bluuebunny/crossref_metadata_2025_split huggingface dataset:
How do membrane proteins sense water stress?
Authors: Poolman Bert , Blount Paul , Folgering Joost H. A. , Friesen Robert H. E. , Moe Paul C. , Heide Tiemen van der 
Published: March 2003

SummaryMaintenance of cell turgor is a prerequisite for almost any form of life as it provides a mechanical force for the expansion of the cell envelope. As changes in extracellular osmolality will have similar physicochemical effects on cells from all biological kingdoms, the responses to osmotic stress may be alike in all organisms. The primary response of bacteria to osmotic upshifts involves the activation of transporters, to effect the rapid accumulation of osmo‐protectants, and sensor kinases, to increase the transport and/or biosynthetic capacity for these solutes. Upon osmotic downshift, the excess of cytoplasmic solutes is released via mechanosensitive channel proteins. A number of breakthroughs in the last one or two years have led to tremendous advances in our understanding of the molecular mechanisms of osmosensing in bacteria. The possible mechanisms of osmosensing, and the actual evidence for a particular mechanism, are presented for well studied, osmoregulated transport systems, sensor kinases and mechanosensitive channel proteins. The emerging picture is that intracellular ionic solutes (or ionic strength) serve as a signal for the activation of the upshift‐activated transporters and sensor kinases. For at least one system, there is strong evidence that the signal is transduced to the protein complex via alterations in the protein–lipid interactions rather than direct sensing of ion concentration or ionic strength by the proteins. The osmotic downshift‐activated mechanosensitive channels, on the other hand, sense tension in the membrane but other factors such as hydration state of the protein may affect the equilibrium between open and closed states of the proteins.
The Tol/Pal system function requires an interaction between the C‐terminal domain of TolA and the N‐terminal domain of TolB
Authors: Walburger Anne , Lazdunski Claude , Corda Yves 
Published: March 2003

SummaryThe Tol/Pal system of Escherichia coli is composed of the YbgC, TolQ, TolA, TolR, TolB, Pal and YbgF proteins. It is involved in maintaining the integrity of the outer membrane, and is required for the uptake of group A colicins and DNA of filamentous bacteriophages. To identify new interactions between the components of the Tol/Pal system and gain insight into the mechanism of colicin import, we performed a yeast two‐hybrid screen using the different components of the Tol/Pal system and colicin A. Using this system, we confirmed the already known interactions and identified several new interactions. TolB dimerizes and the periplasmic domain of TolA interacts with YbgF and TolB. Our results indicate that the central domain of TolA (TolAII) is sufficient to interact with YbgF, that the C‐terminal domain of TolA (TolAIII) is sufficient to interact with TolB, and that the amino terminal domain of TolB (D1) is sufficient to bind TolAIII. The TolA/TolB interaction was confirmed by cross‐linking experiments on purified proteins. Moreover, we show that the interaction between TolA and TolB is required for the uptake of colicin A and for the membrane integrity. These results demonstrate that the TolA/TolB interaction allows the formation of a trans‐envelope complex that brings the inner and outer membranes in close proximity.
Autoinduction of the ompR response regulator by acid shock and control of the Salmonella enterica acid tolerance response
Authors: Bang Iel Soo , Audia Jonathon P. , Park Yong Keun , Foster John W. 
Published: March 2003

Summary Salmonella enterica serovar Typhimurium periodically experiences acid stress
in a variety of host and non‐host environments. An encounter with non‐lethal acid
stress (pH > 4) induces an assortment of physiological changes, called
the acid tolerance response (ATR), that helps the cell to tolerate extreme low pH
(pH 3). These physiological changes differ in log phase and stationary phase cells
and are controlled by different regulatory proteins. OmpR is an acid‐induced response
regulator critical to the stationary phase ATR but not to the log phase ATR. As OmpR
also controls the expression of the acid‐induced viru‐lence operon ssrAB,
acid shock induction of ompR was examined to gain insight into how Salmonella
links virulence with survival at extreme acid pH. The results indicate that acid
pH induces ompR from a promoter different from that used for basal expression.
Transcription from this promoter is repressed by the histone‐like protein H‐NS and
requires OmpR‐P for induction. The classic sensor kinase EnvZ and acetyl phosphate
collaborate to produce the optimum level of OmpR‐P needed for autoinduction. Although
OmpR‐P is required for acid‐induced expression of ompR in wild‐type cells,
OmpR is not needed for ompR transcription in the absence of H‐NS. Thus, the
role of OmpR‐P in autoinduction is to help to counteract repression by H‐NS. This
evidence, combined with the finding that relaxing DNA supercoiling with novobiocin
also increased ompR transcription, suggests that acid stress induces ompR by altering local DNA topology, not by changing the phosphorylation status of OmpR.
Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: a second chromosomal example of translation initiated at AUU
Authors: Binns Nigel , Masters Millicent 
Published: March 2003

SummaryExpression of the gene pcnB, encoding the dispensable Escherichia coli
poly(A) polymerase (PAPI), which is toxic when overproduced, was investigated. Its
promoter was identified and found to be moderately strong when used to express a
β‐galactosidase reporter. Expression levels were not affected by increasing
or decreasing PcnB concentration. Translation of pcnB was found to initiate
from the non‐canonical initiation codon AUU. The only other coli gene reported
to use AUU as initiation codon is infC, which encodes the initiation factor IF‐3. AUU, in common with other rarely used initiation codons, is discriminated against by IF‐3, resulting in the aborting of most AUU‐promoted initiation events. This enables AUU to form part of an autoregulatory circuit controlling IF‐3 production. We show that InfC discrimination reduces PcnB production fivefold. This is the first instance of this mechanism being used to limit severely the production of a potentially toxic product.
Eclipse period without sequestration in Escherichia coli
Authors: Olsson Jan , Dasgupta Santanu , Berg Otto G. , Nordström Kurt 
Published: March 2003

SummaryThe classical Meselson–Stahl density shift experiment was used to determine the length of the eclipse period in Escherichia coli, the minimum time period during which no new initiation is allowed from a newly replicated origin of chromosome replication, oriC. Populations of bacteria growing exponentially in heavy (15NH4+ and 13C6‐glucose) medium were shifted to light (14NH4+ and 12C6‐glucose) medium. The HH‐, HL‐ and LL‐DNA were separated by CsCl density gradient centrifugation, and their relative amounts were determined using radioactive gene‐specific probes. The eclipse period, estimated from the kinetics of conversion of HH‐DNA to HL‐ and LL‐DNA, turned out to be 0.60 generation times for the wild‐type strain. This was invariable for widely varying doubling times (35, 68 and 112 min) and was independent of the chromosome locus at which the eclipse period was measured. For strains with seqA, dam and damseqA mutants, the length of the eclipse period was 0.16, 0.40 and 0.32 generation times respectively. Thus, initiations from oriC were repressed for a considerable proportion of the generation time even when the sequestration function seemed to be severely compromised. The causal relationship between the length of the eclipse period and the synchrony of initiations from oriC is discussed.
Conjugal transfer of the virulence plasmid of Salmonella enterica is regulated by the leucine‐responsive regulatory protein and DNA adenine methylation
Authors: Camacho Eva M. , Casadesús Josep 
Published: March 2003

SummaryHost‐encoded functions that regulate the transfer operon (tra) in the virulence

plasmid of Salmonella enterica (pSLT) were identified with a genetic screen.

Mutations that decreased tra operon expression mapped in the lrp gene,

which encodes the leucine‐responsive regulatory protein (Lrp). Reduced tra

operon expression in an Lrp− background is caused by lowered transcription

of the traJ gene, which encodes a transcriptional activator of the tra

operon. Gel retardation assays indicated that Lrp binds a DNA region upstream of

the traJ promoter. Deletion of the Lrp binding site resulted in lowered and

Lrp‐independent traJ transcription. Conjugal transfer of pSLT decreased 50‐fold

in a Lrp− background. When a FinO− derivative

of pSLT was used, conjugal transfer from an Lrp− donor decreased

1000‐fold. Mutations that derepressed tra operon expression mapped in dam,

the gene encoding Dam methyltransferase. Expression of the tra operon and

conjugal transfer remain repressed in an Lrp− Dam−

background. These observations support the model that Lrp acts as a conjugation activator

by promoting traJ transcription, whereas Dam methylation acts as a conjugation repressor by activating FinP RNA synthesis. This dual control of conjugal transfer may also operate in other F‐like plasmids such as F and R100.
Molecular microbiology and pathogenesis of Helicobacter and Campylobacter updated: a meeting report of the 11th conference on Campylobacter, Helicobacter and related organisms
Authors: Bereswill Stefan , Kist Manfred 
Published: March 2003

SummaryThe genome analysis of the gastrointestinal pathogens Helicobacter and Campylobacter has stimulated a wealth of new research activities, which are presented every 2 years at the international conferences on Campylobacter, Helicobacter and Related Organisms (CHRO). Both organisms represent excellent models for the identification of new molecular mechanisms involved in pathogenesis, host response and physiolological adaptation in course of acute and chronic infectious diseases. The investigation of their global distribution, pronounced genetic and antigenic diversity as well as the molecu‐lar mechanisms allowing long‐term persistence in hostile and unusual microbial habitats, is a challenge for scientists of many different disciplines world‐wide. With a focus on the molecular microbiology aspects, this review summarizes recent trends in Helicobacter and Campylobacter research by highlighting selected presentations at the 11th CHRO conference. The topics include the discovery of new virulence factors, functional analysis of protein secretion systems, host signalling pathways, adaptation to stress conditions, global gene regulation, and genetic variability.
The control of the yeast H2O2 response by the Msn2/4 transcription factors
Authors: Hasan Rukhsana , Leroy Christophe , Isnard Anne‐Dominique , Labarre Jean , Boy‐Marcotte Emmanuelle , Toledano Michel B. 
Published: March 2003

SummaryWe have analysed the contribution of the Msn2/4 transcription factors and the Ras‐cAMP‐proteine kinase A (PKA) pathway to the control of the yeast H2O2 response. Strains deleted for MSN2 and MSN4 are hypersensitive to H2O2, although they can still adapt to this oxidant. They are also unable to induce 27 proteins of the H2O2 stimulon as shown by quantitative two‐dimensional gel analysis. This peculiar H2O2 tolerance defect, the nature of the proteins of the Msn2/4 regulon, and the partial overlap of this regulon with the Yap1 H2O2‐response regulon, suggest an independent and distinctive role of these two H2O2 stress response pathways. A strain lacking PDE2, and therefore carrying high intracellular cAMP levels, is also hypersensitive to H2O2. In the presence of exogenous cAMP, this strain does not induce the entire H2O2 Msn2/4 regulon and some other proteins. This, and the normal H2O2 induction of a gene reporter under control of the Yap1 regulator when intracellular cAMP level are high, demonstrate that the Ras‐cAMP pathway negatively affects the H2O2 stress response through Msn2/4. However, the high H2O2 sensitivity of a strain lacking the PKA‐negative regulatory subunit Bcy1, is not only the consequence of the inhibition of Msn2/4 but also of Yap1 through a yet undefined mechanism.
Genes of non‐typeable Haemophilus influenzae expressed during interaction with human epithelial cell lines
Authors: Ulsen Peter van , Schilfgaarde Muriel van , Dankert Jacob , Jansen Henk , Alphen Loek van 
Published: March 2003

SummaryNon‐typeable Haemophilus influenzae may infect the lower respiratory airways of chronic obstructive pulmonary disease patients. We characterized genes of non‐typeable H. influenzae expressed during interaction with two human respiratory tract‐derived epithelial cell lines. A library of 8000 clones was constructed in H. influenzae Rd (rec1) by cloning chromosomal fragments upstream of a promoterless cat gene. Exposure of this library to NCI‐H292 epithelial cell layers in the presence of chloramphenicol (Cam) resulted in survival of bacteria expressing cat. A total of 52 clones were selected that were resistant to Cam in the presence of epithelial cells of cell line NCI‐H292. These did not (n = 42) or hardly grow (n = 10) on sBHI plates containing Cam and were sensitive to Cam in cell culture medium alone. All clones, moreover, survived Cam in the presence of Hep2 epithelial cell layers. Sequence analysis showed that four clones contained sequences without homology to Rd or any other sequence, and therefore contained promoters and parts of open reading frames (ORFs) of novel genes. The other 48 clones were homologous to Rd, and characterization was based upon this genome. Six different functional classes were distinguished: (i) metabolic processes; (ii) stress response; (iii) gene expression; (iv) cell envelope biosynthesis; (v) DNA‐related processes and cell division; and (vi) ORFs encoding proteins of unknown function. The contribution of identified genes to non‐typeable H. influenzae adaptation to the epithelial cell environment is discussed.
RNA editing: complexity and complications
Authors: Stuart Kenneth , Panigrahi Aswini K. 
Published: March 2003

SummaryRNA editing in Trypanosomatids creates functional mitochondrial mRNAs by extensive uridylate (U) insertion and deletion as specified by small guide RNAs (gRNAs). Editing is catalysed by the multiprotein editosome. Over 20 of its protein components have been identified and additional proteins are likely to function in editing and its regulation. The functions of only a few editosome proteins have been determined. Surprisingly, there are related pairs or sets of editosome proteins, and insertion and deletion editing appear to be functionally and perhaps spatially separate. A model for the editosome is proposed, which has a catalysis domain with separate sectors for insertion and deletion editing. It also contains domains for anchor duplex and upstream RNA binding, which position the sequence to be edited in the catalysis domain.
Never say never again: protein glycosylation in pathogenic bacteria
Authors: Benz Inga , Schmidt M. Alexander 
Published: March 2003

SummaryIn recent years, accumulating evidence for glycosylated bacterial proteins has overthrown an almost dogmatic belief that prokaryotes are not able to synthesize glycoproteins. Now it is widely accepted that eubacteria express glycoproteins. Although, at present, detailed information about glycosylation and structure–function relationships is available for only few eubacterial proteins, the variety of different components and structures observed already indicates that the variations in bacterial glycoproteins seem to exceed the rather limited display found in eukaryotes. Numerous virulence factors of bacterial pathogens have been found to be covalently modified with carbohydrate residues, thereby identifying these factors as true glycoproteins. In several bacterial species, gene clusters suggested to represent a general pro‐tein glycosylation system have been identified. In other cases, genes encoding highly specific glycosyltransferases have been found to be directly linked with virulence genes. These findings raise interesting questions concerning a potential role of glycosylation in pathogenesis. In this review, we will therefore focus on protein glycosylation in Gram‐negative bacterial pathogens.
YopH prevents monocyte chemoattractant protein 1 expression in macrophages and T‐cell proliferation through inactivation of the phosphatidylinositoI 3‐kinase pathway
Authors: Sauvonnet Nathalie , Lambermont Isabelle , Bruggen Pierre van der , Cornelis Guy R. 
Published: March 2003

SummaryPhosphatidylinositol 3‐kinase (PI 3‐kinase) and its target protein kinase B (Akt) are involved in various processes including internalization, chemotaxis and proliferation. We analysed the activation of Akt in J774 macrophages infected with virulent (pYV+) or avirulent (pYV−) Yersinia enterocolitica. During the early stage of infection with pYV+ and pYV− bacteria, Akt and its targets, glycogen synthase kinase 3 (GSK‐3) and forkhead transcription factor (FKHRL1), became phosphorylated. This phosphorylation induction was inhibited by wortmannin and thus dependent on PI 3‐kinase. When infection was carried out with pYV+ bacteria but not with pYV− bacteria, Akt and its targets became dephosphorylated at later time points. Using single knock‐out mutants in bacterial effector genes, we have determined that the tyrosine phosphatase YopH was responsible for the inactivation of the PI 3‐kinase cascade. In macrophages, this inactivation correlated with the downregulation of mRNA coding for monocyte chemoattractant protein 1 (MCP‐1), suggesting that YopH inhibits recruitment of macrophages to lymph nodes. We also analysed the effects of Y. enterocolitica infection on the proliferation of T lymphocytes. Consistent with the observation that YopH inactivated the Akt pathway, YopH inhibited PI 3‐kinase‐dependent secretion of interleukin 2 and proliferation. These data reveal a new effect of YopH in Yersinia pathogenesis.
A peroxide‐induced zinc uptake system plays an important role in protection against oxidative stress in Bacillus subtilis
Authors: Gaballa Ahmed , Helmann John D. 
Published: March 2003

SummaryIn Bacillus subtilis, hydrogen peroxide (H2O2) induces expression of the PerR regulon including catalase (KatA), alkyl hydroperoxide reductase and the DNA‐binding protein MrgA. We have identified the P‐type metal‐transporting ATPase ZosA (formerly YkvW) as an additional member of the perR regulon. Expression of zosA is induced by H2O2 and repressed by the PerR metalloregulatory protein, which binds to two Per boxes in the promoter region. Physiological studies implicate ZosA in Zn(II) uptake. ZosA functions together with two Zur‐regulated uptake systems and one known efflux system to maintain Zn(II) homeostasis. ZosA is the major pathway for zinc uptake in cells growing with micromolar levels of Zn(II) that are known to repress the two Zur‐regulated transporters. A perR mutant is sensitive to high levels of zinc, and this sensitivity is partially suppressed by a zosA mutation. ZosA is important for resistance to both H2O2 and the thiol‐oxidizing agent diamide. This suggests that increased intracellular Zn(II) may protect thiols from oxidation. In contrast, catalase is critical for H2O2 resistance but does not contribute significantly to diamide resistance. Growth of cells with elevated zinc significantly increases resistance to high concentrations of H2O2, and this effect requires ZosA. Our results indicate that peroxide stress leads to the upregulation of a dedicated Zn(II) uptake system that plays an important role in H2O2 and disulphide stress resistance.
Characterization of a fungal protein kinase from Cryphonectria parasitica and its transcriptional upregulation by hypovirus
Authors: Kim Myoung‐Ju , Choi Jin‐Won , Park Seung‐Moon , Cha Byeong‐Jin , Yang Moon‐Sik , Kim Dae‐Hyuk 
Published: March 2003

SummaryThe chestnut blight fungus Cryphonectria parasitica and its hypovirus comprise useful model system to study the mechanisms of hypoviral infection. We used degenerate primers based on fungal protein kinases to isolate a gene, cppk1, which encodes a novel Ser/Thr protein kinase of C. parasitica. The gene showed highest homology to ptk1, a Ser/Thr protein kinase from Trichoderma reesei. The encoded protein had a predicted mass of 70.5 kDa and a pI of 7.45. Northern blot analyses revealed that the cppk1 transcript was expressed from the beginning of culture, with a slight increase by 5 days of culture. However, its expression was specifically affected by the presence of virus, and it was transcriptionally upregulated in the fungal strain infected with the hypovirus. A kinase assay using Escherichia coli‐derived CpPK1 revealed CpPK1‐specific phosphorylated proteins with estimated masses of 50 kDa and 44 kDa. In addition, the phosphorylation of both proteins was higher in a cell‐free extract from the hypovirulent strain. The increased expression of cppk1 by the introduction of an additional copy results in a subset of viral symptoms of reduced pigmentation and conidiation in a virus‐free isolate. cppk1 overexpression also causes the downregulation of mating factor genes Mf2/1 and Mf2/2, resulting in female sterility. The present study suggests that the hypovirus disturbs fungal signalling by transcriptional upregulation of cppk1, which results in reduced pigmentation and conidiation and female sterility.
A Rho‐dependent phase‐variable transcription terminator controls expression of the FimE recombinase in Escherichia coli
Authors: Joyce Susan A. , Dorman Charles J. 
Published: March 2003

SummaryThe fim switch is a 314 bp segment of invertible chromosomal DNA that is responsible for phase‐variable expression of type 1 fimbriae in Escherichia coli. The switch harbours the promoter of the fimA gene. This codes for the type 1 fimbrial subunit protein and, when the promoter is directed towards fimA (phase ON), the bacteria are fimbriate and, when it is directed away, the cells are afimbriate. The switch lies immediately downstream from the fimE gene, coding for a tyrosine site‐specific recombinase that catalyses inversion of the switch from the ON to the OFF phase. It has been suggested previously that, because the fim switch lies immediately downstream from the fimE gene, expression of FimE could be subject to control by antisense RNA in phase OFF bacteria in which the promoter harboured within the fim switch is oriented against the direction of transcription of the fimE gene. In this study, no effect of inducible fimE antisense RNA, expressed in cis or in trans, on FimE expression was detected. In phase ON cells, fimE mRNA extends across the switch into fimA, whereas in phase OFF cells, it terminates within the switch. This termination is Rho dependent and is abolished in a rho mutant. The extended fimE found in phase ON cells is more stable and results in an approximately fivefold increase in FimE protein compared with phase OFF bacteria. In the absence of Rho factor, fimE mRNA is equally stable in phase ON and phase OFF cells, and the levels of FimE recombinase are also equal.