Biology subjects

Rogers, D. W.

Publications and source records attributed to Rogers, D. W..

6 recordsLinked to original sources

bioRxiv2026

Forging an evolutionary individual from separate replicators

Major evolutionary transitions occur when independently replicating particles unite into a higher-level individual. How selection comes to work on particle collectives and generates reliable heredity is unresolved. By packaging red and green plasmids in yeast cells we made plasmid communities units of selection: cell boundaries supplied discreteness, segregation generated variation, and cell division reproduced communities. Communities colouring cells yellow were preferentially propagated. Initially, yellow parents rarely produced yellow offspring, but continued selection aligned replicative fates of the two plasmids favouring recombinants that fused with the endogenous 2-micron element. Chimera stability was secured by mutations in FLP1, which encodes a recombinase that otherwise resolves fused replicons. Reliable collective heredity, here, a derived product of higher-level selection, marked completion of an evolutionary transition in individuality.

evolutionary biology↗

bioRxiv2026

Model-based inference of gene expression noise from single-cell RNA-sequencing data

The heterogeneity of expression levels among genetically identical cells, termed gene expression noise, is a property of the gene expression process whose importance in the biology of organisms and their evolution is increasingly recognized. Measuring gene expression noise requires single-cell expression data, as obtained from single-cell RNA sequencing (scRNASeq). Its estimation, however, is challenging owing to (i) the presence of technical noise in addition to biological noise, and (ii) the heterogeneity of cell types in the sampled population. We propose a maximum-likelihood framework to infer biological noise from scRNASeq data, while accounting for technical noise, dropout probabilities, and distinct cell sequencing depths. We demonstrate the parameter identifiability using simulations and that the resulting noise estimates are uncorrelated from the mean gene expression, and therefore do not need extra correction in downstream analyses, easing intra- and inter-genome comparisons. Using two technical replicates of scR-NASeq data from the wild yeast Saccharomyces paradoxus, we show that expression noise can be inferred in a reproducible manner.

bioinformatics↗

bioRxiv2026

Transcriptomic dissection of genetically diverse Wrinkly Spreader mutants reveals hidden layers of complexity

Understanding the genetic basis of adaptive traits requires linking mutation to phenotypic change and fit-ness. The Wrinkly Spreader (WS) mutants of Pseudomonas fluorescens SBW25, which colonize the air-liquid interface (ALI) in static microcosms, provide a model for dissecting genotype-phenotype relationships. Muta-tions generating the WS phenotype cause constitutive activation of regulatory pathways synthesising cyclic bis-(3,5)-dimeric guanosine monophosphate (c-di-GMP) leading to over-production of cellulose encoded by the wss operon. Using RNA-seq on 14 independently evolved WS mutants, each carrying a single characterised mutation in one of 14 different genes affecting production of c-di-GMP, we report that transcriptional responses are highly genotype specific, with few differentially expressed genes (DEGs) shared among WS mutants. Genes showing greatest variance in expression included fimbrial and matrix-associated loci such as fap, cupE and pga. fap and cupE were the only fimbriae-related loci active in these mutants. Targeted deletions of these candidate loci revealed subtle phenotypic and fitness effects. Closer examination of the fap locus showed that its expression is genotype dependent, restricted to a minority of cells, and associated with stability in early stages of mat formation. Overall, our results confirm that previous suppressor-based approaches have captured the major genetic components of the WS phenotype: cellulose encoded by the wss operon and regulated by elevated c-di-GMP. At the same time, it is apparent that morphology-based screens have failed to detect genes having more subtle effects, whose contributions influence success of WS mutants at the ALI. These findings reveal additional layers of complexity that underscore the polygenic nature of the WS phenotype.

microbiology↗

bioRxiv2024

Experimental capture of genomic islands defines a widespread class of genetic element capable of non-autonomous transfer

Bacteria acquire new genes by horizontal gene transfer (HGT), typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages and certain integrative and conjugative elements (ICEs) are well characterized, the broader diversity of MGEs remains poorly understood. Here, we propagated the bacterium Pseudomonas fluorescens SBW25 in the presence of filtrate obtained from garden compost communities. Genome sequencing of derived colonies revealed acquisition of three different mobile elements, each integrated immediately downstream of tmRNA, flanked by direct repeats, and encoding a tyrosine integrase (intY) and putative phage defense systems. Absent are genes with recognized roles in autonomous transfer. Interrogation of DNA sequence databases showed that similar elements are widespread in the genus Pseudomonas and beyond, with Vibrio Pathogenicity Island-1 (VPI-1) from V. cholerae as a notable example. Bioinformatic analyses demonstrate frequent horizontal transfer among diverse hosts. Detailed analysis of a single element, I55, showed that it is transferred between cells by a jumbo phage, and confers a fitness benefit via a type II restriction-modification system. Significance StatementThe impact of horizontal gene transfer on the evolution of bacteria outpaces that driven by spontaneous mutation, but knowledge of the range of mediators, the genes mobilized, and the mechanisms of movement have largely depended on inferences stemming from bioinformatics. Here we describe a real-time evolution experiment in which a single focal strain propagated with filtrate from a complex microbial community captured genetic elements carrying a diverse cargo of genes whose mobility was previously uncharacterized. The elements represent a widespread class of mobile DNA dependent only on a tyrosine integrase targeting a highly conserved genomic site. Genetic analysis of one element shows that it confers a significant fitness advantage via defense against bacteriophages, and hijacks a jumbo bacteriophage for intercellular transfer. Our findings reveal new insights into the hidden diversity and dynamics of MGEs in natural environments. ClassificationBiological Sciences / Microbiology

microbiology↗

bioRxiv2018

Evolution of mating types in finite populations: the precarious advantage of being rare

Sexually reproducing populations with self-incompatibility bear the cost of limiting potential mates to individuals of a different type. Rare mating types escape this cost since they are unlikely to encounter incompatible partners, leading to the deterministic prediction of continuous invasion by new mutants and an ever increasing number of types. However, rare types are also at an increased risk of being lost by random drift. Calculating the number of mating types that a population can maintain requires consideration of both the deterministic advantages and the stochastic risks. By comparing the relative importance of selection and drift, we show that a population of size N can maintain a maximum of approximately N1/3 mating types for intermediate population sizes while for large N we derive a formal estimate. Although the number of mating types in a population is quite stable, the rare type advantage promotes turnover of types. We derive explicit formulas for both the invasion and turnover probabilities in finite populations.

evolutionary biology↗

bioRxiv2017

Ribosome reinitiation can explain length-dependent translation of messenger RNA

Models of mRNA translation usually presume that transcripts are linear; upon reaching the end of a transcript each terminating ribosome returns to the cytoplasmic pool before initiating anew on a different transcript. A consequence of linear models is that faster translation of a given mRNA is unlikely to generate more of the encoded protein, particularly at low ribosome availability. Recent evidence indicates that eukaryotic mRNAs are circularized, potentially allowing terminating ribosomes to preferentially reinitiate on the same transcript. Here we model the effect of ribosome reinitiation on translation and show that, at high levels of reinitiation, protein synthesis rates are dominated by the time required to translate a given transcript. Our model provides a simple mechanistic explanation for many previously enigmatic features of eukaryotic translation, including the negative correlation of both ribosome densities and protein abundance on transcript length, the importance of codon usage in determining protein synthesis rates, and the negative correlation between transcript length and both codon adaptation and 5' mRNA folding energies. In contrast to linear models where translation is largely limited by initiation rates, our model reveals that all three stages of translation - initiation, elongation, and termination/reinitiation - determine protein synthesis rates even at low ribosome availability.

molecular biology↗