Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals

Abstract

Non-random gene organization in eukaryotes plays a significant role in genome evolution. Here, we investigate the origin of a biosynthetic gene cluster for production of defence compounds in oat—the avenacin cluster. We elucidate the structure and organisation of this 12-gene cluster, characterise the last two missing pathway steps, and reconstitute the entire pathway in tobacco by transient expression. We show that the cluster has formed de novo since the divergence of oats in a subtelomeric region of the genome that lacks homology with other grasses, and that gene order is approximately colinear with the biosynthetic pathway. We speculate that the positioning of the late pathway genes furthest away from the telomere may mitigate against a ‘self-poisoning’ scenario in which toxic intermediates accumulate as a result of telomeric gene deletions. Our investigations reveal a striking example of adaptive evolution underpinned by remarkable genome plasticity.

Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology

“…In addition, genome analysis of poppy revealed that noscapine and thebaine clusters occur separately on the same chromosome while R -reticuline-synthesizing genes were found to be loosely clustered (Guo et al, 2018 ; Li et al, 2020 ). A similar pattern of compact clustering is also observed in oat avenacin cluster (Qi et al, 2004 ; Li et al, 2021a ). Recently, elucidation of complete cluster organization of avenacins revealed that all genes are organized in a co-linear manner in relation to the biosynthetic steps of the pathway, and ten genes are arranged on the end of long arm of the chromosome 1 while the other two glycosyl transferases (GTs) are present in proximal scaffold (Li et al, 2021a ).…”

“…Genome analysis of A. strigosa revealed the presence of avenacin cluster in sub-telomeric regions, with the presence of the early pathway genes near to the telomere, and the existence of terminal pathway genes away from the telomere. These typical positioning co-linearity of genes in the cluster is considered to avoid the deletions of terminal pathway genes, thus preventing the accumulation of toxic intermediates (Li et al, 2021a ). On the other hand, maize DIMBOA gene cluster is also located at the tip (telomeric region) of the chromosome for facilitating an adaptive evolution and a coordinated regulation (Dutartre et al, 2012 ).…”

“…Further, these gene clusters are co-inherited to progeny as an environmental adaptation for functions such as development and defense responses. In addition, negative selection pressure against the accumulation of toxic intermediates could lead to the formation of gene clusters in plants (Li et al, 2021a ). Based on the observations related to the dynamic evolution of gene clusters, it is conclusive that plant genome is highly flexible and capable of associating non-homologous genes into a single coordinated cluster.…”

The emerging role of biosynthetic gene clusters in plant defense and plant interactions

“…Clustering has thus facilitated delineation of various plant biosynthetic pathways, including complex pathways for alkaloids [31,47] and terpenes [48]. Additionally, once a BGC is discovered in one plant species, similar clusters can in some cases be identified in related species by searching for clustered orthologs or syntenic regions [27,30].…”

“…In instances where biosynthetic pathway genes are clustered and genome sequences are available, discovery of one gene in a pathway can lead to identification of others, simply by searching for flanking genes with relevant functional annotations. Clustering has thus facilitated delineation of various plant biosynthetic pathways, including complex pathways for alkaloids [ 31 , 47 ] and terpenes [ 48 ]. Additionally, once a BGC is discovered in one plant species, similar clusters can in some cases be identified in related species by searching for clustered orthologs or syntenic regions [ 27 , 30 ].…”