Research

The rise and success of secondary red algae

This project focused on the evolution and selection of a particular metalloenzyme family, the superoxide dismutases (SOD), which utilize the redox sensitive and thus biogeochemically significant metals Fe, Mn, Cu/Zn, or Ni.  I successfully showed that in the secondary red algae, diatoms, historically high Mn measurements could be accounted for by the protective role and constitutive expression of MnSODs in the plastid.  This was previously unknown to the field ( Wolfe-Simon et al., 2006).  In addition, the importance of Mn to secondary red algae also suggests a possible role for Mn in their ascent to dominance of the marine system during the Mesozoic.  Furthermore, the Mn and FeSOD genes are related due to an ancient gene duplication event.  I reviewed (Wolfe-Simon et al., 2005) and extended our understanding of the molecular evolution and phylogenetic radiation of the Mn and FeSOD isoforms in photoautotrophs by running detailed maximum likelihood and Bayesian phylogenetic analyses (Wolfe-Simon et al., in review).  The eukaryotic subcellular residence of the proteins today suggests that they were inherited originally from the symbiont ancestor which led to the rise of the modern eukaryotic organelles (Wolfe-Simon et al. 2006).

Arsenic and the origins of life

Arsenic as a prebiotic chemical analog of phosphate ( Wolfe-Simon, Davies, & Anbar, 2009). Essentially, arsenic (in the oxidized 5+ state as arsenate) is biologically, so similar to phosphate that many enzymes cannot recognize the difference. This constitutes the basis for much of the toxicity of arsenate and so most detoxification pathways in biology aim to reduce arsenate to more volatile forms for easier removal from biological systems. However, due to the increased mobility of reduced arsenic species, often the toxicity of arsenic increases as the redox state decreases.

Inorganically, As and P have very similar atomic radii and electronegativity (especially, compared to nitrogen which is directly above both on the periodic table). In fact, in contrast to phosphorus, arsenic readily forms sulfides and thus may have been available to early life at hydrothermal vents and similar environments. Given the distinct similarity between these two elements my coauthors and I assemble plausible TESTABLE hypotheses regarding the liklihood of life arising to either originally incorporate arsenate in a functional sense, and/or more speculatively, alternative forms of life utilizing a genetic system entirely based on arsenic. Check out our hypothesis (Wolfe-Simon, Davies, & Anbar, 2009) and decide for yourself!

To futher this hypothesis, we have embarked on two different approaches to test assimilatory arsenic utilization. Firstly, as part of the NASA Astrobiology Institute we are examining arsenate-rich environments to hunt and enrich cultures for organisms utilizing arsenate in novel and unique modes. Here is a good recent review on what is known about arsenic microbial pathways put in an astrobiological context (Oremland, Saltikov, Wolfe-Simon & Stolz, 2009).

In concert with this in situ and/or in vivo type work, we are also collaborating with Dr. Steve Benner and Dr. Nicole Leal at The Foundation for Applied Molecular Evolution and Dr. Marcelo Guzman to measure the spontanous incorporation of arsenate into a DNA backbone.

There are other approaches to search for life "as we do not know it" here on Earth. For more information, check out this paper (Davies, Benner, Cleland, Lineweaver, McKay & Wolfe-Simon, 2009).

Proterozoic primary production and trace metals

Did trace metal availability support the dominance of cyanobacteria during a substantial amount of Earth's early history? Currently, my data suggest that cyanobacteria have biological mechanisms to cope with reduced Fe and reduced Cu conditions as compared to algae and other photosynthetic eukaryotes (Wolfe-Simon & Anbar, for submission to Metallomics).  Cyanobacteria dominated the oceans until approximately 0.5-0.8 billion years ago (Ga) despite drastic environmental changes.  Eukaryotic photoautotrophs evolved during this time (2.7-1.5 Ga) but their rise to ecological prominence and multicellularity was delayed. Biochemical strategies to cope with changing metal availability may have been critical. A major change in metal availability was the decrease in ocean Fe after 1.8 Ga. This decrease would have been accompanied by a decrease in Cu if the oceans became euxinic (reduced and sulfur rich) at this time.  Hence, I am investigating differences in the ways that cyanobacteria and algae cope with Fe and Cu stress. I found that the Cu quota of the cyanobacterium Synechocystis PCC6803 does not increase under Fe-deficiency. This contrasts with previous studies with eukaryotic photoautotrophs showing increased use of Cu under Fe-deficiency.  For cyanobacteria, production of compensatory Cu proteins presumably involves reallocation of intracellular Cu rather than increased Cu uptake.  The implication is that cyanobacteria were better equipped to cope with Fe ocean redox changes at this time when Cu may have been scarce.

How did the redox conditions of the environment, and thus micronutrient availability, help drive the rise of algae? As trace metal concentrations have varied over Earth history, a major geochemical trend is the shift from abundantly soluble Fe to Cu due to the affect of increased oxygen in the atmosphere over geologic time (see above).  There is evidence in the literature that algae and other photosynthetic eukaryotes biochemically utilize Cu in a stoichiometrically larger proportion than cyanobacteria.  I have tested the evolutionary validity of this hypothesis and shown the increased cellular quota of Cu as well as the more economical and efficient use of Cu in green algae when compared to cyanobacteria.  For example, green algae increase their expression of the PSI Cu protein plastocyanin when under Fe-deficiency to replace the Fe-containing protein cytochrome c₆.  Furthermore, they modulate their expression of other Fe-rich PSI proteins including PsaA and psaC.  Another example relates back to my doctoral work in that higher plants utilize CuZnSOD while more primitive plants (including some early eukaryotic photoautotrophs) rely on the constitutive expression of FeSOD.  By combining controlled laboratory experiments, biochemical analyses, and molecular genetic modeling I will be able to forge a deeper understanding of historically relevant events for the Proterozoic evolution of photosynthetic life.

Biological control on the stalled rise of oxygen: maybe cyanobacteria had an alternative, non-metal based, secret

In a global sense, I am specifically interested in the effect of oxygen on Earth. Together with colleagues at Harvard, I have taken a lead role in developing a hypothesis to understand the geologically slow evolution of oxygen on Earth (Johnston*, Wolfe-Simon*, Pearson, & Knoll, 2009). Over geologic time, the global rise in atmospheric O₂ is attributed to the evolution and wide spread proliferation of oxygenic photosynthesis in cyanobacteria. However, cyanobacteria maintain a metabolic flexibility that may not always result in O₂ release. Specifically, cyanobacteria can use a variety of alternative electron donors, rather than water, that are also readily oxidized. These may include sulfur, iron, and arsenic. Cyanobacteria are thus not uniquely constrained towards O₂ production. Changes in the bioavailability of these key elements may have had dramatic consequences for and resulted in the slow accumulation of O₂ in the atmosphere. In particular, by using facultative anoxygenic photosynthesis the cells maintain advantageous anaerobic conditions for N₂-fixation. Although other types of bacteria are capable of N₂-fixation, cyanobacteria singularly possess the dynamic capability of generating and surviving O₂. These two processes pull the cells in opposite directions, metabolically speaking, around an aerobic-anaerobic continuum. Such a strategy also confers a distinct competitive advantage for cyanobacteria over photosynthetic eukaryotes, as they can endure widespread euxinia and maintain their cellular N quota. In an anoxic and/or sulfidic ocean, cyanobacteria would be expected to dominate over eukaryotic algae. I am pursuing Bayesian constructed phylogenetic distributions of specific genes and the metabolic role of key enzymes that form the basis of this hypothesis. Furthermore, the consequences of this proposed ecosystem structure altered the redox balance of the fluid Earth (atmosphere and oceans) and can help explain the o bserved long-term geochemical stasis and slow rates of eukaryotic diversification. The underlying control for global oxygenation was a synergistic interplay between the evolution and elastic physiology of cyanobacteria as they impacted the redox state of early Earth. I am eager to pursue this hypothesis and develop lab and field based experiments to understand how this biological phenomena occurs and to characterize its environmental implications. Never underestimate the elegant flexibility of physiology.

Biology does matter!

Fe-deficient primary production, zooplankton and the carbon cycle

Coming soon...

Molybdenum and the nitrogen cycle

Nitrogen is vital for all known oxygenic photoautotrophs. The three main pathways leading to nitrogen assimilation all require Mo (Glass, Wolfe-Simon & Anbar, Geobiology 2009). Nitrogenase (Nif), responsible for the biological fixation of N₂ gas to ammonia, is known to posses one atom of Mo per functional subgroup. Nitrate reductase (NarB) also has one atom of Mo and reduced nitrate to nitrite for further processing by the cell. Heterocystous diazotrophic cyanobacteria seem to have a variety of coping mechanisms for dealing with changes in Mo concentrations (Glass, Wolfe-Simon, Elser & Anbar, Limnol. Ocean. 2010) that may have evolutionarily significant roots. This project forms the basis for the PhD thesis of Jennifer Glass . Jennifer is a PhD candidate working under the guidance of Ariel Anbar in the School of Earth and Space Exploration at Arizona State University. Jennifer worked with me during my postdoctoral fellowship at ASU and continues to be a close collaborator. For further information on this project, please follow this link.