Abstract
BackgroundXylose-based ethanol production by recombinant S. cerevisiae is of great interest to basic and applied bioenergy research. By expressing three different fungal pathways in two S. cerevisiae hosts respectively, we found that the xylose utilization efficiency by recombinant S. cerevisiae depends not only on the choice of xylose pathway but also on the choice of host, exhibiting an obvious host or context dependence. To investigate molecular mechanisms of this context dependence, we applied RNA-seq analysis in this study for a systematic characterization of the xylose utilization via different pathways in different S. cerevisiae hosts.ResultsBased on the RNA-seq analysis, the transcripts that were regulated during xylose utilization have been identified. Three transcription factors involved in regulation of amino acid metabolism, responses to oxidative stresses, and degradation of aggregated proteins, respectively, were found to participate in xylose metabolism regulation regardless of which pathway was expressed and which host the xylose pathway was expressed in. Nine transcription factors, involved in homeostasis, regulation of amino acid metabolism, and stress responses, were identified as the key modules responsible for the host-specific responses to the same xylose pathway. In addition, the transcriptional regulations of xylose utilization in different yeast hosts were compared to two reference regulation patterns, which indicated that diverse regulation strategies were adopted by different hosts for improved xylose utilization.ConclusionsThis study provides the first transcriptomic study of the host dependence of xylose utilization in S. cerevisiae. Both the conserved regulatory modules for xylose metabolism and the key modules responsible for host dependence were identified. As indicated by the functions of the conserved transcription factors involved in xylose metabolism regulation, the xylose utilization in recombinant S. cerevisiae may be affected by both carbohydrate metabolism regulation and stress responses. Based on the comparison of transcriptional regulation patterns, the metabolic optimizations of xylose utilization in different hosts went toward different directions, which may explain the host dependence observed in this study. The knowledge revealed by this study could provide valuable insights towards the improvement of metabolic engineering strategies for cellulosic ethanol production.
Highlights
Xylose-based ethanol production by recombinant S. cerevisiae is of great interest to basic and applied bioenergy research
By systematically grouping the differentially expressed genes by the transcription factors (TFs) and comparing the profiles of TFs in the CTY and INVSc1 hosts respectively (Figure 1), we found three TFs were used by both hosts for regulating xylose metabolism
Physiology of host dependence in xylose metabolism of S. cerevisiae To optimize xylose utilization, the fungal xylose pathway has been independently engineered in two S. cerevisiae hosts, CTY and INVSc1, by tuning the promoter strengths of three key genes (i.e., xylose reductase (XR), xylitol dehydrogenase (XDH), and xylulose kinase (XKS))
Summary
Xylose-based ethanol production by recombinant S. cerevisiae is of great interest to basic and applied bioenergy research. Engineering S. cerevisiae to utilize xylose for ethanol production is of great interest to the biofuel industry because it can reduce the cost of feedstock for bioethanol production and substantially minimize the emission of greenhouse gases [1,2]. To achieve this objective, a heterologous xylose pathway, consisting of xylose reductase (XR), xylitol dehydrogenase (XDH), and xylulose kinase (XKS), is usually functionally expressed in S. cerevisiae [3,4,5], followed by the optimization of xylose fermentation behaviors via a series of metabolic engineering approaches such as promoter engineering [6,7] and evolutionary engineering [8]. The xylose metabolism of recombinant S. cerevisiae depends on the pathway and the host
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