The Need for Integrated Approaches in Metabolic Engineering

Lechner, Anna; Brunk, Elizabeth; Keasling, Jay D.

doi:10.1101/cshperspect.a023903

Cited by 47 publications

(33 citation statements)

References 120 publications

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“…Более сложно организованные объекты, такие как животные и растения, со временем тоже по-требуют большей процессивности. Особенно остро во-прос эффективности методов преобразования генома для микроорганизмов встал, когда методы биоинформатики и аналитические подходы позволили предсказывать и анализировать сложные модельные эксперименты, требу-ющие модификации и тонкой регуляции большого числа генов и метаболических путей (Lechner et al, 2016). Уже сейчас для отдельных задач в биологии необходимы сот-ни и тысячи модификаций.…”

Section: Mainstream Technologies In Genetics and Cell Biology Vavilovunclassified

Methods of yeast genome editing

Розанов¹,

Шляхтун²,

Текутьева³

et al. 2017

Vestn. VOGiS

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Yeasts are a convenient model eukaryote used for genome studies and genome editing. Saccharomyces cerevisiae is the species most widely employed in bio technology, since it is easily cultivated in bioreactors and is absolutely safe. The last decade saw a significant development of methods of yeast genetic engineer ing and the creation of novel instruments adapted from other fields, which allowed one to significantly accelerate the construction of new strains. The most prominent examples are the proteins used for directed DNA editing. For a long time, yeast genome engineer ing was based on the yeasts' system of homologous recombination. It was sufficient for several decades before the development of highthroughput methods. Many highthroughput methods were developed in the second decade of the XXI century, including those used in genomics, transcriptomics, proteomics, metabolomics, interactomics, etc. Modern bioinfor matic databases now allow one to rapidly process the increasing flow of information and model cellular pro cesses. As a result, the rate of analysis and prediction of targets for genome editing is currently higher than the rate of genome editing, which led to the develop ment of new methods of genetic engineering. This process was particularly pronounced for microorgan isms. Modern tasks require tens, hundreds, sometimes even thousands of genome modifications, which made researchers to look for new techniques. As a result, the instruments used for more complex objects, such as animals, plants, and cell lines, were adapted for yeasts. Modern methods for yeast genome editing allow introducing several modifications into the genome in a single step. In this study, we review the methods of directed genome editing and their applications and perspectives for yeasts.Key words: yeast; Saccharomyces cerevisiae; genetic engineering; ZFN; zinc fingers; TALENS; CRISPR/Cas; Argonaut; NgAgo.Дрожжи являются модельным эукариотическим организмом, на котором отрабатываются многие предположения о работе генома, а также методы его редактирования. Наиболее часто в исследо вательских работах используют Saccharomyces cerevisiae, которые очень хорошо приспособлены физиологически к культивированию в условиях биореактора и признаны абсолютно безопасными. В по следнее десятилетие методы генетической инженерии дрожжей претерпели значительные изменения. Появились новые инстру менты, которые пришли из смежных направлений и позволили значительно ускорить процесс получения новых штаммов. Прежде всего это белки для направленного внесения изменений в после довательность ДНК. Длительное время методы редактирования генома дрожжей базировались на использовании их собственной системы гомологичной рекомбинации. Она удобна и удовлетво ряла потребности исследователей на протяжении нескольких де сятилетий, до того времени, когда на первый план стали выходить высокопроизводительные методы. Во втором десятилетии XXI века произошло бурное развитие высокопроизводительных подходов, в первую очередь методов анализа в биологии: геномики, транс крипто...

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Section: Mainstream Technologies In Genetics and Cell Biology Vavilovunclassified

Methods of yeast genome editing

Розанов¹,

Шляхтун²,

Текутьева³

et al. 2017

Vestn. VOGiS

View full text Add to dashboard Cite

show abstract

“…A common problem in the field of biotechnology is the unpredictability inherent in engineering complex biological systems. The use of a whole-system approach can prevent some of the obstacles encountered in bioengineering, including toxicity due to metabolite over-production (Fletcher et al, 2016), metabolic bottlenecks (Lechner et al, 2016), and low product titers (Otero and Nielsen, 2013). Systems metabolic engineering relies on the generation and analysis of large datasets to identify key genetic components that contribute to high-yield production phenotypes.…”

Section: Introductionmentioning

confidence: 99%

Genetic-metabolic coupling for targeted metabolic engineering

Cardinale

Farfan

Sommer

2017

Preprint

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“…To some, synthetic biology means simply "synthesizing a lot of DNA," perhaps even entire genomes (Ellington 2016;Glass 2016). To others, synthetic biology is a new name for the much older field of metabolic engineering, but on a grander scale than modestly constructing a microbe that manufactures a single natural product using a single heterologously expressed gene (Lechner et al 2016).…”

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confidence: 99%