GRINS: Genetic elements that recode assembly-line polyketide synthases and accelerate their diversification

Abstract

Assembly-line polyketide synthases (PKSs) are large and complex enzymatic machineries with a multimodular architecture, typically encoded in bacterial genomes by biosynthetic gene clusters. Their modularity has led to an astounding diversity of biosynthesized molecules, many with medical relevance. Thus, understanding the mechanisms that drive PKS evolution is fundamental for both functional prediction of natural PKSs as well as for the engineering of novel PKSs. Here, we describe a repetitive genetic element in assembly-line PKS genes which appears to play a role in accelerating the diversification of closely related biosynthetic clusters. We named this element GRINS: genetic repeats of intense nucleotide skews. GRINS appear to recode PKS protein regions with a biased nucleotide composition and to promote gene conversion. GRINS are present in a large number of assembly-line PKS gene clusters and are particularly widespread in the actinobacterial genus Streptomyces. While the molecular mechanisms associated with GRINS appearance, dissemination, and maintenance are unknown, the presence of GRINS in a broad range of bacterial phyla and gene families indicates that these genetic elements could play a fundamental role in protein evolution.

Insights into azalomycin F assembly-line contribute to evolution-guided polyketide synthase engineering and identification of intermodular recognition

“…Recently, gene duplication and conversion have been proposed to explain the evolution of the PKS assembly-lines 29 , 30 . Nivina and coworkers showed that the gene conversion of genetic repeats of intense nucleotide skews (GRINS) recode and accelerate the diversification of the PKS assembly-line, and recombination between GRINS was also observed via a bioinformatics analysis 30 , 31 .…”

Insights into azalomycin F assembly-line contribute to evolution-guided polyketide synthase engineering and identification of intermodular recognition

“…Therefore, an in-depth understanding of the catalytic mechanism and evolution process of polyketide synthase has theoretical guiding significance for engineering the PKS assembly-line in a more universal strategy. Considering that the broad distribution of homologous modules within a PKS assembly-line especially in cis-AT PKS assembly-lines 29 , we provided a proof-of-concept of an evolution-oriented engineering strategy for PKS assembly-lines via emulating the recombination process of homologous modules.…”

“…Genetic repeats of intense nucleotide skews (GRINS) Other regions of high sequence identity Recently, gene duplication and conservation have been proposed to explain the evolution of the PKS assembly-lines 28,29 . Nivina and coworkers showed that the gene conversion of genetic repeats of intense nucleotide skews (GRINS) recode and accelerate the diversification of the PKS assemblyline, and recombination between GRINS was also observed via a bioinformatics analysis 29,30 . Considering the GRINS analysis of AZL PKS, we found two nearly identical GRINS in the KS-AT-DH-KR tetradomain in modules 3 and 6 (Fig.…”

Evolution Inspired Engineering of Megasynthetases

“…It is yet unclear whether this architectural and genetic unit also corresponds to an evolutionary unit that has been preserved in megasynthases 24,26 . Phylogenetic and computational analyses of the PKS family have led to a proposed redefinition of module boundaries from the “historical” KS-AT-(DH-KR-ER)-ACP to the “alternative” AT-(DH-KR-ER)-ACP-KS 27,28 , and highlighted the presence of genetic repeats 29 (GRINS = genetic repeats of intense nucleotide skews) in a large number of PKS. The latter play a putative role in accelerating diversification of closely related BGCs by promoting gene conversion.…”