Phosphoproteomic Comparison of Four Eimeria tenella Life Cycle Stages

Ma, Xiu-Wen; Liu, Baohong; Gong, Zhenxing; Qu, Zigang; Cai, Jianping

doi:10.3390/ijms222212110

Cited by 9 publications

(8 citation statements)

References 62 publications

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“…TC-seq [ 27 ], Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of temporal patterns of time course data, can be applied to cluster genes based on gene expression patterns. In this study, TC-seq was employed for clustering the DEGs mentioned in 2.3.…”

Section: Methodsmentioning

confidence: 99%

Identification immune response genes in psoriasis after treatment with secukinumab

et al. 2023

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Background Secukinumab is a fully human IgG1κ MoAb that selectively binds to IL-17A with high affinity, and it has been proven effective for the treatment of psoriasis. However, the immune response pathways and mechanisms during the treatment are still masked. Therefore, the current study was designed to investigate the potential immune response genes via bioinformatics approaches. Methods Gene expression data of severe plaque-type psoriasis was retrieved from the GEO database. Quantification of immune infiltration by ssGSEA and identification of differentially infiltrated immune cells were conducted to validate the treatment effect of secukinumab. After data processing, differentially expressed genes were identified between the treatment and untreated group. TC-seq was employed to analyze the trend of gene expression and clustering analysis. IL-17 therapeutic immune response genes were selected by taking the intersection of the genes inside the key cluster set and the MAD3-PSO geneset. Based on these therapeutic response genes, protein–protein interaction networks were built for key hub gene selection. These hub genes would work as potential immune response genes, and be validated via an external dataset. Results Enrichment scores calculated by ssGSEA illustrated that the immune infiltration level of T cells had a strong difference before and after medication, which validated the treatment effect of Secukinumab. 1525 genes that have significantly different expression patterns before and after treatment were extracted for further analysis, and the enrichment result shows that these genes have the function related to epidermal development, differentiation, and keratinocytes differentiation. After overlapping candidate genes with MAD3-PSO gene set, 695 genes were defined as anti-IL7A treatment immune response genes, which were mainly enriched in receptor signaling and IL-17 signaling pathways. Hub gene were pinpointed from the PPI network constructed by anti-IL7A treatment immune response genes, their expression pattern fits TC-seq gene expression pattern. Conclusion Our study revealed the potential anti-IL7A treatment immune response genes, and the central hub genes, which may act critical roles in Secukinumab, induced immune response. This would open up a novel and effective avenue for the treatment of psoriasis.

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Section: Methodsmentioning

confidence: 99%

Identification immune response genes in psoriasis after treatment with secukinumab

et al. 2023

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“…The resulting MS/MS data were processed using Maxquant search engine (v.1.6.15.0, http://www.maxquant.org/). 34 Tandem mass spectra were searched against the UniProtKB_ Eimeria tenella database (Eimeria_tenella_5802_-UP_20200314, 8595 sequences) concatenated with a reverse decoy database. Trypsin/P was specified as cleavage enzyme allowing up to four missing cleavages.…”

Section: Ms/ms Analysismentioning

confidence: 99%

“…Cluster membership were visualized by a heat map using the "heatmap.2" function from the "gplots" R-package. 34…”

Section: Ms/ms Analysismentioning

confidence: 99%

Label-free quantitative detection and comparative analysis of lysine acetylation during the different life stages of Eimeria tenella

Gong

et al. 2023

J. Proteome Res.

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Proteome-wide lysine acetylation has been documented in apicomplexan parasite Toxoplasma gondii and Plasmodium falciparum. Here, we conducted the first lysine acetylome in unsporulated oocysts (USO), sporulated 7 h oocysts (SO 7h), sporulated oocysts (SO), sporozoites (S), and the second generation merozoites (SMG) of Eimeria tenella through a 4D label-free quantitative technique. Altogether, 8532 lysine acetylation sites on 2325 proteins were identified in E. tenella, among which 5445 sites on 1493 proteins were quantified. In addition, 557, 339, 478, 248, 241, and 424 differentially expressed proteins were identified in the comparisons SO7h vs USO, SO vs SO7h, SO vs USO, S vs SO, SMG vs S, and USO vs SMG, respectively. The bioinformatics analysis of the acetylome showed that the lysine acetylation is widespread on proteins of diverse functions. Moreover, the dynamic changes of lysine acetylome among E. tenella different life stages revealed significant regulation during the whole process of E. tenella growth and stage conversion. This study provides a beginning for the investigation of the regulate role of lysine acetylation in E. tenella and may provide new strategies for anticoccidiosis drug and vaccine development. Raw data are publicly available at iProX with the data set identifier PXD040368.

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“…Three species, E. acervulina , E. maxima , and E. tenella , are most common in young chickens and become highly pathogenic when they mature ( Clark et al., 2016 ). Several cysteine proteases related to the UCH and OTU domain family of deubiquitinase enzymes have shown their expression at different phases of the E. tenella life cycle ( Ma et al., 2021 ). RNA-dependent RNA polymerase of E. tenella was found to be associated with the deubiquitinating enzyme of the OTU domain family protein of the host.…”

Section: Functional Role Of Dubs Indifferent Parasitesmentioning

confidence: 99%

The emerging role of Deubiquitinases (DUBs) in parasites: A foresight review

Kumar

Mandal

et al. 2022

Front. Cell. Infect. Microbiol.

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Before the discovery of the proteasome complex, the lysosomes with acidic proteases and caspases in apoptotic pathways were thought to be the only pathways for the degradation of damaged, unfolded, and aged proteins. However, the discovery of 26S and 20S proteasome complexes in eukaryotes and microbes, respectively, established that the degradation of most proteins is a highly regulated ATP-dependent pathway that is significantly conserved across each domain of life. The proteasome is part of the ubiquitin-proteasome system (UPS), where the covalent tagging of a small molecule called ubiquitin (Ub) on the proteins marks its proteasomal degradation. The type and chain length of ubiquitination further determine whether a protein is designated for further roles in multi-cellular processes like DNA repair, trafficking, signal transduction, etc., or whether it will be degraded by the proteasome to recycle the peptides and amino acids. Deubiquitination, on the contrary, is the removal of ubiquitin from its substrate molecule or the conversion of polyubiquitin chains into monoubiquitin as a precursor to ubiquitin. Therefore, deubiquitylating enzymes (DUBs) can maintain the dynamic state of cellular ubiquitination by releasing conjugated ubiquitin from proteins and controlling many cellular pathways that are essential for their survival. Many DUBs are well characterized in the human system with potential drug targets in different cancers. Although, proteasome complex and UPS of parasites, like plasmodium and leishmania, were recently coined as multi-stage drug targets the role of DUBs is completely unexplored even though structural domains and functions of many of these parasite DUBs are conserved having high similarity even with its eukaryotic counterpart. This review summarizes the identification & characterization of different parasite DUBs based on in silico and a few functional studies among different phylogenetic classes of parasites including Metazoan (Schistosoma, Trichinella), Apicomplexan protozoans (Plasmodium, Toxoplasma, Eimeria, Cryptosporidium), Kinetoplastidie (Leishmania, Trypanosoma) and Microsporidia (Nosema). The identification of different homologs of parasite DUBs with structurally similar domains with eukaryotes, and the role of these DUBs alone or in combination with the 20S proteosome complex in regulating the parasite survival/death is further elaborated. We propose that small molecules/inhibitors of human DUBs can be potential antiparasitic agents due to their significant structural conservation.

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Phosphoproteomic Comparison of Four Eimeria tenella Life Cycle Stages

Cited by 9 publications

References 62 publications

Identification immune response genes in psoriasis after treatment with secukinumab

Identification immune response genes in psoriasis after treatment with secukinumab

Label-free quantitative detection and comparative analysis of lysine acetylation during the different life stages of Eimeria tenella

The emerging role of Deubiquitinases (DUBs) in parasites: A foresight review

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