How Organisms Adapt to New Enzymes and Pathways

Brandeis University, Waltham MA

Investigators

Abstract

Bacteria and other organisms live in a constantly changing, often hostile environment. To survive, they must adapt by developing new enzymes and new metabolic processes. These new activities might, for example, enable them to destroy a new antibiotic or detoxify an environmental pollutant, or might enable them to use that same pollutant as a source of nutrients, to boldly grow where no microbe has grown before. The new activities may also suddenly cause a harmless microbe to become a deadly human pathogen. Darwin anticipated all of the major mechanisms for the generation of phenotypic diversity in living organisms except one: the horizontal transfer of genetic information from one organism to other, resulting in the immediate acquisition of a new enzyme or, in some cases, an entire new metabolic pathway. With the advent of complete genome sequences, it is now clear that at least a quarter, sometimes more, of the genes in a bacterium have probably been acquired from outside in this way. This natural process also mimics what scientists do in the lab when they try to engineer microbes to produce useful substances or degrade environmental toxins. Yet little is known about how organisms respond to the introduction of a new enzyme or set of enzymes and how they subsequently modify both the new genes and their own to generate a new species with new properties. The overall aim of this project is to develop a model system for studying the origin, control and integration of new enzymes and new metabolic pathways, and to utilize this system to discover the factors that govern their evolution; to develop new ways of modeling them effectively; and to understand how their presence influences - and is influenced by - the core pathways already present in the organism. To address this fundamental biological question, a team with expertise in microbial genetics and physiology, mechanistic enzymology, molecular biology, structural biology, and systems biology, including bioinformatics, has been assembled, and a model system has been chosen. The project will transfer the enzymes of the mandelamide pathway from the soil bacterium Pseudomonas putida into E. coli, and follow their evolution as the organism adapts to use them to grow on lactamide as a carbon source. Understanding how a cell responds to new enzymes and pathways is of great importance to biology because this process is a key part of the fundamental machinery of evolution at the cellular level. The project will yield new basic information about how organisms adapt and evolve. It will also provide guidelines for the more effective engineering of new activities into bacteria for industrial and environmental uses. The interdisciplinary nature of this project means that people with a wide range of backgrounds can contribute and can benefit from the results. The project also provides opportunities for secondary school teachers and students from minority and non-Ph.D.-granting institutions to explore a wide range of basic questions and to learn a broad range of techniques. We intend to make the results widely available in a variety of forms that can be used from secondary education through to advanced applied research projects.