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Chapter 4: Methods for Metabolic Engineering of a Filamentous Trichoderma reesei
In this work, we describe genetic tools and techniques for engineering Trichoderma reesei for the production of farnesene. Enhanced production of farnesene was used as an example of this methodology; as were the overexpression of a key enzyme, HMGS, in the MVA pathway.
Modification of the glycolytic pathway in Pyrococcus furiosus and the implications for metabolic engineering
Not provided.
Integrating Aquatic Metabolism and Net Ecosystem CO2 Balance in Short- and Long-Hydroperiod Subtropical Freshwater Wetlands
Abstract How aquatic primary productivity influences the carbon (C) sequestering capacity of wetlands is uncertain. We evaluated the magnitude and variability in aquatic C dynamics and compared them to net ecosystem CO 2 exchange (NEE) and ecosystem respiration ( R eco ) rates within calcareous freshwater wetlands in Everglades National Park. We continuously recorded 30-min measurements of dissolved oxygen (DO), water level, water temperature ( T water ), and photosynthetically active radiation (PAR). These measurements were coupled with ecosystem CO 2 fluxes over 5 years (2012–2016) in a long-hydroperiod peat-rich, freshwater marsh and a short-hydroperiod, freshwater marl prairie. Daily net aquatic primary productivity (NAPP) rates indicated both wetlands were generally net heterotrophic. Gross aquatic primary productivity (GAPP) ranged from 0 to − 6.3 g C m −2 day −1 and aquatic respiration ( R Aq ) from 0 to 6.13 g C m −2 day −1 . Nonlinear interactions between water level, T water , and GAPP and R Aq resulted in high variability in NAPP that contributed to NEE. Net aquatic primary productivity accounted for 4–5% of the deviance explained in NEE rates. With respect to the flux magnitude, daily NAPP was a greater proportion of daily NEE at the long-hydroperiod site (mean = 95%) compared to the short-hydroperiod site (mean = 64%). Although we have confirmed the significant contribution of NAPP to NEE in both long- and short-hydroperiod freshwater wetlands, the decoupling of the aquatic and ecosystem fluxes could largely depend on emergent vegetation, the carbonate cycle, and the lateral C flux.
IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss
Abstract Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana . To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3 , a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis , and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4 . Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.
Impact of europium and samarium on growth and metabolism of two anaerobic wastewater microorganisms: Sporacetigenium mesophilum and Clostridium sporogenes
Increases in environmental fluxes of rare earth elements (REEs) stemming from increased demand for these technology critical elements may affect microbial ecosystem functions important for pollutant degradation and nutrient cycling. Here, this study investigates the responses of Sporacetigenium mesophilum and Clostridium sporogenes, two anaerobic fermenters, to varying concentrations of two REE, namely europium and samarium. Eu and Sm are adjacent lanthanides but differ significantly in their redox behavior. We tested Eu and Sm concentrations ranging from < 1 to 600 µM. Despite the close phylogenetic relatedness of the two bacteria, we observed species-specific as well as REE-specific and incubation time-dependent sensitivities. S. mesophilum exhibited pronounced inhibition of hydrogen production and growth with exposure to ≥ 60 µM of Eu, but with 6 µM Eu, a hormetic effect was observed—hydrogen production was enhanced relative to the control. With Sm, the only impact observed on S. mesophilum was inhibition at the highest concentration (600 µM) tested. For C. sporogenes, growth inhibition was observed only at 600 µM Eu or Sm, and no hormesis was observed with either REE. This study offers both significant benefits and novelty by addressing the emerging environmental concern of REE pollution, particularly the effects of Eu and Sm on anaerobic microorganisms relevant to wastewater treatment. It provides valuable insights into REE impacts under anaerobic conditions, which are essential for understanding potential disruptions to organic matter degradation and nutrient cycling processes.
Genome-scale metabolic model accurately predicts fermentation of glucose by Chromochloris zofingiensis
Not Available
The molecular aspects of absorption and metabolism of carotenoids and retinoids in vertebrates
Abstract not provided
Chemical-free production of multiple high-value bioproducts from metabolically engineered transgenic sugarcane ‘oilcane’ bagasse and their recovery using nanofiltration
Bioenergy crops have potential for being a sustainable and renewable feedstock for biofuels and various value- added bioproducts. The study utilizes recently developed transgenic sugarcane (‘oilcane’) bagasse for chemical- free coproduction of high-value bioproducts, i.e., furfurals, HMF, acetic acid, cellulosic sugars, and vegetative lipids. Hydrothermal pretreatment was optimized at 210°C for 5 min to coproduce 6.91%, 2.67%, 5.07%, 2.42% and 37.82% (w/w) furfurals, HMF, acetic acid, vegetative lipids, and cellulosic sugars, respectively from lignocellulosic biomass. Additionally, nanofiltration system in-series was successfully established to recover sugars, furfurals, HMF, and acetic acid from the pretreatment liquor. 1st nanofiltration with Duracid NF mem- brane rejected ~99% sugars. Concentrated sugars with significantly reduced inhibitory products were obtained in retentate for fermentation. 2nd nanofiltration with NF90 membrane used permeate of 1st nanofiltration as feed and rejected ~ 86% furfurals. Furthermore, the work demonstrates the feasibility of coproducing and recovering multiple biochemicals from lignocellulosic biomass.
Inducible flippase-mediated metabolic engineering of Rhodosporidium toruloides for enhanced 3-hydroxypropionic acid production from corn stover hydrolysate
Rhodosporidium toruloides has gained increasing interests as a promising non-model host organism to produce a wide range of bioproducts from lignocellulosic biomass. Increasing the bioproduct titers, rates, and yields remains a challenge, largely due to a lack of robust and well-characterized genetic tools in this host. Here we developed an inducible flippase (FLP) and flippase recognition target (FRT) system that enables genetic manipulations without the need for additional selection markers. Synthetic inducible promoters were established, enabling regulation of FLP expression and efficient antibiotic marker removal. Leveraging this system, we engineered a strain to optimize 3-hydroxypropionic acid (3HP) production. Over four rounds of iterative genomic editing to resolve pathway bottlenecks, we achieved a 3HP titer of 69.4 g/L in fed-batch fermentation - the highest level reported in yeast from lignocellulosic hydrolysates. The engineered high 3HP producing strain offers a robust platform for sustainable bio-based chemical production from lignocellulosic feedstocks.
Xylose metabolic engineering of Issatchenkia orientalis for 3-hydroxypropionic acid production from cellulosic hydrolysate without nutrient supplementation
Bioconversion of lignocellulosic biomass offers a promising alternative to petroleum-based chemical production. However, inefficient xylose utilization and toxic compounds in cellulosic hydrolysate limit microbial fermentation, as the hydrolysate contains substantial amounts of xylose in addition to glucose. To address these challenges, we engineered Issatchenkia orientalis to produce 3-hydroxypropionic acid (3-HP) directly from sorghum hydrolysate under low-pH conditions. A heterologous xylose utilization pathway consisting of XYL1, XYL2, and XYL3 from Scheffersomyces stipitis was introduced into an engineered 3-HP producing strain, enabling efficient conversion of xylose to 3-HP. The engineered strain produced 46.8 g/L 3-HP from sorghum hydrolysate without nutrient supplementation. To eliminate the lag phase under low-pH conditions, fermentation was conducted at pH 6.0 for the first three days, after which pH control was discontinued and in situ 3-HP accumulation buffered the culture. This partial pH control strategy increased 3-HP productivity by 55% from 0.20 to 0.31 g/L∙h, while maintaining low-pH conditions. Introducing an additional copy of XYL2 further increased 3-HP titer to 53.5 g/L and the yield by 33%, from 0.30 to 0.40 g/g sugars, with pH reaching 4.5 at the end of fermentation. This represents one of the highest reported 3-HP titers and yields from cellulosic hydrolysate without additional nutrient supplementation. This work demonstrates a nutrient-independent and low-pH bioprocess for upgrading lignocellulosic hydrolysate into 3-HP, highlighting the industrial potential of engineered xylose-utilizing I. orientalis for sustainable production of platform chemicals from renewable feedstocks.