Microorganisms are capable of surviving and reproducing in various environments. Many of these environments produce stresses such as nutrient limitation, acid/base, thermal stress, oxidation, desiccation and exposure to bile salts and antimicrobial peptides, which affect the reaction kinetics and the performance of the organism under these conditions. For example, bacteria living in the alimentary canal must be able to sense and respond according to changes in pH and bile salts that they encounter in their environment. To survive, microorganisms have evolved both physiological and genetic mechanisms to tolerate extreme conditions. The production of specific key sets of proteins, maintaining pH homeostasis plus other passive and active mechanisms act as survival strategies.
Key words: stress responses, survival strategies, and unfavorable environmental conditions
Microorganisms used in research laboratories and various industries such as food and fermentation technologies are supplied with plenty of nutrients and grown at optimal temperature, pH, oxygen levels and solute concentrations. However in the various natural ecosystems, conditions that allow maximum growth are few and most organisms live in a constant state of stress. Moreover, the extent of the change in the various environmental parameters will determine whether the organism continues to grow, is killed, or survives in a state of dormancy. In order to survive potentially lethal changes, organisms must be able to percept every particular stimuli and induce the appropriate response against the vast array of stresses. Responses to these conditions not only have an impact on growth and survival but also influence the degree of virulence of certain pathogens and their ability to resist antimicrobial drugs.
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The stringent response is used by microorganisms to adapt to lack of amino acids and fatty acids. It controls operons regulating the transcription of rRNA and tRNA. By decreasing the rate of rNA synthesis, it reduces the rate of protein synthesis and stops certain energy draining functions for example cell replication and cell cycle. The stringent response is expressed by the stringent factor RelA and spoT in response to lack of amino acid in the environment.
Some bacteria can also make use of alternative sources of energy by making use of the catabolite repression mechanism during deficiency of certain nutrients especially carbon source in the environment. For example the lac operon in E.coli allows the bacteria to use lactose once glucose is depleted. This allows the organisms to make use of available nutrient sources in the environment whenever their primary sources of energy is completely depleted or lacking in the surrounding environment.
The Pho system is a mechanism which is activated during the presence of very low levels of phosphates available in the surrounding environment of the microorganisms. This mechanism like catabolite repression also causes the microorganisms to make use of other sources of phosphates other than inorganic phosphates from the environment. For example instead of using inorganic phosphates the microorganisms can use organic sources of phosphates. This system also causes an increased production of alkaline phosphatases which is responsible for dephosphorylating phosphate groups so that they can be absorbed into the cells.
During starvation some bacteria have the capability to produce endospores which is a differentiation to a reproducing form. Endospore formation is usually repressed in the presence of glucose and other growth substances. Spore formation in certain bacteria is regulated by sigma factors during the lack of essential elements for growth and reproduction. Endospore formation is a survival strategy developed by certain bacteria that enable them to be dormant and survive in nutrient deficient environments for longer period of time without reproducing until optimum conditions for growth and reproduction returns back.
Weak acids are present in several fruits and vegetables. They are utilised as preservatives for low pH foods such as salad dressings and wines. Maintaining the microbial stability in the food prevents spoilage, which is usually caused by yeasts, molds and lactic acid bacteria. Weak acid preservatives influence the cell's ability to stabilise pH homeostasis, disrupt substrate transport and prevent metabolic pathways to take place. This results in a hurdle for microbes to grow and flourish. However, despite the high level of preservative used, osmophilic yeasts such as Zygosaccharamyces.rouxii can still survive to cause spoilage of the food. Also, microorganisms gain resistance to strong doses of weak acid if they were previously exposed to mild concentrations. In the presence of weak acid preservatives, bacteria can survive but unable to grow.
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Reacting with the cell wall, cell membrane, metabolic enzymes and DNA molecules can cause growth inhibition. The preservatives may also influence the cell yield, ATP levels which results in the malfunctioning of the substrate transport and oxidative phosphorylation. Nevertheless, fungi have developed the H+-translocating ATPase of the plasma membrane to neutralize the effect of weak acids and stabilise pH. Resistance mechanisms are more difficult in Gram-negative bacteria than in Gram-positive bacteria as the tolerance is determined by the structure and chemical composition of the outer layers of the cell.
The electron transport chain relies on the catalytic spin pairing of triplet oxygen to produce energy. During this process, toxic compounds of oxygen are formed which damage the DNA molecules, proteins and lipid components of the cell. One of the harmful compounds is superoxide, which react with other chemical reactions releasing even more highly reactive oxygen derivatives such as hydrogen peroxide and hydroxyl radicals. Peroxynitrite anion can also be produced which interacts with proteins such methionine, cysteine, tyrosine and tryptophan. Consequently, enzyme inactivation, growth deficiencies and DNA damage can result.
Nevertheless, aerobic microorganisms are protected from those toxic compounds by the enzyme superoxide dismutase (SOD) and catalase. Cytoplasmic SOD protects the DNA and proteins from oxidation whereas periplasmic SOD protects the membrane components from the harmful superoxide. Anaerobes defend themselves by using NADH oxidase which catalyses the direct four electron reduction of oxygen to water. The superoxide reductase system has the benefit of removing superoxide without the production of molecular oxygen.
Thermal stress and envelope (extracytoplasmic) stress:
Heat Shock Proteins are required for thermo-tolerance. Studies on Salmonella enterica shows that a molecular switch which act as thermometer check for thermal changes and the production of HSPs. Upon a increase in temperature, intramolecular hydrogen bonds blocking translation of rpoH mRNA which encodes for σH are broken and translation follows. σH binds to RNA polymerase and directs the transcription of more than 30 HSPs, which function as molecular chaperones, proteases and misfolded proteins. A negative feedback loop control the over expression of HSPs. At low temperature, DnaK- DnaJ chaperone complex binds to σH, however upon heat stress, DnaK- DnaJ chaperone complex binds to the misfolded proteins allowing more RNA polymerase and σH binding, therefore increased HSPs expression. While the σH regulon controls the accumulation of misfolded proteins in the cytoplasmic membrane, the σE controls multiple envelope and extracytoplasmic accumulation of misfolded proteins. The σE regulon include periplasmic chaperones, proteases and other factors associated with extracytoplasmic functions.
A decrease in temperature would alter the fluidity of the cell membrane resulting in leakage of the cell components. However, most cells remodel their membrane lipid composition to ensure membrane function such as solute transport is maintained. Major homeoviscous adaptations involve increased in fatty acid saturation and shortening of the average fatty acid length which disturb the interactions and packing between adjoining chains resulting in an increase in membrane fluidity. Moreover, repression of the heat shock proteins and induction of cold shock proteins (Csp) have been observed in E.coli. After a reduction from 37 oC to 10 oC, CspA, which regulates transcription, recognizes gene promoters and induces the production of more cold shock proteins. Another cold shock protein Hcs66 act as a molecular chaperone, which ensures refolding of proteins and the conformation of proteins, is maintained.
Antimicrobial Peptide (AP) stress:
Soil bacteria (e.g. Paenibacillus polymyxa) produce antimicrobial peptides ( polymyxins and bacteriocins/lantibiotics) in order to kill competing microbes for nutrient.
Different types of APs have been observed to have negative impact on a wide range of microbes. APs produced by eukaryotic organisms are cationic and non-cationic APs. The cationic AP (alpha and beta) includes defensins, cathelicidins and thrombocidins and the non-cationic APs, which exhibit much lower antimicrobial.
The AP resistance mediated by LPS modification includes the addition of 4-aminoarabinose (Ara4N) and phosphoenthanolamine(pEtN) to one or both phosphate groups in the lipid A moiety thus reducing the overall negative charge at the outer membrane.
pEtN addition to the first heptose phosphate residue in the core of the polysaccharide is mediated by the gene product cptA. Also, the dephosphorylation of the second core heptose phosphate by the pmrG gene product helps in AP resistance.
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Another mechanism of LPS modification is the alteration of the acylation character of lipid A moiety. The addition of palmitate to the second position of the N-linked 3-hydroxymyristate on the proximal glucosamine of lipid A is catalyzed by the product of the PhoP-regulated pagP gene.
The production of a surface-associated protease that degrades AP before it can interact with the outer membrane and the pgtE gene encodes a surface protease that exhibits some specificity for alpha-helical APs such as C18G and human cathelicidin.
Bile is composed of various substances like proteins, ions, pigments, cholesterol and salts. It is present throughout the gastrointestinal tract and protects the body from microorganisms. However, enteric bacteria are still able to survive in the environment as they have developed several mechanisms to protect themselves and allow them to proliferate. Bile salts affect mainly the bacterial cell membranes and if the membrane is breached, the DNA molecules can be harmed as well by the production of reactive oxygen compounds.Eventually, all essential processes like replication will stop and will result in cell death. Mechanism developed by the enteric bacteria is not only about surmounting the damage of the cell membrane or DNA molecule but is also a combination of defense and repair processes. They have efflux pumps to dislodge the bile salts from the cell, thus preventing further damage.
Multi dug resistance:
Infectious diseases are getting more and more difficult to treat because of the rise of multidrug-resistant bacteria. There are several mechanisms, which have developed in bacteria gifting them the antibiotic resistance. The processes allow the bacteria to survive by chemically altering the antibiotic or removing it from the cell in an inactive form. Target site can also be modified so that the antibiotic does not recognize it and act upon it. Moreover, an existing enzyme can change itself to react with the antibiotic in such a way that the microorganism is not harmed.
Antibiotic resistance trait can be inherited in bacteria making it naturally resistant. For example, an outer membrane is formed on the cell wall of the bacterium, providing a protective shield against the antibiotic. The trait can also be gained from the mutations, which may have occurred in the DNA or from receiving DNA molecules known as plasmids from a foreign source. There is the vertical gene transfer and the horizontal gene transfer.
The vertical gene transfer is an operation driven by the principles of natural selection. A spontaneous mutation takes place in the chromosome giving resistance to a member of the bacterial population. In the presence of the antibiotic, the non-mutants will definitely be killed whereas the resistant mutant is allowed to grow and proliferate.
On the other hand, horizontal gene transfer is a series of actions whereby plasmids are transferred from one bacterium to another one, either of the same species or between different species. There are three mechanisms present. Firstly, conjugation is a process where there is direct cell contact between the two bacteria and then the transfer occurs. Secondly, transformation takes place where plasmids are absorbed by bacteria from the external environment. Lastly, transduction occurs when bacteriophages exchange DNA between two closely related bacteria.
For many microbial cells, hypertonic conditions are when there is water loss from the cytoplasm hence causing the cell to shrink (plasmolysis).
Hypotonic conditions occur when there is an influx of water into the cytoplasm which thus causes the cell to swell (plasmolysis) and can lead to osmotic lysis.
The function of osmoregulatory mechanism is maintaining the cell viability by proper turgor within limits.
Movement of water is mostly by diffusion and the rapid process occurs through water-selective channels called aquaporins. Due to sudden osmotic upshifts or downshifts, the AqpZ channels of E. coli have been able to allow large water fluxes in both directions. By regulating the total osmotic solute pool, turgor is maintained in the cytoplasm and the relative level of solutes in the periplasm (in Gram-negative bacteria) immediately outside the cytoplasmic membrane. In low-osmolality media, cytosolic osmolality is largely due to ionic solutes (e.g., K+ ions); in high-osmolality media it largely involves neutral solutes (e.g., trehalose).
Turgor pressure drops and growth slows when the osmolality of the surrounding environment increases hence macromolecular biosynthesis is inhibited and respiration rates decrease. This results in the most rapid response to this osmotic upshock which is an increase in K+ ion influx through three uptake systems in E. coli: Trk, Kdp, and Kup.
Under high osmolality condition, the Trk and Kdp systems are the major systems for K+ uptake, since they can achieve sufficiently high rates of uptake. The Trk system is composed of three components: TrkA (peripheral membrane protein), TrkE(membrane associated), and either TrkH (in E. coli ; membrane-spanning protein) or TrkG (E. coli and other bacteria; membrane-spanning protein). The Trk system binds NAD (H) via TrkA and may regulate K+ ion uptake.
The Kdp system is a three-component system composed of KdpA (membrane-spanning protein),KdpB (integral membrane protein), and KdpC (peripheral membrane protein).
KdpB is a P-type ATPase and provides the energy to drive K+ ion influx.
The Kup is a single, large membrane-spanning protein having a significant cytoplasmic tail domain. Moreover, K+ ion accumulation results from plasmolysis and the closing of stretch-sensitive K+ ion efflux channels.
The increase in K+ ion influx resulting from high external osmolality is a decrease in intracellular putrescine levels due to increased excretion.
Glutamate is the major anionic compound involved in osmoregulation and hence is synthesized and therefore accumulates quickly due to osmotic upshock and is totally dependent on K+ ion uptake. Two enzymes synthesize Glutamate: glutamate dehydrogenase (GDH) and glutamate synthase (GS) in E. coli and other enteric bacteria.
The disaccharide trehalose as a compatible solute, is often accumulated by many microbes.
In the periplasm of Gram-negative bacteria,there are presence of membrane-derived oligosaccharides(MDOs) and these are substituted with sn-1-phosphoglycerol and phosphoethanolamine derived from the membrane phospholipids and also with O-succinyl ester residues.
It is referred as water loss due to drying or water stress and affects greatly the survival of microbial cells on inanimate surfaces and environmental habitats such as soil.
Extracellular defenses such as bacterial glycocalyces (composed of exopolysaccharides and associated proteins) have an important role in protecting the bacteria by forming a gel-like extracellular matrix that holds a significant amount of bound water. Thus this water is lost slowly to the evaporative and matric forces.
Colloidal surface structures help in slowing the drying process. The regulatory protein CsgD in S.Typhimurium controls the biosynthesis extracellular cellulose and the thin aggregate fimbriae(curli) which are the major factors in desiccation resistance.
Also, the O-antigen polysaccharide chain of LPS protects the S.Typhimurium from complete desiccation.
During drying, the disaccharide trehalose acts as a compatible solute and aids in maintaining the structure and function of proteins and membrane lipids. The trehalose may also replace water under conditions of extreme desiccation therefore preventing denaturation of proteins and hence stabilizing membrane phospholipids.
Iron stress in many bacteria is regulated by the ferric uptake regulator (Fur) which is the global Fe homeostasis regulator and ryhB (sRNA). During Fe starvation, Fur is inactivated and ryhB becomes expressed. The expression of ryhB reduces the use of Fe by non-essential proteins thus making Fe available for essential Fe-using proteins such as ribonucleotide reductase involved in DNA synthesis and repair. RyhB is also involved in the repression of Fur mRNA translation which prevents the Fur repression of Fe metabolising genes (for example for Fe uptake) in low Fe conditions.
RyhB can also interact with mRNA shiA, which encodes for shikimate transporter increasing the uptake of shikimate from the surrounding environment. Shikimate is essential for the biogenesis of siderophores which are important in the acquisition of more Fe from the external environment due to their very high affinity for Fe3+.Enterochellin is an example of one of the main siderophore synthesised by enterobacteriaceae family for example in E.coli, Shigella, Salmonella and Klebsiella.
Once Fe is repleted in the external environment, there is a decrease in the production of siderophores to prevent excessive uptake of Fe which may be harmful to the cell. The further uptake of Fe is usually repressed by the formation of the Fur- Fe2+ complex.
At least 3 different ryhB-like systems have been identified in other bacteria:
1. Pseudomonas aeruginosa; 2 tandem sRNAs regulated by Fur is used to repress mRNAs encoding Fe-using proteins during Fe starvation
2. Neisseria meningitidis; the sRNA, NrrF, is involved in the rapid degradation of sdhCDAB mRNA during Fe starvation
3. Bacillus subtilis; the Fur regulated sRNA, FsrA, represses several Fe-using proteins for example succinate dehydrogenase
Microorganisms have developed several mechanisms in order to adapt themselves to frequently unfavorable environmental conditions. The mechanisms are usually stress-specific and they are generated for survival of the organism in high lethal levels of the stress in the organism. The organisms have sometimes evolved stress mechanism induced by one stress factor only but which allows the organisms to survive several other different stresses. These stress mechanism allows the organisms to anticipate, prepare for possible adverse environmental conditions in the future and thus increasing their chances of survival. The control of these stress mechanisms are controlled by a number of protein regulators and systems and allow the organism to persist whether in a host or non-host environment for longer periods of time. Although much research have been already been done in the subject in order to study the various stress mechanisms that have been developed to maintain survival of the organism, there still remains much to be covered in the field inviting future incentives into the field.