The evolution of gene collectives: How natural selection drives chemical innovation

Abstract

DNA sequencing has become central to the study of evolution. Comparing the sequences of individual genes from a variety of organisms has revolutionized our understanding of how single genes evolve, but the challenge of analyzing polygenic phenotypes has complicated efforts to study how genes evolve when they are part of a group that functions collectively. We suggest that biosynthetic gene clusters from microbes are ideal candidates for the evolutionary study of gene collectives; these selfish genetic elements evolve rapidly, they usually comprise a complete pathway, and they have a phenotype-a small molecule-that is easy to identify and assay. Because these elements are transferred horizontally as well as vertically, they also provide an opportunity to study the effects of horizontal transmission on gene evolution. We discuss known examples to begin addressing two fundamental questions about the evolution of biosynthetic gene clusters: How do they propagate by horizontal transfer? How do they change to create new molecules?

Fig. 1.

Propagation of gene clusters. (a) Horizontal transfer of the yersiniabactin gene cluster. The yersiniabactin gene clusters from Y. pestis KIM and P. syringae phaseolicola 1448A are shown, with related genes depicted in the same color to highlight intracluster gene rearrangements. (b) Horizontal transfer of the andrimid gene cluster. The andrimid gene clusters from Pantoea agglomerans CU2194 and Vibrionales bacterium SWAT-3 are shown; the only syntenic difference is the insertion of a single gene at the 3′ end of the latter cluster.

Fig. 2.

How individual genes in a cluster change. (a) A loss-of-function mutation leads to building-block diversity in FK520. Two modules from the FK520 PKS component FkbB are shown; the first module (red) has an active DH domain, whereas the second module (blue) has a mutationally inactivated DH domain (denoted by a lowercase “dh”). As a result, the first module modifies its three-carbon building block (red) so that it has a double bond, whereas the second module performs one fewer modification step to its building block (blue), leaving a hydroxyl group instead of a double bond. (b) Mutation and rearrangement of adenylation (A) domains creates diversity among the iturin family NRPs. The portions of the bacillomycin (Bam), iturin (Itu), and mycosubtilin (Myc) synthetases that insert the last 4 aa are shown at the top. A domains that are homologous to each other are depicted in the same color, and the building block they insert is listed above the domain. The chemical structures of bacillomycin D, iturin A, and mycosubtilin are shown at the bottom, and the residues are colored to correspond with the A domains. Mutation and divergent evolution of an ancestral A domain likely gave rise to the Glu/Gln- and Ser/Thr-inserting A domain families, whereas intragenic A domain rearrangement probably led to the differences among the three synthetases. (c) Module duplications within the mycolactone gene cluster. Modules that share >98% amino acid sequence identity are shown in the same color, and the chemical structure of mycolactone is shown with the building blocks resulting from the action of each module colored correspondingly. (d) Intergenic rearrangements lead to the chimerism between rapamycin and FK520. The chemical structures of rapamycin and FK520 are shown, with the identical “left halves” colored red and the distinct “right halves” colored black. Portions of the rapamycin and FK520 gene clusters are shown below, with homologous sections shown in the same color and divergent sections colored gray.

Fig. 3.

Changes to the number and identity of genes comprising a cluster. (a) Differences in the complement of peripheral genes encoding “tailoring” enzymes are a source of diversity in the glycopeptide antibiotics. The chemical structures of A47934 and teicoplanin are shown, with chemical groups unique to each molecule colored magenta, blue, green, or red. The A47934 and teicoplanin gene clusters are shown below, with the genes unique to each cluster colored yellow. (b) Differential tailoring of a common core in the aminoglycoside antibiotics. The chemical structures of neomycin B and butirosin B are shown with the 2-deoxystreptamine colored black, two peripheral components shared between these molecules colored red and blue, and peripheral components unique to each molecule colored brown and magenta. The neomycin and butirosin gene clusters are shown below, with genes shared between the two clusters colored green. (c) Subcluster joining gives rise to a new gene cluster. The chemical structures of clorobiocin, simocyclinone, and landomycin are shown with the aminocoumarin groups colored red and the anthracycline groups colored blue. The gene clusters for each molecule are shown at the right, with the aminocoumarin-producing subclusters colored red and the anthracycline-producing subclusters colored blue. Genes encoding putative conjugating enzymes are colored green.

Fig. 4.

Divergent biosynthetic evolution. (a) Genes with origins in primary metabolism. The 3,5-AHBA biosynthetic enzyme RifG and its homolog in the shikimate biosynthetic pathway, AroB, catalyze similar reactions. Shikimate is the precursor to the aromatic amino acids, whereas 3,5-AHBA is a precursor to the polyketides rifamycin and geldanamycin. The 3,5-AHBA-producing subcluster from the rifamycin gene cluster is shown below, with rifG colored green. (b) Duplication and divergence of gene clusters. Five lantibiotic gene clusters from the lacticin 481 family are shown; related genes are depicted in the same color to highlight the common features of the clusters. Adapted from ref. .

Fig. 5.

Convergent biosynthetic evolution. (a) Desferrioxamine, enterobactin, and carboxymycobactin are functionally convergent in that these unrelated molecules all bind iron. Their chemical structures are with chemical groups that are ligands to the iron, which is colored red. (b) Two different pathways for the formation of the terpene building-block isopentenyl pyrophosphate (IPP). The mevalonate pathway (red) converts acetyl-CoA to IPP using seven enzymes, whereas the nonmevalonate pathway (blue) uses six unrelated enzymes to convert glyceraldehyde-3-phosphate and pyruvate to IPP. (c) Convergent biosynthesis of the gibberellins. The plant (blue) and fungal (red) biosynthetic pathways for giberellic acid 3 involve two different sequences of chemical tailoring steps that yield identical small-molecule products.

Fig. 6.

Ancestral subclusters. A four-gene subcluster found in many different genetic contexts diverts the primary metabolite chorismate to an activated form of the secondary metabolite 2,3-dihydroxybenzoate (DHB). The chemical structures of the DHB-containing molecules enterobactin (ent), vibriobactin (vib), and vanchrobactin (vab) are shown with the DHB groups colored red. Their gene clusters are shown below, with the DHB subcluster genes shown in color. A portion of the vibriobactin gene cluster has been omitted for clarity.