Biology subjects

Paez-Espino, D.

Publications and source records attributed to Paez-Espino, D..

6 recordsLinked to original sources

bioRxiv2025

Viruses associated with Nitrososphaerota archaea: diversity, evolution and horizontal gene transfers

Nitrososphaeria, an archaeal class containing all ammonium-oxidizing archaea (AOA) and their closely related clades (e.g. Ca. Caldarchaeales), is a widely distributed archaeal lineage across diverse ecosystems. Due to the difficulty of isolation and cultivation, the viral diversity and evolution associated with non-marine AOA lineages and Ca. Caldarchaeales remain largely uncharacterized. Here, based on globally sampled genomes and metagenomes, we assembled a genomic catalogue associated with AOA, including 283 species-level viruses and 415 species-level mobile genetic elements (MGEs). Notably, 259 previously unrecognized species-level viruses or MGEs associated with Ca. Caldarchaeales were identified. Across the two major Nitrososphaeria lineages, we uncovered an expansion of archaeal viral families: 11 families associated with AOA, including seven new head-tailed lineages, one of which comprises a mega archaeal virus with a genome size exceeding 220 kb; ten families associated with Ca. Caldarchaeales, including four novel head-tailed groups and two previously unknown rod-shaped family (Demeterviridae and Gaiaviridae). Phylogenetic inference showed that rod-shaped viruses associated with Ca. Caldarchaeales and methanogens are phylogenetically intertwined and likely share a common ancestor with Hoswirudivirus, a Sulfolobales-associated rod-shaped virus characterized by two copies of the coat gene. Through structural modelling, a rare fusion of the coat protein in Demeterviridae was observed, in which a single open reading frame within a gene island adjacent to a glycosyl transferase appears capable of forming a complete capsomer. This provides new insights into the origin and evolution of Adnaviria viral realm. Functional genomics analyses further revealed that these novel rod-shaped viruses encode virus-specific rare quinone biosynthesis genes and arsenic response transcriptional regulator genes, providing potential clues to their mechanisms of adaptation to hyperthermal environments. Collectively, our work uncovers the hidden genomic, evolution and functional diversity of Nitrososphaeria viromes for the first time and closes a long-standing gap in archaeal virome research. HighlightsO_LIFirst genomic catalogue of viruses and MGEs linked to Nitrososphaeria. C_LIO_LIDiscovery of diverse novel archaeal viral families. C_LIO_LINew insights into rod-shaped virus evolution and archaeal virus-host adaptation. C_LI

bioinformatics↗

bioRxiv2023

Global Biogeography of the Soil Virosphere

Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities, and interactions with the soil microbiome remains limited. Here, we present the Global Soil Virus (GSV) Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and comprised of 616,935 uncultivated viral genomes (UViGs) and 38,508 unique viral operational taxonomic units (vOTUs). Rarefaction curves from the GSV Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared vOTUs across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.

ecology↗

bioRxiv2022

A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages

High-throughput RNA sequencing offers unprecedented opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA viral contigs. Via analysis of the 330k novel RNA-dependent RNA polymerases (RdRP), this expansion corresponds to a five-fold increase of RNA virus diversity. Extended RdRP phylogeny supports monophyly of the five established phyla, reveals two putative new bacteriophage phyla and numerous putative novel classes and orders. The dramatically expanded Lenarviricota phylum, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome diversity. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts. Gene content analysis revealed multiple domains previously not found in RNA viruses and implicated in virus-host interactions. This vast collection of new RNA virus genomes provides insights into RNA virus evolution and should become a major resource for RNA virology.

genomics↗

bioRxiv2021

Individuals at risk for developing rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential

Rheumatoid arthritis (RA) is an autoimmune disease characterized in seropositive individuals by the presence of anti-cyclic citrullinated protein (CCP) antibodies. RA is linked to the intestinal microbiota, yet the association of microbes with CCP serology and their contribution to RA is unclear. We describe intestinal phage communities of individuals at risk for developing RA, with or without anti-CCP antibodies, whose first degree relatives have been diagnosed with RA. We show that at-risk individuals harbor intestinal phage compositions that diverge based on CCP serology, are dominated by Lachnospiraceae phages, and originate from disparate ecosystems. These phages encode unique repertoires of auxiliary metabolic genes (AMGs) which associate with anti-CCP status, suggesting that these phages directly influence the metabolic and immunomodulatory capability of the microbiota. This work sets the stage for the use of phages as preclinical biomarkers and provides insight into a possible microbial-based causation of RA disease development.

microbiology↗

bioRxiv2019

Untapped viral diversity in global soil metagenomes

Viruses outnumber every other biological entity on Earth, and soil viruses are particularly diverse compared to other habitats. However, we have limited understanding of soil viruses because of the tremendous variation in soil ecosystems and because of the lack of appropriate screening tools. Here, we determined the global distribution of more than 24,000 soil viral sequences and their potential hosts, including >1,600 sequences associated with giant viruses. The viral sequences, derived from 668 terrestrial metagenomes, greatly extend existing knowledge of soil viral diversity and viral biogeographical distribution. We screened these sequences to identify a suite of cosmopolitan auxiliary metabolic genes (AMGs) encoding enzymes involved in soil organic carbon decomposition across soil biomes. Additionally, we provide evidence for viral facilitation of multi-domain linkages in soils by locating a fungal chitosanase in bacteriophages, generating a new paradigm of how viruses can serve as exchange vectors of carbon metabolism across domains of life.

microbiology↗

bioRxiv2017

A thermostable Cas9 with increased lifetime in human plasma

CRISPR-Cas9 is a powerful technology that has enabled genome editing in a wide range of species. However, the currently developed Cas9 homologs all originate from mesophilic bacteria, making them susceptible to proteolytic degradation and unsuitable for applications requiring function at elevated temperatures. Here, we show that the Cas9 protein from the thermophilic bacterium Geobacillus stearothermophilus (GeoCas9) catalyzes RNA-guided DNA cleavage over a wide temperature range and has an enhanced protein lifetime in human plasma. GeoCas9 is active at temperatures up to 70{degrees}C, compared to 45{degrees}C for Streptococcus pyogenes Cas9 (SpyCas9), which greatly expands the temperature range for CRISPR-Cas9 applications. By comparing features of two closely related Geobacillus homologs, we created a variant of GeoCas9 that doubles the DNA target sequences that can be recognized by this system. We also found that GeoCas9 is an effective tool for editing mammalian genomes when delivered as a ribonucleoprotein (RNP) complex. Together with an increased lifetime in human plasma, the thermostable GeoCas9 provides the foundation for improved RNP delivery in vivo and expands the temperature range of CRISPR-Cas9.

biochemistry↗