Genomic and transcriptomic analysis of Candida intermedia reveals the genetic determinants for its xylose-converting capacity

Abstract

Background: An economically viable production of biofuels and biochemicals from lignocellulose requires microorganisms that can readily convert both the cellulosic and hemicellulosic fractions into product. The yeast Candida intermedia displays a high capacity for uptake and conversion of several lignocellulosic sugars including the abundant pentose d-xylose, an underutilized carbon source since most industrially relevant microorganisms cannot naturally ferment it. Thus, C. intermedia constitutes an important source of knowledge and genetic information that could be transferred to industrial microorganisms such as Saccharomyces cerevisiae to improve their capacity to ferment lignocellulose-derived xylose. Results: To understand the genetic determinants that underlie the metabolic properties of C. intermedia, we sequenced the genomes of both the in-house-isolated strain CBS 141442 and the reference strain PYCC 4715. De novo genome assembly and subsequent analysis revealed C. intermedia to be a haploid species belonging to the CTG clade of ascomycetous yeasts. The two strains have highly similar genome sizes and number of protein-encoding genes, but they differ on the chromosomal level due to numerous translocations of large and small genomic segments. The transcriptional profiles for CBS 141442 grown in medium with either high or low concentrations of glucose and xylose were determined through RNA-sequencing analysis, revealing distinct clusters of co-regulated genes in response to different specific growth rates, carbon sources and osmotic stress. Analysis of the genomic and transcriptomic data also identified multiple xylose reductases, one of which displayed dual NADH/NADPH co-factor specificity that likely plays an important role for co-factor recycling during xylose fermentation. Conclusions: In the present study, we performed the first genomic and transcriptomic analysis of C. intermedia and identified several novel genes for conversion of xylose. Together the results provide insights into the mechanisms underlying saccharide utilization in C. intermedia and reveal potential target genes to aid in xylose fermentation in S. cerevisiae.

The Brazilian Amazonian rainforest harbors a high diversity of yeasts associated with rotting wood, including many candidates for new yeast species

“…shehatae (both present in our samples), and some members of the genus Spathaspora are considered prominent species for the conversion of xylose to ethanol (Cadete & Rosa, 2018; Cadete et al, 2015; Morais et al, 2020). Among other species we reported here, C. tropicalis , C. intermedia , C. maltosa , and species of the genera Cyberlindnera , Sugiyamaella , Wickerhamomyces , Meyerozyma , and Pichia were also reported to ferment xylose into ethanol and/or xylitol (Barros et al, 2021; Bazoti et al, 2017; Geijer et al, 2020; Morais et al, 2020; Narisetty et al, 2021; Sena et al, 2017).…”

Using Genomics to Shape the Definition of the Agglutinin-Like Sequence (ALS) Family in the Saccharomycetales

“…Among the 62 Metschnikowiaceae species, ALS sequences were found primarily in species closely related to C. auris and C. lusitaniae including Candida haemulonii , Candida duobushaemulonis , and Candida pseudohaemulonii , all of which have been observed as pathogens ( Jurardo-Martin et al, 2020 ). C. intermedia , noted for its ability to ferment xylose, as well as a rare cause of catheter-related fungemia ( Ruan et al, 2010 ; Geijer et al, 2020 ) also had ALS sequences. No ALS sequences were detected in the Cephaloascaceae , although only 2 genomes were available ( Table 4 ).…”

RNA sequencing reveals metabolic and regulatory changes leading to more robust fermentation performance during short-term adaptation of Saccharomyces cerevisiae to lignocellulosic inhibitors

“…Cells were centrifuged at 0 °C at 3800 × g. After washing, the cell pellet was resuspended in RNAlater (Invitrogen, USA) and kept at -20 °C until analyzed. RNA was extracted using a TRIzol–chloroform method, as described by Geijer et al [ 85 ], followed by on-column DNase digestion using the RNeasy PowerPlant Kit and RNase-free DNAse set from Qiagen (Germany). The RNA samples were analyzed with a Fragment Analyzer (Agilent, USA) and all samples were confirmed to have an RNA integrity number above 5.5.…”