Abstract: Understanding how prokaryotic genomes coordinate nucleotide composition and gene distribution is a central yet unresolved question in genome evolution. Across different genomes, GC-content, nucleotide asymmetries, and biased gene distribution between replication strands are tightly associated, but existing explanations typically address only individual components and lack a unified causal framework. Here, by analyzing 4012 complete sequences, we show that the variation in GC-content, together with intrinsic constraints imposed by the genetic code and selection, can account for the coordinated evolution of GC-skew, AT-skew, and gene strand bias (GS-bias). We show that decreasing GC-content inevitably influences both synonymous codon usage and amino acid usage, thereby enforcing stronger GC- and AT-skews in coding genes and driving a shift between “typical” (GC-skew > 0, AT-skew < 0, and GS-bias > 0 in the leading strand) and “atypical” (GC-skew > 0, AT-skew > 0, and GS-bias > 0) modes of organization. Grounded in first principles, we propose an evolutionary framework that integrates previously proposed hypotheses. This framework explains why atypical organization emerges primarily in low-GC genomes, reveals that mutational biases likely evolved to accommodate the skew requirements of coding genes, and highlights the importance of internal constraints on prokaryotic genome evolution.