Dataset Information

Comparative Wnt dependent Hydra ECM proteome

ABSTRACT: Comparative proteome of extracted Hydra vulgaris AEP extracellular matrix form Wnt9/10 knock out and Azakenpaullone treated animals. Used to analyse the changes in molecular composition of the mesoglea (ECM) of normal and Wnt depleted animals

INSTRUMENT(S): Q Exactive

ORGANISM(S): Hydra Vulgaris

TISSUE(S): Connective Tissue

SUBMITTER: Frank Stein

LAB HEAD: Suat Oezbek

PROVIDER: PXD039846 | Pride | 2023-05-10

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Bert_210716_P1746_MR_SK_Hydra_TP_TMT12_fr1.raw	Raw
	Bert_210716_P1746_MR_SK_Hydra_TP_TMT12_fr10.raw	Raw
	Bert_210716_P1746_MR_SK_Hydra_TP_TMT12_fr11.raw	Raw
	Bert_210716_P1746_MR_SK_Hydra_TP_TMT12_fr12.raw	Raw
	Bert_210716_P1746_MR_SK_Hydra_TP_TMT12_fr2.raw	Raw

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Publications

Wnt/β-catenin signaling induces axial elasticity patterns of Hydra extracellular matrix.

Veschgini Mariam M Suzuki Ryo R Kling Svenja S Petersen Hendrik O HO Bergheim Bruno Gideon BG Abuillan Wasim W Linke Philipp P Kaufmann Stefan S Burghammer Manfred M Engel Ulrike U Stein Frank F Özbek Suat S Holstein Thomas W TW Tanaka Motomu M

iScience 20230316 4

The extracellular matrix (ECM) plays crucial roles in animal development and diseases. Here, we report that Wnt/β-catenin signaling induces the ECM remodeling during Hydra axis formation. We determined the micro- and nanoscopic arrangement of fibrillar type I collagen along Hydra's body axis using high-resolution microscopy and X-ray scattering. Elasticity mapping of the ECM ex vivo revealed distinctive elasticity patterns along the body axis. A proteomic analysis of the ECM ...[more]

PMID: 37009232

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Project description:Proteomics, the temporal study of proteins expressed by an organism, is a powerful technique that can reveal how organisms respond to biological perturbations, such as disease and environmental stress. Yet, the use of proteomics for addressing ecological questions has been limited, partly due to inadequate protocols for the sampling and preparation of animal tissues from the field. Although RNAlater is an ideal alternative to freezing for tissue preservation in transcriptomics studies, its suitability for the field could be more broadly examined. Moreover, existing protocols require samples to be preserved immediately to maintain protein integrity, yet the effects of delays in preservation on proteomic analyses have not been thoroughly tested. Hence, we optimised a proteomic workflow for wild-caught samples. First, we conducted a preliminary in-lab test using SDS-PAGE analysis on aquaria-reared Octopus berrima confirming that RNAlater can effectively preserve proteins up to 6 h after incubation, supporting its use in the field. Subsequently, we collected arm tips from wild-caught Octopus berrima and preserved them in homemade RNAlater immediately, 3 h, and 6 h after euthanasia. Processed tissue samples were analysed by liquid chromatography tandem mass spectrometry to ascertain protein differences between time delay in tissue preservation, as well as the influence of sex, tissue type, and tissue homogenisation methods. Over 3500 proteins were identified from all tissues, with bioinformatic analysis revealing protein abundances were largely consistent regardless of sample treatment. However, nearly 10 % additional proteins were detected from tissues homogenised with metal beads compared to liquid nitrogen methods, indicating the beads were more efficient at extracting proteins. Our optimised workflow demonstrates that sampling non-model organisms from remote field sites is achievable and can facilitate extensive proteomic coverage without compromising protein integrity.

Dataset Information

Comparative Wnt dependent Hydra ECM proteome

Dataset's files

Publications

Wnt/β-catenin signaling induces axial elasticity patterns of <i>Hydra</i> extracellular matrix.

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