2026-10-12T13:00:41Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33958611 2026-09-21T17:57:39Z category_8 category_13 category_14 category_24 category_39 category_734 category_61 category_64 category_132 category_133 portal_5 item_type_3 month_year_09_2026

<p>Datasets analyzed in the present study.</p> Ruiqi Yuan (25084989) Jianzhi Zhang (14669) Microbiology Genetics Molecular Biology Evolutionary Biology Ecology Biological Sciences not elsewhere classified Developmental Biology Cancer Infectious Diseases Plant Biology three bacterial species promoter strengths measured individual promoter strengths analyze eight multi escherichia coli </ div >< p expression slope — dependent expression hypothesis chromosomal gene positioning two hypotheses explain replication origin (< mean expression hypothesis expression slope dependent expression gene expression two environments terminus (< eight datasets chromosomal position expression level gene ’ ter </ oric </ small fraction significant decrease replicated earlier relative support relative contributions positional gradients mutations altering moderate effects likely shaped incompletely offset genes near genes involved dose effect disproportionately contributed compensatory evolution circular chromosomes >), particularly <div><p>In bacteria with circular chromosomes, genes near the replication origin (<i>oriC</i>) are replicated earlier and consequently attain higher copy numbers than genes near the terminus (<i>ter</i>), particularly during rapid growth. Hence, mutations altering a gene’s chromosomal position can affect its expression level and be subject to selection. Two non–mutually exclusive hypotheses regarding the target of this selection have been proposed. The mean expression hypothesis (MEH) posits that the target is a gene’s average expression across environments, whereas the growth-dependent expression hypothesis (GEH) proposes that the target is the growth dependence of gene expression, quantified by the expression slope—the change in expression level per unit change in growth rate. To test these hypotheses and assess their relative support, we analyze eight multi-environment protein expression datasets from three bacterial species, as well as <i>Escherichia coli</i> promoter strengths measured in two environments. Consistent with both MEH and GEH, we observe a significant decrease in both mean expression and expression slope from <i>oriC</i> to <i>ter</i> in six and four of the eight datasets, respectively. In regression models predicting gene position, the relative contributions of the two hypotheses differ across species. However, even when combined, the two hypotheses explain only a small fraction of chromosomal gene positioning, in part because the replication-dose effect is incompletely offset by compensatory evolution of individual promoter strengths. The positional gradients in mean and growth-dependent expression are disproportionately contributed by genes involved in translation and transcription. We conclude that patterns of bacterial chromosomal gene positioning are consistent with moderate effects of selection on both mean and growth-dependent expression.</p></div> 2026-09-21T17:57:33Z Dataset Dataset 10.1371/journal.pgen.1012316.t001 https://figshare.com/articles/dataset/_p_Datasets_analyzed_in_the_present_study_p_/33958611 CC BY 4.0