Gene Modules Co-regulated with Biosynthetic Gene Clusters for Allelopathy between Rice and Barnyardgrass

Abstract

Allelopathy is a central process in crop–weed interactions and is mediated by the release of allelochemicals that result in adverse growth effects on one or the other plant in the interaction. The genomic mechanism for the biosynthesis of many critical allelochemicals is unknown but may involve the clustering of non-homologous biosynthetic genes involved in their formation and regulatory gene modules involved in controlling the coordinated expression within these gene clusters. In this study, we used the transcriptomes from mono- or co-cultured rice and barnyardgrass to investigate the nature of the gene clusters and their regulatory gene modules involved in the allelopathic interactions of these two plants. In addition to the already known biosynthetic gene clusters in barnyardgrass we identified three potential new clusters including one for quercetin biosynthesis and potentially involved in allelopathic interaction with rice. Based on the construction of gene networks, we identified one gene regulatory module containing hub transcription factors, significantly positively co-regulated with both the momilactone A and phytocassane clusters in rice. In barnyardgrass, gene modules and hub genes co-expressed with the gene clusters responsible for 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) biosynthesis were also identified. In addition, we found three genes in barnyardgrass encoding indole-3-glycerolphosphate synthase that regulate the expression of the DIMBOA cluster. Our findings offer new insights into the regulatory mechanisms of biosynthetic gene clusters involved in allelopathic interactions between rice and barnyardgrass, and have potential implications in controlling weeds for crop protection.

Horizontal Transfers Lead to the Birth of Momilactone Biosynthetic Gene Clusters in Grass

“…In barnyardgrass ( E. crus-galli ), CYP76L1-hgt is co-expressed with other MABGC genes (Sultana et al, 2019). A recent study in rice demonstrated that CYP76L1-hgt from barnyardgrass is functionally equivalent to CYP76M8 in catalyzing the 6β-hydroxylation of syn-pimaradiene (Kitaoka et al, 2021), implying a function of CYP76L1-hgt in momilactone biosynthesis.…”

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

“…Barnyard grass, a noxious weed of rice fields, has acquired orthologous gene clusters involved in the biosynthesis of momilactone and DIMBOA, respectively. In addition, barnyard grass is known to possess a quercetin producing gene cluster, which is highly upregulated during the interaction of the weed with the host (Sultana et al, 2019 ). Gene clusters of rice (phytocassanes and momilactones) might have evolved as an adaptive strategy to counter pathogenic invasions (Swaminathan et al, 2009 ).…”

“…to possess a quercetin producing gene cluster, which is highly upregulated during the interaction of the weed with the host (Sultana et al, 2019). Gene clusters of rice (phytocassanes and momilactones) might have evolved as an adaptive strategy to counter pathogenic invasions (Swaminathan et al, 2009).…”

Allelopathic Potential of Rice Cultivars Sowing in Santa Catarina State on Weedy Rice

“…This author also demonstrated that when S. bicolor developed in the presence of the velvetleaf weed (Abutilon theophrasti), the synthesis of the allelochemical sorgoleone was greater, indicating that interspecific competition has an important role in modulating the synthesis of allelochemicals. For rice crop, Sultana et al (2019) demonstrated that the expression of five genes related to the synthesis of allelochemicals in barnyardgrass (E. crus-galli) was higher when the weed developed in co-culture with rice.…”

“…A series of secondary metabolites synthesized by rice can suppress the growth of weeds, including fatty acids, indols, momylactones, phenolics and terpenes (Khanh et al, 2005). One of the most active allelochemicals synthesized by rice is momilactone B, which has a high capacity to inhibit plant growth (Sultana et al, 2019). Momilactone B is a diterpene synthesized from the mevalonic acid and methylerythritol phosphate pathway (Macias et al, 2019).…”