Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus

Henson, William R.; Campbell, Tayte; DeLorenzo, Drew M.; Gao, Yu; Berla, Bertram M.; Kim, Soo Ji; Foston, Marcus; Moon, Tae Seok; Dantas, Gautam

doi:10.1016/j.ymben.2018.06.009

Cited by 56 publications

(103 citation statements)

References 86 publications

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“…This provides strong evidence that the ortho pathway is the exclusive route for phenol degradation. The labeling result is consistent with our previous gene knockout analyses (Henson et al, 2018a). Specifically, when muconate cycloisomerase, an ortho pathway enzyme, was disrupted, R. opacus was no longer able to grow on phenol.…”

Section: Resultssupporting

confidence: 91%

“…Proteinogenic amino acid synthesis in R. opacus undergoes minimal changes when grown on different carbon sources. R. opacus is known to store high concentrations of lipids in late growth phases, and reportedly can accumulate lipids up to 80% of its dry cell weight under low-nitrogen stress (Alvarez et al, 1996;Henson et al, 2018a). In the exponential growth phase when nitrogen is still available, ~0.3 g lipid per gram dry cell weight was accumulated in biomass samples.…”

Section: Resultsmentioning

confidence: 99%

“…It is important to note that while transcriptomics can illuminate how genes are regulated, it does not strictly correlate to enzyme activities or flux values due to variations in translational rate and allosteric regulation. Using data generated in the previous report, we compared the transcription levels of central pathway enzymes in glucose-and phenol-fed cultures of wild type R. opacus and R. opacus PVHG6, a mutant strain which was adaptively evolved for improved growth on a mixture of aromatic compounds ( Figure 3C) (Henson et al, 2018a). When consuming glucose, R. opacus expressed phenol hydroxylase at low levels, while its key enzymes for glycolysis are mostly highly expressed.…”

Section: Resultsmentioning

confidence: 99%

“…RNA-seq analysis. Raw transcriptomic sequences were downloaded from the Sequence Read Archive (SRA) accession number SRP131196 (Henson et al, 2018a). Sequences were quality trimmed using Trimmomatic (Bolger et al, 2014) before mapping to the Chinese Academy of Science reference genome of R. opacus (ASM59954v1) (Chen et al, 2014) using Bowtie2 (Langmead and Salzberg, 2012).…”

Section: Methodsmentioning

confidence: 99%

“…Isolated from a gas works plant, this strain is capable of accumulating triacylglycerol (TAG), the precursor for biodiesel up to 80% of its dry cell weight (Alvarez et al, 1996). Studies of its mechanisms of aromatic tolerance and TAG accumulation have found promising results for its use in the conversion of lignin-derived aromatic substrates (DeLorenzo et al, 2017;Henson et al, 2018a;Henson et al, 2018b;Yoneda et al, 2016). R. opacus has been extensively studied for its growth kinetics and transcriptional activities, yet key knowledge gaps from genotype to phenotype still remain.…”

Section: Introductionmentioning

confidence: 99%

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Section: Resultssupporting

confidence: 91%

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confidence: 99%

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Engineering Pseudomonas putida for improved utilization of syringyl aromatics

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Lignin is a largely untapped source for the bioproduction of value-added chemicals.Pseudomonas putida KT2440 has emerged as a strong candidate for bioprocessing of lignin feedstocks due to its resistance to several industrial solvents, broad metabolic capabilities, and genetic amenability. Here we demonstrate the engineering of P. putida for the ability to metabolize syringic acid, one of the major products that comes from the breakdown of the syringyl component of lignin. The rational design was first applied for the construction of strain Sy-1 by overexpressing a native vanillate demethylase. Subsequent adaptive laboratory evolution (ALE) led to the generation of mutations that achieved robust growth on syringic acid as a sole carbon source. The best mutant showed a 30% increase in the growth rate over the original engineered strain. Genomic sequencing revealed multiple mutations repeated in separate evolved replicates. Reverse engineering of mutations identified in agmR, gbdR, fleQ, and the intergenic region of gstB and yadG into the parental strain recaptured the improved growth of the evolved strains to varied extent. These findings thus reveal the ability of P. putida to utilize lignin more fully as a feedstock and make it a more economically viable chassis for chemical production.adaptive lab evolution (ALE), Pseudomonas putida KT2440, syringyl lignin-derived aromatics | INTRODUCTIONLignin is a complex organic polymer that makes up 20%-35% of plant cell walls. It is polymerized from three monolignols: p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol, which are categorized as the corresponding hydroxy (H), guaiacyl (G), and syringyl (S) lignin components (Figure 1a;Feofilova & Mysyakina, 2016). Depending on the type of plants, the ratio of H, G, and S subunits in lignin varies, where the grass lignin consists of all subunits, the softwood lignin often has low S component

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Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database

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Appl Microbiol Biotechnol

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Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.

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Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus

Cited by 56 publications

References 86 publications

A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630

A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630

Engineering Pseudomonas putida for improved utilization of syringyl aromatics

Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database

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