Quantitative proteome analysis of Caenorhabditis elegans upon exposure to nematicidal Bacillus thuringiensis

Treitz, Christian; Cassidy, Liam; Höckendorf, Aylin; Leippe, Matthias; Tholey, Andreas

doi:10.1016/j.jprot.2014.09.027

Cited by 56 publications

(58 citation statements)

References 78 publications

(108 reference statements)

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“…Only proteins identified by at least two matched peptides were considered for proteomic analysis (Treitz et al, 2015). As the three replicates of each sample showed high reproducibility with high significant linear correlations (Spearman's and Pearson's correlations, P < 0.001), we grouped each three replicates and calculated the average abundances (fmol or fmol μg −1 ) of each protein.…”

Section: Methodsmentioning

confidence: 99%

“…As the three replicates of each sample showed high reproducibility with high significant linear correlations (Spearman's and Pearson's correlations, P < 0.001), we grouped each three replicates and calculated the average abundances (fmol or fmol μg −1 ) of each protein. The fmol averages of each sample were also normalized by the median using the Perseus Software (v1.5.1.6; www.maxquant.org, Treitz et al, 2015). Moreover, using each protein's molecular weight from the database, the fmol quantity of each protein was converted to nanograms for the triplicates, and by summing the average ng of all proteins we obtained the total average ng in each sample (Saka et al, 2011).…”

Section: Methodsmentioning

confidence: 99%

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Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp.

et al. 2017

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Arthropod-borne Rickettsia species are obligate intracellular bacteria which are pathogenic for humans. Within this genus, Rickettsia slovaca and Rickettsia conorii cause frequent and potentially severe infections, whereas Rickettsia raoultii and Rickettsia massiliae cause rare and milder infections. All four species belong to spotted fever group (SFG) rickettsiae. However, R. slovaca and R. raoultii cause scalp eschar and neck lymphadenopathy (SENLAT) and are mainly associated with Dermacentor ticks, whereas the other two species cause Mediterranean spotted fever (MSF) and are mainly transmitted by Rhipicephalus ticks. To identify the potential genes and protein profiles and to understand the evolutionary processes that could, comprehensively, relate to the differences in virulence and pathogenicity observed between these four species, we compared their genomes and proteomes. The virulent and milder agents displayed divergent phylogenomic evolution in two major clades, whereas either SENLAT or MSF disease suggests a discrete convergent evolution of one virulent and one milder agent, despite their distant genetic relatedness. Moreover, the two virulent species underwent strong reductive genomic evolution and protein structural variations, as well as a probable loss of plasmid(s), compared to the two milder species. However, an abundance of mobilome genes was observed only in the less pathogenic species. After infecting Xenopus laevis cells, the virulent agents displayed less up-regulated than down-regulated proteins, as well as less number of identified core proteins. Furthermore, their similar and distinct protein profiles did not contain some genes (e.g., ompA/B and rickA) known to be related to rickettsial adhesion, motility and/or virulence, but may include other putative virulence-, antivirulence-, and/or disease-related proteins. The identified evolutionary forces herein may have a strong impact on intracellular expressions and strategies in these rickettsiae, and that may contribute to the emergence of distinct virulence and diseases in humans. Thus, the current multi-omics data provide new insights into the evolution and fitness of SFG virulence and pathogenicity, and intracellular pathogenic bacteria.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp.

et al. 2017

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“…We mentioned previously that genes encoding TTL proteins have been identified as effector-modulating host immunity factors in APNs and PPNs (Goverse and Smant, 2014; Mantelin et al , 2015). Curiously, numerous transthyretin-like proteins in C. elegans are significantly up-regulated in DAF-16- and IIS-dependent manners (Depuydt et al , 2013) and are thus associated with innate immunity against microbial nematicides (Treitz et al , 2015). The TTL gene family may be an example of potential nematode effectors that are secreted in response to the oxidative stress response induced by its host plant.…”

Section: Section Ii: Potential Key Regulators Of Oxidative Stress Resmentioning

confidence: 99%

Plant-parasitic nematodes: towards understanding molecular players in stress responses

Gillet

Bournaud

Júnior

et al. 2017

Ann Bot

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Background Plant–parasitic nematode interactions occur within a vast molecular plant immunity network. Following initial contact with the host plant roots, plant-parasitic nematodes (PPNs) activate basal immune responses. Defence priming involves the release in the apoplast of toxic molecules derived from reactive species or secondary metabolism. In turn, PPNs must overcome the poisonous and stressful environment at the plant–nematode interface. The ability of PPNs to escape this first line of plant immunity is crucial and will determine its virulence. Scope Nematodes trigger crucial regulatory cytoprotective mechanisms, including antioxidant and detoxification pathways. Knowledge of the upstream regulatory components that contribute to both of these pathways in PPNs remains elusive. In this review, we discuss how PPNs probably orchestrate cytoprotection to resist plant immune responses, postulating that it may be derived from ancient molecular mechanisms. The review focuses on two transcription factors, DAF-16 and SKN-1, which are conserved in the animal kingdom and are central regulators of cell homeostasis and immune function. Both regulate the unfolding protein response and the antioxidant and detoxification pathways. DAF-16 and SKN-1 target a broad spectrum of Caenorhabditis elegans genes coding for numerous protein families present in the secretome of PPNs. Moreover, some regulatory elements of DAF-16 and SKN-1 from C. elegans have already been identified as important genes for PPN infection. Conclusion DAF-16 and SKN-1 genes may play a pivotal role in PPNs during parasitism. In the context of their hub status and mode of regulation, we suggest alternative strategies for control of PPNs through RNAi approaches.

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“…Here, we performed a quantitative proteome analysis using an isobaric labeling/2D‐LC approach described earlier to provide a reference dataset showing the protein level differences of E. coli K‐12 strain MG1655 grown on acetate versus glucose.…”

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confidence: 99%

Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose

et al. 2016

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Relative protein abundances of Escherichia coli MG1655 growing exponentially on minimal medium with acetate or glucose as the sole carbon source were investigated in a quantitative shotgun proteome analysis with TMT6-plex isobaric tags. Peptides were separated by high resolution high/low pH 2D-LC, using an optimized fraction pooling scheme followed by mass spectrometric analysis. Quantitative data were acquired for 2099 proteins covering 49% of the predicted E. coli proteins, showing system-wide effects of growth conditions. In total, 507 proteins showed a fold change of at least 1.5 and 205 proteins changed by more than twofold. Significant differences in abundance were observed for most of the proteins in the central carbon metabolism and in proteins relevant for amino acid and protein synthesis, processing of environmental information and scavenging of a variety of alternate carbon sources. Periplasmic-binding proteins were also more abundant on acetate, especially proteins involved in scavenging extracellular resources such as sugars. All MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (dataset identifier PXD003863).

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Quantitative proteome analysis of Caenorhabditis elegans upon exposure to nematicidal Bacillus thuringiensis

Cited by 56 publications

References 78 publications

Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp.

Multi-omics Analysis Sheds Light on the Evolution and the Intracellular Lifestyle Strategies of Spotted Fever Group Rickettsia spp.

Plant-parasitic nematodes: towards understanding molecular players in stress responses

Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose

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