Engineering natural isolates of Saccharomyces cerevisiae for consolidated bioprocessing of cellulosic feedstocks

Saccharomyces cerevisiae has gained much attention as a potential host for cellulosic bioethanol production using consolidated bioprocessing (CBP) methodologies, due to its high-ethanol-producing titres, heterologous protein production capabilities, and tolerance to various industry-relevant stresses. Since the secretion levels of heterologous proteins are generally low in domesticated strains of S. cerevisiae, natural isolates may offer a more diverse genetic background for improved heterologous protein secretion, while also displaying greater robustness to process stresses. In this study, the potential of natural and industrial S. cerevisiae strains to secrete a core set of cellulases (CBH1, CBH2, EG2, and BGL1), encoded by genes integrated using CRISPR/Cas9 tools, was evaluated. High levels of heterologous protein production were associated with a reduced maximal growth rate and with slight changes in overall strain robustness, compared to the parental strains. The natural isolate derivatives YI13_BECC and YI59_BECC displayed superior secretion capacity for the heterologous cellulases at high incubation temperature and in the presence of acetic acid, respectively, compared to the reference industrial strain MH1000_BECC. These strains also exhibited multi-tolerance to several fermentation-associated and secretion stresses. Cultivation of the strains on crystalline cellulose in oxygen-limited conditions yielded ethanol concentrations in the range of 4-4.5 g/L, representing 35-40% of the theoretical maximum ethanol yield after 120 h, without the addition of exogenous enzymes. This study therefore highlights the potential of these natural isolates to be used as chassis organisms in CBP bioethanol production. KEY POINTS: • Process-related fermentation stresses influence heterologous protein production. • Transformants produced up to 4.5 g/L ethanol, ~ 40% of the theoretical yield in CBP. • CRISPR/Cas9 was feasible for integrating genes in natural S. cerevisiae isolates.

A Broad Continuum of E. coli Traits in Nature Associated with the Trade-off Between Self-preservation and Nutritional Competence

A trade-off between reproduction and survival is a characteristic of many organisms. In bacteria, growth is constrained when cellular resources are channelled towards environmental stress protection. At the core of this trade-off in Escherichia coli is RpoS, a sigma factor that diverts transcriptional resources towards general stress resistance. The constancy of RpoS levels in natural isolates is unknown. A uniform RpoS content in E. coli would impart a narrow range of resistance properties to the species, whereas a diverse set of RpoS levels in nature should result in a diverse range of stress susceptibilities. We explore the diversity of trade-off settings and phenotypes by measuring the level of RpoS protein in strains of E. coli cohabiting in a natural environment. Strains from a stream polluted with domestic waste were investigated in monthly samples. Analyses included E. coli phylogroup classification, RpoS protein level, RpoS-dependent stress phenotypes and the sequencing of rpoS mutations. The most striking finding was the continuum of RpoS levels, with a 100-fold range of RpoS amounts consistently found in individuals in the stream. Approximately 1.8% of the sampled strains carried null or non-synonymous mutations in rpoS. The natural isolates also exhibited a broad (>100-fold) range of stress resistance responses. Our results are consistent with the view that a multiplicity of survival-multiplication trade-off settings is a feature of the species E. coli. The phenotypic diversity resulting from the trade-off permits bet-hedging and the adaptation of E. coli strains to a very broad range of environments.

Single nucleotide polymorphism (SNP) frequencies and distribution reveal complex genetic composition of seven novel natural isolates of Cydia pomonella granulovirus

The co-evolution between baculoviruses and their insect hosts results in selection of virus populations. To explore this phenomenon at the molecular level, seven natural isolates of Cydia pomonella granulovirus (CpGV) collected from orchards in northwest China were studied using Illumina next generation sequencing (NGS). A total of 540 genome positions with single nucleotide polymorphisms (SNPs) were detected in comparison with known CpGV isolates. New members of previously defined phylogenetic genome groups A, D and E of CpGV, as well as two novel phylogenetic lines, termed genome group F and G, were identified. Combining SNP frequency distribution with the prevalence of genome group-specific SNPs, revealed that six isolates of CpGV were mixtures of different ratios of at least two genotypes, whereas only one isolate, CpGV-WW, was genetically highly homogeneous. This study significantly extends our current understanding of the genetic diversity of CpGV and opens new lines of application of this virus.

A locus in Pristionchus pacificus that is responsible for the ability to give rise to fertile offspring at higher temperatures

Temperature is a stress factor that varies temporally and spatially, and can affect the fitness of cold-blooded organisms, leading to a loss of reproductive output; however, little is understood about the genetics behind the long-term response of organisms to temperature. Here, we approach this problem in the model nematode Pristionchus pacificus by utilising a large collection of natural isolates with diverse phenotypes. From this collection we identify two strains, one from California that can give rise to fertile offspring up to 28°C and one from Japan that is fertile up to 30°C. We show that the optimum temperature and the upper temperature limit for fertility is shifted higher in the Japanese strain suggesting that there is a mechanism that controls the temperature response of fertility across a range of temperatures. By crossing the two strains, and using genetic mapping, we identify a region on chromosome V that is responsible for maintaining fertility at higher temperatures. Thus, we conclude that fitness of P. pacificus at high temperature is under genetic control, suggesting that it could be subject to natural selection.