Biology subjects

Etxebeste, O.

Publications and source records attributed to Etxebeste, O..

6 recordsLinked to original sources

bioRxiv2023

Diversity and biotechnological potential of filamentous fungi isolated from sediments of Basque estuaries

Marine environments harbor a vast diversity of microorganisms, which have developed multiple strategies to adapt to challenging conditions and represent a valuable source for new products such as pigments, enzymes and bioactive compounds. From all microorganisms inhabiting marine environments, fungi have been the least studied, despite their ubiquitous presence and great biotechnological potential. Here, we focused on the isolation and characterization of filamentous fungi from marine sediment samples, which were collected along the Basque coast in Spain. Through phenotypic characterization, we identified isolates potentially able to produce secondary metabolites or grow on minimal culture medium supplemented with recalcitrant algal polysaccharides. Based on this screening, two Sordariomycetes isolates were selected for further analyses through genome sequencing and omics techniques: 1) a Marquandomyces marquandii strain able to stain the culture medium in yellow, indicative of secretion of pigments and secondary metabolites and 2) an Albophoma yamanashiensis strain able to grow in minimal culture medium supplemented with the recalcitrant algal polysaccharide fucoidan. Fungal co-culture experiments suggested an inhibitory effect of the secretome of M. marquandii on fungal growth. Under culture conditions inducing pigment secretion, a set of secondary metabolite gene clusters were differentially expressed, as analysed by RNA-seq. On the other hand, transcriptomic and proteomic experiments on A. yamanashiensis unveiled the enzymatic activities expressed in response to the presence of fucoidan. Overall, our results indicate that the isolated marine fungal strains could serve as a source of new enzymatic activities and secondary metabolites.

microbiology↗

bioRxiv2023

Identification and functional characterization of the putative members of the CTDK-1 kinase complex as regulators of growth and development in the genus Aspergillus.

The genus Aspergillus includes industrially, medically and agriculturally important species. All of them, as do fungi in general, disperse to new niches principally by means of asexual spores. Regarding the genetic/molecular control of asexual development, Aspergillus nidulans is the main reference. In this species, two pathways control the production of conidiophores, the structures bearing asexual spores (conidia). The Upstream Developmental Activation (UDA) pathway transduces environmental signals, determining whether the Central Developmental Pathway (CDP) and the required morphological changes are induced. The transcriptional regulator BrlA links both pathways as loss-of-function mutations in flb (UDA) genes block brlA transcription and, consequently, conidiation. However, the aconidial phenotype of specific flb mutants is reverted under salt-stress conditions. Previously, we generated a collection of {Delta}flbB mutants unable to conidiate on culture medium supplemented with NaH2PO4 (0.65M). Here, we identified a Gly347Stop mutation within flpA as responsible for the FLIP57 phenotype. The putative cyclin FlpA and the remaining putative components of the C-terminal domain kinase-1 (CTDK-1) complex are necessary for proper germination, growth and developmental patterns in both A. nidulans and A. fumigatus. Cellular localization and functional interdependencies of the three proteins are also analyzed. Overall, this work links the putative CTDK-1 complex of aspergilli with growth and developmental control. One-sentence summaryIdentification of a mutation in flpA as inhibitor of conidiation in A. nidulans and functional characterization of FlpA, Stk47 and FlpB as putative members of the C-terminal domain kinase complex CTDK-1 in the genus Aspergillus.

microbiology↗

bioRxiv2021

Fungal Transcription factors: Markers of genetic innovation, network rewiring and conflict between genomics and transcriptomics.

Gene Regulatory Networks (GRNs) are shaped by the democratic/hierarchical relationships among transcription factors (TFs) and associated proteins, together with the cis-regulatory sequences (CRSs) bound by these TFs at target promoters. GRNs control all cellular processes, including metabolism, stress-response, growth and development. Due to the ability to modify morphogenetic and developmental patterns, there is the consensus view that the reorganization of GRNs is a driving force of species evolution and differentiation. Duplication of TF-coding genes, their divergent sequence evolution and gain/loss/modification of CRSs are events rewiring GRNs. Fungi (mainly Saccharomycotina) have served as a reference kingdom for the study of GRN evolution. Here, I studied the genes predicted to encode TFs in the fungus Aspergillus nidulans (Pezizomycotina). The analysis of the expansion of different families of TFs suggests that duplication of TFs impacts the species level and that the expansion in Zn2Cys6 TFs is mainly due to dispersed duplication events. Comparison of genomic annotation and transcriptomic data suggests that a significant percentage of genes should be re-annotated while many others remain silent. Finally, a new regulator of growth and development is identified and characterized. Overall, this study establishes a novel theoretical framework in synthetic biology, since overexpression of silent TF forms would provide additional tools to assess how GRNs are rewired. Impact StatementGRNs controlling fungal sexual and asexual development, stress response, carbon/nitrogen metabolism or secondary metabolism, have been widely characterized in the fungus A. nidulans and, in several cases, were characterized for the first time in this fungus. The functional and genetic relationships among the TFs of these networks are known. By comparing the genomes/proteomes of hundreds of fungal genomes available in public repositories, researchers can track the emergence of regulators of interest, and identify groups of paralog TFs. The present work uses basic bioinformatics tools and standard RNA-seq analysis tools to compare genomic annotation and transcriptomics data, find incorrectly annotated TFs, identify paralog clusters of TFs, track the trajectories of duplication events and expansion of bHLH-type TFs, and identify TFs with a role in the control of growth and development. The study of TFs and GRNs of A. nidulans offers the opportunity to dissect and analyze sequentially the contribution of each cis and trans regulatory element to network rewiring and the modification of developmental patterns. Data SummaryThe data underlying this article are available in supplementary tables and supplementary figures. RNA-seq, genomic and proteomic data used is this article (and previously deposited by others; see references and accession numbers in Materials and Methods) were retrieved from sources (www.ebi.ac.uk/arrayexpress/; www.ncbi.nlm.nih.gov/bioproject/; https://www.ncbi.nlm.nih.gov/geo/) and databases (https://fungidb.org/fungidb/app) in the public domain. Aspergillus nidulans strains generated in this article will be shared on reasonable request to the corresponding author. One-sentence summaryA study of the predicted set of transcriptional regulators in the fungus Aspergillus nidulans, their conservation patterns and the correlation between gene annotations and transcriptomic data

evolutionary biology↗

bioRxiv2020

Defining the transcriptional responses of Aspergillus nidulans to cation/alkaline pH stress and the role of the transcription factor SltA.

Fungi have developed the ability to overcome extreme growth conditions and thrive in hostile environments. The model fungus Aspergillus nidulans tolerates, for example, ambient alkalinity up to pH 10 or molar concentrations of multiple cations. The ability to grow under alkaline pH or saline stress depends on the effective function of, at least, three regulatory pathways mediated by high hierarchy zinc-finger transcription factors: PacC, which mediates the ambient pH regulatory pathway, the calcineurin-dependent CrzA and the cation-homeostasis responsive factor SltA. Using RNA sequencing, we determined the effect of external pH alkalinisation or sodium stress on gene expression. Data show that each condition triggers transcriptional responses with a low degree of overlap. By sequencing the transcriptomes of the null mutant, the role of SltA in the abovementioned homeostasis mechanisms was also studied. Results show that the transcriptional role of SltA is wider than initially expected and implies, for example, the positive control of the PacC-dependent ambient pH regulatory pathway. Overall, our data strongly suggest that the stress-response pathways in fungi include some common but mostly exclusive constituents, and that there is a hierarchy of authority among the main regulators of stress response, with SltA controlling pacC expression at least in A. nidulans.

microbiology↗

bioRxiv2019

Rewiring of transcriptional networks as a major event leading to the diversity of asexual multicellularity in fungi

Complex multicellularity (CM) is characterized by the generation of three-dimensional structures that follow a genetically controlled program. CM emerged at least five times in evolution, one of them in fungi. There are two types of CM programs in fungi, leading, respectively, to the formation of sexual or asexual spores. Asexual spores foment the spread of mycoses, as they are the main vehicle for dispersion. In spite of this key dependence, there is great morphological diversity of asexual multicellular structures in fungi. To advance the understanding of the mechanisms that control initiation and progression of asexual CM and how they can lead to such a remarkable morphological diversification, we studied 503 fungal proteomes, representing all phyla and subphyla, and most known classes. Conservation analyses of 33 regulators of asexual development suggest stepwise emergence of transcription factors. While velvet proteins constitute one of the most ancient systems, the central regulator BrlA emerged late in evolution (with the class eurotiomycetes). Some factors, such as MoConX4, seem to be species-specific. These observations suggest that the emergence and evolution of transcriptional regulators rewire transcriptional networks. This process could reach the species level, resulting in a vast diversity of morphologies.\n\nOne-sentence summaryA study of the evolution of regulators that control the production of asexual spores in fungi.

developmental biology↗

bioRxiv2018

Developmental regulators FlbE/D orchestrate the polarity site-to-nucleus dynamics of the fungal bZIP FlbB

Permanently polarized cells have developed transduction mechanisms linking polarity-sites with gene regulation in the nucleus. In neurons, one mechanism is based on long-distance retrograde migration of transcription factors (TFs). Aspergillus nidulans FlbB is the only known fungal TF shown to migrate retrogradely to nuclei from the polarized region of fungal cells known as hyphae. There, FlbB controls developmental transitions by triggering the production of asexual multicellular structures. FlbB dynamics in hyphae is orchestrated by regulators FlbE and FlbD. At least three FlbE domains are involved in the acropetal transport of FlbB, with a final MyoE/actin filament-dependent step from the subapex to the apex. Experiments employing a T2A viral peptide-containing chimera (FlbE::mRFP::T2A::FlbB::GFP) suggest that apical FlbB/FlbE interaction is inhibited in order to initiate a dynein-dependent FlbB transport to nuclei. FlbD controls the nuclear accumulation of FlbB through a cMyb domain and a C-terminal LxxLL motif. Overall, results elucidate a highly dynamic pattern of FlbB interactions, which enable timely developmental induction. Furthermore, this system establishes a reference for TF-based long-distance signaling in permanently polarized cells.

developmental biology↗