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Friday, July 19, 2019

Exploiting members of the BAHD acyltransferase family to synthesize multiple hydroxycinnamate and benzoate conjugates in yeast.

BAHD acyltransferases, named after the first four biochemically characterized enzymes of the group, are plant-specific enzymes that catalyze the transfer of coenzyme A-activated donors onto various acceptor molecules. They are responsible for the synthesis in plants of a myriad of secondary metabolites, some of which are beneficial for humans either as therapeutics or as specialty chemicals such as flavors and fragrances. The production of pharmaceutical, nutraceutical and commodity chemicals using engineered microbes is an alternative, green route to energy-intensive chemical syntheses that consume petroleum-based precursors. However, identification of appropriate enzymes and validation of their functional expression in heterologous hosts is…

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Friday, July 19, 2019

Contrasting evolutionary genome dynamics between domesticated and wild yeasts.

Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus. These population-level high-quality genomes with comprehensive annotation enable precise definition of chromosomal boundaries between cores and subtelomeres and a high-resolution view of evolutionary genome dynamics. In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae…

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Friday, July 19, 2019

Iterative optimization of xylose catabolism in Saccharomyces cerevisiae using combinatorial expression tuning.

A common challenge in metabolic engineering is rapidly identifying rate-controlling enzymes in heterologous pathways for subsequent production improvement. We demonstrate a workflow to address this challenge and apply it to improving xylose utilization in Saccharomyces cerevisiae. For eight reactions required for conversion of xylose to ethanol, we screened enzymes for functional expression in S. cerevisiae, followed by a combinatorial expression analysis to achieve pathway flux balancing and identification of limiting enzymatic activities. In the next round of strain engineering, we increased the copy number of these limiting enzymes and again tested the eight-enzyme combinatorial expression library in this new background.…

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Sunday, July 7, 2019

HINGE: long-read assembly achieves optimal repeat resolution.

Long-read sequencing technologies have the potential to produce gold-standard de novo genome assemblies, but fully exploiting error-prone reads to resolve repeats remains a challenge. Aggressive approaches to repeat resolution often produce misassemblies, and conservative approaches lead to unnecessary fragmentation. We present HINGE, an assembler that seeks to achieve optimal repeat resolution by distinguishing repeats that can be resolved given the data from those that cannot. This is accomplished by adding “hinges” to reads for constructing an overlap graph where only unresolvable repeats are merged. As a result, HINGE combines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de…

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Sunday, July 7, 2019

Genome sequences of Cyberlindnera fabianii 65, Pichia kudriavzevii 129, and Saccharomyces cerevisiae 131 isolated from fermented masau fruits in Zimbabwe.

Cyberlindnera fabianii 65, Pichia kudriavzevii 129, and Saccharomyces cerevisiae 131 have been isolated from the microbiota of fermented masau fruits. C. fabianii and P. kudriavzevii especially harbor promising features for biotechnology and food applications. Here, we present the draft annotated genome sequences of these isolates. Copyright © 2017 van Rijswijck et al.

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Sunday, July 7, 2019

Construction of efficient xylose-fermenting Saccharomyces cerevisiae through a synthetic isozyme system of xylose reductase from Scheffersomyces stipitis.

Engineered Saccharomyces cerevisiae has been used for ethanol production from xylose, the abundant sugar in lignocellulosic hydrolyzates. Development of engineered S. cerevisiae able to utilize xylose effectively is crucial for economical and sustainable production of fuels. To this end, the xylose-metabolic genes (XYL1, XYL2 and XYL3) from Scheffersomyces stipitis have been introduced into S. cerevisiae. The resulting engineered S. cerevisiae strains, however, often exhibit undesirable phenotypes such as slow xylose assimilation and xylitol accumulation. This work was undertaken to construct an improved xylose-fermenting strain by developing a synthetic isozyme system of xylose reductase (XR). The DXS strain having both wild…

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Sunday, July 7, 2019

The dynamic three-dimensional organization of the diploid yeast genome.

The budding yeast Saccharomyces cerevisiae is a long-standing model for the three-dimensional organization of eukaryotic genomes. However, even in this well-studied model, it is unclear how homolog pairing in diploids or environmental conditions influence overall genome organization. Here, we performed high-throughput chromosome conformation capture on diverged Saccharomyces hybrid diploids to obtain the first global view of chromosome conformation in diploid yeasts. After controlling for the Rabl-like orientation using a polymer model, we observe significant homolog proximity that increases in saturated culture conditions. Surprisingly, we observe a localized increase in homologous interactions between the HAS1-TDA1 alleles specifically under galactose induction and…

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Sunday, July 7, 2019

LRCstats, a tool for evaluating long reads correction methods.

Third-generation sequencing (TGS) platforms that generate long reads, such as PacBio and Oxford Nanopore technologies, have had a dramatic impact on genomics research. However, despite recent improvements, TGS reads suffer from high-error rates and the development of read correction methods is an active field of research. This motivates the need to develop tools that can evaluate the accuracy of noisy long reads correction tools.We introduce LRCstats, a tool that measures the accuracy of long reads correction tools. LRCstats takes advantage of long reads simulators that provide each simulated read with an alignment to the reference genome segment they originate from,…

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Sunday, July 7, 2019

Genome sequence of Saccharomyces cerevisiae strain Kagoshima No. 2, used for Brewing the Japanese distilled spirit Shochu.

Here, we report a draft genome sequence of Saccharomyces cerevisiae strain Kagoshima no. 2, which is used for brewing shochu, a traditional distilled spirit in Japan. The genome data will facilitate an understanding of the evolutional traits and genetic background related to the characteristic features of strain Kagoshima no. 2. Copyright © 2017 Mori et al.

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Sunday, July 7, 2019

Meeting report on experimental approaches to evolution and ecology using yeast and other model systems.

The fourth EMBO-sponsored conference on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems (https://www.embl.de/training/events/2016/EAE16-01/), was held at the EMBL in Heidelberg, Germany, October 19-23, 2016. The conference was organized by Judith Berman (Tel Aviv University), Maitreya Dunham (University of Washington), Jun-Yi Leu (Academia Sinica), and Lars Steinmetz (EMBL Heidelberg and Stanford University). The meeting attracted ~120 researchers from 28 countries and covered a wide range of topics in the fields of genetics, evolutionary biology, and ecology with a unifying focus on yeast as a model system. Attendees enjoyed the Keith Haring inspired yeast florescence microscopy artwork…

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Sunday, July 7, 2019

Single molecule sequencing-guided scaffolding and correction of draft assemblies.

Although single molecule sequencing is still improving, the lengths of the generated sequences are inevitably an advantage in genome assembly. Prior work that utilizes long reads to conduct genome assembly has mostly focused on correcting sequencing errors and improving contiguity of de novo assemblies.We propose a disassembling-reassembling approach for both correcting structural errors in the draft assembly and scaffolding a target assembly based on error-corrected single molecule sequences. To achieve this goal, we formulate a maximum alternating path cover problem. We prove that this problem is NP-hard, and solve it by a 2-approximation algorithm.Our experimental results show that our approach…

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Sunday, July 7, 2019

HISEA: HIerarchical SEed Aligner for PacBio data.

The next generation sequencing (NGS) techniques have been around for over a decade. Many of their fundamental applications rely on the ability to compute good genome assemblies. As the technology evolves, the assembly algorithms and tools have to continuously adjust and improve. The currently dominant technology of Illumina produces reads that are too short to bridge many repeats, setting limits on what can be successfully assembled. The emerging SMRT (Single Molecule, Real-Time) sequencing technique from Pacific Biosciences produces uniform coverage and long reads of length up to sixty thousand base pairs, enabling significantly better genome assemblies. However, SMRT reads are…

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Sunday, July 7, 2019

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D.

Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction. Assembly of the reads derived from all three technologies resulted in complete sequences for…

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