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Abstract

Operons (clusters of co-regulated genes with related functions) are common features of bacterial genomes. More recently, functional gene clustering has been reported in eukaryotes, from yeasts to filamentous fungi, plants, and animals. Gene clusters can consist of paralogous genes that have most likely arisen by gene duplication. However, there are now many examples of eukaryotic gene clusters that contain functionally related but non-homologous genes and that represent functional gene organizations with operon-like features (physical clustering and co-regulation). These include gene clusters for use of different carbon and nitrogen sources in yeasts, for production of antibiotics, toxins, and virulence determinants in filamentous fungi, for production of defense compounds in plants, and for innate and adaptive immunity in animals (the major histocompatibility locus). The aim of this article is to review features of functional gene clusters in prokaryotes and eukaryotes and the significance of clustering for effective function. Keywords Metabolism
Natural products
Antibiotics
Pathogens
Defense
Chromatin
Development
Innate and adaptive immunity

Introduction Operons (clusters of co-regulated genes with related functions) are a well-known feature of prokaryotic genomes. Archeal and bacterial genomes generally contain a small number of highly conserved operons and a much larger number of unique or rare ones [1]. Functional gene clustering also occurs in eukaryotes, from yeasts to filamentous fungi, mammals, nematodes, and plants [2]. The members of these eukaryotic gene clusters contribute to a common function but do not usually share sequence similarity. These gene clusters therefore represent functional gene organizations with operon-like features (physical clustering and co-regulation), although the genes are not usually transcribed as a single mRNA as is the case in prokaryotes. This article reviews facets of genome organization in prokaryotes and eukaryotes that are of relevance for understanding the significance of the establishment, maintenance, and dissipation of functional gene clusters and the evolutionary forces that shape genome architecture. Classical operons The term ‘‘operon’’ was coined by Jacob and Monod [3–۵], who characterized the first defined classical operon, the lac operon, in Escherichia coli. The lac operon consists of three structural genes that are required for lactose utilisation, lacZ, lacY, and lacA (Fig. 1). These genes encode a b-galactosidase, a lac permease, and a transacetylase, respectively. The first step in lactose metabolism is catalyzed by b-galactosidase, which cleaves lactose into galactose and glucose. Lactose is then taken up by the transmembrane protein, lac permease

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