The Natural History of Nitrogen Fixation
Jason Raymond*, Janet L. Siefert, Christopher R. Staples* and Robert E. Blankenship*
* Department of Chemistry and Biochemistry, Arizona State University, Tempe
Department of Statistics, Rice University, Houston
E-mail: firstname.lastname@example.org .
In recent years, our understanding of biological nitrogen fixation has been bolstered by a diverse array of scientific techniques. Still, the origin and extant distribution of nitrogen fixation has been perplexing from a phylogenetic perspective, largely because of factors that confound molecular phylogeny such as sequence divergence, paralogy, and horizontal gene transfer. Here, we make use of 110 publicly available complete genome sequences to understand how the core components of nitrogenase, including NifH, NifD, NifK, NifE, and NifN proteins, have evolved. These genes are universal in nitrogen fixing organisms—typically found within highly conserved operons—and, overall, have remarkably congruent phylogenetic histories. Additional clues to the early origins of this system are available from two distinct clades of nitrogenase paralogs: a group composed of genes essential to photosynthetic pigment biosynthesis and a group of uncharacterized genes present in methanogens and in some photosynthetic bacteria. We explore the complex genetic history of the nitrogenase family, which is replete with gene duplication, recruitment, fusion, and horizontal gene transfer and discuss these events in light of the hypothesized presence of nitrogenase in the last common ancestor of modern organisms, as well as the additional possibility that nitrogen fixation might have evolved later, perhaps in methanogenic archaea, and was subsequently transferred intothe bacterial domain.
Nitrogen Fixing Archaea, Article # 2… Nitrogen Fixation at 92°C by a Hydrothermal Vent Archaeon
Mausmi P. Mehta* and John A. Baross
A methanogenic archaeon isolated from deep-sea hydrothermal vent fluid was found to reduce N2 to NH3 at up to 92°C, which is 28°C higher than the current upper temperature limit of biological nitrogen fixation. The 16S ribosomal RNA gene of the hyperthermophilic nitrogen fixer designated FS406-22, was 99% similar to that of non–nitrogen fixing Methanocaldococcus jannaschii DSM 2661. At its optimal growth temperature of 90°C, FS406-22 incorporated 15N2 and expressed nifH messenger RNA.This increase in the temperature limit of nitrogen fixationcould reveal a broader range of conditions for life in the subseafloorbiosphere and other nitrogen-limited ecosystems than previouslyestimated.
School of Oceanography, University of Washington, Seattle, WA 98195, USA.
Nitrogen Fixing Archaea # 3…
Annual Review of Microbiology
Vol. 61: 349-377 (Volume publication date October 2007)
First published online as a Review in Advance on June 18, 2007
Nitrogen Regulation in Bacteria and Archaea
John A. Leigh and Jeremy A. Dodsworth
A wide range of Bacteria and Archaea sense cellular 2-oxoglutarate (2OG) as an indicator of nitrogen limitation. 2OG sensor proteins are varied, but most of those studied belong to the PII superfamily. Within the PII superfamily, GlnB and GlnK represent a widespread family of homotrimeric proteins (GlnB-K) that bind and respond to 2OG and ATP. In some bacterial phyla, GlnB-K proteins are covalently modified, depending on enzymes that sense cellular glutamine as an indicator of nitrogen sufficiency. GlnB-K proteins are central clearing houses of nitrogen information and bind and modulate a variety of nitrogen assimilation regulators and enzymes. NifI1 and NifI2 comprise a second widespread family of PII proteins (NifI) that are heteromultimeric, respond to 2OG and ATP, and bind and regulate dinitrogenase in Euryarchaeota and many Bacteria.
Acronyms and Definitions
2OG: 2-oxoglutarate (α-ketoglutarate)
Adenylyltransferase (ATase): adenylylates and deadenylylates GS
DRAG: dinitrogenase reductase activating glycohydrolase
DRAT: dinitrogenase reductase ADP-ribosyltransferase
GlnB-K: a family of homotrimeric PII proteins that bind and modulate a variety of nitrogen assimilation functions
GOGAT: glutamate synthase (glutamine:2-oxoglutarate aminotransferase)
GS: glutamine synthetase
NifI: a family of heteromultimeric PII proteins that bind and modulate dinitrogenase in nitrogen fixing methanogenic Archaea and many Bacteria
PII protein: a widespread superfamily of proteins that sense 2OG and control nitrogen regulatory functions
Uridylyltransferase/uridylyl-removing enzyme (UTase/UR): uridylylates and deuridylylates some GlnB-K-type PII proteins