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2002 Annual Science Report

University of California, Los Angeles Reporting  |  JUL 2001 – JUN 2002

Genomic Evolution and the Tree of Life

4 Institutions
3 Teams
0 Publications
0 Field Sites
Field Sites

Project Progress

Trees constructed from whole-genome comparisons using the presence or absence of protein-coding genes continue to resemble those obtained from single genes, notably ribosomal ribonucleic acid (RNA) genes (House and Fitz-Gibbon, 2002). However, the confounding effects of lateral gene transfers and genome size variations are being investigated in a cross-team collaboration that is an activity of the Evolutionary Genomics Focus Group (James A. Lake, Co-Chair). Although most analyses resolve the Archaea as a stand-alone (monophyletic) group, the presence of DNA-winding proteins (histones) intermediate in crystal structure between the ones in methanogens and eukaryotes (Fahrner et al., 2001) lends some support to the idea that some Archaea are more closely related to eukaryotes than are others.

Whole-genome comparisons yield useful information in different parts of the Tree of Life. A first-order comparison of four, fully sequenced, eukaryote genomes (human, fly, worm, and yeast) fails to support the currently favored ?ecdysozoa? hypothesis that all molting animals (arthropods, nematodes, priapulids, etc.) share a common ancestry separate from the non-molting animal phyla (Fitz-Gibbon, Runnegar, and House, submitted).

Sorel Fitz-Gibbon?s Ph.D. project, the complete genome of the microaerophilic archaeal hypothermophile, Pyrobaculum aerophilum (Fitz-Gibbon et al., 2002), provides an explanation for a surprising intolerance of elemental sulfur in this metabolically versatile microorganism: Frameshift mutations have disrupted two crucial sulfur-metabolizing genes. This serendipitous discovery suggests that synthetic replacement genes may be used to develop a genetic system for this geobiologically relevant model organism.

Retortamonad flagellates, an anaerobic protist group, have been shown to be closely related to diplomonads such as Giardia (Silberman et al., 2002). According to UCLA microbiologists Jeffrey D. Silberman and Patricia J. Johnson and their collaborator at Dalhousie University, Andrew J. Roger, this implies that all known living eukaryotes are descended from an ancestor that postdated the endosymbiotic event that gave rise to the energy-producing organelle, the mitochondrion. This view is not shared by members of other NAI teams who believe that Giardia and its close relatives predated the endosymbiotic event. Silberman and his collaborators are focusing on genes that have been imported by the endosymbiont and then lost to the host nucleus later on. Whether these genes are cryptic relics of the endosymbiont or were obtained by more recent lateral gene transfers will ultimately arbitrate this cross-team debate.

    Bruce Runnegar
    Project Investigator

    David Jacobs

    Patricia Johnson

    James Lake

    James Ferry

    James Garey

    Christopher House

    Ravi Jain

    Jeffrey Miller

    Andrew Roger

    Karl Stetter

    Sorel Fitz-Gibbon
    Research Staff

    Ruth Gates
    Research Staff

    Maria Rivera
    Research Staff

    Jeffrey Silberman
    Research Staff

    Jonathan Moore
    Doctoral Student

    Objective 4.0
    Expand and interpret the genomic database of a select group of key microorganisms in order to reveal the history and dynamics of evolution.

    Objective 5.0
    Describe the sequences of causes and effects associated with the development of Earth's early biosphere and the global environment.

    Objective 6.0
    Define how ecophysiological processes structure microbial communities, influence their adaptation and evolution, and affect their detection on other planets.

    Objective 7.0
    Identify the environmental limits for life by examining biological adaptations to extremes in environmental conditions.

    Objective 12.0
    Define climatological and geological effects upon the limits of habitable zones around the Sun and other stars to help define the frequency of habitable planets in the universe.