PXD006834

PXD006834 is an original dataset announced via ProteomeXchange.

Title	Transposon sequencing uncovers an essential regulatory function of phosphoribulokinase for methylotrophy
Description	Methylotrophy is the ability of organisms to grow at the expense of reduced one-carbon compounds such as methanol or methane. Here, we used transposon sequencing combining hyper-saturated transposon mutagenesis with high-throughput sequencing to define the essential methylotrophy genome of Methylobacterium extorquens PA1, a model methylotroph. To distinguish genomic regions required for growth only on methanol from general required genes, we contrasted growth on methanol with growth on succinate, a non-methylotrophic reference substrate. About 500'000 insertions were mapped for each condition, resulting in a median insertion distance of 5 base pairs. We identified 147 genes and 76 genes as specific for growth on methanol and succinate, respectively, and a set of 590 genes as required under both growth conditions. For the integration of metabolic functions, we reconstructed a genome-scale metabolic model and performed in silico essentiality analysis. In total, the approach uncovered 95 previously not described genes as crucial for methylotrophy, including genes involved in respiration, carbon metabolism, transport, and regulation. Strikingly, regardless of the absence of the Calvin cycle in the methylotroph, the screen led to the identification of the gene for phosphoribulokinase as essential during growth on methanol but not on succinate. Genetic experiments in addition to metabolomics and proteomics revealed that phosphoribulokinase serves a key regulatory function. Our data support a model according to which ribulose-1,5 bisphosphate is an essential metabolite that induces a transcriptional regulator driving one-carbon assimilation.
HostingRepository	PRIDE
AnnounceDate	2017-07-11
AnnouncementXML	Submission_2017-08-22_05:16:08.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lucas Hemmerle
SpeciesList	scientific name: Methylobacterium extorquens PA1; NCBI TaxID: 419610;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-29 23:20:18	ID requested
1	2017-07-11 04:56:26	announced
⏵ 2	2017-08-22 05:16:09	announced	Updated publication reference for PubMed record(s): 28823675.

Ochsner AM, Christen M, Hemmerle L, Peyraud R, Christen B, Vorholt JA, Transposon Sequencing Uncovers an Essential Regulatory Function of Phosphoribulokinase for Methylotrophy. Curr Biol, 27(17):2579-2588.e6(2017) [pubmed]

curator keyword: Biological

submitter keyword: Methylobacterium extorquens PA1, LC-MS/MS, Label-free Quantification

Julia A. Vorholt
contact affiliation	Department of Biology, Institute of Microbiology, ETH Zürich, Switzerland
contact email	jvorholt@ethz.ch
lab head
Lucas Hemmerle
contact affiliation	ETH Zürich
contact email	helucas@ethz.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD006834
     1. Label: PRIDE project
     2. Name: Transposon sequencing uncovers an essential regulatory function of phosphoribulokinase for methylotrophy