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

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.

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

International Journal of Molecular Sciences ◽

10.3390/ijms21051904 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1904 ◽

Cited By ~ 1

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.

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Evolution of Proteins and Gene Expression Levels are Coupled in Drosophila and are Independently Associated with mRNA Abundance, Protein Length, and Number of Protein-Protein Interactions

Molecular Biology and Evolution ◽

10.1093/molbev/msi122 ◽

2005 ◽

Vol 22 (5) ◽

pp. 1345-1354 ◽

Cited By ~ 174

Author(s):

B. Lemos

Keyword(s):

Gene Expression ◽

Protein Interactions ◽

Mrna Abundance ◽

Protein Protein Interactions ◽

Expression Levels ◽

Protein Length ◽

Evolution Of Proteins ◽

Gene Expression Levels

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Single-Molecule Methods for the Large-Scale Characterization of Expression Levels and Protein-Protein Interactions in Shewanella Oneidensis MR-1

10.2172/1010284 ◽

2008 ◽

Author(s):

Shimon Weiss ◽

Xavier Michalet

Keyword(s):

Single Molecule ◽

Protein Interactions ◽

Large Scale ◽

Shewanella Oneidensis ◽

Protein Protein Interactions ◽

Expression Levels ◽

Scale Characterization

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Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula

International Journal of Molecular Sciences ◽

10.3390/ijms22147537 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7537

Author(s):

Yuanyuan Zhao ◽

Junchao Zhang ◽

Zhanmin Sun ◽

Yixiong Tang ◽

Yanmin Wu

Keyword(s):

Medicago Truncatula ◽

Protein Interactions ◽

Stress Responses ◽

Regulatory Networks ◽

Developmental Stages ◽

Interaction Network ◽

Polycomb Group ◽

Protein Protein Interactions ◽

Group I ◽

Gene Structures

Polycomb group (PcG) proteins, which are important epigenetic regulators, play essential roles in the regulatory networks involved in plant growth, development, and environmental stress responses. Currently, as far as we know, no comprehensive and systematic study has been carried out on the PcG family in Medicago truncatula. In the present study, we identified 64 PcG genes with distinct gene structures from the M. truncatula genome. All of the PcG genes were distributed unevenly over eight chromosomes, of which 26 genes underwent gene duplication. The prediction of protein interaction network indicated that 34 M. truncatula PcG proteins exhibited protein–protein interactions, and MtMSI1;4 and MtVRN2 had the largest number of protein–protein interactions. Based on phylogenetic analysis, we divided 375 PcG proteins from 27 species into three groups and nine subgroups. Group I and Group III were composed of five components from the PRC1 complex, and Group II was composed of four components from the PRC2 complex. Additionally, we found that seven PcG proteins in M. truncatula were closely related to the corresponding proteins of Cicer arietinum. Syntenic analysis revealed that PcG proteins had evolved more conservatively in dicots than in monocots. M. truncatula had the most collinearity relationships with Glycine max (36 genes), while collinearity with three monocots was rare (eight genes). The analysis of various types of expression data suggested that PcG genes were involved in the regulation and response process of M. truncatula in multiple developmental stages, in different tissues, and for various environmental stimuli. Meanwhile, many differentially expressed genes (DEGs) were identified in the RNA-seq data, which had potential research value in further studies on gene function verification. These findings provide novel and detailed information on the M. truncatula PcG family, and in the future it would be helpful to carry out related research on the PcG family in other legumes.

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Tracking chromatin state changes using μMap photo-proximity labeling

10.1101/2021.09.28.462236 ◽

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.

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Characterization of the Key Region and Key Phosphorylation Sites of EcaICE1 for its Molecular Interaction with EcaHOS1 Protein in Eucalyptus camaldulensis

10.21203/rs.2.21485/v1 ◽

2020 ◽

Author(s):

Ling Cheng ◽

Weihua Zhang ◽

Jianlin Hu ◽

Ziyang Zhang ◽

Yan Liu ◽

...

Keyword(s):

Cold Stress ◽

Protein Interactions ◽

Phosphorylation Site ◽

Eucalyptus Camaldulensis ◽

Phosphorylation Sites ◽

Protein Protein Interactions ◽

Amino Acid Region ◽

Mda Content ◽

Proteasome Pathway

Abstract Background ICE1 (inducer of CBF expression 1), a MYC-like bHLH transcriptional activator, plays an important role in plant under cold stress via regulating transcriptional expression of downstream cold-responsive genes. Ubiquitination-proteasome pathway mediated by high expression of osmotically responsive gene1 (HOS1) can effectively induce the degradation of ICE1 and decrease the expression of expression of CBFs and their downstream genes under cold stress response in Arabidopsis , but the knowledge about ubiquitination regulation of ICE1 by HOS1 is still unknown in woody plants.Results The complete EcaICE1 gene and a new E3 ubiquitin ligase gene EcaHOS1 were amplified from the tissue culture seedlings of Eucalyptus camaldulensis . Yeast two-hybrid (Y2H) and BiFC assay results showed that EcaICE1 can interact with EcaHOS1 protein in the nucleus, and further Y2H assay demonstrated that the 126-185 amino acid region at the N-terminus of EcaICE1 protein was indispensable for its interaction with EcaHOS1 protein. Moreover, we found that the amino acids at positions 143, 145, 158 and 184 within the key interaction region were the potential phosphorylation sites of EcaICE1 based on bioinformatics analysis, and that only the substitution of Serine (Ser) 158 by Alanine (Ala) blocked the protein-protein interactions between EcaICE1 and EcaHOS1 by Y2H and β-galactosidase assays using site-direct mutagenesis. Overexpression of EcaICE1 and its mutations in Arabidopsis could significantly increase POD and SOD activities with a reduction for MDA content and up-regulate four cold-responsive genes ( CBF3 , KIN1 , COR15 and COR47A ) in the transgenic lines.Conclusion We first reported that EcaICE1 could interact with EcaHOS1 protein in Eucalyptus , and identified Ser 158 of EcaICE1 as the key phosphorylation site for its interaction with EcaHOS1 protein.

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Tracking chromatin state changes using µMap photo-proximity labeling

10.21203/rs.3.rs-955662/v1 ◽

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.

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