PXD058004-1

PXD058004 is an original dataset announced via ProteomeXchange.

Title	Signal sequence characteristics of periplasm and thylakoid lumen proteins in cyanobacteria revealed using a proximity-based proteomics generated spatial proteome
Description	Cyanobacteria have an inner and outer cell membrane enclosing the periplasm and cell wall and an additional set of membranes called the thylakoid membranes enclosing thylakoid lumen. The periplasm and thylakoid lumen have unique proteomes, but the mechanisms sorting proteins to these locations have remained elusive. Here, proximity-based proteomics using APEX2 was performed in the cyanobacteria Synechococcus sp. PCC 7002 to identify the proteomes of the cytoplasm, thylakoid lumen, and the periplasm and outer membrane (P-OM). This revealed specific roles for the thylakoid lumen in photosynthesis and energy generation, as well as roles for the periplasm in metabolite transport and binding, cell motility, and cell wall maintenance. Forty proteins were localized to both the thylakoid lumen proteome and the periplasm and outer membrane proteomes, however, their biological functions remain unclear. We also analyzed the correlation between signal sequences characteristics and differential protein localization to either the thylakoid lumen or the P-OM. In PCC 7002, as well as Synechocystis sp. PCC 6803 and Nostoc sp. PCC 7120, thylakoid lumen proteins translocated across membranes by the Secretory (Sec) system possess more hydrophobic and more alpha helical signal sequence H-regions that than P-OM proteins. Signal sequences of homologous proteins in PCC 7421, a species of cyanobacteria with a combined thylakoid lumen and periplasmic space, did not possess such differences. Therefore, the pattern of increased H-region hydrophobicity and alpha helix content is specific to cyanobacteria with a separate thylakoid lumen space, and likely contributes to proper protein sorting between the thylakoid lumen or periplasm.
HostingRepository	PRIDE
AnnounceDate	2026-02-09
AnnouncementXML	Submission_2026-02-08_16:37:00.360.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD058004
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christopher Ebmeier
SpeciesList	scientific name: Synechococcus sp. PCC 7002 x Microcystis aeruginosa TAIHU98 coculture; NCBI TaxID: NEWT:1856682;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2024-11-18 11:59:25	ID requested
⏵ 1	2026-02-08 16:37:01	announced

Dahlgren K, Ebmeier CC, Koke E, Cameron JC, Spatial proteomics reveals signal sequence characteristics correlated with localization in cyanobacteria. Plant Physiol, 198(4):(2025) [pubmed]

10.6019/PXD058004;

10.1093/plphys/kiaf186;

submitter keyword: Signal sequence, cyanobacteria, protein localization, APEX2, proximity-based proteomics

Jeffrey C. Cameron, PhD
contact affiliation	Principle Investigator • Institute Fellow • Assistant Professor Department of Chemistry and Biochemistry & Renewable and Sustainable Energy Institute
contact email	jeffrey.c.cameron@colorado.edu
lab head
Christopher Ebmeier
contact affiliation	University of Colorado Boulder
contact email	christopher.ebmeier@colorado.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD058004
     1. Label: PRIDE project
     2. Name: Signal sequence characteristics of periplasm and thylakoid lumen proteins in cyanobacteria revealed using a proximity-based proteomics generated spatial proteome