PXD046220

PXD046220 is an original dataset announced via ProteomeXchange.

Title	The functional proteome landscape of a cosmopolitan oceanic bacterium
Description	SAR11 bacteria, the most abundant organisms in the global ocean, are also the most studied example of streamlining, an adaptation to extremely low nutrient ecosystems. Streamlined cells are small and have small genomes with a high coding density, and frequently have reduced transcriptional regulation, an apparent trade-off between metabolic versatility and optimization for the efficient uptake of dissolved compounds. To understand the regulation of gene functions in streamlined cells, we developed a proteome map for SAR11 type strain HTCC1062 under 13 growth conditions. We detected 95% of the previously predicted proteome, corrected 24 predicted coding regions, and discovered 80 previously unannotated proteins, many with frame-shifted or overlapping reading frames. Our findings demonstrate these streamlined cells have an even higher coding density than reported previously. HTCC1062 cells expressed almost their entire genome (> 87.7% of predicted proteins) in all growth conditions, demonstrating they allocate relatively little coding capacity to auxillary functions deployed infrequently in response to environmental challenges and opportunities. Most proteins involved in fundamental cellular processes were stably present, but some transport proteins and other proteins with roles in central metabolism, protein synthesis and cell division appeared in 11 co-regulated protein modules. A highly compact genome and relatively stable proteome, augmented by an unusual regulon structure that supports homeostasis in response to a small set of environmental challenges, appear to be critical elements in the organization of these simple, free-living planktonic cells
HostingRepository	iProX
AnnounceDate	2023-10-18
AnnouncementXML	Submission_2023-10-18_20:33:16.281.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Dongxu Li
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2023-10-18 20:32:36	ID requested
⏵ 1	2023-10-18 20:33:16	announced

Dataset with its publication pending

submitter keyword: SAR11 bacteria，genome streamlining，proteome landscape

Dazhi Wang
contact affiliation	Xiamen University
contact email	dzwang@xmu.edu.cn
lab head
Dongxu Li
contact affiliation	Xiamen University
contact email	lidongxu@stu.xmu.edu.cn
dataset submitter

iProX dataset URI