Biology subjects

Abrahao, J. S.

Publications and source records attributed to Abrahao, J. S..

4 recordsLinked to original sources

bioRxiv2026

Mimicin, an antimicrobial protein encoded by mimivirus

Antimicrobial peptides (AMPs) are innate defense molecules found in all domains of life. Giant viruses of amoeba are known to thrive among complex microbial relationships within its hosts cells, hinting at the existence of virus-derived antimicrobial strategies. Here we show that viruses belonging to the Mimiviridae and Marseilleviridae families contain a higher density of in silico predicted AMPs per genome size than other viruses of amoeba. The investigation of potential AMPs led to the description of Mimicin, a taxonomically restricted 74 amino acid long protein coded by few mimiviruses. Mimicin contains three smaller predicted AMP sequences within it and has a broad in vitro antimicrobial activity against different bacteria, a yeast and two non-enveloped phages. In contrast, it has no activity against a marseillevirus, a mimivirus or human cell lines. When tested against bacterial endosymbionts co-cultured with Acanthamoeba terricola, Mimicin and its SIM-31 portion were able to control the attenuated Protochlamydia amoebophila but not the highly virulent Parachlamydia acanthamoebae. Based on deposited transcriptomic data, Mimicin is coded by an early gene more active during the beginning of the infection process. No structure could be predicted using Alphafold, while additional structural analysis indicate that Mimicin could be a highly disordered protein. In conclusion, we describe evidence of a biologically relevant antimicrobial activity derived from a giant virus. Mimicin highlights the relevance of AMPs from giant viruses for microbial ecology and opens the way for investigating their biotechnological and clinical potential.

microbiology↗

bioRxiv2024

Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland

Giant viruses of protists are a diverse and likely ubiquitous group of organisms. Here, we describe Jyvaskylavirus, the first giant virus isolated from Finland. This clade B marseillevirus was found in Acanthamoeba castellanii from a composting soil sample in Jyvaskyla, Central Finland. Its genome shares similarities with other marseilleviruses. Helium ion microscopy and electron microscopy of infected cells unraveled stages of the Jyvaskylavirus lifecycle. We reconstructed the Jyvaskylavirus particle to 6.3 [A] resolution using cryo-EM. The [~]2,500 [A] diameter virion displays structural similarities to other Marseilleviridae giant viruses. The capsid comprises of 9,240 copies of the major capsid protein ORF184, which possesses a double jellyroll fold arranged in trimers forming pseudo-hexameric capsomers. Below the capsid shell, the internal membrane vesicle encloses the genome. Through cross-structural and -sequence comparisons with other Marseilleviridae using AI-based software in model building and prediction, we elucidated ORF142 as the penton protein, which plugs the twelve vertices of the capsid. Five additional ORFs were identified, with models predicted and fitted into densities that either cap the capsomers externally or stabilize them internally. The isolation of Jyvaskylavirus suggests that these viruses may be widespread in the boreal environment and provide structural insights extendable to other marseilleviruses.

microbiology↗

bioRxiv2020

A mysterious 80 nm amoeba virus with a near-complete "ORFan genome" challenges the classification of DNA viruses

Here we report the discovery of Yaravirus, a new lineage of amoebal virus with a puzzling origin and phylogeny. Yaravirus presents 80 nm-sized particles and a 44,924 bp dsDNA genome encoding for 74 predicted proteins. More than 90% (68) of Yaravirus predicted genes have never been described before, representing ORFans. Only six genes had distant homologs in public databases: an exonuclease/recombinase, a packaging-ATPase, a bifunctional DNA primase/polymerase and three hypothetical proteins. Furthermore, we were not able to retrieve viral genomes closely related to Yaravirus in 8,535 publicly available metagenomes spanning diverse habitats around the globe. The Yaravirus genome also contained six types of tRNAs that did not match commonly used codons. Proteomics revealed that Yaravirus particles contain 26 viral proteins, one of which potentially representing a novel capsid protein with no significant homology with NCLDV major capsid proteins but with a predicted double-jelly roll domain. Yaravirus expands our knowledge of the diversity of DNA viruses. The phylogenetic distance between Yaravirus and all other viruses highlights our still preliminary assessment of the genomic diversity of eukaryotic viruses, reinforcing the need for the isolation of new viruses of protists. Significance statementMost of the known viruses of amoeba have been seen to share many features that eventually prompted authors to classify them into common evolutionary groups. Here we describe Yaravirus, an entity that could represent either the first isolated virus of Acanthamoeba spp. out of the group of NCLDVs or, in alternative evolutive scenario, it is a distant and extremely reduced virus of this group. Contrary to what is observed in other isolated viruses of amoeba, Yaravirus is not represented by a large/giant particle and a complex genome, but at the same time carries an important number of previously undescribed genes, including one encoding a novel major capsid protein. Metagenomic approaches also testified for the rarity of Yaravirus in the environment.

microbiology↗

bioRxiv2019

Boiling Acid Mimics Intracellular Giant Virus Genome Release

Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four metastable infection intermediates in Samba virus (lineage A Mimiviridae) as visualized by cryo-EM, cryo-ET, and SEM. Each of these four intermediates reflects a stage that occurs in vivo. We show that these genome release stages are conserved in other, diverse giant viruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved amongst disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.

biophysics↗