Comprehensive structural annotation of Pichia pastoris transcriptome and the response to various carbon sources using deep paired-end RNA sequencing

BMC Genomics

Research Article

Minghui He¹  Yanrui Ye²  Li Pan²  Ying Lin²  Shuli Liang²  Shuangyan Han²  Bin Wang²  Suiping Zheng²  Xiaoning Wang³ 

[1] Beijing Genomics Institute at Shenzhen, 518000, Shenzhen, China;School of Bioscience and Bioengineering, South China University of Technology, 510006, Guangzhou, Guangdong, China;School of Bioscience and Bioengineering, South China University of Technology, 510006, Guangzhou, Guangdong, China;School of life Science, General Hospital of PLA, 100853, Beijing, China;

关键词: RNA-Seq;    Transcriptome;    Pichia pastoris;    Methanol induction;    Internal ribosome entry site (IRES);    Translation initiation mechanism;   

DOI  :  10.1186/1471-2164-13-738

 received in 2012-01-16, accepted in 2012-12-18,  发布年份 2012

来源: Springer

【 摘 要 】

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.

【 授权许可】

Unknown   
© Liang et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.