bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative analysis of expression of two circadian clock‐controlled gene clusters coding for the bidirectional hydrogenase in the cyanobacterium Synechococcus sp. PCC7942
Authors: Schmitz Oliver , Boison Gudrun , Bothe Hermann 
Published: March 2003

Hydrogen metabolism is of central interest in cyanobacterial research because of its potential applications. The gene expression and physiological role of the cyanobacterial bidirectional NAD(P)+‐reducing hydrogenase are poorly understood. Transcription rates of hoxEF and hoxUYH encoding this enzyme have been studied in Synechococcus sp. PCC7942. PhoxU activity was about three times higher than that of PhoxE. Circadian phasing of both promoters was found to be synchronous and influenced expression levels by at least one order of magnitude. This is the first demonstration of circadian control of gene expression for any hydrogenase. For the majority of PhoxU‐driven messages, transcription presumably terminates between hoxU and hoxH. Being part of a polycistronic hoxUYHW… operon, hoxW, encoding a protease involved in C‐terminal processing of the hydrogenase large‐subunit HoxH, is mainly expressed by its own promoter, PhoxW. The complex transcript formation may be a key feature for controlling bidirectional hydrogenase expression in vivo.
The att locus of Rhodococcus fascians strain D188 is essential for full virulence on tobacco through the production of an autoregulatory compound
Authors: Maes Tania , Vereecke Danny , Ritsema Tita , Cornelis Karen , Thu Hang Ngo Thi , Van Montagu Marc , Holsters Marcelle , Goethals Koen 
Published: March 2003

The ability of Rhodococcus fascians strain D188 to provoke leafy gall formation on a variety of plant species is correlated with the linear plasmid pFiD188, on which different pathogenicity loci were identified. The att locus affects the severity of symptom development on tobacco, whereas the fas locus is essential for virulence. To gain insight into the function of the att locus, sequence and expression analyses were performed. The att locus contains nine open reading frames homologous to arginine and β‐lactam biosynthetic genes. att gene expression is transcriptionally induced by leafy gall extracts, but not by extracts of uninfected plants, and depends on the attR gene that encodes a LysR‐type transcriptional regulator. The att locus proves to be essential for the formation of inducing factors (IFs) that are present in gall extracts. Because the induction of the fas locus also requires the presence of IFs in gall extracts, the att locus is proposed to play an important role in regulating the expression of the virulence loci of R. fascians.
The LuxS‐dependent autoinducer AI‐2 controls the expression of an ABC transporter that functions in AI‐2 uptake in Salmonella typhimurium
Authors: Taga Michiko E. , Semmelhack Julia L. , Bassler Bonnie L. 
Published: March 2003

In a process called quorum sensing, bacteria communicate with one another using secreted chemical signalling molecules termed autoinducers. A novel autoinducer called AI‐2, originally discovered in the quorum‐sensing bacterium Vibrio harveyi, is made by many species of Gram‐negative and Gram‐positive bacteria. In every case, production of AI‐2 is dependent on the LuxS autoinducer synthase. The genes regulated by AI‐2 in most of these luxS‐containing species of bacteria are not known. Here, we describe the identification and characterization of AI‐2‐regulated genes in Salmonella typhimurium. We find that LuxS and AI‐2 regulate the expression of a previously unidentified operon encoding an ATP binding cassette (ABC)‐type transporter. We have named this operon the lsr (luxS regulated) operon. The Lsr transporter has homology to the ribose transporter of Escherichia coli and S. typhimurium. A gene encoding a DNA‐binding protein that is located adjacent to the Lsr transporter structural operon is required to link AI‐2 detection to operon expression. This gene, which we have named lsrR, encodes a protein that represses lsr operon expression in the absence of AI‐2. Mutations in the lsr operon render S. typhimurium unable to eliminate AI‐2 from the extracellular environment, suggesting that the role of the Lsr apparatus is to transport AI‐2 into the cells. It is intriguing that an operon regulated by AI‐2 encodes functions resembling the ribose transporter, given recent findings that AI‐2 is derived from the ribosyl moiety of S‐ribosylhomocysteine.
The universal stress protein paralogues of Escherichia coli are co‐ordinately regulated and co‐operate in the defence against DNA damage
Authors: Gustavsson N. , Diez . A. , Nyström T. 
Published: March 2003

SummaryWe have cloned, characterized and inactivated genes encoding putative UspA paralogues in Escherichia coli. The yecG (uspC), yiiT (uspD)
and ydaA (uspE) genes were demonstrated to encode protein pro‐ducts
and these were mapped to spots in the E. coli proteomic database. Expression
analysis using chromosomal transcriptional lacZ fusions and two‐dimensional
gels revealed that all usp genes analysed are regulated in a similar fashion.
Thus, uspC, D and E are all induced in stationary phase and
by a variety of stresses causing growth arrest of cells. Induction is independent
of rpoS but is abolished in a ΔrelAΔspoT
(ppGpp0) background and rescued by suppressor mutations rendering the
β‐subunit of RNA polymerase to behave like a stringent polymerase. Ectopic
elevation of ppGpp levels in growing cells, by overproducing the RelA protein, triggered
the induction of all usp genes. The expression of all usp genes was
also elevated by a mutation in the ftsK cell division gene, and this super‐induction
could be suppressed by inactivating recA indicating that the usp paralogues
are involved in the management of DNA. Indeed, uspC, uspD and uspE
deletion mutants were all found to be sensitive to UV exposure. Overexpression of
UspD could compensate for the lack of a chromosomal uspD gene but not a uspA
gene. Similarly, UspA overproduction could only compensate for the lack of chromosomal
uspA. Moreover, combination of usp mutations had no additive effect on UV sensitivity indicating that they are all co‐operating and required in the same pathway, which could explain the co‐ordinated regulation of the genes.
Genetic and functional analysis of the phosphorylcholine moiety of commensal Neisseria lipopolysaccharide
Authors: Serino Laura , Virji Mumtaz 
Published: March 2003

SummaryPhosphorylcholine (ChoP) is a common surface feature of many mucosal organisms, including Neisseria spp., in which it is present exclusively on pili of pathogenic Neisseria and on the lipopolysaccharide (LPS) of commensal Neisseria (Cn). Its presence in Cn has been confirmed by nuclear magnetic resonance. It appears that choline is the main source for the production of ChoP by Cn. We have sequenced a locus, containing four genes (licA–D) with 47–73% identity to the lic1 locus of Haemophilus influenzae (Hi) and 21–40% identity to lic genes in Streptococcus pneumoniae, involved in the production and incorporation of ChoP. The arrangement of the Cn genes and the presence of CAAT repeats, responsible for phase variation of ChoP expression, resemble Hi and differ from S. pneumoniae. Cn DNA flanking the lic locus contains genes ilvE and NMA2149 with >85% identity to the pathogenic Neisseria genes. However, there are no lic genes in the corresponding location or elsewhere in pathogenic Neisseria. This suggests either the loss of the locus from pathogenic Neisseria or a horizontal transfer of genes to Cn, perhaps from H. influenzae spp. As in Hi, ChoP enhances adherence to and invasion of human epithelial cells via the receptor for platelet‐activating factor. However, ChoP expression also increases susceptibility to serum killing mediated by complement and C‐reactive protein. Taken together, these observations support the hypothesis that the ability of many organisms to switch off ChoP expression rapidly represents an important adaptation to dif‐ferent environments encountered during the colonization/infection process and that the ChoP moiety apparently synthesized by distinct means in pathogenic and commensal Neisseria represents an advantage in the colonization properties of these bacteria.
Osmotic stress‐coupled maintenance of polar growth in Aspergillus nidulans
Authors: Han Kap‐Hoon , Prade Rolf A. 
Published: March 2003

SummaryFree‐living cells monitor extracellular ‘osmotic strength’ and respond metabolically to offset unfavourable osmotic intracellular solute concentrations. Here, we report the reconstruction of the Aspergillus nidulans salt stress‐controlling
MAP kinase pathway, based on homology analysis with known yeast genes. In A. nidulans,
salt stress HOG genes, such as pbsA, hogA, ptpA and msnA,
are upregulated when exposed to high concentrations of salt and, in a hogA
deletion mutant (SIK1), the accumulation of pbsA is strongly reduced, suggesting a salt‐specific feedback induction mechanism. Growth of SIK1 appears to be unchanged in unstressed cells, but hyphal extension rates are reduced by as much as 60% in the presence of salt. Microscopic observation revealed abnormal hyperbranched hyphal tips, disproportionate accumulation of nuclei and absence of septa. Thus, the inability to maintain turgor pressure depresses cell expansion and results in slower volume increases. In addition, SIK1 fails to partition the apical cell; thus, nuclei are not likely to arrest mitosis in interphase as in normal cells, but continue to divide, accumulating to high levels.
Quorum sensing Escherichia coli regulators B and C (QseBC): a novel two‐component regulatory system involved in the regulation of flagella and motility by quorum sensing in E. coli
Authors: Sperandio Vanessa , Torres Alfredo G. , Kaper James B. 
Published: March 2003

SummaryQuorum sensing is a cell‐to‐cell signalling mechanism in which bacteria secrete hormone‐like compounds called autoinducers. When these auto‐inducers reach a certain threshold concentration, they interact with bacterial transcriptional regulators, thereby regulating gene expression. Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 as well as E. coli K‐12 produces the autoinducer‐2 (AI‐2), which is synthesized by the product of the luxS gene, and previous work from our laboratory has shown that genes encoding the EHEC type III secretion system were activated by quorum sensing. Recently, by hybridizing an E. coli K‐12 gene array with cDNA synthesized from RNA extracted from EHEC strain 86‐24 and its isogenic luxS mutant, we observed that other potential virulence‐associated factors, such as genes encoding the expression and assembly of flagella, motility and chemotaxis, were also activated by quorum sensing. The array data also indicated that several genes encoding putative E. coli regulators were controlled by quorum sensing. In this report, we describe a two‐component system regulated by quorum sensing that shares homology with Salmonella typhimurium PmrAB, which we have named quorum sensing E. coli regulator B and C (QseBC). The qseBC genes, previously identified only as open reading frames b3025 and b3026, are organized in an operon in the E. coli chromosome, with qseB encoding the response regulator and qseC the sensor kinase. We confirmed the regulation of qseBC by quorum sensing using qseB::lacZ transcriptional fusions and characterized the phenotypes of an isogenic qseC mutation in EHEC. This mutant expressed less flagellin and had reduced motility compared with the wild‐type and complemented strains. Transcription of flhD, fliA, motA and fliC::lacZ fusions was decreased in the qseC mutant, suggesting that qseBC is a transcriptional regulator of flagella genes. A qseC mutant was also generated in E. coli K‐12 strain MC1000 that showed the same phenotypes as the EHEC mutant, indicating that qseBC regulates flagella and motility by quorum sensing in both EHEC and K‐12. QseBC activates transcription of flhDC, which is the master regulator for the flagella and motility genes and, in the absence of flhD, QseBC failed to activate the transcription of fliA. Motility of a luxS, but not of a qseC, mutant can be restored by providing AI‐2 exogenously as preconditioned media, suggesting that the qseC mutant is unable to respond to AI‐2. However, QseC has no effect on the expression of other quorum sensing‐controlled genes such as those encoding for the type III secretion system. These data indicate that QseBC is one component of the quorum‐sensing regulatory cascade in both EHEC and K‐12 that is involved in the regulation of flagella and motility genes, but that additional regulators in this cascade remain to be characterized.
The WD40‐repeat protein CreC interacts with and stabilizes the deubiquitinating enzyme CreB in vivo in Aspergillus nidulans
Authors: Lockington Robin A. , Kelly Joan M. 
Published: March 2003

SummaryGenetic dissection of carbon catabolite repression in Aspergillus nidulans

has identified two genes, creB and creC, which, when mutated, affect

expression of many genes in both carbon catabolite repressing and derepressing conditions.

The creB gene encodes a functional deubiquitinating enzyme and the creC

gene encodes a protein that contains five WD40 repeat motifs, and a proline‐rich

region . These findings have allowed the in vivo molecular analysis of a cellular

switch involving deubiquitination. We demonstrate that overexpression of the CreB

deubiquitinating enzyme can partially compensate for a lack of the CreC WD40‐repeat

protein in the cell, but not vice versa and, thus, the CreB deubiquitinating

enzyme acts downstream of the CreC WD40‐repeat protein. We demonstrate using co‐immunoprecipitation

ex‐periments that the CreB deubiquitinating enzyme and the CreC WD40‐repeat protein

interact in vivo in both carbon catabolite repressing and carbon catabolite derepressing conditions. Further, we show that the CreC WD40‐repeat protein is required to prevent the proteolysis of the CreB deubiquitinating enzyme in the absence of carbon catabolite repression. This is the first case in which a regulatory deubiquitinating enzyme has been shown to interact with another protein that is required for the stability of the deubiquitinating enzyme.
An rRNA mutation identifies the apicoplast as the target for clindamycin in Toxoplasma gondii
Authors: Camps Manel , Arrizabalaga Gustavo , Boothroyd John 
Published: March 2003

Summary Toxoplasma gondii is a protozoan sensitive to several inhibitors of prokaryotic

translation (e.g. clindamycin, macrolides and tetracyclines). A priori, two

prokaryotic‐like organelles, the ‘apicoplast’ (a non‐photosynthetic

plastid) and the mitochondrion, are likely targets for these drugs. Without using

overt mutagenesis, we selected two independent clones (ClnR‐4 and ClnR‐21)

with strong and stable clindamycin resistance. Several lines with substantial but

lower levels of resistance were also isolated with (XR‐46) or without (ClnR‐23)

overt mutagenesis. The ClnR‐4 and ClnR‐21 mutants uniquely

possess a G→U point mutation at position 1857 of the apicoplast large‐subunit

rRNA, whereas no mutation was identified in this region for ClnR‐23 or

XR‐46. Position 1857 corresponds to position 2061 in Escherichia coli where

it is predicted to bind clindamycin. The mutation is present in all the apicoplast

rDNA copies (an estimated 12 per organelle), indicative of a strong selective advantage

in the presence of clindamycin. In the absence of drug, however, such a mutation

is unlikely to be neutral, as the G is a critical contributor to the transpeptidation

reaction and absolutely conserved in all kingdoms. This may explain why ClnR‐4

shows a slight growth defect in vitro. These mutants provide direct genetic

evidence that apicoplast translation is the target for clindamycin in Toxoplasma. Further, their sensitivity profiles to other antibiotics specific for the large ribosomal subunit (macrolides and chloramphenicol) and, intriguingly, the small subunit (doxycycline) argue that these drugs also target the apicoplast ribosome.
Overexpression of the putative thiol conjugate transporter TbMRPA causes melarsoprol resistance in Trypanosoma brucei
Authors: Shahi Sanjay K. , Krauth‐Siegel R. Luise , Clayton Christine E. 
Published: March 2003

SummaryMelaminophenyl arsenical drugs are a mainstay of chemotherapy against late‐stage African sleeping sickness, but drug resistance is increasingly prevalent. We describe here the characterization of two genes encoding putative metal–thiol conjugate transporters from Trypanosoma brucei. The two proteins, TbMRPA and
TbMRPE, were each overexpressed in trypanosomes, with or without co‐expression
of two key enzymes in trypanothione biosynthesis, ornithine decarboxylase and gamma‐glutamyl‐cysteine
synthetase. Overexpression of gamma‐glutamyl‐cysteine synthetase resulted in a twofold
increase in cellular trypanothione, whereas overexpression of ornithine decarboxylase
had no effect on the trypanothione level. The overexpression of TbMRPA resulted
in a 10‐fold increase in the IC50 of melarsoprol. The overexpression of
the trypanothione biosynthetic enzymes alone gave two‐ to fourfold melarsoprol resistance,
but did not enhance resistance caused by MRPA. Overexpression of TbMRPE had little effect on susceptibility to melarsoprol but did give two‐ to threefold resistance to suramin.
A genome‐wide strategy for the identification of essential genes in Staphylococcus aureus
Authors: Forsyth R. Allyn , Haselbeck Robert J. , Ohlsen Kari L. , Yamamoto Robert T. , Xu Howard , Trawick John D. , Wall Daniel , Wang Liangsu , Brown‐Driver Vickie , Froelich Jamie M. , C. Kedar G. , King Paula , McCarthy Melissa , Malone Cheryl , Misiner Brian , Robbins David , Tan Zehui , Zhu Zhan‐yang , Carr Grant , Mosca Deborah A. , Zamudio Carlos , Foulkes J. Gordon , Zyskind Judith W. 
Published: March 2003

SummaryTo address the need for new approaches to antibiotic drug development, we have identified a large number of essential genes for the bacterial pathogen, Staphylococcus

aureus, using a rapid shotgun antisense RNA method. Staphylococcus aureus

chromosomal DNA fragments were cloned into a xylose‐inducible expression plasmid

and transformed into S. aureus. Homology comparisons between 658 S. aureus

genes identified in this particular antisense screen and the Mycoplasma genitalium

genome, which contains 517 genes in total, yielded 168 conserved genes, many of which

appear to be essential in M. genitalium and other bacteria. Examples are presented in which expression of an antisense RNA specifically reduces its cognate mRNA. A cell‐based, drug‐screening assay is also described, wherein expression of an antisense RNA confers specific sensitivity to compounds targeting that gene product. This approach enables facile assay development for high throughput screening for any essential gene, independent of its biochemical function, thereby greatly facilitating the search for new antibiotics.
Studies on the role of the metK gene product of Escherichia coli K‐12
Authors: Wei Yuhong , Newman E. B. 
Published: March 2003

SummaryWe show here that the metK gene is essential to the growth of Escherichia

coli K‐12 and can be deleted only in the presence of a rescue plasmid carrying

a functional metK gene. When metK expression was limited, genomic DNA

methylation decreased and cell division was hampered. Through primer extension, the

transcription start site of metK was located at 140 bp upstream of the translation

start site. The frequently used metK84 mutant has been shown to

carry an A(r)G transition in the −10 region of the metK promoter. This accounts for its low level of S‐adenosylmethionine (SAM) synthetase and SAM deficiency.
The luxS gene is involved in cell–cell signalling for toxin production in Clostridium perfringens
Authors: Ohtani Kaori , Hayashi Hideo , Shimizu Tohru 
Published: March 2003

SummaryA Gram‐positive anaerobic pathogen, Clostridium perfringens, causes clostridial
myonecrosis or gas gangrene in humans by producing numerous extracellular toxins
and enzymes that act in concert to degrade host tissues. C. perfringens possesses
a homologue of the luxS gene that is reported to be responsible for the production
of autoinducer 2 (AI‐2), which participates in quorum sensing in bacteria. The luxS
mutant was constructed using C. perfringens strain 13, and the role of the
luxS gene in toxin production was examined. The cell‐free culture supernatant
from wild‐type strain 13 greatly stimulated the luminescence of Vibrio harveyi
BB170, whereas that from the luxS mutant caused no significant stimulation,
indicating that the luxS gene is necessary for AI‐2 production in C. perfringens.
The luxS mutant showed a reduced level of production of alpha‐, kappa‐ and
theta‐toxins. In the luxS mutant, the transcription of the theta‐toxin gene
(pfoA) was lower at mid‐exponential growth phase, whereas alpha‐ and kappa‐toxin
gene transcription was not significantly affected. The production of toxins in the
luxS mutant was stimulated by the addition of the culture supernatant from
the wild‐type cells, possibly because of the presence of AI‐2. Moreover, the expression
of the pfoA gene in the luxS mutant was apparently activated when the
mutant cells were cultured in the presence of culture supernatants from the wild‐type
C. perfringens, Escherichia coli DH5α carrying the luxS
gene of C. perfringens. A deletion analysis of the luxS operon showed
that the luxS gene alone is responsible for cell–cell signalling, and
that the metB or cysK genes located upstream of luxS are not
involved in regulating toxin production. Our results indicate that cell–cell
signalling by AI‐2 plays an important role in the regulation of toxin production
in C. perfringens.
The FtsH protease is involved in development, stress response and heat shock control in Caulobacter crescentus
Authors: Fischer B. , Rummel G. , Aldridge P. , Jenal Urs 
Published: March 2003

SummaryThe ftsH gene of Caulobacter crescentus has been isolated and identified as a component of the general stress response of this organism. In C. crescentus, ftsH expression is transiently induced after temperature upshift and in stationary phase. Consistent with this, mutants deprived of the FtsH protease are viable at normal growth conditions, but are highly sensitive to elevated temperature, increased salt concentration or the presence of antibiotics. Overexpression of ftsH resulted in an increased salt but not thermotolerance, emphasizing the importance of the FtsH protease in stress response. Mutants lacking FtsH were unable to undergo morphological and physiological adaptation in stationary phase and, upon starvation, experienced a more pronounced loss of viability than cells containing FtsH. In addition, cells lacking FtsH had an increased cellular concentration of the heat shock sigma factor σ32, indicating that, as in Escherichia coli, the FtsH protease is involved in the control of the C. crescentus heat shock response. In agreement with this, transcription of the heat‐induced σ32‐dependent gene dnaK was derepressed at normal temperature when FtsH was absent. In contrast, the groEL gene, which is controlled in response to heat stress by both σ32 and a HcrA/CIRCE mechanism, was not derepressed in an ftsH mutant. Finally, FtsH is involved in C. crescentus development and cell cycle control. ftsH mutants were unable to synthesize stalks efficiently and had a severe cell division phenotype. In the absence of FtsH, swarmer cells differentiated into stalked cells faster than when FtsH was present, even though the entire cell cycle was longer under these conditions. Thus, directly or indirectly, the FtsH protease is involved in the inherent biological clock mechanism, which controls the timing of cell differentiation in C. crescentus.