Dataset Information

Proteomic analysis of E. coli MG1655 after removal of oriC

ABSTRACT: The project aim was to describe proteomic changes in E. coli MG1655 strain after removal of oriC. Temperature-sensitive transcriptional repressor cI857 and its target promoter was used to control the expression of a serine recombinase from bacteriophage phiC31 (phiC31 integrase). cI857 is a temperature-sensitive mutant that represses its target promoter at 30°C, but the repression is relieved at 37°C. We generated an E. coli “switcher” strain in which the oriC sequence in the chromosome is flanked by phiC31-integrase-specific attP and attB sites and in this strain the oriC is irreversibly excised when cells are incubated at 37°C.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli

SUBMITTER: Villu Kasari

LAB HEAD: Arvi Jõers

PROVIDER: PXD029931 | Pride | 2021-12-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	210308_03_Orbi2_KN_SER_G180_T210_K2rmas_1-83-2_2_25ug_iRT_150pg.raw	Raw
	210308_05_Orbi2_KN_SER_G180_T210_K2rmas_3-84-6_2_25ug_iRT_150pg.raw	Raw
	210308_07_Orbi2_KN_SER_G180_T210_K2rmas_3-83-3_2_25ug_iRT_150pg.raw	Raw
	210308_09_Orbi2_KN_SER_G180_T210_K2rmas_4-84-6_2_25ug_iRT_150pg.raw	Raw
	210308_11_Orbi2_KN_SER_G180_T210_K2rmas_1-84-6_2_25ug_iRT_150pg.raw	Raw

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Publications

Decoupling Growth and Production by Removing the Origin of Replication from a Bacterial Chromosome.

Kasari Marje M Kasari Villu V Kärmas Mirjam M Jõers Arvi A

ACS synthetic biology 20220707 8

Efficient production of biochemicals and proteins in cell factories frequently benefits from a two-stage bioprocess in which growth and production phases are decoupled. Here, we describe a novel growth switch based on the permanent removal of the origin of replication (oriC) from the Escherichia coli chromosome. Without oriC, cells cannot initiate a new round of replication, and they stop growing while their metabolism remains active. Our system relies on a serine recombinas ...[more]

PMID: 35798328

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Project description:Extensive changes in replication timing occur during early mouse development, but their biological significance remains uncertain. To identify evolutionarily conserved features of replication timing and their relationships to epigenetic properties in humans, we profiled replication timing genome-wide in four human embryonic stem cell (hESC) lines, hESC-derived neural precursor cells (NPCs), lymphoblastoid cells, and two independently derived human induced pluripotent stem cell lines (hiPSCs). Results confirm the conservation of coordinately replicated megabase-sized units of chromosomes (replication domains) with stable cell type specific molecular boundaries that consolidate into larger replication domains during differentiation. Replication timing changes encompassed units of 400-800 kb and were coordinated with changes in transcription similar to mouse. Moreover, significant cell-type specific conservation of replication timing profiles was observed across regions of conserved synteny, despite significant species variation in the alignment of replication timing to isochore GC/LINE-1 content. Replication profiling also revealed a closer genome-wide epigenetic alignment of hESCs to mouse epiblast-derived stem cells (mEpiSCs) than to mouse ESCs. Finally, we identify a signature of chromatin modifications marking the boundaries of early replicating domains and a remarkably strong link between spatial proximity of chromatin as measured by Hi-C analysis and replication timing. Together, our results reveal evolutionarily conserved elements of the replication program in mammalian early development, demonstrate the power of replication profiling to identify important epigenetic distinctions between closely related stem cell populations (e.g. ESCs vs. EpiSCs), and strengthen the hypothesis that replication domains are structural and functional units of 3D chromosomal architecture. 8 cell types, with a total of 13 individual replicates (i.e. 5 in duplicates, 3 in single replicates)