Comparative genomics and transcriptomics of Pichia pastoris

Area of Science:

• Microbiology
• Genomics
• Biotechnology

Background:

• Pichia pastoris is a key host for recombinant biopharmaceuticals due to its high cell density and low protein burden.
• Limited genomic and transcriptomic data has hindered Pichia strain engineering.
• Confusion exists between Komagataella pastoris and Komagataella phaffii (both branded as Pichia), impacting host performance understanding.

Purpose of the Study:

• To provide standardized, high-quality comparative genomic and transcriptomic data for key Pichia strains.
• To clarify the genetic distinctions between K. pastoris and K. phaffii.
• To lay the groundwork for rational strain engineering to enhance biopharmaceutical production.

Main Methods:

• Utilized long-read (PacBio) and short-read (Illumina) sequencing for high-coverage genome assembly.
• Generated gap-free genome assemblies for K. pastoris and K. phaffii strains.
• Analyzed genomic features, including syntenic rearrangements and linear plasmids.
• Investigated transcriptomic profiles across different carbon sources.

Main Results:

• Achieved highly contiguous, gap-free genomes for K. pastoris and K. phaffii (GS115).
• Identified substantial genomic rearrangements and a linear plasmid in K. phaffii.
• Characterized 35 non-synonymous mutations in the K. phaffii GS115 strain impacting performance.
• Revealed consistent high expression of core genes and selective expression of others across carbon sources, identifying novel promoters.

Conclusions:

• Established a foundational understanding of genome structure, cultivation, and gene expression relationships in Pichia.
• Generated critical genomic and transcriptomic resources for Pichia research.
• Facilitated rational, organism-wide strain engineering for improved biopharmaceutical production hosts.