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The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans (2008)

N. King ; M. J. Westbrook ; S. L. Young ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 451(7180): 783-8. doi: 10.1038/nature06617.

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Publication Date: 2008-02-15

Description: Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562698/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562698/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉King, Nicole -- Westbrook, M Jody -- Young, Susan L -- Kuo, Alan -- Abedin, Monika -- Chapman, Jarrod -- Fairclough, Stephen -- Hellsten, Uffe -- Isogai, Yoh -- Letunic, Ivica -- Marr, Michael -- Pincus, David -- Putnam, Nicholas -- Rokas, Antonis -- Wright, Kevin J -- Zuzow, Richard -- Dirks, William -- Good, Matthew -- Goodstein, David -- Lemons, Derek -- Li, Wanqing -- Lyons, Jessica B -- Morris, Andrea -- Nichols, Scott -- Richter, Daniel J -- Salamov, Asaf -- Sequencing, J G I -- Bork, Peer -- Lim, Wendell A -- Manning, Gerard -- Miller, W Todd -- McGinnis, William -- Shapiro, Harris -- Tjian, Robert -- Grigoriev, Igor V -- Rokhsar, Daniel -- R01 CA058530/CA/NCI NIH HHS/ -- R01 CA058530-14/CA/NCI NIH HHS/ -- R01 GM077197/GM/NIGMS NIH HHS/ -- R01 HG004164/HG/NHGRI NIH HHS/ -- R01 HG004164-01/HG/NHGRI NIH HHS/ -- R37 HD028315/HD/NICHD NIH HHS/ -- England -- Nature. 2008 Feb 14;451(7180):783-8. doi: 10.1038/nature06617.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology and the Center for Integrative Genomics, University of California, Berkeley, California 94720, USA. nking@berkeley.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18273011" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Cell Adhesion ; Conserved Sequence ; Eukaryotic Cells/classification/cytology/*metabolism ; Evolution, Molecular ; Extracellular Matrix/metabolism ; Gene Expression Regulation ; Genetic Speciation ; Genome/*genetics ; Hedgehog Proteins/chemistry/genetics ; Humans ; Introns/genetics ; Phosphotyrosine/metabolism ; *Phylogeny ; Protein Structure, Tertiary/genetics ; Receptors, Notch/chemistry/genetics ; Signal Transduction/genetics ; Transcription Factors/genetics/metabolism ; Transcription, Genetic

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Negative feedback that improves information transmission in yeast signalling (2008)

R. C. Yu ; C. G. Pesce ; A. Colman-Lerner ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 456(7223): 755-61. doi: 10.1038/nature07513.

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Publication Date: 2008-12-17

Description: Haploid Saccharomyces cerevisiae yeast cells use a prototypic cell signalling system to transmit information about the extracellular concentration of mating pheromone secreted by potential mating partners. The ability of cells to respond distinguishably to different pheromone concentrations depends on how much information about pheromone concentration the system can transmit. Here we show that the mitogen-activated protein kinase Fus3 mediates fast-acting negative feedback that adjusts the dose response of the downstream system response to match the dose response of receptor-ligand binding. This 'dose-response alignment', defined by a linear relationship between receptor occupancy and downstream response, can improve the fidelity of information transmission by making downstream responses corresponding to different receptor occupancies more distinguishable and reducing amplification of stochastic noise during signal transmission. We also show that one target of the feedback is a previously uncharacterized signal-promoting function of the regulator of G-protein signalling protein Sst2. Our work suggests that negative feedback is a general mechanism used in signalling systems to align dose responses and thereby increase the fidelity of information transmission.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716709/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2716709/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yu, Richard C -- Pesce, C Gustavo -- Colman-Lerner, Alejandro -- Lok, Larry -- Pincus, David -- Serra, Eduard -- Holl, Mark -- Benjamin, Kirsten -- Gordon, Andrew -- Brent, Roger -- P50 HG002370/HG/NHGRI NIH HHS/ -- P50 HG002370-01A1/HG/NHGRI NIH HHS/ -- P50 HG002370-01A1S1/HG/NHGRI NIH HHS/ -- P50 HG002370-02/HG/NHGRI NIH HHS/ -- P50 HG002370-03/HG/NHGRI NIH HHS/ -- P50 HG002370-03S1/HG/NHGRI NIH HHS/ -- P50 HG002370-04/HG/NHGRI NIH HHS/ -- P50 HG002370-04S1/HG/NHGRI NIH HHS/ -- P50 HG002370-05/HG/NHGRI NIH HHS/ -- P50 HG002370-05S1/HG/NHGRI NIH HHS/ -- P50 HG02370/HG/NHGRI NIH HHS/ -- R01 GM097479/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Dec 11;456(7223):755-61. doi: 10.1038/nature07513.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Sciences Institute, 2168 Shattuck Avenue, Berkeley, California 94704, USA. ryu@molsci.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19079053" target="_blank"〉PubMed〈/a〉

Keywords: Dose-Response Relationship, Drug ; Feedback, Physiological/*physiology ; GTPase-Activating Proteins/metabolism ; Mitogen-Activated Protein Kinases/*metabolism ; Pheromones/*metabolism/pharmacology ; Protein Binding ; Saccharomyces cerevisiae/drug effects/metabolism/*physiology ; Saccharomyces cerevisiae Proteins/*metabolism ; *Signal Transduction/drug effects

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Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

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Messenger RNA targeting to endoplasmic reticulum stress signalling sites (2008)

T. Aragon ; E. van Anken ; D. Pincus ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 457(7230): 736-40. doi: 10.1038/nature07641.

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Publication Date: 2008-12-17

Description: Deficiencies in the protein-folding capacity of the endoplasmic reticulum (ER) in all eukaryotic cells lead to ER stress and trigger the unfolded protein response (UPR). ER stress is sensed by Ire1, a transmembrane kinase/endoribonuclease, which initiates the non-conventional splicing of the messenger RNA encoding a key transcription activator, Hac1 in yeast or XBP1 in metazoans. In the absence of ER stress, ribosomes are stalled on unspliced HAC1 mRNA. The translational control is imposed by a base-pairing interaction between the HAC1 intron and the HAC1 5' untranslated region. After excision of the intron, transfer RNA ligase joins the severed exons, lifting the translational block and allowing synthesis of Hac1 from the spliced HAC1 mRNA to ensue. Hac1 in turn drives the UPR gene expression program comprising 7-8% of the yeast genome to counteract ER stress. Here we show that, on activation, Ire1 molecules cluster in the ER membrane into discrete foci of higher-order oligomers, to which unspliced HAC1 mRNA is recruited by means of a conserved bipartite targeting element contained in the 3' untranslated region. Disruption of either Ire1 clustering or HAC1 mRNA recruitment impairs UPR signalling. The HAC1 3' untranslated region element is sufficient to target other mRNAs to Ire1 foci, as long as their translation is repressed. Translational repression afforded by the intron fulfils this requirement for HAC1 mRNA. Recruitment of mRNA to signalling centres provides a new paradigm for the control of eukaryotic gene expression.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768538/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768538/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aragon, Tomas -- van Anken, Eelco -- Pincus, David -- Serafimova, Iana M -- Korennykh, Alexei V -- Rubio, Claudia A -- Walter, Peter -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Feb 5;457(7230):736-40. doi: 10.1038/nature07641. Epub 2008 Dec 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158-2517, USA. Tomas.Aragon@ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19079237" target="_blank"〉PubMed〈/a〉

Keywords: 3' Untranslated Regions/genetics ; Basic-Leucine Zipper Transcription Factors/genetics ; Conserved Sequence ; Endoplasmic Reticulum/*metabolism ; Gene Expression Regulation, Fungal/genetics ; Introns/genetics ; Membrane Glycoproteins/metabolism ; Protein Biosynthesis ; Protein-Serine-Threonine Kinases/metabolism ; RNA Splicing ; RNA, Fungal/genetics/*metabolism ; RNA, Messenger/genetics/*metabolism ; Repressor Proteins/genetics ; Saccharomyces cerevisiae/*cytology/*genetics ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; *Signal Transduction ; *Stress, Physiological/genetics

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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