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Oliveira, C. C.

Publications and source records attributed to Oliveira, C. C..

8 recordsLinked to original sources
bioRxiv2026

Identification and functional characterization of novel murine DIS3L2 isoforms

RNases are key factors for the posttranscriptional control of gene expression due to their involvement in processing, degradation and quality control of all classes of RNA in eukaryotes. DIS3L2 is an evolutionarily conserved exoribonuclease involved in cytoplasmic RNA degradation pathways that regulate gene expression. Macrophages undergo great change in gene expression of specific genes that allow these cells to perform multiple functions in addition to defense against infection. Here, we analyzed the change in expression of macrophages genes in response to Leishmania major infection, and show evidence that the levels of RNases such as the RNA exosome, XRN1, and DIS3L2, are modulated by the infection. We then identified three DIS3L2 variants that are differentially expressed in murine macrophages and other cell lines. DIS3L2 isoforms show similar RNA binding affinity, but differences in exonucleolytic activity in in vitro assays. Furthermore, we characterized the interactome of the DIS3L2 variants, which shows similarities with respect to ribosomal proteins, but differences that hint at specific functions for each isoform. This work uncovers previously uncharacterized DIS3L2 isoforms that are active, whose functions have yet to be identified.

molecular biology↗
bioRxiv2026

Phosphorylation patterns of pre-ribosomal proteins associated with the RNA exosome

The RNA exosome is an essential and ubiquitous RNase with exonucleolytic activity, involved in ribosome biogenesis and RNA quality control in eukaryotes. It is present both in nucleus and cytoplasm, and interacts with specific cofactors in each cell compartment, which are essential for recruitment and activity control of the exosome. Posttranslational modifications are known to regulate enzyme activity and protein interaction, although their precise roles are individually specific. In this study, we investigated the phosphorylation status of proteins associated with the nuclear (Rrp6) and core (Rrp46) subunits of the RNA exosome in Saccharomyces cerevisiae. Using co-immunoprecipitation followed by phosphopeptide enrichment and high-resolution mass spectrometry, we identified 121 phosphorylation sites on proteins functionally related to rRNA processing. Differential phosphorylation patterns between Rrp6 and Rrp46 co-immunoprecipitations are consistent with distinct exosome assemblies and suggest potential regulatory roles for phosphorylation. The results shown here highlight the role of phosphorylation in the recruitment and control of the exosome in RNA processing and degradation, offering new insights into the posttranscriptional control of gene expression.

molecular biology↗
bioRxiv2025

UDP-glucose Activation of a G-protein/Sucrose Synthase Signaling Supercomplex

Arabidopsis thaliana REGULATOR OF G PROTEIN SIGNALING 1 (AtRGS1, hereafter, RGS1) within the heterotrimeric G protein complex plays a role in sensing extracellular signals. High millimolar concentrations of some sugars induce RGS1 endocytosis and therefore G protein activation. However, this is not likely a direct, rather an indirect effect through a sugar metabolite. One metabolite at the plasma membrane where RGS1 resides is UDP-glucose (UDPG) produced by SUCROSE SYNTHASE (SUS) enzymes, previously shown to interact with RGS1. Our direct measurements indicate that the Kd for UDPG binding to RGS1 (2.4 {micro}M) is consistent with UDPG activation of RGS1 with an EC50 of 17 {micro}M to rapidly trigger G protein activation within minutes. RGS1 associates directly with SUS1 and SUS4, exhibiting affinities (Kd = 161 nM and 106 nM, respectively) that are markedly tighter than the corresponding Km values for UDPG formation (40 {micro}M and 70 {micro}M, respectively). Therefore, SUS may be one source for this RGS1 ligand in a manner analogous to "metabolite funneling" in enzymology. UDPG induces rapid phosphorylation of RGS1 at the C-terminal phosphorylation cluster, a site previously implicated in RGS1 endocytosis and G protein activation. UDPG activation of RGS1 changes the global transcript profiles in various processes, largely involving plant defense. These results provide the first molecular evidence for UDPG as a newly recognized low-molecular weight signal controlling key aspects of plant physiology.

plant biology↗
bioRxiv2025

New Insights into nuclear import and nucleolar localization of yeast RNA exosome subunits

The RNA exosome is a multiprotein complex essential for RNA maturation and degradation. In budding yeast, a nine-subunit protein complex (Exo9) associated with Rrp44 forms Exo10 in the cytoplasm and, in complex with Rrp6, Exo11 in the nucleus. Depending on its subcellular localization, the exosome interacts with different cofactors and RNA substrates. In the cytoplasm, Exo10 associates with the SKI complex via Ski7, while in the nucleus, Exo11 interacts with the TRAMP complex. Within the nucleolus, the exosome participates in ribosomal RNA (rRNA) processing, facilitated by Mtr4-dependent adaptors Utp18 and Nop53. In this manuscript, we have performed a comprehensive study that addresses the targeting mechanism and precise subcellular localization of all members of the Exo11 complex. We observed a high concentration of all Exo11 subunits in the nucleolus and identified the importins Srp1 () and Kap95 ({beta}) as responsible for the nuclear import of Exo9 subunits. Notably, Exo9 subunits localization was not significantly disrupted in the simultaneous absence of NLS-containing subunits Rrp6 and Rrp44, suggesting redundant nuclear import pathways for Exo9. Additionally, we show evidence that Ski7 may play a role in the Exo9 retention in the cytoplasm. To explore the exosome sub-nucleolar localization, we compared Rrp43 with nuclear exosome cofactors and show that it is enriched in the same nucleolar region as Mtr4 and Nop53. In conclusion, our findings provide a detailed characterization of Exo11 distribution, highlight the primary nuclear import mechanisms for Exo9, and reveal the specific localization of the exosome within the granular component (GC) of the yeast nucleolus, suggesting a spatial regulation of the RNA processing pathway. Highlights- Comprehensive study of the localization of all exosome subunits in yeast. - Identification of karyopherins involved in exosome nuclear import. - Ski7 dependent cytoplasmic retention of exosome. - Yeast sub-nucleolar organization of exosome and its cofactors.

molecular biology↗
bioRxiv2024

Characterization and Functional Assessment of Epicardial Secretome: Epicardium-Derived Extracellular Vesicles and Matrix

AimThe epicardium, an epithelial layer covering the heart, plays pivotal roles in embryonic heart development and responses to cardiac damage. Epicardial secreted molecular agents are known to be involved in the regulation of these phenomena, but how this regulation occurs is poorly understood. In this study, we have investigated extracellular vesicle (EV) and extracellular matrix (ECM) components of epicardial secretions using a continuous mouse embryonic epicardial-derived cell (EPIC) line. Methods and resultsEpicardial-derived EVs were isolated using differential ultracentrifugation from EPIC cultured at 1% (EVs-H1%), 5% (EVs-H5%), and 21% oxygen (EVs-N). EVs protein content was determined by tandem mass tag (TMT) proteomic analysis. The results showed that epicardial-derived EVs cargo is sensitive to the oxygen level of their parenteral cells, increasing their content on glycolytic proteins. Moreover, hypoxic-derived EVs were found to both increase EPIC proliferation and affect the metabolism of Primary Human Umbilical Vein Endothelial Cells (HUVECs). On the other hand, epicardial-derived extracellular matrix (EPIC-ECM) was characterized by subjecting decellularized EPIC to shotgun proteomics and comparing it to decellularized perinatal hearts and Matrigel(R). We found that EPIC-ECM composition closely resembles that of embryonic cardiac tissue. Although the structural and basement membrane-associated proteins of EPIC-ECM were similar to those found in Matrigel(R)(R), EPIC-ECM exhibited higher protein diversity and was a more potent inducer of HUVEC proliferation. ConclusionThis work represents the first comprehensive and systematic proteomic analysis of two important components of the epicardial-derived secretome. Our experiments reveal that the epicardium responds to hypoxia by secreting EVs capable of modifying the metabolic responses of surrounding cells. Furthermore, EPIC-ECM promotes endothelial cell proliferation. These findings demonstrate the significant signaling abilities of the epicardial secretome, consistent with reports of endothelial responses following cardiac ischemic damage.

developmental biology↗
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↗
bioRxiv2018

Therapeutic blockade of Activin-A improves NK cell function and anti-tumor immunity

Natural killer (NK) cells are innate lymphocytes that play a major role in immunosurveillance against tumor initiation and metastasis spread. Signals and checkpoints that regulate NK cell fitness and function in the tumor microenvironment are not well defined. Transforming grow factor (TGF)-{beta} is a recognized suppressor of NK cells that inhibits IL-15 dependent signaling events and induces cellular transdifferentiation, however the role of other SMAD signaling pathways in NK cells is unknown. In this report, we show that NK cells express the type I Activin receptor, ALK4, which upon binding its ligand Activin-A, phosphorylates SMAD2/3 to efficiently suppress IL-15-mediated NK cell metabolism. Activin-A impairs human and mouse NK cell proliferation and downregulates intracellular granzyme B levels to impair tumor killing. Similar to TGF-{beta}, Activin-A also induced SMAD2/3 phosphorylation and drove NK cells to upregulate several ILC1-like surface markers including CD69, TRAIL and CD49a. Activin-A also induced these changes on TGF-{beta} receptor deficient NK cells, highlighting that Activin-A and TGF-{beta} are independent pathways that drive SMAD2/3-mediated NK cell suppression. Finally, therapeutic inhibition of Activin-A by Follistatin significantly slowed orthotopic melanoma growth in mice. These data highlight independent SMAD2/3 pathways target NK cell fitness and function and identify a novel therapeutic axis to promote tumor immunity.\n\nOne Sentence Summary: Activin-A can directly inhibit NK cell effector functions, promote NK cells transdifferentiation into ILC1-like cells and suppress anti-melanoma immunity.

immunology↗