Biology subjects

Zaher, H.

Publications and source records attributed to Zaher, H..

4 recordsLinked to original sources

bioRxiv2024

Genome-wide association analysis of flowering date in a collection of cultivated olive tree

1.Flowering date in perennial fruit trees is an important trait for fruit production. Depending on the winter and spring temperatures, flowering of olive may be advanced, delayed, or even suppressed. Deciphering the genetic control of flowering date is thus key to help selecting cultivars better adapted to the current climate context. Here, we investigated the genetic determinism of full flowering date stage in cultivated olive based on capture sequencing data of 318 genotypes from the worldwide olive germplasm bank of Marrakech, Morocco. The genetic structure of this collection was organized in three clusters that were broadly attributed to eastern, central, and western Mediterranean regions, based on the presumed origin of genotypes. Flowering dates, collected over seven years, were used to estimate the genotypic best linear unbiased predictors, which were then analyzed in a genome-wide association study. Loci with small effects were significantly associated with the studied trait, by either a single- or a multi-locus approach. The three most robust loci were located on chromosomes 01 and 04, and on a scaffold, and explained 7.1%, 6.2%, and 6.5 % of the trait variance, respectively. A significantly higher accuracy in the best linear unbiased predictors of flowering date prediction was reported with Ridge-compared to LASSO-based genomic prediction model. Along with genomic association results, this suggests a complex polygenic determinism of flowering date, as seen in many other fruit perennials. These results and the screening of associated regions for candidate genes open perspectives for further studies and breeding programs targeting flowering date.

genetics↗

bioRxiv2021

Differential viral RNA methylation contributes to pathogen blocking in Wolbachia-colonized arthropod

Arthropod endosymbiont Wolbachia pipientis is part of a global biocontrol strategy to reduce the replication of mosquito-borne RNA viruses such as alphaviruses. We previously demonstrated the importance of a host cytosine methyltransferase, DNMT2, in Drosophila and viral RNA as a cellular target during pathogen-blocking. Here we report on the role of DNMT2 in Wolbachia-induced alphavirus inhibition in Aedes species. Expression of DNMT2 in mosquito tissues, including the salivary glands, is elevated upon virus infection. Notably, this is suppressed in Wolbachia-colonized animals, coincident with reduced virus replication and decreased infectivity of progeny virus. Ectopic expression of DNMT2 in cultured Aedes cells is proviral, increasing progeny virus infectivity, and this effect of DNMT2 on virus replication and infectivity is dependent on its methyltransferase activity. Finally, examining the effects of Wolbachia on modifications of viral RNA by LC-MS show a decrease in the amount of 5-methylcytosine modification consistent with the down-regulation of DNMT2 in Wolbachia colonized mosquito cells and animals. Collectively, our findings support the conclusion that disruption of 5-methylcytosine modification of viral RNA is a vital mechanism operative in pathogen blocking. These data also emphasize the essential role of epitranscriptomic modifications in regulating fundamental alphavirus replication and transmission processes.

microbiology↗

bioRxiv2019

Short translational ramp determines efficiency of protein synthesis

It is generally assumed that translation efficiency is governed by translation initiation. However, the efficiency of protein synthesis is regulated by multiple factors including tRNA abundance, codon composition, mRNA motifs and amino-acid sequence1-4. These factors influence the rate of protein synthesis beyond the initiation phase of translation, typically by modulating the rate of peptide-bond formation and to a lesser extent that of translocation. The slowdown in translation during the early elongation phase, known as the 5 translational ramp, likely contributes to the efficiency of protein synthesis 5-9. Multiple mechanisms, which could explain the molecular basis for this translational ramp, have been proposed that include tRNA abundance bias6,9, the rate of translation initiation10-15, mRNA and ribosome structure 11,12,14,16-18, or retention of initiation factors during early elongation events 19. Here, we show that the amount of synthesized protein (translation efficiency) depends on a short translational ramp that comprises the first 5 codons in mRNA. Using a library of more than 250,000 reporter sequences combined with in vitro and in vivo protein expression assays, we show that differences in the short ramp can lead to 3 to 4 orders of magnitude changes in protein abundance. The observed difference is not dependent on tRNA abundance, efficiency of translation initiation, or overall mRNA structure. Instead, we show that translation is regulated by amino-acid-sequence composition and local mRNA sequence. Single-molecule measurements of translation kinetics indicate substantial pausing of ribosome and abortion of protein synthesis on the 4th or 5th codon for distinct amino acid or nucleotide compositions. Introduction of preferred sequence motifs, only at the exact positions within the mRNA, improves protein synthesis for recombinant proteins, indicating an evolutionarily conserved mechanism for controlling translational efficiency.

molecular biology↗

bioRxiv2018

Natural selection on gene-specific codon usage bias is common across eukaryotes

Although the actual molecular evolutionary forces that shape differences in codon usage across species remain poorly understood, majority of synonymous mutations are assumed to be functionally neutral because they do not affect protein sequences. However, empirical studies suggest that some synonymous mutations can have phenotypic consequences. Here we show that in contrast to the current dogma, natural selection on gene-specific codon usage bias is common across Eukaryota. Furthermore, by using bioinformatic and experimental approaches, we demonstrate that specific combinations of rare codons contribute to the spatial and sex-related regulation of some protein-coding genes in Drosophila melanogaster. Together, these data indicate that natural selection can shape gene-specific codon usage bias, which therefore, represents an overlooked genomic feature that is likely to play an important role in the spatial and temporal regulation of gene functions. Hence, the broadly accepted dogma that synonymous mutations are in general functionally neutral should be reconsidered.

evolutionary biology↗