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Title: Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium

The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponentialmore » and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.« less
Authors:
ORCiD logo [1] ;  [2] ;  [3] ;  [3] ;  [3] ;  [3] ;  [2]
  1. Federico Santa Maria Technical Univ., Valparaiso (Chile). Daniel Alkalay Lowitt Biotechnology Center
  2. Univ. of Massachusetts, Amherst, MA (United States). Microbiology Dept.
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Publication Date:
Report Number(s):
PNNL-SA-131719
Journal ID: ISSN 1932-6203
Grant/Contract Number:
AC02-05CH11231; AC05-76RL01830
Type:
Published Article
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 12; Journal Issue: 10; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Research Org:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Univ. of Massachusetts, Amherst, MA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Univ. of Massachusetts Amherst (United States)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; lignin; formates; glucose; gene expression; Enterobacter; glucose metabolism; gene regulation; laccases
OSTI Identifier:
1400337
Alternate Identifier(s):
OSTI ID: 1430727

Orellana, Roberto, Chaput, Gina, Markillie, Lye Meng, Mitchell, Hugh, Gaffrey, Matt, Orr, Galya, and DeAngelis, Kristen M. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium. United States: N. p., Web. doi:10.1371/journal.pone.0186440.
Orellana, Roberto, Chaput, Gina, Markillie, Lye Meng, Mitchell, Hugh, Gaffrey, Matt, Orr, Galya, & DeAngelis, Kristen M. Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium. United States. doi:10.1371/journal.pone.0186440.
Orellana, Roberto, Chaput, Gina, Markillie, Lye Meng, Mitchell, Hugh, Gaffrey, Matt, Orr, Galya, and DeAngelis, Kristen M. 2017. "Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium". United States. doi:10.1371/journal.pone.0186440.
@article{osti_1400337,
title = {Multi-time series RNA-seq analysis of Enterobacter lignolyticus SCF1 during growth in lignin-amended medium},
author = {Orellana, Roberto and Chaput, Gina and Markillie, Lye Meng and Mitchell, Hugh and Gaffrey, Matt and Orr, Galya and DeAngelis, Kristen M.},
abstractNote = {The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.},
doi = {10.1371/journal.pone.0186440},
journal = {PLoS ONE},
number = 10,
volume = 12,
place = {United States},
year = {2017},
month = {10}
}

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