scholarly journals Identification and Functional Study of Chitin Metabolism and Detoxification-Related Genes in Glyphodes pyloalis Walker (Lepidoptera: Pyralidae) Based on Transcriptome Analysis

2020 ◽  
Vol 21 (5) ◽  
pp. 1904 ◽  
Author(s):  
Zuo-min Shao ◽  
Yi-jiangcheng Li ◽  
Xiao-rui Zhang ◽  
Jie Chu ◽  
Jia-hui Ma ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Transcriptome Analysis ◽  
Effective Control ◽  
Functional Study ◽  
Transcriptome Data ◽  
Protein Protein Interactions ◽  
Glutathione S Transferase ◽  
Expression Levels ◽  
Glyphodes Pyloalis ◽  
Lepidoptera Pyralidae

Glyphodes pyloalis Walker (Lepidoptera: Pyralididae) is a serious pest in the sericulture industry, which has caused damage and losses in recent years. With the widespread use of insecticides, the insecticide resistance of G. pyloalis has becomes increasingly apparent. In order to find other effective methods to control G. pyloalis, this study performed a transcriptome analysis of the midgut, integument, and whole larvae. Transcriptome data were annotated with KEGG and GO, and they have been shown to be of high quality by RT-qPCR. The different significant categories of differentially expressed genes between the midgut and the integument suggested that the transcriptome data could be used for next analysis. With the exception of Dda9 (GpCDA5), 19 genes were involved in chitin metabolism, most of which had close protein–protein interactions. Among them, the expression levels of 11 genes, including GpCHSA, GpCDA1, GpCDA2, GpCDA4, GPCHT1, GPCHT2a, GPCHT3a, GPCHT7, GpTre1, GpTre2, and GpRtv were higher in the integument than in the midgut, while the expression levels of the last eight genes, including GpCHSB, GpCDA5, GpCHT2b, GpCHT3b, GpCHT-h, GpPAGM, GpNAGK, and GpUAP, were higher in the midgut than in the integument. Moreover, 282 detoxification-related genes were identified and can be divided into 10 categories, including cytochrome P450, glutathione S-transferase, carboxylesterase, nicotinic acetylcholine receptor, aquaporin, chloride channel, methoprene-tolerant, serine protease inhibitor, sodium channel, and calcium channel. In order to further study the function of chitin metabolism-related genes, dsRNA injection knocked down the expression of GpCDA1 and GpCHT3a, resulting in the significant downregulation of its downstream genes. These results provide an overview of chitin metabolism and detoxification of G. pyloalis and lay the foundation for the effective control of this pest in the sericulture industry.

scholarly journals Identification of Glutathione S-Transferase Genes in Hami Melon (Cucumis melo var. saccharinus) and Their Expression Analysis Under Cold Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Wen Song ◽  
Fake Zhou ◽  
Chunhui Shan ◽  
Qin Zhang ◽  
Ming Ning ◽  
...  
Keyword(s):  
Cold Stress ◽  
Expression Analysis ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Glutathione S Transferase ◽  
Expression Levels ◽  
Cellular Detoxification ◽  
Cold Tolerant ◽  
Gene Structures ◽  
Stress Related Genes

As a group of multifunctional enzymes, glutathione S-transferases (GSTs) participate in oxidative stress resistance and cellular detoxification. Here, we identified 39 CmGST genes with typical binding sites from the Hami melon genome, and they can be classified into seven subfamilies. Their molecular information, chromosomal locations, phylogenetic relationships, synteny relationships, gene structures, protein–protein interactions, structure of 3-D models, and expression levels under cold stress were analyzed. Expression analysis indicates that cold-tolerant Jia Shi-310 (JS) had higher GST enzyme activities and expression levels of 28 stress-related genes under cold stress. Some CmGSTs belonging to Tau, Phi, and DHAR classes play significant roles under cold stress, and they could be regarded as candidate genes for further studies. The present study systematically investigated the characterization of the Hami melon GST gene family, extending our understanding of Hami melon GST mediated stress-response mechanisms in this worldwide fruit.

scholarly journals Tracking chromatin state changes using μMap photo-proximity labeling

2021 ◽  
Author(s):  
Ciaran P Seath ◽  
Antony J Burton ◽  
David W. C. MacMillan ◽  
Tom W Muir
Keyword(s):  
Cell Fate ◽  
Small Molecule ◽  
Protein Interactions ◽  
Control Cell ◽  
Global Changes ◽  
Therapeutic Effects ◽  
Protein Protein Interactions ◽  
Chromatin Remodelers ◽  
Expression Levels ◽  
Epigenetic Drug

Interactions between biomolecules, particularly proteins, underlie all cellular processes, and ultimately control cell fate. Perturbation of native interactions through mutation, changes in expression levels, or external stimuli leads to altered cellular physiology and can result in either disease or therapeutic effects. Mapping these interactions and determining how they respond to stimulus is the genesis of many drug development efforts, leading to new therapeutic targets and improvements in human health. However, in the complex environment of the nucleus it is challenging to determine protein-protein interactions due to low abundance, transient or multi-valent binding, and a lack of technologies that are able to interrogate these interactions without disrupting the protein binding surface under study. Chromatin remodelers, modifying enzymes, interactors, and transcription factors can all be redirected by subtle changes to the microenvironment, causing global changes in protein expression levels and subsequent physiology. Here, we describe the Chroma-μMap method for the traceless incorporation of Ir-photosensitizers into the nuclear microenvironment using engineered split inteins. These Ir-catalysts can activate diazirine warheads to form reactive carbenes within a ~10 nm radius, cross-linking with proteins within the immediate microenvironment for analysis via quantitative chemoproteomics. We demonstrate this concept on nine different nuclear proteins with varied function and in each case, elucidating their microenvironments. Additionally, we show that this short-range proximity labelling method can reveal the critical changes in interactomes in the presence of cancer-associated mutations, as well as treatment with small-molecule inhibitors. Chroma-μMap improves our fundamental understanding of nuclear protein-protein interactions, as well as the effects that small molecule therapeutics have on the local chromatin environment, and in doing so is expected to have a significant impact on the field of epigenetic drug discovery in both academia and industry.

scholarly journals Tracking chromatin state changes using µMap photo-proximity labeling

2021 ◽  
Author(s):  
Tom Muir ◽  
Ciaran Seath ◽  
David MacMillan ◽  
Antony Burton
Keyword(s):  
Cell Fate ◽  
Small Molecule ◽  
Protein Interactions ◽  
Control Cell ◽  
Global Changes ◽  
Therapeutic Effects ◽  
Protein Protein Interactions ◽  
Chromatin Remodelers ◽  
Expression Levels ◽  
Epigenetic Drug

Abstract Interactions between biomolecules, particularly proteins, underlie all cellular processes, and ultimately control cell fate. Perturbation of native interactions through mutation, changes in expression levels, or external stimuli leads to altered cellular physiology and can result in either disease or therapeutic effects. Mapping these interactions and determining how they respond to stimulus is the genesis of many drug development efforts, leading to new therapeutic targets and improvements in human health. However, in the complex environment of the nucleus it is challenging to determine protein-protein interactions due to low abundance, transient or multi-valent binding, and a lack of technologies that are able to interrogate these interactions without disrupting the protein binding surface under study. Chromatin remodelers, modifying enzymes, interactors, and transcription factors can all be redirected by subtle changes to the microenvironment, causing global changes in protein expression levels and subsequent physiology. Here, we describe the Chroma-µMap method for the traceless incorporation of Ir-photosensitizers into the nuclear microenvironment using engineered split inteins. These Ir-catalysts can activate diazirine warheads to form reactive carbenes within a ~10 nm radius, cross-linking with proteins within the immediate microenvironment for analysis via quantitative chemoproteomics. We demonstrate this concept on nine different nuclear proteins with varied function and in each case, elucidating their microenvironments. Additionally, we show that this short-range proximity labeling method can reveal the critical changes in interactomes in the presence of cancer-associated mutations, as well as treatment with small-molecule inhibitors. Chroma-µMap improves our fundamental understand-ing of nuclear protein-protein interactions, as well as the effects that small molecule therapeutics have on the local chromatin environment, and in doing so is expected to have a significant impact on the field of epigenetic drug discovery in both academia and industry.

scholarly journals A protein-domain microarray identifies novel protein–protein interactions

2002 ◽  
Vol 367 (3) ◽  
pp. 697-702 ◽  
Author(s):  
Alexsandra ESPEJO ◽  
Jocelyn CÔTÉ ◽  
Andrzej BEDNAREK ◽  
Stephane RICHARD ◽  
Mark T. BEDFORD
Keyword(s):  
Protein Interactions ◽  
Cellular Protein ◽  
Protein Domain ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Glutathione S Transferase ◽  
Binding Profile ◽  
Peptide Motifs ◽  
Small Nuclear Ribonucleoprotein ◽  
Interaction Map

Protein domains mediate protein—protein interactions through binding to short peptide motifs in their corresponding ligands. These peptide recognition modules are critical for the assembly of multiprotein complexes. We have arrayed glutathione S-transferase (GST) fusion proteins, with a focus on protein interaction domains, on to nitrocellulose-coated glass slides to generate a protein-domain chip. Arrayed protein-interacting modules included WW (a domain with two conserved tryptophans), SH3 (Src homology 3), SH2, 14.3.3, FHA (forkhead-associated), PDZ (a domain originally identified in PSD-95, DLG and ZO-1 proteins), PH (pleckstrin homology) and FF (a domain with two conserved phenylalanines) domains. Here we demonstrate, using peptides, that the arrayed domains retain their binding integrity. Furthermore, we show that the protein-domain chip can ‘fish’ proteins out of a total cell lysate; these domain-bound proteins can then be detected on the chip with a specific antibody, thus producing an interaction map for a cellular protein of interest. Using this approach we have confirmed the domain-binding profile of the signalling molecule Sam68 (Src-associated during mitosis 68), and have identified a new binding profile for the core small nuclear ribonucleoprotein SmB′. This protein-domain chip not only identifies potential binding partners for proteins, but also promises to recognize qualitative differences in protein ligands (caused by post-translational modification), thus getting at the heart of signal transduction pathways.

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