De novo origination of a new protein-coding gene in Saccharomyces cerevisiae

Abstract

Origination of new genes is an important mechanism generating genetic novelties during the evolution of an organism. Processes of creating new genes using preexisting genes as the raw materials are well characterized, such as exon shuffling, gene duplication, retroposition, gene fusion, and fission. However, the process of how a new gene is de novo created from noncoding sequence is largely unknown. On the basis of genome comparison among yeast species, we have identified a new de novo protein-coding gene, BSC4 in Saccharomyces cerevisiae. The BSC4 gene has an open reading frame (ORF) encoding a 132-amino-acid-long peptide, while there is no homologous ORF in all the sequenced genomes of other fungal species, including its closely related species such as S. paradoxus and S. mikatae. The functional protein-coding feature of the BSC4 gene in S. cerevisiae is supported by population genetics, expression, proteomics, and synthetic lethal data. The evidence suggests that BSC4 may be involved in the DNA repair pathway during the stationary phase of S. cerevisiae and contribute to the robustness of S. cerevisiae, when shifted to a nutrient-poor environment. Because the corresponding noncoding sequences in S. paradoxus, S. mikatae, and S. bayanus also transcribe, we propose that a new de novo protein-coding gene may have evolved from a previously expressed noncoding sequence.

Figure 1.—

Results of Southern hybridization showing that only S. cerevisiae has a detectable signal of the BSC4 gene. M, marker; 1, S. bayanus; 2, S. kudriavzevii; 3, S. mikatae; 4, S. paradoxus; 5, S. cerevisiae. The phylogenetic relation of the four species is indicated under the lane numbers.

Figure 2.—

Alignment of the orthologous sequences of BSC4 from Saccharomyces bayanus (Sbay), S. mikatae (Smik), S. paradoxus (Spar), and S. cerevisiae (Scer). The conserved nucleotides are shaded.

Figure 3.—

(A) Synteny relationships in the BSC4 region in different fungi species. (B) Phylogenetic tree of the fungi species used in A. Sbay, S. bayanus; Smik, S. mikatae; Spar, S. paradoxus; Scer, S. cerevisiae; Agos, Ashbya gossypii; Spom, Schizosaccharomyces pombe; Ylip, Yarrowia lipolytica; Ncra, Neurospora crassa. The dashed arrows in A indicate an orthologous relationship.

Figure 3.—

(A) Synteny relationships in the BSC4 region in different fungi species. (B) Phylogenetic tree of the fungi species used in A. Sbay, S. bayanus; Smik, S. mikatae; Spar, S. paradoxus; Scer, S. cerevisiae; Agos, Ashbya gossypii; Spom, Schizosaccharomyces pombe; Ylip, Yarrowia lipolytica; Ncra, Neurospora crassa. The dashed arrows in A indicate an orthologous relationship.

Figure 4.—

RT–PCR results. “−” indicates the RT–PCR-negative controls in which everything is the same as the positive (+) except omitting reverse transcriptase. Sbay, S. bayanus; Smik, S. mikatae; Spar, S. paradoxus; Scer, S. cerevisiae.

Figure 5.—

Comparisons of expression changes among BSC4, RPN4, and ACT1 based on the microarray data of Gasch et al. (2000). ACT1 is selected because it is considered as a good internal control in most yeast expression quantification experiments and it also indicates that the upregulation of gene expression is neither a whole-genome pattern nor a system error of the microarray. The y-axis denotes the log₂ value of fold change, and the x-axis denotes the culture time after the time point 0. YPD cultures were grown at 30° to OD₆₀₀ = 0.3, at which point the cell culture was collected to serve as the time = 0 reference. Samples were recovered at 2, 4, 6, 8, 10, and 12 hr and 1, 2, 3, and 5 days of culture incubation. The partial coexpression pattern of BSC4 and RPN4 in stationary phase is shown.