Debora Leite, Utku Avici, Michael Hahn and Mark BuckeridgeFluorescence microscopy image of the cell wall of sugarcane: the glycomic code determines its architectureDebora Leite, Utku Avici, Michael Hahn and Mark Buckeridge
“Do plant cell walls have a code?” That question, which is somewhat rhetorical, is the title of an article published in the November 1, 2015, issue of Plant Science by a pair of botanists at the Biosciences Institute of the University of São Paulo (IB-USP): Professor Marcos Buckeridge, a specialist in plant physiology, and Eveline Tavares, a postdoctoral researcher at the Institute. Buckeridge and Tavares believe the answer is yes, that is, a glycomic code provides instructions so that the wall—a rigid yet flexible layer that gives structural support and protection to certain types of cells—can produce a given architecture, one that is more or less rigid or resilient, for example.
If genomics involves the study of genes and proteomics deals with proteins, glycomics examines the role of carbohydrates, which are organic molecules composed of carbon, hydrogen and oxygen. This group, also called saccharides, includes sugars, starch and cellulose. The cell wall comprises between 50% and 60% of a plant’s biomass and is rich in complex carbohydrates (the polysaccharides cellulose, hemicellulose and pectin), as well as structural proteins and lignin, a polymer that gives it rigidity. “The way in which the monosaccharides, the simplest carbohydrates, come together and form polysaccharides, the larger molecules present in the cell walls of plants, is not random,” says Buckeridge. “That mechanism contains important information about how the wall is structured and how it can be broken.”
A code is a set of rules establishing a correspondence between two independent worlds, comprised of different elements: the signs, the basic information, and the meaning of the encoded information. A third element, the adapters, bridges the gap between the two worlds and gives meaning to the code. “The meaning of a sign can be a process, an action or even a structure that has a biological role,” says Tavares. To understand the thinking of the USP researchers, it can be useful to draw a parallel between the glycomic code and the genetic code, which is the most recognized biological code.
DNA is made up of a sequence of four different types of nucleotides (the nitrogenous bases adenine (A), cytosine (C), guanine (G) or thymine (T)), plus monosaccharide deoxyribose and a phosphate. The nucleotides are the code signs. They join together through the action of enzymes and the synthesis (playing the role of adapter) occurs to form a larger molecule, the DNA itself. Genes, which are formed by the nucleotides and are grouped in longer sequences of DNA (chromosomes), represent the meaning of the code. Each gene has a distinct biological function and is responsible for producing a particular protein. “The isolated nucleotides have completely different properties from those of the DNA molecule, even if the DNA is made up of them,” says Buckeridge.
The same logic governs how the glycomic code works. In this case, the signs are the monosaccharides, the simplest forms of carbohydrates, such as glucose, fructose and galactose. A group of enzymes promotes the union of these small molecules of sugars and causes the synthesis (adaptor) of larger molecules, polysaccharides, which function—now having been provided with instructions—as energy reserves (starch) or structural components of the plant’s cell walls.
There are three known types of cell walls in plants. Each variant is characterized by a distinct combination of three major polysaccharides: cellulose, pectin and hemicellulose. The various combinations and quantities of these large carbohydrate molecules generate structures with particular architectures, and therefore different chemical and mechanical properties. “Using the example of the relationship between nucleotides and DNA: the monosaccharides are molecules with properties completely different from the polysaccharides present in the cell wall,” says Buckeridge. To date, 14 types of monosaccharides have been isolated as building blocks of the polysaccharides that form the walls of plants.
Second-generation ethanol
The idea of a glycomic code able to regulate a plant’s cell wall characteristics is based on Buckeridge’s 20 years of work in the field of bioenergy. Buckeridge published his first article on the subject in a 2014 issue of the journal BioEnergy Research. He is a well-known authority on how to obtain second-generation ethanol, a biofuel extracted from the breakdown of plant cell walls, that is, from sugarcane bagasse, corn cobs or even wood.
Unlike simple sugars, the monosaccharides, found in the juice of the sugarcane, which are ready to ferment and be turned into ethanol, the polysaccharides of sugarcane bagasse are stored in a virtually inaccessible structure. The enzymes responsible for hydrolysis, a process that changes non-fermentable polysaccharides into fermentable monosaccharides by adding water, can not penetrate the cell wall and break it down. “The theory of a glycomic code is a very interesting one,” says Edivaldo Ximenes Ferreira Filho, a biochemist at the enzymology laboratory of the University of Brasília (UnB). “When it comes to bioenergy, a better understanding of how the cell walls of plants such as sugarcane form can be useful for learning how to break down these structures and produce second-generation ethanol.”
Project
Using a systems biology approach to develop a model for whole plant functioning (nº 2011/52065-3); Grant Mechanism Research Program in Partnership for Technological Innovation (PITE) and FAPESP-Microsoft Research Agreement; Principal Investigator Marcos Buckeridge (IB-USP); Investment R$547,964.97.
Scientific article
TAVARES, E.Q.P. and BUCKERIDGE, M.S. Do plant cell walls have a code? Plant Science. November 1, 2015.
