Scaling laws of bacterial and archaeal plasmids

The capacity of a plasmid to express genes is constrained by its length and copy number. However, the interplay between these parameters and their constraints on plasmid evolution have remained elusive due to the absence of comprehensive quantitative analyses. Here, we present ‘Pseudoalignment and P...

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Vydáno v:	Nature communications Ročník 16; číslo 1; s. 6023 - 14
Hlavní autoři:	Maddamsetti, Rohan, Shyti, Irida, Wilson, Maggie L., Son, Hye-In, Baig, Yasa, Zhou, Zhengqing, Lu, Jia, You, Lingchong
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London Nature Publishing Group UK 02.07.2025 Nature Publishing Group Nature Portfolio
Témata:	45 631/114/2409 631/181 631/208/212/2305 631/326/41 631/326/41/2530 Archaea - genetics Bacteria Bacteria - genetics Biology Chromosomes Computational Biology - methods Computer applications Constraints Copy number Correlation Datasets Estimates Evolution Evolution, Molecular Functional morphology Gene Dosage Gene expression Genes Genetic engineering Genome, Archaeal - genetics Genome, Bacterial - genetics Genomes Genomics Humanities and Social Sciences Microorganisms multidisciplinary Parameters Plasmids Plasmids - genetics Scaling Scaling laws Science Science (multidisciplinary)
ISSN:	2041-1723, 2041-1723
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Shrnutí:	The capacity of a plasmid to express genes is constrained by its length and copy number. However, the interplay between these parameters and their constraints on plasmid evolution have remained elusive due to the absence of comprehensive quantitative analyses. Here, we present ‘Pseudoalignment and Probabilistic Iterative Read Assignment’ (pseuPIRA), a computational method that overcomes previous computational bottlenecks, enabling rapid and accurate determination of plasmid copy numbers at large scale. We apply pseuPIRA to all microbial genomes in the NCBI RefSeq database with linked short-read sequencing data (4644 bacterial and archaeal genomes including 12,006 plasmids). The analysis reveals three scaling laws of plasmids: first, an inverse power-law correlation between plasmid copy number and plasmid length; second, a positive linear correlation between protein-coding genes and plasmid length; and third, a positive correlation between metabolic genes per plasmid and plasmid length, particularly for large plasmids. These scaling laws imply fundamental constraints on plasmid evolution and functional organization, indicating that as plasmids increase in length, they converge toward chromosomal characteristics in copy number and functional content. The capacity of a plasmid to express genes is constrained by parameters such as its length and copy number. Here, Maddamsetti et al. present a computational method that enables rapid and accurate determination of plasmid copy numbers at a large scale, revealing fundamental constraints on these parameters and thus on plasmid evolution and functional organization.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	2041-1723 2041-1723
DOI:	10.1038/s41467-025-61205-2