Science Progress (2004), 87 (3)

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Science Progress (2004), 87 (3), 131-136

Responses to chemical, physical

and biological stresses: involvement

of extracellular alarmones,

pheromones and varisensors

ROBIN J. ROWBURY

Introduction

The first article in this special issue1 seems at first slightly out of

place, in that it considers the synthesis, properties and roles of the

ribosome modulation factor (RMF) and related agents. In fact, this

article is firmly related to stress effects of potentially lethal agents

and conditions and on responses to these, with the author reviewing

particularly RMF effects on responses to stationary-phase stress and

to thermal and acid stresses. First, the group of agents El-Sharoud

considers interact with ribosomes allowing bacteria to survive

stresses in the stationary-phase. These agents do more than this,

however, in that they both protect organisms from potentially lethal

chemical stress agents in the stationary-phase, but also from the

same and other agents in exponential phase. RMF has two major

properties namely: (1) leading to ribosome dimerisation, the active

70S particles dimerising to form inactive 100S ones, whilst (2) this

ribosome binding component also influences rRNA degradation. It

appears that the latter property is more important as a means of protecting

organisms from stress. Of interest is the finding that ppGpp

controls RMF synthesis, probably explaining why this component,

which is not influenced by the sigma factor, RpoS, nonetheless increases

in level in stationary-phase.

Science Progress (2004), 87 (3), 137-152

Ribosome inactivation for

preservation: concepts and

reservations

WALID M. EL-SHAROUD

The role of the bacterial ribosome in the cellular response to environmental

stress has been widely considered over last decade. Certain ribosomeassociated

proteins have been shown to induce conformational changes

that lead to the formation of inactive forms of ribosomes that are presumed

to be more stable during stationary phase. This was found to aid the

survival of bacteria in this phase. Such proteins include ribosome modulation

factor (RMF), YfiA and YhbH. Examining the influence of RMF on the

survival of E. coli under heat, acid and osmotic stress showed that it was

important for bacterial viability under these environmental pressures.

However, the mechanism by which this protein exerts its effect has not

been fully elucidated. The present work reviews the involvement of

ribosomes in determining cell behaviour during stress. It focuses on the

action of the ribosome-associated proteins and their role in inactivating

ribosomes for preserving their integrity and aiding cell survival under

stress.

Keywords: bacterial ribosome, cellular response to environmental

stress, RMF, YfiA, YhbH

Science Progress (2004), 87 (3), 153-177

Applied and ecological aspects of

oxidative-stress damage to

bacterial spores and to oral

microbes

ROBERT E. MARQUIS

Bacterial cells have adapted in a variety of ways to resist oxidative

stresses and damage in their everyday lives in a predominantly aerobic

world. The nearly universal occurrence of resistance mechanisms against

oxidative stresses, particularly those due to reactive oxygen species

(ROS), suggests that most, if not all, bacteria have to deal with oxidative

assaults. A primary source of oxidative stress is aerobic metabolism,

which leads to production of ROS such as hydrogen peroxide, superoxide

radical, perhydroxyl radical, hydroxyl radical and a variety of other toxic

metabolites, including organic peroxides and other organics or inorganics

able to transfer electrons to sites of oxidative damage. Anaerobes as well

as aerobic and facultative organisms are subject to oxidative stresses, often

as a result of their own metabolism of O2 or that of associated facultative

organisms. If anaerobes would just ignore oxygen instead of metabolizing

it, they would not have to deal with toxic metabolites of their own

making. Another major source of oxidative stress comes from the use of

oxidative agents in the disinfection-sterilization industry. Notable examples

are hypochlorite for water purification and hydrogen peroxide

used for industrial sterilization. Antimicrobials such as isoniazide and

mitomycin C also act oxidatively to cause damage. In this article, aseptic

packaging and processing involving use of hydrogen peroxide for sterilization

of packaging materials is reviewed as an example of oxidative

stress imposed on bacterial spores and vegetative cells from outside the

organisms or the microbial community. The other example considered is

related to oral microbiology and infectious disease in which oxidative

stress may arise from the metabolism of the oral microbiota or may come

from outside through use of oral care products.

Keywords: spores, oral bacteria, reactive oxygen species, aseptic

technology, oral infectious diseases

Science Progress (2004), 87 (3), 179-191

Bacterial sensitivity to

bacteriophage in the aquatic

environment

MARTIN DAY

There are several unusual features about phage when you first encounter

them as a biologist. They are small, but conform to one of a few morphological

types. Next their genomes can be composed of DNA or RNA and be

single or double stranded. Finally they are numerically more abundant

than prokaryotes and a significant proportion of them form an association

in their microbial host populations termed lysogeny. The latter findings

indicate that they are numerically significant in microbial populations.

Since bacterial and phage abundance or lack of it is related in environments,

this implies that the phage populations ‘titrate’ their hosts, and

more probably the host’s physiological status. Microbial populations wax

and wane with nutritional inputs and there is a dynamic relationship between

phage population sizes and host numbers and physiology. Overlay

this with the different phage life cycle strategies, exemplified at the extremes

by phage lambda (temperate) and phage T4 (virulent), then it becomes

apparent that phage are a component in nutrient cycling in ecology.

But their contribution does not stop there. Many are capable of transduction,

moving DNA from one cell into another. So they can also aid the evolutionary

progress of microbial populations by allowing them to share

genes, just as gene exchange via plasmids and transformation does. Our

perception of bacteria has been derived from pure culture studies and we

are just being able to appreciate how subtle their ecological interactions

are. This is no less true of the studies on bacteriophage, which are almost

all based on laboratory experimentation, where the hosts are physiologically

stressed by growing in ‘high nutritional and optimum conditions’.

The natural environment is naturally discontinuous and life evolved in

this. Thus our perceptions of bacteriophage and their life cycle patterns

derived from laboratory experimentation may be a little off the mark when

we come to understand how they and their hosts interact in the niches

available to them. It is worth just considering this as you read the article,

as I suspect phage behaviours are more intimately involved in, and

moderated by the physiological stresses in the life cycle of bacteria than

we currently believe.

Keywords: bacterial sensitivity, bacteriophage, aquatic environment

Science Progress (2004), 87 (3), 193-225

Enterobacterial responses to

external protons, including

responses that involve early warning

against stress and the functioning

of extracellular pheromones,

alarmones and varisensors

ROBIN J. ROWBURY

Several striking findings, related to biological effects of external acidity,

are reviewed here. The first of these relates to the role of PhoE in the penetration

of H+ and protonated metabolites into the cell. PhoE is an anion

pore and would not be expected to take up protons. The work reviewed

here, however, shows that the loss or repression of PhoE leads to poor H+

passage through the outer membrane (OM), whilst derepression of PhoE

leads to facilitated passage. It is now believed that H+ crosses through the

PhoE pore in association possibly with oligopeptides, and that other protonated

molecules, such as the acid tolerance EIC, use the same means to

cross the OM. Additionally, several processes that form early warning systems

against acidity are reviewed here. First, the properties of the acid tolerance

EIC alarmones allow them to diffuse to regions not yet facing acid

stress, and there give early warning and induce sensitive organisms to tolerance.

Second, some agents, such as glucose, induce acid tolerance in organisms,

long before these organisms are exposed to catabolically-produced

acidity, preparing them, in advance, to resist this impending acid

challenge. Third, the occurrence of multiple forms of ESCs (i.e. of

varisensors) ensures that where organisms have been grown under conditions

that sensitise them to acid stress, the ESCs formed are modified so as

to be activated at much higher pH values, ensuring that lethality by acid is

reduced or abolished. Fourthly, normally only EICs induce tolerance.

Strikingly, however, pH 8.5 or 9.0-grown cells are induced to tolerance by

ESC formed at pH 6.5. This is believed to provide another early warning

system, protecting alkali-grown cells against sudden acidification of media.

Two other finding reviewed here should be emphasised. First, the hydrophobic

antibiotic novobiocin is ineffective against enterobacteria, due

to its failure to penetrate the OM barrier. This only applies to cultures in

pH 7.0 media,however, cells growing at pH 5.0 being exquisitely sensitive

to novobiocin, due to a conformational change to the antibiotic at acidic

pH, which allows ready penetration through the OM. Second, acidic pHs

affect the synthesis and effects of another antibiotic, namely colicin V.

Thus pH 5.0 prevents both synthesis of this agent and its effects on sensitive

cells. Exposure to external acidity leads to numerous other effects, including

those that influence growth, cell division, plasmid transfer and

chemotaxis; these have also been reviewed here.

Keywords: Alarmones, cross-talk, early-warning, Escherichia coli, extracellular

sensors, intercellular communication, pheromones, stress tolerance

induction, varisensors.