Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1

Abstract

BackgroundHansenula polymorpha DL1 is a methylotrophic yeast, widely used in fundamental studies of methanol metabolism, peroxisome biogenesis and function, and also as a microbial cell factory for production of recombinant proteins and metabolic engineering towards the goal of high temperature ethanol production.ResultsWe have sequenced the 9 Mbp H. polymorpha DL1 genome and performed whole-genome analysis for the H. polymorpha transcriptome obtained from both methanol- and glucose-grown cells. RNA-seq analysis revealed the complex and dynamic character of the H. polymorpha transcriptome under the two studied conditions, identified abundant and highly unregulated expression of 40% of the genome in methanol grown cells, and revealed alternative splicing events. We have identified subtelomerically biased protein families in H. polymorpha, clusters of LTR elements at G + C-poor chromosomal loci in the middle of each of the seven H. polymorpha chromosomes, and established the evolutionary position of H. polymorpha DL1 within a separate yeast clade together with the methylotrophic yeast Pichia pastoris and the non-methylotrophic yeast Dekkera bruxellensis. Intergenome comparisons uncovered extensive gene order reshuffling between the three yeast genomes. Phylogenetic analyses enabled us to reveal patterns of evolution of methylotrophy in yeasts and filamentous fungi.ConclusionsOur results open new opportunities for in-depth understanding of many aspects of H. polymorpha life cycle, physiology and metabolism as well as genome evolution in methylotrophic yeasts and may lead to novel improvements toward the application of H. polymorpha DL-1 as a microbial cell factory.

Mating-type switching by chromosomal inversion in methylotrophic yeasts suggests an origin for the three-locusSaccharomyces cerevisiaesystem

“…The region immediately to the left of the silenced MAT genes and the leftmost copy of the 2-kb IR in H. polymorpha (as drawn in Fig. 2) has several characteristics that indicate it could be a regional centromere (20,43). It coincides with a trough of G+C content (SI Appendix, Fig.…”

“…The IRs are at bases 424,078 to 426,143 and 444,674 to 446,739 (2,066 bp), are identical to each other, and have 94% identity to the NCYC495 IRs. The centromere is to the right of the MAT locus at 447-459 kb (20).…”

“…Species in the CTG clade have only one MAT-like locus and do not switch (36,37). More recently, genomes have been sequenced from a third clade within the Saccharomycotina which includes the methanol-assimilating species Hansenula polymorpha (20) and Pichia pastoris (21,38) and relatives such as Dekkera bruxellensis (22,23) and Kuraishia capsulata (24). For convenience we refer to this clade as the "methylotrophs."…”

A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes

“…Even the highly GC-rich genomes of Ogataea parapolymorpha (Ravin et al 2013) and Kuraishia capsulata (Morales et al 2013) have fewer CUG codons, suggesting a general strong reduction of CUG-codon usage after the split of Yarrowia.…”

Growth-dependent surface characteristics of Hansenula Polymorpha: implications for expanded bed adsorption chromatography

“…However, it is crucial to understand these interactions from a fundamental perspective. H. polymorpha like other methylotrophic yeast strains has a rigid bilayer cell wall, mainly composed of mannoproteins linked convalently to glucans, to lesser extent chitin, and is located outside of the plasma membrane [21][22][23][24]. This cell wall/ surface undergo rearrangements during cell growth and this physicochemical/ or specific molecular character of the cell surface composition can be key to better understand the interaction to solid supports [25,26].…”