Where a Gene Sits on the Bacterial Chromosome May Shape Its Expression Through Selection

In the crowded interior of a bacterial cell, location matters. A new study published in PLOS Genetics by Ruiqi Yuan and Jianzhi Zhang suggests that the positions of genes along bacterial chromosomes are not random, but instead bear the fingerprints of natural selection acting on how much proteins those genes produce. The research, which draws on eight large protein expression datasets from three bacterial species, provides some of the most systematic evidence yet that where a gene sits relative to the replication origin can influence both its average expression and the way its expression changes as cells grow faster or slower.

The biological logic behind the finding begins with a quirk of bacterial genome architecture. Most bacteria carry a single circular chromosome that is copied by two replication forks starting from a fixed site called the origin, or oriC, and meeting at the opposite point, the terminus, or ter. This arrangement means that genes lying close to the origin are copied earlier in the cell cycle and, crucially, are present in more copies than genes near the terminus. The disparity becomes especially pronounced during rapid growth, when bacterial cells initiate new rounds of replication before the previous ones finish. Under those conditions, an origin-proximal gene may exist in several copies at once, while a terminus-proximal gene lingers as a single copy. More gene copies generally mean more messenger RNA templates, and therefore more protein, all else being equal.

That copy-number gradient creates an opportunity for evolution. If moving a gene closer to the origin raises its expression, then mutations that relocate genes, or that fine-tune their promoters to compensate for their position, could be favored or disfavored by selection. Scientists have proposed two hypotheses about what exactly selection is optimizing. The first, called the mean expression hypothesis, holds that selection cares about a gene’s average expression level across the range of environments a bacterium encounters. Under this view, highly expressed genes should gradually drift toward the origin over evolutionary time, where the replication-dose effect boosts their output. The second, the growth-dependent expression hypothesis, focuses instead on the slope of expression: how much a gene’s expression changes per unit change in growth rate. Genes whose products are needed more urgently during fast growth, such as the machinery of protein synthesis, would benefit from placement near the origin, where the dose effect amplifies their growth-linked responsiveness.

Testing these ideas requires expression measurements across many growth conditions, and that is precisely what Yuan and Zhang assembled. They analyzed eight multi-environment protein expression datasets spanning three bacterial species, together with measurements of promoter strength in Escherichia coli taken under two different environments. For each gene, they could estimate both its mean expression across conditions and its expression slope with respect to growth rate, and then ask whether these quantities vary systematically with chromosomal position from origin to terminus.

The answer, in short, is yes, but with important nuances. Consistent with both hypotheses, the researchers observed a significant decrease in mean expression from origin to terminus in six of the eight datasets. The expression slope showed the same directional gradient in four of the eight datasets. In other words, genes near the replication origin tend not only to be more highly expressed on average, but also to ramp up their expression more steeply as growth accelerates. Both patterns match the predictions of the replication-dose model, and both are consistent with the idea that selection has shaped gene placement, at least in part, through the copy-number consequences of chromosomal position.

To weigh the two hypotheses against each other, the team built regression models that predict a gene’s chromosomal position from its expression properties. The relative contributions of mean expression and growth-dependent expression turned out to differ across species, suggesting that no single rule governs gene positioning in all bacteria. In some lineages the average-expression signal dominates, while in others the growth-dependence signal carries more weight. The authors emphasize that the two hypotheses are not mutually exclusive; a gene’s position may simultaneously reflect selection on its typical output and on how that output scales with growth rate.

Perhaps the most sobering result is how little of the overall pattern these two forces explain. Even when combined, the mean expression and growth-dependent expression hypotheses accounted for only a small fraction of the variation in chromosomal gene positioning. The researchers attribute this partly to the incompleteness of the replication-dose effect itself: compensatory evolution of individual promoter strengths can erode the positional gradient. A gene that drifted toward the terminus, for example, might evolve a stronger promoter that restores its expression to the required level, weakening the observable correlation between position and expression. Chromosomal location, in other words, is one lever among many that evolution can pull when tuning gene expression, and its influence is partially masked by the others.

The study also identified which kinds of genes drive the positional gradients. The patterns in both mean expression and growth-dependent expression were disproportionately contributed by genes involved in translation and transcription, the core processes of making proteins and reading them out of DNA. These are exactly the functions whose demand rises sharply during rapid growth, so their enrichment near the origin fits the growth-dependent hypothesis particularly well. Genes with other functions contributed far less to the gradients, indicating that the selective pressure of replication-associated gene dosage has acted most strongly on the expression economics of the cell’s growth machinery.

Taken together, the findings paint a picture of bacterial chromosome organization as a landscape shaped by moderate but real selective forces. The authors conclude that patterns of chromosomal gene positioning are consistent with selection acting on both mean and growth-dependent expression, with the strength and balance of these effects varying among species. The work reframes the bacterial chromosome not merely as a container of genes but as an expression-regulating structure in its own right, where the geography of replication imprints a dose gradient that evolution has exploited, and partially erased, over millions of years.

For the broader field, the study offers a framework for interpreting genome organization in terms of expression physiology rather than sequence alone. As multi-environment expression datasets accumulate for more bacterial species, the comparative approach used by Yuan and Zhang can be extended to test whether the origin-to-terminus gradients in mean expression and growth responsiveness are universal features of prokaryotic genomes or lineage-specific adaptations. It also raises new questions about the interplay between gene relocation, promoter evolution, and the demands of fast growth, questions that sit at the intersection of genome evolution, gene regulation, and the ecology of microbial life. What emerges from this analysis is a subtle but compelling message: in bacteria, the address of a gene on its chromosome is part of its regulatory identity, and natural selection has been reading, and writing, that address all along.

Subject of Research: Evolutionary shaping of bacterial chromosomal gene positioning by selection on mean and growth-dependent gene expression

Article Title: Bacterial chromosomal gene positioning is likely shaped by selection on both mean and growth-dependent expression

Article References: Yuan, R., & Zhang, J. (2026). Bacterial chromosomal gene positioning is likely shaped by selection on both mean and growth-dependent expression. PLOS Genetics, 22(9), e1012316. https://doi.org/10.1371/journal.pgen.1012316

Image Credits: AI Generated

DOI: 10.1371/journal.pgen.1012316

Keywords: bacteria, chromosome organization, gene expression, replication origin, gene dosage, natural selection, PLOS Genetics, Escherichia coli, promoter evolution, translation, transcription, genome evolution