Engineering topics

Lu, Fachuang

Publications and source records attributed to Lu, Fachuang.

5 records

DOE OSTI2025

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

ABSTRACT A randomly barcoded transposon insertion sequencing (RB-TnSeq) library of Novosphingobium aromaticivorans DSM12444 was grown in media containing either glucose or the β-5-linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) as the sole carbon source. The cultures were grown to saturation and then sequenced, yielding the barcode abundance data sets presented here.

Metz, Fletcher↗

DOE OSTI2024

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

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.

Metz, Fletcher↗

DOE OSTI2024

Catabolism of β-5 linked aromatics by Novosphingobium aromaticivorans

ABSTRACT Aromatic compounds are an important source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived from plant lignin can potentially be converted into commodity chemicals through depolymerization followed by microbial funneling of monomers and low molecular weight oligomers. This study investigates the catabolism of the β-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans . We used genome-wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidate genes elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans . Specifically, a newly identified γ-formaldehyde lyase, PcfL, opens the phenylcoumaran ring to form a stilbene and formaldehyde. A lignostilbene dioxygenase, LsdD, then cleaves the stilbene to generate the aromatic monomers vanillin and 5-formylferulate (5-FF). We also showed that the aldehyde dehydrogenase FerD oxidizes 5-FF before it is decarboxylated by LigW, yielding ferulic acid. We found that some enzymes involved in the β-5 catabolism pathway can act on multiple substrates and that some steps in the pathway can be mediated by multiple enzymes, providing new insights into the robust flexibility of aromatic catabolism in N. aromaticivorans . A comparative genomic analysis predicted that the newly discovered β-5 aromatic catabolic pathway is common within the order Sphingomonadales. IMPORTANCE In the transition to a circular bioeconomy, the plant polymer lignin holds promise as a renewable source of industrially important aromatic chemicals. However, since lignin contains aromatic subunits joined by various chemical linkages, producing single chemical products from this polymer can be challenging. One strategy to overcome this challenge is using microbes to funnel a mixture of lignin-derived aromatics into target chemical products. This approach requires strategies to cleave the major inter-unit linkages of lignin to release monomers for funneling into valuable products. In this study, we report newly discovered aspects of a pathway by which the Novosphingobium aromaticivorans DSM12444 catabolizes aromatics joined by the second most common inter-unit linkage in lignin, the β-5 linkage. This work advances our knowledge of aromatic catabolic pathways, laying the groundwork for future metabolic engineering of this and other microbes for optimized conversion of lignin into products.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

NMR Database of Lignin and Cell Wall Model Compounds

This database was designed to provide a coherent, single source of NMR data of lignin and other plant cell wall model compounds. The database exists as an Adobe pdf cross-platform file for viewing and printing. This is the latest public version of the Database, version 2024/08 updated from the 2009 version.

cell wall↗

DOE OSTI2024

PagMYB128 regulates secondary cell wall formation by direct activation of cell wall biosynthetic genes during wood formation in poplar

The biosynthesis of cellulose, lignin, and hemicelluloses in plant secondary cell walls (SCWs) is regulated by a hierarchical transcriptional regulatory network. Here, this network features orthologous transcription factors shared between poplar and Arabidopsis, highlighting a foundational similarity in their genetic regulation. However, knowledge on the discrepant behavior of the transcriptional-level molecular regulatory mechanisms between poplar and Arabidopsis remains limited. In this study, we investigated the function of PagMYB128 during wood formation and found it had broader impacts on SCW formation compared to its Arabidopsis ortholog, AtMYB103. Transgenic poplar trees overexpressing PagMYB128 exhibited significantly enhanced xylem development, with fiber cells and vessels displaying thicker walls, and an increase in the levels of cellulose, lignin, and hemicelluloses in the wood. In contrast, plants with dominant repression of PagMYB128 demonstrated the opposite phenotypes. RNA sequencing and reverse transcription – quantitative polymerase chain reaction showed that PagMYB128 could activate SCW biosynthetic gene expression, and chromatin immunoprecipitation along with yeast one-hybrid, and effector–reporter assays showed this regulation was direct. Further analysis revealed that PagSND1 (SECONDARY WALL-ASSOCIATED NAC-DOMAIN PROTEIN1) directly regulates PagMYB128 but not cell wall metabolic genes, highlighting the pivotal role of PagMYB128 in the SND1-driven regulatory network for wood development, thereby creating a feedforward loop in SCW biosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗