A phylogenetic approach to the early evolution of autotrophy: the case of the reverse TCA and the reductive acetyl-CoA pathways

In recent decades, a number of hypotheses on the autotrophic origin of life have been presented. These proposals invoke the emergence of reaction networks leading from CO or CO2 to the organic molecules required for life. It has also been suggested that the last (universal) common ancestor (LCA or LUCA) of all extant cell lineages was a chemolitho-autotrophic thermophilic anaerobe. The antiquity of some carbon fixation pathways, the phylogenetic basal distribution of some autotrophic organisms, and the catalytic properties of iron-sulfur minerals have been advanced in support of these ideas. Here we critically examine the phylogenetic distribution and evolution of enzymes that are essential for two of the most ancient autotrophic means of metabolism: the reductive tricarboxylic acid (rTCA) cycle and the reductive acetyl-CoA pathway. Phylogenetic analysis of citryl-CoA synthetase and of citryl-CoA lyase, key enzymatic components of the rTCA cycle, and of CO dehydrogenase/acetyl-CoA synthase, a key enzyme in the reductive acetyl-CoA pathway, revealed that all three enzymes have undergone major lateral transfer events and therefore cannot be used as proof of the LCA’s metabolic abilities nor as evidence of an autotrophic origin of life. [Int Microbiol 2014; 17(2):91-97]Keywords: autotrophic pathways · reverse Krebs cycle · Wood–Ljungdahl pathway · origin of life · last common ancestor (LCA, LUCA

Gut Microbiota Cannot Compensate the Impact of (quasi) Aposymbiosis in Blattella germanica

The German cockroach Blattella germanica is a good model to study complex symbiotic relationships because the following two symbiotic systems coexist in a single individual: the endosymbiont Blattabacterium (living inside specialized cells called bacteriocytes) and the gut microbiota. Although the role of the endosymbiont has been fully elucidated, the function of the gut microbiota remains unclear. The study of the gut microbiota will benefit from the availability of insects deprived of Blattabacterium. Our goal is to determine the effect of the removal (or, at least, the reduction) of the endosymbiont population on the cockroach's fitness, in a normal gut microbiota community. For this purpose, we treated our cockroach population with rifampicin to decrease the amount of endosymbiont in the following generation. As the treatment also affects rifampicin-sensitive gut bacteria, we allowed it to recover for at least 20 days before sampling. We found that after this antibiotic treatment, the endosymbiont population remained extremely reduced and only the microbiota were able to recover, although it could not compensate for the endosymbiont role, and the host's fitness was drastically affected. This accomplished reduction, however, is not homogenous and requires further study to develop stable quasi-aposymbiotic cockroaches

gNOMO : a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms

The study of bacterial symbioses has grown exponentially in the recent past. However, existing bioinformatic workflows of microbiome data analysis do commonly not integrate multiple meta-omics levels and are mainly geared toward human microbiomes. Microbiota are better understood when analyzed in their biological context; that is together with their host or environment. Nevertheless, this is a limitation when studying non-model organisms mainly due to the lack of well-annotated sequence references. Here, we present gNOMO, a bioinformatic pipeline that is specifically designed to process and analyze non-model organism samples of up to three meta-omics levels: metagenomics, metatranscriptomics and metaproteomics in an integrative manner. The pipeline has been developed using the workflow management framework Snakemake in order to obtain an automated and reproducible pipeline. Using experimental datasets of the German cockroach Blattella germanica, a non-model organism with very complex gut microbiome, we show the capabilities of gNOMO with regard to meta-omics data integration, expression ratio comparison, taxonomic and functional analysis as well as intuitive output visualization. In conclusion, gNOMO is a bioinformatic pipeline that can easily be configured, for integrating and analyzing multiple meta-omics data types and for producing output visualizations, specifically designed for integrating paired-end sequencing data with mass spectrometry from non-model organisms

Disposición del alumnado al uso de herramientas de comunicación síncrona en la docencia universitaria

En los últimos años han sido numerosas las iniciativas de innovación educativa que han propuesto el uso de las herramientas de comunicación síncrona como recurso tecnológico de soporte a la docencia universitaria. Dichas propuestas han demostrado sus beneficios en contextos de aplicación concretos como por ejemplo: la tutorización virtual o la internacionalización y movilidad en másteres y doctorados. Sin embargo, su alcance limitado dificulta a menudo la extrapolación de resultados a otros ámbitos docentes y, por tanto, la transformación de actividades que se pueden catalogar como piloto en soluciones de implantación consolidada. Con el trasfondo de la declaración del año 2015 como Año Internacional de la Evaluación, en este trabajo presentamos los resultados de un estudio dirigido a conocer la opinión del alumnado sobre el uso de herramientas de comunicación por Internet en la docencia universitaria. El estudio ha involucrado a 436 estudiantes matriculados en asignaturas de cursos diversos en titulaciones de ingeniería, magisterio, criminología y ciencias del deporte, en universidades públicas y privadas. Los resultados muestran una caracterización del interés, las expectativas y las preferencias de los alumnos con respecto a la incorporación de las herramientas informáticas de comunicación síncronas como mecanismo de apoyo y mejora del proceso de aprendizaje.In recent years there have been numerous innovative educational initiatives that have proposed the use of synchronous communication tools to support university teaching. These proposals have proven their worth in specific application contexts such as: virtual tutoring, internationalization and mobility in masters and doctorates. However, their sometimes limited scope often makes it difficult to generalize results to other contexts and, thus, to pass from pilots to consolidated solutions. Within the framework of 2015 being declared as the International Year of Evaluation, this paper presents the results of a survey aimed to obtain the opinion of students regarding the use of synchronous communication tools for university teaching. The survey involved 436 students enrolled in subjects of various grade levels in degrees sucha as engineering, teaching, criminology and sports science, both in public and private universities. The results show a characterization of the interest, expectations and preferences of students with respect to the incorporation of computer communication tools as a mechanism to improve the learning process.Educació

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

We identified rare coding variants associated with Alzheimer’s disease (AD) in a 3-stage case-control study of 85,133 subjects. In stage 1, 34,174 samples were genotyped using a whole-exome microarray. In stage 2, we tested associated variants (P<1×10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, an additional 14,997 samples were used to test the most significant stage 2 associations (P<5×10-8) using imputed genotypes. We observed 3 novel genome-wide significant (GWS) AD associated non-synonymous variants; a protective variant in PLCG2 (rs72824905/p.P522R, P=5.38×10-10, OR=0.68, MAFcases=0.0059, MAFcontrols=0.0093), a risk variant in ABI3 (rs616338/p.S209F, P=4.56×10-10, OR=1.43, MAFcases=0.011, MAFcontrols=0.008), and a novel GWS variant in TREM2 (rs143332484/p.R62H, P=1.55×10-14, OR=1.67, MAFcases=0.0143, MAFcontrols=0.0089), a known AD susceptibility gene. These protein-coding changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified AD risk genes. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to AD development

The effect of rifampicin on the symbiotic systems of Blattella germanica

Resumen del trabajo presentado a la VII Biennial Congress of Sociedad Española de Biología Evolutiva (SEBE), celebrada en Sevilla (España) del 5 al 7 de febrero de 2020.Two symbiotic systems have been described, endosymbiosis and ectosymbiosis, and generally insects harbour one of the two. However, Blattella germanica is an omnivorous insect in which both systems coexist: Blattabacterium cuenotii, an endosymbiont located in specialised cells (bacteriocytes) in the fat body, and a rich microbiota located in the hindgut. Blattabacterium is an obligate endosymbiont with an essential role in the nitrogen recycling and essential amino acids biosynthesis, as it has been proposed after its genome sequencing. The gut microbiome is a complex population similar to the human gut microbiome, with many potential functions that still have to be elucidated. To assess if there is a crosstalk between both symbiotic systems in B. germanica, despite being located in separate compartments, we planned to reduce the Blattabacterium population by antibiotic treatment, but affecting as little as possible to its microbiota. To do that, we treated adults with rifampicin (antibiotic that attacks Blattabacterium as well as Gram-negative and some Gram-positive bacteria) in short periods of time (12 days, when Blattabacterium is extracellular to infect the nextgeneration oocytes), during three generations. We have measured in adult females the amount of Blattabacterium by qPCR and the changes of the bacterial community of the gut microbiota by sequencing the 16S rRNA gene. We have also determined several fitness parameters (developmental time, sexual maturation time, reproductive rate and mortality) to assess the effect on the host of the reduction of the endosymbiont. Results indicate that the gut microbiota is not able to carry out Blattabacterium’s role.Peer reviewe

Correlated Biochemical and ultrastructural changes in nitrogen-starved Euglena Gracilis

10 pages, figures, and tables statisticsGrowth of Euglena gracilis Z Pringsheim under photoheterotrophic conditions in a nitrogen-deprived medium resulted in progressive loss of chroroplastic material until total bleaching of the cells ocurred. Biochemical analysis and ultrastructural observation of the first stages of the starvation process demonstrated and early lag phase (from 0 to 9 h) in which cells increased in size, followed by a period of cell division, apparently supportde by the mobilization of some chroroplastic proteins such as the photosynthetic CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase-oxygenasePeer reviewe

Of cockroaches and symbionts: Recent advances in the characterization of the relationship between Blattella germanica and its dual symbiotic system

This article belongs to the Collection Feature Review Papers for Life.Mutualistic stable symbioses are widespread in all groups of eukaryotes, especially in insects, where symbionts have played an essential role in their evolution. Many insects live in obligate relationship with different ecto- and endosymbiotic bacteria, which are needed to maintain their hosts’ fitness in their natural environment, to the point of even relying on them for survival. The case of cockroaches (Blattodea) is paradigmatic, as both symbiotic systems coexist in the same organism in two separated compartments: an intracellular endosymbiont (Blattabacterium) inside bacteriocytes located in the fat body, and a rich and complex microbiota in the hindgut. The German cockroach Blattella germanica is a good model for the study of symbiotic interactions, as it can be maintained in the laboratory in controlled populations, allowing the perturbations of the two symbiotic systems in order to study the communication and integration of the tripartite organization of the host–endosymbiont–microbiota, and to evaluate the role of symbiotic antimicrobial peptides (AMPs) in host control over their symbionts. The importance of cockroaches as reservoirs and transmission vectors of antibiotic resistance sequences, and their putative interest to search for AMPs to deal with the problem, is also discussed.This research was funded by the European Regional Development Fund (ERDF) and Ministerio de Ciencia, Innovación y Universidades (MICINN, Spain), grant number PGC2018-099344-B-I00; Conselleria d’Educació, Generalitat Valenciana (Spain), grant number PROMETEO/2018/133.Peer reviewe

Blattella germanica displays a large arsenal of antimicrobial peptide genes

Defence systems against microbial pathogens are present in most living beings. The German cockroach Blattella germanica requires these systems to adapt to unhealthy environments with abundance of pathogenic microbes, in addition to potentially control its symbiotic systems. To handle this situation, four antimicrobial gene families (defensins, termicins, drosomycins and attacins) were expanded in its genome. Remarkably, a new gene family (blattellicins) emerged recently after duplication and fast evolution of an attacin gene, which is now encoding larger proteins with the presence of a long stretch of glutamines and glutamic acids. Phylogenetic reconstruction, within Blattellinae, suggests that this duplication took place before the divergence of Blattella and Episymploce genera. The latter harbours a long attacin gene (pre-blattellicin), but the absence of the encoded Glx-region suggests that this element evolved recently in the Blattella lineage. A screening of AMP gene expression in available transcriptomic SR projects of B. germanica showed that, while some AMPs are expressed during almost the whole development, others are restricted to shorter periods. Blattellicins are highly expressed only in adult females. None of the available SR tissue projects could be associated with blattellicins’ expression, suggesting that it takes place in other tissues, maybe the gut.This work was funded by European Regional Development Fund (ERDF) and Ministerio de Ciencia, Innovación y Universidades (Spain) (PGC2018-099344-B-I00) and Generalitat Valenciana (Prometeo/2018/A/133). MMB is granted with a FPU fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain) (FPU15-01203).Peer reviewe

Fighting against microbes: The cosmopolitan German cockroach

Resumen del póster presentado al XLII Congreso de la Sociedad Española de Genética, celebrado de forma virtual del 14 al 18 de junio de 2021.Insects kill pathogens through different mechanisms. One of the most relevant is the production of several types of small proteins called antimicrobial peptides (AMPs), which mainly act on microbial membranes producing the cell lysis. However, the presence of beneficial microbiota, or a permanent endosymbiont species located in specialized cells, may generate the evolutionary recruitment of one of these AMPs to control the symbiont populations. The German cockroach Blattella germanica requires these systems to adapt to unhealthy environments with abundance of pathogenic microbes. It also possesses a rich beneficial gut microbiota and an ancient endosymbiont (Blattabacterium cuenoti), whose association with the order Blattodea started more than 200 million years ago. To handle this situation, four antimicrobial gene families (defensins, termicins, drosomycins and attacins) were expanded in its genome. Remarkably, a new gene family (blattellicins) emerged recently after duplication and fast evolution of an attacin gene, which is now encoding larger proteins with the presence of a long stretch of glutamines and glutamic acids. Phylogenetic reconstruction, within Blattellinae, suggests that this duplication took place before the divergence of Blattella and Episymploce genera. The latter harbours a long attacin gene (pre-blattellicin), but the absence of the encoded Glx-region suggests that this element evolved recently in the Blattella lineage. A screening of AMP gene expression in available transcriptomic SR projects of B. germanica showed that, while some AMPs are expressed during almost the whole development, others are restricted to shorter periods. Blattellicins are highly expressed only in adult females. Because none of the available SR tissue projects could be associated with blattellicins’ expression, RNA seq experiments with several adult tissue samples will be performed to identify where they are expressed.This work was supported by European Regional Development Fund (ERDF) and Ministerio de Economía, Industria y Competitividad (Spain) (PGC2018-099344-B-I00) and Generalitat Valenciana (Prometeo/2018/A/133).Peer reviewe