Journal article
Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets
Biotechnology for biofuels, Vol.14(1), pp.116-116
05/10/2021
DOI: 10.1186/s13068-021-01964-4
PMCID: PMC8112048
PMID: 33971924
Abstract
BackgroundMass spectrometry-based proteomics can identify and quantify thousands of proteins from individual microbial species, but a significant percentage of these proteins are unannotated and hence classified as proteins of unknown function (PUFs). Due to the difficulty in extracting meaningful metabolic information, PUFs are often overlooked or discarded during data analysis, even though they might be critically important in functional activities, in particular for metabolic engineering research.ResultsWe optimized and employed a pipeline integrating various "guilt-by-association" (GBA) metrics, including differential expression and co-expression analyses of high-throughput mass spectrometry proteome data and phylogenetic coevolution analysis, and sequence homology-based approaches to determine putative functions for PUFs in Clostridium thermocellum. Our various analyses provided putative functional information for over 95% of the PUFs detected by mass spectrometry in a wild-type and/or an engineered strain of C. thermocellum. In particular, we validated a predicted acyltransferase PUF (WP_003519433.1) with functional activity towards 2-phenylethyl alcohol, consistent with our GBA and sequence homology-based predictions.ConclusionsThis work demonstrates the value of leveraging sequence homology-based annotations with empirical evidence based on the concept of GBA to broadly predict putative functions for PUFs, opening avenues to further interrogation via targeted experiments.
Details
- Title: Subtitle
- Identification and characterization of proteins of unknown function (PUFs) in Clostridium thermocellum DSM 1313 strains as potential genetic engineering targets
- Creators
- Suresh Poudel - University of Tennessee at KnoxvilleAlexander L. Cope - University of Tennessee at KnoxvilleKaela B. O'Dell - Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USAAdam M. Guss - University of Tennessee at KnoxvilleHyeongmin Seo - University of Tennessee at KnoxvilleCong T. Trinh - University of Tennessee at KnoxvilleRobert L. Hettich - Oak Ridge National Laboratory
- Resource Type
- Journal article
- Publication Details
- Biotechnology for biofuels, Vol.14(1), pp.116-116
- Publisher
- Springer Nature
- DOI
- 10.1186/s13068-021-01964-4
- PMID
- 33971924
- PMCID
- PMC8112048
- ISSN
- 1754-6834
- eISSN
- 1754-6834
- Number of pages
- 19
- Grant note
- Center for Bioenergy Innovation (CBI), a U.S. Department of Energy Bioenergy Research Center - Office of Biological and Environmental Research in the DOE Office of Science; United States Department of Energy (DOE)
- Language
- English
- Date published
- 05/10/2021
- Academic Unit
- Chemical and Biochemical Engineering
- Record Identifier
- 9984696714802771
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