To survive adverse and fluctuating conditions, microorganisms possess mechanisms to recognize diverse environmental changes and mount an appropriate response. Microorganisms frequently react simultaneously to a wide variety of stresses, and the various stress response systems interact with each other by a complex of global regulatory networks.
Stress response systems can. Implications for Food Technology and Food Safety. Stress Responses of Lactic Acid Bacteria. Wood T. Ribosome dependence of persister cell formation and resuscitation. Gutgsell N. The pseudouridine synthase RluD is required for normal ribosome assembly and function in Escherichia coli. Jackman J. Wiley Interdiscip. Lorenz C. Eargle J. Zhang J. Giege R. EcoSal Plus.
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Stabilization of RNA stacking by pseudouridine. Wang S. Urbonavicius J. Three modifications in the D and T arms of tRNA influence translation in Escherichia coli and expression of virulence genes in Shigella flexneri. Ishida K. Pseudouridine at position 55 in tRNA controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium Thermus thermophilus. Gehrig S. Identification of modifications in microbial, native tRNA that suppress immunostimulatory activity.
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Gustilo E. Agris P. Olejniczak M. Durand J. Transfer RNA modification, temperature and DNA superhelicity have a common target in the regulatory network of the virulence of Shigella flexneri: The expression of the virF gene.
Aubee J. Thompson K. Putrescine or a combination of methionine and arginine restores virulence gene expression in a tRNA modification-deficient mutant of Shigella flexneri: A possible role in adaptation of virulence. Jelenc P. Nucleoside triphosphate regeneration decreases the frequency of translation errors.
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Support Center Support Center. External link. Please review our privacy policy. Structure Determination. X-ray Cristallography.
All modifications. Difficult to obtain crystals. Cryo Electron Microscopy. Heterogeneous resolution. Nuclear Magnetic Resonance.
Size limit. Nucleoside analysis. DMRM [ 34 ]. Known modifications. Fragmentation pattern and retention time of modifications must be known. NLS [ 34 ]. Various modifications. Fragment analysis. Relative quantification can be assessed with reference in vitro RNA. Without reference RNase digests [ 39 ].
Determination of base composition and localization by comparing mass-spectrometry results with expected RNase fragments. NGS-based methods. RNA deep-sequencing direct method. A-to-I [ 54 ]. Methylations [ 55 ]. Based on RT stops or misincorporations.
Nanopore RNA sequencing [ 56 , 57 ]. Software is still in development. Indirect methods: chemical treatments. ICE-Seq [ 58 , 59 ]. No need of DNA seq. Bisulfite-Seq [ 60 ]. Riboxi-Seq [ 61 ]. RiboMethSeq [ 62 , 63 ]. Pseudo-Seq [ 64 ].
PSI-Seq [ 65 ]. HydraPsi-Seq [ 66 ]. SLAM-Seq [ 67 ]. ARM-Seq [ 68 ]. TRAC-Seq [ 69 ]. AlkAniline-Seq [ 70 ]. Indirect methods: IP. NAD capture-Seq [ 77 ]. Affinity gel electrophoresis. Mercury-sulfur affinity [ 78 ]. APM treatment Acrylo-aminophenylmercuric chloride.
A 40 kDa protein has been reported to be associated with RNA polymerase purified from heat shocked cells. The pattern of HSP synthesis is dependent on the severity of the heat stress with two distinct phases being discernible in the heat shock response. Unlike in L. Sixteen HSPs have been identified in V. One of the major low molecular mass HSP, a 16 kDa protein is preferentially degraded following shift down of temperature.
This protein is induced at a much lower level at high temperature in cells maintained in the laboratory for a prolonged period. These laboratory maintained cells showed increased sensitivity to heat and low pH. During laboratory subculturing of V. All these functions can be restored by a single passage of the cells in guinea pig Roy et al Whether the 16 kDa protein has any role in virulence is yet to be investigated.
This protein is antigenic and antibodies against this inner membrane protein could be detected in sera of convales- cent cholera patients. The only HSP located at the outer membrane of V. The deduced amino acid sequence of the rpoH like gene of V. HSPs participate in immune response to bacterial infections and development of autoimmune diseases Murray and Young Different classes of HSPs from different bacteria can directly induce cytokine expressions and secretion in macro- phage Retzlaff et al Hsp60 has been found to be a common antigen of many bacterial pathogens including species of Pseudomonas, Mycobacterium, Borrelia, Salmonella, Legionella, Coxiella and Rickettsia Shinnick In Borellia burgdorferi, there are two HSP60 of molecular masses 60 and 66 kDa which have been implicated in developing autoimmune pathologies such as arthritis Carreiro et al The HSP70 of the organism, however, did not react with immune sera from Lyme disease patients.
It has been shown that S. This abundance of HSP may be one reason for their immuno- dominance. However, using a different macrophage Abshire and Neidhardt failed to detect induction of these HSPs following phagocytosis by S. It has been postulated that since HSP60 is highly conserved, the host may frequently encounter this antigen through infection with various other microorganisms thereby constantly boosting the immune response to HSP Kaufmann et al The major antigen in V. Oxygen stress The expression of adherence and invasion factors of several pathogenic bacteria is regulated by oxygen concentration.
High oxygen usually represses whereas low oxygen induces invasiveness. During switch from aerobic to anaerobic growth condition, a set of genes are induced and some genes are repressed Iuchi and Lin One regulatory network is the Fnr fumerate-nitrate reductase -dependent control in response to anaerobiosis. The frd and nar gene products are required for the reduction of fumarate and nitrate so that they can serve as alternative electron acceptors for oxidative phosphorylation even in the absence of oxygen.
Under semi-anaerobic conditions, the cytochrome d oxidase, which has low Km value for oxygen is induced under the control of ArcA—ArcB, a two component sensor regulator system responsive to a shift from aerobic to anaerobic growth. ArcA—ArcB-dependent regulation re- presses transcription of several genes involved in aerobic metabolism. The response to switch from aerobic to anaerobic growth conditions has been examined in detail in Salmonella sp and a number of invasion genes that are expressed under low oxygen environment have been identified.
The gene does not have significant similarity to other sequences present in the Gene Bank. The upstream of the orgA ORF has two direct repeats similar to those identified for the fnr-dependent promoters. These repeats overlap with the putative promoter of orgA. Osmotic stress For a pathogenic bacterium which passes from environmental waters to the human body for infection, osmolarity is an important criterion to distinguish between the external and host associated environments.
Thus, an increase in osmolarity is associated with expression of virulence factors in many pathogenic organisms. The two component regulatory system OmpR-EnvZ encoded by the OmpB locus is responsibIe for sensing and responding to the signal and controls the expression of the vir genes as well as the chromosomal ompF-ompC genes enconding the osmoregulated porins which are probably necessary for intracellular survival Bernardini et al Thus, ompB deletion mutants of S.
However, envZ mutations alone caused a decrease in expression of vir genes, but did not abolish their derepression under high osmolarity. These results suggested that although EnvZ is a major factor required for optimal expression of virulence genes, it is not the only component involved in the response of vir genes to osmolarity and cross talk between OmpR and an alternative component could restore osmoinduction of vir genes in EnvZ deficient mutants.
Recent reports suggest that OmpC may actually be involved in the invasion of epithelial cells by S. Interestingly, OmpC is expressed constitutively under conditions of high and low osmolarity in S. Unlike in S. Since antibiotics that reduce the superhelicity of DNA caused a decrease in the expression of invA, osmolarity may control expression of invasion genes by changing DNA super- coiling.
This is further supported by the observation that invA expression was reduced at low temperatures, a condition known to cause a reduction in the linking number of DNA. Although expression of the invasion genes is independent of ompR, mutations in ompR lead to an attenuation of virulence that cannot be accounted for only by changes in the concentrations of OmpC and OmpF, suggesting that other genes under the control of the ompR regulatory system may contribute to Salmonella virulence Chat- field et al
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