Recent advances in the intellectual property landscape of filamentous fungi

For centuries, filamentous fungi have been used in the making of food and beverages, and for decades for the production of enzymes and pharmaceuticals. In the last decades, the intellectual property (IP) landscape for fungal technology has seen an ever increasing upward trend, introducing new and promising applications utilising fungi. In this review, we highlight fungi-related patent applications published during the last 5 years (2015–2020), identify the key players in each field, and analyse future trends. New developments in the field of fungal technology include the increased use of filamentous fungi as a food source (mycoprotein), using fungi as biodegradable materials, in wastewater treatment, in integrated biorefineries and as biological pest agents. Biotechnology companies in Europe and the US are currently leading when it comes to the number of patents in these areas, but Asian companies and research institutes, in particular in China, are becoming increasingly important players, for example in pesticide formulation and agricultural practices.

Integration of a multi-step heterologous pathway in Saccharomyces cerevisiae for the production of abscisic acid

BACKGROUND

The sesquiterpenoid abscisic acid (ABA) is mostly known for regulating developmental processes and abiotic stress responses in higher plants. Recent studies show that ABA also exhibits a variety of pharmacological activities. Affordable and sustainable production will be required to utilize the compound in agriculture and as a potential pharmaceutical. Saccharomyces cerevisiae is an established workhorse for the biotechnological production of chemicals. In this study, we constructed and characterised an ABA-producing S. cerevisiae strain using the ABA biosynthetic pathway from Botrytis cinerea.

RESULTS

Expression of the B. cinerea genes bcaba1, bcaba2, bcaba3 and bcaba4 was sufficient to establish ABA production in the heterologous host. We characterised the ABA-producing strain further by monitoring ABA production over time and, since the pathway contains two cytochrome P450 enzymes, by investigating the effects of overexpressing the native S. cerevisiae or the B. cinerea cytochrome P450 reductase. Both, overexpression of the native or heterologous cytochrome P450 reductase, led to increased ABA titres. We were able to show that ABA production was not affected by precursor or NADPH supply, which suggested that the heterologous enzymes were limiting the flux towards the product. The B. cinerea cytochrome P450 monooxygenases BcABA1 and BcABA2 were identified as pathway bottlenecks and balancing the expression levels of the pathway enzymes resulted in 4.1-fold increased ABA titres while reducing by-product formation.

CONCLUSION

This work represents the first step towards a heterologous ABA cell factory for the commercially relevant sesquiterpenoid.

FadR-Based Biosensor-Assisted Screening for Genes Enhancing Fatty Acyl-CoA Pools in Saccharomyces cerevisiae

Fatty acid-derived compounds have a range of industrial applications, from chemical building blocks to biofuels. Due to the highly dynamic nature of fatty acid metabolism, it is difficult to identify genes modulating fatty acyl-CoA levels using a rational approach. Metabolite biosensors can be used to screen genes from large-scale libraries in vivo in a high throughput manner. Here, a fatty acyl-CoA sensor based on the transcription factor FadR from Escherichia coli was established in Saccharomyces cerevisiae and combined with a gene overexpression library to screen for genes increasing the fatty acyl-CoA pool. Fluorescence-activated cell sorting, followed by data analysis, identified genes enhancing acyl-CoA levels. From these, overexpression of RTC3, GGA2, and LPP1 resulted in about 80% increased fatty alcohol levels. Changes in fatty acid saturation and chain length distribution could also be observed. These results indicate that the use of this acyl-CoA biosensor combined with a gene overexpression library allows for identification of gene targets improving production of fatty acids and derived products.

Redirection of lipid flux toward phospholipids in yeast increases fatty acid turnover and secretion

Bio-based production of fatty acids and fatty acid-derived products can enable sustainable substitution of petroleum-derived fuels and chemicals. However, developing new microbial cell factories for producing high levels of fatty acids requires extensive engineering of lipid metabolism, a complex and tightly regulated metabolic network. Here we generated a Saccharomyces cerevisiae platform strain with a simplified lipid metabolism network with high-level production of free fatty acids (FFAs) due to redirected fatty acid metabolism and reduced feedback regulation. Deletion of the main fatty acid activation genes (the first step in β-oxidation), main storage lipid formation genes, and phosphatidate phosphatase genes resulted in a constrained lipid metabolic network in which fatty acid flux was directed to a large extent toward phospholipids. This resulted in simultaneous increases of phospholipids by up to 2.8-fold and of FFAs by up to 40-fold compared with wild-type levels. Further deletion of phospholipase genes PLB1 and PLB2 resulted in a 46% decrease in FFA levels and 105% increase in phospholipid levels, suggesting that phospholipid hydrolysis plays an important role in FFA production when phospholipid levels are increased. The multiple deletion mutant generated allowed for a study of fatty acid dynamics in lipid metabolism and represents a platform strain with interesting properties that provide insight into the future development of lipid-related cell factories.

Metabolic engineering of Saccharomyces cerevisiae for overproduction of triacylglycerols

Triacylglycerols (TAGs) are valuable versatile compounds that can be used as metabolites for nutrition and health, as well as feedstocks for biofuel production. Although Saccharomyces cerevisiae is the favored microbial cell factory for industrial production of biochemicals, it does not produce large amounts of lipids and TAGs comprise only ~1% of its cell dry weight. Here, we engineered S. cerevisiae to reorient its metabolism for overproduction of TAGs, by regulating lipid droplet associated-proteins involved in TAG synthesis and hydrolysis. We implemented a push-and-pull strategy by overexpressing genes encoding a deregulated acetyl-CoA carboxylase, ACC1^S659A/S1157A(ACC1**), as well as the last two steps of TAG formation: phosphatidic phosphatase (PAH1) and diacylglycerol acyltransferase (DGA1), ultimately leading to 129 mg∙gCDW⁻¹ of TAGs. Disruption of TAG lipase genes TGL3, TGL4, TGL5 and sterol acyltransferase gene ARE1 increased the TAG content to 218 mg∙gCDW⁻¹. Further disruption of the beta-oxidation by deletion of POX1, as well as glycerol-3-phosphate utilization through deletion of GUT2, did not affect TAGs levels. Finally, disruption of the peroxisomal fatty acyl-CoA transporter PXA1 led to accumulation of 254 mg∙gCDW⁻¹. The TAG levels achieved here are the highest titer reported in S. cerevisiae, reaching 27.4% of the maximum theoretical yield in minimal medium with 2% glucose. This work shows the potential of using an industrially established and robust yeast species for high level lipid production.

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Saccharomyces cerevisiae was engineered towards triacylglycerol (TAG) accumulation.

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Overexpression of TAG biosynthesis genes, and deletion of degradation pathways were targeted.

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Final strain reached 254 mg/gCDW TAG on 2% glucose media, achieving 27.4% of the maximum theoretical yield.

Dynamic regulation of fatty acid pools for improved production of fatty alcohols in Saccharomyces cerevisiae

Background

In vivo production of fatty acid-derived chemicals in Saccharomyces cerevisiae requires strategies to increase the intracellular supply of either acyl-CoA or free fatty acids (FFAs), since their cytosolic concentrations are quite low in a natural state for this organism. Deletion of the fatty acyl-CoA synthetase genes FAA1 and FAA4 is an effective and straightforward way to disable re-activation of fatty acids and drastically increase FFA levels. However, this strategy causes FFA over-accumulation and consequential release to the extracellular medium, which results in a significant loss of precursors that compromises the process yield. In the present study, we aimed for dynamic expression of the fatty acyl-CoA synthetase gene FAA1 to regulate FFA and acyl-CoA pools in order to improve fatty alcohol production yields.

Results

We analyzed the metabolite dynamics of a faa1Δ faa4Δ strain constitutively expressing a carboxylic acid reductase from Mycobacterium marinum (MmCAR) and an endogenous alcohol dehydrogenase (Adh5) for in vivo production of fatty alcohols from FFAs. We observed production of fatty acids and fatty alcohols with different rates leading to high levels of FFAs not being converted to the final product. To address the issue, we expressed the MmCAR + Adh5 pathway together with a fatty acyl-CoA reductase from Marinobacter aquaeolei to enable fatty alcohol production simultaneously from FFA and acyl-CoA, respectively. Then, we expressed FAA1 under the control of different promoters in order to balance FFA and acyl-CoA interconversion rates and to achieve optimal levels for conversion to fatty alcohols. Expressing FAA1 under control of the HXT1 promoter led to an increased accumulation of fatty alcohols per OD₆₀₀ up to 41% while FFA levels were decreased by 63% compared with the control strain.

Conclusions

Fine-tuning and dynamic regulation of key metabolic steps can be used to improve cell factories when the rates of downstream reactions are limiting. This avoids loss of precursors to the extracellular medium or to competing reactions, hereby potentially improving the process yield. The study also provides knowledge of a key point of fatty acid regulation and homeostasis, which can be used for future design of cells factories for fatty acid-derived chemicals.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0663-3) contains supplementary material, which is available to authorized users.

Adenosine diphosphate platelet dysfunction on thromboelastogram is independently associated with increased morality in traumatic brain injury

PURPOSE

The purpose of this study is to determine if adenosine diphosphate (ADP) platelet dysfunction on thromboelastogram (TEG) is associated with increased in-hospital mortality in patients with head trauma. The hypothesis is that ADP dysfunction is associated with increased mortality.

METHODS

This retrospective review evaluated trauma patients admitted to a level 1 trauma center from February 2011 to October 2013 who received a TEG. Patients were included if the TEG was drawn within the first 24 h of admission and the head abbreviated injury score was greater than or equal to three. Patients were categorized as severe ADP dysfunction if the degree of ADP inhibition on TEG exceeded 60 %.

RESULTS

A total of 90 patients were included (no ADP dysfunction n = 37; ADP dysfunction n = 53). Initial Glasgow Coma Scale [GCS (12 ± 4 vs. 11 ± 5; p = 0.26)] and use of pre-injury antiplatelet agents (30 vs. 28 %; p = 0.88) were similar. Patients with ADP dysfunction on TEG had a higher in-hospital mortality rate (8 vs. 32 %; p < 0.01). ADP dysfunction was independently associated with in-hospital mortality upon fixed logistic regression (OR 6.2; 95 % CI 1.2-33) while controlling for age, gender, hypotension, pre-injury antiplatelet agents, GCS and Injury Severity Score.

CONCLUSION

ADP dysfunction on TEG is associated with increased mortality in patients with traumatic brain injury.

Intragenic recombination has a critical role on the evolution of Legionella pneumophila virulence-related effector sidJ

SidJ is a Dot/Icm effector involved in the trafficking or retention of ER-derived vesicles to Legionella pneumophila vacuoles whose mutation causes an observable growth defect, both in macrophage and amoeba hosts. Given the crucial role of this effector in L. pneumophila virulence we investigated the mechanisms shaping its molecular evolution. The alignment of SidJ sequences revealed several alleles with amino acid variations that may influence the protein properties. The identification of HGT events and the detection of balancing selection operating on sidJ evolution emerge as a clear result. Evidence suggests that intragenic recombination is an important strategy in the evolutionary adaptive process playing an active role on sidJ genetic plasticity. This pattern of evolution is in accordance with the life style of L. pneumophila as a broad host-range pathogen by preventing host-specialization and contributing to the resilience of the species.

Effect of delaying same-admission cholecystectomy on outcomes in patients with diabetes

Background

Recent studies have suggested that same-admission delayed cholecystectomy is a safe option. Patients with diabetes have been shown to have less favourable outcomes after cholecystectomy, but the impact of timing of operation for acute cholecystitis during the same admission is unknown.

Methods

This was a retrospective analysis of patients undergoing laparoscopic cholecystectomy for acute cholecystitis between 2004 and 2010, from the American College of Surgeons National Surgical Quality Improvement Program database. Patients with no significant co-morbidities (American Society of Anesthesiologists grade I or II) were included. Propensity score matching (PSM) was used to match patients with diabetes with those who did not have diabetes, in a ratio of 1 : 3, to ensure homogeneity of the two groups. Logistic regression models were applied to adjust for differences between early (within 24 h) and delayed (24 h or more) surgical treatment. The primary outcome was development of local and systemic infectious complications. Secondary outcomes were duration of operation and length of hospital stay.

Results

From a total of 2892 patients, 144 patients with diabetes were matched with 432 without diabetes by PSM. Delaying cholecystectomy for at least 24 h after admission in patients with diabetes was associated with significantly higher odds of developing surgical-site infections (adjusted odds ratio 4·11, 95 per cent confidence interval 1·11 to 15·22; P = 0·034) and a longer hospital stay. For patients with no diabetes, however, delaying cholecystectomy had no impact on complications or length of hospital stay.

Conclusion

Patients with diabetes who undergo laparoscopic cholecystectomy 24 h or more after admission may have an increased risk of postoperative surgical-site infection and a longer hospital stay than those undergoing surgery within 24 h of admission.

Dalteparin versus Enoxaparin for the prevention of venous thromboembolic events in trauma patients

BACKGROUND

The use of low-molecular-weight heparin (LMWH) for the chemoprophylaxis of venous thromboembolism (VTE) in trauma patients is supported by Level-1 evidence. Because Enoxaparin was the agent used in the majority of studies for establishing the efficacy of LMWH in VTE, it remains unclear if Dalteparin provides an equivalent effect.

OBJECTIVE

To compare Dalteparin to Enoxaparin and investigate their equivalence as VTE prophylaxis in trauma.

PATIENTS/SETTING

Trauma patients receiving VTE chemoprophylaxis in the Surgical Intensive Care Unit of a Level-1 Trauma Center from 2009 (Enoxaparin) to 2010 (Dalteparin) were included.

MEASUREMENTS

The primary outcome was the incidence of clinically significant VTE. Secondary outcomes included heparin-induced thrombocytopenia (HIT), major bleeding, and drug acquisition cost savings. Equivalence margins were set between -5 and 5 %.

MAIN RESULTS

A total of 610 patient records (277 Enoxaparin, 333 Dalteparin) were reviewed. The two study groups did not differ significantly: blunt trauma 67 vs. 62 %, p = 0.27; mean Injury Severity Score (ISS) 17 ± 10 vs. 16 ± 10, p = 0.34; Acute Physiology and Chronic Health Evaluation (APACHE) II score 17 ± 9 vs. 17 ± 10, p = 0.76; time to first dose of LMWH 69 ± 98 vs. 65 ± 67 h, p = 0.57). The rates of deep venous thrombosis (DVT) (3.2 vs. 3.3 %, p = 1.00), pulmonary emboli (PE) (1.8 vs. 1.2 %, p = 0.74), and overall VTE (5.1 vs. 4.5 %, p = 0.85) did not differ. The absolute difference in the incidence of overall VTE was 0.5 % [95 % confidence interval (CI): -2.9, 4.0 %, p = 0.85]. The 95 % CI was within the predefined equivalence margins. There were no significant differences in the frequency of HIT or major bleeding. The total year-on-year cost savings, achieved with 277 patients during the switch to Dalteparin, was estimated to be $107,778.

CONCLUSIONS

Dalteparin is equivalent to Enoxaparin in terms of VTE in trauma patients and can be safely used in this population, with no increase in complications and significant cost savings.