Biology subjects

Loureiro, C.

Publications and source records attributed to Loureiro, C..

9 recordsLinked to original sources

bioRxiv2026

Elucidating biosynthetic pathways related to the synthesis of small halogenated peptidic natural products in marine sponge microbiomes

Marine sponges are known sources of bioactive natural products (NPs), many of which are produced by associated bacterial symbionts via encoded biosynthetic gene clusters (BGCs). A particularly interesting subclass of sponge-derived NPs is comprised of small, brominated alkaloids, which are recovered from diverse habitats and host sponge taxonomies. Despite having been described decades ago, most of these NPs do not have an elucidated biosynthetic origin. We queried metagenomes of several sponge species by making use of a minimal set of core enzymes that we postulate to be necessary to produce these small peptidic NPs: an FADH2-dependent halogenase and an AMP-binding adenylation enzyme. This revealed a variety of novel BGC architectures, many of which showed conservation among sponge host phylogenies and were encoded in the genomes of diverse sponge-associated bacteria. Furthermore, we identified a BGC in the sponge G. barretti that is potentially linked to the production of the iconic barettins, given its enzymatic machinery and specific acidobacterial origin. The present work contributes to the challenging quest to link orphan brominated NPs to their parent BGCs in the sponge holobiont and beyond.

bioinformatics↗

bioRxiv2026

Distinct taxonomic groups of sponge symbionts have the biosynthetic capacity for the production of ether lipids

The marine sponge holobiont, composed of the sponge host and its microbial symbionts, is a known source of abundant and diverse ether lipids (ELs). Apart from their structural role in the cytoplasmic membrane of archaea and some bacteria, ELs have often been linked to signaling functions and defense against pathogens. Despite the relevance of ELs, their biosynthesis, as well as the identity of their producers, remain elusive. Here, we report the analysis of potential ether lipid producing genes and gene clusters, detected in marine sponge metagenomes as well as public sponge genomes. We show that the sponge holobiont has the capacity to synthesize ELs via several pathways, and suggest the ability of the sponge holobiont to synthesize ELs under different O2 levels. Finally, targeted lipidome analysis confirmed that ELs are present in the lipid profiles of all of the studied sponge holobiont samples, and indicates that the biosynthesis of the plasmalogens detected is likely restricted to the sponge host itself, based on the detected hydrocarbon chain lengths. This work provides a basis for the challenging quest to decipher intricate EL biosynthesis in marine sponges and their associated microbes.

microbiology↗

bioRxiv2025

BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters

Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medicines and crop protection agents. Here, we present BiG-SCAPE and BiG-SLiCE 2.0, next-generation methods that facilitate scalable, accurate and interactive gene cluster analyses. BiG-SCAPE 2.0 updates its classification, alignment methods, and visualizations, enabling more accurate analysis, up to 8x faster runtimes and halved memory requirements. BiG-SLiCE 2.0 updates its distance metric, pHMM database, and classification logic, resulting in increased sensitivity nearing that of BiG-SCAPE. Analysis of 260,630 biosynthetic gene clusters from publicly available genomes reveals that both tools generate concurring estimates of gene cluster diversity, thus providing significantly extended methodological support for recent evidence indicating that the vast majority of natural product diversity remains unexplored. Together, these updates will facilitate global genome mining efforts for natural product discovery and microbiome analyses scalable with current data sizes.

bioinformatics↗

bioRxiv2024

Single-cell transcriptional dynamics in a living vertebrate

The ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. With these tools, we obtained single-cell, real-time measurements of transcriptional dynamics of the segmentation clock. Our measurements challenge the traditional view of smooth clock oscillations and instead suggest a model of discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity in the context of vertebrate organisms can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.

developmental biology↗

bioRxiv2022

Autorepression-based conditional gene expression system in yeast for variation-suppressed control of protein dosage

Conditional control of gene expression allows an experimenter to investigate many aspects of a genes function. In the model organism Saccharomyces cerevisiae, a number of methods to control gene expression are widely practiced, including induction by metabolites, small molecules, and even light. However, all current methods suffer from at least one of a set of drawbacks, including need for specialized growth conditions, leaky expression, or the requirement of specialized equipment. Here we describe protocols using two transformations to construct strains that carry a new controller, in which all these drawbacks are overcome. In these strains, the expression of a controlled gene (gene of interest, or GOI) is repressed by the bacterial repressor TetR, and induced by anhydrotetracycline. TetR also regulates its own expression, creating an autorepression loop. This autorepression allows tight control of gene expression/ protein dosage with low cell to cell variation in expression. A second repressor, TetR-Tup1, prevents any leaky expression. We also present a protocol showing a particular workhorse application of such strains, to generate synchronized cell populations. We turn off the expression of the cell cycle regulator CDC20 completely, arresting the cell population, and then back on so that the synchronized cells resume cell cycle progression. This control system can be applied to any endogenous or exogenous gene for precise expression. Basic Protocol 1Generating a parent WTC846 strain. Basic Protocol 2Generating a WTC846 strain with controlled expression of the targeted gene Alternate Protocol 1CRISPR-mediated promoter replacement Basic Protocol 3Cell cycle synchronization/Arrest and Release using the WTC846-K3::CDC20 strain

genetics↗

bioRxiv2022

Comparative metagenomic analysis of biosynthetic diversity across sponge microbiomes highlights metabolic novelty, conservation and diversification

Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about their global distribution landscape and the symbionts that produce them. As the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont and measure their diversity across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three sponge species from the Atlantic Ocean and the Mediterranean Sea. This dataset reveals striking novelty in its encoded biosynthetic potential, with less than 1% of the recovered gene cluster families (GCF) showing similarity to any characterized biosynthetic gene cluster (BGC). When zooming in on the microbial communities of each sponge, we observed higher variability of both secondary metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we also identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species, and a true GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases (NRPS) that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts, and to the cryptic biosynthetic potential contained in this environmental niche.

microbiology↗

bioRxiv2021

Nuclei are mobile processors enabling specialization in a gigantic single-celled syncytium

In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleated syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters, and if nuclei within the cell diversify into heterogeneous states. Here we performed spatial transcriptome analysis of the slime mold Physarum polycephalum in the plasmodium state under different environmental conditions, and used single-nucleus RNA-sequencing to dissect gene expression heterogeneity among nuclei. Our data identifies transcriptome regionality in the organism that associates with proliferation, syncytial substructures, and localized environmental conditions. Further, we find that nuclei are heterogenous in their transcriptional profile, and may process local signals within the plasmodium to coordinate cell growth, metabolism, and reproduction. To understand how nuclei variation within the syncytium compares to heterogeneity in single-nucleated cells, we analyzed states in single Physarum amoebal cells. We observed amoebal cell states at different stages of mitosis and meiosis, and identified cytokinetic features that are specific to nuclei divisions within the syncytium. Notably, we do not find evidence for predefined transcriptomic states in the amoebae that are observed in the syncytium. Our data shows that a single-celled slime mold can control its gene expression in a region-specific manner while lacking cellular compartmentalization, and suggests that nuclei are mobile processors facilitating local specialized functions. More broadly, slime molds offer the extraordinary opportunity to explore how organisms can evolve regulatory mechanisms to divide labor, specialize, balance competition with cooperation, and perform other foundational principles that govern the logic of life.

cell biology↗

bioRxiv2018

Quantitative insights into the cyanobacterial cell economy

Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological adaptations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial adaptations to different growth rates have implications to understand and optimize photosynthetic productivity.

microbiology↗

bioRxiv2017

A minimal model of protein allocation during phototrophic growth

Photoautotrophic growth depends upon an optimal allocation of finite cellular resources to diverse intracellular processes. Commitment of a certain mass fraction of the proteome to a specific cellular function, typically reduces the proteome available for other cellular functions. Here, we develop a minimal semi-quantitative kinetic model of cyanobacterial phototrophic growth to describe such trade-offs of cellular protein allocation. The model is based on coarse-grained descriptions of key cellular processes, in particular carbon uptake, metabolism, photosynthesis, and protein translation. The model is parametrized using literature data and experimentally obtained growth curves. Of particular interest are the resulting cyanobacterial growth laws as fundamental characteristics of cellular growth. We show that the model gives rise to similar growth laws as observed for heterotrophic organisms, with several important differences due to the distinction between light energy and carbon uptake. We discuss recent experimental data supporting the model results and show that minimal growth models have implications for our understanding of the limits of phototrophic growth and bridge a gap between molecular physiology and ecology.

systems biology↗