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AKIR-1 protein-protein interactions in C. elegans

ABSTRACT: We combined transgenic AKIR-1::GFP C. elegans strain and label-free quantitative affinity purification to identify protein interaction partners of AKIR-1. An additonal pull-down experiment was performed to study AKIR-1 interactions under Drechmeria coniospora infection.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Caenorhabditis Elegans

TISSUE(S): Whole Body

SUBMITTER: Jia-Xuan Chen

LAB HEAD: Matthias Selbach

PROVIDER: PXD008074 | Pride | 2018-06-19

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	MaxQuant_Output_AKIR1_GFP_infected.zip	Other
	MaxQuant_Output_AKIR1_GFP_uninfected.zip	Other
	MaxQuant_Output_untagged_control.zip	Other
	Statler_20150313_JC_Jola_aki1_S1_CON.raw	Raw
	Statler_20150313_JC_Jola_aki1_S1_GFP.raw	Raw

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Publications

Evolutionary plasticity in the innate immune function of Akirin.

Polanowska Jolanta J Chen Jia-Xuan JX Soulé Julien J Omi Shizue S Belougne Jerome J Taffoni Clara C Pujol Nathalie N Selbach Matthias M Zugasti Olivier O Ewbank Jonathan J JJ

PLoS genetics 20180723 7

Eukaryotic gene expression requires the coordinated action of transcription factors, chromatin remodelling complexes and RNA polymerase. The conserved nuclear protein Akirin plays a central role in immune gene expression in insects and mammals, linking the SWI/SNF chromatin-remodelling complex with the transcription factor NFκB. Although nematodes lack NFκB, Akirin is also indispensable for the expression of defence genes in the epidermis of Caenorhabditis elegans following natural fungal infect ...[more]

PMID: 30036395

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MALT-1 mediates IL-17 neural signaling to regulate C. elegans behavior, immunity and longevity

Project description:The interaction partners of C. elegans soluble IL-17 signaling components were profiled using IP/MS. In vivo interactions were profiled for ACTL-1-FLAG, PIK-1-Myc, MALT-1::GFP, NFKI-1::GFP and their respective controls. Quantification of NFKI-1::GFP interactions was performed by labelling immunoprecipitated proteins using tandem mass tags.

2020-05-27 | PXD018000 | Pride

wt vs daf-2 C. elegans protein turnover

Project description:Most aging hypotheses revolve around the accumulation of some sort of damage resulting in gradual physiological decline and ultimately death. Avoiding protein damage accumulation by enhanced turnover should slow down the aging process and extend lifespan. However, lowering translational efficiency extends rather than shortens lifespan in C. elegans. We studied turnover of individual proteins in the conserved Insulin/Insulin-like Growth Factor (IGF-1) receptor mutant daf-2 by combining Stable Isotope Labeling by Nitrogen-15 in Caenorhabditis elegans and LC-MS/MS. Intriguingly, the majority of proteins displayed prolonged half-lives in daf-2, while others remained unchanged, signifying that longevity is not supported by high protein turnover. This slow-down of protein turnover was most prominent for components of the translation machinery and mitochondria. In contrast, the high turnover of lysosomal hydrolases and very low turnover of cytoskeletal proteins remained largely unchanged in daf-2. The slow-down of protein dynamics and decreased abundance of the translational machinery may point at the importance of anabolic attenuation in lifespan extension as suggested by the hyperfunction theory.

2016-09-27 | PXD002317 | Pride

Protein turnover during C. elegans aging

Project description:Protein turnover rates severely decline in aging organisms, including C. elegans. However, limited information is available on turnover dynamics at the individual protein level during aging. We followed changes in protein turnover at one-day resolution using a multiple-pulse 15N-labeling and accurate mass spectrometry approach. Forty percent of the proteome shows gradual slowdown in turnover with age, while only few proteins show increased turnover. Decrease in protein turnover was consistent for the minority of functional protein subsets, including tubulins and vitellogenins, while for most functionally related protein pools randomly diverging turnover patterns were observed with age. Our data suggests severe dysregulation of protein turnover of the translation machinery, whereas protein turnover of UPS and antioxidant systems are well-preserved over time. Hence, we presume that maintenance of quality control mechanisms is a protective strategy in aging worms, although the ultimate proteome collapse is inescapable.

2017-07-11 | PXD002901 | Pride

mut-16 and other mutator-class genes modulate 22G and 26G siRNA pathways in Caenorhabditis elegans

Project description:Argonaute-associated siRNAs and Piwi-associated piRNAs have overlapping roles in silencing mobile genetic elements in animals. In C. elegans, mutator-class (mut) genes mediate siRNA-guided repression of transposons as well as exogenous RNA-directed gene silencing (RNAi), but their roles in endogenous RNA silencing pathways are not well understood. To characterize the endogenous small RNAs dependent on mutator-class genes, small RNA populations from a null allele of mut-16, as well as a regulatory mut-16(mg461) allele that disables only somatic RNAi, were subjected to deep sequencing. Small RNA analysis in wild type and mut-16 mutant C. elegans strains

2011-02-01 | E-GEOD-26165 | biostudies-arrayexpress

The C. elegans proteome response to alternative food source bacteria

Project description:Understanding how C. elegans interacts with the bacteria it feeds upon enables us to better comprehend the complex interactions occurring at the interface of host and microbe. Here we have assessed the proteome of C. elegans after growth on bacteria capable of colonising the gut via a comparative analysis of C. elegans grown on two environmentally obtained species of Ochrobactrum (MYb71 and MYb237) verses C. elegans grown on E. coli OP50. A total of 4,677 C. elegans proteins were identified, with quantification under our criteria possible for more than 84% (3,941) of these proteins. Significant alterations in protein abundances were observed for 122 proteins, 48 higher in abundance and 74 lower in abundance. We observed an increase in abundance of proteins potentially regulated via host signalling pathways, in addition to several proteins involved in the breakdown and detoxification of foreign entities (e.g. lipase, proteases, glutathione metabolism). Of the proteins decreased in abundance, a number are involved in both degradation (branch chain amino acids) and biosynthesis (cysteine, methionine, glycine, serine and threonine) of amino acids. While enzymes associated with the degradation of peptidoglycan were also less abundant (Lys-4, Lys-5). The differences observed in C. elegans following growth on alternative food source bacteria, as opposed to the normal E. coli OP50, help to highlight the subtle nuances that are, more often than not, overlooked in classical host pathogen studies.

2018-03-13 | PXD008105 | Pride

Protein interactors of MEG-1 in C. elegans embryos

Project description:In animals with germ plasm, specification of the germline involves “germ granules”, cytoplasmic condensates that enrich maternal transcripts in the germline founder cells. In C. elegans embryos, P granules enrich maternal transcripts, but surprisingly P granules are not essential for germ cell fate specification. Here we have described a second condensate in the C. elegans germ plasm. Like canonical P-bodies found in somatic cells, “germline P-bodies” contain regulators of mRNA decapping and deadenylation and, in addition, the intrinsically-disordered proteins MEG-1 and MEG-2 and the TIS11-family RNA-binding protein POS-1. Embryos lacking meg-1 and meg-2 do not stabilize P-body components, miss-regulate POS-1 targets, miss-specify the germline founder cell, and do not develop a germline. Our findings suggest that specification of the germ line involves at least two distinct condensates that independently enrich and regulate maternal mRNAs in the germline founder cells.

2022-10-05 | PXD036610 | Pride

microRNA decay analysis in the first larval stage Caenorhabditis elegans

Project description:microRNAs (miRNAs) constitute a class of small non-coding RNAs (~22nt). They are thought to be generally stable with half-lives of many hours or even days. However, several miRNAs have been reported to decay rapidly in specific situations. In order to examine miRNA stability on a global scale, we quantify relative decay rates of miRNA in first larval stage C. elegans worms that are treated with a transcription inhibitor alpha-amanitin by deep sequencing. Several miRNAs including members of the miR-35 and miR-51 families exhibit accelerated decay. Moreover, biogenesis of miRNAs involves generation of a miRNA duplex intermediate consisting of the miRNA guide strand (miR) and the miRNA passenger strand (miR*). miR and miR* names were originally assigned based on the relative abundance of each strand, with the less abundant strand presumed to be inactive, and thus the miR*. However, subsequent research showed that at least individual miR*s can have biological activity. Our sequencing data reveal that miR*s, operationally defined on the basis of their relative abundance at time point t=1h, are substantially less stable than miRs. This would appear to support the notion that miR*s mainly constitute processing byproducts rather than a less abundant class of functional miRNAs. Examination of microRNA decay rates in the first larval stage C. elegans worms.

2014-02-06 | E-GEOD-46753 | biostudies-arrayexpress

Influence of p38 MAPK (PMK-1) on the heat stress response of C. elegans

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2012-11-05 | E-GEOD-41205 | biostudies-arrayexpress

The proteomic response of C. elegans to two protective Pseudomonas symbionts

Project description:The two C. elegans natural microbiota isolates Pseudomonas lurida MYb11 and Pseudomonas fluorescens MYb115 protect the host against pathogens through distinct mechanisms. While P. lurida produces an antimicrobial compound and directly inhibits pathogen growth, P. fluorescens MYb115 protects the host without affecting pathogen growth. It is unknown how these two protective microbes affect host biological processes. We used a proteomics approach to elucidate the C. elegans response to MYb11 and MYb115. We found that both Pseudomonas isolates increase vitellogenin protein production in adult day 1 animals, which confirms previous findings on the effect of microbiota on C. elegans reproductive timing. Moreover, the C. elegans responses to MYb11 and MYb115 exhibit common signatures with the response to other vitamin B12-producing bacteria, emphasizing the importance of vitamin B12 in C. elegans-microbe metabolic interactions.

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Transcription profiling of C. elegans pocket protein ortholog, lin-35

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