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Mechanistic and Structural Basis for Plant Metabolic Evolution

Research Summary

Joseph Noel probes the adaptive changes that have occurred in plant-specialized metabolism as these enzyme networks emerged and evolved from their ancestral roots in primary metabolism at the dawn of terrestrial plants nearly 500 million years ago. His research examines the evolutionary principles underlying the biosynthesis of plant natural products, including isoprenoids, phenylpropanoids, polyketides, and fatty acid–derived metabolites.

What shapes natural selection of enzymes and metabolic pathways during the emergence and expansion of chemical diversity in living systems? This fundamental question in evolutionary biology remains largely unanswered. For sessile organisms possessing the developmental and ecological complexity of plants, this adaptive process is especially critical. The chemicals produced by these metabolic pathways are key mediators of intra- and interspecies interactions resulting in speciation, survival, and ecological homeostasis.

Early land plants arose from freshwater ecological niches. Their success on land—driven by evolutionary adaptations such as their ability to screen out damaging ultraviolet radiation, to resist desiccation, and to master self-support and fluid conduction—had far-reaching consequences for the complexity of terrestrial ecosystems that followed. The early success of land plants and the ongoing diversification of the green plant lineage was then and is to this day due in large part to their ability to biosynthesize specialized or so-called secondary metabolites.

Through photosynthesis, early land plants provided major nutritional stores that precipitated the dawn and development of almost all early terrestrial life forms, including tetrapods, insects, fungi, and even microorganisms. The rise of land plants, in turn, profoundly impacted the global climate. For example, carbon fixation by early land plants is considered one of the major factors that led to the significant drop of atmospheric CO2 levels and a corresponding increase of O2 levels during the late Paleozoic era. These changes in atmospheric composition precipitated more physiological innovations, e.g., the evolution of aerial locomotion in insects and the origin of megaphyll leaves in plants.

Plant-specialized metabolism has made a momentous contribution to the biodiversity of terrestrial Earth. Specialized metabolic pathways and their chemical output are a rich evolutionary record of where biosynthetic pathways, natural chemicals, and biosynthetic enzymes have been (vestigial biochemical traits); the adaptive advantages these complex enzymatic systems hold in the present (emergent function); and where these pathways may be heading in the future (functional plasticity).

Our decade-long study of these metabolic pathways has coalesced around four fundamental questions: (1) Can one discern the phylogenetic routes through which plant secondary metabolic enzymes evolved from their primary metabolic ancestors? (2) What are the biophysical features inherited by these enzymes that give rise to evolvability and/or restrain such evolutionary processes? (3) How was the evolutionary directionality maintained, if at all, before the emergence of the defining activities that provided obvious selective advantages? (4) What role did catalytic promiscuity play in shaping the evolvability of these biosynthetic systems? Answering these questions will not only extend our understanding of the biochemical strategies that early land plants adopted in their adaptation to a myriad of terrestrial environments but also shape our appreciation of mutability and the origins of new enzyme function in general.

Metabolic Building Blocks of Isoprenoids (Terpenes)
Isopentenyl diphosphate (IPP) and its isomer, dimethylallyl diphosphate (DMAPP), are essential precursors to all isoprenoids, including steroids, terpenes, carotenoids, and a multitude of other primary and secondary metabolites. Their biosynthesis occurs through the classical MVA (mevalonate) pathway in eukaryotes; through the more recently discovered DXP (1-deoxy-D-xylulose 5-phosphate) pathway in plastid-bearing eukaryotes and bacteria; and through a variant of the MVA pathway referred to as the modified, lost, or alternative MVA pathway in Archaea.

Our most recent work is focused on the "lost pathway" originally thought to exist only in the Archaea. In 2006, Laura Grochowski and her colleagues (Virginia Polytechnic Institute and State University) characterized the enzyme isopentenyl phosphate kinase (IPK) from the thermophilic archaeon Methanocaldococcus jannaschii, which catalyzes the ATP-dependent phosphorylation of isopentenyl phosphate (IP) to IPP. This enzyme fulfilled the last step of a postulated two-step modification of the MVA pathway required to complete this lost pathway in Archaea. We first established the specificity and mechanism of IPK using a combination of x-ray crystallography, structure-based design, and mutagenesis. With the structure as a starting point, we discovered that a number of eukaryotic IPK orthologs exist, suggesting our current understanding of isoprenoid building block metabolism employing either the MVA or DXP pathways is incomplete. Most notably, the IPK gene appears in every plant, which suggests that the alternative MVA pathway may retain an essential function within this branch of eukaryotes. Knockout experiments in Arabidopsis thaliana for putative genes of this newly discovered wrinkle in the clinically important MVA pathway (target of statin drugs) will help determine whether the alternative branch of the MVA pathway plays an essential role in plants, whether compensation from other isoprenoid pathways can recover its function, and what role if any the two branches of the MVA pathway play in primary and secondary isoprenoid biosynthesis.

Terpene Synthase Evolution and Global Climate
Cyclic sesquiterpenes may be the plant-derived volatile organic compounds that are most sensitive to tropospheric climatic and chemical changes. Our goal is to (1) quantify the effects of temperature, CO2, and O3on the biochemistry of plant sesquiterpene metabolic pathways; (2) determine the impact of promiscuous enzymes involved in terpenoid biosynthesis on plant responses and adaptation to environmental conditions associated with climate changes; and (3) elucidate the genomic and enzymatic molecular mechanisms that control plant responses to these abiotic factors. Our current research in this direction is focused on the discovery of how plants, with their natural terpene chemodiversity, interact with and respond to troposphere climate and chemistry. To achieve this, we are developing a phylogenetic and biochemical understanding of a model sesquiterpene biosynthetic system tuned by evolution for enhanced plant fitness.

Evolutionary Routes of an Ancient Plant Metabolic Network—Phenylpropanoids
To understand the molecular evolution shaping the diversity of plant phenylpropanoids, particularly the ubiquitous class of compounds known as flavonoids, stilbenes (resveratrol), and polyketides, we employ techniques of modern genomics, enzymology, plant biology, and biochemistry. With these techniques, we are pursuing a deep phylogenetic examination of putative evolutionary intermediates that gave rise to the ubiquitous plant enzyme, chalcone synthase (CHS). We first performed phylogenetic analyses using an angiosperm CHS as the query against the sequenced genomes near the root of the green plant lineage, including Chlamydomonas (unicellular algae), Physcomitrella (bryophyte, nonvascular moss), and Selaginella (water-conducting vascular lycophyte). We also carried out RNAseq assemblies of two charophyte algae species, a lineage of freshwater algae immediately sister to land plants and closely related to bryophytes.

This analysis identified a clade that includes CHS orthologs from bryophytes (basal green plants) to angiosperms (derived green plants) and additional plant CHS-like enzymes with divergent function from CHS. Parallel to the CHS clade, vascular plants contain a clade of type III polyketide synthases (PKSs), composed of genes that are specifically expressed in reproductive organs.

Our analysis of genomically encoded emergent enzyme function placed two Selaginella genes, three Physcomitrella genes, and three charophyte algae genes in between the CHS clade and a clade containing ketoacyl synthases of primary metabolism. We hypothesize that these CHS-like type III PKSs represent—as well as possible in extant species—the ancestral forms of CHS, back to the time when early land plants emerged from their aquatic environments. Understanding the structure and function of the CHS-like enzymes at these key divergence branches will provide a molecular foundation for a more precise understanding of the evolutionary path toward the origin of CHS function during early land plant evolution. This may also elucidate the key adaptive innovations that afford iterative carbon-carbon bond formation in a multitude of biologically and clinically important enzymes, the PKSs.

Grants from the National Science Foundation provided partial support for these projects.

As of May 30, 2012

Scientist Profile

Investigator
Salk Institute for Biological Studies
Biochemistry, Plant Biology