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Zhang ZB, Xiong T, Wang XJ, Chen YR, Wang JL, Guo CL, Ye ZY. Lineage-specific gene duplication and expansion of DUF1216 gene family in Brassicaceae. PLoS One 2024; 19:e0302292. [PMID: 38626181 PMCID: PMC11020792 DOI: 10.1371/journal.pone.0302292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/01/2024] [Indexed: 04/18/2024] Open
Abstract
Proteins containing domain of unknown function (DUF) are prevalent in eukaryotic genome. The DUF1216 proteins possess a conserved DUF1216 domain resembling to the mediator protein of Arabidopsis RNA polymerase II transcriptional subunit-like protein. The DUF1216 family are specifically existed in Brassicaceae, however, no comprehensive evolutionary analysis of DUF1216 genes have been performed. We performed a first comprehensive genome-wide analysis of DUF1216 proteins in Brassicaceae. Totally 284 DUF1216 genes were identified in 27 Brassicaceae species and classified into four subfamilies on the basis of phylogenetic analysis. The analysis of gene structure and conserved motifs revealed that DUF1216 genes within the same subfamily exhibited similar intron/exon patterns and motif composition. The majority members of DUF1216 genes contain a signal peptide in the N-terminal, and the ninth position of the signal peptide in most DUF1216 is cysteine. Synteny analysis revealed that segmental duplication is a major mechanism for expanding of DUF1216 genes in Brassica oleracea, Brassica juncea, Brassica napus, Lepidium meyneii, and Brassica carinata, while in Arabidopsis thaliana and Capsella rubella, tandem duplication plays a major role in the expansion of the DUF1216 gene family. The analysis of Ka/Ks (non-synonymous substitution rate/synonymous substitution rate) ratios for DUF1216 paralogous indicated that most of gene pairs underwent purifying selection. DUF1216 genes displayed a specifically high expression in reproductive tissues in most Brassicaceae species, while its expression in Brassica juncea was specifically high in root. Our studies offered new insights into the phylogenetic relationships, gene structures and expressional patterns of DUF1216 members in Brassicaceae, which provides a foundation for future functional analysis.
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Affiliation(s)
- Zai-Bao Zhang
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Xiao-Jia Wang
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Yu-Rui Chen
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Jing-Lei Wang
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Cong-Li Guo
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Zi-Yi Ye
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
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2
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Giangrieco I, Ciardiello MA, Tamburrini M, Tuppo L, Mari A, Alessandri C. Plant and Arthropod IgE-Binding Papain-like Cysteine Proteases: Multiple Contributions to Allergenicity. Foods 2024; 13:790. [PMID: 38472904 DOI: 10.3390/foods13050790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/05/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Papain-like cysteine proteases are widespread and can be detected in all domains of life. They share structural and enzymatic properties with the group's namesake member, papain. They show a broad range of protein substrates and are involved in several biological processes. These proteases are widely exploited for food, pharmaceutical, chemical and cosmetic biotechnological applications. However, some of them are known to cause allergic reactions. In this context, the objective of this review is to report an overview of some general properties of papain-like cysteine proteases and to highlight their contributions to allergy reactions observed in humans. For instance, the literature shows that their proteolytic activity can cause an increase in tissue permeability, which favours the crossing of allergens through the skin, intestinal and respiratory barriers. The observation that allergy to PLCPs is mostly detected for inhaled proteins is in line with the reports describing mite homologs, such as Der p 1 and Der f 1, as major allergens showing a frequent correlation between sensitisation and clinical allergic reactions. In contrast, the plant food homologs are often digested in the gastrointestinal tract. Therefore, they only rarely can cause allergic reactions in humans. Accordingly, they are reported mainly as a cause of occupational diseases.
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Affiliation(s)
- Ivana Giangrieco
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), 80131 Naples, Italy
| | | | - Maurizio Tamburrini
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), 80131 Naples, Italy
| | - Lisa Tuppo
- Institute of Biosciences and BioResources (IBBR), National Research Council of Italy (CNR), 80131 Naples, Italy
| | - Adriano Mari
- Associated Centers for Molecular Allergology (CAAM), 00100 Rome, Italy
- Allergy Data Laboratories (ADL), 04100 Latina, Italy
| | - Claudia Alessandri
- Associated Centers for Molecular Allergology (CAAM), 00100 Rome, Italy
- Allergy Data Laboratories (ADL), 04100 Latina, Italy
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3
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Zou Z, Zheng Y, Xie Z. Analysis of Carica papaya Informs Lineage-Specific Evolution of the Aquaporin (AQP) Family in Brassicales. PLANTS (BASEL, SWITZERLAND) 2023; 12:3847. [PMID: 38005748 PMCID: PMC10674200 DOI: 10.3390/plants12223847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/15/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023]
Abstract
Aquaporins (AQPs), a type of intrinsic membrane proteins that transport water and small solutes across biological membranes, play crucial roles in plant growth and development. This study presents a first genome-wide identification and comparative analysis of the AQP gene family in papaya (Carica papaya L.), an economically and nutritionally important fruit tree of tropical and subtropical regions. A total of 29 CpAQP genes were identified, which represent five subfamilies, i.e., nine plasma intrinsic membrane proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), seven NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). Although the family is smaller than the 35 members reported in Arabidopsis, it is highly diverse, and the presence of CpXIP genes as well as orthologs in Moringa oleifera and Bretschneidera sinensis implies that the complete loss of the XIP subfamily in Arabidopsis is lineage-specific, sometime after its split with papaya but before Brassicaceae-Cleomaceae divergence. Reciprocal best hit-based sequence comparison of 530 AQPs and synteny analyses revealed that CpAQP genes belong to 29 out of 61 identified orthogroups, and lineage-specific evolution was frequently observed in Brassicales. Significantly, the well-characterized NIP3 group was completely lost; lineage-specific loss of the NIP8 group in Brassicaceae occurred sometime before the divergence with Cleomaceae, and lineage-specific loss of NIP2 and SIP3 groups in Brassicaceae occurred sometime after the split with Cleomaceae. In contrast to a predominant role of recent whole-genome duplications (WGDs) on the family expansion in B. sinensis, Tarenaya hassleriana, and Brassicaceae plants, no recent AQP repeats were identified in papaya, and ancient WGD repeats are mainly confined to the PIP subfamily. Subfamily even group-specific evolution was uncovered via comparing exon-intron structures, conserved motifs, the aromatic/arginine selectivity filter, and gene expression profiles. Moreover, down-regulation during fruit ripening and expression divergence of duplicated CpAQP genes were frequently observed in papaya. These findings will not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further studies of AQP genes in papaya and species beyond.
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Affiliation(s)
- Zhi Zou
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.Z.); (Z.X.)
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4
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Zhang X, Tao L, Wei G, Yang M, Wang Z, Shi C, Shi Y, Huang A. Plant-derived rennet: research progress, novel strategies for their isolation, identification, mechanism, bioactive peptide generation, and application in cheese manufacturing. Crit Rev Food Sci Nutr 2023:1-13. [PMID: 37902764 DOI: 10.1080/10408398.2023.2275295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Rennet, an aspartate protease found in the stomach of unweaned calves, effectively cuts the peptide bond between Phe105-Met106 in κ-casein, hydrolyzing the casein micelles to coagulate the milk and is a crucial additive in cheese production. Rennet is one of the most used enzymes of animal origin in cheese making. However, using rennet al.one is insufficient to meet the increasing demand for cheese production worldwide. Numerous studies have shown that plant rennet can be an alternative to bovine rennet and exhibit a good renneting effect. Therefore, it is crucial and urgent to find a reliable plant rennet. Based on our team's research on rennet enzymes of plant origin, such as from Dregea sinensis Hemsl. and Moringa oleifer Lam., for more than ten years, this paper reviews the relevant literature on rennet sources, isolation, identification, rennet mechanism, functional active peptide screening, and application in cheese production. In addition, it proposes the various techniques for targeted isolation and identification of rennet and efficient screening of functionally active peptides, which show excellent prospects for development.
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Affiliation(s)
- Xueting Zhang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Liang Tao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Guangqiang Wei
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Min Yang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zilin Wang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Chongying Shi
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yanan Shi
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Aixiang Huang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, China
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5
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Song P, Zhang X, Wang S, Xu W, Wang F, Fu R, Wei F. Microbial proteases and their applications. Front Microbiol 2023; 14:1236368. [PMID: 37779686 PMCID: PMC10537240 DOI: 10.3389/fmicb.2023.1236368] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Proteases (proteinases or peptidases) are a class of hydrolases that cleave peptide chains in proteins. Endopeptidases are a type of protease that hydrolyze the internal peptide bonds of proteins, forming shorter peptides; exopeptidases hydrolyze the terminal peptide bonds from the C-terminal or N-terminal, forming free amino acids. Microbial proteases are a popular instrument in many industrial applications. In this review, the classification, detection, identification, and sources of microbial proteases are systematically introduced, as well as their applications in food, detergents, waste treatment, and biotechnology processes in the industry fields. In addition, recent studies on techniques used to express heterologous microbial proteases are summarized to describe the process of studying proteases. Finally, future developmental trends for microbial proteases are discussed.
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Affiliation(s)
- Peng Song
- College of Life Sciences, Liaocheng University, Liaocheng, China
- Shandong Aobo Biotech Co. Ltd., Liaocheng, China
- Jiangxi Zymerck Biotech Co. Ltd., Nanchang, China
| | - Xue Zhang
- College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Shuhua Wang
- Shandong Aobo Biotech Co. Ltd., Liaocheng, China
| | - Wei Xu
- College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Fei Wang
- College of Life Sciences, Liaocheng University, Liaocheng, China
| | - Rongzhao Fu
- Jiangxi Zymerck Biotech Co. Ltd., Nanchang, China
| | - Feng Wei
- College of Life Sciences, Liaocheng University, Liaocheng, China
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6
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Kordiš D, Turk V. Origin and Early Diversification of the Papain Family of Cysteine Peptidases. Int J Mol Sci 2023; 24:11761. [PMID: 37511529 PMCID: PMC10380794 DOI: 10.3390/ijms241411761] [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: 06/21/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Peptidases of the papain family play a key role in protein degradation, regulated proteolysis, and the host-pathogen arms race. Although the papain family has been the subject of many studies, knowledge about its diversity, origin, and evolution in Eukaryota, Bacteria, and Archaea is limited; thus, we aimed to address these long-standing knowledge gaps. We traced the origin and expansion of the papain family with a phylogenomic analysis, using sequence data from numerous prokaryotic and eukaryotic proteomes, transcriptomes, and genomes. We identified the full complement of the papain family in all prokaryotic and eukaryotic lineages. Analysis of the papain family provided strong evidence for its early diversification in the ancestor of eukaryotes. We found that the papain family has undergone complex and dynamic evolution through numerous gene duplications, which produced eight eukaryotic ancestral paralogous C1A lineages during eukaryogenesis. Different evolutionary forces operated on C1A peptidases, including gene duplication, horizontal gene transfer, and gene loss. This study challenges the current understanding of the origin and evolution of the papain family and provides valuable insights into their early diversification. The findings of this comprehensive study provide guidelines for future structural and functional studies of the papain family.
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Affiliation(s)
- Dušan Kordiš
- Department of Molecular and Biomedical Sciences, J. Stefan Institute, 1000 Ljubljana, Slovenia
| | - Vito Turk
- Department of Biochemistry, Molecular and Structural Biology, J. Stefan Institute, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
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7
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Lin NS, Hirayama K, Kitamura M, Koide S, Kitajima H, Harada T, Mayama S, Umemura K. Fabrication of a Floatable Micron-Sized Enzyme Device Using Diatom Frustules. ACS OMEGA 2023; 8:21145-21153. [PMID: 37332799 PMCID: PMC10268610 DOI: 10.1021/acsomega.3c02104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023]
Abstract
Immobilization of enzymes has been widely reported due to their reusability, thermal stability, better storage abilities, and so on. However, there are still problems that immobilized enzymes do not have free movements to react to substrates during enzyme reactions and their enzyme activity becomes weak. Moreover, when only the porosity of support materials is focused, some problems such as enzyme distortion can negatively affect the enzyme activity. Being a solution to these problems, a new function "floatability" of enzyme devices has been discussed. A "floatable" micron-sized enzyme device was fabricated to enhance the free movements of immobilized enzymes. Diatom frustules, natural nanoporous biosilica, were used to attach papain enzyme molecules. The floatability of the frustules, evaluated by macroscopic and microscopic methods, was significantly better than that of four other SiO2 materials, such as diatomaceous earth (DE), which have been widely used to fabricate micron-sized enzyme devices. The frustules were fully suspended at 30 °C for 1 h without stirring, although they settled at room temperature. When enzyme assays were performed at room temperature, 37, and 60 °C with or without external stirring, the proposed frustule device showed the highest enzyme activity under all conditions among papain devices similarly prepared using other SiO2 materials. It was confirmed by the free papain experiments that the frustule device was active enough for enzyme reactions. Our data indicated that the high floatability of the reusable frustule device, and its large surface area, is effective in maximizing enzyme activity due to the high probability to react to substrates.
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Affiliation(s)
- Nay San Lin
- Department
of Physics, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 1628601, Japan
| | - Kota Hirayama
- Department
of Physics, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 1628601, Japan
| | - Masaki Kitamura
- Department
of Physics, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 1628601, Japan
| | - Shinji Koide
- Department
of Physics, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 1628601, Japan
| | - Hiromasa Kitajima
- Department
of Integrated Science and Technology, Faculty of Science and Technology, Oita University, Dannoharu, 700, Oita City 870-1192, Japan
| | - Takunori Harada
- Department
of Integrated Science and Technology, Faculty of Science and Technology, Oita University, Dannoharu, 700, Oita City 870-1192, Japan
| | - Shigeki Mayama
- Tokyo
Diatomology Lab, 2-3-2
Nukuikitamachi, Koganei, Tokyo 184-0015, Japan
| | - Kazuo Umemura
- Department
of Physics, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku, Tokyo 1628601, Japan
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8
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Keshapaga UR, Jathoth K, Singh SS, Gogada R, Burgula S. Characterization of high-yield Bacillus subtilis cysteine protease for diverse industrial applications. Braz J Microbiol 2023; 54:739-752. [PMID: 37157054 PMCID: PMC10235272 DOI: 10.1007/s42770-023-00992-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 04/25/2023] [Indexed: 05/10/2023] Open
Abstract
Bacterial proteases have extensive applications in various fields of industrial microbiology. In this study, protease-producing organisms were screened on skimmed milk agar media using serial dilution. Through microbial biomass production, biochemical tests, protease-specific activity, and 16 s RNA gene sequencing, the isolates were identified as Bacillus subtilis and submitted to NCBI. The strain accession numbers were designated as A1 (MT903972), A2 (MT903996), A4 (MT904091), and A5 (MT904796). The strain A4 Bacillus subtilis showed highest protease-specific activity as 76,153.84 U/mg. A4 Bacillus subtilis was unaffected by Ca2+, Cu2+, Fe2+, Hg2+, Mg2+, Na, Fe2+, and Zn2+ but was inhibited by 80% by Mn2+ (5 mM). The protease activity was inhibited by up to 30% by iodoacetamide (5 mM). These findings confirm the enzyme to be a cysteine protease which was further confirmed by MALDI-TOF. The identified protease showed 71% sequence similarity with Bacillus subtilis cysteine protease. The crude cysteine protease significantly aided in fabric stain removal when added to a generic detergent. It also aided in the recovery of silver from used X-ray films and de-hairing of goat skin hides and showed decent application in meat tenderization. Thus, the isolated cysteine protease has high potential for industrial applications.
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Affiliation(s)
- Usha Rani Keshapaga
- Department of Microbiology, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Kalyani Jathoth
- Department of Microbiology, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Surya Satyanarayana Singh
- Department of Biochemistry , University College of Science, Osmania University , Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Raghu Gogada
- Department of Biochemistry , University College of Science, Osmania University , Tarnaka, Hyderabad, 500 007, Telangana, India
| | - Sandeepta Burgula
- Department of Microbiology, University College of Science, Osmania University, Tarnaka, Hyderabad, 500 007, Telangana, India.
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Xia X, Song S, Zhou T, Zhang H, Cui H, Zhang F, Hayat K, Zhang X, Ho CT. Preparation of Saltiness-Enhancing Enzymatic Hydrolyzed Pea Protein and Identification of the Functional Small Peptides of Salt Reduction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:8140-8149. [PMID: 37202341 DOI: 10.1021/acs.jafc.3c02046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
According to the correlation of saltiness determined by electronic tongue and perceived NaCl concentration, favorable enzymatic hydrolysis parameters were achieved to prepare the saltiness enhancing mixture peptides from pea protein. Six peptide fractions (F1, F2, F3, F4, F5, and F6) were isolated using Sephadex G-10 gel filtration. Among them, fraction F4 (0.1%) exhibited the highest saltiness (5.90 ± 0.03). The amino acid sequences of five main peptides identified by time-of-flight mass spectrometry were Tyr-Trp (367.40 Da), Gly-Glu-His-Glu (470.43 Da), Glu-Arg-Phe-Gly-Pro (604.65 Da), Gly-Ala-Gly-Lys (331.37 Da), and Pro-Gly-Ala-Gly-Asn (414.41 Da). Tyr-Trp (0.01%) in 0.4% NaCl solution had a 20% saltiness-enhancement compared with 0.4% NaCl solution. More salivary aldosterone was secreted after tasting hydrolysate or Tyr-Trp solutions via enzyme-linked immunosorbent assay, reflecting the improvement of human sensitivity to saltiness. Thereby, the saltiness-enhancing effect was confirmed for the small peptides from hydrolyzed pea protein and the main contributor was further identified.
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Affiliation(s)
- Xue Xia
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122 Jiangsu, P. R. China
| | - Shiqing Song
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 200235, P. R. China
| | - Tong Zhou
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122 Jiangsu, P. R. China
| | - Han Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122 Jiangsu, P. R. China
| | - Heping Cui
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122 Jiangsu, P. R. China
| | - Foxin Zhang
- Anhui Qiang Wang Flavouring Food Co., Ltd., No. 1 Shengli Road, Jieshou, Fuyang, 236500 Anhui, P. R. China
| | - Khizar Hayat
- Department of Kinesiology, Nutrition, and Health, Miami University, Oxford, Ohio 45056, United States
| | - Xiaoming Zhang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122 Jiangsu, P. R. China
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, 65 Dudley Road, New Brunswick, New Jersey 08901, United States
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Transcriptomic Analysis of Radish (Raphanus sativus L.) Roots with CLE41 Overexpression. PLANTS 2022; 11:plants11162163. [PMID: 36015466 PMCID: PMC9416626 DOI: 10.3390/plants11162163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/02/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022]
Abstract
The CLE41 peptide, like all other TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF) family CLE peptides, promotes cell division in (pro-)cambium vascular meristem and prevents xylem differentiation. In this work, we analyzed the differential gene expression in the radish primary-growing P35S:RsCLE41-1 roots using the RNA-seq. Our analysis of transcriptomic data revealed a total of 62 differentially expressed genes between transgenic radish roots overexpressing the RsCLE41-1 gene and the glucuronidase (GUS) gene. For genes associated with late embryogenesis, response to abscisic acid and auxin-dependent xylem cell fate determination, an increase in the expression in P35S:RsCLE41-1 roots was found. Among those downregulated, stress-associated genes prevailed. Moreover, several genes involved in xylem specification were also downregulated in the roots with RsCLE41-1 overexpression. Unexpectedly, none of the well-known targets of TDIFs, such as WOX4 and WOX14, were identified as DEGs in our experiment. Herein, we discuss a suggestion that the activation of pathways associated with desiccation resistance, which are more characteristic of late embryogenesis, in roots with RsCLE41-overexpression may be a consequence of water deficiency onset due to impaired vascular specification.
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11
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Yingqi H, Lv Y, Zhang J, Ahmad N, Li Y, Wang N, Xiuming L, Na Y, Li X. Identification and functional characterization of safflower cysteine protease 1 as negative regulator in response to low-temperature stress in transgenic Arabidopsis. PLANTA 2022; 255:106. [PMID: 35445865 DOI: 10.1007/s00425-022-03875-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
We performed genome-wide and heterologous expression analysis of the safflower cysteine protease family and found that inhibition of CtCP1 expression enhanced plant cold resistance. Cysteine protease (CP) is mainly involved in plant senescence and stress responses. However, the molecular mechanism of endogenous cysteine protease inhibition in plant stress tolerance is yet unknown. Here, we report the discovery and functional characterization of a candidate CP1 gene from safflower. The conserved structural topology of CtCPs revealed important insights into their possible roles in plant growth and stress responses. The qRT-PCR results implied that most of CtCP genes were highly expressed at fading stage suggesting that they are most likely involved in senescence process. The CtCP1 expression was significantly induced at different time points under cold, NaCl, H2O2 and PEG stress, respectively. The in-vitro activity of heterologously expressed CtCP1 protein showed highest protease activity for casein and azocasein substrates. The expression and phenotypic data together with antioxidant activity and physiological indicators revealed that transgenic plants inhibited by CtCP1-anti showed higher tolerance to low temperature than WT and CtCP1-OE plants. Our findings demonstrated the discovery of a new Cysteine protease 1 gene that exerted a detrimental effect on transgenic Arabidopsis under low-temperature stress.
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Affiliation(s)
- Hong Yingqi
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Yanxi Lv
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Jianyi Zhang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Naveed Ahmad
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Youbao Li
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Nan Wang
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China
| | - Liu Xiuming
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China.
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
- Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
| | - Yao Na
- College of Life Sciences, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun, 130118, China.
| | - Xiaokun Li
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
- Biomedical Collaborative Innovation Center of Zhejiang Province, Wenzhou University, Wenzhou, 325035, Zhejiang, China.
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12
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Kang J, Gong P, Ge M, Sadeghnezhad E, Liu Z, Zhang M, Shangguan L, Fang J. "The PLCP gene family of grapevine (Vitis vinifera L.): characterization and differential expression in response to Plasmopara Viticola". BMC PLANT BIOLOGY 2021; 21:499. [PMID: 34717550 PMCID: PMC8556938 DOI: 10.1186/s12870-021-03279-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 10/19/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND Papain-like cysteine proteases (PLCPs), a large group of cysteine proteases, are structurally related to papain. The members belonging to PLCPs family contribute to plant immunity, senescence, and defense responses in plants. The PLCP gene family has been identified in Arabidopsis, rice, soybean, and cotton. However, no systematic analysis of PLCP genes has been undertaken in grapevine. Since Plasmopara viticola as a destructive pathogen could affect immunity of grapes in the field, we considered that the members belonged to PLCPs family could play a crucial role in defensive mechanisms or programmed cell death. We aimed to evaluate the role of PLCPs in 2 different varieties of grapevines and compared the changes of their expressions with the transcriptional data in response to P. viticola. RESULTS In this study, 23 grapevine PLCP (VvPLCP) genes were identified by comprehensive bioinformatics analysis. Subsequently, the chromosomal localizations, gene structure, conserved domains, phylogenetic relationship, gene duplication, and cis-acting elements were analyzed. Numerous cis-acting elements related to plant development, hormone, and stress responses were identified in the promoter of the VvPLCP genes. Phylogenetic analysis grouped the VvPLCP genes into nine subgroups. The transcription of VvPLCP in different inoculation time points and varieties indicated that VvPLCP may have vital functions in grapevine defense against Plasmopara viticola. According to transcriptome data and qPCR analysis, we observed the increasing expression levels of VvRD21-1 at 72 h after inoculation in resistant variety, inferring that it was related to grape downy mildew resistance. Meanwhile, 3 genes including VvXBCP1, VvSAG12-1, and VvALP1 showed higher expression at 24 h after pathogen inoculation in the susceptible variety and might be related to the downy mildew phenotype. We nominated these four genes to function during hypersensitive response (HR) process, inferring that these genes could be associated with downy mildew resistance in grapes. CONCLUSIONS Our results provide the reference for functional studies of PLCP gene family, and highlight its functions in grapevine defense against P. viticola. The results help us to better understand the complexity of the PLCP gene family in plant immunity and provide valuable information for future functional characterization of specific genes in grapevine.
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Affiliation(s)
- Jun Kang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Peijie Gong
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China.
| | - Mengqing Ge
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Ehsan Sadeghnezhad
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Zhongjie Liu
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Mengwei Zhang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Lingfei Shangguan
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
| | - Jinggui Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China.
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Abstract
Proteases are ubiquitous enzymes, having significant physiological roles in both synthesis and degradation. The use of microbial proteases in food fermentation is an age-old process, which is today being successfully employed in other industries with the advent of ‘omics’ era and innovations in genetic and protein engineering approaches. Proteases have found application in industries besides food, like leather, textiles, detergent, waste management, agriculture, animal husbandry, cosmetics, and pharmaceutics. With the rising demands and applications, researchers are exploring various approaches to discover, redesign, or artificially synthesize enzymes with better applicability in the industrial processes. These enzymes offer a sustainable and environmentally safer option, besides possessing economic and commercial value. Various bacterial and fungal proteases are already holding a commercially pivotal role in the industry. The current review summarizes the characteristics and types of proteases, microbial source, their current and prospective applications in various industries, and future challenges. Promoting these biocatalysts will prove significant in betterment of the modern world.
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14
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Tacias-Pascacio VG, Morellon-Sterling R, Castañeda-Valbuena D, Berenguer-Murcia Á, Kamli MR, Tavano O, Fernandez-Lafuente R. Immobilization of papain: A review. Int J Biol Macromol 2021; 188:94-113. [PMID: 34375660 DOI: 10.1016/j.ijbiomac.2021.08.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Papain is a cysteine protease from papaya, with many applications due to its broad specificity. This paper reviews for first time the immobilization of papain on different supports (organic, inorganic or hybrid supports) presenting some of the features of the utilized immobilization strategies (e.g., epoxide, glutaraldehyde, genipin, glyoxyl for covalent immobilization). Special focus is placed on the preparation of magnetic biocatalysts, which will permit the simple recovery of the biocatalyst even if the medium is a suspension. Problems specific to the immobilization of proteases (e.g., steric problems when hydrolyzing large proteins) are also defined. The benefits of a proper immobilization (enzyme stabilization, widening of the operation window) are discussed, together with some artifacts that may suggest an enzyme stabilization that may be unrelated to enzyme rigidification.
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Affiliation(s)
- Veymar G Tacias-Pascacio
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico; Tecnológico Nacional de México/Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Roberto Morellon-Sterling
- Departamento de Biocatálisis. ICP-CSIC./Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid. Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid. Spain
| | - Daniel Castañeda-Valbuena
- Tecnológico Nacional de México/Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales, Universidad de Alicante, Alicante, Spain
| | - Majid Rasool Kamli
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddad 21589, Saudi Arabia; Center of excellence in Bionanoscience Research, King Abdulaziz University, Jeddad 21589, Saudi Arabia
| | - Olga Tavano
- Faculty of Nutrition, Alfenas Federal Univ., 700 Gabriel Monteiro da Silva St, Alfenas, MG 37130-000, Brazil
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis. ICP-CSIC./Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid. Spain; Center of Excellence in Bionanoscience Research, External advisory board, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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15
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Li Y, Niu L, Wu X, Faleri C, Tai F, Zhang M, Liu H, Wang W, Cai G. Genome-Wide Identification and Comparison of Cysteine Proteases in the Pollen Coat and Other Tissues in Maize. FRONTIERS IN PLANT SCIENCE 2021; 12:709534. [PMID: 34630461 PMCID: PMC8494779 DOI: 10.3389/fpls.2021.709534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/24/2021] [Indexed: 05/07/2023]
Abstract
Cysteine proteases, belonging to the C1-papain family, play a major role in plant growth and development, senescence, and immunity. There is evidence to suggest that pollen cysteine protease (CP) (ZmCP03) is involved in regulating the anther development and pollen formation in maize. However, there is no report on the genome-wide identification and comparison of CPs in the pollen coat and other tissues in maize. In this study, a total of 38 homologous genes of ZmCP03 in maize were identified. Subsequently, protein motifs, conserved domains, gene structures, and duplication patterns of 39 CPs are analyzed to explore their evolutionary relationship and potential functions. The cis-elements were identified in the upstream sequence of 39 CPs, especially those that are related to regulating growth and development and responding to environmental stresses and hormones. The expression patterns of these genes displayed remarked difference at a tissue or organ level in maize based on the available transcriptome data in the public database. Quantitative reverse transcription PCR (RT-qPCR) analysis showed that ZmCP03 was preferably expressed at a high level in maize pollen. Analyses by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblot, immunofluorescence and immunogold electron microscopy all validated the cellular localization of ZmCP03 in both the pollen coat and pollen cytoplasm. In addition, 142 CP genes from Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and cotton (Gossypium hirsutum), together with 39 maize CPs, were retrieved to analyze their evolution by comparing with orthologous genes. The results suggested that ZmCP03 was relatively conservative and stable during evolution. This study may provide a referential evidence on the function of ZmCP03 in pollen development and germination in maize.
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Affiliation(s)
- Yanhua Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Liangjie Niu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xiaolin Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Claudia Faleri
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Fuju Tai
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Fuju Tai
| | - Man Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hui Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- Wei Wang
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, Siena, Italy
- Giampiero Cai
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16
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Zhai Y, Cui Y, Song M, Vainstein A, Chen S, Ma H. Papain-Like Cysteine Protease Gene Family in Fig ( Ficus carica L.): Genome-Wide Analysis and Expression Patterns. FRONTIERS IN PLANT SCIENCE 2021; 12:681801. [PMID: 34122493 PMCID: PMC8193581 DOI: 10.3389/fpls.2021.681801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/03/2021] [Indexed: 05/05/2023]
Abstract
The papain-like cysteine proteases (PLCPs) are the most abundant family of cysteine proteases in plants, with essential roles in biotic/abiotic stress responses, growth and senescence. Papain, bromelain and ficin are widely used in food, medicine and other industries. In this study, 31 PLCP genes (FcPCLPs) were identified in the fig (Ficus carica L.) genome by HMM search and manual screening, and assigned to one of nine subfamilies based on gene structure and conserved motifs. SAG12 and RD21 were the largest subfamilies with 10 and 7 members, respectively. The FcPCLPs ranged from 1,128 to 5,075 bp in length, containing 1-10 introns, and the coding sequence ranged from 624 to 1,518 bp, encoding 207-505 amino acids. Subcellular localization analysis indicated that 24, 2, and 5 PLCP proteins were targeted to the lysosome/vacuole, cytoplasm and extracellular matrix, respectively. Promoter (2,000 bp upstream) analysis of FcPLCPs revealed a high number of plant hormone and low temperature response elements. RNA-seq revealed differential expression of 17 FcPLCPs in the inflorescence and receptacle, and RD21 subfamily members were the major PLCPs expressed in the fruit; 16 and 5 FcPLCPs responded significantly to ethylene and light, respectively. Proteome analyses revealed 18 and 5 PLCPs in the fruit cell soluble proteome and fruit latex, respectively. Ficins were the major PLCP in fig fruit, with decreased abundance in inflorescences, but increased abundance in receptacles of commercial-ripe fruit. FcRD21B/C and FcALP1 were aligned as the genes encoding the main ficin isoforms. Our study provides valuable multi-omics information on the FcPLCP family and lays the foundation for further functional studies.
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Affiliation(s)
- Yanlei Zhai
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yuanyuan Cui
- College of Horticulture, China Agricultural University, Beijing, China
| | - Miaoyu Song
- College of Horticulture, China Agricultural University, Beijing, China
| | - Alexander Vainstein
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shangwu Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Huiqin Ma
- College of Horticulture, China Agricultural University, Beijing, China
- *Correspondence: Huiqin Ma,
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17
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Yuan S, Ke D, Li R, Li X, Wang L, Chen H, Zhang C, Huang Y, Chen L, Hao Q, Yang H, Cao D, Chen S, Guo W, Shan Z, Yang Z, Zhang X, Qiu D, Guan Y, Zhou X. Genome-wide survey of soybean papain-like cysteine proteases and their expression analysis in root nodule symbiosis. BMC PLANT BIOLOGY 2020; 20:517. [PMID: 33183238 PMCID: PMC7659060 DOI: 10.1186/s12870-020-02725-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/26/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes and play important roles in root nodule symbiosis (RNS), while the whole-genome studies of PLCP family genes in legume are quite limited, and the roles of Glycine max PLCPs (GmPLCPs) in nodulation, nodule development and senescence are not fully understood. RESULTS In the present study, we identified 97 GmPLCPs and performed a genome-wide survey to explore the expansion of soybean PLCP family genes and their relationships to RNS. Nineteen paralogous pairs of genomic segments, consisting of 77 GmPLCPs, formed by whole-genome duplication (WGD) events were identified, showing a high degree of complexity in duplication. Phylogenetic analysis among different species showed that the lineage differentiation of GmPLCPs occurred after family expansion, and large tandem repeat segment were specifically in soybean. The expression patterns of GmPLCPs in symbiosis-related tissues and nodules identified RNS-related GmPLCPs and provided insights into their putative symbiotic functions in soybean. The symbiotic function analyses showed that a RNS-related GmPLCP gene (Glyma.04G190700) really participate in nodulation and nodule development. CONCLUSIONS Our findings improved our understanding of the functional diversity of legume PLCP family genes, and provided insights into the putative roles of the legume PLCPs in nodulation, nodule development and senescence.
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Affiliation(s)
- Songli Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Danxia Ke
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Rong Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiangyong Li
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Lei Wang
- College of Life Sciences & Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal University, Xinyang, China
| | - Haifeng Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chanjuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Limiao Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Qingnan Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hongli Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shuilian Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhihui Shan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zhonglu Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dezhen Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuefeng Guan
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Xinan Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China.
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18
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da Silva Júnior NR, Vital CE, de Almeida Barros R, Faustino VA, Monteiro LP, Barros E, de Oliveira EE, de Oliveira Ramos HJ, de Almeida Oliveira MG. Intestinal proteolytic profile changes during larval development of Anticarsia gemmatalis caterpillars. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 103:e21631. [PMID: 31587381 DOI: 10.1002/arch.21631] [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: 04/08/2019] [Revised: 08/26/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
Soybean is one of most consumed and produced grains in the world, and Anticarsia gemmatalis is a pest that causes great damage to this crop due to severe defoliation during its larval phase. Plants have mechanisms that lead to the inhibition of proteases in the intestine of these herbivores, hampering their development. Understanding this complex protease inhibitor is important for pest control. The objective of this study was to evaluate the enzymatic profiles of the intestinal proteases of the soybean caterpillar at different instars. For this, the proteolytic profile of the gut in the third, fourth, and fifth instars were analyzed. Irreversible inhibitors of proteases were separately incubated with A. gemmatalis enzyme extracts at the third, fourth, and fifth instar to assess the contribution of these proteases to total proteolytic activity. The enzymatic extracts were also evaluated with specific substrates to confirm changes in the specific activities of trypsin-like, chymotrypsin-like, and cysteine proteases at different instars. The results showed that the protease profile of A. gemmatalis gut changes throughout its larval development. The activity of cysteine proteases was more intense in the first instar. On the contrary, the serine proteases showed major activities in the late stages of the larval phase. Zymogram analysis and protein identification by liquid chromatography-mass spectrometry indicated serine protease as the main protease class expressed in the fifth instar. These results may shift the focus from the rational development of the protease inhibitor to A. gemmatalis and other Lepidoptera, as the expression of major proteases is not constant.
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Affiliation(s)
- Neilier R da Silva Júnior
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, BIOAGRO/INCT-IPP, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Camilo E Vital
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, BIOAGRO/INCT-IPP, Universidade Federal de Viçosa, Viçosa, Brazil
- Center of Analysis of Biomolecules, NuBioMol, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Rafael de Almeida Barros
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, BIOAGRO/INCT-IPP, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Verônica A Faustino
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, BIOAGRO/INCT-IPP, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Luana P Monteiro
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, BIOAGRO/INCT-IPP, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Edvaldo Barros
- Center of Analysis of Biomolecules, NuBioMol, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Humberto J de Oliveira Ramos
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, BIOAGRO/INCT-IPP, Universidade Federal de Viçosa, Viçosa, Brazil
- Center of Analysis of Biomolecules, NuBioMol, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Maria G de Almeida Oliveira
- Department of Biochemistry and Molecular Biology, Laboratory of Enzymology and Biochemistry of Proteins and Peptides, BIOAGRO/INCT-IPP, Universidade Federal de Viçosa, Viçosa, Brazil
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19
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Han Z, Kraiyot S, Kittikun AH, Zhou W, Li J. Fractionation and activity profiling of fruit bromelain from pineapples of Phuket variety growing in Thailand. J Food Biochem 2019; 43:e13011. [PMID: 31393018 DOI: 10.1111/jfbc.13011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/16/2019] [Accepted: 07/22/2019] [Indexed: 11/27/2022]
Abstract
Bromelain is a type of protease found in both fruits and stems of pineapples. Stem bromelain has been extensively studied and is commercially available for applications in various industries. In contrast, studies of fruit bromelain are quite limited since most of pineapples have been consumed freshly, canned or juiced. Nowadays, the consumption of canned fruits, including canned pineapples has decreased greatly. Fruit bromelain could be a new growth point for pineapple industry. In this study, fruit bromelain was extracted from the pineapple juice of Phuket variety and some of its properties were studied. The enzyme was purified by precipitation using ammonium sulfate fractionation followed by ion-exchange and gel filtration chromatography. Consequently, the protease purification level was increased by 95.2 fold. The final specific activity was getting to 448,590 U/mg on average, dominated by cysteine proteases, with optimal activity at 45°C and pH ranging from 6 to 8. The study facilitates the molecular and application research of fruit bromelain. PRACTICAL APPLICATIONS: The research has been carried out at Funong Food Technology Co., Ltd., Guangdong, China, which produces primarily pineapple chunks and juice. As plenty of by-products, like peels and cores of pineapples, are produced, the techniques are employed to extract bromelain from the by-products. The techniques reported in this work are not new or advanced, however, they are applicable during the manufacturing process and the related equipment is easy to set up and operate. What's more, the practical application of the techniques is cost-effective for the manufactories. Take Funong Food Technology Co., Ltd. as an example, they was using 80% saturation ammonium sulfate to precipitate protein from pineapple juice and obtained a bromelain with activity of approximately 8,000 U/mg and yield of 1.7 kg per ton of juice. With the application of the techniques reported in this work, bromelain was first extracted by ammonium sulfate gradient precipitation, and then purified through ion-exchange and gel filtration chromatography. Each step of precipitation and purification generates a different level of activity and recovery of bromelain, ranging from around 2,506 to 448,590 U/mg, which allows for the production of bromelain according to the requirement of the market and brings more profits.
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Affiliation(s)
- Zhiping Han
- College of Chemistry and Chemical Engineering, Lingnan Normal University, Zhanjiang, China
| | - Saelim Kraiyot
- Department of Industrial Biotechnology, Prince of Songkla University, Hat Yai, Thailand
| | - Aran H Kittikun
- Department of Industrial Biotechnology, Prince of Songkla University, Hat Yai, Thailand
| | - Wei Zhou
- Chinese Academy of Tropical Agricultural Sciences, Agricultural Product Processing Research Institute, Zhanjiang, China
| | - Jihua Li
- Chinese Academy of Tropical Agricultural Sciences, Agricultural Product Processing Research Institute, Zhanjiang, China
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20
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Razzaq A, Shamsi S, Ali A, Ali Q, Sajjad M, Malik A, Ashraf M. Microbial Proteases Applications. Front Bioeng Biotechnol 2019; 7:110. [PMID: 31263696 PMCID: PMC6584820 DOI: 10.3389/fbioe.2019.00110] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/01/2019] [Indexed: 11/13/2022] Open
Abstract
The use of chemicals around the globe in different industries has increased tremendously, affecting the health of people. The modern world intends to replace these noxious chemicals with environmental friendly products for the betterment of life on the planet. Establishing enzymatic processes in spite of chemical processes has been a prime objective of scientists. Various enzymes, specifically microbial proteases, are the most essentially used in different corporate sectors, such as textile, detergent, leather, feed, waste, and others. Proteases with respect to physiological and commercial roles hold a pivotal position. As they are performing synthetic and degradative functions, proteases are found ubiquitously, such as in plants, animals, and microbes. Among different producers of proteases, Bacillus sp. are mostly commercially exploited microbes for proteases. Proteases are successfully considered as an alternative to chemicals and an eco-friendly indicator for nature or the surroundings. The evolutionary relationship among acidic, neutral, and alkaline proteases has been analyzed based on their protein sequences, but there remains a lack of information that regulates the diversity in their specificity. Researchers are looking for microbial proteases as they can tolerate harsh conditions, ways to prevent autoproteolytic activity, stability in optimum pH, and substrate specificity. The current review focuses on the comparison among different proteases and the current problems faced during production and application at the industrial level. Deciphering these issues would enable us to promote microbial proteases economically and commercially around the world.
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Affiliation(s)
- Abdul Razzaq
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Sadia Shamsi
- School of Medicine, Medical Sciences and Nutrition, The Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Arfan Ali
- 1-FB, Genetics, Four Brothers Group, Lahore, Pakistan
| | - Qurban Ali
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Sajjad
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Arif Malik
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
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Biguanide is a modifiable pharmacophore for recruitment of endogenous Zn 2+ to inhibit cysteinyl cathepsins: review and implications. Biometals 2019; 32:575-593. [PMID: 31044334 PMCID: PMC6647370 DOI: 10.1007/s10534-019-00197-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/13/2019] [Indexed: 01/28/2023]
Abstract
Excessive activities of cysteinyl cathepsins (CysCts) contribute to the progress of many diseases; however, therapeutic inhibition has been problematic. Zn2+ is a natural inhibitor of proteases with CysHis dyads or CysHis(Xaa) triads. Biguanide forms bidentate metal complexes through the two imino nitrogens. Here, it is discussed that phenformin (phenylethyl biguanide) is a model for recruitment of endogenous Zn2+ to inhibit CysHis/CysHis(X) peptidolysis. Phenformin is a Zn2+-interactive, anti-proteolytic agent in bioassay of living tissue. Benzoyl-L-arginine amide (BAA) is a classical substrate of papain-like proteases; the amide bond is scissile. In this review, the structures of BAA and the phenformin-Zn2+ complex were compared in silico. Their chemistry and dimensions are discussed in light of the active sites of papain-like proteases. The phenyl moieties of both structures bind to the "S2" substrate-binding site that is typical of many proteases. When the phenyl moiety of BAA binds to S2, then the scissile amide bond is directed to the position of the thiolate-imidazolium ion pair, and is then hydrolyzed. However, when the phenyl moiety of phenformin binds to S2, then the coordinated Zn2+ is directed to the identical position; and catalysis is inhibited. Phenformin stabilizes a "Zn2+ sandwich" between the drug and protease active site. Hundreds of biguanide derivatives have been synthesized at the 1 and 5 nitrogen positions; many more are conceivable. Various substituent moieties can register with various arrays of substrate-binding sites so as to align coordinated Zn2+ with catalytic partners of diverse proteases. Biguanide is identified here as a modifiable pharmacophore for synthesis of therapeutic CysCt inhibitors with a wide range of potencies and specificities. Phenformin-Zn2+ Complex.
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Zhang S, Xu Z, Sun H, Sun L, Shaban M, Yang X, Zhu L. Genome-Wide Identification of Papain-Like Cysteine Proteases in Gossypium hirsutum and Functional Characterization in Response to Verticillium dahliae. FRONTIERS IN PLANT SCIENCE 2019; 10:134. [PMID: 30842780 PMCID: PMC6391353 DOI: 10.3389/fpls.2019.00134] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/28/2019] [Indexed: 05/12/2023]
Abstract
Cotton, a natural fiber producing crop of huge importance, is often prone to attack of Verticillium dahliae. Papain-like cysteine proteases (PLCPs) constitute a large family in plants and were proposed to involve in plant defense against pathogen attack in a number of studies. However, there is no detailed characterization of PLCP genes in cotton against infection of V. dahliae. In this study, we carried out a genome-wide analysis in cotton and identified seventy-eight PLCPs, which were divided into nine subfamilies based on their evolution phylogeny: RD21 (responsive to desiccation 21), CEP (cysteine endopeptidase), XCP (xylem cysteine peptidase), XBCP3 (xylem bark cysteine peptidase 3), THI, SAG12 (senescence-associated gene 12), RD19 (responsive to desiccation 19), ALP (aleurain-like protease) and CTB (cathepsin B-like). Genes in each subfamily exhibit a similar structure and motif composition. The expression patterns of these genes in different organs were examined, and subfamily RD21 was the most abundant in these families. Expression profiles under abiotic stress showed that thirty-five PLCP genes were induced by multiple stresses. Further transcriptome analysis showed that sixteen PLCP genes were up-regulated in response to V. dahliae in cotton. Among those, GhRD21-7 showed a higher transcription level than most other PLCP genes. Additionally, over-expression of GhRD21-7 led to enhanced resistance and RNAi lines were more susceptible to V. dahliae in cotton. Our results provide valuable information for future functional genomic studies of PLCP gene family in cotton.
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Balakireva AV, Deviatkin AA, Zgoda VG, Kartashov MI, Zhemchuzhina NS, Dzhavakhiya VG, Golovin AV, Zamyatnin AA. Proteomics Analysis Reveals That Caspase-Like and Metacaspase-Like Activities Are Dispensable for Activation of Proteases Involved in Early Response to Biotic Stress in Triticum aestivum L. Int J Mol Sci 2018; 19:ijms19123991. [PMID: 30544979 PMCID: PMC6320887 DOI: 10.3390/ijms19123991] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/04/2018] [Accepted: 12/08/2018] [Indexed: 12/15/2022] Open
Abstract
Plants, including Triticum aestivum L., are constantly attacked by various pathogens which induce immune responses. Immune processes in plants are tightly regulated by proteases from different families within their degradome. In this study, a wheat degradome was characterized. Using profile hidden Markov model (HMMer) algorithm and Pfam database, comprehensive analysis of the T. aestivum genome revealed a large number of proteases (1544 in total) belonging to the five major protease families: serine, cysteine, threonine, aspartic, and metallo-proteases. Mass-spectrometry analysis revealed a 30% difference between degradomes of distinct wheat cultivars (Khakasskaya and Darya), and infection by biotrophic (Puccinia recondita Rob. ex Desm f. sp. tritici) or necrotrophic (Stagonospora nodorum) pathogens induced drastic changes in the presence of proteolytic enzymes. This study shows that an early immune response to biotic stress is associated with the same core of proteases from the C1, C48, C65, M24, M41, S10, S9, S8, and A1 families. Further liquid chromatography-mass spectrometry (LC-MS) analysis of the detected protease-derived peptides revealed that infection by both pathogens enhances overall proteolytic activity in wheat cells and leads to activation of proteolytic cascades. Moreover, sites of proteolysis were identified within the proteases, which probably represent targets of autocatalytic activation, or hydrolysis by another protease within the proteolytic cascades. Although predicted substrates of metacaspase-like and caspase-like proteases were similar in biotrophic and necrotrophic infections, proteolytic activation of proteases was not found to be associated with metacaspase-like and caspase-like activities. These findings indicate that the response of T. aestivum to biotic stress is regulated by unique mechanisms.
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Affiliation(s)
- Anastasia V Balakireva
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia.
| | - Andrei A Deviatkin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia.
| | - Victor G Zgoda
- Institute of Biomedical Chemistry, Pogodinskaya str., 10, bld. 8, Moscow 119121, Russia.
| | - Maxim I Kartashov
- All Russian Research Institute of Phytopathology, VNIIF, Bolshie Vyazemi, Odintsovsky distr., Moscow region 143050, Russia.
| | - Natalia S Zhemchuzhina
- All Russian Research Institute of Phytopathology, VNIIF, Bolshie Vyazemi, Odintsovsky distr., Moscow region 143050, Russia.
| | - Vitaly G Dzhavakhiya
- All Russian Research Institute of Phytopathology, VNIIF, Bolshie Vyazemi, Odintsovsky distr., Moscow region 143050, Russia.
| | - Andrey V Golovin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia.
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia.
| | - Andrey A Zamyatnin
- Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya str., 8, bld. 2, Moscow 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
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