods, especially the Bradford and Lowry assays.
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Affiliation(s)
- Shawn M Wilder
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA.
| | - Cody L Barnes
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK, USA
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14
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Christopher M, Sreeja-Raju A, Sankar M, Gokhale DV, Pandey A, Sukumaran RK. Lignocellulose degradation by Penicillium janthinellum enzymes is influenced by its variable secretome and a unique set of feedstock characteristics. BIORESOURCE TECHNOLOGY 2022; 365:128129. [PMID: 36252760 DOI: 10.1016/j.biortech.2022.128129] [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: 09/01/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Substrate characteristics and proteins that affect lignocellulose-hydrolysis by the hypercellulolytic fungus Penicillium janthinellum NCIM 1366 (PJ-1366) were investigated. The hydrolysis rate of PJ-1366 enzymes was very high, with upto 75 % of the reaction being completed in initial 4 h. Comparison of the hydrolytic efficiencies on differently pretreated biomass indicated that the greatest (negative) effect was imparted by lignin, suggesting that improving ligninase activity of the PJ-1366 enzymes may help to improve hydrolysis. Larger pore sizes and higher crystallinity of substrates, which favor enzyme penetration and processive hydrolysis, positively influenced hydrolysis efficiency. For alkali-pretreated substrates, 16 FPU/g of PJ-1366 cellulases released the sugar-equivalent of using 10 FPU/g of a commercial biomass hydrolyzing enzyme. By correlation analysis, 41 proteins, including 20 CAZymes were identified, whose abundance in the secretome positively correlated with the cellulase activities of the culture filtrate. These proteins may be considered as the primary drivers of FPase/CMCase/pNPGase/xylanase activity in PJ-1366.
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Affiliation(s)
- Meera Christopher
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Athiraraj Sreeja-Raju
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Meena Sankar
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | - Ashok Pandey
- Centre for Innovation & Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226 001, Uttar Pradesh, India; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun 248 007, Uttarakhand, India; Centre for Energy and Environmental Sustainability, Lucknow 226 029, Uttar Pradesh, India
| | - Rajeev K Sukumaran
- Biofuels and Biorefineries Section, Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Pappanamcode, Thiruvananthapuram 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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15
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Kim J, Ahn J, Ahn C. Characterization of novel bacteriocin produced by bacteriocinogenic Carnobacterium maltaromaticum isolated from raw milk. Microb Pathog 2022; 173:105872. [PMID: 36368602 DOI: 10.1016/j.micpath.2022.105872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
This study was designed to assess newly isolated bacteriocin-producing strain as potential food preservative. A bacteriocin producing lactic acid bacterium, named Carnobacterium maltaromatium KCA018, was screened from raw milk using deferred and spot-on-the-lawn assays. The crude cell free supernatant (CFS) was purified to obtain proteinaceous bacteriocin by ammonium sulfate precipitation (assigned as bacteriocin KCA) and tested for bacteriocin production, physical stability, antimicrobial activity, and bacteriocin-encoding gene detection. The growth curves of C. maltaromatium KCA018 reached late exponential phase after 15 h of incubation at 25 °C and 30 °C (Fig. 2). The maximum production of bacteriocin KCA was reached after 12 h of incubation at 25 °C, showing the antimicrobial activity of more than 3000 AU/ml against Listeria monocytogenes. The purified bacteriocin KCA was stable up to 67 °C for 30 min of exposure and between pH 4 and 7, showing more than 6000 AU/ml. The antibacterial activity of bacteriocin KCA was lost in the presence of pronase, proteinase K, and trypsin. Purified bacteriocin KCA showed higher antibacterial activity against Gram-positive bacteria than against Gram-negative bacteria. The CFS and purified bacteriocin KCA effectively inhibited the growth of L. monocytogenes ATCC 1911, E. faecalis ATCC 19433, and E. feacium ATCC 11576. The molecular weight of purified bacteriocin KCA was estimated at approximately 5 kDa. The positive amplification was observed for pisA and cbnBM1 with approximately between 100 and 200 bp. The newly identified bacteriocin can be a promising preservative for application in food.
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Affiliation(s)
- Junhwan Kim
- Department of Biomedical Science, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea; Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, Gangwon, 24341, Republic of Korea.
| | - Cheol Ahn
- Cell Biotech, Gimpo, Gyunggi, 10003, Republic of Korea
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16
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Barrett K, Zhao H, Hao P, Bacic A, Lange L, Holck J, Meyer AS. Discovery of novel secretome CAZymes from Penicillium sclerotigenum by bioinformatics and explorative proteomics analyses during sweet potato pectin digestion. Front Bioeng Biotechnol 2022; 10:950259. [PMID: 36185449 PMCID: PMC9523869 DOI: 10.3389/fbioe.2022.950259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Novel selective enzymatic refining of sweet potato processing residues requires judicious enzyme selection and enzyme discovery. We prepared a pectinaceous cell wall polysaccharide fraction from sweet potato using an enzymatic a treatment to preserve the natural linkages and substitutions. Polysaccharide composition and linkage analysis data confirmed the pectinaceous polysaccharide fraction to be a rhamnogalacturonan I-rich fraction with a high content of arabinogalactan Type I. We hypothesized that the post-harvest tuber pathogenic fungus Penicillium sclerotigenum would harbor novel enzymes targeting selective sweet potato pectin modification. As part of the study, we also report the first genome sequence of P. sclerotigenum. We incubated the sweet potato pectinaceous fraction with P. sclerotigenum. Using proteomics accompanied by CUPP-bioinformatics analysis, we observed induced expression of 23 pectin-associated degradative enzymes. We also identified six abundantly secreted, induced proteins that do not correspond to known CAZymes, but which we suggest as novel enzymes involved in pectin degradation. For validation, the predicted CUPP grouping of putative CAZymes and the exo-proteome data obtained for P. sclerotigenum during growth on sweet potato pectin were compared with proteomics and transcriptomics data reported previously for pectin-associated CAZymes from Aspergillus niger strain NRRL3. The data infer that P. sclerotigenum has the capacity to express several novel enzymes that may provide novel opportunities for sweet potato pectin modification and valorization of sweet potato starch processing residues. In addition, the methodological approach employed represents an integrative systematic strategy for enzyme discovery.
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Affiliation(s)
- Kristian Barrett
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Hai Zhao
- Chengdu Institute of Biology, Chinese Academy of Science, Chengdu, China
| | - Pengfei Hao
- La Trobe Institute for Agriculture and Food, La Trobe University, Melbourne, VIC, Australia
| | - Antony Bacic
- La Trobe Institute for Agriculture and Food, La Trobe University, Melbourne, VIC, Australia
| | - Lene Lange
- LLa BioEconomy, Research & Advisory, Valby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Anne S. Meyer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
- *Correspondence: Anne S. Meyer,
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17
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Adebayo IA, Habib MAH, Sarmiento ME, Acosta A, Yaacob NS, Ismail MN. Proteomic analysis of Malaysian Horseshoe crab (Tachypleus gigas) hemocytes gives insights into its innate immunity host defence system and other biological processes. PLoS One 2022; 17:e0272799. [PMID: 35947629 PMCID: PMC9365167 DOI: 10.1371/journal.pone.0272799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/26/2022] [Indexed: 11/18/2022] Open
Abstract
Horseshoe crabs are one of the most studied invertebrates due to their remarkable innate immunity mechanism and biological processes. In this work, the proteins of the lipopolysaccharides (LPS)-stimulated and non-stimulated hemocytes of Malaysian Tachypleus gigas were profiled using LC-MS/MS. A total of 154 proteins were identified in both types of samples. Additionally, seventy-seven proteins were commonly found in both conditions, while 52 and 25 proteins were uniquely found in the LPS-stimulated and non-stimulated hemocytes, respectively. ATP-dependent energy-generating proteins such as actins and BLTX actin-related proteins were detected in both stimulated and non-stimulated T. gigas hemocytes, but more of such proteins were found in the former type. Proteins such as tachylectin-2, coagulogen, c-reactive proteins, histones, hemocyanin, and DNA polymerase, which play key roles in the organism’s innate immunity, were differentially expressed in the hemocytes following LPS challenge. In conclusion, the proteins identified in the hemolymph of T. gigas are vital for the organism’s molecular functions, biological processes, and activation of innate immunity.
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Affiliation(s)
- Ismail Abiola Adebayo
- Faculty of Biomedical Sciences, Department of Microbiology and Immunology, Kampala International University, Ishaka, Bushenyi, Uganda
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
- Department of Clinical Biology, School of Medicine and Pharmacy, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
| | - Maria E. Sarmiento
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Nik Soriani Yaacob
- Department of Chemical Pathology, School of Medical Sciences, Universiti Sains Malaysia (USM), Kelantan, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Bayan Lepas, Pulau Pinang, Malaysia
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, USM, Pulau Pinang, Malaysia
- * E-mail:
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18
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Zhang D, Yang Z, Song X, Zhang F, Liu Y. TMT-based proteomic analysis of liquorice root in response to drought stress. BMC Genomics 2022; 23:524. [PMID: 35854220 PMCID: PMC9297632 DOI: 10.1186/s12864-022-08733-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Drought stress is a serious threat to land use efficiency and crop yields worldwide. Understanding the mechanisms that plants use to withstand drought stress will help breeders to develop drought-tolerant medicinal crops. Liquorice (Glycyrrhiza uralensis Fisch.) is an important medicinal crop in the legume family and is currently grown mostly in northwest China, it is highly tolerant to drought. Given this, it is considered an ideal crop to study plant stress tolerance and can be used to identify drought-resistant proteins. Therefore, to understand the effects of drought stress on protein levels of liquorice, we undertook a comparative proteomic analysis of liquorice seedlings grown for 10 days in soil with different relative water content (SRWC of 80%, 65%, 50% and 35%, respectively). We used an integrated approach of Tandem Mass Tag labeling in conjunction with LC-MS/MS. RESULTS A total of 7409 proteins were identified in this study, of which 7305 total proteins could be quantified. There were 837 differentially expressed proteins (DEPs) identified after different drought stresses. Compared with CK, 123 DEPs (80 up-regulated and 43 down-regulated) were found in LS; 353 DEPs (254 up-regulated and 99 down-regulated) in MS; and 564 DEPs (312 up-regulated and 252 down-regulated) in SS.The number of differentially expressed proteins increased with increasing water stress, and the number of up-regulated proteins was higher than that of down-regulated proteins in the different drought stress treatments compared with the CK. Used systematic bioinformatics analysis of these data to identify informative proteins we showed that osmolytes such as cottonseed sugars and proline accumulated under light drought stress and improved resistance. Under moderate and severe drought stress, oxidation of unsaturated fatty acids and accumulation of glucose and galactose increased in response to drought stress. Under moderate and severe drought stress synthesis of the terpene precursors, pentacene 2,3-epoxide and β-coumarin, was inhibited and accumulation of triterpenoids (glycyrrhetinic acid) was also affected. CONCLUSIONS These data provide a baseline reference for further study of the downstream liquorice proteome in response to drought stress. Our data show that liquorice roots exhibit specific response mechanisms to different drought stresses.
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Affiliation(s)
- Dong Zhang
- College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010011, China.,Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Zhongren Yang
- College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010011, China. .,Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Inner Mongolia Agricultural University, Hohhot, 010011, China.
| | - Xiaoqing Song
- College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010011, China.,Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Fenglan Zhang
- College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010011, China.,Inner Mongolia Key Laboratory of Wild Peculiar Vegetable Germplasm Resource and Germplasm Enhancement, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Yan Liu
- College of Horticultural and Plant Protection, Inner Mongolia Agricultural University, Hohhot, 010011, China.
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19
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Identification of Somatic Proteins in Haemonchus Contortus Infective Larvae (L 3) and Adults. Helminthologia 2022; 59:143-151. [PMID: 36118367 PMCID: PMC9444209 DOI: 10.2478/helm-2022-0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/05/2022] [Indexed: 11/26/2022] Open
Abstract
Haemonchus contortus is considered the most pathogenic nematode in sheep production systems based on grazing. Comparing infective larvae (L3) with adult parasites can lead to the identification of proteins that play an important role in parasite-host interactions. In this study, we report a list of H. contortus somatic proteins and made a comparative analysis of somatic proteins of L3 and adult worms. L3 and adult parasites were subjected to protein extraction and subsequently to peptide fractionation. Peptides were analysed by mass spectrometry and LC-MS/MS data analysis. Data analysis and search on SEQUEST and MASCOT against H. contortus from the WormBase ParaSite database resulted in the identification of 775 unique peptide sequences corresponding to 227 proteins at 1 % FDR. From these, 18 proteins were specific to L3 and 63 to adult parasites. The gene ontology (GO) enrichment analysis of the proteins specific to L3 and adult worms to gain insight into cellular components, molecular functions and biological processes that affect the parasite-host interaction showed some differences between the two parasite stages. The list of proteins found provides a database to identify target proteins that could be useful as biomarkers of the infection or in the generation of anthelmintic drugs that inhibit proteins essential for the establishment of the infection and the survival of adult parasites. They can also serve as new candidates for vaccine research.
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20
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Angiopathic activity of LRG1 is induced by the IL-6/STAT3 pathway. Sci Rep 2022; 12:4867. [PMID: 35318338 PMCID: PMC8938720 DOI: 10.1038/s41598-022-08516-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/07/2022] [Indexed: 12/14/2022] Open
Abstract
Leucine-rich α-2-glycoprotein 1 (LRG1) is a secreted glycoprotein that under physiological conditions is produced predominantly by the liver. In disease, its local induction promotes pathogenic neovascularisation while its inhibition leads to reduced dysfunctional angiogenesis. Here we examine the role of interleukin-6 (IL-6) in defective angiogenesis mediated by LRG1. IL-6 treatment induced LRG1 expression in endothelial cells and ex vivo angiogenesis cultures and promoted vascular growth with reduced mural cell coverage. In Lrg1−/− explants, however, IL-6 failed to stimulate angiogenesis and vessels exhibited improved mural cell coverage. IL-6 activated LRG1 transcription through the phosphorylation and binding of STAT3 to a conserved consensus site in the LRG1 promoter, the deletion of which abolished activation. Blocking IL-6 signalling in human lung endothelial cells, using the anti-IL6 receptor antibody Tocilizumab, significantly reduced LRG1 expression. Our data demonstrate that IL-6, through STAT3 phosphorylation, activates LRG1 transcription resulting in vascular destabilisation. This observation is especially timely in light of the potential role of IL-6 in COVID-19 patients with severe pulmonary microvascular complications, where targeting IL-6 has been beneficial. However, our data suggest that a therapy directed towards blocking the downstream angiopathic effector molecule LRG1 may be of greater utility.
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21
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Xu Y, Yan F, Zong Y, Li J, Gao H, Liu Y, Wang Y, Zhu Y, Wang Q. Proteomic and lipidomics analyses of high fatty acid AhDGAT3 transgenic soybean reveals the key lipase gene associated with the lipid internal mechanism. Genome 2022; 65:153-164. [PMID: 34995159 DOI: 10.1139/gen-2021-0043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vegetable oil is one of the most important components of human nutrition. Soybean (Glycine max) is an important oil crop worldwide and contains rich unsaturated fatty acids. Diacylglycerol acyltransferase (DGAT) is a key rate-limiting enzyme in the Kennedy pathway from diacylglycerol (DAG) to triacylglycerol (TAG). In this study, we conducted further research using T3 AhDGAT3 transgenic soybean. A high-performance gas chromatography flame ionization detector showed that oleic acid (18:1) content and total fatty acid content of transgenic soybean were significantly higher than those of the wild type (WT). However, linoleic acid (18:2) was much lower than that in the WT. For further mechanistic studies, 20 differentially expressed proteins (DEPs) and 119 differentially expressed metabolites (DEMs) were identified between WT (JACK) and AhDGAT3 transgenic soybean mature seeds using proteomic and lipidomics analyses. Combined proteomic and lipidomics analyses showed that the upregulation of the key DEP (lipase GDSL domain-containing protein) in lipid transport and metabolic process induced an increase in the total fatty acid and 18:1 composition, but a decrease in the 18:2 composition of fatty acids. Our study provides new insights into the deep study of molecular mechanism underlying the enhancement of fatty acids in transgenic soybeans, especially oleic acid and total fatty acid, which are enhanced by over-expression of AhDGAT3.
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Affiliation(s)
- Yang Xu
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Fan Yan
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Yu Zong
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Jingwen Li
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Han Gao
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Yajing Liu
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Ying Wang
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Youcheng Zhu
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
| | - Qingyu Wang
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
- College of Plant Science, Jilin University, No.5333 Xi'an Road, Changchun City, 130062, China
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22
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Wong EYL, Loh GOK, Goh CZ, Tan YTF, Ng SSM, Law KB, Cheah KY, Mohd HF, Peh KK. Sample preparation and quantification of polar drug, allopurinol, in human plasma using LCMSMS. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2022; 28:35-46. [PMID: 35668610 DOI: 10.1177/14690667221105837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A fast, selective and reproducible LC-MS/MS method with simple sample preparation was developed and validated for a polar compound, allopurinol in human plasma, using acyclovir as internal standard (IS). Chromatographic separation was achieved using Agilent Poroshell 120 EC-C18 (100 × 2.1 mmID, 2.7 µm) analytical column. The mobile phase was comprised of 0.1%v/v formic acid-methanol (95:05; v/v), at a flow rate of 0.45 mL/min. The effect of different protein precipitation agents used in sample preparation such as methanol, acetonitrile, a mixture of acetonitrile-methanol and a mixture of acetonitrile-acetone were evaluated to optimize the extraction efficiency of allopurinol and IS. The use of acetone-acetonitrile (50:50, v/v) as protein precipitating agent shortened the sample preparation time and improved the recovery of allopurinol to above 93%. The IS-normalised matrix factors at two concentration levels were 1.0, with CV of 5.1% and 4.2%. Allopurinol in plasma was stable at benchtop for 24 h, in autosampler tray for 48 h, in instrumentation room for 48 h, in freezer after 7 freeze-thaw cycles and in freezer for 140 days. Allopurinol stock standard solutions were stable for 140 days at room temperature and in the chiller. The short sample run time of the validated bioanalytical method allowed high throughput analysis of plasma samples in pharmacokinetic study of an allopurinol formulation. The robustness and reproducibility of the bioanalytical method was reaffirmed through incurred sample reanalysis (ISR).
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Affiliation(s)
| | | | - Chen Zhu Goh
- 619929Bioxis Sdn Bhd, Simpang Ampat, Pulau Pinang, Malaysia
| | | | - Sharon Shi Min Ng
- Centre for Clinical Trial, Institute for Clinical Research, 576396Ampang Hospital, Ministry of Health, Ampang, Selangor, Malaysia
| | - Kian Boon Law
- Centre for Clinical Trial, Institute for Clinical Research, 576396Ampang Hospital, Ministry of Health, Ampang, Selangor, Malaysia
| | - Kit Yee Cheah
- Centre for Clinical Trial, Institute for Clinical Research, 576396Ampang Hospital, Ministry of Health, Ampang, Selangor, Malaysia
| | - Hani Farhana Mohd
- Centre for Clinical Trial, Institute for Clinical Research, 576396Ampang Hospital, Ministry of Health, Ampang, Selangor, Malaysia
| | - Kok Khiang Peh
- School of Pharmaceutical Sciences, 26689Universiti Sains Malaysia, Minden, Penang, Malaysia
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23
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Zheng W, Yang P, Sun C, Zhang Y. Comprehensive comparison of sample preparation workflows for proteomics. Mol Omics 2022; 18:555-567. [DOI: 10.1039/d2mo00076h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mass spectrometry-based proteomics experiments can be subject to a large variability, which forms an obstacle to obtaining deep and accurate protein identification. Here, to obtain an optimal sample preparation workflow...
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24
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Does the Food Ingredient Pectin Provide a Risk for Patients Allergic to Non-Specific Lipid-Transfer Proteins? Foods 2021; 11:foods11010013. [PMID: 35010137 PMCID: PMC8750200 DOI: 10.3390/foods11010013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/27/2022] Open
Abstract
Pectin, a dietary fiber, is a polysaccharide that is widely used in food industry as a gelling agent. In addition, prebiotic and beneficial immunomodulatory effects of pectin have been demonstrated, leading to increased importance as food supplement. However, as cases of anaphylactic reactions after consumption of pectin-supplemented foods have been reported, the present study aims to evaluate the allergy risk of pectin. This is of particular importance since most of the pectin used in the food industry is extracted from citrus or apple pomace. Both contain several allergens such as non-specific lipid transfer proteins (nsLTPs), known to induce severe allergic reactions, which could impair the use of pectins in nsLTP allergic patients. Therefore, the present study for the first time was performed to analyze residual nsLTP content in two commercial pectins using different detection methods. Results showed the analytical sensitivity was diminished by the pectin structure. Finally, spiking of pectin with allergenic peach nsLTP Pru p 3 led to the conclusion that the potential residual allergen content in both pectins is below the threshold to induce anaphylactic reactions in nsLTP-allergic patients. This data suggests that consumption of the investigated commercial pectin products provides no risk for inducing severe reactions in nsLTP-allergic patients.
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25
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Kischkel B, Boniche-Alfaro C, Menezes IDG, Rossi SA, Angeli CB, de Almeida SR, Palmisano G, Lopes-Bezerra L, Nosanchuk JD, Taborda CP. Immunoproteomic and Immunopeptidomic Analyses of Histoplasma capsulatum Reveal Promiscuous and Conserved Epitopes Among Fungi With Vaccine Potential. Front Immunol 2021; 12:764501. [PMID: 34880863 PMCID: PMC8645968 DOI: 10.3389/fimmu.2021.764501] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/29/2021] [Indexed: 12/27/2022] Open
Abstract
As there are more than 6 million human deaths due to mycoses each year, there is an urgent need to develop fungal vaccines. Moreover, given the similarities among pathogenic fungi, it may be possible to create a multi-fungi vaccine. In this study, we combined immunoproteomic and immunopeptidomic methods, for which we have adapted a technique based on co-immunoprecipitation (Co-IP) that made it possible to map Histoplasma capsulatum epitopes for the first time in a natural context using murine dendritic cells (DCs) and macrophages (Mφ). Although polysaccharide epitopes exist, this research focused on mapping protein epitopes as these are more immunogenic. We used different algorithms to screen proteins and peptides identified by two-dimensional electrophoresis (2-D) and Co-IP. Seventeen proteins were revealed by 2-D gels, and 45 and 24 peptides from distinct proteins were presented by DCs and Mφ, respectively. We then determined which epitopes were restricted to MHC-I and II from humans and mice and showed high promiscuity, but lacked identity with human proteins. The 4 most promising peptides were synthesized, and the peptides with and without incorporation into glucan particles induced CD4+ and CD8+ T cell proliferation and produced a Th1 and Th17 response marked by the secretion of high levels of IFN-γ, IL-17 and IL-2. These epitopes were from heat shock protein 60, enolase, and the ATP-dependent molecular chaperone HSC82, and they each have a high degree of identity with proteins expressed by other medically important pathogenic fungi. Thus, the epitopes described in this study have the potential for use in the development of vaccines that could result in cross-protection among fungal species.
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Affiliation(s)
- Brenda Kischkel
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Camila Boniche-Alfaro
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Isabela de Godoy Menezes
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Suelen Andreia Rossi
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.,Department of Dermatology, Tropical Medicine Institute, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | - Claudia Blanes Angeli
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Sandro Rogério de Almeida
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Leila Lopes-Bezerra
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil
| | - Joshua D Nosanchuk
- Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, New York, NY, United States.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY, United States
| | - Carlos Pelleschi Taborda
- Department of Microbiology, Biomedical Sciences Institute, University of São Paulo, São Paulo, Brazil.,Department of Dermatology, Tropical Medicine Institute, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
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26
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Bai C, Zheng Y, Watkins CB, Fu A, Ma L, Gao H, Yuan S, Zheng S, Gao L, Wang Q, Meng D, Zuo J. Revealing the Specific Regulations of Brassinolide on Tomato Fruit Chilling Injury by Integrated Multi-Omics. Front Nutr 2021; 8:769715. [PMID: 34926549 PMCID: PMC8681340 DOI: 10.3389/fnut.2021.769715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/04/2021] [Indexed: 12/28/2022] Open
Abstract
Tomato fruit is susceptible to chilling injury (CI) when stored at low temperatures, limiting its storage potential, and resulting in economic loss if inappropriate temperatures are used. Brassinolide (BR) is a plant growth regulator that is known to decrease the susceptibility of fruit to CI. In this study, transcriptome, metabolome, and proteome analysis revealed the regulation mechanism of BR treatment in alleviating tomato fruit CI. The results showed that the differentially expressed metabolites mainly included amino acids, organic acids, carbohydrates, and lipids. Differentially expressed genes (DEGs) were involved in plant cold stress response (HSFA3, SHSP, and TPR), fruit redox process (POD, PAL, and LOX), related to the fruit texture (CESA, β-Gal, and PAE), plant hormone signal transduction (ACS3, ARF, and ERF,), transcription factors (TCP, bHLH, GATA). Moreover, differentially expressed proteins were associated with fruit texture (CESA, PE, PL, and CHI), plant oxidation processes (LOX, GPX, CAT, and POD), plant cold stress response (HSF, HSP20, HSP70, and HSP90B), plant hormone signal transduction (BSK1 and JAR1) and transcription factors (WRKY and MYB). Our study showed that BR alleviates CI symptoms of tomato fruit by regulating LOX in the α-linolenic acid metabolism pathway, enhancing jasmonic acid-CoA (JA-CoA) synthesis, inhibiting cell wall and membrane lipid damage. The results provided a theoretical basis for further study on the CI mechanism of tomato fruit.
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Affiliation(s)
- Chunmei Bai
- Key Laboratory of Vegetable Post-harvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
| | - Yanyan Zheng
- Key Laboratory of Vegetable Post-harvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Christopher B. Watkins
- School of Integrative Plant Science, Horticulture Section, College of Agriculture and Life Science, Cornell University, Ithaca, NY, United States
| | - Anzhen Fu
- Key Laboratory of Vegetable Post-harvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Lili Ma
- Key Laboratory of Vegetable Post-harvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - HongWu Gao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
| | - Shuzhi Yuan
- Key Laboratory of Vegetable Post-harvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shufang Zheng
- Key Laboratory of Vegetable Post-harvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Lipu Gao
- Key Laboratory of Vegetable Post-harvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qing Wang
- Key Laboratory of Vegetable Post-harvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
| | - Jinhua Zuo
- Key Laboratory of Vegetable Post-harvest Processing, Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Institute of Agri-Food Processing and Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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27
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Xu Y, Yan F, Liu Y, Wang Y, Gao H, Zhao S, Zhu Y, Wang Q, Li J. Quantitative proteomic and lipidomics analyses of high oil content GmDGAT1-2 transgenic soybean illustrate the regulatory mechanism of lipoxygenase and oleosin. PLANT CELL REPORTS 2021; 40:2303-2323. [PMID: 34427748 DOI: 10.1007/s00299-021-02768-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Proteomic and lipidomics analyses of WT and GmDGAT1-2 transgenic soybeans showed that GmDGAT1-2 over-expression induced lipoxygenase down-regulatation and oleoin up-regulatation, which significantly changed the compositions and total fatty acid. The main goal of soybean breeding is to increase the oil content. Diacylglycerol acyltransferase (DGAT) is a key rate-limiting enzyme in fatty acid metabolism and may regulate oil content. Herein, 10 GmDGAT genes were isolated from soybean and transferred into wild-type (WT) Arabidopsis. The total fatty acid was 1.2 times higher in T3 GmDGAT1-2 transgenic Arabidopsis seeds than in WT. Therefore, GmDGAT1-2 was transferred into WT soybean (JACK), and four T3 transgenic soybean lines were obtained. The results of high-performance gas chromatography and Soxhlet extractor showed that, compared with those of JACK, oleic acid (18:1), and total fatty acid levels in transgenic soybean plants were much higher, but linoleic acid (18:2) was lower than WT. Palmitic acid (16:0), stearic acid (18:0), and linolenic acid (18:3) were not significantly different. For mechanistic studies, 436 differentially expressed proteins (DEPs) and 180 differentially expressed metabolites (DEMs) were identified between WT (JACK) and transgenic soybean pods using proteomic and lipidomics analyses. Four lipoxygenase proteins were down-regulated in linoleic acid metabolism while four oleosin proteins were up-regulated in the final oil formation. The results showed an increase in the total fatty acid and 18:1 composition, and a decrease in the 18:2 composition of fatty acid. Our study brings new insights into soybean genetic transformation and the deep study of molecular mechanism that changes the total fatty acid, 18:1, and 18:2 compositions in GmDGAT1-2 transgenic soybean.
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Affiliation(s)
- Yang Xu
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Fan Yan
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Yajing Liu
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Ying Wang
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Han Gao
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Shihui Zhao
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Youcheng Zhu
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China
| | - Qingyu Wang
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China.
| | - Jingwen Li
- Jilin Key Laboratory for Crop Genetic Engineering, College of Plant Science, Jilin University, Changchun, 130062, China.
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28
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Zhang X, Luo W, Yao Y, Luo X, Han C, Zhong Y, Zhang B, Li D, Han L, Huang S, Greisen P, Shang Y. Enhanced chemoselectivity of a plant cytochrome P450 through protein engineering of surface and catalytic residues. ABIOTECH 2021; 2:215-225. [PMID: 36303887 PMCID: PMC9590459 DOI: 10.1007/s42994-021-00056-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/07/2021] [Indexed: 10/31/2022]
Abstract
Cytochrome P450s (P450s) are the most versatile catalysts utilized by plants to produce structurally and functionally diverse metabolites. Given the high degree of gene redundancy and challenge to functionally characterize plant P450s, protein engineering is used as a complementary strategy to study the mechanisms of P450-mediated reactions, or to alter their functions. We previously proposed an approach of engineering plant P450s based on combining high-accuracy homology models generated by Rosetta combined with data-driven design using evolutionary information of these enzymes. With this strategy, we repurposed a multi-functional P450 (CYP87D20) into a monooxygenase after redesigning its active site. Since most plant P450s are membrane-anchored proteins that are adapted to the micro-environments of plant cells, expressing them in heterologous hosts usually results in problems of expression or activity. Here, we applied computational design to tackle these issues by simultaneous optimization of the protein surface and active site. After screening 17 variants, effective substitutions of surface residues were observed to improve both expression and activity of CYP87D20. In addition, the identified substitutions were additive and by combining them a highly efficient C11 hydroxylase of cucurbitadienol was created to participate in the mogrol biosynthesis. This study shows the importance of considering the interplay between surface and active site residues for P450 engineering. Our integrated strategy also opens an avenue to create more tailoring enzymes with desired functions for the metabolic engineering of high-valued compounds like mogrol, the precursor of natural sweetener mogrosides. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-021-00056-z.
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Affiliation(s)
- Xiaopeng Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
| | - Wei Luo
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500 China
| | - Yinying Yao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China.,National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xuming Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
| | - Chao Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yang Zhong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China.,Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of Ministry of Agriculture, Sino-Dutch Joint Lab of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Bo Zhang
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500 China
| | - Dawei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
| | - Lida Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China
| | - Per Greisen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518116 China.,Novo Nordisk Research Center Seattle Inc, Seattle, WA 98109 USA
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The CAAS-YNNU-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650500 China
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Sagu ST, Huschek G, Homann T, Rawel HM. Effect of Sample Preparation on the Detection and Quantification of Selected Nuts Allergenic Proteins by LC-MS/MS. Molecules 2021; 26:4698. [PMID: 34361856 PMCID: PMC8348345 DOI: 10.3390/molecules26154698] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 11/20/2022] Open
Abstract
The detection and quantification of nut allergens remains a major challenge. The liquid chroma-tography tandem mass spectrometry (LC-MS/MS) is emerging as one of the most widely used methods, but sample preparation prior to the analysis is still a key issue. The objective of this work was to establish optimized protocols for extraction, tryptic digestion and LC-MS analysis of almond, cashew, hazelnut, peanut, pistachio and walnut samples. Ammonium bicar-bonate/urea extraction (Ambi/urea), SDS buffer extraction (SDS), polyvinylpolypyrroli-done (PVPP) extraction, trichloroacetic acid/acetone extraction (TCA/acetone) and chloro-form/methanol/sodium chloride precipitation (CM/NaCl) as well as the performances of con-ventional tryptic digestion and microwave-assisted breakdown were investigated. Overall, the protein extraction yields ranged from 14.9 ± 0.5 (almond extract from CM/NaCl) to 76.5 ± 1.3% (hazelnut extract from Ambi/urea). Electrophoretic profiling showed that the SDS extraction method clearly presented a high amount of extracted proteins in the range of 0-15 kDa, 15-35 kDa, 35-70 kDa and 70-250 kDa compared to the other methods. The linearity of the LC-MS methods in the range of 0 to 0.4 µg equivalent defatted nut flour was assessed and recovery of internal standards GWGG and DPLNV(d8)LKPR ranged from 80 to 120%. The identified bi-omarkers peptides were used to relatively quantifier selected allergenic protein form the inves-tigated nut samples. Considering the overall results, it can be concluded that SDS buffer allows a better protein extraction from almond, peanut and walnut samples while PVPP buffer is more appropriate for cashew, pistachio and hazelnut samples. It was also found that conventional overnight digestion is indicated for cashew, pistachio and hazelnut samples, while microwave assisted tryptic digestion is recommended for almond, hazelnut and peanut extracts.
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Affiliation(s)
- Sorel Tchewonpi Sagu
- Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany; (S.T.S.); (T.H.)
| | - Gerd Huschek
- GV-Institut für Getreideverarbeitung GmbH, Arthur-Scheunert-Allee 40/41, 14558 Nuthetal, Germany;
| | - Thomas Homann
- Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany; (S.T.S.); (T.H.)
| | - Harshadrai M. Rawel
- Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany; (S.T.S.); (T.H.)
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30
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Vighi IL, Seixas Neto A, Sousa GF, Carvalho JO, da Silva Pinto L. Standardization of a protein extraction protocol for the proteomic analysis of the leaves of
Oryza sativa
L. cv. BRS AG. SEPARATION SCIENCE PLUS 2021. [DOI: 10.1002/sscp.202100019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Isabel Lopes Vighi
- Postgraduate program in Biotechnology, Bioinformatics, and Proteomics Laboratory (BioPro Lab.), Technological Development Center Federal University of Pelotas Capão do Leão Brazil
| | - Amilton Seixas Neto
- Postgraduate Program in Microbiology and Parasitology (PPGMPar) Technological Development Center Federal University of Pelotas Capão do Leão Brazil
| | - Guilherme Feijó Sousa
- Postgraduate program in Biotechnology, Bioinformatics, and Proteomics Laboratory (BioPro Lab.), Technological Development Center Federal University of Pelotas Capão do Leão Brazil
| | - Juliana Oliveira Carvalho
- Postgraduate program in Biotechnology, Bioinformatics, and Proteomics Laboratory (BioPro Lab.), Technological Development Center Federal University of Pelotas Capão do Leão Brazil
| | - Luciano da Silva Pinto
- Postgraduate program in Biotechnology, Bioinformatics, and Proteomics Laboratory (BioPro Lab.), Technological Development Center Federal University of Pelotas Capão do Leão Brazil
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31
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Optimization of Protein Isolation and Label-Free Quantitative Proteomic Analysis in Four Different Tissues of Korean Ginseng. PLANTS 2021; 10:plants10071409. [PMID: 34371612 PMCID: PMC8309323 DOI: 10.3390/plants10071409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022]
Abstract
Korean ginseng is one of the most valuable medicinal plants worldwide. However, our understanding of ginseng proteomics is largely limited due to difficulties in the extraction and resolution of ginseng proteins because of the presence of natural contaminants such as polysaccharides, phenols, and glycosides. Here, we compared four different protein extraction methods, namely, TCA/acetone, TCA/acetone-MeOH/chloroform, phenol-TCA/acetone, and phenol-MeOH/chloroform methods. The TCA/acetone-MeOH/chloroform method displayed the highest extraction efficiency, and thus it was used for the comparative proteome profiling of leaf, root, shoot, and fruit by a label-free quantitative proteomics approach. This approach led to the identification of 2604 significantly modulated proteins among four tissues. We could pinpoint differential pathways and proteins associated with ginsenoside biosynthesis, including the methylerythritol 4-phosphate (MEP) pathway, the mevalonate (MVA) pathway, UDP-glycosyltransferases (UGTs), and oxidoreductases (CYP450s). The current study reports an efficient and reproducible method for the isolation of proteins from a wide range of ginseng tissues and provides a detailed organ-based proteome map and a more comprehensive view of enzymatic alterations in ginsenoside biosynthesis.
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32
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Comparative Analysis of Universal Protein Extraction Methodologies for Screening of Lipase Activity from Agricultural Products. Catalysts 2021. [DOI: 10.3390/catal11070816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Protein extraction techniques are absolutely required for the research of biological catalysts. The present study compared four universal protein extraction methodologies (ammonium sulfate precipitation, TCA/acetone precipitation, and two commercial kits) to provide practical information on protein extraction in order to discover a novel lipase in agricultural products. Yields of protein extraction from 24 domestic agricultural products and their specific activities were evaluated and compared with each other. TCA/acetone precipitation showed a relatively higher extraction yield (on average, 3.41 ± 1.08 mg protein/0.1 g sample) in crude protein extraction, whereas the Pierce™ Plant Total Protein Extraction Kit showed the highest specific lipase activity on average in both spectrophotometric (266.61 ± 235.78 μU/mg protein) and fluorometric (41.52 ± 32.63 μU/mg protein) assays. Our results suggest that commercial kits for the rapid extraction of soluble functional proteins would be a better choice than conventional precipitation techniques to perform the high-throughput screening of enzyme activity from plant sources. Finally, several agricultural products such as cordyceps, pepper, bracken, and hemp, all of which exhibited an excellent specific lipase activity, were proposed as promising candidates for a source of novel lipases.
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33
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Quantification of Acyl-Acyl Carrier Proteins for Fatty Acid Synthesis Using LC-MS/MS. Methods Mol Biol 2021; 2295:219-247. [PMID: 34047980 DOI: 10.1007/978-1-0716-1362-7_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The fatty acid biosynthetic cycle is predicated on an acyl carrier protein (ACP) scaffold where two carbon acetyl groups are added in a chain elongation process through a series of repeated enzymatic steps. The chain extension is terminated by hydrolysis with a thioesterase or direct transfer of the acyl group to a glycerophospholipid by an acyltransferase. Methods for analysis of the concentrations of acyl chains attached to ACPs are lacking but would be informative for studies in lipid metabolism. We describe a method to profile and quantify the levels of acyl-ACPs in plants, bacteria and mitochondria of animals and fungi that represent Type II fatty acid biosynthetic systems. ACPs of Type II systems have a highly conserved Asp-Ser-Leu-Asp (DSLD) amino acid sequence at the attachment site for 4'-phosphopantetheinyl arm carrying the acyl chain. Three amino acids of the conserved sequence can be cleaved away from the remainder of the protein using an aspartyl protease. Thus, partially purified protein can be enzymatically hydrolyzed to produce an acyl chain linked to a tripeptide via the 4'-phosphopantetheinyl group. After ionization and fragmentation, the corresponding fragment ion is detected by a triple quadrupole mass spectrometer using a multiple reaction monitoring method. 15N isotopically labeled acyl-ACPs generated in high amounts are used with an isotope dilution strategy to quantify the absolute levels of each acyl group attached to the acyl carrier protein scaffold.
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34
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Jin D, Liu H, Bu L, Ke Q, Li Z, Han W, Zhu S, Liu C. Comparative Analysis of Whey Proteins in Human Milk Using a Data-Independent Acquisition Proteomics Approach during the Lactation Period. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:4319-4330. [PMID: 33788563 DOI: 10.1021/acs.jafc.1c00186] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Human milk (HM) is the primary source of nutrients and bioactive components that supports the growth and development of infants. However, the proteins present in human milk may change depending on the period of lactation. In this light, the objective of the present study was to evaluate the effect of lactation period on HM utilizing a data-independent acquisition (DIA) approach to identify the differences in HM whey protein proteomes. As part of the study, whey proteins of January, February, and June in human milk were studied. The results identified a total of 1563 proteins in HM whey proteins of which 114 groups were subunits of differentially expressed proteins as revealed by cluster analysis. Protein expression was observed to be affected by the period of lactation with expression levels of plasminogen, thrombospondin-1, and tenascin higher during January, keratin, type I cytoskeletal 9 highest in February, and transcobalamin-1 highest in June. The results of this study contribute to expand our understanding of the human whey proteome but also provide strong evidence for the nutritional difference of HM during different lactation periods.
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Affiliation(s)
- Dengpeng Jin
- The Key Laboratory of Food Quality and Safety of Guangdong Province, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Huan Liu
- The Key Laboratory of Food Quality and Safety of Guangdong Province, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Lingling Bu
- The Key Laboratory of Food Quality and Safety of Guangdong Province, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Qianhua Ke
- The Key Laboratory of Food Quality and Safety of Guangdong Province, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhongyi Li
- The Key Laboratory of Food Quality and Safety of Guangdong Province, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Wenna Han
- The Key Laboratory of Food Quality and Safety of Guangdong Province, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Siyu Zhu
- The Key Laboratory of Food Quality and Safety of Guangdong Province, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Chunhong Liu
- The Key Laboratory of Food Quality and Safety of Guangdong Province, College of Food Science, South China Agricultural University, Guangzhou 510642, China
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35
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Alberton D, Valdameri G, Moure VR, Monteiro RA, Pedrosa FDO, Müller-Santos M, de Souza EM. What Did We Learn From Plant Growth-Promoting Rhizobacteria (PGPR)-Grass Associations Studies Through Proteomic and Metabolomic Approaches? FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.607343] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Plant growth stimulation by microorganisms that interact in a mutually beneficial manner remains poorly understood. Understanding the nature of plant-bacteria interactions may open new routes for plant productivity enhancement, especially cereal crops consumed by humans. Proteomic and metabolomic analyses are particularly useful for elucidating these mechanisms. A complete depiction of these mechanisms will prompt researchers to develop more efficient plant-bacteria associations. The success of microorganisms as biofertilizers may replace the current massive use of chemical fertilizers, mitigating many environmental and economic issues. In this review, we discuss the recent advances and current state of the art in proteomics and metabolomics studies involving grass-bacteria associations. We also discuss essential subjects involved in the bacterial plant-growth promotion, such, nitrogen fixation, plant stress, defense responses, and siderophore production.
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36
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Burdějová L, Moravcová D, Strouhalová D, Lunerová K. Pressurized water extraction - the fast and efficient method for isolation of bioactive proteins from Viscum album leaves. J Pharm Biomed Anal 2020; 195:113850. [PMID: 33429253 DOI: 10.1016/j.jpba.2020.113850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 10/22/2022]
Abstract
New strategies for the fast, efficient, and environmentally friendly extraction of proteins are required to isolate desired bioactive compounds from a technological point of view. In this study, utilization of the pressurized water extraction (PWE) at low temperature (40 °C) for isolation of mistletoe proteins was investigated. PWE effectiveness, based on protein fingerprints, were compared with those obtained by conventional extractions using 10 mmol L-1 Tris-HCl buffer pH 8.3, 50 mmol L-1 phosphate buffer pH 7, or deionized water. The extracts were precipitated using acetone, trichloroacetic acid (TCA), and 20% (w/v) TCA/acetone and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. PWE was more or equally efficient for isolation of mistletoe proteins than evaluated conventional extraction methods. The proteomic analysis combining mass spectrometry and database searching confirmed the presence of 35 proteins in PWE extracts precipitated by acetone, which was the most compounds identified from all studied extracts. The PWE high extraction power was revealed for multiple viscotoxin isoforms and specific enzymes indispensable for the synthesis of terpenes.
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Affiliation(s)
- Lenka Burdějová
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Veveří 97, 602 00 Brno, Czech Republic.
| | - Dana Moravcová
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Veveří 97, 602 00 Brno, Czech Republic.
| | - Dana Strouhalová
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Veveří 97, 602 00 Brno, Czech Republic.
| | - Kamila Lunerová
- State Office for Nuclear Safety of the Czech Republic, The National Institute for Nuclear, Chemical and Biological Protection, Kamenná 71, 262 31 Milín, Czech Republic.
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37
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Perez-Perri JI, Noerenberg M, Kamel W, Lenz CE, Mohammed S, Hentze MW, Castello A. Global analysis of RNA-binding protein dynamics by comparative and enhanced RNA interactome capture. Nat Protoc 2020; 16:27-60. [PMID: 33208978 DOI: 10.1038/s41596-020-00404-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/24/2020] [Indexed: 02/06/2023]
Abstract
Interactions between RNA-binding proteins (RBPs) and RNAs are critical to cell biology. However, methods to comprehensively and quantitatively assess these interactions within cells were lacking. RNA interactome capture (RIC) uses in vivo UV crosslinking, oligo(dT) capture, and proteomics to identify RNA-binding proteomes. Recent advances have empowered RIC to quantify RBP responses to biological cues such as metabolic imbalance or virus infection. Enhanced RIC exploits the stronger binding of locked nucleic acid (LNA)-containing oligo(dT) probes to poly(A) tails to maximize RNA capture selectivity and efficiency, profoundly improving signal-to-noise ratios. The subsequent analytical use of SILAC and TMT proteomic approaches, together with high-sensitivity sample preparation and tailored statistical data analysis, substantially improves RIC's quantitative accuracy and reproducibility. This optimized approach is an extension of the original RIC protocol. It takes 3 d plus 2 weeks for proteomics and data analysis and will enable the study of RBP dynamics under different physiological and pathological conditions.
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Affiliation(s)
| | - Marko Noerenberg
- Department of Biochemistry, University of Oxford, Oxford, UK.,MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, Scotland, UK
| | - Wael Kamel
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Caroline E Lenz
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, Oxford, UK.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK.,The Rosalind Franklin Institute, Oxfordshire, UK
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, Oxford, UK. .,MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, Scotland, UK.
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Iles RK, Zmuidinaite R, Iles JK, Carnell G, Sampson A, Heeney JL. Development of a Clinical MALDI-ToF Mass Spectrometry Assay for SARS-CoV-2: Rational Design and Multi-Disciplinary Team Work. Diagnostics (Basel) 2020; 10:E746. [PMID: 32987950 PMCID: PMC7600155 DOI: 10.3390/diagnostics10100746] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic caused by the SARS-CoV-2 coronavirus has stretched national testing capacities to breaking points in almost all countries of the world. The need to rapidly screen vast numbers of a country's population in order to control the spread of the infection is paramount. However, the logistical requirement for reagent supply (and associated cost) of RT-PCR based testing (the current front-line test) have been hugely problematic. Mass spectrometry-based methods using swab and gargle samples have been reported with promise, but have not approached the task from a systematic analysis of the entire diagnostic process. Here, the pipeline from sample processing, the biological characteristics of the pathogen in human biofluid, the downstream bio- and physical-chemistry and the all-important data processing with clinical interpretation and reporting, are carefully compiled into a single high-throughput and reproducible rapid process. Utilizing MALDI-ToF mass spectrometric detection to viral envelope glycoproteins in a systems biology-multidisciplinary team approach, we have achieved a multifaceted clinical MALDI ToF MS screening test, primarily (but not limited to) SARS-CoV-2, with direct application to other future epidemics/pandemics that may arise. The clinical information generated not only includes SARS-CoV-2 coronavirus detection-(Spike protein fragments S1, S2b, S2a peaks), but other respiratory viral infections detected as well as an assessment of generalised oral upper respiratory immune response (elevated total Ig light chain peak) and a measure of the viral immune response (elevated intensity of IgA heavy chain peak). The advantages of the method include; (1) ease of sampling, (2) speed of analysis, and much reduced cost of testing. These features reveal the diagnostic utility of MALDI-ToF mass spectrometry as a powerful and economically attractive global solution.
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Affiliation(s)
- Ray K. Iles
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
- NISAD, Medicon Village, SE-223 81 Lund, Sweden
| | - Raminta Zmuidinaite
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Jason K. Iles
- MAPSciences the iLAB, Stannard Way, Bedford MK44 3RZ, UK; (R.Z.); (J.K.I.)
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - George Carnell
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Alex Sampson
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
| | - Jonathan L. Heeney
- Laboratory of Viral Zoonotics, Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK; (G.C.); (A.S.); (J.L.H.)
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Nickerson JL, Doucette AA. Rapid and Quantitative Protein Precipitation for Proteome Analysis by Mass Spectrometry. J Proteome Res 2020; 19:2035-2042. [DOI: 10.1021/acs.jproteome.9b00867] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jessica L. Nickerson
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alan A. Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
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40
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Yadav S, Srivastava A, Biswas S, Chaurasia N, Singh SK, Kumar S, Srivastava V, Mishra Y. Comparison and optimization of protein extraction and two-dimensional gel electrophoresis protocols for liverworts. BMC Res Notes 2020; 13:60. [PMID: 32028996 PMCID: PMC7006083 DOI: 10.1186/s13104-020-4929-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/28/2020] [Indexed: 12/25/2022] Open
Abstract
Objective Liverworts possess historical adaptive strategies for abiotic stresses because they were the first plants that shifted from water to land. Proteomics is a state-of-the-art technique that can capture snapshots of events occurring at the protein level in many organisms. Herein, we highlight the comparison and optimization of an effective protein extraction and precipitation protocol for two-dimensional gel electrophoresis (2-DE) of liverworts. Results We compared three different protein extraction methods, i.e.,1.5 M Tris–HCl (pH 8.8), 50 mM Tris–HCl (pH 7.5), and polyvinylpolypyrrolidone (PVPP) extraction, followed by three precipitation methods, i.e., 80% ethanol, 80% acetone, and 20% tricholoroacetic acid (TCA)–acetone, in a liverwort Dumortiera hirsuta. Among these methods, 50 mM Tris–HCl (pH 7.5) extraction, followed by 20% TCA–acetone precipitation, appeared to be more suitable for 2-DE. Furthermore, we performed modifications during protein washing, re-solubilization in rehydration buffer and isoelectric focusing (IEF). The modifications provided us better results in terms of protein yield, resolution, spot numbers, and intensities for 2-DE gels of D. hirsuta and other two liverworts, i.e., Marchantia paleacea and Plagiochasma appendiculatum. Furthermore, we randomly selected spots from the 2-DE gel of D. hirsuta and identified using mass spectrometry, which confirms the applicability of this protocol for liverworts proteomics.
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Affiliation(s)
- Sandhya Yadav
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Akanksha Srivastava
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Subhankar Biswas
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Neha Chaurasia
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, 793022, India
| | - Sushil Kumar Singh
- Botanical Survey of India Northern Regional Centre, 192, Kaulagarh Road, Dehradun, Uttarakhand, 248003, India
| | - Sanjiv Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 10691, Stockholm, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, 10691, Stockholm, Sweden.
| | - Yogesh Mishra
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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Niu L, Wu Z, Liu H, Wu X, Wang W. 2-DE-based proteomic analysis of protein changes associated with etiolated mesocotyl growth in Zea mays. BMC Genomics 2019; 20:758. [PMID: 31640549 PMCID: PMC6805590 DOI: 10.1186/s12864-019-6109-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/20/2019] [Indexed: 02/06/2023] Open
Abstract
Background The mesocotyl connects the coleoptilar node and the basal part of the seminal root of maize (Zea mays) seedling. The mesocotyl pushes the shoot of the seedling out of the soil during seed germination; thus, its growth is highly related to deep-sowing tolerance. Although many studies on the maize mesocotyl have been carried out at physiological and molecular levels, the proteomic changes associated with cellular and physiological activities during mesocotyl growth are still unknown. Results In the present study, the maize hybrid Zhengdan 958 was used to study mesocotyl growth and accompanying protein changes. The dark-grown etiolated mesocotyls exhibited a slow-fast-slow feature, with significant changes in the levels of indole-3-acetic acid (IAA) and cellulose and the activity of peroxidase (POD). In particular, POD activity increased with mesocotyl growth, showing higher activity at the mature (lower) end of the mesocotyl. For the proteomic analysis, soluble proteins were extracted from etiolated mesocotyls dark-grown for 48 h, 84 h, and 132 h, corresponding to the initial, rapid, and slow growth periods, respectively, and subjected to separation by two-dimensional gel electrophoresis (2-DE). As a result, 88 differentially abundant proteins (DAPs) were identified using MALDI-TOF-TOF analysis. At 48 h, most DAPs were stress proteins, heat shock proteins and storage proteins; at 84 h, oxidation/reduction proteins, carbohydrate biogenesis-related proteins and cytoskeleton-related proteins were highly accumulated; at 132 h, the most striking DAPs were those involved in the synthesis and modification of the cell wall and the biogenesis of carbohydrates. Gene ontology (GO) analysis showed that changes in the abundance and proportion of DAPs were consistent with cellular and physiological activities and biological processes during mesocotyl growth. The accumulation of nine DAPs of interest was verified by immunoblotting and RT-qPCR. Conclusions The present study revealed that the protein patterns in 2-D gels differed greatly with mesocotyl growth. At different growth periods, a specific set of DAPs participate in various biological processes and underlie the cellular and physiological activities of the mesocotyl. These results contributed to the understanding of mesocotyl growth and the cultivation of maize lines with deep-sowing tolerance.
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Affiliation(s)
- Liangjie Niu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhaokun Wu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hui Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaolin Wu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
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Min CW, Gupta R, Agrawal GK, Rakwal R, Kim ST. Concepts and strategies of soybean seed proteomics using the shotgun proteomics approach. Expert Rev Proteomics 2019; 16:795-804. [PMID: 31398080 DOI: 10.1080/14789450.2019.1654860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/08/2019] [Indexed: 12/30/2022]
Abstract
Introduction: The last decade has yielded significant developments in the field of proteomics, especially in mass spectrometry (MS) and data analysis tools. In particular, a shift from gel-based to MS-based proteomics has been observed, thereby providing a platform with which to construct proteome atlases for all life forms. Nevertheless, the analysis of plant proteomes, especially those of samples that contain high-abundance proteins (HAPs), such as soybean seeds, remains challenging. Areas covered: Here, we review recent progress in soybean seed proteomics and highlight advances in HAPs depletion methods and peptide pre-fractionation, identification, and quantification methods. We also suggest a pipeline for future proteomic analysis, in order to increase the dynamic coverage of the soybean seed proteome. Expert opinion: Because HAPs limit the dynamic resolution of the soybean seed proteome, the depletion of HAPs is a prerequisite of high-throughput proteome analysis, and owing to the use of two-dimensional gel electrophoresis-based proteomic approaches, few soybean seed proteins have been identified or characterized. Recent advances in proteomic technologies, which have significantly increased the proteome coverage of other plants, could be used to overcome the current complexity and limitation of soybean seed proteomics.
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Affiliation(s)
- Cheol Woo Min
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
| | - Ravi Gupta
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265 , Kathmandu , Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited , Birgunj , Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO 13265 , Kathmandu , Nepal
- GRADE (Global Research Arch for Developing Education) Academy Private Limited , Birgunj , Nepal
- Faculty of Health and Sport Sciences, University of Tsukuba , Tsukuba , Ibaraki , Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and industry Convergence Research Institute, Pusan National University , Miryang , Korea
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Niu L, Ding H, Zhang J, Wang W. Proteomic Analysis of Starch Biosynthesis in Maize Seeds. STARCH-STARKE 2019. [DOI: 10.1002/star.201800294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Liangjie Niu
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
| | - Huiying Ding
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
| | - Jinghua Zhang
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
| | - Wei Wang
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
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Jiang Y, Zhou S, Chu W. The effects of dietary Bacillus cereus QSI-1 on skin mucus proteins profile and immune response in Crucian Carp (Carassius auratus gibelio). FISH & SHELLFISH IMMUNOLOGY 2019; 89:319-325. [PMID: 30970281 DOI: 10.1016/j.fsi.2019.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 04/03/2019] [Accepted: 04/05/2019] [Indexed: 06/09/2023]
Abstract
The objective of this study was to investigate the effect of dietary quorum quenching bacterium Bacillus cereus QSI-1 on skin mucus protein pattern and innate immune response in Crucian Carp (Carassius auratus gibelio). The differential proteomes of skin mucus of Crucian Carp were analyzed after administration of Bacillus cereus QSI-1 by isobaric tags for relative and absolute quantitation (iTRAQ) labeling, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 1974 proteins were quantified. Using a 1.5-fold change in expression as a physiological significant benchmark, 264 differentially expressed proteins were reliably quantified by iTRAQ analysis, including 130 up- and 134 down-regulated proteins after dietary Bacillus cereus QSI-1. Some Proteins that were involved in immunity included protein S100, annexin, histone H3, lymphocyte cytosolic protein 1, heat shock protein, L-plastin, keratin 91, etc. Furthermore, fish fed 5 × 108 CFU/g Bacillus cereus QSI-1 supplemented diet showed an increase in alternative complement activity and lysozyme activity but expressed a decrease in superoxide dismutase activity in skin mucus (P < 0.05). However, administration of Bacillus cereus QSI-1 had no significant effects on total immunoglobulin level (P > 0.05). These results demonstrated that dietary administration of Bacillus cereus QSI-1 affects skin mucus protein profile and innate immune response in Crucian Carp, and also can enhance the disease resistance of Crucian Carp against A. hydrophila. This is the first report on proteomics analysis of skin mucus proteins in Crucian Carp after administration of quorum quenching bacterium Bacillus cereus, and the results will help to understand the mucosal immune responses to probiotics at the protein level in fish.
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Affiliation(s)
- Yuanhe Jiang
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Shuxin Zhou
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China
| | - Weihua Chu
- Department of Pharmaceutical Microbiology, School of Life Science and Technology, China Pharmaceutical University, Nanjing, 210009, China.
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