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1.
Widespread use of unconventional targeting signals in mitochondrial ribosome proteins.
Bykov, YS, Flohr, T, Boos, F, Zung, N, Herrmann, JM, Schuldiner, M
The EMBO journal. 2022;(1):e109519
Abstract
Mitochondrial ribosomes are complex molecular machines indispensable for respiration. Their assembly involves the import of several dozens of mitochondrial ribosomal proteins (MRPs), encoded in the nuclear genome, into the mitochondrial matrix. Proteomic and structural data as well as computational predictions indicate that up to 25% of yeast MRPs do not have a conventional N-terminal mitochondrial targeting signal (MTS). We experimentally characterized a set of 15 yeast MRPs in vivo and found that five use internal MTSs. Further analysis of a conserved model MRP, Mrp17/bS6m, revealed the identity of the internal targeting signal. Similar to conventional MTS-containing proteins, the internal sequence mediates binding to TOM complexes. The entire sequence of Mrp17 contains positive charges mediating translocation. The fact that these sequence properties could not be reliably predicted by standard methods shows that mitochondrial protein targeting is more versatile than expected. We hypothesize that structural constraints imposed by ribosome assembly interfaces may have disfavored N-terminal presequences and driven the evolution of internal targeting signals in MRPs.
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2.
Multi-omics based strategy for toxicity analysis of acrylamide in Saccharomyces cerevisiae model.
Lin, Z, Luo, P, Huang, D, Wu, Y, Li, F, Liu, H
Chemico-biological interactions. 2021;:109682
Abstract
Although the toxicity of acrylamide (ACR) has been extensively investigated in different experimental models, its perturbations to multiple nodes of the cellular signaling network have not been systematically associated. In this study, changes at different omics layers in ACR exposed Saccharomyces cerevisiae cells were monitored using a multi-omics strategy. The results of the analysis highlighted the impairment of oxidative-reductive balance, energy metabolism, lipid metabolism, nucleotide metabolism, and ribosome function in yeast cells. Response to acute ACR damage, glutathione synthesis was upregulated, the process of protein degradation was accelerated, and the autophagy flux was initiated. Meanwhile, yeast upregulates gene expression levels of enzymes in carbohydrate metabolism and speeds up the oxidation process of fatty acids to compensate for energy depletion. Importantly, the multi-omics strategy captures features that have rarely been addressed in previous studies on the toxicology of ACR, including blocked de novo nucleotide synthesis, decreased levels of metabolic enzyme cofactors thiamine and D-biotin, increased intracellular concentrations of neurotoxic N-methyl d-aspartic acid and l-glutamic acid, and release of death mediators ceramide. The ACR perturbation network constructed in this work and the discovery of new damage features provide a theoretical basis for subsequent point-to-point toxicological studies.
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3.
Lipid Droplets and Their Autophagic Turnover via the Raft-Like Vacuolar Microdomains.
Rahman, MA, Kumar, R, Sanchez, E, Nazarko, TY
International journal of molecular sciences. 2021;(15)
Abstract
Although once perceived as inert structures that merely serve for lipid storage, lipid droplets (LDs) have proven to be the dynamic organelles that hold many cellular functions. The LDs' basic structure of a hydrophobic core consisting of neutral lipids and enclosed in a phospholipid monolayer allows for quick lipid accessibility for intracellular energy and membrane production. Whereas formed at the peripheral and perinuclear endoplasmic reticulum, LDs are degraded either in the cytosol by lipolysis or in the vacuoles/lysosomes by autophagy. Autophagy is a regulated breakdown of dysfunctional, damaged, or surplus cellular components. The selective autophagy of LDs is called lipophagy. Here, we review LDs and their degradation by lipophagy in yeast, which proceeds via the micrometer-scale raft-like lipid domains in the vacuolar membrane. These vacuolar microdomains form during nutrient deprivation and facilitate internalization of LDs via the vacuolar membrane invagination and scission. The resultant intra-vacuolar autophagic bodies with LDs inside are broken down by vacuolar lipases and proteases. This type of lipophagy is called microlipophagy as it resembles microautophagy, the type of autophagy when substrates are sequestered right at the surface of a lytic compartment. Yeast microlipophagy via the raft-like vacuolar microdomains is a great model system to study the role of lipid domains in microautophagic pathways.
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4.
Improvement of ethanol production in fed-batch fermentation using a mixture of sugarcane juice and molasse under very high-gravity conditions.
Cruz, ML, de Resende, MM, Ribeiro, EJ
Bioprocess and biosystems engineering. 2021;(3):617-625
Abstract
Ethanol fermentation in very high gravity (VHG) saves energy consumption for ethanol distillation. As the technology offers high ethanol yield and low waste generation and it can be operated at low cost, it could be more efficient at an industrial scale than other ethanol production methods. This work studied ethanol production using a fed-batch bioreactor with a working volume of 1.5 L. The main objective of this research was evaluate the effects of temperature, sugar concentration, and cellular concentration using a Central Composite Design (CCD). Experimental conditions were selected using the surface response technique obtained from the CCD, and the results were validated to test the reproducibility. The following operating conditions were selected: temperature of 27.0 °C, sugar concentration 300.0 g/L, and cell concentration 15.0% (v/v). Under these conditions, after 30 h of fermentation the ethanol concentration, productivity and yield were 135.0 g/L, 4.42 g/(L·h) and 90.0%, respectively. All sugar was completely consumed.
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5.
Urm1: A Non-Canonical UBL.
Termathe, M, Leidel, SA
Biomolecules. 2021;(2)
Abstract
Urm1 (ubiquitin related modifier 1) is a molecular fossil in the class of ubiquitin-like proteins (UBLs). It encompasses characteristics of classical UBLs, such as ubiquitin or SUMO (small ubiquitin-related modifier), but also of bacterial sulfur-carrier proteins (SCP). Since its main function is to modify tRNA, Urm1 acts in a non-canonical manner. Uba4, the activating enzyme of Urm1, contains two domains: a classical E1-like domain (AD), which activates Urm1, and a rhodanese homology domain (RHD). This sulfurtransferase domain catalyzes the formation of a C-terminal thiocarboxylate on Urm1. Thiocarboxylated Urm1 is the sulfur donor for 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), a chemical nucleotide modification at the wobble position in tRNA. This thio-modification is conserved in all domains of life and optimizes translation. The absence of Urm1 increases stress sensitivity in yeast triggered by defects in protein homeostasis, a hallmark of neurological defects in higher organisms. In contrast, elevated levels of tRNA modifying enzymes promote the appearance of certain types of cancer and the formation of metastasis. Here, we summarize recent findings on the unique features that place Urm1 at the intersection of UBL and SCP and make Urm1 an excellent model for studying the evolution of protein conjugation and sulfur-carrier systems.
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6.
Modeling the Ethanol Tolerance of the Probiotic Yeast Saccharomyces cerevisiae var. boulardii CNCM I-745 for its Possible Use in a Functional Beer.
Ramírez-Cota, GY, López-Villegas, EO, Jiménez-Aparicio, AR, Hernández-Sánchez, H
Probiotics and antimicrobial proteins. 2021;(1):187-194
Abstract
Saccharomyces yeasts are able to ferment simple sugars to generate levels of ethanol that are toxic to other yeasts and bacteria. The tolerance to ethanol of different yeasts depends also on the incubation temperature. In this study, the ethanol stress responses of S. cerevisiae and the probiotic yeast S. boulardii CNCM I-745 were evaluated at two temperatures. The growth kinetics parameters were obtained by fitting the Baranyi and Roberts model to the experimental data. The four-parameter logistic Hill equation was used to describe the ethanol tolerance of the yeasts at the temperatures of 28 and 37 °C. Adequate determination coefficients were obtained (R2 > 0.91) in all cases. S. boulardii grown at 28 °C was selected as the yeast with the best ethanol tolerance (6-8%) for use in the elaboration of functional craft beers.
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7.
Tryptophan Derivatives by Saccharomyces cerevisiae EC1118: Evaluation, Optimization, and Production in a Soybean-Based Medium.
Dei Cas, M, Vigentini, I, Vitalini, S, Laganaro, A, Iriti, M, Paroni, R, Foschino, R
International journal of molecular sciences. 2021;(1)
Abstract
Given the pharmacological properti es and the potential role of kynurenic acid (KYNA) in human physiology and the pleiotropic activity of the neurohormone melatonin (MEL) involved in physiological and immunological functions and as regulator of antioxidant enzymes, this study aimed at evaluating the capability of Saccharomyces cerevisiae EC1118 to release tryptophan derivatives (dTRPs) from the kynurenine (KYN) and melatonin pathways. The setting up of the spectroscopic and chromatographic conditions for the quantification of the dTRPs in LC-MS/MS system, the optimization of dTRPs' production in fermentative and whole-cell biotransformation approaches and the production of dTRPs in a soybean-based cultural medium naturally enriched in tryptophan, as a case of study, were included in the experimental plan. Variable amounts of dTRPs, with a prevalence of metabolites of the KYN pathway, were detected. The LC-MS/MS analysis showed that the compound synthesized at highest concentration is KYNA that reached 9.146 ± 0.585 mg/L in fermentation trials in a chemically defined medium at 400 mg/L TRP. Further experiments in a soybean-based medium confirm KYNA as the main dTRPs, whereas the other dTRPs reached very lower concentrations. While detectable quantities of melatonin were never observed, two MEL isomers were successfully measured in laboratory media.
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8.
Use of Hanseniaspora guilliermondii and Hanseniaspora opuntiae to enhance the aromatic profile of beer in mixed-culture fermentation with Saccharomyces cerevisiae.
Bourbon-Melo, N, Palma, M, Rocha, MP, Ferreira, A, Bronze, MR, Elias, H, Sá-Correia, I
Food microbiology. 2021;:103678
Abstract
Beer production is predominantly carried out by Saccharomyces species, such as S. cerevisiae and S. pastorianus. However, the introduction of non-Saccharomyces yeasts in the brewing process is now seen as a promising strategy to improve and differentiate the organoleptic profile of beer. In this study, 17 non-Saccharomyces strains of 12 distinct species were isolated and submitted to a preliminary sensory evaluation to determine their potential for beer bioflavouring. Hanseniaspora guilliermondii IST315 and H. opuntiae IST408 aroma profiles presented the highest acceptability and were described as having 'fruity' and 'toffee' notes, respectively. Their presence in mixed-culture fermentations with S. cerevisiae US-05 did not influence attenuation and ethanol concentration of beer but had a significant impact in its volatile composition. Notably, while both strains reduced the total amount of ethyl esters, H. guilliermondii IST315 greatly increased the concentration of acetate esters, especially when sequentially inoculated, leading to an 8.2-fold increase in phenylethyl acetate ('rose', 'honey' aroma) in the final beverage. These findings highlight the importance of non-Saccharomyces yeasts in shaping the aroma profile of beer and suggest a role for Hanseniaspora spp. in improving it.
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9.
Hybrid neural network modeling and particle swarm optimization for improved ethanol production from cashew apple juice.
da Silva Pereira, A, Pinheiro, ÁDT, Rocha, MVP, Gonçalves, LRB, Cartaxo, SJM
Bioprocess and biosystems engineering. 2021;(2):329-342
Abstract
A hybrid neural model (HNM) and particle swarm optimization (PSO) was used to optimize ethanol production by a flocculating yeast, grown on cashew apple juice. HNM was obtained by combining artificial neural network (ANN), which predicted reaction specific rates, to mass balance equations for substrate (S), product and biomass (X) concentration, being an alternative method for predicting the behavior of complex systems. ANNs training was conducted using an experimental set of data of X and S, temperature and stirring speed. The HNM was statistically validated against a new dataset, being capable of representing the system behavior. The model was optimized based on a multiobjective function relating efficiency and productivity by applying the PSO. Optimal estimated conditions were: S0 = 127 g L-1, X0 = 5.8 g L-1, 35 °C and 111 rpm. In this condition, an efficiency of 91.5% with a productivity of 8.0 g L-1 h-1 was obtained at approximately 7 h of fermentation.
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10.
Monitoring single-cell dynamics of entry into quiescence during an unperturbed life cycle.
Jacquel, B, Aspert, T, Laporte, D, Sagot, I, Charvin, G
eLife. 2021
Abstract
The life cycle of microorganisms is associated with dynamic metabolic transitions and complex cellular responses. In yeast, how metabolic signals control the progressive choreography of structural reorganizations observed in quiescent cells during a natural life cycle remains unclear. We have developed an integrated microfluidic device to address this question, enabling continuous single-cell tracking in a batch culture experiencing unperturbed nutrient exhaustion to unravel the coordination between metabolic and structural transitions within cells. Our technique reveals an abrupt fate divergence in the population, whereby a fraction of cells is unable to transition to respiratory metabolism and undergoes a reversible entry into a quiescence-like state leading to premature cell death. Further observations reveal that nonmonotonous internal pH fluctuations in respiration-competent cells orchestrate the successive waves of protein superassemblies formation that accompany the entry into a bona fide quiescent state. This ultimately leads to an abrupt cytosolic glass transition that occurs stochastically long after proliferation cessation. This new experimental framework provides a unique way to track single-cell fate dynamics over a long timescale in a population of cells that continuously modify their ecological niche.