Biology subjects

Pereiro, E.

Publications and source records attributed to Pereiro, E..

8 recordsLinked to original sources

bioRxiv2025

Intracellular amorphous calcium carbonate biomineralization in methanotrophic gammaproteobacteria was acquired by horizontal gene transfer from cyanobacteria

Some bacteria genetically control the biomineralization of intracellular amorphous calcium carbonates (iACC) with potential implications for microbial physiology, evolution, bioremediation and biogeochemical cycling. Until now, this capacity has been documented in Cyanobacteria, the giant gammaproteobacterium Achromatium and a few magnetotactic Pseudomonadota and Nitrospirota. Here, we report the discovery of iACC biomineralization in members of the Methylococcaceae, a family of aerobic methanotrophic Gammaproteobacteria. A homolog of the ccyA gene, previously considered a diagnostic marker for iACC formation in Cyanobacteria, was identified in several Methylococcaceae genomes, based on a search of the conserved C-terminal (GlyZip)3 domain of the encoded calcyanin protein, with a sequence coverage higher than 60% and an E-value lower than 1e-20. Moreover, two cultivated strains, Methylococcus geothermalis and Methylococcus mesophilus, whose genomes contained the ccyA gene, were consistently shown to form iACC granules. The ccyA genes of Methylococcaceae and Microcystis share higher sequence similarity (47%) than with other Cyanobacteria (around 30%) within their common (GlyZip)3 domain, suggesting horizontal gene transfer (HGT) from an ancestral Microcystis-like cyanobacterium to Methylococcaceae. This finding extends the known taxonomic distribution of ccyA and suggests that the capability to biomineralize iACC was acquired by HGT, possibly in environments such as those close to the oxyclines of lakes, where Cyanobacteria and Methylococcaceae commonly co-exist. The discovery of iACC in methane-oxidizing Methylococcaceae highlights a previously unrecognized coupling between calcium carbonate biomineralization and methane cycling in aquatic environments, suggesting that iACC formation may play an overlooked role in microbial carbon storage and local geochemical regulation.

microbiology↗

bioRxiv2025

Bridging the resolution gap in cryo-CLEM by introducing cryo-SXT: cryo-CLXEM

Cryo-imaging in cellular biology provides the means to visualize the cellular interieur at close-to-native conditions. A cornerstone in the field has been cryo-correlative light and electron microscopy (cryo-CLEM), with cryo-visible light fluorescent microscopy (cryo-VLFM) providing the specificity by tagging macromolecules or structures and cryo-electron tomography (cryo-ET) for the structural details at molecular level. The large resolution gap between these techniques, however, is limiting this correlative workflow as cryo-ET targets are often smaller than the resolution limit of cryo-VLFM. Here we introduce cryo-soft X-ray tomography (cryo-SXT) as an intermediate step that can compensate for the partial view and limited resolution of cryo-VLFM by providing invaluable cellular context information in 3D to the cryo-ET dataset within an integrated workflow.

cell biology↗

bioRxiv2025

Multiple Xpa In vivo crystallization routes in HEK 293 human cells

Phase changes of macromolecules in living cells gained recently a major interest in cell biology as liquid liquid phase separation or liquid solid phase transition phenomenon being observed in increasing number of biological or pathological processes. Comprehensive characterization of these phases remains challenging and requires new methodological approaches for their complete description across spatial and temporal scales. We propose a combination of imaging methods applied to a model system and report the in vivo crystallization pathways of a macromolecule from its solution to crystalline states at the cell population level down to the meso scale. Combining various live fluorescence based techniques and a high resolution cryo imaging technique within unaltered cryopreserved cells, we could described the unexpectedly wide landscape of the in vivo crystalline states of the fluorescent coral derived protein xpa, gain information of crystal growth dynamics in cellulo, and provide hypothesis of the crystal nucleation requirements of this stochastic process.

biophysics↗

bioRxiv2023

Progression of herpesvirus infection remodels mitochondrial organization and metabolism

Viruses target mitochondria to promote their replication, and infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteracting viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Here we show extensive transcriptional remodeling of protein-encoding host genes involved in the respiratory chain, apoptosis, and structural organization of mitochondria as herpes simplex virus type 1 lytic infection proceeds from early to late stages of infection. High-resolution microscopy and interaction analyses unveiled infection-induced emergence of rough, thin, and elongated mitochondria relocalized at the perinuclear area, a significant increase in the number and clustering of ER-mitochondria contact sites, and thickening and shortening of mitochondrial cristae. Finally, metabolic analyses demonstrated that reactivation of ATP production is accompanied by increased mitochondrial Ca2+ content and proton leakage as the infection proceeds. Overall, the significant structural and functional changes in the mitochondria triggered by the viral invasion are tightly connected to the progression of the virus infection.

microbiology↗

bioRxiv2021

Cryo soft X-ray tomography to explore Escherichia coli nucleoid remodelling by Hfq master regulator

Bacterial chromosomic DNA is packed within a membrane-less structure, the nucleoid, thanks to proteins called Nucleoid Associated Proteins (NAPs). The NAP composition of the nucleoid varies during the bacterial life cycle and is growth phase-dependent. Among these NAPs, Hfq is one of the most intriguing as it plays both direct and indirect roles on DNA structure. Indeed, Hfq is best known to mediate post-transcriptional regulation by using small noncoding RNA (sRNA). Although Hfq presence in the nucleoid has been demonstrated for years, its precise role is still unclear. Recently, it has been shown in vitro that Hfq belongs to the bridging family of NAPs. Its bridging mechanism relies on the formation of the amyloid-like structure of Hfq C-terminal region. Here, using cryo soft X-ray tomography imaging of native unlabelled cells and using a semi-automatic analysis and segmentation procedure, we show that Hfq significantly remodels the Escherichia coli nucleoid, especially during the stationary growth phase. Hfq influences both nucleoid volume and absorbance. Hfq cumulates direct effects and indirect effects due to sRNA-based regulation of other NAPs. Taken together, our findings reveal a new role for this protein in nucleoid remodelling that may serve in response to stress conditions and in adapting to changing environments. This implies that Hfq regulates nucleoid compaction directly via its interaction with DNA, but also at the post-transcriptional level via its interaction with RNA.

microbiology↗

bioRxiv2020

Cellular pathways of calcium transport and concentration towards mineral formation in sea urchin larvae

Sea urchin larvae have an endoskeleton consisting of two calcitic spicules. The primary mesenchyme cells (PMCs) are the cells that are responsible for spicule formation. PMCs endocytose sea water from the larval internal body cavity into a network of vacuoles and vesicles, where calcium ions are concentrated until they precipitate in the form of amorphous calcium carbonate (ACC). The mineral is subsequently transferred to the syncytium, where the spicule forms. Using cryo-soft X-ray microscopy (cryo-SXM) we imaged intra-cellular calcium-containing particles in the PMCs and acquired Ca-L2,3 X-ray absorption near edge spectra (XANES) of these Ca-particles. Using the pre-peak/main peak (L2/ L2) intensity ratio, which reflects the atomic order in the first Ca coordination shell, we determined the state of the calcium ions in each particle. The concentration of Ca in each of the particles was also determined by the integrated area in the main Ca absorption peak. We observed about 700 Ca-particles with order parameters, L2/ L2, ranging from solution to hydrated and anhydrous ACC, and with concentrations ranging between 1-15 M. We conclude that in each cell the calcium ions exist in a continuum of states. This implies that most, but not all water, is expelled from the particles. This cellular process of calcium concentration may represent a widespread pathway in mineralizing organisms. SignificanceOrganisms form mineralized skeletons, many of which are composed of calcium salts. Marine organisms extract calcium ions from sea water. One of the main unresolved issues is how organisms concentrate calcium by more than 3 orders of magnitude, to achieve mineral deposition in their skeleton. Here we determine the calcium state in each of the calcium-containing vesicles inside the spicule-building cells of sea urchin larvae. We show that within one cell there is a wide range of concentrations and states from solution to solid. We hypothesize that calcium concentration increases gradually in each vesicle, starting from sea water levels and until mineral is deposited. This model might well be relevant to other phyla, thus advancing the understanding of biomineralization processes.

biophysics↗

bioRxiv2020

Four-dimensional characterization of the Babesia divergens asexual life cycle: from the trophozoite to the multiparasite stage

Babesia is an apicomplexan parasite of significance that causes the disease known as babesiosis in domestic and wild animals and in humans worldwide. Babesia infects vertebrate hosts and reproduces asexually by a form of binary fission within erythrocytes/red blood cells (RBCs), yielding a complex pleomorphic population of intraerythrocytic parasites. Seven of them, clearly visible in human RBCs infected with Babesia divergens, are considered the main forms and named single, double and quadruple trophozoites, paired and double paired-pyriforms, tetrad or Maltese Cross, and multiparasite stage. However, these main intraerythrocytic forms coexist with RBCs infected with transient parasite combinations of unclear origin and development. In fact, little is understood about how Babesia builds this complex population during its asexual life cycle. By combining the emerging technique cryo soft X-ray tomography and video microscopy, main and transitory parasites were characterized in a native whole cellular context and at nanometric resolution. As a result, the architecture and kinetic of the parasite population has been elucidated. Importantly, the process of multiplication by binary fission, involving budding, was visualized in live parasites for the first time, revealing that fundamental changes in cell shape and continuous rounds of multiplication occur as the parasites go through their asexual multiplication cycle. Based on these observations, a four-dimensional (4D) asexual life cycle model has been designed highlighting the origin of the tetrad, double paired-pyriform and multiparasite stages and the transient morphological forms that, surprisingly, intersperse in a chronological order between one main stage and the next along the cycle. IMPORTANCEBabesiosis is a disease caused by intraerythrocytic Babesia parasites, which possess many clinical features that are similar to those of malaria. This worldwide disease, is increasing in frequency and geographical range, and has a significant impact on human and animal health. Babesia divergens is one of the species responsible for human and cattle babesiosis causing death unless treated promptly. When B. divergens infects its vertebrate hosts it reproduces asexually within red blood cells. During its asexual life cycle, B. divergens builds a population of numerous intraerythrocytic (IE) parasites of difficult interpretation. This complex population is largely unexplored, and we have therefore combined three and four dimensional (3D and 4D) imaging techniques to elucidate the origin, architecture, and kinetic of IE parasites. Unveil the nature of these parasites have provided a vision of the B. divergens asexual cycle in unprecedented detail and a key step to develop control strategies against babesiosis

microbiology↗

bioRxiv2020

Downregulation of the essential Rrp44 ribonuclease causes extensive ultra-structure cell modifications in Trypanosoma brucei

Rrp44/Dis3 is an essential protein conserved in all eukaryotes that functions in the maturation of many different RNA precursors and RNA surveillance. The Trypanosoma brucei Rrp44/Dis3 homologue (TbRRP44) is required for maturation of pre-rRNA, spliced leader, and U3 snoRNA precursors. Its depletion leads to inhibition of cell proliferation and eventually to cell death. In this work, we showed that TbRRP44 depletion causes a massive expansion of acidic and lysosome-derived vacuoles, enlargement of cell and nuclei sizes without changes in DNA content, mitochondrial inactivation, and autophagy induction. Consistently, 3D reconstructions using cryo-soft X-ray tomography revealed extreme vacuolation of the cytoplasm and numerous cellular alterations, including an increase in size and number of calcium-containing vesicles and lipid droplets. These multiple defects indicate that a combination of alterations converge to induce lysosome expansion. With time, the cytoplasm is taken up by lysosome-derived vacuoles, which may be a final stage leading to the cell death triggered by TbRRP44 depletion. These studies provide the first evidence on the ultra-structure cell modifications caused by deficiency of this essential ribonuclease in T. brucei.

cell biology↗