Biology subjects

Ngan, W. Y.

Publications and source records attributed to Ngan, W. Y..

3 recordsLinked to original sources

bioRxiv2024

Empirical evidence of a role for insertion sequences in the repair of DNA breaks in bacterial genomes

Insertion Sequences (ISs) are mobile pieces of DNA that are widespread in bacterial genomes. IS movements typically involve (i) excision of the IS element, (ii) cutting of the target site DNA, and (iii) IS element insertion. This process generates a new copy of the IS element, as well as a short duplication at the target site. It has been noted that, when observing extant IS element copies in a genome, occasionally no Target Site Duplication (TSD) is readily identifiable. This has been attributed to degeneration of the TSD at some point after the insertion event. Here, we provide evidence that some IS movement events - namely, those that occur in association with large-scale genome rearrangements - occur without generating TSDs. In support of this hypothesis, we provide two direct, empirical observations of such IS transposition events: an IS481 movement occurring with a large duplication in Pseudomonas fluorescens SBW25, and an IS5/IS1182 movement plus a large deletion in Escherichia coli C. Additionally, we use sequencing data from the Lenski long-term evolution experiment to provide a further 14 examples of IS150 movements in E. coli B that are associated with large deletions and do not carry TSDs. Overall, our results indicate that some IS elements can insert into, and thus repair, existing DNA breaks in bacterial genomes.

evolutionary biology↗

bioRxiv2022

Large-scale duplication events underpin population-level flexibility in bacterial tRNA gene copy number

The complement of tRNA genes within a genome is typically considered to be a (relatively) stable characteristic of an organism. Here we demonstrate that bacterial tRNA gene set composition can be more flexible than previously appreciated, particularly regarding tRNA gene copy number. We report the high-rate occurrence of spontaneous, large-scale, tandem duplication events in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The identified duplications are up to [~]1 Mb in size ([~]15 % of the wildtype genome) and are predicted to change the copy number of up to 917 genes, including several tRNA genes. The observed duplications are inherently unstable: they occur, and are subsequently lost, at extremely high rates. We propose that this unusually plastic type of mutation provides a mechanism by which tRNA gene set diversity can be rapidly generated, while simultaneously preserving the underlying tRNA gene set in the absence of continued selection. That is, if a tRNA set variant provides no fitness advantage, then high-rate segregation of the duplication ensures the maintenance of the original tRNA gene set. However, if a tRNA gene set variant is beneficial, the underlying duplication fragment(s) may persist for longer and provide raw material for further, more stable, evolutionary change.

evolutionary biology↗

bioRxiv2022

The layered costs and benefits of translational redundancy

The rate and accuracy of translation hinges upon multiple components - including transfer RNA (tRNA) pools, tRNA modifying enzymes, and rRNA molecules - many of which are redundant in terms of gene copy number or function. It has been hypothesized that the redundancy evolves under selection, driven by its impacts on growth rate. However, we lack empirical measurements of the fitness costs and benefits of redundancy, and we have poor understanding of how this redundancy is organized across components. We manipulated redundancy in multiple translation components of Escherichia coli by deleting 28 tRNA genes, 3 tRNA modifying systems, and 4 rRNA operons in various combinations. We find that redundancy in tRNA pools is beneficial when nutrients are plentiful, and costly under nutrient limitation. This nutrient-dependent cost of redundant tRNA genes stems from upper limits to translation capacity and growth rate, and therefore varies as a function of the maximum growth rate attainable in a given nutrient niche. The loss of redundancy in rRNA genes and tRNA modifying enzymes had similar nutrient-dependent fitness consequences. Importantly, these effects are also contingent upon interactions across translation components, indicating a layered hierarchy from copy number of tRNA and rRNA genes to their expression and posttranscriptional modification. Overall, our results indicate both positive and negative selection on redundancy in translation components, depending on a species evolutionary history with feasts and famines.

evolutionary biology↗