Biology subjects

Maachi, A.

Publications and source records attributed to Maachi, A..

5 recordsLinked to original sources

bioRxiv2026

The DGKK mRNA is a primary target of the Prader-Willi syndrome-associated snoRNA SNORD116

Box C/D small nucleolar RNAs (SNORDs) classically guide site-specific modification of ribosomal RNAs through antisense elements located upstream of their D[prime] and D boxes, termed ASE1 and ASE2. Yet many orphan SNORDs have no established primary targets, including the paternally expressed multicopy SNORD116 family implicated in Prader-Willi syndrome. Our previous comparative analysis identified the DGKK/Dgkk interaction as the most evolutionarily persistent candidate involving the highly conserved SNORD116 ASE1 sequence and showed that SNORD116 depletion increases DGKK RNA abundance in human cells. Here, we re-evaluated this interaction alongside a focused set of recently published candidates and asked whether evolutionary persistence was accompanied by independent evidence of regulation. DGKK/Dgkk showed reproducible increases following transient SNORD116 loss across human iPSC-derived neural cells and in brain tissues from Snord116-knockout mice. Its predicted SNORD116 interaction site combined a marked local depletion of human sequence variation with an overlapping cis-regulatory interval identified in mouse. SNORD116 deficiency was also associated with increased endogenous DGK[kappa]; protein across several mouse brain regions, including the hypothalamus. More broadly, comparison across the candidate set showed that evolutionary persistence, duplex stability and expression response did not systematically align, indicating that sequence-based properties alone do not allow reliable prediction of responses to SNORD116 loss. Together, these data support DGKK/Dgkk as the best-supported primary regulatory target of SNORD116 to date and establish it as a model for dissecting the regulatory mechanism of this orphan snoRNA family.

molecular biology↗

bioRxiv2026

Genetic diversity of tomato brown rugose fruit virus in Morocco

Tomato brown rugose fruit virus (Tobamovirus fructirugosum) is an emerging virus that affects tomatoes, capsicum, and chili. Since its first detection in Jordan in 2015, the virus was reported in more than 40 countries across all the continents. In Morocco, the virus was reported for the first time in October 2021. However, its genetic diversity remains unexplored. In this work, we used a collection of tomato fruits from local markets to investigate the variability of the virus in the country. We explored the different pressures acting on the N-terminus of the RNA-dependent RNA polymerase, the movement protein, and the coat protein genes. Then, we used haplotype network analyses to reveal the population structure within the Moroccan isolates and studied their relationships with the ones from the world. We found that genetic diversity is low, which is consistent with the global situation. No signatures of diversifying selection were detected across the analyzed genes. However, the virus sequences from Morocco showed a clear geographic structure, suggesting that geographic factors probably combined with agricultural practices may contribute to shaping the population structure of ToBRFV in Morocco.

microbiology↗

bioRxiv2025

Multiple origins, one function: evolutionary pathways of HSP70 proteins in viruses

Heat shock proteins 70 (HSP70) are highly conserved molecular chaperones found across all domains of life, where they play essential roles in cellular stress responses. While HSP70 homologs have been previously identified in closteroviruses (ssRNA viruses), their broader presence and evolutionary history in viruses remain poorly understood. In this study, we conducted a comprehensive search of viral protein databases and identified HSP70 homologs in viruses beyond ssRNA, including dsDNA viruses from the classes Megaviricetes and Caudoviricetes. These viral HSP70s exhibit diverse gene organizations, copy numbers, and structural features. Notably, HSP70s from Megaviricetes showed up to three gene copies per genome and distinct structural motifs, while those from closteroviruses displayed higher sequence and structural diversity, suggesting faster evolutionary rates. Structural and phylogenetic analyses revealed two major clusters of viral HSP70s, with dsDNA virus HSP70s closely resembling those of their protist hosts, supporting the hypothesis of horizontal gene transfer. In contrast, ssRNA virus HSP70s formed a distinct, highly divergent group. Our findings suggest multiple independent acquisitions of HSP70 genes by viruses and provide new insights into their evolutionary trajectories and potential functional adaptations.

evolutionary biology↗

bioRxiv2023

Evidence for gene transfer between mycoviruses and their host: Curvulaviridae as a case study

Gene transfer between distinct evolutionary lineages has been recognized as a frequent event occurring between viruses and their hosts. This phenomenon has been studied to some extent in animal and plant viruses, not so much in the case of mycoviruses, for which the evolutionary origins of their proteins remain poorly understood. In this study, we have tested the hypothesis of a mosaic origin for mycoviruses genomes, with the RNA-dependent RNA-polymerase (RdRp) being of viral origin and the coat protein (CP) resulting from one or more transfer events from the host genome. Firstly, phylogenetic trees were constructed for the RdRps and the CPs from a selection of viruses to address for possible incongruent evolutionary histories. Moreover, a PSI-BLAST search using the CP sequences from the different mycovirus groups retrieved hypothetical proteins (HP) with many orthologues in fungal genomes showing significant sequence homology with the CP from the members within the Curvulaviridae family. The structures of these HPs, predicted in silico using AlphaFold, tend to show high similarity with viral CPs suggesting the occurrence of gene transfer between viruses and fungi, although no clear function has been yet attributed to these genes in the host. Phylogenetic analyses suggest that this gene transfer could have occurred in multiple independent events. Additional selection analysis supports the notion that the most parsimonious explanation is the transfer of the HP from the host to an ancestral viral genome followed by fast evolution to accommodate the newly acquired protein to function as a CP.

microbiology↗

bioRxiv2020

Date palm virus A: first plant virus found in date palm trees

In this work, a novel ssRNA (+) viral genomic sequence with gene organization typical of members of the subfamily Quinvirinae (family Betaflexiviridae) was identified using high throughput sequencing data of date palm obtained from the Sequence Read Archive database. The viral genome sequence consists of 7860 nucleotides and contains five ORFs encoding for the replication protein (Rep), triple gene block proteins 1, 2, 3 (TGB 1, 2 and 3) and coat protein (CP). Phylogenetic analysis based on the Rep and the CP amino acid sequences showed the closest relationship to garlic yellow mosaic-associated virus (GYMaV). Based on the demarcation criteria of the family Betaflexiviridae, this new virus, provisionally named date palm virus A (DPVA), could constitute a member of a novel genus. However, considering that DPVA and GYMaV share the same genomic organization and that they cluster together on the Rep phylogenetic analysis, they could also constitute a novel genus together, highlighting the necessity of a revision of the taxonomic criteria of the family Betaflexiviridae.

plant biology↗