Biology subjects

Rossi, J.

Publications and source records attributed to Rossi, J..

10 recordsLinked to original sources

bioRxiv2025

Retrotransposon-mediated duplication of SSU1 in high SO2 tolerant Brettanomyces bruxellensis winery isolates

Brettanomyces bruxellensis is an industrially relevant yeast and major spoilage organism in wine, where tolerance to sulphur dioxide (SO2), the primary preservative used for its control, varies between strains. To investigate the genetic basis of SO2 tolerance in winery populations, 26 isolates from Australian wineries were phenotypically characterised and sequenced using long-read technology. Isolates showed a wide range of SO2 tolerance that correlated with phylogenetic clade and ploidy. Haplotype phasing of SSU1, a sulphite efflux pump linked to SO2 tolerance, identified nine distinct haplotypes, including the previously described high-tolerance H1 allele. Highly tolerant strains carried duplications of H1, frequently associated with retrotransposon insertions and chromosomal rearrangements at the SSU1 locus. Comparative analyses with laboratory-evolved strains confirmed that retrotransposons facilitated the acquisition of additional SSU1 copies. These findings suggest that transposon-mediated structural variation drives adaptive increases in SO2 tolerance in B. bruxellensis populations.

microbiology↗

bioRxiv2025

Cryo-EM structures reveal the PP2A-B55α and Eya3 interaction that can be disrupted by a peptide inhibitor

We have previously shown that Eya3 recruits PP2A-B55 to dephosphorylate pT58 on Myc, increasing Myc stability and enhancing primary tumor growth of triple-negative breast cancer (TNBC). However, the molecular details of how Eya3 recruits PP2A-B55 remain unclear. Here we determined the cryo-EM structures of PP2A-B55 bound with Eya3, with an inhibitory peptide B55i, and in its unbound state. These studies demonstrate that Eya3 binds B55 through an extended peptide in the NTD of Eya3. The Eya3 peptide and other PP2A-B55 substrates and protein/peptide inhibitors including B55i bind to a similar area on the B55 surface but the molecular details of the binding differ. We further demonstrated that the B55i peptide inhibits the B55 and Eya3 interaction in vitro. B55i peptide expressed on a plasmid increases pT58 and decreases Myc protein level in TNBC cells, suggesting the potential of B55i or similar peptides as therapies for TNBC.

molecular biology↗

bioRxiv2025

Development of conditional-siRNA programmable riboswitch for targeting adverse cardiac remodeling

Heart Failure (HF) remains a global epidemic and a significant healthcare burden, with an unmet need for novel therapies to target the preceding pathological hypertrophy in vulnerable patients. Here we report the development of novel conditional-siRNA (Cond- siRNA) constructs that are selectively activated by disease-specific RNA biomarkers to enable cell-specific inhibition of a target disease-causing RNA. We designed a Cond- siRNA that can be activated by nppa mRNA, upregulated specifically in CMs under pathological stress, to silence the key pro-hypertrophic gene calcineurin by the effector siRNA. In cellular models including neonatal rat ventricular myocyte (NRVM) and rat cardiomyocyte cell-line (H9C2), Cond-siRNA exhibited low baseline activity in the absence of the disease biomarker but achieved targeted calcineurin silencing upon nppa mRNA induction by phenylephrine (PE)-induced stress in a two-dimensional (2D) cell culture system and pressure overload in three-dimensional (3D) heart-on a chip system. NRVM transfection with the Cond-siRNA resulted in a decreased expression of calcineurin mRNA specifically after PE or pressure-overload treatment, but not after vehicle treatment, proving nppa mRNA-specific activation of the effector siRNA against calcineurin. Specificity was confirmed as Cond-siRNA did not significantly silence calcineurin in cardiac fibroblasts and T cells, lacking nppa expression. Reduced calcineurin protein levels and NFATc1 nuclear translocation correlated with decreased NRVM hypertrophy after PE treatment, confirming Cond-siRNAs efficacy. This study offers proof-of-concept for Cond-siRNA as a targeted therapy to mitigate hypertrophic progression, paving the way for novel HF treatments. One sentence summaryConditional-siRNA targeting adverse cardiac remodeling GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/633434v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1b6532borg.highwire.dtl.DTLVardef@10e3836org.highwire.dtl.DTLVardef@8c839eorg.highwire.dtl.DTLVardef@1152883_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast

The recognition of 5 splice site (5 ss) is one of the earliest steps of pre-mRNA splicing. To better understand the mechanism and regulation of 5 ss recognition, we selectively humanized components of the yeast U1 snRNP to reveal the function of these components in 5 ss recognition and splicing. We targeted U1C and Luc7, two proteins that interact with and stabilize the yeast U1 (yU1) snRNA and the 5 ss RNA duplex. We replaced the Zinc-Finger (ZnF) domain of yU1C with its human counterpart, which resulted in cold-sensitive growth phenotype and moderate splicing defects. Next, we added an auxin-inducible degron to yLuc7 protein and found that Luc7-depleted yU1 snRNP resulted in the concomitant loss of PRP40 and Snu71 (two other essential yeast U1 snRNP proteins), and further biochemical analyses suggest a model of how these three proteins interact with each other in the U1 snRNP. The loss of these proteins resulted in a significant growth retardation accompanied by a global suppression of pre-mRNA splicing. The splicing suppression led to mitochondrial dysfunction as revealed by a release of Fe2+ into the growth medium and an induction of mitochondrial reactive oxygen species. Together, these observations indicate that the human U1C ZnF can substitute that of yeast, Luc7 is essential for the incorporation of the Luc7-Prp40-Snu71 trimer into yeast U1 snRNP, and splicing plays a major role in the regulation of mitochondria function in yeast.

biochemistry↗

bioRxiv2023

Chloroplasts lacking class I glutaredoxins are functional but show a delayed recovery of protein cysteinyl redox state after oxidative challenge

Redox status of protein cysteinyl residues is mediated via glutathione (GSH)/glutaredoxin (GRX) and thioredoxin (TRX)-dependent redox cascades. An oxidative challenge can induce post-translational protein modifications on thiols, such as protein S-glutathionylation. Class I GRX are small thiol-disulfide oxidoreductases that reversibly catalyse S-glutathionylation and protein disulfide formation. TRX and GSH/GRX redox systems can provide partial backup for each other in several subcellular compartments, but not in the plastid stroma where TRX/light-dependent redox regulation of primary metabolism takes place. While the stromal TRX system has been studied at detail, the role of class I GRX on plastid redox processes in vivo is still unknown. We generate knockout lines of GRXC5 as the only chloroplast class I GRX of the moss Physcomitrium patens. While we find that class I PpGRXC5 has high activities in glutathione-dependent oxidoreductase assays using hydroxyethyl disulfide or redox-sensitive GFP2 (roGFP2) as substrates in vitro, {Delta}grxc5 plants show no detectable growth defect or stress sensitivity, in contrast to mutants with a less negative stromal EGSH ({Delta}gr1). Using stroma-targeted roGFP2, we show increased protein Cys oxidation and decreased reduction rates after oxidative challenge in {Delta}grxc5 plants in vivo, indicating kinetic uncoupling of the protein Cys redox state from glutathione redox potential. Protein Cys disulfide and S-glutathionylation formation rates after H2O2 treatment remained unchanged. Lack of class I GRX function in the stroma did not result in impaired carbon fixation. Our observations suggest specific roles for class I GRX in the efficient redox equilibration between EGSH and protein Cys in the plastid stroma as well as negligible cross-talk with metabolic regulation via the TRX system. We propose a model for stromal class I GRX function as efficient kinetic couplers of protein Cys redox state to the dynamic stromal EGSH and highlight the importance of identifying in vivo target proteins of GRXC5. One sentence summaryRemoval of class I GRX activity in the chloroplast stroma of P. patens kinetically uncouples GRX-dependent cysteine redox changes from the local glutathione redox potential, without an effect on NPQ or photosynthetic carbon reactions.

plant biology↗

bioRxiv2023

Inhalation Delivered RNA Aptamer for Therapeutics against SARS-CoV2

The continual emergence and re-emergence of infectious diseases has led to a pressing need for the development of swift and targeted therapeutic interventions. SARS-CoV-2, the causative agent of COVID-19, is a prime example of such a rapidly spreading virus[1]. The global crisis caused by this virus has propelled researchers to explore and adopt novel techniques in the hopes of effectively combating its spread[2]. One such innovative approach is the use of aptamers--single-stranded RNA molecules that can bind targets with high specificity.

molecular biology↗

bioRxiv2022

Handedness is associated with less common input to spinal motor neurons innervating different hand muscles

Whether the neural control of manual behaviours differs between the dominant and non-dominant hand is poorly understood. This study aimed to determine whether the level of common synaptic input to motor neurons innervating the same or different muscles differs between the dominant and the non-dominant hand. Seventeen participants performed two motor tasks with distinct mechanical requirements: an isometric pinch and an isometric rotation of a pinched dial. Each task was performed at 30% of maximum effort and was repeated with the dominant and non-dominant hand. Motor units were identified from two intrinsic (flexor digitorum interosseous and thenar) and one extrinsic muscle (flexor digitorum superficialis) from high-density surface electromyography recordings. Two complementary approaches were used to estimate common synaptic inputs. First, we calculated the coherence between groups of motor neurons from the same and from different muscles. Then, we estimated the common input for all pairs of motor neurons by correlating the low-frequency oscillations of their discharge rate. Both analyses led to the same conclusion, indicating less common synaptic input between motor neurons innervating different muscles in the dominant hand than in the non-dominant hand, which was only observed during the isometric rotation task. No differences in common input were observed between motor neurons of the same muscle. This lower level of common input could confer higher flexibility in the recruitment of motor units, and therefore, in mechanical outputs. Whether this difference between the dominant and non-dominant arm is the cause or the consequence of handedness remains to be determined. Key points- How the neural control of manual behaviours differs between the dominant and non-dominant hand remains poorly understood. - We decoded the spiking activities of spinal motor neurons innervating one extrinsic and two intrinsic hand muscles during isometric tasks. - We estimated the common synaptic input to motor neurons innervating the same or different muscles. - There is less common synaptic input between motor neurons innervating different muscles in the dominant than in the non-dominant hand during isometric rotation tasks. - No differences in common input were observed between motor neurons of the same muscle. - Lower level of common input could confer higher flexibility in the recruitment of motor units.

neuroscience↗

bioRxiv2022

Structural snapshots of nitrosoglutathione binding and reactivity underlying S-nitrosylation of photosynthetic GAPDH

S-nitrosylation is a redox post-translational modification widely recognized to play an important role in cellular signaling as it can modulate protein function and conformation. At the physiological level, nitrosoglutathione (GSNO) is considered the major physiological NO-releasing compound due to its ability to transfer the NO moiety to protein thiols. GSNO can also induce protein S-glutathionylation but the structural determinants regulating its redox specificity are not fully elucidated. In this study, we employed photosynthetic glyceraldehyde-3-phosphate dehydrogenase from Chlamydomonas reinhardtii (CrGAPA) to investigate the molecular mechanisms underlying GSNO-dependent thiol oxidation. We first observed that GSNO causes enzyme inhibition by specifically inducing S-nitrosylation. Treatment with reducing agents restores CrGAPA activity completely. While the cofactor NADP+ only partially protects from GSNO-mediated S-nitrosylation, the resultant inactivation is completely blocked by the presence of the substrate 1,3-bisphosphoglycerate, indicating that the S-nitrosylation of the catalytic Cys149 is responsible of CrGAPA inactivation. The crystal structures of CrGAPA in complex with NADP+ and NAD+ reveal a general structural similarity with other photosynthetic GAPDH. Starting from the 3D structure, we carried out molecular dynamics simulations to identify the protein residues involved in GSNO binding. Quantum mechanical/molecular mechanical calculations were performed to investigate the reaction mechanism of GSNO with CrGAPA Cys149 and to disclose the relative contribution of protein residues in modulating the activation barrier of the trans-nitrosylation reaction. Based on our findings, we provide functional and structural insights into the response of CrGAPA to GSNO-dependent regulation, possibly expanding the mechanistic features to other protein cysteines susceptible to be oxidatively modified by GSNO.

plant biology↗

bioRxiv2020

Structural and functional insights into nitrosoglutathione reductase from Chlamydomonas reinhardtii

Protein S-nitrosylation plays a fundamental role in cell signaling and nitrosoglutathione (GSNO) is considered as the main nitrosylating signaling molecule. Enzymatic systems controlling GSNO homeostasis are thus crucial to indirectly control the formation of protein S-nitrosothiols. GSNO reductase (GSNOR) is the key enzyme controlling GSNO levels by catalyzing its degradation in the presence of NADH. Here, we found that protein extracts from the microalga Chlamydomonas reinhardtii catabolize GSNO via two enzymatic systems having specific reliance on NADPH or NADH and different biochemical features. Scoring the Chlamydomonas genome for orthologs of known plant GSNORs, we found two genes encoding for putative and almost identical GSNOR isoenzymes. One of the two, here named CrGSNOR1, was heterologously expressed and purified. The kinetic properties of CrGSNOR1 were determined and the high-resolution three-dimensional structures of the apo and NAD+-bound forms of the enzyme were solved. These analyses revealed that CrGSNOR1 has a strict specificity towards GSNO and NADH, and a conserved 3D-folding with respect to other plant GSNORs. The catalytic zinc ion, however, showed an unexpected variability of the coordination environment. Furthermore, we evaluated the catalytic response of CrGSNOR1 to thermal denaturation, thiol-modifying agents and oxidative modifications as well as the reactivity and position of accessible cysteines. Despite being a cysteine-rich protein, CrGSNOR1 contains only two solvent-exposed/reactive cysteines. Oxidizing and nitrosylating treatments have null or limited effects on CrGSNOR1 activity, highlighting a certain resistance of the algal enzyme to redox modifications. The molecular mechanisms and structural features underlying the response to thiol-based modifications are discussed. One-sentence summaryGSNOR1 from Chlamydomonas reinhardtii displays an unusual variability of the catalytic zinc coordination environment and an unexpected resistance to thiol-based redox modifications

plant biology↗

bioRxiv2020

Illuminating a Phytochrome Paradigm - a Light-Activated Phosphatase in Two-Component Signaling Uncovered

Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (AgP1). Whereas AgP1 acts as a conventional histidine kinase, we identify DrBphP as a light-sensitive phosphatase. While AgP1 binds its cognate response regulator only transiently, DrBphP does so strongly, which is rationalized at the structural level. Our data pinpoint two key residues affecting the balance between kinase and phosphatase activities, which immediately bears on photoreception and two-component signaling. The opposing output activities in two highly similar bacteriophytochromes inform the use of light-controllable histidine kinases and phosphatases for optogenetics.

biochemistry↗