Biology subjects

Fabre, M. L.

Publications and source records attributed to Fabre, M. L..

6 recordsLinked to original sources

bioRxiv2026

An Aspergillus lncRNA atlas reveals a novel modulator of aflatoxin biosynthesis

Long non-coding RNAs (lncRNAs) represent a significant fraction of the transcriptome and are vital regulators in eukaryotes, yet their functional landscape in fungi remains largely undefined. Here we present a transcriptomic atlas of 8,553 lncRNAs across four evolutionarily and biotechnologically diverse Aspergillus species. We observed marked diversity in the long non-coding repertoire between species, with only 39% shared between at least two species. However, conserved lncRNAs are expressed at significantly higher levels and across more conditions than species-specific ones, revealing a functional hierarchy within the non-coding transcriptome. We also identify subtelomeres and transposable elements as hotspots for lncRNA innovation in Aspergillus, albeit at the cost of reduced expression. Integrating genomic and transcriptomic data, we show that lncRNAs predominantly exhibit distance-dependent cis-coexpression with neighboring genes and, through guilt-by-association, we identify their participation in global modules governing primary and secondary metabolism. This framework enabled the discovery of aflalinc, a species- and condition-specific lncRNA in A. flavus that plays a role in regulating the aflatoxin biosynthetic gene cluster. Crucially, deletion of this lncRNA severely reduced the production of aflatoxin B, a highly potent agent of acute toxicity and driver of hepatocarcinoma, without affecting growth, conidiation, or sclerotia formation. In addition, examination of an independent dataset confirms the strength of the co-expression networks and uncovers stage-specific functions for lincRNAs in the maturation of A. fumigatus biofilms. Together, these findings establish lncRNAs as integral components of fungal biology and demonstrate that they can modulate mycotoxin production and biofilm formation, with broad implications for controlling fungal threats to food safety and human health.

microbiology↗

bioRxiv2025

Proteomic Characterization of Spodoptera frugiperda Granulovirus Occlusion Bodies

Lepidopteran-infecting baculoviruses represent one of the most promising alternatives for pest biocontrol. In particular, Spodoptera frugiperda granulovirus (SfGV) infects the fall armyworm Spodoptera frugiperda, an increasingly important pest for maize and other crops around the world. SfGV has been investigated due to its capacity to enhance other baculovirus infectivity and as a biopesticide itself. Although the proteome of SfGV occlusion bodies (OB) is fundamental for their infectivity properties, we still lack a detailed understanding of its protein components and how they compare with other baculoviruses. To tackle this problem, we performed mass spectrometry-based proteomics analysis on SfGV OB obtained from infected larvae. We could detect 72 proteins included in SfGV OB and confirm the presence of two enhancins. EmPAI-based semi-quantification highlighted the presence of two granulovirus proteins, ORF101 and ORF141, shared with other GV proteomic studies. ORF101 was shown to form aggregates in insect cells. Bioinformatic analysis determined that ORF101 is an Ac5 family protein and at the same time shares striking similarities with AcMNPV P10. Prediction and comparison of OB protein structures allowed the detection of a common structural fold among 6 proteins PEP-1, PEP-2, Pep-P10, ORF007, ORF025, and Bro-f. Finally, comparison of four reported ODV proteomic studies of different GVs indicated that ORF040, ORF101, ORF141 and Bro-f are common components in GV OBs.

molecular biology↗

bioRxiv2024

Comparative pan-genomics reveals divergent adaptations in clinically-relevant members of the Fusarium solani species complex

The Fusarium solani species complex (FSSC) is a group of dual-kingdom fungal pathogens capable of causing devastating disease on a wide range of host plants and life-threatening infections in humans that are difficult to treat. In this study, we generate highly contiguous genomes for three clinical isolates of Fusarium keratoplasticum and three clinical isolates of Fusarium petroliphilum and compare them with other genomes of the FSSC from plant and animal sources. We find that human pathogenicity is polyphyletic within the FSSC, including within F. keratoplasticum. Pan-genome analysis revealed extensive gene presence-absence in the complex, with only 41% of genes (11,079/27,068) found in all samples and the presence of accessory chromosomes encoding isolate- and species-specific genes. Definition of long non-coding RNAs (lncRNAs) in F. keratoplasticum and F. petroliphilum demonstrated that they show a similarly high degree of presence-absence variation but are integrated into the transcriptional network to a similar degree as protein-coding genes, suggesting broad and extensive cellular roles. Elucidation of secondary metabolic potential identified many actively transcribed biosynthetic gene clusters with unknown products and identified several lncRNAs as putative regulators of specific metabolite clusters. Finally, examination of the FSSC for Starship gigantic mobile genetic elements revealed that F. keratoplasticum had the largest number with a median of four elements per genome and an overall pattern of Starships in the FSSC that were incongruent with the phylogeny, suggesting multiple horizontal transfer events. This study provides valuable insights into the evolutionary dynamics and genomic architecture of the FSSC, with implications for understanding multi-kingdom virulence, something of increasing relevance as climate change potentially increases the number of fungal species that can grow at human temperatures.

genomics↗

bioRxiv2020

Genomic Diversity in a Population of Spodoptera frugiperda Nucleopolyhedrovirus

Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) represents a strong candidate to develop environmental-friendly pesticides against the fall armyworm (Spodoptera frugiperda), a widespread pest that poses a severe threat to different crops around the world. However, little is known regarding the genomic diversity present inside SfMNPV isolates and how it shapes the interactions between virus and host. Here, the genomic diversity present inside an isolate of SfMNPV was explored using high-throughput sequencing for the first time. We identified 704 intrahost single nucleotide variants, from which 184 are nonsynonymous mutations distributed among 82 different coding sequences. We detected several structural variants affecting SfMNPV genome, including two previously reported deletions inside the egt region. A comparative analysis between polymorphisms present in different SfMNPV isolates and our intraisolate diversity data suggests that coding regions with higher genetic diversity are associated with oral infectivity or unknown functions. In this context, through molecular evolution studies we provide evidence of diversifying selection acting on sf29, a putative collagenase which could contribute to the oral infectivity of SfMNPV. Overall, our results contribute to deepen our understanding of the coevolution between SfMNPV and the fall armyworm and will be useful to improve the applicability of this virus as a biological control agent. HighlightsO_LIWe characterized the genomic diversity within a population of SfMNPV. C_LIO_LICoding regions with higher genetics diversity are associated with oral infectivity or unknown functions. C_LIO_LISeveral structural variants contribute to the genomic diversity of SfMNPV. C_LIO_LISf29, a putative collagenase, shows signs of adaptive evolution. C_LI

microbiology↗

bioRxiv2020

Codon-usage optimization in the prokaryotic tree of life: How synonymous codons are differentially selected in sequence domains with different expression levels and degrees of conservation.

Prokaryote genomes exhibit a wide range of GC contents and codon usages, both resulting from an interaction between mutational bias and natural selection. In order to investigate the basis underlying specific codon changes, we performed a comprehensive analysis of 29-different prokaryote families. The analysis of core-gene sets with increasing ancestries in each family lineage revealed that the codon usages became progressively more adapted to the tRNA pools. While, as previously reported, highly-expressed genes presented the more optimized codon usage, the singletons contained the less selectively-favored codons. Results showed that usually codons with the highest translational adaptation were preferentially enriched. In agreement with previous reports, a C-bias in 2- to 3-fold codons, and a U-bias in 4-fold codons occurred in all families, irrespective of the global genomic-GC content. Furthermore, the U-biases suggested that U3-mRNA-U34-tRNA interactions were responsible for a prominent codon optimization in both the more ancestral core and the highly expressed genes. A comparative analysis of sequences that encode conserved-(cr) or variable-(vr) translated products, with each one being under high- (HEP) and low- (LEP) expression levels, demonstrated that the efficiency was more relevant (by a factor of 2) than accuracy to modelling codon usage. Finally, analysis of the third position of codons (GC3) revealed that, in genomes of global-GC contents higher than 35-40%, selection favored a GC3 increase; whereas in genomes with very low-GC contents, a decrease in GC3 occurred. A comprehensive final model is presented where all patterns of codon usage variations are condensed in five-distinct behavioral groups. IMPORTANCEThe prokaryotic genomes--the current heritage of the more ancient life forms on earth-- are comprised of diverse gene sets; all characterized by varied origins, ancestries, and spatial-temporal-expression patterns. Such genetic diversity has for a long time raised the question of how cells shape their coding strategies to optimize protein demands (i.e., product abundance) and accuracy (i.e., translation fidelity) through the use of the same genetic code in genomes with GC-contents that range from less than 20 to over 80%. In this work, we present evidence on how codon usage is adjusted in the prokaryote tree of life, and on how specific biases have operated to improve translation. Through the use of proteome data, we characterized conserved and variable sequence domains in genes of either high- or low-expression level, and quantitated the relative weight of efficiency and accuracy--as well as their interaction--in shaping codon usage in prokaryotes.

microbiology↗

bioRxiv2018

\"Protein composition of the occlusion bodies of Epinotia aporema granulovirus\"

Within family Baculoviridae, members of the Betabaculovirus genus are employed as biocontrol agents against lepidopteran pests, either alone or in combination with selected members of the Alphabaculovirus genus. Epinotia aporema granulovirus (EpapGV) is a fast killing betabaculovirus that infects the bean shoot borer (E. aporema) and is a promising biopesticide. Because occlusion bodies (OBs) play a key role in baculovirus horizontal transmission, we investigated the composition of EpapGV OBs. Using mass spectrometry-based proteomics we could identify 56 proteins that are included in the OBs during the final stages of larval infection. Our data provides experimental validation of several annotated hypothetical coding sequences. Proteogenomic mapping against genomic sequence detected a previously unannotated ac110-like core gene and a putative translation fusion product of ORFs epap48 and epap49. Comparative studies of the proteomes available for the family Baculoviridae highlight the conservation of core gene products as parts of the occluded virion. Two proteins specific for betabaculoviruses (Epap48 and Epap95) are incorporated into OBs. Moreover, quantification based on emPAI values showed that Epap95 is one of the most abundant components of EpapGV OBs.

microbiology↗