ArticleBMC genomics2012
Comprehensive structural annotation of Pichia pastoris transcriptome and the response to various carbon sources using deep paired-end RNA sequencing.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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36 citing papers in PubMed, 77 citations in OpenAlex.
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- Comparative proteomics analysis ofSynthetic and systems biotechnology · 2022Article
- Comparative transcriptome and metabolome analyses reveal the methanol dissimilation pathway of Pichia pastoris.BMC genomics · 2022Article
- Engineering of Promoters for Gene Expression in Pichia pastoris.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Comparative transcriptomic analysis-based identification of the regulation of foreign proteins with different stabilities expressed inFrontiers in microbiology · 2022Article
- Global transcriptome profiling reveals genes responding to overproduction of a small secretory, a high cysteine- and a high glycosylation-bearing protein inBiotechnology reports (Amsterdam, Netherlands) · 2021Article
- Transcriptome analysis on fructose as the sole carbon source enhancing perylenequinones production of endophytic fungus3 Biotech · 2020Article
- Transcriptomic Analysis ofFrontiers in microbiology · 2020Article
- Statistically Designed Medium Reveals Interactions between Metabolism and Genetic Information Processing for Production of Stable Human Serum Albumin inBiomolecules · 2019Article
- Transcriptomic Analysis of the Influence of Methanol Assimilation on the Gene Expression in the RecombinantGenes · 2019Article
- Screening for functional IRESes using α-complementation system of β-galactosidase inBiotechnology for biofuels · 2019Article
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe methylotrophic yeast Pichia pastoris is widely used as a bioengineering platform for producing industrial and biopharmaceutical proteins, studying protein expression and secretion mechanisms, and analyzing metabolite synthesis and peroxisome biogenesis. With the development of DNA microarray and mRNA sequence technology, the P. pastoris transcriptome has become a research hotspot due to its powerful capability to identify the transcript structures and gain insights into the transcriptional regulation model of cells under protein production conditions. The study of the P. pastoris transcriptome helps to annotate the P. pastoris transcript structures and provide useful information for further improvement of the production of recombinant proteins.
resultsWe used a massively parallel mRNA sequencing platform (RNA-Seq), based on next-generation sequencing technology, to map and quantify the dynamic transcriptome of P. pastoris 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 (IRESes) were first identified within the UTRs of genes from P. pastoris, encoding kinases and the proteins involved in the control of growth. We also provide a transcriptional regulation model for P. pastoris grown on different carbon sources.
conclusionsWe suggest that the IRES-dependent translation initiation mechanism also exists in P. pastoris. Retained introns (RIs) are determined as the main AS event and are produced predominantly by an intron definition (ID) mechanism. Our 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.
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