Biology subjects

Gutierrez, P. A.

Publications and source records attributed to Gutierrez, P. A..

5 recordsLinked to original sources

bioRxiv2025

Expanding the Orchidaceae Virome Through Analysis of Public-Domain Sequencing Data

Orchidaceae is one of the largest plant families, renowned for its ornamental appeal, uses in food, cosmetics, and medicine, and its vital importance in ecosystem health and biodiversity. However, despite their diversity and economic significance, knowledge about the viruses associated with orchid species remains limited. Fortunately, the widespread adoption of high-throughput sequencing enables the collection of indirect information about the viruses associated with various plant hosts. In this work, we conducted an integrated data analysis of viruses associated with Orchidaceae by reexamining 2,789 public RNA-seq datasets encompassing 41 genera, 18 subtribes, and five subfamilies. We identified sequences associated with 163 viruses, 13 representing new associations with Orchidaceae. Additionally, 117 sequences likely represent putative novel species, including six tentative new genera within Benyviridae, Betaflexiviridae, Phenuiviridae, and Tymoviridae. Analysis of the updated Orchidaceae virome revealed a strong correlation between the pairs Alphaflexiviridae/Virgaviridae, Rhabdoviridae/Partitiviridae, and Partitiviridae/Secoviridae and a negative correlation between Alphaflexiviridae/Partitiviridae; Virgaviridae/Partitiviridae; Rhabdoviridae/Alphaflexiviridae; Betaflexiviridae/Alphaflexiviridae; and Secoviridae/Alphaflexiviridae in addition to correlations between virus genera and orchid lifestyles. A network analysis of the host range of orchid viruses was also performed in addition to a preliminary estimate of the size of the Orchidaceae virome. IMPORTANCEDespite their diversity, little is known about viruses associated with orchids. Plant viruses significantly threaten agriculture and may harm orchid conservation. Without detailed characterization of the orchid virome and suitable diagnostic tools, viruses could unintentionally enter ecosystems and cultivation fields from contaminated sources. Sequence information is crucial for developing detection tests for quick virus identification, supporting disease management strategies, and producing virus-free plants. In addition, understanding ecological factors contributing to virus transmission--like primary infection sources, vectors, and alternative hosts--is essential for selecting control measures to prevent viral diseases and manage outbreaks. Data mining provides a cost-effective method to bridge knowledge gaps, highlight trends that are useful for plant virus surveillance, and inform epidemiological decisions. The analysis presented here offers a global perspective on the Orchidaceae virome that could guide future research and virus vigilance programs and enhance our understanding of plant virus diversity.

bioinformatics↗

bioRxiv2024

Adaptation of turnip mosaic virus to Arabidopsis thaliana involves rewiring of VPg - host proteome interactions

The outcome of a viral infection depends on a complex interplay between the host physiology and the virus, mediated through numerous protein-protein interactions. In a previous study we used high-throughput yeast two-hybrid (HT-Y2H) to identify proteins in Arabidopsis thaliana that bind to the proteins encoded by the turnip mosaic virus (TuMV) genome. Furthermore, after experimental evolution of TuMV lineages in plants with mutations in defense-related or proviral genes, most mutations observed in the evolved viruses affected the VPg cistron. Among these mutations, D113G was a convergent mutation selected in many lineages across different plant genotypes. In contrast, mutation R118H specifically emerged in the jin1 mutant with affected jasmonate signaling. Using the HT-Y2H system, we analyzed the impact of these two mutations on VPgs interaction with plant proteins. Interestingly, both mutations severely compromised the interaction of VPg with the translation initiation factor eIF(iso)4E, a crucial interactor for potyvirus infection. Moreover, mutation D113G, but not R118H, adversely affected the interaction with RHD1, a zinc-finger homeodomain transcription factor involved in regulating DNA demethylation. Our results suggest that RHD1 enhances plant tolerance to TuMV infection.

evolutionary biology↗

bioRxiv2023

Conserved Roles for the Dynein Intermediate Chain and Ndel1 in Assembly and Activation of Dynein

Cytoplasmic dynein, the primary retrograde microtubule transport motor within cells, must be activated for processive motility through the regulated assembly of a dynein-dynactin-adapter (DDA) complex. The interaction between dynein and dynactin was initially ascribed to the N-terminus of the dynein intermediate chain (IC) and a coiled-coil of the dynactin subunit p150Glued. However, cryo-EM structures of DDA complexes have not resolve these regions of the IC and p150Glued, raising questions about the importance of this interaction. The IC N-terminus (ICN) also interacts with the dynein regulators Nde1/Ndel1, which compete with p150Glued for binding to ICN. Using a combination of approaches, we reveal that the ICN plays critical, evolutionarily conserved roles in DDA assembly by interacting with dynactin and Ndel1, the latter of which recruits the DDA assembly factor LIS1 to the dynein complex. In contrast to prior models, we find that LIS1 cannot simultaneously bind to Ndel1 and dynein, indicating that LIS1 must be handed off from Ndel1 to dynein in temporally discrete steps. Whereas exogenous Ndel1 or p150Glued disrupts DDA complex assembly in vitro, neither perturbs preassembled DDA complexes, indicating that the IC is stably bound to p150Glued within activated DDA complexes. Our study reveals previously unknown regulatory steps in the dynein activation pathway, and provides a more complete model for how the activities of LIS1/Ndel1 and dynactin/cargo-adapters are integrated to regulate dynein motor activity.

biochemistry↗

bioRxiv2022

Single-cell RNA-sequencing data analysis reveals a highly correlated triphasic transcriptional response to SARS-CoV-2 infection

Single-cells RNA sequencing (scRNA-seq) is currently one of the most powerful techniques available to study the transcriptional response of cells to external perturbations. However, the use of conventional bulked RNA-seq analysis methods can miss important patterns underlying in the scRNA-seq data. Here, we present a reanalysis of scRNA-seq data from human bronchial epithelial cells and colon and ileum organoids using pseudo-time profiles based on the degree of virus accumulation which reflect the progress of infection. Our analysis revealed a transcriptional response to infection characterized by three distinct up- and down-regulatory phases, that cannot be detected using classical two-group comparisons. Interrogation of results, focused on genes involved in interferon-response, transcription factors and RNA-binding proteins, suggests a highly correlated transcriptional response for most genes. In addition, correlation network analysis revealed a distinct response of genes involved in translation and mitochondrially-encoded genes. Based on our data, we propose a model where modulation of nucleocytoplasmic traffic by the viral protein nsp1 explains the triphasic transcriptional response to SARS-CoV-2 infection.

bioinformatics↗

bioRxiv2017

Differential Effects of LIS1 On Processive Dynein-Dynactin Motility

Cytoplasmic dynein is the primary minus-end directed microtubule motor protein in cells. LIS1 is a highly conserved dynein regulatory factor that binds directly to the dynein motor domain, uncoupling the enzymatic and mechanical cycles of the motor, and stalling dynein on the microtubule track. Dynactin, another ubiquitous dynein regulatory factor, acts to release dynein from an autoinhibited state, leading to a dramatic increase in fast, processive dynein motility. How these opposing activities are integrated to control dynein motility is unknown. Here we used fluorescence single-molecule microscopy to study the interaction of LIS1 with the processive dynein-dynactin-BicD2N (DDB) complex. Surprisingly, in contrast to the prevailing model for LIS1 function established in the context of dynein alone, we find that binding of LIS1 to DDB does not strongly disrupt processive motility. Motile DDB complexes bind up to two LIS1 dimers, and mutational analysis suggests LIS1 binds directly to the dynein motor domains during DDB movement. Interestingly, LIS1 enhances DDB velocity in a concentration dependent manner, in contrast to observations of LIS1s effects on the motility of isolated dynein. Thus, LIS1 exerts concentration dependent effects on dynein motility, and can synergize with dynactin to enhance processive movement in the absence of load.

biochemistry↗