PXD015007-2

PXD015007 is an original dataset announced via ProteomeXchange.

Title	Multiomic studies of inhibitory effects of lignocellulose-derived inhibitors on xylose utilization in Zymomonas mobilis using chemical defined synthetic hydrolysates
Description	Previously we found that modified Zymomonas mobilis is able to convert glucose to ethanol when fermenting highly concentrated hydrolysates such as 9% glucan-loading AFEX-pretreated corn stover hydrolysate (ACSH), but that xylose conversion after glucose depletion is greatly impaired. We hypothesized that impaired xylose conversion is caused by lignocellulose-derived inhibitors (LDIs) present in highly concentrated hydrolysates. To investigate the effects of LDIs on xylose utilization in Z. mobilis, we generated synthetic hydrolysates (SynHs) that contains nutrients and LDI at concentrations found in authentic 9% ACSH. Comparative fermentations of Z. mobilis 2032 using SynH with or without LDI were performed, and samples were collected for endproduct, transcriptomic, metabolomic, and proteomic analyses. Our data suggest that the overall flux of xylose metabolism is reduced in the presence of LDIs. However, the expression of most genes involved in glucose and xylose assimilation was not affected by LDIs nor did we observe blocks in glucose and xylose metabolic pathways. Several LDI-specific effects were observed including intracellular accumulation of mannose-1P and mannose-6P, down regulation of a Type I secretion system (ZMO0252-0255), and upregulation of sulfur metabolism genes and the RND family efflux pump system (ZMO0282_0283_0285). This efflux pump system is involved in detoxification. Together, our findings identify cellular responses to LDIs and possible causes of impaired xylose conversion that will enable future strain engineering of Z. mobilis.
HostingRepository	PRIDE
AnnounceDate	2019-10-28
AnnouncementXML	Submission_2019-12-06_06:42:51.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Evgenia Shishkova
SpeciesList	scientific name: Zymomonas mobilis; NCBI TaxID: 542;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-13 01:14:45	ID requested
1	2019-10-28 02:02:38	announced
⏵ 2	2019-12-06 06:42:53	announced	2019-12-06: Updated publication reference for PubMed record(s): 31787963.
3	2024-10-22 04:57:13	announced	2024-10-22: Updated project metadata.

Zhang Y, Vera JM, Xie D, Serate J, Pohlmann E, Russell JD, Hebert AS, Coon JJ, Sato TK, Landick R, . Front Microbiol, 10():2596(2019) [pubmed]

submitter keyword: Zymomonas mobilis, lignocellulosic hydrolysate, biofuels, microbial conversion, xylose metabolism, multiomics

Prof. Joshua J Coon
contact affiliation	Professor of Biomolecular Chemistry and Chemistry at University of Wisconsin-Madison
contact email	jcoon@chem.wisc.edu
lab head
Evgenia Shishkova
contact affiliation	University of Wisconsin - Madison
contact email	shishkova@wisc.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD015007
     1. Label: PRIDE project
     2. Name: Multiomic studies of inhibitory effects of lignocellulose-derived inhibitors on xylose utilization in Zymomonas mobilis using chemical defined synthetic hydrolysates