Biology subjects

Stevani, C. V.

Publications and source records attributed to Stevani, C. V..

3 recordsLinked to original sources

bioRxiv2025

Microbial diversity of Atlantic Rainforest ponds assessed by nanopore sequencing

Despite their limited size, ponds are ecologically important habitats that harbor rich microbial communities and play key roles in global biodiversity and biogeochemical cycling. In this study, we conducted a metagenomic survey of microbial diversity in three ponds - Vermelha, Grande, and Furnas - situated within the Atlantic Rainforest biome in Brazil. Vermelha and Grande are natural, remote, and minimally impacted by human activity, whereas Furnas is an artificial pond with greater human accessibility. Using a long-read nanopore shotgun metagenomics approach, we sequenced DNA extracted from pond water, assembled metagenomes, and performed taxonomic classification and functional annotation. Furthermore, 21 metagenome-assembled genomes (MAGs) were recovered. Our results reveal striking biodiversity contained within ponds, with pond-specific microbial community structures and functional profiles. In addition to bacterial communities, some dsDNA bacteriophages and eukaryotic viruses were also detected. Functional annotation identified putative antimicrobial resistance genes (ARGs), most of them in Furnas, potentially reflecting human impact. Cyanotoxin biosynthesis genes were detected as well, predominantly in Vermelha. Our findings underscore the ecological distinctiveness of each pond and demonstrate the utility of nanopore-based metagenomics for investigating microbial biodiversity in understudied freshwater ecosystems, with implications for conservation and biotechnological exploration. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=126 SRC="FIGDIR/small/660208v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1941bd9org.highwire.dtl.DTLVardef@b06d66org.highwire.dtl.DTLVardef@de6df3org.highwire.dtl.DTLVardef@1048bbd_HPS_FORMAT_FIGEXP M_FIG Through nanopore metagenomic sequencing, this work uncovered the microbiome of the 3 analysed freshwater ponds of the Brazilian Atlantic Forest. Results include the taxonomic profile present in each sample, countless genes identified and 21 MAGs recovered. C_FIG

bioinformatics↗

bioRxiv2024

Velamins: the first green-light emitting class of wild-type Ca2+-regulated photoproteins isolated from the ctenophore Velamen parallelum

Ca2+-regulated photoproteins (CaPhs) consist of single-chain globular proteins to which coelenterazine, a widely distributed marine luminogenic substrate (the luciferin), binds along with molecular oxygen, producing a stable peroxide. Upon Ca2+ addition, CaPhs undergo conformational changes leading to the cyclization of the peroxide and the formation of a high-energy intermediate. Subsequently, its decomposition yields coelenteramide in an excited state and results in the emission of a flash of light. To date, all CaPhs reported produce blue light ({lambda}max 465-495 nm). Here, we report the cloning and functional characterization of a novel class of wild-type CaPhs capable of emitting green light: velamins, isolated from the bioluminescent ctenophore Velamen parallelum. Ten unique photoprotein-like sequences were recovered and grouped in three main clusters. Representative sequences were cloned, expressed, purified, and regenerated into the active His-tagged -, {beta}-, and {gamma}-velamins. Upon injection of a calcium-containing buffer into the velamin, a flash of green light ({lambda}max 500-508 nm) was observed across pH values ranging from 7 to 9. Whilst -velamin isoforms exhibited the highest light emission activity, {beta}- and {gamma}-velamins were found to be more thermostable at higher temperatures. Velamins are the only known wild-type Ca2+-regulated photoproteins that exhibit the longest wavelength in light emission, making them a promising model for studying spectral modulation. As a result, velamins hold potential for enhancing the sensitivity of signal detection in analytical systems, particularly when dealing with complex biological matrices.

biochemistry↗

bioRxiv2020

L-DOPA dioxygenase of the fly agaric toadstool: revision of the dodA gene sequence and mechanism of enzymatic pigment production

O_SCPLOWLC_SCPLOW-DOPA extradiol dioxygenases (DODAs) catalyze the production of betalains and hygroaurins pigments. The sequence of the DODAs found in Caryophyllales and Basidiomycetes are not conserved, although betalains are produced both by plants and fungi. Here we revise the coding region of the dodA gene of fly agaric [Amanita muscaria (L.) Lam.] and describe an alternative start codon downstream that enables the heterologous expression of AmDODA, a promiscuous O_SCPLOWLC_SCPLOW-DOPA dioxygenase. AmDODA is 43-amino acid residues shorter than the recombinant DODA previously reported but catalyzes the formation of two isomeric seco-DOPAs that are the biosynthetic precursors of betalains and hygroaurins. The putative active site of AmDODA contains two distinct His-His-Glu motifs that can explain the dual cleavage of O_SCPLOWLC_SCPLOW-DOPA according to the mechanism proposed for non-heme iron-dependent dioxygenases. Upon addition of excess O_SCPLOWLC_SCPLOW-DOPA, both the betaxanthin and hygroaurin adducts of O_SCPLOWLC_SCPLOW-DOPA are produced. The kinetic parameters of enzymatic catalysis at pH 8.5 are similar to those reported for other O_SCPLOWLC_SCPLOW-DOPA dioxygenases. The rate constants for the conversion of O_SCPLOWLC_SCPLOW-DOPA into the betalamic acid and muscaflavin were estimated by kinetic modelling allowing the proposal of a mechanism of pigment formation. These results contribute to understanding the biosynthesis of bacterial, fungal and plant pigments, for the biotechnological production of hygroaurins, and for the development of more promiscuous dioxygenases for environmental remediation.

biochemistry↗