THE ORIGIN OF THE FUNDAMENTAL METABOLIC PATHWAYS AND THE SUBSEQUENT RISE OF THE GREAT METABOLIC DIVERSITY IN MICROBES ARE MAJORSTEPS IN LIFES EVOLUTION ON EARTH AND POTENTIALLY OTHER HABITABLE PLANETS. UNDERSTANDING HOW DIFFERENT METABOLISMS MAY ARISEAND WHAT CONDITIONS SELECT FOR WHAT TYPES OF METABOLIC NETWORKS IS A KEY QUESTION FOR THE ORIGIN OF LIFE. THE EVOLUTIONARY EMERGENCEOF DIVERSE METABOLISMS DEPENDS NOT ONLY ON ENVIRONMENTAL CONDITIONS BUT ON THE MICROBIAL INTERACTIONS SUCH AS COMPETITION ANDMUTUALISM AS WELL. SO FAR THE ROLE OF CHANGING MICROBIAL INTERACTIONS IN THE ORIGIN OF METABOLIC PATHWAYS UNDER DYNAMIC CONDITIONSHAS NOT BEEN INVESTIGATED IN DETAIL. HERE WE PROPOSE TO COMBINE TWO NOVEL MODELING APPROACHES FROM TWO DISPARATE DISCIPLINES TOEXPLORE HOW MICROBIAL METABOLIC NETWORKS ARISE AND EVOLVE IN DYNAMIC COMPETITIVE ENVIRONMENTS. WE WILL EMBED A RECENTLY DEVELOPEDMETABOLIC MODELING APPROACH FOR THE ELEMENTARY FLUX MODE ANALYSIS UNDER NONEQUILIBRIUM CONDITIONS (THE DYNAMIC REDUCTION OFUNBALANCED METABOLISM DRUM) IN AN ECO-EVOLUTIONARY MODELING FRAMEWORK OF TRAIT EVOLUTION (ADAPTIVE DYNAMICS) TO INVESTIGATEHOW DIFFERENT METABOLIC NETWORKS ARISE AND COMPETE IN DIFFERENT ENVIRONMENTS. THE RESULTING NEW EVOLUTIONARY SYSTEMS BIOLOGYMATHEMATICAL FRAMEWORK (EVODRUM) IS A POWERFUL TOOL THAT WILL ALLOW EXTENSIVE EXPLORATIONS OF HOW EARLY METABOLISMS APPEAREDAND WERE MAINTAINED BY NATURAL SELECTION AND THUS WILL BE USEFUL FOR THE FIELD OF EARLY MICROBIAL EVOLUTION. EVODRUM EXTENDSAND MODIFIES THE IDEA OF GATHERING THE EVOLUTIONARILY POSSIBLE REACTIONS BY DEFINING A LARGE -- IDEALLY UNIVERSAL -- MUTATION SPACE INWHICH EVOLUTION CAN PROCEED. IN LINE WITH THE ADAPTIVE DYNAMICS FRAMEWORK EVOLUTION IS DRIVEN BY A STEP BY STEP MUTANT/RESIDENTINVASION DYNAMICS WITH A DEFINED MUTATION RATE. THE NOVELTY OF THE PROPOSED APPROACH IS THAT IT INVESTIGATES THE METABOLICALLY EXPLICITTRAIT CHANGES AND EVOLUTION AS A RESULT OF SELECTION THROUGH COMPETITIVE INTERACTIONS OF DIFFERENT PHENOTYPES. IT ALLOWS INCORPORATINGMETABOLIC ACCUMULATION AND EVOLUTIONARY INNOVATIONS.WE WILL HAVE FOUR MAJOR FOCI IN THE PROPOSED RESEARCH. 1) WE WILL FULLY DEVELOP THIS NOVEL FRAMEWORK AND APPLY IT TO SEVERAL SIMPLEMETABOLIC NETWORKS WITH SEVERAL RESOURCES AND TEMPORALLY FLUCTUATING CONDITIONS. IN PARTICULAR WE WILL INVESTIGATE HOW THE NUMBEROF MUTATIONS THE MUTATION RATE AND NEUTRAL MUTATIONS THE CONCENTRATIONS OF AVAILABLE RESOURCES AND THEIR TEMPORAL VARIATION AFFECTTHE METABOLIC NETWORK EVOLUTION 2) WE WILL APPLY AND VALIDATE OUR APPROACH ON THE GENOME-SCALE METABOLIC NETWORK OF ESCHERICHIACOLI. WE WILL INVESTIGATE THE CONDITIONS LEADING TO THE DEVELOPMENT OF FERMENTATION VS RESPIRATION STRATEGIES AND THE DIAUXIC METABOLICSHIFTS AND THE EFFECT OF HORIZONTAL GENE TRANSFER (HGT) CORRESPONDING TO THE ADDITION OF BIG BLOCKS OF REACTIONS ON THE EVOLUTIONARYOUTCOME. WE WILL LOOK AT THE CHANGES IN MODULARITY AND CONNECTIVITY IN METABOLIC NETWORKS DURING EVOLUTION. 3) WE WILL USE OURMETHOD TO UNDERSTAND THE EVOLUTION OF NITROGEN FIXATION IN EARLY MARINE CYANOBACTERIA AND THEIR ADAPTATION TO DIFFERENT CONDITIONS. 4)EVODRUM WILL BE USED TO STUDY THE EVOLUTION OF SIMPLE MICROBIAL COMMUNITIES WITH COMPETITIVE AND MUTUALISTIC INTERACTIONS FIRST WITHMODIFIED E. COLI STRAINS WITH A POSSIBILITY OF CROSS-FEEDING AND SECOND WITH A MARINE MICROBIAL CONSORTIUM INVOLVING NITROGEN FIXERS.RELEVANCE STATEMENT. THE PROPOSED WORK IS DIRECTLY RELEVANT TO THE 'EARLY EVOLUTION OF LIFE AND THE BIOSPHERE' AREA OF RESEARCH IN THISSOLICITATION. IT COMBINES FOR THE FIRST TIME TWO DISTINCT MODELING FRAMEWORKS TO INVESTIGATE THE ORIGIN AND THE DIVERSIFICATION OF DIFFERENTMETABOLIC PATHWAYS IN MICROBES UNDER CHANGING CONDITIONS AND EXPLORES HOW MICROBIAL INTERACTIONS SHAPE THE EVOLUTION OF DIVERSEMETABOLISMS. THIS WORK WILL HELP GAIN INSIGHTS INTO THE EVOLUTION OF EARLY METABOLIC NETWORKS IN MICROBES AND MICROBIAL INTERACTIONS.
$360,000FY2020National Aeronautics and Space AdministrationNASA
Michigan State University, East Lansing MI