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Sun Y, Wang Y, Li Y, Li H, Wang C, Zhang Q. Comparative transcriptome and proteome analyses of the longissimus dorsi muscle for explaining the difference between donkey meat and other meats. Anim Biotechnol 2023; 34:3085-3098. [PMID: 36271875 DOI: 10.1080/10495398.2022.2134883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Domestic donkeys (Equus asinus) have been maintained mainly for service purposes in the past. Nowadays, there is an increasing interest in donkey milk and meat production in several countries, including China. Donkey meat is highly consumed because of its nutritional value and unique flavor. However, genomic studies on donkey meat are limited. Therefore, in this study, we aimed to examine the molecular difference of longissimus dorsi muscles of donkey, cow, and goat. RNA sequencing and Proteome sequencing technology were used to analyze the transcriptome and proteome of the longissimus dorsi muscle of donkey, cow, and goat. A total of 1338 and 1780 differentially expressed genes (DEGs) were identified in donkey meat compared with that in cow and goat meat, respectively. Most of the DEGs were involved in biological processes, including small GTPase-mediated signal transduction, protein ubiquitination, protein glycosylation, and MAP kinase tyrosine/serine/threonine phosphatase activity. Additionally, 764 and 1024 differentially expressed proteins (DEPs) were identified in cow vs. donkey, and goat vs. donkey, respectively; these DEPs were mainly involved in metabolism. Genetic variation and regulatory factors can combine as a database to provide more valuable molecular information for further analysis.
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Affiliation(s)
- Yan Sun
- Shandong Provincial Key Laboratory of Animal Biotochnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
| | - Yonghui Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Yuhua Li
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Haijing Li
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotochnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, China
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2
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Coelho D, Ribeiro D, Osório H, de Almeida AM, Prates JAM. Integrated Omics analysis of pig muscle metabolism under the effects of dietary Chlorella vulgaris and exogenous enzymes. Sci Rep 2022; 12:16992. [PMID: 36216870 PMCID: PMC9551059 DOI: 10.1038/s41598-022-21466-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/27/2022] [Indexed: 12/29/2022] Open
Abstract
Monogastric feeding is dependent on costly conventional feedstuffs. Microalgae such as Chlorella vulgaris are a sustainable alternative; however, its recalcitrant cell wall hinders monogastric digestion. Carbohydrate Active Enzyme (CAZyme) supplementation is a possible solution. The objective of this work was to evaluate the effect of 5% dietary C. vulgaris (CV) and enzymatic supplementation (CV + R-Rovabio® Excel AP; CV + M-four CAZyme mix) on muscle transcriptome and proteome of finishing pigs, in an integrated approach. Control pigs increased the abundance of contractile apparatus (MYH1, MYH2, MYH4) and energy metabolism (CKMT1, NDUFS3) proteins, demonstrating increased nutrient availability. They had increased expression of SCD, characteristic of increased glucose availability, via the activation of SREBP-1c and ChREBP. CV and CV + R pigs upregulated proteolytic and apoptotic genes (BAX, DDA1), whilst increasing the abundance of glucose (UQCRFS1) and fatty acid catabolism (ACADS) proteins. CV + R pigs upregulated ACOT8 and SIRT3 genes as a response to reduced nutrient availability, maintaining energy homeostasis. The cell wall specific CAZyme mix, CV + M, was able to comparatively reduce Omics alterations in the muscle, thereby reducing endogenous nutrient catabolism compared to the CV + R and CV.
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Affiliation(s)
- Diogo Coelho
- CIISA - Centro de Investigação Interdisciplinar Em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Alto da Ajuda, 1300-477, Lisbon, Portugal
- Laboratório Associado Para Ciência Animal E Veterinária (AL4AnimalS), Lisbon, Portugal
| | - David Ribeiro
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - Hugo Osório
- i3S - Instituto de Investigação E Inovação Em Saúde, Universidade Do Porto, 4200-135, Porto, Portugal
- IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Universidade Do Porto, 4200-135, Porto, Portugal
- Departamento de Patologia, Faculdade de Medicina, Universidade Do Porto, 4200-319, Porto, Portugal
| | - André Martinho de Almeida
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisbon, Portugal
| | - José António Mestre Prates
- CIISA - Centro de Investigação Interdisciplinar Em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Alto da Ajuda, 1300-477, Lisbon, Portugal.
- Laboratório Associado Para Ciência Animal E Veterinária (AL4AnimalS), Lisbon, Portugal.
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3
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Chen R, Song Y, Yang M, Wen C, Liu Q, Zhuang S, Zhou Y. Effect of Dietary Betaine on Muscle Protein Deposition, Nucleic Acid and Amino Acid Contents, and Proteomes of Broilers. Animals (Basel) 2022; 12:ani12060736. [PMID: 35327133 PMCID: PMC8944442 DOI: 10.3390/ani12060736] [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: 01/05/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022] Open
Abstract
To investigate the effect of betaine supplementation on growth performance, muscle protein deposition, muscle nucleic acid and amino acid contents, and muscle proteome of broilers, 160 one-day-old male partridge shank broiler chickens were randomly divided into 2 groups with 8 replicates of 10 broilers each. Broilers were fed a basal diet alone, or a basal diet supplemented with 1000 mg/kg betaine. Compared with the control group, the betaine group significantly increased (p < 0.05) the broilers average daily gain, the levels of serum insulin-like growth factor-1 (IGF-1), growth hormone (GH), total protein (TP), the contents of muscle absolute protein deposition, RNA, Ser, Glu, Met, and Phe, and the ratio of RNA/DNA, and decreased (p < 0.05) the feed conversion ratio and serum blood urea nitrogen content. Moreover, proteomic analysis revealed 35 differentially abundant proteins (DAPs) in the betaine group compared with the control group, including 27 upregulated proteins and 8 downregulated proteins (p < 0.05). These DAPs were mainly related to cell differentiation, small molecule metabolic process, and tissue development. In conclusion, diets supplemented with 1000 mg/kg betaine improved growth performance and muscle protein deposition of broilers. Increased serum GH, IGF-1, and TP contents, and alterations in muscle nucleic acids, amino acids, and protein abundance levels were involved in this process.
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Zhou CY, Pan DD, Cao JX, Zhou GH. A comprehensive review on molecular mechanism of defective dry-cured ham with excessive pastiness, adhesiveness, and bitterness by proteomics insights. Compr Rev Food Sci Food Saf 2021; 20:3838-3857. [PMID: 34118135 DOI: 10.1111/1541-4337.12779] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/14/2021] [Accepted: 05/03/2021] [Indexed: 02/01/2023]
Abstract
Excessive bitterness, pastiness, and adhesiveness are the main organoleptic and textural defects of dry-cured ham, which often cause a lot of financial losses to manufacturers and seriously damage the quality of the product. These sensory and textural defects are related to the protein degradation of dry-cured ham. Proteomics shows great potential to improve our understanding of the molecular mechanism of sensory and textural defects and identify biomarkers for monitoring their quality traits. This review presents some of the major achievements and considerations in organoleptic and textural defects of dry-cured ham by proteomics analysis in the recent decades and gives an overview about how to correct sensory and textural defects of dry-cured ham. Proteomics reveals that muscle proteins derived from myofibril and cytoskeleton and involved in metabolic enzymes and oxygen transport have been identified as potential biomarkers in defective dry-cured ham. Relatively high residual activities of cathepsin B and L are responsible for the excessive degradation of these protein biomarkers in defective dry-cured ham. Ultrasound-assisted mild thermal or high-pressure treatment shows a good correction for the organoleptic and textural defects of dry-cured ham by changing microstructure and conformation of muscle proteins by accelerating degradation of proteins and polypeptides into free amino acids.
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Affiliation(s)
- Chang-Yu Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China.,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China.,Key Laboratory of Meat Processing and Quality Control, MOE, Nanjing Agricultural University, Nanjing, P.R. China.,Key Laboratory of Meat Processing, MOA, Nanjing Agricultural University, Nanjing, P.R. China.,Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, P.R. China
| | - Dao-Dong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China.,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Jin-Xuan Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China.,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food & Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Guang-Hong Zhou
- Key Laboratory of Meat Processing and Quality Control, MOE, Nanjing Agricultural University, Nanjing, P.R. China.,Key Laboratory of Meat Processing, MOA, Nanjing Agricultural University, Nanjing, P.R. China.,Jiangsu Synergetic Innovation Center of Meat Processing and Quality Control, Nanjing Agricultural University, Nanjing, P.R. China
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Li T, Li Q, Li H, Xiao X, Ahmad Warraich D, Zhang N, Chen Z, Hou J, Liu T, Weng X, Liu Z, Hua J, Liao M. Pig-specific RNA editing during early embryo development revealed by genome-wide comparisons. FEBS Open Bio 2020; 10:1389-1402. [PMID: 32433824 PMCID: PMC7327910 DOI: 10.1002/2211-5463.12900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/15/2020] [Indexed: 12/19/2022] Open
Abstract
Posttranscriptional modification of mRNA sequences through RNA editing can increase transcriptome and proteome diversity in eukaryotes. Studies of fetal and adult tissues showed that adenosine‐to‐inosine RNA editing plays a crucial role in early human development, but there is a lack of global understanding of dynamic RNA editing during mammalian early embryonic development. Therefore, here we used RNA sequencing data from human, pig and mouse during early embryonic development to detect edited genes that may regulate stem cell pluripotency. We observed that although most of the RNA editing sites are located in intergenic, intron and UTR, a few editing sites are in coding regions and may result in nonsynonymous amino acid changes. Some editing sites are predicted to change the structure of a protein. We also report that HNF1A, TBX3, ACLY, ECI1 and ERDR1 are related to embryonic development and cell division.
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Affiliation(s)
- Tongtong Li
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Qun Li
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Hao Li
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Xia Xiao
- College of Life Sciences, Northwest A&F University, Yangling, China
| | | | - Ning Zhang
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Ziyun Chen
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Junyao Hou
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Tong Liu
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaogang Weng
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jinlian Hua
- College of Veterinary Medicine, Shaanxi Centre of Stem Cells Engineering & Technology, Northwest A&F University, Yangling, China
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Yangling, China
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6
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Ren W, Badgery W, Ding Y, Guo H, Gao Y, Zhang J. Hepatic transcriptome profile of sheep (Ovis aries) in response to overgrazing: novel genes and pathways revealed. BMC Genet 2019; 20:54. [PMID: 31272371 PMCID: PMC6610972 DOI: 10.1186/s12863-019-0760-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/26/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Overgrazing is a major factor that causes steppe degradation in Inner Mongolian, resulting in extensive ecosystem damage. Scarcity of grass means sheep are smaller and therefore mutton and cashmere production is greatly reduced, which has resulted in massive annual economic losses. Liver is the primary metabolic organ in mammals. It is also the key source of energy supply and detoxification of metabolites in animals, has a close relationship with animal growth. However, investigations on the responses of sheep induced by consequence of overgrazing, particularly those relating to liver-related molecular mechanisms and related metabolic pathways, remain elusive. RESULTS The body weight daily gain of sheep, immune organ indices (liver and spleen), and serum parameters related to immune response, protein synthesis and energy supply (IgG, albumin, glucose and non-esterified fatty acid) were significantly lower in the overgrazing group. Other serum parameters including alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase, total bilirubin, blood urea nitrogen and interleukin-6 were significantly higher in the overgrazing group. For the RNA-Seq results, we identified approximately 50 differentially expressed genes, of which half of were up-regulated and the other half were down-regulated (overgrazing group versus light grazing group). Bioinformatics analysis identified two enriched KEGG pathways including peroxisome proliferator-activated receptor (PPAR) signaling pathway (related to lipolysis) and ECM-receptor interaction (related to liver injury and apoptosis). Additionally, several of the down-regulated genes were related to detoxification and immune response. CONCLUSIONS Overall, based on the high-throughput RNA sequencing profile integrated with the results of serum biochemical analyses, consequences of lower forage availability and quality under overgrazing condition induced altered expression levels of genes participating in energy metabolism (particularly lipid metabolism) and detoxification and immune responses, causing lipolysis and impaired health status, which might be key reasons for the reduced growth performance of sheep. This investigation provides a novel foundation for the development of sheep hepatic gene interactive networks that are a response to the degraded forage availability under overgrazing condition.
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Affiliation(s)
- Weibo Ren
- Key Laboratory of Forage Grass, Ministry of Agriculture, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, Inner Mongolia, China
| | - Warwick Badgery
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW, 2800, Australia
| | - Yong Ding
- Key Laboratory of Forage Grass, Ministry of Agriculture, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, Inner Mongolia, China
| | - Huiqin Guo
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010019, Inner Mongolia, China
| | - Yang Gao
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130018, Jilin, China
| | - Jize Zhang
- Key Laboratory of Forage Grass, Ministry of Agriculture, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, 010010, Inner Mongolia, China.
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7
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De novo transcriptomic profiling of the clonal Leymus chinensis response to long-term overgrazing-induced memory. Sci Rep 2018; 8:17912. [PMID: 30559460 PMCID: PMC6297159 DOI: 10.1038/s41598-018-35605-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/07/2018] [Indexed: 01/26/2023] Open
Abstract
Sheepgrass (Leymus chinensis) is one of the dominant grass species present on typical steppes of the Inner Mongolia Plateau. However, L. chinensis has developed a dwarfing phenotype in response to the stressful habitat in grasslands that are severely degraded due to heavy grazing. The lack of transcriptomic and genomic information has prohibited the understanding of the transgenerational effect on physiological alterations in clonal L. chinensis at the molecular level in response to livestock grazing. To solve this problem, transcriptomic information from the leaves of clonal L. chinensis obtained from overgrazed (GR) and non-grazed (NG) grasslands was studied using a paired-end Illumina HiSeq 2500 sequencing platform. First, despite the influence of grazing being absent during the growth of clonal offspring in our hydroponic experiment, compared with those from the NG group, clonal L. chinensis from the GR group exhibited significant dwarf-type morphological traits. A total of 116,356 unigenes were subsequently generated and assembled de novo, of which 55,541 could be annotated to homologous matches in the NCBI non-redundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The expression of 3,341 unigenes significantly differed between the GR group and the NG group with an absolute value of Log2 ratio ≥ 1. The altered expression of genes involved in defence and immune responses, pathogenic resistance and cell development indicates that livestock grazing induces a transgenerational effect on the growth inhibition of clonal L. chinensis. The results of the present study will provide important large-scale transcriptomic information on L. chinensis. Furthermore, the results facilitated our investigation of grazing-induced transgenerational effects on both the morphological and physiological characteristics of L. chinensis at the molecular levels.
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8
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Shi J, Zhang L, Lei Y, Shen H, Yu X, Luo Y. Differential proteomic analysis to identify proteins associated with quality traits of frozen mud shrimp ( Solenocera melantho ) using an iTRAQ-based strategy. Food Chem 2018; 251:25-32. [DOI: 10.1016/j.foodchem.2018.01.046] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/28/2017] [Accepted: 01/04/2018] [Indexed: 12/16/2022]
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9
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Navarrete-Perea J, Isasa M, Paulo JA, Corral-Corral R, Flores-Bautista J, Hernández-Téllez B, Bobes RJ, Fragoso G, Sciutto E, Soberón X, Gygi SP, Laclette JP. Quantitative multiplexed proteomics of Taenia solium cysts obtained from the skeletal muscle and central nervous system of pigs. PLoS Negl Trop Dis 2017; 11:e0005962. [PMID: 28945737 PMCID: PMC5634658 DOI: 10.1371/journal.pntd.0005962] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 10/10/2017] [Accepted: 09/13/2017] [Indexed: 01/01/2023] Open
Abstract
In human and porcine cysticercosis caused by the tapeworm Taenia solium, the larval stage (cysts) can infest several tissues including the central nervous system (CNS) and the skeletal muscles (SM). The cyst’s proteomics changes associated with the tissue localization in the host tissues have been poorly studied. Quantitative multiplexed proteomics has the power to evaluate global proteome changes in response to different conditions. Here, using a TMT-multiplexed strategy we identified and quantified over 4,200 proteins in cysts obtained from the SM and CNS of pigs, of which 891 were host proteins. To our knowledge, this is the most extensive intermixing of host and parasite proteins reported for tapeworm infections.Several antigens in cysticercosis, i.e., GP50, paramyosin and a calcium-binding protein were enriched in skeletal muscle cysts. Our results suggested the occurrence of tissue-enriched antigen that could be useful in the improvement of the immunodiagnosis for cysticercosis. Using several algorithms for epitope detection, we selected 42 highly antigenic proteins enriched for each tissue localization of the cysts. Taking into account the fold changes and the antigen/epitope contents, we selected 10 proteins and produced synthetic peptides from the best epitopes. Nine peptides were recognized by serum antibodies of cysticercotic pigs, suggesting that those peptides are antigens. Mixtures of peptides derived from SM and CNS cysts yielded better results than mixtures of peptides derived from a single tissue location, however the identification of the ‘optimal’ tissue-enriched antigens remains to be discovered. Through machine learning technologies, we determined that a reliable immunodiagnostic test for porcine cysticercosis required at least five different antigenic determinants. Human and porcine cysticercosis caused by Taenia solium is a parasite disease still endemic in developing countries. The cysts can be located in different host tissues, including different organs of the central nervous system and the skeletal muscles. The molecular mechanisms associated with the tissue localization of the cysts are not well understood. Here, we described the proteome changes of the cysts obtained from different host tissues from infected pigs using quantitative multiplex proteomics. We explored the diversity of host proteins identified in the cyst’s protein extracts and we also explored the immune-localization of several host-related proteins within the cysts, and propose their possible function. We identified several proteins and antigens enriched for a given tissue localization. Several synthetic peptides designed from these tissue-enriched antigens were tested trough ELISA. Using a combination of peptide mixtures and machine learning technologies we were able to distinguish non cysticercotic and cysticercotic pig’s sera. The tissue-enriched proteins/antigens could be useful for the development of improved immuno-diagnostic tests capable of discriminate the tissue-localization of the cysts.
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Affiliation(s)
- José Navarrete-Perea
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Marta Isasa
- Dept. of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joao A Paulo
- Dept. of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ricardo Corral-Corral
- Dept. of Biochemistry and Structural Biology, Institute of Cell Physiology, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Jeanette Flores-Bautista
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Beatriz Hernández-Téllez
- Dept. of Tissue and Cell Biology, School of Medicine, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Raúl J Bobes
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Gladis Fragoso
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Edda Sciutto
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Xavier Soberón
- Instituto Nacional de Medicina Genómica, Ciudad de México, México.,Dept. of Biocatalysis and Cellular Engineering, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Morelos, México
| | - Steven P Gygi
- Dept. of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Juan P Laclette
- Dept. of Immunology, Institute for Biomedical Research, Universidad Nacional Autónoma de México, Ciudad de México, México
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10
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Sharma Ghimire P, Ouyang H, Wang Q, Luo Y, Shi B, Yang J, Lü Y, Jin C. Insight into Enzymatic Degradation of Corn, Wheat, and Soybean Cell Wall Cellulose Using Quantitative Secretome Analysis of Aspergillus fumigatus. J Proteome Res 2016; 15:4387-4402. [PMID: 27618962 DOI: 10.1021/acs.jproteome.6b00465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lignocelluloses contained in animal forage cannot be digested by pigs or poultry with 100% efficiency. On contrary, Aspergillus fumigatus, a saprophytic filamentous fungus, is known to harbor 263 glycoside hydrolase encoding genes, suggesting that A. fumigatus is an efficient lignocellulose degrader. Hence the present study uses corn, wheat, or soybean as a sole carbon source to culture A. fumigatus under animal physiological condition to understand how cellulolytic enzymes work together to achieve an efficient degradation of lignocellulose. Our results showed that A. fumigatus produced different sets of enzymes to degrade lignocelluloses derived from corn, wheat, or soybean cell wall. In addition, the cellulolytic enzymes produced by A. fumigatus were stable under acidic condition or at higher temperatures. Using isobaric tags for a relative and absolute quantification (iTRAQ) approach, a total of ∼600 extracellular proteins were identified and quantified, in which ∼50 proteins were involved in lignocellulolysis, including cellulases, hemicellulases, lignin-degrading enzymes, and some hypothetical proteins. Data are available via ProteomeXchange with identifier PXD004670. On the basis of quantitative iTRAQ results, 14 genes were selected for further confirmation by RT-PCR. Taken together, our results indicated that the expression and regulation of lignocellulolytic proteins in the secretome of A. fumigatus were dependent on both nature and complexity of cellulose, thus suggesting that a different enzyme system is required for degradation of different lignocelluloses derived from plant cells. Although A. fumigatus is a pathogenic fungus and cannot be directly used as an enzyme source, as an efficient lignocellulose degrader its strategy to synergistically degrade various lignocelluloses with different enzymes can be used to design enzyme combination for optimal digestion and absorption of corn, wheat, or soybean that are used as forage of pig and poultry.
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Affiliation(s)
- Prakriti Sharma Ghimire
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100101, China
- Himalayan Environment Research Institute (HERI) , Bouddha-6, Kathmandu, Nepal
| | - Haomiao Ouyang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Qian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Yuanming Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Bo Shi
- Feed Research Institute, Chinese Academy of Agricultural Sciences , Beijing 100081, China
| | - Jinghua Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Yang Lü
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
| | - Cheng Jin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
- University of Chinese Academy of Sciences , Beijing 100101, China
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11
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Yan XH. Molecular nutrition: basic understanding of the digestion, absorption, and metabolism of nutrients. J Zhejiang Univ Sci B 2015; 16:413-6. [PMID: 26055903 DOI: 10.1631/jzus.b1500130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Xiang-hua Yan
- College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China
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