Codon usage variability determines the correlation between proteome and transcriptome fold changes

Background: The availability of high throughput experimental methods has made possible to observe the relationships between proteome and transcirptome. The protein abundances show a positive but weak correlation with the concentrations of their cognate mRNAs. This weak correlation implies that there are other crucial effects involved in the regulation of protein translation, different from the sole availability of mRNA. It is well known that ribosome and tRNA concentrations are sources of variation in protein levels. Thus, by using integrated analysis of omics data, genomic information, transcriptome and proteome, we aim to unravel important variables affecting translation. Results: We identified how much of the variability in the correlation between protein and mRNA concentrations can be attributed to the gene codon frequencies. We propose the hypothesis that the influence of codon frequency is due to the competition of cognate and near-cognate tRNA binding; which in turn is a function of the tRNA concentrations. Transcriptome and proteome data were combined in two analytical steps; first, we used Self-Organizing Maps (SOM) to identify similarities among genes, based on their codon frequencies, grouping them into different clusters; and second, we calculated the variance in the protein mRNA correlation in the sampled genes from each cluster. This procedure is justified within a mathematical framework. Conclusions: With the proposed method we observed that in all the six studied cases most of the variability in the relation protein-transcript could be explained by the variation in codon composition

Genome sequence of Methylocystis hirsuta CSC1, a polyhydroxyalkanoate producing methanotroph

Producción CientíficaPolyhydroxyalkanoates (PHAs) are biodegradable plastics that can be produced by some methanotrophic organisms such as those of the genus Methylocystis. This allows the conversion of a detrimental greenhouse gas into an environmentally friendly high added‐value bioproduct. This study presents the genome sequence of Methylocystis hirsuta CSC1 (a high yield PHB producer). The genome comprises 4,213,043 bp in 4 contigs, with the largest contig being 3,776,027 bp long. Two of the other contigs are likely to correspond to large size plasmids. A total of 4,664 coding sequences were annotated, revealing a PHA production cluster, two distinct particulate methane monooxygenases with active catalytic sites, as well as a nitrogen fixation operon and a partial denitrification pathway.Ministerio de Ciencia e Innovación (Proyect CTM2015‐70442‐R)Junta de Castilla y León (programa de apoyo a proyectos de investigación – Ref. Project UIC 71

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

<p>Background:</p> <p>The genome-scale metabolic model of Saccharomyces cerevisiae, first presented in 2003, was the first genome-scale network reconstruction for a eukaryotic organism. Since then continuous efforts have been made in order to improve and expand the yeast metabolic network.</p> <p>Results:</p> <p>Here we present iTO977, a comprehensive genome-scale metabolic model that contains more reactions, metabolites and genes than previous models. The model was constructed based on two earlier reconstructions, namely iIN800 and the consensus network, and then improved and expanded using gap-filling methods and by introducing new reactions and pathways based on studies of the literature and databases. The model was shown to perform well both for growth simulations in different media and gene essentiality analysis for single and double knock-outs. Further, the model was used as a scaffold for integrating transcriptomics, and flux data from four different conditions in order to identify transcriptionally controlled reactions, i.e. reactions that change both in flux and transcription between the compared conditions.</p> <p>Conclusion:</p> <p>We present a new yeast model that represents a comprehensive up-to-date collection of knowledge on yeast metabolism. The model was used for simulating the yeast metabolism under four different growth conditions and experimental data from these four conditions was integrated to the model. The model together with experimental data is a useful tool to identify condition-dependent changes of metabolism between different environmental conditions.</p

Characterization of the keratinolytic activity of three streptomyces strains and impact of their co-cultivation on this activity

Producción CientíficaIn this study, we describe the characterization of three efficient chicken feather-degrading Streptomyces bacteria isolated from honeybee samples and assess the impact of their co-cultivation on this activity and antistaphylococcal activity. Streptomyces griseoaurantiacus AD2 was the strain showing the highest keratinolytic activity (4000 U × mL−1), followed by Streptomyces albidoflavus AN1 and Streptomyces drozdowiczii AD1, which both generated approximately 3000 U × mL−1. Moreover, a consortium constituted of these three strains was able to use chicken feathers as its sole nutrient source and growth in such conditions led to a significant increase in antibiotic production. S. griseoaurantiacus AD2 was the only strain that exhibited weak antimicrobial activity against Staphylococcus aureus. UPLC analyses revealed that a significant number of peaks detected in the extracts of co-cultures of the three strains were missing in the extracts of individual cultures. In addition, the production of specialized metabolites, such as undecylprodigiosin and manumycin A, was clearly enhanced in co-culture conditions, in agreement with the results of the antimicrobial bioassays against S. aureus. Our results revealed the benefits of co-cultivation of these bacterial species in terms of metabolic wealth and antibiotic production. Our work could thus contribute to the development of novel microbial-based strategies to valorize keratin waste.Fondo Europeo de Desarrollo Regional (FEDER), (grant TCUE 2021–2023) - (project 067/229111)Unión Europea, H2020-MSCA-IF-2016 - (grant UE-18-VANRESTREP-740080

Genome scale metabolic modeling reveals the metabolic potential of three Type II methanotrophs of the genus Methylocystis

Producción CientíficaGenome Scale Metabolic Models (GSMMs) of the recently sequenced Methylocystis hirsuta and two other methanotrophs from the genus Methylocystis have been reconstructed. These organisms are Type II methanotrophs with the ability of accumulating Polyhydroxyalkanoates under nutrient limiting conditions. For the first time, GSMMs have been reconstructed for Type II methanotrophs. These models, combined with experimental biomass and PHB yields of Methylocystis hirsuta, allowed elucidating the methane oxidation mechanism by the enzyme pMMO (particulate methane monooxygenase) in these organisms. In contrast to Type I methanotrophs, which use the “direct coupling mechanism”, Type II methanotrophs appear to use the so called “redox arm mechanism”. The utilization of the “redox arm mechanism”, which involves the coupling between methane oxidation and complex I of the respiratory chain, was confirmed by inhibition of complex I with catechol. Utilization of the “redox arm” mechanism leads to lower biomass yields on methane compared to Type I methanotrophs. However, the ability of Type II methanotrophs to redirect high metabolic carbon fluxes towards acetoacetyl-CoA under nitrogen limiting conditions makes these organisms promising platforms for metabolic engineering.Marie Curie grant H2020-MSCA-IF-2016 CH4BioVal (GA nº 750126).Junta de Castilla y León (Ref. Project VA281P18)Ministerio de Ciencia e Innovación (Proyect CLU 2017-09, CTM2015-70442-R

Genome Scale Metabolic Model of the versatile methanotroph Methylocella silvestris

BACKGROUND: Methylocella silvestris is a facultative aerobic methanotrophic bacterium which uses not only methane, but also other alkanes such as ethane and propane, as carbon and energy sources. Its high metabolic versatility, together with the availability of tools for its genetic engineering, make it a very promising platform for metabolic engineering and industrial biotechnology using natural gas as substrate. RESULTS: The first Genome Scale Metabolic Model for M. silvestris is presented. The model has been used to predict the ability of M. silvestris to grow on 12 different substrates, the growth phenotype of two deletion mutants (ΔICL and ΔMS), and biomass yield on methane and ethanol. The model, together with phenotypic characterization of the deletion mutants, revealed that M. silvestris uses the glyoxylate shuttle for the assimilation of C1 and C2 substrates, which is unique in contrast to published reports of other methanotrophs. Two alternative pathways for propane metabolism have been identified and validated experimentally using enzyme activity tests and constructing a deletion mutant (Δ1641), which enabled the identification of acetol as one of the intermediates of propane assimilation via 2-propanol. The model was also used to integrate proteomic data and to identify key enzymes responsible for the adaptation of M. silvestris to different substrates. CONCLUSIONS: The model has been used to elucidate key metabolic features of M. silvestris, such as its use of the glyoxylate shuttle for the assimilation of one and two carbon compounds and the existence of two parallel metabolic pathways for propane assimilation. This model, together with the fact that tools for its genetic engineering already exist, paves the way for the use of M. silvestris as a platform for metabolic engineering and industrial exploitation of methanotrophs

The effect of temperature during culture enrichment on methanotrophic polyhydroxyalkanoate production

Producción CientíficaClimate change and plastic pollution are likely the most relevant environmental problems of the 21st Century. Thus, one of the most promising solutions to remedy both environmental problems simultaneously is the bioconversion of greenhouse gases, such as methane (CH4), into bioplastics (PHAs). However, the optimization of this bioconversion platform is still required to turn CH4 biotransformation into a cost-effective and cost-competitive process. In this context, the research presented here aimed at elucidating the best temperature culture conditions to enhance both PHA accumulation and methane degradation. Six different enrichments were carried out at 25, 30 and 37 °C using different inocula and methane as the only energy and carbon source. CH4 biodegradation rates, specific growth rates, PHA accumulations and the community structure were characterized. Higher temperatures (30 and 37 °C) increased the PHAs accumulation up to 30% regardless of the inoculum. Moreover, Methylocystis became the dominant genus (∼30% of the total population) regardless of the temperature and inoculum used. This research demonstrated for the first time the fundamental role of temperature in increasing both the accumulation of PHAs and methane abatement during the enrichment of PHA cell-factories from methane, thus enhancing the cost-effectiveness of the process.Ministerio de Economía, Industria y Competitividad, TheEuropean FEDER program and the European Commission (CTM2015-73228-JIN, H2020-MSCA-IF-2016: CH4BioVal-GA:750126 and Red NOVEDAR)

Evaluation of Cx43 gap junction inhibitors using a quantitative structure-activity relationship model

Producción CientíficaGap junctions (GJs) made of connexin-43 (Cx43) are necessary for the conduction of electrical impulses in the heart. Modulation of Cx43 GJ activity may be beneficial in the treatment of cardiac arrhythmias and other dysfunctions. The search for novel GJ-modulating agents using molecular docking allows for the accurate prediction of binding affinities of ligands, which, unfortunately, often poorly correlate with their potencies. The objective of this study was to demonstrate that a Quantitative Structure-Activity Relationship (QSAR) model could be used for more precise identification of potent Cx43 GJ inhibitors. Using molecular docking, QSAR, and 3D-QSAR, we evaluated 16 known Cx43 GJ inhibitors, suggested the monocyclic monoterpene d-limonene as a putative Cx43 inhibitor, and tested it experimentally in HeLa cells expressing exogenous Cx43. The predicted concentrations required to produce 50% of the maximal effect (IC50) for each of these compounds were compared with those determined experimentally (pIC50 and eIC50, respectively). The pIC50ies of d-limonene and other Cx43 GJ inhibitors examined by our QSAR and 3D-QSAR models showed a good correlation with their eIC50ies (R = 0.88 and 0.90, respectively) in contrast to pIC50ies obtained from molecular docking (R = 0.78). However, molecular docking suggests that inhibitor potency may depend on their docking conformation on Cx43. Searching for new potent, selective, and specific inhibitors of GJ channels, we propose to perform the primary screening of new putative compounds using the QSAR model, followed by the validation of the most suitable candidates by patch-clamp techniques.Consejo de Investigación de Lituania - (grant S-MIP-23-105

Recent trends and advances in biogas upgrading and methanotrophs-based valorization

Producción CientíficaThe global quest for sustainability in industrial activities and waste management has recently boosted biogas production worldwide. However, the rapid decrease in the levelized cost of electricity of renewable energies will soon entail electricity prices from biogas much higher than those from solar or wind power. In this context, the upgrading of biogas into biomethane represents an alternative to on-site biogas combustion. Membrane separation technology is rapidly dominating the biogas upgrading market and displacing scrubbing and adsorption technologies driven by the recent breakthroughs in material science. Similarly, biogas biorefineries have recently emerged as an innovative platform for biogas valorization capable of biotransforming methane into added value products. The limited number of bioproducts naturally synthesized by methanotrophs can be boosted via metabolic engineering of methanotrophs, while novel bioreactor configurations capable of supporting a cost-effective methane mass transfer from the gas phase to the methanotrophic broth are currently under investigation to facilitate the full scale implementation of biogas biorefineries.Junta de Castilla y Leon - FEDER (program CLU 2017–09, CL-EI-2021–07 and UIC 315)European Commission-H2020-MSCA-IF-2019 project UP-GRAD (894515)Ministerio de Ciencia, Innovación y Universidades (project IJC2019–040495-I

Genetic modifications in bacteria for the degradation of synthetic polymers: a review

Producción CientíficaSynthetic polymers, commonly known as plastics, are currently present in all aspects of our lives. Although they are useful, they present the problem of what to do with them after their lifespan. There are currently mechanical and chemical methods to treat plastics, but these are methods that, among other disadvantages, can be expensive in terms of energy or produce polluting gases. A more environmentally friendly alternative is recycling, although this practice is not widespread. Based on the practice of the so-called circular economy, many studies are focused on the biodegradation of these polymers by enzymes. Using enzymes is a harmless method that can also generate substances with high added value. Novel and enhanced plastic-degrading enzymes have been obtained by modifying the amino acid sequence of existing ones, especially on their active site, using a wide variety of genetic approaches. Currently, many studies focus on the common aim of achieving strains with greater hydrolytic activity toward a different range of plastic polymers. Although in most cases the depolymerization rate is improved, more research is required to develop effective biodegradation strategies for plastic recycling or upcycling. This review focuses on a compilation and discussion of the most important research outcomes carried out on microbial biotechnology to degrade and recycle plastics.Fundación Ramón Areces - (CLU 2017-09 and ProgStrain