Structure, replication efficiency and fragility of yeast ARS elements

Dhar, Manoj K.; Sehgal, Shelly; Kaul, Sanjana

doi:10.1016/j.resmic.2012.03.003

Cited by 44 publications

(32 citation statements)

References 84 publications

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“…Although this motif is necessary for DNA replication, it is not sufficient for Ori function. In contrast to Saccharomyces cerevisiae, Saccharomyces pombe Oris do not contain a core consensus sequence [5]. S. pombe Oris are AT-rich (from 0.5 to 3 kb in length) and contain several functionally important DNA sequence elements for their activity.…”

Section: Introductionmentioning

confidence: 99%

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Genome-scale identification of active DNA replication origins

Cayrou

Grégoire

Coulombe

et al. 2012

Methods

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Section: Introductionmentioning

confidence: 99%

“…This is the only eukaryote in which ORC specifically recognizes a 17 bp AT-rich consensus sequence called ACS (for ARS Consensus Sequence) [5]. Although this motif is necessary for DNA replication, it is not sufficient for Ori function.…”

Section: Introductionmentioning

confidence: 99%

Genome-scale identification of active DNA replication origins

Cayrou

Grégoire

Coulombe

et al. 2012

Methods

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“…A potential epigenetic factor is DNA replication and the requirement for regularly spaced ARSs along chromosomes. Whereas ARSs are typically spaced by 30-40 kb in S. cerevisiae (32), insertion of the 35-kb sequence carrying the glycolytic genes resulted in a spacing between adjacent confirmed ARSs (ARS504.2 and ARS507, and ARS912 and ARS913) of 82 and 74 kb for chromosomes V and IX, respectively (33). In their design for a synthetic chromosome III, Annaluru et al kept a conservative approach by maintaining 12 of the 19 native ARSs, with a maximum spacing between ARSs of ∼50 kb (34).…”

Section: Discussionmentioning

confidence: 99%

Pathway swapping: Toward modular engineering of essential cellular processes

Kuijpers

Solis-Escalante

Luttik

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Recent developments in synthetic biology enable one-step implementation of entire metabolic pathways in industrial microorganisms. A similarly radical remodelling of central metabolism could greatly accelerate fundamental and applied research, but is impeded by the mosaic organization of microbial genomes. To eliminate this limitation, we propose and explore the concept of "pathway swapping," using yeast glycolysis as the experimental model. Construction of a "single-locus glycolysis" Saccharomyces cerevisiae platform enabled quick and easy replacement of this yeast's entire complement of 26 glycolytic isoenzymes by any alternative, functional glycolytic pathway configuration. The potential of this approach was demonstrated by the construction and characterization of S. cerevisiae strains whose growth depended on two nonnative glycolytic pathways: a complete glycolysis from the related yeast Saccharomyces kudriavzevii and a mosaic glycolysis consisting of yeast and human enzymes. This work demonstrates the feasibility and potential of modular, combinatorial approaches to engineering and analysis of core cellular processes.pathway swapping | glycolysis | Saccharomyces cerevisiae | modular genomes R eplacement of petrochemistry by bio-based processes is a key element for sustainable development and requires microbes equipped with novel-to-nature capabilities. Recent developments in synthetic biology enable introduction of entire metabolic pathways and, thereby, new functionalities for product formation and substrate consumption, into microbial cells (1). However, industrial relevance of the resulting strains critically depends on optimal interaction of the newly introduced pathways with the core metabolism of the host cell. Central metabolic pathways such as glycolysis, tricarboxylic acid cycle, and pentose phosphate pathways, are essential for synthesis of precursors, for providing free energy (ATP), and for redox-cofactor balancing. Optimization of productivity, product yield, and robustness therefore requires modifications in the configuration and/or regulation of these core metabolic functions.Engineering of central metabolism is in some respects more challenging than the functional expression of heterologous product pathways. Millions of years of evolution of microorganisms have endowed their metabolic and regulatory networks with a level of complexity that cannot be efficiently reengineered by iterative, single-gene modifications. Enzymes of central metabolism are encoded by hundreds of genes that, especially in eukaryotes, are scattered across microbial genomes. Moreover, inactivation and subsequent replacement of genes involved in central metabolism is complicated by functional redundancy of isoenzymes (2, 3) as well as by the essential role of many of the corresponding biochemical reactions. Microbial platforms in which the configuration of key pathways can be remodelled in a swift, combinatorial manner would provide an invaluable asset for fundamental research and engineering of central metabolism.Wherea...

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“…Many of these elements were originally identified as sequences of a few hundred base pairs that confer plasmids (otherwise devoid of their own replication origin) the ability to replicate in budding yeast cells following transformation experiments and were thus coined as autonomously replicating sequences (ARSs). Key functional aspects of ARS elements include the ability to recruit a variety of factors involved in triggering DNA replication (with the origin recognition complex being a critical one) and the intrinsic propensity to easily unwind to facilitate the DNA replication process (for a review, see Dhar et al 2012). Whereas many ARSs are bona fide origins of replication in their natural chromosomal contexts, some are not, thus necessitating the use of sophisticated techniques to unequivocally designate a specific ARS as a true chromosomal origin of replication.…”

Section: Genomic Regions Involved In Chromosome Maintenancementioning

confidence: 99%

Budding Yeast for Budding Geneticists: A Primer on the Saccharomyces cerevisiae Model System

2014

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The budding yeast Saccharomyces cerevisiae is a powerful model organism for studying fundamental aspects of eukaryotic cell biology. This Primer article presents a brief historical perspective on the emergence of this organism as a premier experimental system over the course of the past century. An overview of the central features of the S. cerevisiae genome, including the nature of its genetic elements and general organization, is also provided. Some of the most common experimental tools and resources available to yeast geneticists are presented in a way designed to engage and challenge undergraduate and graduate students eager to learn more about the experimental amenability of budding yeast. Finally, a discussion of several major discoveries derived from yeast studies highlights the far-reaching impact that the yeast system has had and will continue to have on our understanding of a variety of cellular processes relevant to all eukaryotes, including humans.

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Structure, replication efficiency and fragility of yeast ARS elements

Cited by 44 publications

References 84 publications

Genome-scale identification of active DNA replication origins

Genome-scale identification of active DNA replication origins

Pathway swapping: Toward modular engineering of essential cellular processes

Budding Yeast for Budding Geneticists: A Primer on the Saccharomyces cerevisiae Model System

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