Towards a genome-scale metabolic model for the Kluyveromyces lactis yeast

The interest in Kluyveromyces lactis (K. lactis) has begun in academia due to its ability to metabolize the betaglycoside (1). Since then, this yeast has been considered a model organism for studies in genetics and physiology (2). This yeast had its genome sequenced back in 2004 (3) and recently we have published a full metabolic re-annotation of its genome (4). This re-annotation can be used, among other applications, to reconstruct genome-scale metabolic models. These models allow anticipating a given organism's phenotype from its genome sequence. The reconstruction of biochemical networks is, currently, a valid alternative to microorganisms modelling as the output provided by the in silico simulations permits focusing on experiments with promising results. Thus, we propose a new fully compartmentalised genome-scale metabolic model for K. lactis, the iOD1759 which comprises 1759 metabolic genes

Reconstructing genome-scale metabolic models with Merlin

The reconstruction of genome-scale metabolic models is based on the well-known stoichiometry of biochemical reactions. Usually the main objective of a reconstruction is the in silico simulation of the phenotypic behaviour of a microorganism, under different environmental and genetic conditions, thus representing an important tool in Metabolic Engineering. The genome of the yeast Kluyveromyces lactis was used as a case study for this method, providing information for the first stage of the reconstruction of this eukaryote. Given and input of 5085 gene sequences, Merlin identified more than 4200 distinct organisms and approximately 394.000 genes with sequence similarities to the K. lactis genome. This information, after user appraisal, will be used to assemble a metabolic model with the reactions catalysed by the enzymes encoded in the genome. Such model, in the SBML format, can be used as a first raw approach to the study of the K. lactis metabolism

Genome-wide metabolic (re-) annotation of Kluyveromyces lactis

Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic analysis. Nevertheless, until now, no complete metabolic functional annotation has been performed to the proteins encoded in the Kluyveromyces lactis genome. Results In this work, a new metabolic genome-wide functional re-annotation of the proteins encoded in the Kluyveromyces lactis genome was performed, resulting in the annotation of 1759 genes with metabolic functions, and the development of a methodology supported by merlin (software developed in-house). The new annotation includes novelties, such as the assignment of transporter superfamily numbers to genes identified as transporter proteins. Thus, the genes annotated with metabolic functions could be exclusively enzymatic (1410 genes), transporter proteins encoding genes (301 genes) or have both metabolic activities (48 genes). The new annotation produced by this work largely surpassed the Kluyveromyces lactis currently available annotations. A comparison with KEGG's annotation revealed a match with 844 (~90%) of the genes annotated by KEGG, while adding 850 new gene annotations. Moreover, there are 32 genes with annotations different from KEGG. Conclusions The methodology developed throughout this work can be used to re-annotate any yeast or, with a little tweak of the reference organism, the proteins encoded in any sequenced genome. The new annotation provided by this study offers basic knowledge which might be useful for the scientific community working on this model yeast, because new functions have been identified for the so-called metabolic genes. Furthermore, it served as the basis for the reconstruction of a compartmentalized, genome-scale metabolic model of Kluyveromyces lactis, which is currently being finished.This work was partially supported by the MIT-Portugal Program in Bioengineering (MIT-Pt/BS-BB/0082/2008) and a PhD grant (SFRH / BD / 47307 / 2008) from Portuguese FCT (Fundacao para a Ciencia e Tecnologia)

Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates

The yeast Kluyveromyces lactis has received attention both from academia and industry due to some important features, such as its capacity to grow in lactose-based media, its safe status, its suitability for large-scale cultivation and for heterologous protein synthesis. It has also been considered as a model organism for genomics and metabolic regulation. Despite this, very few studies were carried out hitherto under strictly controlled conditions, such as those found in a chemostat. Here we report a set of quantitative physiological data generated during chemostat cultivations with the K. lactis CBS 2359 strain, obtained under glucose-limiting and fully aerobic conditions. This dataset serve as a basis for the comparison of K. lactis with the model yeast Saccharomyces cerevisiae in terms of their elemental compositions, as well as for future metabolic flux analysis and metabolic modelling studies with K. lactis.This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE2020 (POCI-01-0145-FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. T.O.B. would like to express his gratitude for funds provided by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Brasília, Brazil).info:eu-repo/semantics/publishedVersio

Erratum to: Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates

In the original publication of the article, the below mentioned errors have appeared. The correct text is provided in this erratum. In the abstract section, the sentence ‘‘This dataset serve’’ should be replaced as ‘‘This dataset serves’’. Also, the reference ‘‘Basso TO, Gomes FS, Lopes ML, et al (2014) Homo- and heterofermentative lactobacilli differently affect sugarcane-based fuel ethanol fermentation.Antonie Van Leeuwenhoek105:169–177. doi:10.1007/s10482-013-0063-6’’ should be replaced as ‘‘Basso TO, Dario MG, Tonso A, Stambuk BU, GombertAK(2010)Insufficienturacilsupplyinfullyaerobic chemostat cultures of Saccharomyces cerevisiae leads torespiro-fermentative metabolism anddouble nutrientlimitation. Biotechnol Lett 32:973–977. doi: 10.1007/ s10529-010-0248-2’’. Finally, in the Table 2 footnote, ‘‘according to (Heijnen 1981)’’ should be replaced as ‘‘according to Heijnen (1981)’’.info:eu-repo/semantics/publishedVersio

Recent progress in the discovery of macrocyclic compounds as potential anti-infective therapeutics

Novel therapeutic strategies are urgently needed for the treatment of serious diseases caused by viral, bacterial and parasitic infections, because currently used drugs are facing the problem of rapidly emerging resistance. There is also an urgent need for agents that act on novel pathogen-specific targets, in order to expand the repertoire of possible therapies. The high throughput screening of diverse small molecule compound libraries has provided only a limited number of new lead series, and the number of compounds acting on novel targets is even smaller. Natural product screening has traditionally been very successful in the anti-infective area. Several successful drugs on the market as well as other compounds in clinical development are derived from natural products. Amongst these, many are macrocyclic compounds in the 1-2 kDa size range. This review will describe recent advances and novel drug discovery approaches in the anti-infective area, focusing on synthetic and natural macrocyclic compounds for which in vivo proof of concept has been established. The review will also highlight the Protein Epitope Mimetics (PEM) technology as a novel tool in the drug discovery process. Here the structures of naturally occurring antimicrobial and antiviral peptides and proteins are used as starting points to generate novel macrocyclic mimetics, which can be produced and optimized efficiently by combinatorial synthetic methods. Several recent examples highlight the great potential of the PEM approach in the discovery of new anti-infective agents

De l’angine simple à l’abcès périamygdalien [From tonsillitis to peritonsillar abscess]

Acute tonsillitis is a common disease. The tonsillar infection can be uni- or bilateral with a high rate of spontaneous recovery. In some cases, a peritonsillar cellulitis or abscess can occur, characterized by an inflammatory reaction of the peritonsillar space. The red flags consist of a gradually worsening odynodysphagia, an ipsilateral swelling of the soft palate, a trismus (infrequent in children) and in some cases a change of voice (« hot potato voice »). A needle puncture of the swollen soft palate is then required. If pus is found, a surgical drainage by either hot tonsillectomy or incision under local anesthesia with an appropriate antibiotic therapy must be carried out

Exploring the longitudinal relationships between the use of grammar in text messaging and performance on grammatical tasks

Research has demonstrated that use of texting slang (textisms) when text messaging does not appear to impact negatively on children's literacy outcomes and may even benefit children's spelling attainment. However, less attention has been paid to the impact of text messaging on the development of children's and young people's understanding of grammar. This study therefore examined the interrelationships between children's and young adults' tendency to make grammatical violations when texting and their performance on formal assessments of spoken and written grammatical understanding, orthographic processing and spelling ability over the course of 1 year. Zero-order correlations showed patterns consistent with previous research on textism use and spelling, and there was no evidence of any negative associations between the development of the children's performance on the grammar tasks and their use of grammatical violations when texting. Adults' tendency to use ungrammatical word forms ('does you') was positively related to performance on the test of written grammar. Grammatical violations were found to be positively associated with growth in spelling for secondary school children. However, not all forms of violation were observed to be consistently used in samples of text messages taken 12 months apart or were characteristic of typical text messages. The need to differentiate between genuine errors and deliberate violation of rules is discussed, as are the educational implications of these findings

iOD962 - the first genome-scale metabolic model of Kluyveromyces lactis

The genome-scale metabolic model of Kluyveromyces lactis was reconstructed from its genome annotation. The result was the partially compartmentalized (5 compartments) iOD962 metabolic model composed of 2038 reactions and 1561 metabolites. Previous chemostate experiments were used to adjust the maintenance ATP parameter, and the model proved valuable when predicting the biomass, oxygen and carbon dioxide yields. Also, the in silico knockouts predicted accurately the in vivo phenotypes, when compared to published experiments. This model allowed determining a minimal medium for cultivating K. lactis and will surely allow elucidating insights on the milk yeast metabolism as well as identifying engineering targets for the improvement of the production of by-products of interest by performing in silico simulations