Biology subjects

Durand, E.

Publications and source records attributed to Durand, E..

3 recordsLinked to original sources

bioRxiv2018

In situ and high-resolution Cryo-EM structure of the Type VI secretion membrane complex

Bacteria have evolved macromolecular machineries that secrete effectors and toxins to survive and thrive in diverse environments. The type VI secretion system (T6SS) is a contractile machine that is related to Myoviridae phages. The T6SS is composed of a baseplate that contains a spike onto which an inner tube is built, surrounded by a contractile sheath. Unlike phages that are released to and act in the extracellular medium, the T6SS is an intracellular machine inserted in the bacterial membranes by a trans-envelope complex. This membrane complex (MC) comprises three proteins: TssJ, TssL and TssM. We previously reported the low-resolution negative stain electron microscopy structure of the enteroaggregative Escherichia coli MC and proposed a rotational 5-fold symmetry with a TssJ:TssL:TssM stoichiometry of 2:2:2. Here, cryo-electron tomography analysis of the T6SS MC confirmed the 5-fold symmetry in situ and identified the regions of the structure that insert into the bacterial membranes. A high resolution model obtained by single particle cryo-electron microscopy reveals its global architecture and highlights new features: five additional copies of TssJ, yielding a TssJ:TssL:TssM stoichiometry of 3:2:2, a 11-residue loop in TssM, protruding inside the lumen of the MC and constituting a functionally important periplasmic gate, and hinge regions. Based on these data, we revisit the model on the mechanism of action of the MC during T6SS assembly and function.

microbiology↗

bioRxiv2018

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Transposable elements (TEs) have initially been viewed as pure genomic parasites but are now recognized as central genome architects and powerful agents of rapid adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either recent or old insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. TE fragments that have been maintained in both species, i.e. those that are orthologous, tend to be located on average closer to genes than those that are retained in one species only. Moreover, compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing TE insertions when they are close to genes. Overall, our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.

evolutionary biology↗

bioRxiv2018

The high turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

Little is known about the rate of emergence of genes de novo, how they spread in populations and what their initial properties are. We examined wild yeast (Saccharomyces paradoxus) populations to characterize the diversity and turnover of intergenic ORFs over short evolutionary time-scales. With ~34,000 intergenic ORFs per individual genome for a total of ~64,000 orthogroups identified, we found de novo ORF formation to have a lower estimated turnover rate than gene duplication. Hundreds of intergenic ORFs show translation signatures similar to canonical genes. However, they have lower translation efficiency, which could reflect a mechanism to reduce their production cost or simply a lack of optimization. We experimentally confirmed the translation of many of these ORFs in laboratory conditions using a reporter assay. Translated intergenic ORFs tend to display low expression levels with sequence properties that generally are close to expectations based on intergenic sequences. However, some of the very recent translated intergenic ORFs, which appeared less than 110 Kya ago, already show gene- like characteristics, suggesting that the raw material for functional innovations could appear over short evolutionary time-scales.

evolutionary biology↗