Relationship between G+C content, ORF‐length and mRNA concentration in <i>Saccharomyces cerevisiae</i>

Marı́n, Antonio; Gallardo, Mercedes; Kato, Yuki; Shirahige, Katsuhiko; Gutiérrez, Gabriel; Ohta, Kouji; Aguilera, Andrés

doi:10.1002/yea.992

Cited by 42 publications

(40 citation statements)

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“…A transcription initiation enhancer element (Cavener and Ray, 1991) was introduced 5# of the initiation codon. GC content was adjusted from 47% in the 5# coding region to 33% (Marín et al, 2003), and rare yeast codons were replaced. Using eight partially overlapping long-mer oligonucleotides, the optimized 561-bp 5# region of PsCYP720B4 was synthesized by PCR and ligated to 891 bp of the native 3# region.…”

Section: Expression Of Diterpene Synthases and Pscyp720b4 In Yeastmentioning

confidence: 99%

Evolution of Diterpene Metabolism: Sitka Spruce CYP720B4 Catalyzes Multiple Oxidations in Resin Acid Biosynthesis of Conifer Defense against Insects

et al. 2011

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Diterpene resin acids (DRAs) are specialized (secondary) metabolites of the oleoresin defense of conifers produced by diterpene synthases and cytochrome P450s of the CYP720B family. The evolution of DRA metabolism shares common origins with the biosynthesis of ent-kaurenoic acid, which is highly conserved in general (primary) metabolism of gibberellin biosynthesis. Transcriptome mining in species of spruce (Picea) and pine (Pinus) revealed CYP720Bs of four distinct clades. We cloned a comprehensive set of 12 different Sitka spruce (Picea sitchensis) CYP720Bs as full-length cDNAs. Spatial expression profiles, methyl jasmonate induction, and transcript enrichment in terpenoid-producing resin ducts suggested a role of CYP720B4 in DRA biosynthesis. CYP720B4 was characterized as a multisubstrate, multifunctional enzyme by the formation of oxygenated diterpenoids in metabolically engineered yeast, yeast in vivo transformation of diterpene substrates, in vitro assays with CYP720B4 protein produced in Escherichia coli, and alteration of DRA profiles in RNA interference-suppressed spruce seedlings. CYP720B4 was active with 24 different diterpenoid substrates, catalyzing consecutive C-18 oxidations in the biosynthesis of an array of diterpene alcohols, aldehydes, and acids. CYP720B4 was most active in the formation of dehydroabietic acid, a compound associated with insect resistance of Sitka spruce. We identified patterns of convergent evolution of CYP720B4 in DRA metabolism and ent-kaurene oxidase CYP701 in gibberellin metabolism and revealed differences in the evolution of specialized and general diterpene metabolism in a gymnosperm. The genomic and functional characterization of the gymnosperm CYP720B family highlights that the evolution of specialized metabolism involves substantial diversification relative to conserved, general metabolism.

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Section: Expression Of Diterpene Synthases and Pscyp720b4 In Yeastmentioning

confidence: 99%

Evolution of Diterpene Metabolism: Sitka Spruce CYP720B4 Catalyzes Multiple Oxidations in Resin Acid Biosynthesis of Conifer Defense against Insects

et al. 2011

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“…Interestingly, top Rrm3-bound genes were more expressed in npl3D cells, suggesting that replication obstacles occur preferentially at the highest transcribed genes in the absence of Npl3 (Fig. 7B), these genes preferentially being shorter all over the genome (Marin et al 2003). In this sense, although gene ontology analysis revealed that genes involved in ribosome biogenesis or intron-containing genes were significantly overrepresented in npl3D cells, this is consistent with the fact that ribosome biogenesis genes are highly transcribed and represent the major class of intron-containing genes in yeast.…”

Section: Genome-wide Dna Replication Impairment In Npl3d Cells Detectmentioning

confidence: 99%

The Npl3 hnRNP prevents R-loop-mediated transcription–replication conflicts and genome instability

et al. 2013

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Transcription is a major obstacle for replication fork (RF) progression and a cause of genome instability. Part of this instability is mediated by cotranscriptional R loops, which are believed to increase by suboptimal assembly of the nascent messenger ribonucleoprotein particle (mRNP). However, no clear evidence exists that heterogeneous nuclear RNPs (hnRNPs), the basic mRNP components, prevent R-loop stabilization. Here we show that yeast Npl3, the most abundant RNA-binding hnRNP, prevents R-loop-mediated genome instability. npl3D cells show transcription-dependent and R-loop-dependent hyperrecombination and genome-wide replication obstacles as determined by accumulation of the Rrm3 helicase. Such obstacles preferentially occur at long and highly expressed genes, to which Npl3 is preferentially bound in wild-type cells, and are reduced by RNase H1 overexpression. The resulting replication stress confers hypersensitivity to double-strand break-inducing agents. Therefore, our work demonstrates that mRNP factors are critical for genome integrity and opens the option of using them as therapeutic targets in anti-cancer treatment.

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“…Another possibility is that regions of high GC content are associated with a chromatin modification that facilitates recombination (43). Relevant to this point is the observation that there is a very significant positive correlation between GC content of genes and their mRNA levels (40).…”

Section: Vol 26 2006 Global Analysis Of Yeast Meiotic Recombinationmentioning

confidence: 99%

Global Analysis of the Relationship between the Binding of the Bas1p Transcription Factor and Meiosis-Specific Double-Strand DNA Breaks in Saccharomyces cerevisiae

Mieczkowski

Dominska²,

Buck

et al. 2006

Molecular and Cellular Biology

108

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In the yeast Saccharomyces cerevisiae, certain genomic regions have very high levels of meiotic recombination (hot spots). The hot spot activity associated with the HIS4 gene requires the Bas1p transcription factor. To determine whether this relationship between transcription factor binding and hot spot activity is general, we used DNA microarrays to map all genomic Bas1p binding sites and to map the frequency of meiosis-specific double-strand DNA breaks (as an estimate of the recombination activity) of all genes in both wild-type and bas1 strains. We identified sites of Bas1p-DNA interactions upstream of 71 genes, many of which are involved in histidine and purine biosynthesis. Our analysis of recombination activity in wild-type and bas1 strains showed that the recombination activities of some genes with Bas1p binding sites were dependent on Bas1p (as observed for HIS4), whereas the activities of other genes with Bas1p binding sites were unaffected or were repressed by Bas1p. These data demonstrate that the effect of transcription factors on meiotic recombination activity is strongly context dependent. In wild-type and bas1 strains, meiotic recombination was strongly suppressed in large (25-to 150-kb) chromosomal regions near the telomeres and centromeres and in the region flanking the rRNA genes. These results argue that both local and regional factors affect the level of meiotic recombination.From comparisons of genetic and physical maps, it is clear that recombination events are unevenly distributed. Regions with relatively high and low levels of exchange are termed "hot spots" and "cold spots," respectively. As first shown for Saccharomyces cerevisiae (28), meiotic recombination events in many eukaryotes (including humans) are initiated by doublestrand DNA breaks (DSBs) catalyzed by Spo11p, a topoisomerase II-related protein. In general, there is a good correlation between the frequency of DSBs and the rate of local meiotic recombination (36, 43). In the study described here, we use DNA microarrays to measure the rate of DSBs for all open reading frames (ORFs) and intergenic regions. We assume that these measurements will reflect the meiotic recombination activities near the DSB sites, although the nature of the later steps of recombination (strand invasion, extent of heteroduplex formation, etc.) could influence the recombination frequency.From studies of individual hot spots in Saccharomyces cerevisiae, as well as from more global studies, several generalizations concerning hot spots and cold spots can be made. First, DSBs usually occur in intergenic regions rather than within genes (4, 22, 58), suggesting a connection between "open" chromatin and preferred sites for Spo11p-induced cleavage. Second, for some hot spots (␣ hot spots), binding of transcription factors is required for hot spot activity (56) and DSB formation (19). This requirement for transcription factor binding does not indicate a direct connection between transcription and hot spot activity, since deletion of a TATAA sequence, which substa...

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Relationship between G+C content, ORF‐length and mRNA concentration in Saccharomyces cerevisiae

Cited by 42 publications

References 42 publications

Evolution of Diterpene Metabolism: Sitka Spruce CYP720B4 Catalyzes Multiple Oxidations in Resin Acid Biosynthesis of Conifer Defense against Insects

Evolution of Diterpene Metabolism: Sitka Spruce CYP720B4 Catalyzes Multiple Oxidations in Resin Acid Biosynthesis of Conifer Defense against Insects

The Npl3 hnRNP prevents R-loop-mediated transcription–replication conflicts and genome instability

Global Analysis of the Relationship between the Binding of the Bas1p Transcription Factor and Meiosis-Specific Double-Strand DNA Breaks in Saccharomyces cerevisiae

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