Ohio Eminent Scholar of Microbiology
School of Natural Resources, Plant Cellular and Molecular Biology
Ph.D. Syracuse Univ., 1971
Postdoc. Washington State Univ., 1971-1973
Microorganisms are important agents for carbon sequestration and biofuel/bioenergy production on earth. My laboratory is concerned with the molecular regulation, biochemistry, and enzymology of carbon dioxide assimilation and the application of this knowledge to favor the production of energy-rich biofuels by microorganisms from CO2. All organisms require CO2 and many enzyme-catalyzed reactions employ CO2 as a reactant for processes as important and varied as carbohydrate metabolism, lipid biosynthesis, and the production of important metabolic intermediates for the cell. Most importantly, CO2 may also be employed as the sole source of carbon by a large and diverse group of organisms on this planet. For this reason, CO2 fixation is a process that is associated with global issues of health, agricultural productivity, carbon cycling, and industrial productivity. As the chief green house gas in the atmosphere, CO2 is also recognized and implicated in the general warming of the earth's biosphere. For all these reasons, research on various aspects of CO2 fixation control, biochemistry, and ecology have attracted wide interest. In addition, these studies, and the subsequent manipulation of various molecular control mechanisms, have lead to the development of promising microbial systems for the production of biofuels and bioenergy from CO2. The following pages summarize our ongoing and future efforts to probe various aspects of these issues.
Metabolic biochemistry and enzymology
The key and rate limiting step in global CO2 assimilation is catalyzed by the enzyme RubisCO. This enzyme is a very poor catalyst, yet it is the protein that actually fixes the bulk of CO2 on this planet, and is thus most responsible for the biological removal of CO2 from the atmosphere. In addition, RubisCO function directly correlates with plant and crop productivity as well as the growth and reproduction of many significant microbes in the biosphere. The major issue that we study is the basis by which RubisCO discriminates between CO2 and O2, two gaseous substrates that compete for the same active site on the protein. This is a very important issue as O2 normally prevents efficient CO2 fixation. Taking a combined molecular biological and chemical approach we have attacking this problem by constructing novel mutant enzymes with different sensitivity to oxygen. RubisCO and a related protein, the RubisCO-like protein (RLP), also are involved in sulfur salvage reactions in the cell. We are engaged in determining the roles of RubisCO and RLP in sulfur metabolism and determining how the active sites of these proteins accommodate novel substrates.
Molecular control mechanisms
We are interested in how the CO2 fixation (cbb) structural genes are regulated in bacteria, using the metabolically versatile nonsulfur purple bacteria as model systems. In these organisms, the entire cbb regulon is under the control of a specific transcriptional regulator gene, cbbR, whose product, CbbR, positively controls the transcription of the two major operons required for CO2 fixation. In order to turn on transcription, CbbR must be activated in the cell after it binds to specific effector molecules. Understanding the biochemistry of CbbR is thus an important part of this research. In addition, response regulator proteins from specific two-component regulatory systems also impinge on control and these response regulators are able to interact with CbbR to fine-tune the regulatory response. How these different regulators influence the function of CbbR is a major thrust of our laboratory as understanding the means by which these proteins influence the control of CO2 fixation is important for elucidating the overall regulatory mechanism. Moreover, the potential manipulation of these control mechanisms directly influences the type and amount of value-added products that might be made from CO2.
Manipulating biochemistry and molecular control mechanisms for the bioconversion of CO2 to liquid biofuels
We are deeply engaged in using knowledge of the biochemistry and molecular biology of CO2 fixation in both chemoautotrophic and photosynthetic bacteria to enable efficient bioconversion of CO2 into infrastructure-compatible liquid biofuels. These organisms are attractive for such manipulations as they are genetically tractable and use electrons stripped from the oxidation of various substances to reduce CO2 to organic compounds. Using a synthetic biology approach, we are engineering these organisms to maximize CO2 fixation such that various products, including biofuels, may be produced.
Integrative control of the CO2 fixation (cbb), nitrogen fixation (nif) and hydrogen evolution systems; production of H2 as a biofuel
An interesting aspect of our studies on cbb control in photosynthetic bacteria was the finding that the nitrogen fixation (nif) system, and its control, is intimately involved with a global regulatory system, the Reg/Prr system. Indeed, knocking out the cbb system, under conditions where CO2 is normally used as an electron acceptor and not a carbon source, causes these organisms to evolve mutations that allow derepression of nitrogenase synthesis and expression of the nifHDK genes, so that reducing equivalents may now be dissipated as a result of the H+ - reducing hydrogenase activity of nitrogenase. Thus, the organism exquisitely controls how it handles environmental signals related to carbon and nitrogen metabolism. This results in the production of copious quantities of hydrogen gas and over the years we have shown this to be the case for four different nonsulfur purple bacteria that we have studied. Hydrogen is a biofuel of enormous potential significance and our basic mechanistic studies are designed to optimize this process further.
Molecular ecology and RubisCO metagenomics
We have collaborated with marine scientists to understand how the regulation of key CO2 fixation genes, like the RubisCO genes, are controlled in the oceans. This work, a combination of ship-board and laboratory investigations, is devoted to a primary problem, namely the sequestration of CO2 in the environment. Procedures for the direct examination of RubisCO transcripts in the open ocean were developed and applied to the global CO2 fixation problem. As these studies unfolded, it became possible to identify organisms which contribute to active CO2 fixation and sequestration by amplifying and sequencing specific RubisCO transcripts via RT-PCR technology. These studies have also evolved to the point that we are able to isolate and select novel and potentially useful RubisCO genes from metagenomic libraries obtained from this and other environments. Bioselection of RubisCO genes with different properties from the vast body of uncultured organisms provides a significant tool to understand how the active site of this key enzyme has evolved for its particular function. Such studies have the potential to greatly impact the enzymological studies discussed above.
RELEVANT RECENT PUBLICATIONS
Witte B, John D, Wawrik B, Paul JH, Dayan D, & Tabita FR. (2010) Functional prokaryotic RubisCO from an oceanic metagenomic library. Appl Env Microbiol. 76, 2997-3003.
Singh J & Tabita FR. (2009) Roles of RubisCO and the RubisCO-like protein in 5-methylthioadenosine metabolism in the nonsulfur purple bacterium Rhodospirillum rubrum. J Bacteriol. 192, 1324-31.
Satagopan S, Scott SS, Smith TG & Tabita FR. (2009) A Rubisco mutant that confers growth under a normally “inhibitory” oxygen concentration. Biochemistry 48, 9076-83.
Romagnoli S & Tabita FR. (2009) Carbon dioxide metabolism and its regulation in nonsulfur purple photosynthetic bacteria. In, Hunter CN, Daldal F, Thurnauer MC & Beatty JT. The Purple Phototrophic Bacteria. Advances in Photosynthesis and Respiration, Vol. 28, Springer, Dordrecht, The Netherlands, pp. 563-76.
Dangel AW & Tabita FR. (2009) Protein–protein interactions between CbbR and RegA (PrrA), transcriptional regulators of the cbb operons of Rhodobacter sphaeroides. Mol Microbiol. 71, 717-29.
Tabita FR, Hanson TE, Satagopan S, Witte BH & Kreel NE. (2008) The evolution, structure, and function of RubisCO and its homolog the RubisCO-like protein. Phil Trans Royal Soc SerB 363, 563-76.
- Tabita FR. (2007) Rubisco: the enzyme that keeps on giving. Cell 129, 1039-40.
Kreel NE & Tabita FR. (2007) Substitutions at methionine 295 of the Archaeoglobus fulgidus ribulose-1,5-bisphosphate carboxylase/oxygenase affects interactions with oxygen binding and CO2/O2 substrate specificity. J Biol Chem. 282, 1341-51.
Tabita FR, Hanson TE, Li H, Satagopan S, Singh J & Chan S. (2007) Function, structure, and evolution of the RubisCO-like proteins and their RubisCO homologs. Microbiol Mol Biol Rev. 71, 576-99.
Li H, Sawaya MR, Tabita FR & Eisenberg D. (2005) Crystal structure of a novel RuBisCO-like protein from the green sulfur bacterium Chlorobium tepidum. Structure. 13, 779-89.
Dangel AW, Gibson JL, Janssen AP & Tabita FR. (2005) Residues that influence in vivo and in vitro CbbR function in Rhodobacter sphaeroides and identification of a specific region critical for co-inducer recognition. Mol Microbiol. 57, 1397-414.
Smith SA & Tabita FR. (2003) Positive and negative selection of mutant forms of prokaryotic (cyanobacterial) ribulose-1, 5-bisphosphate carboxylase/oxygenase. J Mol Biol 331, 557-69.
Dubbs JM & Tabita FR. (2003) Interactions of the cbbII promoter-operator region with CbbR and RegA(PrrA) regulators indicate distinct mechanisms to control expression of the two cbb operons of Rhodobacter sphaeroides. J Biol Chem. 278, 16443-50.
Finn MW & Tabita FR. (2003) Synthesis of cataltically active form III ribulose 1,5-bisphosphate carboxylase/oxygenase in archaea. J Bacteriol. 185, 3049-59.
Hanson TE & Tabita FR. (2001) A RubisCO-like protein from Chlorobium tepidum that is involved with sulfur metabolism and the response to oxidative stress. Proc Natl Acad Sci USA. 98, 4397-402An influential favorite:
Joshi HM & Tabita FR. (1996) A global two component signal transduction system that integrates the control of photosynthesis, carbon dioxide assimilation, and nitrogen fixation. Proc Natl Acad Sci USA. 93, 14515-20.