Biology subjects

Sanchez-Perez, J.

Publications and source records attributed to Sanchez-Perez, J..

3 recordsLinked to original sources

bioRxiv2021

A phosphorylation code regulates the multi-functional protein RETINOBLASTOMA-RELATED1 in Arabidopsis thaliana

The RETINOBLASTOMA-RELATED (RBR) proteins play a central role coordinating cell division, cell differentiation and cell survival within an environmental and developmental context. These roles reflect RBR ability to engage in multiple protein-protein interactions (PPIs), which are regulated by multi-site phosphorylation. However the functional outcomes of RBR phosphorylation in multicellular organisms remain largely unexplored. Here we test the hypothesis that phosphorylation allows diversification of RBR functions in multicellular context. Using a representative collection of transgenic loss- and gain of function point mutations in RBR phosphosites, we analysed their complementation capacity in Arabidopsis thaliana root meristems. While the number of mutated residues often correlated to the phenotypic strength of RBR phosphovariants, phospho-sites contributed differentially to distinct phenotypes. For example, the pocket-domain has a greater influence on meristematic cell proliferation, whereas the C-terminal region associates to stem cell maintenance. We found combinatorial effects between the T406 phopspho-site with others in different protein domains. Moreover, a phospho-mimetic and a phospho-defective variant, both promoting cell death, indicate that RBR controls similar cell fate choices by distinct mechanisms. Thus, additivity and specificity of RBR phospho-sites fine tune RBR activity across its multiple roles. Interestingly, a mutation disrupting RBR interactions with the LXCXE motif suppresses dominant phospho-defective RBR phenotypes. By probing protein-protein interactions of RBR variants, we found that LXCXE-containing members of the DREAM complex constitute an important component of phosphorylation-regulated RBR function, but also that RBR participates in stress or environmental responses independently of its phosphorylation state. We conclude that developmental-related, but not stress- or environmental-related functions of RBR are defined and separable by a combinatorial phosphorylation code.

plant biology↗

bioRxiv2021

Modern microbial mats from the Chihuahuan Desert provide insights into ecological stability throughout Earth's history

Microbial mats are complex ecological assemblages that are found in the Precambrian fossil record and in extant extreme environments. Hence, these structures are regarded as highly stable ecosystems. In this work, we assess the ecological stability in a modern, fluctuating, hypersaline pond from the Cuatro Cienegas Basin. From the 2016 to 2019 metagenomic sampling of this site, we found that this microbial site is sensitive to disturbances, which leads to high taxonomic replacement. Additionally, the mats have shown to be functionally stable throughout time, and could be differentiated between dry and rainy seasonal states. We speculate that this microbial system could represent modern analogs of ancient microbial mats where functions were preserved over time, whereas composition was subject to diversification in the face of local and planetary perturbations.

ecology↗

bioRxiv2021

MicNet Toolbox: visualizing and deconstructing a microbial network

Understanding both global and local patterns in the structure and interplay of microbial communities has been a fundamental question in ecological research. In this paper, we present a python toolbox that combines two emerging techniques that have been proposed as useful when analyzing compositional microbial data. On one hand, we introduce a visualization module that incorporates the use of UMAP, a recent dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density. On the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple this with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) using simulated community networks with known topologies to show that we are able to discern between network topologies. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. Author SummaryMicrobial communities are complex systems that cannot be wholly understood when studied by its individual components. Hence, global pattern analyses seem to be a promising complement to highly focused local approaches. Here, we introduce the MicNet toolbox, an open-source collection of several analytical methods for visualizing abundance data and creating co-occurrence networks for further analysis. We include two modules: one for visualization and one for network analysis based on graph theory. Additionally, we introduce an enhanced version of SparCC, a method to estimate correlations for co-occurrence network construction, that is faster and can support larger datasets. We performed method validations using simulated data and a simple biological network. Our toolbox is freely available in a github repository at https://github.com/Labevo/MicNetToolbox, and it is accompanied by a web dashboard that could be easily accessed and manipulated by non-specialist users. With this implementation, we attempt to provide a simple and straightforward way to explore and analyze microbial relative abundance data.

bioinformatics↗