PXD031549 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Revealing Pentose Catabolism in Pseudomonas putida |
Description | Pseudomonas alloputida KT2440 (previously misclassified as P. putida KT2440 based on 16S rRNA gene homology) has emerged as an ideal host strain for plan t biomass valorization. However, P. alloputida KT2440 is unable to natively utilize abundant pentose sugars (e.g., xylose and arabinose) in hydrolysate streams, which may account for up to 25% of lignocellulosic biomass. In the last decades, microbes have been engineered to utilize the pentose sugars. However, most of the engineered strains were either slow-growing or displayed phenotypes that could not be replicated. In this work, we successfully isolated five Pseudomonas species with the native capability to utilize glucose, xylose and p-coumarate as a sole carbon source. These isolates were in two clusters; one set of isolates (M2 and M5) and the second set of isolates (BP6 and BP7) showed 85.6% and 96.2% ANI, respectively, to P. alloputida KT24440. BP8 showed 84.6% ANI to P. putida KT2440 and does not belong to any neighboring type strains indicating a new species. Notably, the isolates showed robust growth solely on xylose and higher growth rates (m, 0.36-0.49 h-1) when compared to only known xylose-utilizing Pseudomonas taiwanenesis VLB120 (m, 0.28 h-1) as a control. Unexpectedly, among five isolates, M2 and M5 grew solely on arabinose as well. Comprehensive analysis of genomics, transcriptomics and proteomics revealed the isolates utilize xylose and arabinose via Weimberg pathway (xylD-xylX-xylA) and oxidative pathway (araD-araX-araA), respectively. Furthermore, a preliminary result demonstrated the production of flaviolin solely on xylose and arabinose in the isolate, showing noteworthy potential to be an alternative host for lignocellulosic feedstocks into valuable products. This is the first report on isolating Pseudomonas strains natively capable of utilizing all of the major carbon sources in lignocellulosic biomass, and leading to higher consumption of available substrates and therefore maximizing the product yield. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:45:36.741.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD031549 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Christopher Petzold |
SpeciesList | scientific name: Pseudomonas putida; NCBI TaxID: 303; |
ModificationList | monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Exploris 480 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-02-09 08:07:16 | ID requested | |
1 | 2023-05-10 08:47:37 | announced | |
⏵ 2 | 2023-11-14 08:45:45 | announced | 2023-11-14: Updated project metadata. |
Publication List
Park MR, Gauttam R, Fong B, Chen Y, Lim HG, Feist AM, Mukhopadhyay A, Petzold CJ, Simmons BA, Singer SW, Revealing oxidative pentose metabolism in new Pseudomonas putida isolates. Environ Microbiol, 25(2):493-504(2023) [pubmed] |
10.6019/PXD031549; |
Keyword List
submitter keyword: Pseudomonas,Soil isolates, pentose, xylose, and arabinose |
Contact List
Christopher Petzold |
contact affiliation | Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720 |
contact email | cjpetzold@lbl.gov |
lab head | |
Christopher Petzold |
contact affiliation | Lawrence Berkeley National Laboratory |
contact email | cjpetzold@lbl.gov |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD031549
- Label: PRIDE project
- Name: Revealing Pentose Catabolism in Pseudomonas putida