JOURNAL OF BACTERIOLOGY, Sept. 2005, p. 6253–6254
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0021-9193/05/$08.00⫹0 doi:10.1128/JB.187.18.6253–6254.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
GUEST COMMENTARIES
Universal Stress Proteins in Escherichia coli
Deborah A. Siegele*
Department of Biology, Texas A&M University, College Station, TX 77843-3258
Multiple members of the UspA family of proteins are found
in the genomes of bacteria, archaea, fungi, protozoa, and
plants, but the biological and biochemical functions of these
proteins are not known. In this issue of Journal of Bacteriology,
Nachin et al. (6) describe a functional genomics approach to
determining the cellular function(s) of the UspA family of
proteins. A complex array of phenotypes, affecting motility and
adhesion, extend the biological roles of these proteins beyond
coping with stress. The work of Nachin et al. illustrates both
the promise and challenges of functional genomics, even for an
organism as well studied as Escherichia coli.
The UspA domain (Pfam accession number PF0582) is
found in more than 1,000 different proteins (1). The domain
occurs either in isolation or fused to other domains, as is seen
with KdpD, the sensor kinase regulating high-affinity K⫹ trans-
port (10). KdpD contains an UspA domain in addition to the
conserved KdpD sensor domain (Pfam accession number
PF02702) and the ATPase and phosphoacceptor domains
characteristic of sensor kinases. Proteins that contain only one
UspA domain or have two in tandem represent ca. 80% of the
UspA proteins in Bacteria and Archaea and about 50% of the
family members in Eucarya. The atomic structures of two
UspA domains, MJ0577 from Methanococcus jannaschii (11)
and UspA from Haemophilus influenzae (9), reveal asymmetric
dimers with similar ␣/␤ tertiary folds. However, there are some
important differences. MJ0577 crystallizes with a bound ATP,
while H. influenzae UspA lacks both ATP-binding activity and
conserved ATP-binding residues in the P loop. Interestingly,
these structural differences correlate with groupings defined by
amino acid sequence comparisons. UspA, UspC, UspD, and
the N-terminal domain of UspE fall into one group, and UspF,
UspG, and the C-terminal domain of UspE fall into a second
group (5). UspA from H. influenzae is most similar to E. coli
UspA, while MJ0577 is most similar to E. coli UspG. However,
none of the E. coli UspA paralogs have the G-2X-G-9X-G-
(S/T) motif that is found in MJ0577 and shared by many other
members of the UspA family (9).
Previous work on regulation and analysis of mutant pheno-
types implicated the UspA proteins in stress responses. UspA
in E. coli K-12 was named a universal stress protein in 1992 by
Nyström and Neidhardt, who showed that its synthesis is in-
duced in response to a large number of stresses (7). The only
stress that doesn’t induce synthesis of UspA is cold shock (8).
Synthesis of UspA and at least four of the five UspA paralogs
* Mailing address: Department of Biology, Texas A&M University,
3258 TAMU, College Station, TX 77843-3258. Phone: (979) 862-4022.
Fax: (979) 845-2891. E-mail: d-siegele@tamu.edu.
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is induced by overlapping but nonidentical sets of stresses (2, 3,
4). Synthesis of UspA (uspA), UspC (yecG), UspD (yiiT),
UspE (ydaA), and UspG (ybdQ) is induced by starvation for
glucose or phosphate and upon entry to stationary phase in
rich medium. All five also are induced by treatment with the
uncoupler dinitrophenol and by heat shock. However, the
UspA proteins differ in their responses to oxidative stress and
DNA damaging agents: UspA, UspC, UspD, and UspE are
induced by exposure to mitomycin C, cadmium, and hydrogen
peroxide, but UspG is not. Currently there is no information
on the regulation of UspF (ynaF). These similarities and dif-
ferences in expression pattern correlate with biological roles
defined by analysis of usp mutants.
Mutants missing one of the UspA proteins often have sim-
ilar phenotypes. UspA, UspC, UspD, and UspE are each
needed to protect cells from DNA damage (3, 4). At least five
of the UspA proteins are important for recovery from starva-
tion in E. coli. Inactivation of uspA, uspC, uspD, uspE, or uspG
causes an extended lag when stationary-phase cells are trans-
ferred to fresh medium (2, 3, 4).
These previous studies support the idea that Usp family
members have partially overlapping but distinct biological
functions. To study these, organisms missing combinations of
Usp proteins are needed. The use of engineered and targeted
knockouts in functional genomics allows one to make combi-
nations of mutations that are difficult to obtain by traditional
genetic methods. However, even with targeted knockouts,
there are 63 possible combinations of single and multiple mu-
tations for the six usp genes. Rather than constructing and
testing all possible mutants, Nachin et al. were guided by
groupings based on similarities in regulation and sequence
analysis.
Nachin et al. demonstrate that the E. coli UspA proteins also
have a variety of specialized roles in the cell. UspA and UspD,
but not UspC, UspE, UspF, or UspG, protect cells against
superoxide stress during exponential growth. Strikingly, after
addition of phenazine methosulfate, growth of the ⌬uspA mu-
tant is indistinguishable from that of the wild-type strain for
several generations, until the transition to stationary phase
(see Fig. 1 in reference 6).
Several of the E. coli UspA proteins also function during
steady-state growth in the absence of external stress. This was
known previously for UspA, whose absence alters carbon uti-
lization (8). The work of Nachin et al. shows that intracellular
iron levels appear to be higher in the ⌬uspD mutant than in
wild-type cells, which could account for the superoxide sensi-
tivity of this mutant. Nachin et al. noticed serendipitously that
UspA proteins affect cell surface properties, noting that ⌬uspE
6254 GUEST COMMENTARIES
mutants did not settle to the bottom of the tube when cultures
were left standing on the bench. Deletion of uspC, uspE, or
uspG reduces autoaggregation, while mutants lacking UspF
form larger clumps than wild-type cells. This observation led to
the investigation of adhesion and motility phenotypes. Two
pairs of UspA proteins (UspC-UspE and UspF-UspG) affect
adhesion and motility, but in opposing directions. UspC and
UspE each promote flagellum synthesis and motility and de-
crease adhesion by type 1 fimbriae, while UspF and UspG each
increase adhesion and reduce motility. Surprisingly, deleting
both uspF and uspG restores the wild-type phenotypes.
Despite the progress that has been made in studying the
UspA family of proteins, their biochemical activities and the
mechanisms by which they function remain elusive. This family
of proteins clearly warrants further study. The work described
by Nachin et al. points to new avenues of investigation that will
help to solve this puzzle.
I thank Jim Hu for discussions and helpful comments on the manu-
script.
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C. Yeats, and S. R. Eddy. 2004. The Pfam protein families database. Nucleic
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The views expressed in this Commentary do not necessarily reflect the views of the journal or of ASM.
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