Pichia stipitisgenomics, transcriptomics, and gene clusters

Abstract

Genome sequencing and subsequent global gene expression studies have advanced our understanding of the lignocellulose-fermenting yeast Pichia stipitis. These studies have provided an insight into its central carbon metabolism, and analysis of its genome has revealed numerous functional gene clusters and tandem repeats. Specialized physiological traits are often the result of several gene products acting together. When coinheritance is necessary for the overall physiological function, recombination and selection favor colocation of these genes in a cluster. These are particularly evident in strongly conserved and idiomatic traits. In some cases, the functional clusters consist of multiple gene families. Phylogenetic analyses of the members in each family show that once formed, functional clusters undergo duplication and differentiation. Genome-wide expression analysis reveals that regulatory patterns of clusters are similar after they have duplicated and that the expression profiles evolve along with functional differentiation of the clusters. Orthologous gene families appear to arise through tandem gene duplication, followed by differentiation in the regulatory and coding regions of the gene. Genome-wide expression analysis combined with cross-species comparisons of functional gene clusters should reveal many more aspects of eukaryotic physiology.

Ethanol production by a new pentose‐fermenting yeast strain, Scheffersomyces stipitis UFMG‐IMH 43.2, isolated from the Brazilian forest

“…Although a large number of yeast species able to metabolize xylose and with fermentative capacity have been found, only approximately 1% of them are capable of fermenting xylose to ethanol (HahnHägerdal et al, 2007). Scheffersomyces (Pichia) stipitis is reported to have the ability to ferment a wide variety of sugars, including xylose, glucose, mannose, galactose and cellobiose along with mannan and xylan oligomers (Jeffries and Van Vleet, 2009), and thus it has attracted great interest for use on ethanol production from hemicellulose. Some recent studies describe the ethanol production by different S. stipitis strains, the results being clearly dependent on the microorganism, cultivation medium and conditions employed (Agbogbo and Wenger, 2007;Diaz et al, 2009;Silva et al, 2010).…”

Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

“…Recent transcriptomic study under lignocellulosic biomass inducing condition and oxygen limited condition resulted in the mapping of several important genes (Bullard et al, 2010). Synthetic biology applications in S. stipitis are very less at this moment, and most of them involve the genetic transfer of its efficient biosynthetic genes to S. cerevisiae to make it able to utilize pentose sugars, although the full genome sequencing (Jeffries and Van Vleet, 2009) and the more efficient genetic transformation systems (e.g., plasmid vectors and a loxP/Cre recombination system) and drug resistance markers (Laplaza et al, 2006) might enable better room for genetic modification of this industrial strain.…”

Bioethanol a Microbial Biofuel Metabolite; New Insights of Yeasts Metabolic Engineering

“…Nowadays, Pichia stipitis, C. shehatae, and Pachysolen tannophilus attract a lot of attention as the best known natural xylose-fermenting yeasts [73][74][75]. Although the technical and economical biotransformation of pentoses sugars to ethanol are still challenging [12,[76][77][78][79], many achievements in genetic engineering have been done to ferment arabinose and xylose to lactic acid and ethanol. Technical, economic, and political considerations are the driving force for improving the fermentation of xylose to ethanol.…”