PXD022559

PXD022559 is an original dataset announced via ProteomeXchange.

Title	Subcellular fractionation of Tuwongella immobilis by differential solubilization and analysis by Maxquant LFQ-analysis
Description	The Planctomycetes have unique cell architectures with heavily invaginated membrane networks, as here confirmed by three-dimensional models reconstructed from FIB-SEM images of Tuwongella immobilis and Gemmata obscuriglobus. We studied the subcellular proteomes of T. immobilis, and for comparison Escherichia coli, by differential solubilisation followed by LC-MS/MS analysis. More than one thousand proteins were identified in each species. The first Tris-soluble fraction contained mostly cytoplasmic proteins, whereas membrane proteins dominated the second Triton X-100 cell extract. About 50 proteins were exclusive to the third SDS-soluble extract in E. coli, mostly outer membrane and cell surface proteins. A 5-fold higher number of proteins were identified in this fraction in T. immobilis, including predicted cell surface proteins with a prepilin cleavage motif or a Planctomycetes-specific signal peptide. Surprisingly, 50% of the predicted cytoplasmic proteins were exclusively associated with the SDS-soluble protein fraction in T. immobilis. Proteins involved in signal transduction pathway and transcriptional regulation were highly overrepresented in this set, as were also enzymes involved in DNA repair and processing of stable RNAs. Some of these proteins are unique to the Planctomycetes, while others have evolved by gene duplication and domain shuffling. In cases where the paralogs showed different fractionation patterns, it was the most divergent gene copy that was uniquely associated with the SDS-soluble fraction. These results are consistent with the hypothesis that gene duplication and domain shuffling underlie the evolution of new gene functions in the Planctomycetes. We further suggest that repair and recycling of “ageing” molecules play a more important role in the Planctomycetes than in other bacteria due to their large cell sizes, long generation times and life styles.
HostingRepository	PRIDE
AnnounceDate	2021-04-06
AnnouncementXML	Submission_2021-04-06_00:59:10.180.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christian Seeger
SpeciesList	scientific name: Tuwongella immobilis; NCBI TaxID: 692036;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2020-11-16 03:40:01	ID requested
⏵ 1	2021-04-06 00:59:10	announced

Dataset with its publication pending

submitter keyword: Tuwongella immobilis, subcellular fractionation

Siv Andersson
contact affiliation	Molecular Evolution, Department of Cell and Molecular Biology, Science for Life Laboratory, Biomedical Centre, Uppsala University, SE-751 24 Uppsala, Sweden
contact email	siv.andersson@icm.uu.se
lab head
Christian Seeger
contact affiliation	Department of Cell and Molecular Biology, Molecular Evolution, Uppsala University
contact email	christian.seeger@icm.uu.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD022559
     1. Label: PRIDE project
     2. Name: Subcellular fractionation of Tuwongella immobilis by differential solubilization and analysis by Maxquant LFQ-analysis