Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates

Walker, Caleb; Ryu, Seunghyun; Na, Hyunsoo; Zane, Matthew; LaButti, Kurt; Lipzen, Anna; Haridas, Sajeet; Barry, Kerrie; Grigoriev, Igor V.; Quarterman, Joshua; Slininger, Patricia J.; Dien, Bruce S.; Trinh, Cong T.

doi:10.1128/mra.01040-18

Cited by 14 publications

(18 citation statements)

References 17 publications

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“…The second root contained the remaining four non-conventional isolates, depicting YB392 and YB420 as the most divergent from YB567 followed by YB566. This result was surprising since YB392, YB419 and YB420 were all isolated from corn milling plants within Illinois (20). Interestingly, the closest related species to the Yarrowia clade is Sugiyamaella lignohabitans, an efficient pentose utilizing and facultative anaerobic yeast (21).…”

Section: Phylogenetic Tree Of Y Lipolytica Isolates Shows Close Similarity Between Genomesmentioning

confidence: 99%

Exploring Proteomes of RobustYarrowia lipolyticaIsolates Cultivated in Biomass Hydrolysate Reveal Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation

Walker

Dien

Giannone

et al. 2021

Preprint

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Yarrowia lipolytica is an oleaginous yeast exhibiting robust phenotypes beneficial for industrial biotechnology. The phenotypic diversity found within the undomesticated Y. lipolytica clade from various origins illuminates desirable phenotypic traits not found in the conventional laboratory strain CBS7504, which include xylose utilization, lipid accumulation, and growth on undetoxified biomass hydrolysates. Currently, the related phenotypes of lipid accumulation and degradation when metabolizing non-preferred sugars (e.g., xylose) associated with biomass hydrolysates are poorly understood, making it difficult to control and engineer in Y. lipolytica To fill this knowledge gap, we analyzed the genetic diversity of five undomesticated Y. lipolytica strains and identified singleton genes and genes exclusively shared by strains exhibiting desirable phenotypes. Strain characterizations from controlled bioreactor cultures revealed that the undomesticated strain YB420 used xylose to support cell growth and maintained high lipid levels while the conventional strain CBS7504 degraded cell biomass and lipids when xylose was the sole remaining carbon source. From proteomic analysis, we identified carbohydrate transporters, xylose metabolic enzymes and pentose phosphate pathway proteins stimulated during the xylose uptake stage for both strains. Furthermore, we distinguished proteins in lipid metabolism (e.g., lipase, NADPH generation, lipid regulators, β-oxidation) activated by YB420 (lipid maintenance phenotype) or CBS7504 (lipid degradation phenotype) when xylose was the sole remaining carbon source. Overall, the results relate genetic diversity of undomesticated Y. lipolytica strains to complex phenotypes of superior growth, sugar utilization, lipid accumulation and degradation in biomass hydrolysates.

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Section: Phylogenetic Tree Of Y Lipolytica Isolates Shows Close Similarity Between Genomesmentioning

confidence: 99%

Exploring Proteomes of RobustYarrowia lipolyticaIsolates Cultivated in Biomass Hydrolysate Reveal Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation

Walker

Dien

Giannone

et al. 2021

Preprint

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“…The quantified libraries were then multiplexed with other libraries, and the pool of libraries was then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v.4, and the Illumina cBot instrument to generate a clustered flow cell for sequencing. Sequencing of the flow cell was performed on an Illumina HiSeq 2500 sequencer using HiSeq TruSeq sequencing by synthesis (SBS) kits, v.4, following a 2 × 150-bp (2 × 100-bp for LMP) indexed run recipe (14).…”

Section: Announcementmentioning

confidence: 99%

Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens

López

Peng

Daly

et al. 2019

Microbiol Resour Announc

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“…Yarrowia lipolytica YB567 v1.0 [337]; Zygosaccharomyces rouxii CBS732 [338]; Zymoseptoria ardabiliae STIR04_1.1.1; Zymoseptoria pseudotritici STIR04_2.2.1 [339]; Zymoseptoria brevis Zb18110 [340]; Melampsora allii-populina 12AY07 v1.0; Melampsora americana R15-033-03 v1.0 (unpublished).…”

Section: Introductionmentioning

confidence: 99%

Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes

Hage

Rosso

Tarrago

2021

Free Radical Biology and Medicine

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Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thioloxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met.MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-Rsulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenumcontaining enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom.We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi. Material and methods Search for Msr homologs in fungi.The protein sequence of MsrA (Uniprot accession # C8Z745), MsrB (Uniprot accession # P25566) and fRMsr (Uniprot accession # P36088) from S. cerevisiae, MsrP (Uniprot accession # P76342) and BisC (Uniprot accession # P20099) from Escherichia coli, TorZ (Uniprot accession # P44798) from Haemophilus influenzae, and DorA (Uniprot accession # Q57366) from Rhodobacter sphaeroides were used as BLASTP and TBLASTN [49] queries to identify msr genes in 683 genomes available in the MycoCosm database [50] (https://mycocosm.jgi.doe.gov/mycocosm/home). 2.2.List of all explored fungal genomes.

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Draft Genome Assemblies of Five Robust Yarrowia lipolytica Strains Exhibiting High Lipid Production, Pentose Sugar Utilization, and Sugar Alcohol Secretion from Undetoxified Lignocellulosic Biomass Hydrolysates

Cited by 14 publications

References 17 publications

Exploring Proteomes of RobustYarrowia lipolyticaIsolates Cultivated in Biomass Hydrolysate Reveal Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation

Exploring Proteomes of RobustYarrowia lipolyticaIsolates Cultivated in Biomass Hydrolysate Reveal Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation

Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot Basidiomycete Fungus Dichomitus squalens

Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes

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