Divergence in cis-regulatory elements and subcellular targeting, in the absence of protein function modification, were potent drivers of metabolic evolution, providing a strategy for re-engineering valuable chemical diversity into cultivated crops.
Abstract
The evolution of plant defensive specialized metabolites often involves repurposing existing primary metabolic pathways for novel roles. However, the relative contribution of changes in protein function versus gene regulation and localization in driving such divergency remains less well understood. Here, we investigate the evolutionary origin of long-branched-chain acylsugars—a class of insecticidal metabolites found in wild tomatoes but absent from their domesticated counterpart. We show that this chemical divergency is enabled by a single enzyme, an acyl-CoA synthetase (SpBACS1), that was repurposed to bridge two distinct primary metabolic pathways. We demonstrate that SpBACS1 activates products of amino acid catabolism and primes them as non-canonical starters for elongation by the plastidial fatty acid synthase machinery for acylsugar assembly. Strikingly, the loss of this trait during domestication was not due to impaired enzyme function. Instead, we describe two distinct regulatory mechanisms. First, the cultivated ortholog, SlBACS1, lacks expression in acylsugar-producing trichomes due to promoter sequence divergence, despite retaining enzyme catalytic activity. Concurrently, their paralogs, BACS2, were neolocalized to the mitochondria, functionally isolating them from the chloroplast-based primary fatty acid metabolic elongation pathway. These findings demonstrate how divergence in cis-regulatory elements and subcellular targeting, in the absence of protein function modification, were potent drivers of metabolic evolution, providing a strategy for re-engineering valuable chemical diversity into cultivated crops. Long-branched-chain acylsugars are insecticidal metabolites found in wild tomatoes but not their domesticated counterpart. Here the authors show changes in expression and localization of a key enzyme is responsible for this difference.
Abstract Theanine, a non-protein amino acid predominantly found in tea (Camellia sinensis), is a primary contributor to the characteristic umami and sweet taste of tea infusion and is associated with numerous health benefits. The biosynthesis of its direct precursor, ethylamine, is catalyzed by the enzyme CsAlaDC. The evolutionary origin of this enzyme and the molecular basis for its functional divergence from the serine decarboxylase CsSDC, however, remain poorly understood. In this study, through comprehensive genome-wide identification, phylogenetic, structural, and domain analyses, we demonstrate that CsAlaDC originated from CsSDC via gene duplication followed by functional specialization. Phe106 and Gly168 were identified as indispensable residues governing CsAlaDC enzymatic activity in vitro and in vivo through functional validation. Crucially, we pinpointed two specific codon substitutions—TAC(Tyr112) to TTT(Phe106) and TGT(Cys174) to GGT(Gly168)—as key evolutionary mutations responsible for the functional shift from SDC to AlaDC activity. These findings elucidate the evolutionary trajectory of CsAlaDC and provide mechanistic insights into the molecular regulation of theanine biosynthesis in tea plants.
Hui Zhou, Pei-Xian Bai, Yong-Xin Wang et al.· Horticulture Research· 0 citations
The molecular evidence linking a PnTPS-derived gene to caryophyllene biosynthesis in P. nigrum is provided, highlighting its potential role in plant defense and paving the way for functional validation and genetic improvement strategies aimed at enhancing biotic stress resistance in black pepper.
Aparna K. S., Jaysree R. C., Geethalakshmi Sundararaman· Research journal of biotechn...· 0 citations
Nicotinamide mononucleotide (NMN) is a high-value functional ingredient, yet its efficient biosynthesis in food-grade microorganisms remains limited by an incomplete understanding of regulatory mechanisms. Here, we identified a GntR-family transcription factor (TFs), lp_0262, as a key regulator of NMN metabolism in Lactiplantibacillus plantarum. Characterization of lp_0262 revealed an unusual nonmonotonic regulatory behavior, where both its deletion and overexpression significantly promoted NMN accumulation. Comparative transcriptomic profiling of the Δlp_0262 unveiled a metabolic trade-off characterized by the robust upregulation of NMN biosynthetic genes alongside a paradoxical downregulation of the pentose phosphate pathway (PPP). To overcome this limitation, key oxidative PPP genes (zwf, pgl, and gnd) were reinforced in the Δlp_0262 chassis. The synergistic coupling of regulatory relief and metabolic flux optimization resulted in a maximal NMN titer of 300 μmol L–1, the highest reported for lactic acid bacteria (LAB) to date. These findings provide a promising strategy for engineering NMN-producing food-grade microbial cell factories.
Ling-Hui Kong, Xin-Yu Li, Qing He et al.· Journal of Agricultural and...· 0 citations
Inositol monophosphatase (IMP) is a key enzyme in the inositol signaling pathway and ascorbic acid (AsA) biosynthesis, playing crucial roles in plant growth, development, and abiotic stress responses. Sorghum (
S. bicolor
) is an important cereal crop with remarkable drought and salinity tolerance, yet a systematic analysis of the IMP gene family in sorghum has been lacking. In this study, we identified eight IMP genes (
SbIMP-1–SbIMP-8
) in the sorghum genome. Phylogenetic analysis classified them into six subfamilies, consistent with rice and maize, suggesting a common ancestral origin. Gene structure and motif composition were highly conserved within each subfamily but varied among subfamilies, indicating functional divergence. Synteny analysis revealed strong collinearity between sorghum and maize with mostly one-to-one orthologous relationships, whereas complex one-to-many correspondences were observed with the polyploid
S. spontaneum
, highlighting lineage-specific expansion driven by whole-genome duplication. Promoter cis-element analysis identified numerous stress-related and hormone-responsive elements, including ABRE, DRE, MYB and MYC binding sites. Transcriptome and qRT-PCR analyses under salt (NaCl) and osmotic (PEG) stresses revealed distinct expression patterns:
SbIMP-1
,
SbIMP-3
,
SbIMP-6
,
SbIMP-7
and
SbIMP-8
acted as salt responders. In particular,
SbIMP-4
exhibited a strong salt-specific induction. Promoter enrichment of MYB and MYC binding sites was associated with rapid salt response, whereas the combination of DRE, ABRE and MYB sites in
SbIMP-4
likely underpinned its unique expression profile. This study provides preliminary insights into the expression profiles of SbIMP genes under salt and osmotic stresses, offering a theoretical foundation for molecular breeding aimed at improving abiotic stress response in sorghum and other crops.
Ling Zheng, Xiao-Yu Zhou, Fei Wei et al.· Frontiers in Plant Science· 0 citations
This work reconstructed the evolutionary history of the bacterial glycoside hydrolase subfamily GH5-40 across leafhoppers (Cicadellidae) and identified 87 GH5-40 genes encoding 113 catalytic domains across 23 leafhopper species, with copy numbers ranging from 1 to 19 genes per genome.
