bluuebunny/crossref_metadata_2025_split huggingface dataset:
A distinct 5′ flanking var gene region regulates Plasmodium falciparum variant erythrocyte surface antigen expression in placental malaria
Authors: Vázquez‐Macías Aleida , Martínez‐Cruz Perla , Castañeda‐Patlán María Cristina , Scheidig Christine , Gysin Jürg , Scherf Artur , Hernández‐Rivas Rosaura 
Published: March 2003

SummaryThe Plasmodium falciparum multigene var family codes for approximately 50 variant adhesive proteins expressed in a mutually exclusive manner at the surface of infected red blood cells (iRBCs). Switching expression of var genes can lead to fundamental changes in the adhesive and antigenic properties of iRBCs. For example, a specific phenotypic switch in adhesion from CD36 to chondroitin sulphate A (CSA) is associated with malaria pathogenesis in pregnant women. The factors and DNA elements that control the expression of a particular member of the var gene family during gestational malaria remains enigmatic. Here, we report that the subtelomeric FCR3 varCSA is expressed under the control of a unique DNA element of 1.8 kb, whereas the other members of the var multigene family are flanked by common regulatory elements. The 5′varCSA‐type element is conserved as a single copy in laboratory strains and clinical isolates from Brazil and West Africa and contains two distinct repetitive elements of 150 bp and 60 bp respectively. The 5′varCSA‐type sequence tags a var gene in the 3D7 genome that is homologous to the FCR3 varCSA gene. A recombinant DBLγ domain of this var gene showed specific binding to CSA. This subtelomeric varCSA gene is transcribed in the opposite sense when compared with the usual orientation of telomere‐adjacent var genes. This unique arrangement might explain why the varCSA gene is relatively conserved in genetically distinct parasites despite being located in a highly recombinogenic chromosome compartment. The 5′ untranslated region (UTR) of the varCSA‐type sequence is also transcribed in placental isolates that bind to CSA, illustrating an important role for the unique 5′varCSA‐type sequence in the regulation of var genes involved in malaria pathogenesis in pregnant women. However, this promoter is not always found to be transcribing var genes selected for expression of products that bind to CSA in vitro. Our work identifies a sequence tag for the identification of varCSA genes in placental isolates for the first time.
Activation of the Escherichia coli nfnB gene by MarA through a highly divergent marbox in a class II promoter
Authors: Barbosa Teresa M. , Levy Stuart B. 
Published: March 2003

SummaryMarA is a global regulator that mediates resistance to multiple environmental hazards such as antibiotics, disinfectants and oxidative stress agents by modulating the expression of a large number of genes in the Escherichia coli chromosome. Two E. coli MarA homologues, SoxS and Rob also control, to different extents, genes in the mar/sox/rob regulon. The controlling element for these proteins is a 20 bp ‘marbox’ sequence in the promoter region of regulated genes. Using in vitro assays and mutagenesis of promoter fusions in whole cells, we identified the cis regulatory element involved in MarA upregulation of the oxygen‐insensitive nitroreductase nfnB gene. MarA binds to a marbox that is highly divergent from the previously proposed consensus (eight differences out of 14 specified nucleotides). Although purified SoxS and Rob proteins, like MarA, activated nfnB transcription in vitro, only constitutive expression of chromosomal marA, but not of soxS and rob genes, affected nfnB expression in whole cells. Increased expression, but limited as compared with MarA, was only achieved by plasmid‐mediated overexpression of SoxS and Rob. This study shows that MarA can regulate gene expression through a functional marbox that is considerably divergent from the current consensus sequence. The data suggest that MarA is preferred over SoxS and Rob in upregulating nfnB. The findings imply that other different but physiologically important marbox DNA–MarA interactions take place in the regulation of still uncharacterized members of the mar regulon.
Surface antigenic variation in Giardia lamblia
Authors: Nash Theodore E. 
Published: March 2003

Summary Giardia lamblia
, a common intestinal dwelling protozoan and a cause of diarrhoea in humans and animals world‐wide, undergoes surface antigenic variation. The variant‐specific surface proteins (VSPs) are a family of related, highly unusual proteins that cover the entire surface of the parasite. VSPs are cysteine‐rich proteins containing many CXXC motifs, one or two GGCY motifs, a conserved hydrophobic tail and a Zn finger motif. The biological role(s) of VSPs is unclear. As VSPs are resistant to the effects of intestinal proteases, they likely allow the organism to survive in the protease‐rich small intestine. Although immune escape is commonly mentioned as the reason antigenic variation occurs, VSP expression changes
in vivo even in the absence of an adaptive immune system suggesting the biological role of antigenic variation is more complex. The molecular mechanisms involved in antigenic variation are not known but appear to differ from those known to occur in other protozoa.
Identification of a gene required for the biosynthesis of ornithine‐derived lipids
Authors: Weissenmayer Barbara , Gao Jun‐Lian , López‐Lara Isabel M. , Geiger Otto 
Published: March 2003

SummaryPhospholipids are the membrane‐forming constituents in all living organisms. In addition to phosphorus‐containing lipids, the membranes of numerous bacteria contain significant amounts of phosphorus‐free polar lipids, often derived from amino acids. Although lipids derived from the amino acid ornithine are widespread among bacteria, their biosynthesis is unknown. Here, we describe the isolation of mutants of Sinorhizobium meliloti deficient in the biosynthesis of ornithine‐derived lipids (OL). Complementation of such mutants with a sinorhi‐zobial cosmid gene bank, subcloning of the complementing fragment and sequencing of the subclone led to the identification of a gene (olsA) coding for a presumptive acyltransferase. Amplification of this gene and its expression in OL‐deficient mutant backgrounds of S. meliloti demonstrates that it is required for OL biosynthesis. An OL‐deficient mutant of S. meliloti disrupted in olsA shows wild type‐like growth behaviour and is capable of inducing nitrogen‐fixing nodules on legume hosts. A lyso‐ornithine lipid‐dependent acyltransferase activity forming OL requires acyl‐AcpP as the acyl donor and expression of the olsA gene.
Mechanochemical ATPases and transcriptional activation
Authors: Zhang X. , Chaney M. , Wigneshweraraj Siva R. , Schumacher J. , Bordes P. , Cannon W. , Buck M. 
Published: March 2003

SummaryTranscriptional activator proteins that act upon the σ54‐containing form of the bacterial RNA polymerase belong to the extensive AAA+ superfamily of ATPases, members of which are found in all three kingdoms of life and function in diverse cellular processes, often via chaperone‐like activities. Formation and collapse of the transition state of ATP for hydrolysis appears to engender the interaction of the activator proteins with σ54 and leads to the protein structural transitions needed for RNA polymerase to isomerize and engage with the DNA template strand. The common oligomeric structures of AAA+ proteins and the crea‐tion of the active site for ATP hydrolysis between protomers suggest that the critical changes in protomer structure required for productive interactions with σ54‐holoenzyme occur as a consequence of sensing the state of the γ‐phosphate of ATP. Depending upon the form of nucleotide bound, different functional states of the activator are created that have distinct substrate and chaperone‐like binding activ‐ities. In particular, interprotomer ATP interactions rely upon the use of an arginine finger, a situation reminiscent of GTPase‐activating proteins.
Molecular and functional characterization of kshA and kshB, encoding two components of 3‐ketosteroid 9α‐hydroxylase, a class IA monooxygenase, in Rhodococcus erythropolis strain SQ1
Authors: Geize R. van der , Hessels G. I. , Gerwen R. van , Meijden P. van der , Dijkhuizen L. 
Published: March 2003

Summary9α‐Hydroxylation of 4‐androstene‐3,17‐dione (AD) and 1,4‐androstadiene‐3,17‐dione (ADD) is catalysed by 3‐ketosteroid 9α‐hydroxylase (KSH), a key enzyme in microbial steroid catabolism. Very limited knowledge is presently available on the KSH enzyme. Here, we report for the first time the identification and molecular characterization of genes encoding KSH activity. The kshA and kshB genes, encoding KSH in Rhodococcus erythropolis strain SQ1, were cloned by functional complementation of mutant strains blocked in AD(D) 9α‐hydroxylation. Analysis of the deduced amino acid sequences of kshA and kshB showed that they contain domains typically conserved in class IA terminal oxygenases and class IA oxygenase reductases respectively. By definition, class IA oxygenases are made up of two components, thus classifying the KSH enzyme system in R. erythropolis strain SQ1 as a two‐component class IA monooxygenase composed of KshA and KshB. Unmarked in frame gene deletion mutants of parent strain R. erythropolis SQ1, designated strains RG2 (kshA mutant) and RG4 (kshB mutant), were unable to grow on steroid substrates AD(D), whereas growth on 9α‐hydroxy‐4‐androstene‐3,17‐dione (9OHAD) was not affected. Incubation of these mutant strains with AD resulted in the accumulation of ADD (30–50% conversion), confirming the involvement of KshA and KshB in AD(D) 9α‐hydroxylation. Strain RG4 was also impaired in sterol degradation, suggesting a dual role for KshB in both sterol and steroid degradation.
Modulation of bft expression by the Bacteroides fragilis pathogenicity island and its flanking region
Authors: Franco Augusto A. , Cheng Rodney K. , Goodman Alan , Sears Cynthia L. 
Published: March 2003

SummaryTo establish a recombinant system for high‐level expression of biologically active Bacteroides fragilis toxin (BFT), we studied the expression of bft in non‐toxigenic B. fragilis (NTBF) strains. The bft gene and the B. fragilis pathogenicity island (BfPAI) were cloned into NTBF strains with two distinct genetic patterns: (i) pattern II, strains lacking the BfPAI and its flanking region; and (ii) pattern III, strains lacking the BfPAI but containing its flanking region. Analysis of BFT activity of these recombinant strains on HT29/C1 cells showed that both the BfPAI and its flanking regions are important to optimal BFT activity. Reverse transcription polymerase chain reaction (RT‐PCR) analysis indicated that the BfPAI and its flanking regions modulate bft expression. Further experiments demonstrated that the ≈ 700 bp region upstream of bft is the BfPAI region critical for optimal bft expression. We conclude that both the region flanking the BfPAI and ≈ 700 bp region upstream of bft are crucial to maximal BFT production by ETBF strains.
Type 1 fimbriae and extracellular polysaccharides are preeminent uropathogenic Escherichia coli virulence determinants in the murine urinary tract
Authors: Bahrani‐Mougeot Farah K. , Buckles Eric L. , Lockatell C. V. , Hebel J. R. , Johnson D. E. , Tang C. M. , Donnenberg M. S. 
Published: March 2003

Summary Escherichia coli
is the leading cause of urinary tract infections (UTIs). Despite the association of numerous bacterial factors with uropathogenic
E. coli
(UPEC), few such factors have been proved to be required for UTI in animal models. Previous investigations of urovirulence factors have relied on prior identification of phenotypic characteristics. We used signature‐tagged mutagenesis (STM) in an unbiased effort to identify genes that are essential for UPEC survival within the murine urinary tract. A library of 2049 transposon mutants of the prototypic UPEC strain CFT073 was constructed using mini‐Tn5
km2
carrying 92 unique tags and screened in a murine model of ascending UTI. After initial screening followed by confirmation in co‐infection experiments, 19 survival‐defective mutants were identified. These mutants were recovered in numbers 10
1
‐ to 10
6
‐fold less than the wild type in the bladder, kidneys or urine or at more than one site. The transposon junctions from each attenuated mutant were sequenced and analysed. Mutations were found in: (i) the type 1 fimbrial operon; (ii) genes involved in the biosyn‐thesis of extracellular polysaccharides including group I capsule, group II capsule and enterobacterial common antigen; (iii) genes involved in metabolic pathways; and (iv) genes with unknown function. Five of the genes identified are absent from the genome of the
E. coli
K‐12 strain. Mutations in type 1 fimbrial genes resulted in severely attenuated colonization, even in the case of a mutant with an insertion upstream of the
fim
operon that affected the rate of fimbrial switching from the ‘off’ to the ‘on’ phase. Three mutants had insertions in a new type II capsule biosynthesis locus on a pathogenicity island and were impaired in the production of capsule
in vivo
. An additional mutant with an insertion in
wecE was unable to synthesize enterobacterial common antigen. These results confirm the pre‐eminence of type 1 fimbriae, establish the importance of extracellular polysaccharides in the pathogenesis of UTI and identify new urovirulence determinants.
The dynamic microbe: green fluorescent protein brings bacteria to light
Authors: Southward Carolyn M. , Surette Michael G. 
Published: March 2003

SummaryThe demonstration that the green fluorescent protein (GFP) from the jellyfish Aequorea victoria required no jellyfish‐specific cofactors and could be expressed as a fluorescent protein in heterologous hosts including both prokaryotes and eukaryotes sparked the development of GFP as one of the most common reporters in use today. Over the past several years, the utility of GFP as a reporter has been optimized through the isolation and engineering of variants with increased folding rates, different in vivo stabilities and colour variants with altered excitation and emission spectral properties. One of the great utilities of GFP is as a probe for characterizing spatial and temporal dynamics of gene expression, protein localization and protein–protein interactions in living cells. The innovative application of GFP as a reporter in bacteria has made a significant contribution to microbial cell biology. This review will highlight recent studies that demonstrate the potential of GFP for real‐time analysis of gene expression, protein localization and the dynamics of signalling transduction pathways through protein–protein interactions.
The DNA site utilized by bacteriophage P22 for initiation of DNA packaging
Authors: Wu Hongyu , Sampson Laura , Parr Ryan , Casjens Sherwood 
Published: March 2003

SummaryVirion proteins recognize their cognate nucleic acid for encapsidation into virions through recognition of a specific nucleotide sequence contained within that nucleic acid. Viruses like bacteriophage P22, which have partially circularly permuted, double‐stranded virion DNAs, encapsidate DNA through processive series of packaging events in which DNA is recognized for packaging only once at the beginning of the series. Thus a single DNA recognition event programmes the encapsidation of multiple virion chromosomes. The protein product of P22 gene 3, a terminase component, is thought to be responsible for this recognition. The site on the P22 genome that is recognized by the gene 3 protein to initiate packaging series is called the pac site. We report here a strategy for assaying pac site activity in vivo, and the utilization of this system to identify and characterize the site genetically. It is an asymmetric site that spans 22 basepairs and is located near the centre of P22 gene 3.
The LuxR family protein SpnR functions as a negative regulator of N‐acylhomoserine lactone‐dependent quorum sensing in Serratia marcescens
Authors: Horng Yu‐Tze , Deng Su‐Chen , Daykin Mavis , Soo Po‐Chi , Wei Jun‐Rong , Luh Kwen‐Tay , Ho Shen‐Wu , Swift Simon , Lai Hsin‐Chih , Williams Paul 
Published: March 2003

Summary Serratia marcescens
SS‐1 produces at least four
N
‐acylhomoserine lactones (AHLs) which were identified using high‐resolution mass spectrometry and chemical synthesis, as
N‐
(3‐oxohexanoyl) homo‐serine lactone (3‐oxo‐C6‐HSL),
N
‐hexanoyl‐ (C6‐HSL),
N
‐heptanoyl (C7‐HSL) and
N
‐octanoyl‐ (C8‐HSL) homoserine lactone. These AHLs are synthesized via the LuxI homologue SpnI, and regulate via the LuxR homologue SpnR, the production of the red pigment, prodigiosin, the nuclease, NucA, and a biosurfactant which facilitates surface translocation.
spnR
overexpression and
spnR
gene deletion show that SpnR, in contrast to most LuxR homologues, acts as a negative regulator.
spnI
overexpression, the provision of exogenous AHLs and
spnI
gene deletion suggest that SpnR is de‐repressed by 3‐oxo‐C6‐HSL. In addition, long chain AHLs antagonize the biosurfactant‐mediated surface translocation of
S. marcescens
SS‐1. Upstream of
spnI
there is a gene which we have termed
spnT
.
spnI
and
spnT
form an operon and although database searches failed to reveal any
spnT homologues, overexpression of this novel gene negatively affected both sliding motility and prodigiosin production.
The gene bolA regulates dacA (PBP5), dacC (PBP6) and ampC (AmpC), promoting normal morphology in Escherichia coli
Authors: Santos Jorge M. , Lobo Mónica , Matos António P. A. , De Pedro Miguel A. , Arraiano Cecilia M. 
Published: March 2003

SummaryThe gene bolA has been shown to trigger the formation of osmotically stable round cells when overexpressed in stationary phase. We show that in poor growth conditions bolA is essential for normal cell morphology in stationary phase and under conditions of starvation. During exponential growth bolA promotes round morphology through a mechanism that is strictly dependent on the two main Escherichia colid,d‐carboxypeptidases, PBP5 and PBP6. The results show that bolA controls the levels of transcription of dacA (PBP5), dacC (PBP6) and ampC (AmpC), a class C β‐lactamase, thus connecting for the first time penicillin binding proteins (PBPs) and β‐lactamases at the level of gene regulation. Furthermore, PBP5 and PBP6 are shown to be independently regulated and to have distinct effects on the peptidoglycan layer. The evidence presented demonstrates that bolA is a regulator of cell wall biosynthetic enzymes with different roles in cell morphology and cell division.
Chaperones of the type III secretion pathway: jacks of all trades
Authors: Page Anne‐Laure , Parsot Claude 
Published: March 2003

SummaryThe type III secretion (TTS) pathway is used by many Gram‐negative bacteria to inject virulence proteins into cells of their host. The activity of the TTS apparatus is controlled by external signals and, in certain conditions, production and secretion are not coupled. Storage of some proteins before secretion involves their association with specific chaperones. Three classes of TTS chaperones have been distinguished according to whether they associate with: (i) one; (ii) several effector proteins; or (iii) the two translocators that allow passage of effectors across the membrane of eukaryotic cells. These chaperones are required for stabilization of their substrate(s) and prevention of their premature interactions with other partners during storage. They also play a role in secretion of their substrate(s). Some chaperones are also involved in transcriptional regulation of certain genes in response to the activity of secretion. The flagellar export apparatus is closely related to the TTS apparatus and some proteins of the flagellar export system have also been proposed to be chaperones that prevent premature interactions between the flagellum subunits.
Differential accumulation of Salmonella[Cu, Zn] superoxide dismutases SodCI and SodCII in intracellular bacteria: correlation with their relative contribution to pathogenicity
Authors: Uzzau Sergio , Bossi Lionello , Figueroa‐Bossi Nara 
Published: March 2003

SummaryMost Salmonella enterica strains have two peri‐plasmic [Cu, Zn] superoxide dismutases, SodCI and SodCII, encoded by prophage and chromosomal genes respectively. Both enzymes are thought to play a role in Salmonella pathogenicity by intercepting reactive oxygen species produced by the host's innate immune response. To examine the apparent redundancy, we have compared the levels of epitope‐tagged SodCI and SodCII proteins in bacteria growing in vitro, as well as inside tissue culture cells and in mouse tissues. Concomitantly, we have measured the abilities of mutants of either or both sodC genes to proliferate in infected mice in competition assays. Our results show a striking variation in the relative abundance of the two proteins in different environments. In vitro, both proteins accumulate when bacteria enter stationary phase; however, the increase is much sharper and conspicuous for SodCII than for SodCI. In contrast, SodCI vastly predominates in intracellular bacteria where SodCII levels are negligible. In agreement with these findings, most, if not all, of the contribution of [Cu, Zn] superoxide dismutase activity to murine salmonellosis can be ascribed to the SodCI protein. Overall the results of this work suggest that the duplicate sodC genes of Salmonella have evolved to respond to different sets of conditions encountered by bacteria inside the host and in the environment.
The P1 plasmid is segregated to daughter cells by a ‘capture and ejection’ mechanism coordinated with Escherichia coli cell division
Authors: Li Yongfang , Austin Stuart 
Published: March 2003

SummaryThe fate of the P1 plasmid of Escherichia coli was followed by time‐lapse photomicroscopy. A GFP–ParB fusion marked the plasmid during partition (segregation) to daughter cells at slow growth rate. The process differs from that previously inferred from statistical analysis of fixed cells. A focus of plasmid copies is captured at the cell centre. Immediately before cell division, the copies eject bidirectionally along the long axis of the cell. Cell division traps one or more plasmid copies in each daughter. They are not directed to a prescribed position but are free to move, associate and disassociate. Later, they are captured to the new cell centre to restart the cycle. A null P1 par mutant associates to form a focus, but it is neither captured nor ejected. A dominant negative ParB protein forms a plasmid focus that attaches to the cell centre but never ejects. It remains captive at the centre and blocks host cell division. The cells elongate. Eventually the intact focus is pushed to one side and the cells divide simultaneously in several places at the same time. This suggests that the wild‐type plasmid imposes a regulatory node on the host cell cycle, preventing cell division until its own segregation is completed.
The four different σ54 factors of Rhodobacter sphaeroides are not functionally interchangeable
Authors: Poggio Sebastian , Osorio Aurora , Dreyfus Georges , Camarena Laura 
Published: March 2003

SummaryThe σ54 factor is highly conserved in a large number of bacterial species. From the complete genome sequence of Rhodobacter sphaeroides, it was possible to identify four different sequences encoding potentially functional σ54 factors. In this work, we provide evidence that one of these copies (rpoN2) is specifically required to express the flagellar genes in this bacterium. A mutant strain carrying a lesion in the rpoN2 gene was unable to swim even though the RpoN1 and RpoN3 proteins were present in the cytoplasm. The possibility that the different copies of the σ54 factor might be specific for the transcription of a particular subset of σ54 promoters was reinforced by the fact that a mutant strain carrying a lesion in rpoN1 showed a severe growth defect in nitrogen‐free culture medium, even though the rpoN2 and rpoN4 genes were actively transcribed from a plasmid or from the chromosome. Different mech‐anisms that might be responsible for this specificity are discussed.