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BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Silke Claus ◽  
Sylwia Jezierska ◽  
Liam D. H. Elbourne ◽  
Inge Van Bogaert

AbstractStarmerella bombicola is a non-conventional yeast mainly known for its capacity to produce high amounts of the glycolipids ‘sophorolipids’. Although its product has been used as biological detergent for a couple of decades, the genetics of S. bombicola are still largely unknown. Computational analysis of the yeast’s genome enabled us to identify 254 putative transporter genes that make up the entire transportome. For each of them, a potential substrate was predicted using homology analysis, subcellular localization prediction and RNA sequencing in different stages of growth. One transporter family is of exceptional importance to this yeast: the ATP Binding Cassette (ABC) transporter Superfamily, because it harbors the main driver behind the highly efficient sophorolipid export. Furthermore, members of this superfamily translocate a variety of compounds ranging from antibiotics to hydrophobic molecules. We conducted an analysis of this family by creating deletion mutants to understand their role in the export of hydrophobic compounds, antibiotics and sophorolipids. Doing this, we could experimentally confirm the transporters participating in the efflux of medium chain fatty alcohols, particularly decanol and undecanol, and identify a second sophorolipid transporter that is located outside the sophorolipid biosynthetic gene cluster.


Author(s):  
Priscilla Zwiercheczewski de Oliveira ◽  
Luciana Porto de Souza Vandenberghe ◽  
Cristine Rodrigues ◽  
Gilberto Vinícius de Melo Pereira ◽  
Carlos Ricardo Soccol

2021 ◽  
Author(s):  
Silke Claus ◽  
Sylwia Jezierska ◽  
Liam D.H. Elbourne ◽  
Inge N.A. Van Bogaert

Abstract Starmerella bombicola is a non-conventional yeast mainly known for its capacity to produce high amounts of the glycolipids ‘sophorolipids’. Although its product has been used as biological detergent for a couple of decades, the genetics of S. bombicola are still largely unknown. Computational analysis of the yeast’s genome enabled us to identify 254 putative transporter genes that make up the entire transportome. For each of them, a potential substrate was predicted using homology analysis, subcellular localization prediction and RNA sequencing in different stages of growth. One transporter family is of exceptional importance to this yeast: the ATP Binding Cassette (ABC) transporter Superfamily, because it harbors the main driver behind the highly efficient sophorolipid export. Furthermore, members of this superfamily translocate a variety of compounds ranging from antibiotics to hydrophobic molecules. We conducted an analysis of this family by creating deletion mutants to understand their role in the export of hydrophobic compounds, antibiotics and sophorolipids. Doing this, we could experimentally confirm the transporters participating in the efflux of medium chain fatty alcohols, particularly decanol and undecanol, and identify a second sophorolipid transporter that is located outside the sophorolipid biosynthetic gene cluster.


Biology ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 815
Author(s):  
Guo Liu ◽  
Tao Hou ◽  
Shenglan Guo ◽  
Hongyu Lin ◽  
Meng Chen ◽  
...  

The immature honey pomelo fruit (IPF) is a huge agro-industrial by-product generated during pomelo planting. Although IPF is rich in nutrients, more than 95% of IPF is discarded annually, which causes resource waste and a serious environmental problem. Here, we report a novel continuous phase transition extraction technology (CPTE) to improve the comprehensive utilization of IPF by sequentially generating high value products and solve pollution problems related to their disposal. First, essential oil was successively extracted by CPTE at a yield of 1.12 ± 0.36%, in which 43 species were identified. Second, naringin extraction parameters were optimized using the response surface methodology (RSM), resulting in a maximum extraction rate of 99.47 ± 0.15%. Finally, pectin was extracted at a yield of 20.23 ± 0.66%, which is similar to the contents of commercial pectin. In conclusion, this study suggested that IPF was an excellent potential substrate for the production of value-added components by CPTE.


2021 ◽  
Vol 6 (5) ◽  
pp. 70-72
Author(s):  
Holta Prifti ◽  
Tania Floqi ◽  
Mirel Mico

Recently the use of biomass for biogas production is very limited in Albania. According to data acquistion from the study, the highest share in the entire structure of urban solid waste is that of organic waste 41-61.2%. A large part of these waste are bio digestible and can used for production or utilized as potential substrate in anaerobic digestion to produce biogas, a renewable source of energy and environment friendly too. Live stocks waste and especially cow manure farms are concerned in this study because there are a high number 11813 of them are spread all over Albania. In addition, the amount of cow manure exceeds 37,693.92 ton/year. In this case study is presented a cow farm located near Tirana, capital city of Albania with 200 cow heads which in the future will become 700 cow heads. The total amount of cow manure produced in this farm is 1825 ton/year, a considerable quantity of manure available for biogas production. This paper presents the type of digester, calculation of the biogas production yield, the optained energy, the pay back period of the initial investment and the net present value of this farm batcher digestor.


2021 ◽  
Author(s):  
Sebastian Mathea ◽  
Eidarus Salah ◽  
Cynthia Tallant ◽  
Deep Chatterjee ◽  
Benedict-Tilman Berger ◽  
...  

The human protein kinase ULK3 regulates the timing of membrane abscission, thus being involved in exosome budding and cytokinesis. Herein, we present the first high-resolution structures of the ULK3 kinase domain. Its unique features are explored against the background of other ULK kinases. An inhibitor fingerprint indicates that ULK3 is highly druggable and capable of adopting a wide range of conformations. In accordance with this, we describe a conformational switch between the active and an inactive ULK3 conformation, controlled by the properties of the attached small-molecule binder. Finally, we discuss a potential substrate-recognition mechanism of the full-length ULK3 protein.


2021 ◽  
Author(s):  
Jeffrey C. Medley ◽  
Joseph R. DiPanni ◽  
Luke Schira ◽  
Blake M. Shaffou ◽  
Brandon M. Sebou ◽  
...  

Aberrant centrosome numbers are associated with human cancers. The levels of centrosome regulators positively correlate with centrosome number. Thus, tight control of centrosome protein levels is critical. In Caenorhabditis elegans, the anaphase-promoting complex/cyclosome and co-activator FZR-1 (APC/CFZR-1) ubiquitin ligase negatively regulates centrosome assembly through SAS-5 degradation. In this study, we report the C. elegans ZYG-1 (Plk4 in human) as a potential substrate of APC/CFZR-1. Inhibiting APC/CFZR-1 or mutating a ZYG-1 destruction (D)-box leads to elevated ZYG-1 levels at centrosomes, restoring bipolar spindles and embryonic viability to zyg-1 mutants, suggesting that APC/CFZR-1 influences centrosomal ZYG-1 via D-box motif. We also show the Slimb/βTrCP-binding (SB) motif is critical for ZYG-1 degradation, substantiating a conserved mechanism by which ZYG-1/Plk4 stability is regulated by SCFSlimb/βTrCP-dependent proteolysis via the conserved SB motif in C. elegans. Furthermore, we show that co-mutating ZYG-1 SB and D-box motifs stabilizes ZYG-1 in an additive manner, suggesting that APC/CFZR-1 and SCFSlimb/βTrCP ubiquitin ligases function cooperatively for timely ZYG-1 destruction in C. elegans embryos where ZYG-1 activity remains at threshold level to ensure normal centrosome number.


Author(s):  
Gayathri Unnikrishnan ◽  
Vijayaraghavan Ramasamy

Background: Pineapple peel wastes was seasonal which comprised of peels and rags. Their disposal posed a serious environmental pollution. Since pineapple peel was rich in cellulose, hemicellulose and other carbohydrates it was found to be a potential substrate for methane generation by anaerobic digestion.Methods: Here pineapple peel and pulp wastes were collected. The Hydraulic Retention Time of biogas (HRT) was monitored regularly for nine days and at three days intervals in gas collection bladders (Hans Seamless latex valve bladders). The slurry collected was periodically treated with phosphate solubilizers- Providencia rettgeri, a bacterial solubilizer and Meyerozyma gullerimondi, an yeast solubilizer. The biometric parameters of Ananas comosus was tested after slurry application. The germination percent of Passiflora edulis were also calculated.Result: The best combination of biogas slurry with maximum manorial content for phosphate solubilizers were treatment with cow dung and fruit waste in the ratio 1:2 with high amount of magnesium: 0.0037%, followed by 0.075 N and 0.00054% P which was selected for biometric observations for plants. Pineapple waste were good source for making biogas and slurry obtained could be utilized as carriers for phosphate solubilising liquid fertilizers.


Development ◽  
2021 ◽  
Author(s):  
Shuai Zhou ◽  
Yueshuai Guo ◽  
Haifeng Sun ◽  
Lu Liu ◽  
Liping Yao ◽  
...  

Zygotic genomic activation (ZGA) is a landmark event in the maternal-to-zygotic transition (MZT), and the regulation of ZGA by maternal factors remains to be elucidated. In this study, the depletion of maternal ring finger protein 114 (RNF114), a ubiquitin E3 ligase, led to 2-cell embryos developmental arrest in mice. RNF114 was proven to play a crucial role in major ZGA using immunofluorescence and transcriptome analysis. To study the underlying mechanism, we performed protein profiling in mature oocytes and found a potential substrate for RNF114, Chromobox 5 (CBX5), whose ubiquitination and degradation was regulated by RNF114. The overexpression of CBX5 prevented embryonic development and impeded major ZGA. Furthermore, TAB1 was abnormally accumulated in mutant 2-cell embryos, which was consistent with the result of in vitro knockdown of Rnf114. Knockdown of Cbx5 or Tab1 in maternal RNF114-depleted embryos partially rescued developmental arrest and the defect of major ZGA. In summary, our study reveals that maternal RNF114 plays a precise role in degrading some important substrates during MZT, the mis-regulation of which may impede the appropriate activation of major ZGA in mouse embryos.


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