Transcriptomic data sets for Novosphingobium aromaticivorans grown with the β-5-linked aromatic dimer dehydrodiconiferyl alcohol and the related G-aromatic monomers vanillin and ferulic acid

Metz, Fletcher; Myers, Kevin S.; Lu, Fachuang; Noguera, Daniel R.; Donohue, Timothy J.; Maresca, ed., Julia A.

doi:10.1128/mra.00845-24

Transcriptomic data sets for Novosphingobium aromaticivorans grown with the β-5-linked aromatic dimer dehydrodiconiferyl alcohol and the related G-aromatic monomers vanillin and ferulic acid

Journal Article · Tue Nov 12 00:00:00 EST 2024 · Microbiology Resource Announcements

DOI:https://doi.org/10.1128/mra.00845-24· OSTI ID:2477113

^[1]; ^[2]; Lu, Fachuang ^[2]; Noguera, Daniel R. ^[3]; ^[4]; Maresca, ed., Julia A.

DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA, Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin, USA
DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA, Department of Civil and Environmental Engineering, University of Wisconsin, Madison, Wisconsin, USA
DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, USA, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA, Department of Bacteriology, University of Wisconsin, Madison, Wisconsin, USA

ABSTRACT

The transcriptomes of a 2-pyrone-4,6-dicarboxylic acid-producing strain of Novosphingobium aromaticivorans DSM12444 were determined when grown in minimal medium containing glucose alone or glucose plus vanillin, ferulic acid, or the β-5-linked aromatic dimer dehydrodiconiferyl alcohol as carbon sources. Here, we present the RNA-sequencing data we obtained.

View Journal Article

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0018409

OSTI ID:: 2477113

Journal Information:: Microbiology Resource Announcements, Journal Name: Microbiology Resource Announcements Journal Issue: 11 Vol. 13; ISSN 2576-098X

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

References (16)

Review on Catalytic Cleavage of C–C Inter-unit Linkages in Lignin Model Compounds: Towards Lignin Depolymerisation Guadix-Montero, Susana; Sankar, Meenakshisundaram Topics in Catalysis, Vol. 61, Issue 3-4 https://doi.org/10.1007/s11244-018-0909-2	journal	March 2018
Biological valorization strategies for converting lignin into fuels and chemicals Chen, Zhu; Wan, Caixia Renewable and Sustainable Energy Reviews, Vol. 73 https://doi.org/10.1016/j.rser.2017.01.166	journal	June 2017
Funneling aromatic products of chemically depolymerized lignin into 2-pyrone-4-6-dicarboxylic acid with Novosphingobium aromaticivorans Perez, Jose M.; Kontur, Wayne S.; Alherech, Manar Green Chemistry, Vol. 21, Issue 6 https://doi.org/10.1039/C8GC03504K	journal	January 2019
Integrating lignin depolymerization with microbial funneling processes using agronomically relevant feedstocks Perez, Jose M.; Sener, Canan; Misra, Shamik Green Chemistry, Vol. 24, Issue 7 https://doi.org/10.1039/D1GC03592D	journal	January 2022
Novosphingobium aromaticivorans uses a Nu-class glutathione S -transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin Kontur, Wayne S.; Bingman, Craig A.; Olmsted, Charles N. Journal of Biological Chemistry, Vol. 293, Issue 14 https://doi.org/10.1074/jbc.RA117.001268	journal	February 2018
Fast and accurate short read alignment with Burrows-Wheeler transform Li, H.; Durbin, R. Bioinformatics, Vol. 25, Issue 14 https://doi.org/10.1093/bioinformatics/btp324	journal	May 2009
The Sequence Alignment/Map format and SAMtools Li, H.; Handsaker, B.; Wysoker, A. Bioinformatics, Vol. 25, Issue 16 https://doi.org/10.1093/bioinformatics/btp352	journal	June 2009
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
HTSeq--a Python framework to work with high-throughput sequencing data Anders, S.; Pyl, P. T.; Huber, W. Bioinformatics, Vol. 31, Issue 2 https://doi.org/10.1093/bioinformatics/btu638	journal	September 2014
Rapid, Parallel Identification of Catabolism Pathways of Lignin-Derived Aromatic Compounds in Novosphingobium aromaticivorans Cecil, Jacob H.; Garcia, David C.; Giannone, Richard J. Applied and Environmental Microbiology, Vol. 84, Issue 22 https://doi.org/10.1128/AEM.01185-18	journal	September 2018
Aromatic Dimer Dehydrogenases from Novosphingobium aromaticivorans Reduce Monoaromatic Diketones Linz, Alexandra M.; Ma, Yanjun; Perez, Jose M. Applied and Environmental Microbiology, Vol. 87, Issue 24 https://doi.org/10.1128/AEM.01742-21	journal	November 2021
Engineering Novosphingobium aromaticivorans to produce cis,cis -muconic acid from biomass aromatics Vilbert, Avery C.; Kontur, Wayne S.; Gille, Derek Applied and Environmental Microbiology, Vol. 90, Issue 1 https://doi.org/10.1128/aem.01660-23	journal	January 2024
Isolation and Characterization of a Subsurface Bacterium Capable of Growth on Toluene, Naphthalene, and Other Aromatic Compounds Fredrickson, J. K.; Brockman, F. J.; Workman, D. J. Applied and Environmental Microbiology, Vol. 57, Issue 3 https://doi.org/10.1128/aem.57.3.796-803.1991	journal	January 1991
Aromatic-degrading Sphingomonas isolates from the deep subsurface. Fredrickson, J. K.; Balkwill, D. L.; Drake, G. R. Applied and environmental microbiology, Vol. 61, Issue 5 https://doi.org/10.1128/aem.61.5.1917-1922.1995	journal	January 1995
Catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans Metz, Fletcher; Olsen, Abigail M.; Lu, Fachuang mBio https://doi.org/10.1128/mbio.01718-24	journal	July 2024
The essential Rhodobacter sphaeroides CenKR two-component system regulates cell division and envelope biosynthesis Lakey, Bryan D.; Myers, Kevin S.; Alberge, François PLOS Genetics, Vol. 18, Issue 6 https://doi.org/10.1371/journal.pgen.1010270	journal	June 2022

Similar Records

RB-TnSeq barcode abundance data sets for Novosphingobium aromaticivorans grown on the β-5-linked aromatic dimer dehydrodiconiferyl alcohol

Journal Article · Wed Jan 15 19:00:00 EST 2025 · Microbiology Resource Announcements · OSTI ID:2481156

RNA-seq studying the catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans

Dataset · Wed Feb 28 23:00:00 EST 2024 · OSTI ID:3003592

Production of carotenoids from aromatics and pretreated lignocellulosic biomass by Novosphingobium aromaticivorans

Journal Article · Wed Dec 20 19:00:00 EST 2023 · Applied and Environmental Microbiology · OSTI ID:2222551

Transcriptomic data sets for Novosphingobium aromaticivorans grown with the β-5-linked aromatic dimer dehydrodiconiferyl alcohol and the related G-aromatic monomers vanillin and ferulic acid

Citation Formats

References (16)

Similar Records

Related Subjects