NEW YORK UNIVERSITY - NEW AWARD CONTROL NUMBER: 3405-1553 TEOSYNTE (DE-FOA-0003405) PROJECT TITLE: “TF REGULON ENGINEERING: REDUCING N2O EMISSIONS BY INCREASING NUE IN BIOENERGY CROPS” DESCRIPTION: “IN THIS ARPA-E PROPOSAL, WE WILL USE NOVEL MACHINE LEARNING (ML) APPROACHES TO IDENTIFY AND VERIFY GENES-OF-IMPORTANCE TO NUE AND ENHANCE THEIR FUNCTION IN PLANTS. SINCE MULTIPLE GENES AND PATHWAYS CONTRIBUTE TO NUE, WE FOCUS ON DISCOVERING THE REGULATORY NETWORKS THAT LINK TRANSCRIPTION FACTORS (TFS) TO THE EXPRESSION OF GENES THAT CONTROL NUE, TERMED TF-NUE REGULON. WE THEN ENGINEER MAIZE LINES TO HAVE EQUAL OR GREATER YIELD ON REDUCED N-FERTILIZER AND LOWER N2O EMISSIONS USING SYNTHETIC BIOLOGY PRINCIPLES TO MANIPULATE THESE NUE TF-REGULONS. TO ENABLE THIS NEW TECHNOLOGY, WE WILL CARRY OUT THREE TASKS ACROSS BIOENERGY CROPS TO FIND UNIVERSAL DESIGN TARGETS FOR TF-NUE REGULONS: IN TASK 1, OUR NOVEL ML ALGORITHM “BIPARTITE MACHINE LEARNING” WILL PREDICT TF PAIRS THAT COOPERATE TO IMPACT NUE TRAITS. IN TASK 2, WE WILL VERIFY THE FUNCTION OF INTERACTIVE TFS ON GENES AFFECTING NUE IN A HIGH-THROUGHPUT CELL-BASED SYSTEM TO PRIORITIZE INTERACTIVE TF-NUE REGULONS THAT MOST INFLUENCE FIELD NUE. IN TASK 3, WE WILL USE MODERN SYNTHETIC BIOLOGY TO MANIPULATE INTERACTIVE TF-REGULON SETS IN MAIZE TO INCREASE NUE AND REDUCE N2O IN FIELD TRIALS. THIS INNOVATIVE PIPELINE OF DISCOVERY WILL UNVEIL THE TF REGULONS THAT CONTROL THE AGRICULTURAL TRAIT OF NUE TO REDUCE N2O EMISSIONS AND DISRUPT AN AGRICULTURAL MARKET THAT DEPENDS ON ENVIRONMENTALLY COSTLY N-FERTILIZER.”