Bacterial Stress Responses: What Doesn't Kill Them Can Make Them Stronger

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Bacterial Stress Responses: What Doesn't Kill Them Can Make Them Stronger

Boor KJ. Bacterial Stress Responses: What Doesn't Kill Them Can Make Them

Stronger. PLoS Biol 2006;4(1):e23

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rnal.pbio.0040023

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Bacterial Stress Responses: What Doesn't Kill Them Can Make Them Stronger

J. Boor

Boor is in the Department of Food Science, Cornell University,

Ithaca, New York, United States of America. E-mail: kjb4@...

Published: January 17, 2006

DOI: 10.1371/journal.pbio.0040023

Copyright: © 2006 J. Boor. This is an open-access article

distributed under the terms of the Creative Commons Attribution License, which

permits

unrestricted use, distribution, and reproduction in any medium, provided the

original author and source are credited.

Abbreviation: ECF, extracytoplasmic function

Citation: Boor KJ (2006) Bacterial Stress Responses: What Doesn't Kill Them

Can Make Them Stronger. PLoS Biol 4(1): e23

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An organism's survival from moment to moment depends, at least in part, on

its ability to sense and respond to changes in its environment. Mechanisms for

responding to environmental changes are universally present in living

beings. For example, when mammals perceive a sudden environmental change as

threatening, a rush of adrenaline precipitates the well-known " fight or flight "

response. Such physiological stress responses in complex organisms require

appropriately regulated interactions among numerous organ systems. But how do

single-celled organisms respond to potentially lethal threats? The hope is that

identifying specific mechanisms that contribute to microbial survival under

rapidly changing conditions will provide insight into stress response systems

across life forms.

Bacteria-and especially those capable of persisting in diverse environments,

such as Escherichia coli-provide particularly valuable models for exploring

how single-celled organisms respond to environmental stresses. For example,

most bacteria associated with foodborne infections (e.g., some E. coli

serotypes, Salmonella enterica serovar Typhimurium, Listeria monocytogenes) can

survive under diverse conditions, both inside and outside of the host. To

ultimately cause human infection, a foodborne pathogen must first survive

transit in

food or water, a significant achievement since the majority of commercial

products destined for consumption in the United States are treated with

strategies specifically designed to control or eliminate microbial

contaminants.

Following ingestion, the bacterium must survive exposure to conditions that

have

evolved to provide the host with some protection against pathogenic

microbes. Human bodily defenses include gastric acid (ranging from [pH

2.5-4.5],

largely depending on feeding status), bile salts, and organic acids within the

gastrointestinal tract. To survive these extreme and rapidly changing

conditions, bacteria must sense the changes and then respond with appropriate

alterations in gene _expression and protein activity. Therefore, one important

scientific challenge is to identify mechanisms that control the switch or

switches

that allow free-living bacteria to adjust to and invade a host organism.

The Role of Sigma Factors in Transcription

In bacteria, alterations in gene _expression are often controlled at the

transcriptional level through changes in associations between the catalytic

core

of RNA polymerase and the different sigma factors present in a bacterial

cell [1]. RNA polymerase is the enzyme responsible for recognizing appropriate

genes under specific environmental conditions, and for creating the mRNA

transcripts that can be translated into new proteins. Sigma factors are

dissociable subunits of prokaryotic RNA polymerase. When a sigma factor

associates with

a core RNA polymerase to form RNA polymerase holoenzyme, it directs the

holoenzyme to recognize conserved DNA motifs called promoter sites (or regions)

that precede gene sequences. Sigma factors also contribute to DNA strand

separation, which is a critical step in transcription initiation. The sigma

subunit dissociates from the RNA polymerase core enzyme shortly after

transcription

begins, thus becoming available for reassociation. Associations between

different alternative sigma factors and core RNA polymerase essentially

reprogram

the ability of the RNA polymerase holoenzyme to recognize different promoter

sequences and express entirely new sets of target genes. As the set of genes

controlled by a single sigma factor (also known as the regulon) can number

in the hundreds, sigma factors provide effective mechanisms for simultaneously

regulating large numbers of prokaryotic genes.

How do single-celled organisms respond to potentially lethal threats?

Sigma factors are classified into two structurally unrelated families: É-54

and É-70 families. Subunits comprising the É-54 family are often commonly

referred to as É-N. É-N has been identified in multiple diverse species,

including Legionella pneumophila, Pseudomonas spp., Enterococcus faecalis,

Campylobacter jejuni, and L. monocytogenes. In addition to regulating nitrogen

metabolism in a number of organisms, É-N-dependent genes also contribute to a

diverse array of metabolic processes [2,3]. The É-70 family, which is larger

and

more diverse than the É-54 family, is divided into four groups based on

conservation of their primary sequences and structures [4,5]. The Group I sigma

proteins are the primary sigma factors (e.g., Bacillus subtilis É-A) and are

also

referred to as " housekeeping " sigma factors, as they direct transcription of

genes important for bacterial growth and metabolism. Sigma factors in the

remaining groups are also referred to as alternative sigma factors [6] and

often regulate specific physiological processes, e.g., sporulation. É-70 family

members that contribute to bacterial stress responses (e.g., É-S, É-B, and

some extracytoplasmic function sigma factors) are of particular interest as

mounting evidence suggests that in bacterial pathogens, these regulatory

proteins

serve as links between bacterial abilities to respond to changes imposed by

the host environment and, subsequently, to cause disease (e.g., [7,8]).

Bacteria are classified as Gram-negative or Gram-positive based on

microscopically observed staining properties associated with different cell

membrane

structures. É-S (RpoS) and É-B (SigB) have been identified as general stress

responsive alternative sigma factors in Gram-negative and in Gram-positive

bacteria, respectively. É-S was identified in both E. coli and in S.

Typhimurium

as a Group II sigma factor that activates _expression of numerous genes

required to maintain cell viability as the cell leaves exponential growth

conditions and moves into stationary phase [9,10]. In addition to helping E.

coli

and S. Typhimurium respond to different environmental stress conditions, such

as those associated with entry into stationary phase, É-S also contributes to

_expression of virulence-associated genes [10]. Since its initial discovery,

the presence of É-S and its role in stress response has been confirmed in

multiple, diverse Gram-negative bacterial pathogens, including Pseudomonas

aeruginosa, L. pneumophila, Borrelia burgdorferi, Yersinia enterocolitica, and

Shigella flexneri.

É-B, a Group III sigma factor encoded by sigB, was initially identified and

characterized in B. subtilis [11,12], but has also been identified in L.

monocytogenes, Staphylococcus aureus, B. anthracis, and B. licheniformis. The

B.

subtilis É-B-dependent general stress regulon is large: over 200 genes are

expressed following bacterial exposure to heat, acid, ethanol, salt stress,

entry into stationary phase, or starvation for glucose, oxygen, or phosphate

[13,14]. While disruption of sigB in B. subtilis has no apparent effect on the

organism's ability to sporulate or to grow under many conditions, sigB mutants

are sensitive to oxidative stress [15], and exhibit impaired growth in

ethanol and reduced survival at extreme pH [16]. L. monocytogenes sigB mutants

are

more sensitive than wild type to acid and oxidative stress, as well as to

nutrient depletion [17]. In L. monocytogenes, É-B contributes to _expression of

internalin A and internalin B, two bacterial surface-associated proteins

important for host-cell invasion [7,8].

The extracytoplasmic function (ECF) Group IV sigma factors are conserved

across both Gram-positive and Gram-negative species [18], and comprise a large,

phylogenetically distinct subfamily within the É-70 family. É-E, an ECF sigma

factor that was initially recognized as a heat-shock sigma factor in E. coli

[19], responds to accumulation of specific unfolded proteins in the

periplasm [20]. Members of the ECF subfamily are distinct from the rest of the

É-70

family in that they regulate a wide range of functions involved in sensing and

reacting to conditions in the membrane, periplasm, or extracellular

environment [21]. Sensing of the extracellular environment is achieved via a

signal

transduction mechanism in which the ECF sigma factor is bound to a cognate

inner membrane-bound anti-sigma factor.

The Proteins Regulated by Sigma Factors

To fully understand the biological contributions of regulatory proteins such

as sigma factors, it is critically important to identify genes regulated by

these proteins. To date, investigators have used combinations of global

(e.g., computer-based sequence similarity searches for conserved promoter

sequences, two-dimensional protein gel electrophoresis, microarray analyses) and

more

focused strategies (e.g., in vitro transcription methods, reporter fusion

transposon mutagenesis) to identify sigma factor regulons (e.g., [13,14,22,23]).

In the study by Carol Gross and her colleagues [24], published in this issue

of PLoS Biology, É-E-regulated transcription units were identified in E.

coli K-12 through multiple strategies, including microarray profiling and rapid

amplification of cDNA ends, as well as by using a sophisticated

computer-based DNA motif search strategy that was designed using sigma E

promoter

consensus sequence data garnered by the team from E. coli [24]). The authors

then

used their computer-based search strategy to identify potential sigma E motifs

upstream of genes in E. coli and in eight additional Gram-negative genera.

Broadly speaking, one exciting outcome of this work is the development of an

effective set of bioinformatic tools that will be useful in mining DNA sequence

databases for the presence of conserved sequences by allowing more rapid and

accurate prediction of genes that are coordinately regulated.

The results reported by Rhodius et al. [24] unambiguously confirm the role

of É-E in maintenance of the integrity of the bacterial cell's outer membrane,

but they also highlight a critical role for É-E in regulating _expression of

virulence-associated genes among the pathogenic bacteria included in their

study (e.g., E. coli O157:H7, S. Typhimurium, S. flexneri). These data suggest

the possibility that É-E, which is important for bacterial responses at the

cell surface, may represent an important switch mechanism that facilitates

bacterial transition from a free-living organism to a host-invading pathogen.

Studies of this nature provide powerful new insight into the field of

microbial physiology by enabling rapid identification of genes that may appear

to be

unrelated in function, but that must be coordinately regulated to enable an

organism to survive and respond appropriately under rapidly changing

environmental conditions, such as those encountered by a bacterial pathogen

during the

infection process. These coordinately regulated genes ultimately may prove

to be appropriate targets for development of novel antimicrobial strategies,

thus providing tangible realization of the promise and power of the

application of genomics tools for improving human health.

References

1. Borukhov S, Nudler E (2003) RNA polymerase holoenzyme: Structure,

function and biological implications. Curr Opin Microbiol 6: 93-100. Find this

article online

2. Merrick MJ (1993) In a class of its own-The RNA polymerase sigma

factor sigma 54 (sigma N). Mol Microbiol 10: 903-909. Find this article online

3. Buck M, Gallegos MT, Studholme DJ, Guo Y, Gralla JD (2000) The

bacterial enhancer-dependent É-54 (É-N) transcription factor. J Bacteriol 182:

4129-4136. Find this article online

4. Lonetto M, Gribskov M, Gross CA (1992) The sigma 70 family: Sequence

conservation and evolutionary relationships. J Bacteriol 174: 3843-3849. Find

this article online

5. Gruber TM, Gross CA (2003) Multiple sigma subunits and the partitioning

of bacterial transcription space. Annu Rev Microbiol 57: 441-466. Find this

article online

6. Paget MS, Helmann JD (2003) The sigma 70 family of sigma factors.

Genome Biol 4: 203. Find this article online

7. Kim H, Boor KJ, Marquis H (2004) Listeria monocytogenes É-B

contributes to invasion of human intestinal epithelial cells. Infect Immun 72:

7374-7378. Find this article online

8. Kim H, Marquis H, Boor KJ (2005) É-B contributes to Listeria

monocytogenes invasion by controlling _expression of inlA and inlB.

Microbiology

151: 3215-3222. Find this article online

9. Lange R, Hengge-Aronis R (1991) Identification of a central regulator of

stationary-phase gene _expression in Escherichia coli. Mol Microbiol 5:

49-59. Find this article online

10. Fang FC, Libby SJ, Buchmeier NA, Loewen PC, Switala J, et al. (1992)

The alternative sigma factor katF (rpoS) regulates Salmonella virulence.

Proc Natl Acad Sci U S A 89: 11978-11982. Find this article online

11. Haldenwang WG, Losick R (1979) A modified RNA polymerase transcribes

a cloned gene under sporulation control in Bacillus subtilis. Nature 282:

256-260. Find this article online

12. Haldenwang WG, Losick R (1980) Novel RNA polymerase sigma factor from

Bacillus subtilis. Proc Natl Acad Sci U S A 77: 7000-7004. Find this article

online

13. sohn A, Brigulla M, Haas S, Hoheisel JD, Volker U, Hecker M

(2001) Global analysis of the general stress response of Bacillus subtilis. J

Bacteriol 183: 5617-5631. Find this article online

14. Price CW, Fawcett P, Ceremonie H, Su N, CK, et al. (2001)

Genome-wide analysis of the general stress response in Bacillus subtilis. Mol

Microbiol 41: 757-774. Find this article online

15. Engelmann S, Hecker M (1996) Impaired oxidative stress resistance of

Bacillus subtilis sigB mutants and the role of katA and katE. FEMS Microbiol

Lett 145: 63-69. Find this article online

16. Gaidenko TA, Price CW (1998) General stress transcription factor sigmaB

and sporulation transcription factor sigmaH each contribute to survival of

Bacillus subtilis under extreme growth conditions. J Bacteriol 180: 3730-3733.

Find this article online

17. Ferreira A, O'Byrne CP, Boor KJ (2001) Role of É-B in heat, ethanol,

acid, and oxidative stress resistance and during carbon starvation in Listeria

monocytogenes. Appl Environ Microbiol 67: 4454-4457. Find this article online

18. Lonetto MA, Brown KL, Rudd KE, Buttner MJ (1994) Analysis of the

Streptomyces coelicolor sigE gene reveals the existence of a subfamily of

eubacterial RNA polymerase sigma factors involved in the regulation of

extracytoplasmic functions. Proc Natl Acad Sci U S A 91: 7573-7577. Find this

article

online

19. kson JW, Gross CA (1989) Identification of the sigma E subunit

of Escherichia coli RNA polymerase: A second alternative sigma factor

involved in high-temperature gene _expression. Genes Dev 3: 1462-1471. Find

this

article online

20. Alba BM, Gross CA (2004) Regulation of the Escherichia coli

sigma-dependent envelope stress response. Mol Microbiol 52: 613-619. Find this

article

online

21. Raivio TL, Silhavy TJ (2001) Periplasmic stress and ECF sigma

factors. Annu Rev Microbiol 55: 591-624. Find this article online

22. Huang X, Helmann JD (1998) Identification of target promoters for

the Bacillus subtilis sigma X factor using a consensus-directed search. J Mol

Biol 279: 165-173. Find this article online

23. Kazmierczak MJ, Mithoe SC, Boor KJ, Wiedmann M (2003) Listeria

monocytogenes É-B regulates stress response and virulence functions. J

Bacteriol 185:

5722-5734. Find this article online

24. Rhodius VA, Suh WC, Nonaka G, West J, Gross CA (2005) Conserved and

variable functions of the É-E stress response in related genomes. PLoS Biol

4: e2. Find this article online

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