Dataset Information

Signal sequence characteristics of periplasm and thylakoid lumen proteins in cyanobacteria revealed using a proximity-based proteomics generated spatial proteome

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Synechococcus Sp. Pcc 7002 X Microcystis Aeruginosa Taihu98 Coculture

TISSUE(S): Plant Cell

SUBMITTER: Christopher Ebmeier

LAB HEAD: Jeffrey C. Cameron, PhD

PROVIDER: PXD058004 | Pride | 2026-02-09

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	CCE20220405_Kelsey_Dahlgren_TMTPro_NCE30_hfx1.raw	Raw
	CCE20220405_Kelsey_Dahlgren_TMTPro_NCE32_hfx1.raw	Raw
	CCE20220406_Kelsey_Dahlgren_TMTPro18plex_hfx1.raw	Raw
	CCE20220406_Kelsey_Dahlgren_TMTPro18plex_hfx2.raw	Raw
	CCE20220406_Kelsey_Dahlgren_TMTPro18plex_hfx3.raw	Raw

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Publications

Spatial proteomics reveals signal sequence characteristics correlated with localization in cyanobacteria.

Dahlgren Kelsey K Ebmeier Christopher C CC Koke Emily E Cameron Jeffrey C JC

Plant physiology 20250801 4

Cyanobacteria have an inner and outer cell membrane enclosing the periplasm and cell wall and an additional set of internal membranes (called the thylakoid membranes) enclosing the thylakoid lumen. The periplasm and thylakoid lumen have unique proteomes, but the mechanisms regulating protein sorting to these locations have remained elusive. Here, proximity-based proteomics using the engineered peroxidase APEX2 was performed in the cyanobacteria Synechococcus sp. PCC 7002 to profile the proteomes ...[more]

PMID: 40794799

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Project description:The catalytic core of the RNA polymerase of most eubacteria is composed of two M-NM-1 subunits and M-NM-2, M-NM-2M-bM-^@M-^Y and M-OM-^I subunits. In Escherichia coli, the M-OM-^I subunit (encoded by the rpoZ gene) has been suggested to assist M-NM-2M-bM-^@M-^Y during RNA polymerase core assembly. The function of the M-OM-^I subunit is particularly interesting in cyanobacteria because the cyanobacterial M-NM-2M-bM-^@M-^Y is split to N-terminal M-NM-3 and C-terminal M-NM-2M-bM-^@M-^Y subunits. The M-bM-^HM-^FrpoZ strain of the cyanobacterium Synechocystis sp. PCC 6803 grew well in standard conditions although the mutant cells showed low light-saturated photosynthetic activity, low Rubisco content and accumulated high quantities of protective carotenoids and M-NM-1-tocopherol. The M-bM-^HM-^FrpoZ strain contained 15% less of the primary M-OM-^C factor, SigA, than the control strain, and recruitment of SigA to the RNA polymerase core was inefficient in M-bM-^HM-^FrpoZ. Thus, a cyanobacterial RNA polymerase holoenzyme lacking the M-OM-^I subunit contains less frequently the primary M-OM-^C factor. A DNA microarray analysis revealed that this leads to specific down-regulation of highly expressed genes, like genes encoding subunits for Rubisco, ATP synthase, NADH-dehydrogenase and carbon concentrating mechanisms. On the contrary, many genes showing only low or moderate expression in the control strain were up-regulated in M-bM-^HM-^FrpoZ. A conserved -10 region was detected in promoters showing up or down-regulation in M-bM-^HM-^FrpoZ, but -35 regions of down-regulated genes completely differed from -35 regions of up-regulated genes. Cells from cyanobacteria Synechocystis sp. PCC 6803 named as control strain (CS) and RNA polymerase omega subunit inactivation strain, M-NM-^TrpoZ, were harvested (A730=1, 40 mL) directly from standard growth conditions (continuous illumination at the PPFD of 40 M-BM-5mol m-2s-1, 32M-BM-0C, ambient CO2). From three to four independent experiments were performed at each conditions.