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      Divergent Roles for cAMP–PKA Signaling in the Regulation of Filamentous Growth in Saccharomyces cerevisiae and Saccharomyces bayanus

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          Abstract

          The cyclic AMP – Protein Kinase A (cAMP–PKA) pathway is an evolutionarily conserved eukaryotic signaling network that is essential for growth and development. In the fungi, cAMP–PKA signaling plays a critical role in regulating cellular physiology and morphological switches in response to nutrient availability. We undertook a comparative investigation of the role that cAMP-PKA signaling plays in the regulation of filamentous growth in two closely related budding yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus. Using chemical and genetic perturbations of this pathway and its downstream targets we discovered divergent roles for cAMP-PKA signaling in the regulation of filamentous growth. While cAMP-PKA signaling is required for the filamentous growth response in both species, increasing or decreasing the activity of this pathway leads to drastically different phenotypic outcomes. In S. cerevisiae, cAMP-PKA inhibition ameliorates the filamentous growth response while hyper-activation of the pathway leads to increased filamentous growth; the same perturbations in S. bayanus result in the obverse. Divergence in the regulation of filamentous growth between S. cerevisiae and S. bayanus extends to downstream targets of PKA, including several kinases, transcription factors, and effector proteins. Our findings highlight the potential for significant evolutionary divergence in gene network function, even when the constituent parts of such networks are well conserved.

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          Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae.

          Disruption-deletion cassettes are powerful tools used to study gene function in many organisms, including Saccharomyces cerevisiae. Perhaps the most widely useful of these are the heterologous dominant drug resistance cassettes, which use antibiotic resistance genes from bacteria and fungi as selectable markers. We have created three new dominant drug resistance cassettes by replacing the kanamycin resistance (kan(r)) open reading frame from the kanMX3 and kanMX4 disruption-deletion cassettes (Wach et al., 1994) with open reading frames conferring resistance to the antibiotics hygromycin B (hph), nourseothricin (nat) and bialaphos (pat). The new cassettes, pAG25 (natMX4), pAG29 (patMX4), pAG31 (patMX3), pAG32 (hphMX4), pAG34 (hphMX3) and pAG35 (natMX3), are cloned into pFA6, and so are in all other respects identical to pFA6-kanMX3 and pFA6-kanMX4. Most tools and techniques used with the kanMX plasmids can also be used with the hph, nat and patMX containing plasmids. These new heterologous dominant drug resistance cassettes have unique antibiotic resistance phenotypes and do not affect growth when inserted into the ho locus. These attributes make the cassettes ideally suited for creating S. cerevisiae strains with multiple mutations within a single strain. Copyright 1999 John Wiley & Sons, Ltd.
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            Finding functional features in Saccharomyces genomes by phylogenetic footprinting.

            The sifting and winnowing of DNA sequence that occur during evolution cause nonfunctional sequences to diverge, leaving phylogenetic footprints of functional sequence elements in comparisons of genome sequences. We searched for such footprints among the genome sequences of six Saccharomyces species and identified potentially functional sequences. Comparison of these sequences allowed us to revise the catalog of yeast genes and identify sequence motifs that may be targets of transcriptional regulatory proteins. Some of these conserved sequence motifs reside upstream of genes with similar functional annotations or similar expression patterns or those bound by the same transcription factor and are thus good candidates for functional regulatory sequences.
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              Yeast evolutionary genomics.

              Over the past few years, genome sequences have become available from an increasing range of yeast species, which has led to notable advances in our understanding of evolutionary mechanisms in eukaryotes. Yeasts offer us a unique opportunity to examine how molecular and reproductive mechanisms combine to affect genome architectures and drive evolutionary changes over a broad range of species. This Review summarizes recent progress in understanding the molecular mechanisms--such as gene duplication, mutation and acquisition of novel genetic material--that underlie yeast evolutionary genomics. I also discuss how results from yeasts can be extended to other eukaryotes.
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                Author and article information

                Journal
                G3 (Bethesda)
                Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes, Genomes, Genetics
                G3: Genes|Genomes|Genetics
                Genetics Society of America
                2160-1836
                12 September 2018
                November 2018
                : 8
                : 11
                : 3529-3538
                Affiliations
                [1]Department of Biology, Duke University, Durham, North Carolina
                Author notes
                [1 ]Email: paul.magwene@ 123456duke.edu , Department of Biology, Duke University, Box 90338, Durham, NC 27708
                Author information
                http://orcid.org/0000-0002-7659-2589
                Article
                GGG_200413
                10.1534/g3.118.200413
                6222581
                30213866
                2881ff83-c961-485e-a721-55e020196cb5
                Copyright © 2018 Kayikci, Magwene

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 10 May 2018
                : 27 August 2018
                Page count
                Figures: 6, Tables: 0, Equations: 0, References: 72, Pages: 10
                Categories
                Investigations

                Genetics
                gene network evolution,signal transduction,cyclic-amp,fungal genetics
                Genetics
                gene network evolution, signal transduction, cyclic-amp, fungal genetics

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