Scientists at the South China University of Technology used a massively parallel mRNA sequencing platform (RNA-Seq), based on next-generation sequencing technology, to map and quantify the dynamic transcriptome of Pichia pastoris (a widely used as a bioengineering platform for producing industrial and biopharmaceutical proteins ) at the genome scale under growth conditions with glycerol and methanol as substrates. The results describe the transcription landscape at the whole-genome level and provide annotated transcript structures, including untranslated regions (UTRs), alternative splicing (AS) events, novel transcripts, new exons, alternative upstream initiation codons (uATGs), and upstream open reading frames (uORFs). Internal ribosome entry sites (IRESs) were first identified within the UTRs of genes from P. pastoris, encoding kinases and the proteins involved in the control of growth. They also provide a transcriptional regulation model for P. pastoris grown on different carbon sources.
The researchers suggest that the IRES-dependent translation initiation mechanism also exists in P. pastoris. Retained introns (RI) are determined as the main AS event and are produced predominantly by an intron definition (ID) mechanism.
These results describe the metabolic characteristics of P. pastoris with heterologous protein production under methanol induction and provide rich information for further in-depth studies of P. pastoris protein expression and secretion mechanisms.
- Liang S, Wang B, Pan L, Ye Y, He M, Han S, Zheng S, Wang X, Lin Y. Comprehensive structural annotation of Pichia pastoris transcriptome and the response to various carbon sources using deep paired-end RNA sequencing. BMC Genomics 13(1), 738. [abstract]