Biology subjects

Perez-Gonzalez, A.

Publications and source records attributed to Perez-Gonzalez, A..

8 recordsLinked to original sources

bioRxiv2025

Azotobacter vinelandii glutaredoxin D delivers the core cluster to nitrogenase cofactor scaffold protein NifU

The scaffold protein NifU plays a central role in assembling the precursor [Fe4S4] clusters required for nitrogenase to function. The synthesis of these precursors depends on a catalytic [Fe2S2] group within NifU core ferredoxin domain. Here, we show that the monothiol glutaredoxin GrxD delivers this cluster to the NifU scaffold protein. Consistently, grxD mutants have reduced nitrogenase activity, the result of altered iron allocation to this enzyme. Biochemical assays show that GrxD unidirectionally transfers [Fe2S2] to NifU through protein-protein interaction. This allows GrxD to restore apo-NifU functionality, enabling proper [Fe4S4] synthesis, and NifH activation. These findings are crucial to understand how iron is allocated to nitrogenase for biological nitrogen fixation.

biochemistry↗

bioRxiv2025

Identification of a novel link connecting indole-3-acetamide with abscisic acid biosynthesis and signaling

Plants regulate their developmental programs and their responses to environmental changes through a complex network of small signaling compounds, known as phytohormones. The role of auxins in promoting plant growth has been extensively investigated. Furthermore, previous studies have demonstrated that the accumulation of indole-3-acetamide (IAM), an auxin precursor, results in the suppression of plant growth, particularly primary root elongation. This observation led to the hypothesis that IAM or an IAM derivative exerts negative growth regulatory effects. However, the molecular mechanism by which IAM inhibits plant growth remains largely unelucidated. To gain deeper insight into the molecular mode of action of IAM, we conducted a comprehensive genome-wide association study (GWAS) using a highly diverse collection of 166 wild Arabidopsis accessions from the Iberian Peninsula. Consequently, we identified several genomic regions associated with a reduced response to IAM under controlled in vitro conditions, which included ABA3 and GA2ox2 as candidate genes. Sequence analyses, transcriptomics studies, and comparison of three-dimensional models generated for ABA3 proteins encoded by the two major natural alleles identified in the collection of wild accessions suggested that IAM-triggered inhibition of primary root elongation is closely associated with the formation of abscisic acid (ABA) in Arabidopsis thaliana seedlings. Finally, physiological characterization of mutants for those candidate genes further corroborated that IAM activates ABA signaling. Our results demonstrate that IAM is intricately linked with ABA biosynthesis and signaling, thereby elucidating a novel node in plant hormone crosstalk.

plant biology↗

bioRxiv2025

Molecular sorting of nitrogenase catalytic cofactors

The free-living diazotroph Azotobacter vinelandii produces three genetically distinct but functionally and mechanistically similar nitrogenase isozymes, designated as Mo-dependent, V-dependent, and Fe-only. They respectively harbor nearly identical catalytic cofactors that are distinguished by a heterometal site occupied by Mo (FeMo-cofactor), V (FeV-cofactor), or Fe (FeFe-cofactor). Completion of FeMo-cofactor and FeV-cofactor formation occurs on molecular scaffolds prior to delivery to their catalytic partners. In contrast, completion of FeFe-cofactor assembly occurs directly within its cognate catalytic partner. Because hybrid nitrogenase species that contain the incorrect cofactor type cannot reduce N2 to support diazotrophic growth there must be a way to prevent misincorporation of an incorrect cofactor when different nitrogenase isozyme systems are produced at the same time. Here, we show that fidelity of the Fe-only nitrogenase is preserved by blocking the misincorporation of either FeMo-cofactor or FeV-cofactor during its maturation. This protection is accomplished by a two-domain protein, designated AnfO. It is shown that the N-terminal domain of AnfO binds to an immature form of the Fe-only nitrogenase and the C-terminal domain, tethered to the N-terminal domain by a flexible linker, has the capacity to capture FeMo- and FeV-cofactor. AnfO does not prevent the normal activation of Fe-only nitrogenase because completion of FeFe-cofactor assembly occurs within its catalytic partner and, therefore, is never available for capture by AnfO. These results support a post-translational mechanism involving the molecular sorting of structurally similar metallocofactors that involve both protein-protein interactions and metallocofactor binding while exploiting differential pathways for nitrogenase associated catalytic cofactor assembly.

biochemistry↗

bioRxiv2024

Lineage-specific neutralising antibodies after SARS-CoV-2 mild disease. Immune boosting effect of vaccination

We followed a group of 105 non-vaccinated individuals after Alpha or Delta SARS-CoV-2 mild disease, measuring the viral shedding (qRT-PCR, dPCR and subgenomic RNA-E) and humoral response (commercial immunoassay and pseudovirus and live virus neutralisation) up to six months. Sixty nine patients received a vaccination boost during the follow-up period (n=95). Subgenomic RNA-E showed a shorter period until negativity (mean 2.2 weeks) compared to gRNA (mean 5.2 weeks). A high correlation between qRT-PCR and dPCR was found for viral load estimation, even when no nucleic acid extraction was used in dPCR (R2 = 0.87). Post-convalescent sera showed the strongest neutralisation against the variant of natural exposure, while the neutralisation capacity against Omicron variants was significantly lower compared to the other variants. Additionally, the results suggested that commercial immunoassays may not accurately predict protection against a different variant than the variant of exposure. An immune boosting effect of the SARS-CoV-2 vaccination was evident. Variant-specific neutralising antibodies were detected one month after natural infection. Although short lived, maximum igG response was observed after hybrid immunisation (natural infection + vaccination). This study also points to potential improvements in the clinical management of SARS-CoV-2 cases. Firstly, subgenomic RNA-E is a potentially more accurate biomarker of infectivity than current qRT-PCRs using genomic RNA as target. Secondly, accuracy of high-throughput immunoassays must be validated in order to estimate specific protection and organise vaccination campaigns. Our findings could play a role in the current implementation of SARS-CoV-2 vaccine programs. Author SummaryYears after SARS-CoV-2 related infections challenged the healthcare systems of the whole world, the optimal strategy to deal with diagnosis, quarantines or vaccination patterns is still a matter of debate. The interplay between infectivity and immunity in the different circulating variants is complex, and qPCR for diagnosis may extend quarantines, as detection of viral RNA does not necessarily mean that the virus remains infectious. We studied a group of patients infected with pre-Omicron variants to study how their variant-specific antibodies reacted to the past and present variants of SARS-CoV-2. In both Alpha and Delta, antibodies neutralise their own variants better than other variants that came before and after. Perhaps most importantly, neutralisation was lowest against Omicron variants. We followed the viral shedding dynamics of the patients, testing different PCR techniques and targets. Subgenomic RNA was detectable in nasopharyngeal samples for a shorter time than genomic RNA and it has been suggested as a good marker of infectivity. Using sgRNA instead of genomic RNA as a PCR target could reduce hospital bed occupation and quarantine time. Overall, we hope that these results could help guide pandemic and diagnostic control in the future.

microbiology↗

bioRxiv2021

Deciphering the quality of SARS-CoV-2 specific T-cell response associated with disease severity, immune memory and heterologous response

SARS-CoV-2 specific T-cell response has been associated with disease severity, immune memory and heterologous response to endemic coronaviruses. However, an integrative approach combining a comprehensive analysis of the quality of SARS-CoV-2 specific T-cell response with antibody levels in these three scenarios is needed. In the present study we found that, in acute infection, while mild disease was associated with high T-cell polyfunctionality biased to IL-2 production and inversely correlated with anti-S IgG levels, combinations only including IFN-{gamma} with absence of perforin production predominated in severe disease. Seven months after infection, both non-hospitalized and previously hospitalized patients presented robust anti-S IgG levels and SARS-CoV-2 specific T-cell response. In addition, only previously hospitalized patients showed a T-cell exhaustion profile. Finally, combinations including IL-2 in response to S protein of endemic coronaviruses, were the ones associated with SARS-CoV-2 S-specific T-cell response in pre-COVID-19 healthy donors samples. These results have implications for protective immunity against SARS-CoV-2 and recurrent COVID-19 and may help for the design of new prototypes and boosting vaccine strategies.

immunology↗

bioRxiv2021

Dendritic cell deficiencies persist seven months after SARS-CoV-2 infection

Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2 infection induces an exacerbated inflammation driven by innate immunity components. Dendritic cells (DCs) play a key role in the defense against viral infections, for instance plasmacytoid DCs (pDCs), have the capacity to produce vast amounts of interferon-alpha (IFN-). In COVID-19 there is a deficit in DC numbers and IFN- production, which has been associated with disease severity. In this work, we described that in addition to the DC deficiency, several DC activation and homing markers were altered in acute COVID-19 patients, which were associated with multiple inflammatory markers. Remarkably, previously hospitalized and non-hospitalized patients remained with decreased numbers of CD1c+ myeloid DCs and pDCs seven months after SARS-CoV-2 infection. Moreover, the expression of DC markers as CD86 and CD4 were only restored in previously non-hospitalized patients while integrin {beta}7 and indoleamine 2,3- dyoxigenase (IDO) no restoration was observed. These findings contribute to a better understanding of the immunological sequelae of COVID-19.

immunology↗

bioRxiv2018

Comparative analysis of the effect of genomic isolators flanking transgenes to avoid positional effects in Arabidopsis

HighlightWe have studied the effect of different insulator sequences over transgene expression levels and variability, and over transgene integration, using NGS. Our results compare the benefits obtained by their use.\n\nAbstractFor more than 20 years, plant biologists have tried to achieve complete control of transgene expression, but until gene targeting techniques become routine, flanking transgenes with genetic insulators can help avoid positional effects. Insulators are DNA sequences with barrier activity that protect transgenes from interferences with the host genome. We have, for the first time, compared the effect of three insulator sequences previously described in the literature and of a matrix attachment region from Arabidopsis never tested before. Our results indicate that the use of all sequences increases transgene expression, but only the last one reduces variability between lines and between individuals to a minimum. We have analyzed the integration of insulator-flanked T-DNAs using whole genome re-sequencing (to our knowledge, also the first time) and found chiMAR lines with insertions located within heterochromatic regions of the genome, characterized by DNA methylation that did not spread into the T-DNA, suggesting that chiMAR can shelter transgene insertions from neighboring repressive epigenetic states. Finally, we could also observe a loss of accuracy of the RB insertion in the lines harboring insulators, evidenced by a high frequency of truncation of T-DNAs and of insertion of vector backbone that, however, did not affect transgene expression.

synthetic biology↗

bioRxiv2017

The whole-genome panorama of cancer drivers

The advance of personalized cancer medicine requires the accurate identification of the mutations driving each patients tumor. However, to date, we have only been able to obtain partial insights into the contribution of genomic events to tumor development. Here, we design a comprehensive approach to identify the driver mutations in each patients tumor and obtain a whole-genome panorama of driver events across more than 2,500 tumors from 37 types of cancer. This panorama includes coding and non-coding point mutations, copy number alterations and other genomic rearrangements of somatic origin, and potentially predisposing germline variants. We demonstrate that genomic events are at the root of virtually all tumors, with each carrying on average 4.6 driver events. Most individual tumors harbor a unique combination of drivers, and we uncover the most frequent co-occurring driver events. Half of all cancer genes are affected by several types of driver mutations. In summary, the panorama described here provides answers to fundamental questions in cancer genomics and bridges the gap between cancer genomics and personalized cancer medicine.

cancer biology↗