Nonuniversal usage of the leucine CUG codon in yeasts. Investigation of basidiomycetous yeast.

Sugita, Takashi; Nakase, Takashi

doi:10.2323/jgam.45.193

Cited by 10 publications

(11 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Both super tree (Figure 1) and superalignment (Figure 2) topologies inferred a robust monophyletic clade containing organisms which translate CTG as serine instead of leucine [41-44]. This codon reassignment has been proposed to have occurred ~170 million years ago [45].…”

Section: Resultsmentioning

confidence: 99%

Untitled

et al. 2006

View full text Add to dashboard Cite

Background: To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome sequencing presents an opportunity to reconstruct evolutionary events using entire genomes. As a tool for future comparative, phylogenomic and phylogenetic studies, we used both supertrees and concatenated alignments to infer relationships between 42 species of fungi for which complete genome sequences are available.

show abstract

Section: Resultsmentioning

confidence: 99%

Untitled

et al. 2006

View full text Add to dashboard Cite

show abstract

“…With regard to yeasts, it was originally discovered using cell-free translation experiments, that the standard leucine codon CUG encodes a serine in Candida cylindracea [71]. The same was subsequently found to apply to a variety of other Candida species, including C. albicans and C. tropicalis [72], while a larger exploration of the Candida genus showed 66 species using the CUG codon for serine and 11 others for leucine [73]. This last study included Candida famata, the anamorph of D. hansenii used in our program.…”

Section: Determination Of the Genetic Codementioning

confidence: 99%

Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation

et al. 2000

View full text Add to dashboard Cite

The primary analysis of the sequences for our Hemiascomycete random sequence tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written scripts and computer visualization routines. Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then against protein sequences from other completely sequenced organisms and, finally, against protein sequences from all other organisms. Blast alignments were individually inspected to help recognize genes within our random genomic sequences despite the fact that only parts of them were available. For each yeast species, validated alignments were used to infer the proper genetic code, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cerevisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences. Annotated sequences were submitted to the EMBL database, and the general annotation tables produced served as a basis for our comparative description of the evolution, redundancy and function of the Hemiascomycete genomes described in other articles of this issue. ß

show abstract

“…We chose K. marxianus as the source strain for cloning of an arabinose transporter via genomic DNA library screening in a strain of S. cerevisiae that had been engineered and adapted for growth on arabinose. Unfortunately, P. guilliermondii uses an alternative codon for leucine (Tuite and Santos, ; Sugita and Nakase, ) and would thus not be amenable to transporter cloning through library screening with S. cerevisiae , which uses the standard genetic code. We therefore utilized a differential display technique to identify genes that may be involved in arabinose uptake, such that we could codon‐optimize and express these putative genes in S. cerevisiae .…”

Section: Introductionmentioning

confidence: 99%

Novel transporters from Kluyveromyces marxianus and Pichia guilliermondii expressed in Saccharomyces cerevisiae enable growth on l‐arabinose and d‐xylose

Knoshaug

Vidgren

Magalhães

et al. 2015

Yeast

View full text Add to dashboard Cite

Genes encoding L-arabinose transporters in Kluyveromyces marxianus and Pichia guilliermondii were identified by functional complementation of Saccharomyces cerevisiae whose growth on L-arabinose was dependent on a functioning L-arabinose transporter, or by screening a differential display library, respectively. These transporters also transport D-xylose and were designated KmAXT1 (arabinose-xylose transporter) and PgAXT1, respectively. Transport assays using L-arabinose showed that KmAxt1p has K m 263 mM and V max 57 nM/mg/min, and PgAxt1p has K m 0.13 mM and V max 18 nM/mg/min. Glucose, galactose and xylose significantly inhibit L-arabinose transport by both transporters. Transport assays using D-xylose showed that KmAxt1p has K m 27 mM and V max 3.8 nM/mg/min, and PgAxt1p has K m 65 mM and V max 8.7 nM/mg/min. Neither transporter is capable of recovering growth on glucose or galactose in a S. cerevisiae strain deleted for hexose and galactose transporters. Transport kinetics of S. cerevisiae Gal2p showed K m 371 mM and V max 341 nM/mg/min for L-arabinose, and K m 25 mM and V max 76 nM/mg/ min for galactose. Due to the ability of Gal2p and these two newly characterized transporters to transport both L-arabinose and D-xylose, one scenario for the complete usage of biomass-derived pentose sugars would require only the low-affinity, high-throughput transporter Gal2p and one additional high-affinity general pentose transporter, rather than dedicated D-xylose or L-arabinose transporters. Additionally, alignment of these transporters with other characterized pentose transporters provides potential targets for substrate recognition engineering. Accession Nos: KmAXT1: GZ791039; PgAXT1: GZ791040

show abstract

Nonuniversal usage of the leucine CUG codon in yeasts. Investigation of basidiomycetous yeast.

Cited by 10 publications

References 16 publications

Untitled

Untitled

Genomic Exploration of the Hemiascomycetous Yeasts: 3. Methods and strategies used for sequence analysis and annotation

Novel transporters from Kluyveromyces marxianus and Pichia guilliermondii expressed in Saccharomyces cerevisiae enable growth on l‐arabinose and d‐xylose

Contact Info

Product

Resources

About