Search bioRxiv⌕ Search

Biology subjects

Benvenuto, G.

Publications and source records attributed to Benvenuto, G..

6 recordsLinked to original sources

The first photosynthetic mutant in diatoms targets the subunit γ of plastidial ATP synthase and reveals a key role of thylakoid electrochemical proton gradient in photosynthesis regulation and heterotrophic metabolism.

Diatoms are major phytoplanktonic algae with secondary endosymbiotic plastids that differ in cellular and regulatory traits from those of the green lineage. Here we exploited the heterotrophic growth ability of Cyclotella cryptica to create the first diatom photosynthetic mutant by CRISPR-Cas inactivation of the nucleus-encoded ATP synthase subunit {gamma}. These mutants showed impaired phototrophic capacity and altered thylakoids morphology. In absence of {gamma}-ATP, protons that accumulate in the thylakoid lumen slow down the cytochrome b6f complex, thus keeping the electron carriers downhill oxidized. These results, reversible when the proton gradient is suppressed, demonstrate the existence of a photosynthetic control in diatoms. At variance with the wild type, {gamma} ATP synthase mutants cannot grow heterotrophically in darkness nor in the light when photosystem II is inhibited. This requirement of heterotrophic growth on photosynthetic electron transfer or on the presence of plastidial ATP synthase suggests that the proton motive force (pmf) is a central integrator of the metabolic interaction between photosynthesis and heterotrophy. Our results establish C. crytica as a robust model for analysis of photosynthetic function, regulation and metabolic integration in organisms with secondary plastids. TeaserMutagenesis in the facultative autotroph diatom Cyclotella cryptica enables exploration of essential plastid functions in diatoms

plant biology↗

Single Nucleus Profiling Highlights the All-Brain Echinoderm Nervous System

Metazoans comprise diverse tissues and cell types, each essential for the survival of the organism. Most of these cell types are established early in embryogenesis and persist into adulthood. However, in indirectly developing sea urchins, the continuity between embryonic and adult stages is thus interrupted by a planktonic larval stage that undergoes complete metamorphosis. In addition, while the gene regulatory networks governing distinct embryonic and larval cell lineages are well studied, the molecular and morphological identities of post-metamorphic sea urchin cell types remain poorly understood. Here, we reconstructed the cell type atlas of post-metamorphic Paracentrotus lividus juveniles using single-nucleus transcriptomics, shedding light on the conservation of genetic regulatory mechanisms in post-metamorphic cell types. We identified cell signatures corresponding to eight distinct cell type groups and analyzed at least twenty-nine neuronal cell families, including fifteen unique photoreceptor cell signatures. By combining single cell transcriptomics with spatial gene expression analysis and high-resolution electron microscopy, we identified homologues of vertebrate neuronal genes and photoreceptive opsins expressed throughout the sea urchin body. These findings provide evidence that the echinoderm body plan is not only predominantly head-like, but also exhibits an all-brain organization in an animal previously considered to have a primitive nervous system.

evolutionary biology↗

Evolution of the ribbon-like organization of the Golgi apparatus in animal cells

The Golgi ribbon is a structural organization formed by linked Golgi stacks that is believed to be exclusive to vertebrate cells. Its functional contribution to cellular processes is unclear, yet its disruption is associated with several human pathologies. In this study we address the evolutionary origin of the Golgi ribbon, describe a potential molecular mechanism for its emergence and identify a cellular process in which it may be involved. We observed the ribbon-like architecture in the cells of several metazoan taxa, suggesting its early appearance during animal evolution before the emergence of vertebrates. Supported by AlphaFold2 modelling, we propose that the evolution of the complex between two Golgi resident proteins, Golgin-45 and GRASP, led to the tethering of Golgi stacks into the ribbon-like configuration. Finally, we find that the ribbon is assembled during the early embryogenesis of deuterostome animals, a strong indication of its role in development. Overall, our study indicates that the Golgi ribbon is functionally relevant beyond vertebrates and calls for further investigations to decipher its elusive functions. O_FIG O_LINKSMALLFIG WIDTH=89 HEIGHT=200 SRC="FIGDIR/small/528797v2_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@17a404forg.highwire.dtl.DTLVardef@11413b4org.highwire.dtl.DTLVardef@119c036org.highwire.dtl.DTLVardef@19a512f_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

cell biology↗

The ribbon architecture of the Golgi apparatus is not restricted to vertebrates

The Golgi apparatus plays a central role as a processing and sorting station along the secretory pathway. In multicellular organisms, this organelle displays two structural organizations, whereby its functional subunits, the mini-stacks, are either dispersed throughout the cell or linked into a centralized structure, called Golgi "ribbon". The Golgi ribbon is considered to be a feature typical of vertebrate cells. Here we report that this is not the case. We show that sea urchin embryonic cells assemble Golgi ribbons during early development. Sea urchins are deuterostomes, the bilaterian animal clade to which chordates, and thus vertebrates, also belong. Far from being a structural innovation of vertebrates, the Golgi ribbon therefore appears to be an ancient cellular feature evolved before the split between echinoderms and chordates. Evolutionary conservation of the ribbon architecture surmises that it must play fundamental roles in the biology of deuterostomes.

cell biology↗

Molecular diagnosis and prognosis of cancers of unknown-primary (CUPs): progress from a microRNA-based droplet digital PCR assay

Metastasis is responsible for the majority of cancer-related deaths. Particularly challenging is the management of metastatic cancer of unknown primary site (CUP), whose tissue-of-origin (TOO) remains undetermined even after expensive investigations. CUP therapy is rather unspecific and poorly effective. Molecular approaches developed to identify CUPs potential tissue-of-origin, can overcome some of these issues. In this study, we applied a pre-determined set of microRNAs (miRNAs) to infer the TOO of 53 metastatic cancers of unknown or uncertain origin. We designed a molecular assay to quantify 89 miRNAs at the copy number level, using EvaGreen-based Droplet Digital PCR. We assessed miRNA expression in 159 samples including primary tumors from 17 tumor classes (reference set), metastases of known and unknown origin. We applied two different statistical models for class prediction to obtain CUPs most probable TOOs. Specifically, we used the shrunken centroids using PAMR (Prediction Analysis of Microarrays for R) and the least absolute shrinkage and selection operator (LASSO) models. The molecular test was successfully applied to FFPE samples and provided a site-of-origin identification within one-week from the biopsy procedure. The most frequently predicted origins were gastrointestinal, pancreas, breast and lung. The assay was applied to multiple metastases from the same CUP, collected from different metastatic sites: the molecular prediction revealed an impressive agreement in site-of-origin prediction, intrinsically validating our assay. The final prediction was compared with the clinico-pathological hypothesis of primary site. Moreover, a panel of 14 miRNAs proved to have prognostic value and being associated with overall survival. Our study demonstrated that miRNA expression profiling in CUP samples could be employed as diagnostic and prognostic test. Our molecular analysis can be performed on-request, concomitantly with standard diagnostic workup and in association with genetic profiling, to offer valuable indication about the possible primary site, thereby supporting treatment decisions.

pathology↗

Post-metamorphic skeletal growth in the sea urchin Paracentrotus lividus and implications for body plan evolution

Understanding the molecular and cellular processes that underpin animal development are crucial for understanding the diversity of body plans found on the planet today. Because of their abundance in the fossil record, and tractability as a model system in the lab, skeletons provide an ideal experimental model to understand the origins of animal diversity. We herein use molecular and cellular markers to understand the growth and development of the juvenile sea urchin (echinoid) skeleton. We developed a detailed staging scheme based off of the first [~]four weeks of post-metamorphic life of the regular echinoid Paracentrotus lividus. We paired this scheme with immunohistochemical staining for neuronal, muscular, and skeletal tissues, and fluorescent assays of skeletal growth and cell proliferation to understand the molecular and cellular mechanisms underlying skeletal growth and development of the sea urchin body plan. Our experiments highlight the role of skeletogenic proteins in accretionary skeletal growth and cell proliferation in the addition of new metameric tissues. Furthermore, our work provides a framework for understanding the developmental evolution of sea urchin body plans on macroevolutionary timescales.

developmental biology↗