Functional Analysis of Metabolic Channeling and Regulation in Lignin Biosynthesis: A Computational Approach

Abstract

Lignin is a polymer in secondary cell walls of plants that is known to have negative impacts on forage digestibility, pulping efficiency, and sugar release from cellulosic biomass. While targeted modifications of different lignin biosynthetic enzymes have permitted the generation of transgenic plants with desirable traits, such as improved digestibility or reduced recalcitrance to saccharification, some of the engineered plants exhibit monomer compositions that are clearly at odds with the expected outcomes when the biosynthetic pathway is perturbed. In Medicago, such discrepancies were partly reconciled by the recent finding that certain biosynthetic enzymes may be spatially organized into two independent channels for the synthesis of guaiacyl (G) and syringyl (S) lignin monomers. Nevertheless, the mechanistic details, as well as the biological function of these interactions, remain unclear. To decipher the working principles of this and similar control mechanisms, we propose and employ here a novel computational approach that permits an expedient and exhaustive assessment of hundreds of minimal designs that could arise in vivo. Interestingly, this comparative analysis not only helps distinguish two most parsimonious mechanisms of crosstalk between the two channels by formulating a targeted and readily testable hypothesis, but also suggests that the G lignin-specific channel is more important for proper functioning than the S lignin-specific channel. While the proposed strategy of analysis in this article is tightly focused on lignin synthesis, it is likely to be of similar utility in extracting unbiased information in a variety of situations, where the spatial organization of molecular components is critical for coordinating the flow of cellular information, and where initially various control designs seem equally valid. The organization of cooperating enzymes into complexes is a pervasive feature of metabolism. In particular, this phenomenon has been shown to participate in the regulation of flux through the networks of both primary and secondary metabolism in plants. It remains a challenging task to unravel the organizing principles of such “metabolic channels,” which can be temporary or persistent, and to understand their biological function. In this article, we analyze metabolic channels in the biosynthetic pathway of lignin, a complex polymer that stiffens and fortifies secondary cell walls within woody tissues. This system is well suited because the present analysis can be based on a computational, experimentally validated model demonstrating that several enzymes are spatially associated into channels specific for the production of two lignin monomers. To characterize the functioning of these channels, we develop a novel computational approach that is capable of identifying interesting structural and regulatory features of metabolic channeling and permits the formulation of targeted and readily testable hypotheses. Since the spontaneous or controlled assembly of molecules into functional units is known to occur in many biological contexts where information flow is tightly coordinated, the proposed approach might have broad applications in the field of computational systems biology.