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2014 Annual Science Report

University of Illinois at Urbana-Champaign Reporting  |  SEP 2013 – DEC 2014

Project 10: Identifying Key Innovations in the Origin of the Cell

Project Summary

Identifying essential functions of conserved hypothetical genes holds the key to understanding the origins of key innovations in the origin of the cell. Our goal is to take a comparative genomic approach to define the molecular machinery that differentiate the Bacterial from its sister lineage that later diverged to became the Archaea and Eukaryotes. One of the obstacles clouding our view of these early cells from a comparative approach is the large number of conserved hypothetical genes present in Archaeal and Eukaryote genomes whose cellular functions are unknown. Our approach is to identify which conserved hypothetical genes are essential to the function of the model crenarchaeon Sulfolobus islandicus. The Crenarchaea are one of the major lineages with in the Archaeal domain with close ties in function to the cellular biology of Eukaryotes. The essential gene profile has not been identified within any organism in this lineage and holds the key to understanding the origin of cellular features in central processing of genomic information through replication, recombination, repair and the shaping of the chromosome.

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

Over the past year we have developed a random transposon insertion library with the goal of identifying conserved hypothetical genes, whose cellular functions are essential. To begin with we developed a genetic marker with strong positive selection for agmatine prototrophy. Using selection for this marker we constructed a transposon mutagenesis system and tested for random insertions by selecting and sequencing insertions. In order to saturate the genome and identify essential genes we estimate that we need to select 20,000 individual random insertions in the 2.59 Mbp genomic background of M.16.4. Great progress has been made toward this goal. We currently have nearly 10,000 clones isolated and estimate that our complete ordered random library will be constructed and sequenced by February 2015.

Figure 1.
3 Insertion sites of 210 clones on the genome of a double knockout in the model strain S. islandicus M.16.4.

    Rachel Whitaker
    Project Investigator

    Melinda Baughman

    Changyi Zhang

    Angelo Blancaflor

    Carlos Vega

    Objective 3.4
    Origins of cellularity and protobiological systems

    Objective 4.2
    Production of complex life.

    Objective 5.1
    Environment-dependent, molecular evolution in microorganisms

    Objective 6.1
    Effects of environmental changes on microbial ecosystems

    Objective 6.2
    Adaptation and evolution of life beyond Earth