Rex-family repressors
fine-tune the expression of genes involved in respiration in response to oxygen
levels. These redox-sensing repressors are found in Gram-positive bacterial
species like streptococcus and staphylococcus (Reference 1). T-Rex is isolated from thermus
aquaticus, a type of bacteria that can withstand high temperatures and was first
discovered in the hot springs of Yellowstone National Park (Reference 2).
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| Figure 1: Thermus Aquaticus Rex colored by secondary structure, with DNA attached. PDB file (1XCB), edited by author on PyMol software. | | | |
The geometry of T-Rex is
specific to both NAD and DNA. Molecule binding of NAD occurs in the
large cleft
between each subunit, and up to 2 NAD molecules can bind at a time at
this
domain. The two protruding bumps on T-Rex are the DNA binding domain
(Figure 1). The two
domains for NAD and DNA, respectively, are connected by an alpha helical
arm, which
reaches between domains and locks the subunits of the T-Rex complex
together (Reference 3). Figure 2 offers a cross-sectional view of
T-Rex, exposing the NAD binding domain that can bind two NAD molecules with the alpha-helical arm and the DNA in its
domain.
 |
| Figure 2: Geometric domains of T-Rex. PDB file (1XCB), edited by author on PyMol software and with PowerPoint. |
T-Rex represses respiratory
gene expression until a limited oxygen supply raises the ratio of
intracellular
NADH: NAD+. Both NAD+ and NADH bind to T-Rex, evoking different
reactions. Elevated
NADH levels indicate that oxygen is unavailable, and that the expression
of
genes required in respiration are needed. With NADH bound the NAD domain
in
T-Rex, the two DNA binding domains are located so closely that the shape
of DNA
cannot fit and match the domains, and transcription of DNA continues.
Increased
NAD+ indicate a restoration of oxygen levels and no need for continued
respiration. The binding of NAD+ induces a conformational shift of the
entire
T-Rex complex, opening the DNA domains like a scissors. In this form,
DNA can
bind to T-Rex, thus suppressing transcription activity. Figure 3 shows T-Rex with a) NAD+ bound state and open domains allowing
for DNA binding, and b) NADH bound, inducing a rotation of the repressor
and a contraction of the DNA binding domain disallowing for DNA to bind
(Reference 4).
 |
| Figure 3: T-Rex with a) NAD+ bound state and open DNA binding domains and b) NADH bound and closed state. Figure from McLaughlin paper, reference 3. |
|
In summary, the
intracellular ratio of NADH: NAD+ is a sensitive indicator of the redox state
and whether oxygen is present or not. T-Rex facilitates this oxygen
responsiveness as a signaling method for gene transcription. It is one of the
first well-characterized structures responsible for allosteric gene regulation
by the reduction of NADH to oxidized NAD+.
Don’t you just love T-Rex?
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| Figure 4: PDB file (1XCB), edited by author on PyMol software. |
|
References:
1. Sickmier, E. A. "X-Ray Structure of a Rex Family Repressor/NADH Complex from Thermus Aquaticus."
RCSB Protein Data Bank. Dec. 2005. Web.
2. Shapiro, Leo. "Thermus Aquaticus."
Encyclopedia of Life. Web.
3. Goodsell, David S. "T-Rex."
Protein Structure Initiative. Sept. 2008. Web.
4. McLaughlin, Krystle J. "Structural Basis for NADH/NAD+ Redox Sensing."
Molecular Cell. 38 (2011): 563-75. Web.
