ArticleBiotech (Basel (Switzerland))2026
Co-Directional Chromosomal Clustering of Metabolic Pathway Genes as a Layout Prior for Synthetic Construct Design.
Article in Biotech (Basel (Switzerland)), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Metabolic pathway design tools largely address reaction routes and enzyme choice, whereas a complementary set of questions-how pathway genes are arranged on bacterial chromosomes and whether co-directional neighborhoods can inform multi-gene construct layout-has received comparatively little systematic treatment. Here, we present SynPAL (Synteny-Informed Pathway Assembly and Layout), a computational analysis that scores co-directional clustering of BioCyc pathway genes from genomic coordinates (same replicon and strand, intergenic distance ≤ 2000 bp) and translates the resulting scores into design-oriented hypotheses. On a core panel of 55 prokaryotes (887 analyzable pathways), medium or high clustering occurs for 290 pathways (32.7%), with a mean cluster score of 0.432 versus 0.262 under an organism-matched random-gene-set null; 692/887 pathways remain significant after Benjamini-Hochberg false-discovery-rate control at q<0.05. High scores recover classical operons, including
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