Engineered yeast genomes accurately assembled from pure and mixed samples

Collins, Joseph H.; Keating, Kevin W; Jones, Trent R.; Balaji, Shravani; Marsan, Celeste B.; Çomo, Marina; Newlon, Zachary J.; Mitchell, Tom; Bartley, Bryan; Adler, Aaron; Roehner, Nicholas; Young, Eric M.

doi:10.1038/s41467-021-21656-9

Cited by 17 publications

(33 citation statements)

References 125 publications

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“…These isolates have previously been sequenced [22]. We resequenced these isolates using the Prymetime (v0.2) pipeline which uses both long reads and short reads to obtain a more contiguous genome assembly [61]. Using ERGO's Genome Align tool, we confirmed that there is a 12.8 kb region absent in B11220 but present in B11221.…”

Section: A 128 Kb Deletion Region Encodes Genes Involved In Alternate...mentioning

confidence: 84%

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A correlative study of the genomic underpinning of virulence traits and drug tolerance ofCandida auris

Vaisvil

Schmitt

et al. 2023

Preprint

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The risk ofC. aurisinfection is high because it can colonize the body, resist antifungal treatment, and evade the immune system. The genetic mechanisms for these traits are not well-known. We present an analysis of the genetics and gene expression patterns ofC. auriscarbon metabolism, drug resistance, and macrophage interaction. We chose to study twoC. aurisisolates simultaneously, one drug sensitive (B11220 from Clade II) and one drug resistant (B11221 from Clade III). We found that B11220 was missing a 12.8 kb gene cluster encoding proteins related to alternative sugar utilization, possibly L-rhamnose. We show that B11221 more readily assimilates and utilizes D-galactose and L-rhamnose. B11221 exhibits increased adherence and drug resistance compared to B11220 when grown in these sugars. Transcriptomic analysis of both strains grown on glucose or galactose showed that genes associated with translation were upregulated in B11221. These findings reinforce the growing evidence of a link between metabolism and tolerance. We characterized cell wall composition and macrophage evasion for the two strains. We found that B11221 has far less β-1,3-glucan exposure and resists phagocytosis by macrophages compared to B11220. In a transcriptomic analysis of both strains co-cultured with macrophages we found that B11221 upregulates genes associated with early stages of growth and transcription factors that regulate transport. These key differences in growth and membrane composition could explain the resistance to phagocytosis and increased stress tolerance in general of B11221 and indicates another connection between metabolism and immune system evasion.

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Section: A 128 Kb Deletion Region Encodes Genes Involved In Alternate...mentioning

confidence: 84%

“…Reads were demultiplexed using the native software on the iSeq 100 machine. The C. auris B11220 and B11221 sequences were assembled using the Prymetime (v0.2) pipeline [61], which is a hybrid assembler using long and short reads.…”

Section: Genome Sequencing and Assemblymentioning

confidence: 99%

A correlative study of the genomic underpinning of virulence traits and drug tolerance ofCandida auris

Vaisvil

Schmitt

et al. 2023

Preprint

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“…Moreover, the surface of the yeast colonies is smooth, sticky and easy to pick up and the texture of the colonies is uniform with the color of milky white, black or red. [ 84 ]…”

Section: Biofermentation Technology For Synthesis Of Bc‐based Materialsmentioning

confidence: 99%

“…Moreover, the surface of the yeast colonies is smooth, sticky and easy to pick up and the texture of the colonies is uniform with the color of milky white, black or red. [84] As for the fermentation process of yeast, it decomposes macromolecular substances into small molecules that can be easily metabolic via the system of intracellular and extracellular enzymes. The cultures of the yeasts depend on the liquid medium composed of yeast extract, glucose, and tryptone in deionized water with the proper pH value and temperature of 4.5-5.0 and 20-30 °C.…”

Section: Fermentation Of Yeasts For Bc-based Carbon Materialsmentioning

confidence: 99%

Microbe‐Mediated Biosynthesis of Multidimensional Carbon‐Based Materials for Energy Storage Applications

Shen

Chen

Zhou

et al. 2023

Advanced Energy Materials

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Biosynthesis methods are considered to be a promising technology for engineering new carbon‐based materials or redesigning the existing ones for specific purposes with the aid of synthetic biology. Lots of biosynthetic processes including metabolism, fermentation, biological mineralization, and gene editing have been adopted to prepare novel carbon‐based materials with exceptional properties that cannot be realized by traditional chemical methods, because microbes evolved to possess special abilities to modulate components/structure of materials. In this review, the recent development on carbon‐based materials prepared via different biosynthesis methods and various microbe factories (such as bacteria, yeasts, fungus, viruses, proteins) are systematically reviewed. The types of biotechniques and the corresponding mechanisms for the synthesis of carbon‐based materials are outlined. This review also focuses on the structural design and compositional engineering of carbon‐based nanostructures (e.g., metals, semiconductors, metal oxides, metal sulfides, phosphates, Mxenes) derived from biotechnology and their applications in electrochemical energy storage devices. Moreover, the relationship of the architecture–composition–electrochemical behavior and performance enhancement mechanism is also deeply discussed and analyzed. Finally, the development perspectives and challenges on the biosynthetic carbons are proposed and may pave a new avenue for rational design of advanced materials for the low‐carbon economy.

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“…3,8−10 In this scenario, detecting genetic variations in biological replicates is important to establish a better knowledge about the association of genes and phenotypes. 3,6,11,12 The budding yeast Saccharomyces cerevisiae is a common chassis broadly used in metabolic engineering and synthetic biology studies. 13 Engineering in S. cerevisiae benefits from its well-studied genetics and well-developed genetic engineering tools.…”

Section: ■ Introductionmentioning

confidence: 99%

Integration of Yeast Episomal/Integrative Plasmid Causes Genotypic and Phenotypic Diversity and Improved Sesquiterpene Production in Metabolically Engineered Saccharomyces cerevisiae

Peng,

Weintraub,

et al. 2023

ACS Synth. Biol.

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The variability in phenotypic outcomes among biological replicates in engineered microbial factories presents a captivating mystery. Establishing the association between phenotypic variability and genetic drivers is important to solve this intricate puzzle. We applied a previously developed auxin-inducible depletion of hexokinase 2 as a metabolic engineering strategy for improved nerolidol production in Saccharomyces cerevisiae, and biological replicates exhibit a dichotomy in nerolidol production of either 3.5 or 2.5 g L −1 nerolidol. Harnessing Oxford Nanopore's long-read genomic sequencing, we reveal a potential genetic cause�the chromosome integration of a 2μ sequence-based yeast episomal plasmid, encoding the expression cassettes for nerolidol synthetic enzymes. This finding was reinforced through chromosome integration revalidation, engineering nerolidol and valencene production strains, and generating a diverse pool of yeast clones, each uniquely fingerprinted by gene copy numbers, plasmid integrations, other genomic rearrangements, protein expression levels, growth rate, and target product productivities. Τhe best clone in two strains produced 3.5 g L −1 nerolidol and ∼0.96 g L −1 valencene. Comparable genotypic and phenotypic variations were also generated through the integration of a yeast integrative plasmid lacking 2μ sequences. Our work shows that multiple factors, including plasmid integration status, subchromosomal location, gene copy number, sesquiterpene synthase expression level, and genome rearrangement, together play a complicated determinant role on the productivities of sesquiterpene product. Integration of yeast episomal/integrative plasmids may be used as a versatile method for increasing the diversity and optimizing the efficiency of yeast cell factories, thereby uncovering metabolic control mechanisms.

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Engineered yeast genomes accurately assembled from pure and mixed samples

Cited by 17 publications

References 125 publications

A correlative study of the genomic underpinning of virulence traits and drug tolerance ofCandida auris

A correlative study of the genomic underpinning of virulence traits and drug tolerance ofCandida auris

Microbe‐Mediated Biosynthesis of Multidimensional Carbon‐Based Materials for Energy Storage Applications

Integration of Yeast Episomal/Integrative Plasmid Causes Genotypic and Phenotypic Diversity and Improved Sesquiterpene Production in Metabolically Engineered Saccharomyces cerevisiae

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