bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional genomics of bacterial pathogens: from post‐genomics to therapeutic targets
Authors: Polissi Alessandra , Soria Marco R. 
Published: June 2005

SummaryA wealth of new data have become available to the scientific community as a result of the sequencing of many pathogen genomes. A recent meeting devoted to functional genomics of pathogenic microorganisms confirmed the notion that bacterial genomes are not static, because large blocks of genes can be acquired or deleted. Less complex environments usually result in reduction in genome size, while genome expansion is usually associated with environmental change and complexity. During the meeting, pathogenicity and evolutionary aspects were illustrated for enteric pathogens, as well as the microevolution of the plague bacillus Yersinia pestis. New clues for evolution and pathogenicity were derived from comparative genomics of Listeria species. The genomic organization of Bartonellae, an emerging human pathogen, was also discussed in an evolutionary context. Population and functional genomics of Anthrax‐causing bacteria highlighted current scientific interest in this potential biothreat.
Direct binding of the quorum sensing regulator CepR of Burkholderia cenocepacia to two target promoters in vitro
Authors: Weingart Christine L. , White Catharine E. , Liu Suping , Chai Yunrong , Cho Hongbaek , Tsai Ching‐Sung , Wei Yuping , Delay Nicholas R. , Gronquist Matthew R. , Eberhard Anatol , Winans Stephen C. 
Published: June 2005

SummaryBurkholderia cenocepacia is an opportunistic human pathogen that can aggressively colonize the cystic fibrosis lung. This organism has a LuxR/LuxI‐type quorum sensing system that enables cell–cell communication via exchange of acyl homoserine lactones (AHLs). The CepR and CepI proteins constitute a global regulatory system, controlling expression of at least 40 genes, including those controlling swarming motility and biofilm formation. In this study, we isolated seven lacZ fusions in a clinical isolate of B. cenocepacia that are inducible by octanoyl‐HSL. Induction of all of these genes requires CepR. The cepI promoter was tested for induction by a set of 33 synthetic autoinducers and analogues, and was most strongly induced by long‐chain AHLs lacking 3‐oxo substitutions. Expression of this promoter was inhibited by high concentrations of three different autoinducers, each having six‐carbon acyl chains. When CepR protein was overproduced in Escherichia coli, it accumulated in a soluble form in the presence of octanoyl‐HSL, but accumulated only as insoluble inclusion bodies in its absence. Purified CepR‐OHL complexes bound to specific DNA sequences at the cepI and aidA promoters with high specificity. These binding sites included a 16‐nucleotide imperfect dyad symmetry. Both CepR binding sites are centred approximately 44 nucleotides upstream of the respective transcription start sites.
A genetic screen identifies genes and sites involved in pilin antigenic variation in Neisseria gonorrhoeae
Authors: Sechman Eric V. , Rohrer Melissa S. , Seifert H. Steven 
Published: June 2005

SummaryIt has previously been shown that the frequency of pilin antigenic variation in Neisseria gonorrhoeae (the gonococcus, Gc) is regulated by iron availability. To identify factors involved in pilin variation in an iron‐dependent or an iron‐independent manner, we conducted a genetic screen of transposon‐mutated gonococci using a pilus‐dependent colony morphology phenotype to detect antigenic variation deficient mutants. Forty‐six total mutants representing insertions in 30 different genes were shown to have reduced colony morphology changes resulting from impaired pilin variation. Five mutants exhibited an iron‐dependent decrease in pilin variation, while the remaining 41 displayed an iron‐independent decrease in pilin variation. Based on the levels of antigenic variation impairment, we defined the genes as being essential for, important for, or involved in antigenic variation. DNA repair and DNA transformation frequencies of each mutant were measured to determine whether other recombination‐based processes were also affected in the mutants. Each mutant was placed into one of six classes based on their pilin variation, DNA repair and DNA transformation phenotypes. Among the many genes identified, recR is shown to be an additional member of the gonococcal RecF‐like recombination pathway. In addition, recG and ruvA represent the first evidence that the processing of Holliday junctions is required for pilin antigenic variation. Moreover, two independent insertions in a non‐coding region upstream of the pilE gene suggest that cis‐acting sequences important for pilin variation are found in that region. Finally, insertions that effect expression of the thrB and thrC genes suggest that molecules in the threonine biosynthetic pathway are important for pilin variation. Many of the other genes identified in this genetic screen do not have an obvious role in pilin variation, DNA repair, or DNA transformation.
Bacterial ribosomal RNA in pieces
Authors: Evguenieva‐Hackenberg Elena 
Published: June 2005

SummaryThe exact knowledge on the ribosomal RNA (rRNA) structure is an important prerequisite for work  with rRNA sequences in bioinformatic analyses and in experimental research. Most available rRNA sequences of bacteria are based on gene sequences and on similarity analyses using Escherichia coli rRNA as a standard. Therefore, it is often overlooked that many bacteria harbour mature rRNA ‘in pieces’. In some cases, the processing steps during the fragmentation lead to the removal of rRNA segments that are usually found in the ribosome. In this review, the current knowledge on the mechanisms of rRNA fragmentation and on the occurrence of fragmented rRNA in bacteria is summarized, and the physiological implications of this phenomenon are discussed.
Interactions between folding factors and bacterial outer membrane proteins
Authors: Mogensen Jesper E. , Otzen Daniel E. 
Published: June 2005

SummaryThe outer membrane is the first line of contact between Gram‐negative bacteria and their external environment. Embedded in the outer membrane are integral outer membrane proteins (OMPs) that perform a diverse range of tasks. OMPs are synthesized in the cytoplasm and are translocated across the inner membrane and probably diffuse through the periplasm before they are inserted into the outer membrane in a folded and biologically active form. Passage through the periplasm presents a number of challenges, due to the hydrophobic nature of the OMPs and the choice of membranes into which they can insert. Recently, a number of periplasmic proteins and one OMP have been shown to play a role in OMP biogenesis. In this review, we describe what is known about these folding factors and how they function in a biological context. In particular, we focus on how they interact with the OMPs at the molecular level and present a comprehensive overview of data relating to a possible effect on OMP folding yield and kinetics. Furthermore, we discuss the role of lipo‐chaperones, i.e. lipopolysaccharide and phospholipids, in OMP folding. Important advances have clearly been made in the field, but much work remains to be done, particularly in terms of describing the biophysical basis for the chaperone–OMP interactions which so intricately regulate OMP biogenesis.
CTXφ and Vibrio cholerae: exploring a newly recognized type of phage–host cell relationship
Authors: McLeod Sarah M. , Kimsey Harvey H. , Davis Brigid M. , Waldor Matthew K. 
Published: June 2005

SummaryThe genes encoding cholera toxin, one of the principal virulence factors of the diarrhoeal pathogen Vibrio cholerae, are part of the genome of CTXφ, a filamentous bacteriophage. Thus, CTXφ has played a critical role in the evolution of the pathogenicity of V. cholerae. Unlike the well‐studied F pilus‐specific filamentous coliphages, CTXφ integrates site‐specifically into its host chromosome and forms stable lysogens. Here we focus on the CTXφ life cycle and, in particular, on recent studies of the mechanism of CTXφ integration and the factors that govern lysogeny. These and other processes illustrate the remarkable dependence of CTXφ on host‐encoded factors.
Effect of 5′‐proximal elements on decay of a model mRNA in Bacillus subtilis
Authors: Sharp Josh S. , Bechhofer David H. 
Published: June 2005

SummaryPrevious work showed that a 42‐nucleotide sequence from an SP82 bacteriophage early RNA functions as a 5′ mRNA stabilizer in Bacillus subtilis. Real‐time reverse transcriptase polymerase chain reaction (RT‐PCR) analysis of decay of a model mRNA with alterations at the 5′‐end was used to elucidate the mechanism of SP82‐mediated stability. A predicted 5′‐terminal stem–loop structure was essential for stabilization. Increasing the strength of the 5′‐terminal structure above a minimum level did not result in increased stability. A thorough analysis of the context in which the stabilizing structure occurred included the effects of distance from 5′‐end, translation of downstream coding sequence, and distance between the secondary structure and the ribosome binding site. Our data are consistent with the dominant mRNA decay pathway in B. subtilis being 5′‐end dependent.
Dissecting functional similarities of ribosome‐associated chaperones from Saccharomyces cerevisiae and Escherichia coli
Authors: Rauch Thomas , Hundley Heather A. , Pfund Chris , Wegrzyn Renee D. , Walter William , Kramer Günter , Kim So‐Young , Craig Elizabeth A. , Deuerling Elke 
Published: June 2005

SummaryRibosome‐tethered chaperones that interact with nascent polypeptide chains have been identified in both prokaryotic and eukaryotic systems. However, these ribosome‐associated chaperones share no sequence similarity: bacterial trigger factors (TF) form an independent protein family while the yeast machinery is Hsp70‐based. The absence of any component of the yeast machinery results in slow growth at low temperatures and sensitivity to aminoglycoside protein synthesis inhibitors. After establishing that yeast ribosomal protein Rpl25 is able to recruit TF to ribosomes when expressed in place of its Escherichia coli homologue L23, the ribosomal TF tether, we tested whether such divergent ribosome‐associated chaperones are functionally interchangeable. E. coli TF was expressed in yeast cells that lacked the endogenous ribosome‐bound machinery. TF associated with yeast ribosomes, cross‐linked to yeast nascent polypeptides and partially complemented the aminoglycoside sensitivity, demonstrating that ribosome‐associated chaperones from divergent organisms share common functions, despite their lack of sequence similarity.
The Escherichia coli baby cell column: a novel cell synchronization method provides new insight into the bacterial cell cycle
Authors: Bates David , Epstein Jessica , Boye Erik , Fahrner Karen , Berg Howard , Kleckner Nancy 
Published: June 2005

SummaryWe describe a new method for synchronizing bacterial cells. Cells that have transiently expressed an inducible mutant ‘sticky’ flagellin are adhered to a volume of glass beads suspended in a chromatography column though which growth medium is pumped. Following repression of flagellin synthesis, newborn cells are eluted from the column in large quantities exceeding that of current baby machine techniques by approximately 10‐fold. Eluted cultures of ‘baby cells’ are highly synchronous as determined by analysis of DNA replication, cell division and other events, over time after elution from the column. We also show that use of ‘minutes after elution’ as a time metric permits much greater temporal resolution among sequential chromosomal events than the commonly used metric of cell size (length). The former approach reveals the existence of transient intermediate stages that are missed by the latter approach. This finding has two important implications. First, at a practical level, the baby cell column is a particularly powerful method for temporal analysis. Second, at a conceptual level, replication‐related events are more tightly linked to cell birth (i.e. cell division) than to absolute cell mass.
Co‐ordinated bacteriocin production and competence development: a possible mechanism for taking up DNA from neighbouring species
Authors: Kreth Jens , Merritt Justin , Shi Wenyuan , Qi Fengxia 
Published: June 2005

SummaryIt is important to ensure DNA availability when bacterial cells develop competence. Previous studies in Streptococcus pneumoniae demonstrated that the competence‐stimulating peptide (CSP) induced autolysin production and cell lysis of its own non‐competent cells, suggesting a possible active mechanism to secure a homologous DNA pool for uptake and recombination. In this study, we found that in Streptococcus mutans CSP induced co‐ordinated expression of competence and mutacin production genes. This mutacin (mutacin IV) is a non‐lantibiotic bacteriocin which kills closely related Streptococcal species such as S. gordonii. In mixed cultures of S. mutans and S. gordonii harbouring a shuttle plasmid, plasmid DNA transfer from S. gordonii to S. mutans was observed in a CSP and mutacin IV‐dependent manner. Further analysis demonstrated an increased DNA release from S. gordonii upon addition of the partially purified mutacin IV extract. On the basis of these findings, we propose that Streptococcus mutans, which resides in a multispecies oral biofilm, may utilize the competence‐induced bacteriocin production to acquire transforming DNA from other species living in the same ecological niche. This hypothesis is also consistent with a well‐known phenomenon that a large genomic diversity exists among different S. mutans strains. This diversity may have resulted from extensive horizontal gene transfer.
Ribosome‐based protein folding systems are structurally divergent but functionally universal across biological kingdoms
Authors: Ito Koreaki 
Published: June 2005

SummaryIn bacteria, Trigger factor (TF) is the first chaperone that interacts with nascent polypeptides as soon as they emerge from the exit tunnel of the ribosome. TF binds to the ribosomal protein L23 located next to the tunnel exit of the large subunit, with which it forms a cradle‐like space embracing the polypeptide exit region. It cooperates with the DnaK Hsp70 chaperone system to ensure correct folding of a number of newly translated cytosolic proteins in Escherichia coli. Whereas TF is exclusively found in prokaryotes and chloroplasts, Saccharomyces cerevisiae, a eukaryotic microorganism, has a three‐member Hsp70‐J protein complex, Ssb–Ssz–Zuo, which could act as a ribosome‐associated folding facilitator. In the work reported in this volume of Molecular Microbiology, Rauch et al. (2005, Mol Microbiol, doi:10.1111/j.1365‐2958.2005.04690.x) examined the functional similarity of the ribosome‐associated chaperones in prokaryotes and eukaryotes. In spite of the fact that TF and the Hsp70‐based triad are structurally unrelated, TF can bind to the yeast ribosome via Rpl25 (the L23 counterpart) and can substitute for some, but not all, of the functions assigned to Ssb–Ssz–Zuo in yeast. The functional conservation of the ribosome‐associated chaperones without structural similarity is remarkable and suggests that during evolution nature has employed a common design but divergent components to facilitate folding of polypeptides as they emerge from the ribosomal exit, a fundamental process required for the efficient expression of genetic information.
Development of the endoplasmic reticulum, mitochondrion and apicoplast during the asexual life cycle of Plasmodium falciparum
Authors: van Dooren Giel G. , Marti Matthias , Tonkin Christopher J. , Stimmler Luciana M. , Cowman Alan F. , McFadden Geoffrey I. 
Published: June 2005

SummaryPlasmodium parasites are unicellular eukaryotes that undergo a series of remarkable morphological transformations during the course of a multistage life cycle spanning two hosts (mosquito and human). Relatively little is known about the dynamics of cellular organelles throughout the course of these transformations. Here we describe the morphology of three organelles (endoplasmic reticulum, apicoplast and mitochondrion) through the human blood stages of the parasite life cycle using fluorescent reporter proteins fused to organelle targeting sequences. The endoplasmic reticulum begins as a simple crescent‐shaped organelle that develops into a perinuclear ring with two small protrusions, followed by transformation into an extensive reticulated network as the parasite enlarges. Similarly, the apicoplast and the mitochondrion grow from single, small, discrete organelles into highly branched structures in later‐stage parasites. These branched structures undergo an ordered fission – apicoplast followed by mitochondrion – to create multiple daughter organelles that are apparently linked as pairs for packaging into daughter cells. This is the first in‐depth examination of intracellular organelles in live parasites during the asexual life cycle of this important human pathogen.
Dual regulation of genes involved in acetoin biosynthesis and motility/biofilm formation by the virulence activator AphA and the acetate‐responsive LysR‐type regulator AlsR in Vibrio cholerae
Authors: Kovacikova Gabriela , Lin Wei , Skorupski Karen 
Published: June 2005

SummaryAphA is a quorum sensing‐regulated activator that initiates the virulence cascade in Vibrio cholerae by cooperating with the LysR‐type regulator AphB at the tcpPH promoter on the Vibrio pathogenicity island (VPI). To identify the ancestral chromosomal genes in V. cholerae regulated by AphA, we carried out a microarray analysis and show here that AphA influences the expression of 15 genes not associated with the VPI. One set of genes strongly repressed by AphA is involved in the biosynthesis of acetoin, a product synthesized by a variety of bacteria that plays a role in preventing intracellular acidification and which is essential for the viability of V. cholerae in the presence of glucose. Also present in this operon are two putative signal transduction proteins with EAL and GGDEF domains that oppositely influence motility and biofilm formation. Gel mobility shift assays show that AphA binds to a site upstream of the first gene in the acetoin operon. Transcriptional lacZ fusions indicate that at low cell density AphA represses the expression of the acetoin genes up to 15‐fold. Voges Proskauer tests confirm that deletion of AphA increases the production of acetoin under non‐inducing conditions and also that the LysR‐type regulator AlsR divergently transcribed from the operon is required for its production. This is the first report of a specific repressor protein involved in the transcriptional control of acetoin production as well as the co‐regulation of these genes with those that influence motility and biofilm formation. The results here provide a model for the dual regulation of these processes by acetate and quorum sensing through AlsR and AphA.
Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression
Authors: Browning Douglas F. , Grainger David C. , Beatty Christine M. , Wolfe Alan J. , Cole Jeffrey A. , Busby Stephen J. W. 
Published: June 2005

SummaryExpression from the Escherichia coli nrf operon promoter is activated by the anaerobically triggered transcription factor, FNR, and by the nitrate/nitrite ion‐controlled response regulators, NarL or NarP, but is repressed by the IHF and Fis proteins. Here, we present in vitro studies on the nrf promoter, using permanganate footprinting to measure open complex formation, and DNase I footprinting to monitor binding of the different regulators and the interactions between them. Our results show that open complex formation is completely dependent on FNR and is enhanced by NarL, but is repressed by IHF or Fis. NarL counteracts repression by IHF but is unable to alter repression by Fis. These results suggest mechanisms by which nrf promoter activity is modulated by the different factors. Expression from the nrf promoter is known to be repressed in rich media, especially in the presence of glucose, but the molecular basis of this is not understood. Here, we show that this catabolite repression is relieved by mutations that weaken the DNA site for Fis, improve the DNA site for FNR or improve the promoter −10 or −35 elements. Hence, Fis protein is a major factor responsible for catabolite repression at the nrf promoter, and Fis can override activation by FNR and NarL or NarP.
HxlR, a member of the DUF24 protein family, is a DNA‐binding protein that acts as a positive regulator of the formaldehyde‐inducible hxlAB operon in Bacillus subtilis
Authors: Yurimoto Hiroya , Hirai Reiko , Matsuno Norimichi , Yasueda Hisashi , Kato Nobuo , Sakai Yasuyoshi 
Published: June 2005

SummaryThe HxlR protein from Bacillus subtilis belongs to the DUF24 protein family (InterPro No. IPR002577) of unknown function. The hxlR gene that encodes this protein is located upstream of the hxlAB operon. This operon encodes two key enzymes in the ribulose monophosphate pathway that are involved in formaldehyde fixation, 3‐hexulose‐6‐phosphate synthase and 6‐phospho‐3‐hexuloisomerase. Expression of the hxlAB operon is induced by the presence of formaldehyde. Recombinant HxlR prepared from Escherichia coli showed specific binding to a region of DNA upstream of the hxlAB operon. Using gel‐retardation and DNase I footprinting assays, we identified two 25 bp binding regions for HxlR within the upstream DNA. Surface plasmon resonance analyses suggested that two HxlR dimers sequentially bound to the DNA. Finally, we demonstrated that each of the two binding regions for HxlR was necessary for formaldehyde‐induced expression of the hxlAB operon in B. subtilis. Thus, we have shown that HxlR is a DNA‐binding protein that is necessary for formaldehyde‐induced expression of hxlAB in B. subtilis.
A chaperone‐like HrpG protein acts as a suppressor of HrpV in regulation of the Pseudomonas syringae pv. syringae type III secretion system
Authors: Wei Chia‐Fong , Deng Wen‐Ling , Huang Hsiou‐Chen 
Published: June 2005

SummaryThe cloned hrp/hrc cluster of Pseudomonas syringae pv. syringae 61 (Pss61) contains 28 proteins, and many of those are assembled into a type III secretion system (TTSS) that is responsible for eliciting the hypersensitive response (HR) in non‐host plants and causing diseases on host plants (Huang et al., 1995). hrpG, the second gene in the hrpC operon, encodes a 15.4 kDa cytoplasmic protein whose predicted structure is similar to SicP (E‐value: 0.19), a TTSS chaperone of Salmonella typhimurium. Two non‐polar hrpG mutants, Pss61‐N826 and Pss61‐N674, were produced to investigate the biological function of hrpG gene. Pss61‐N826, generated by replacing the coding sequence of hrpG with an nptII gene lacking both the promoter and the terminator, was found to be capable of eliciting the wild‐type HR; whereas Pss61‐N674 generated by replacement of a terminatorless nptII gene in the hrpG coding sequence showed the delayed HR phenotype. Northern and Western blotting analyses showed that the expression of hrpZ, hrcJ and hrcQb genes residing on two different operons in Pss61‐N674 was reduced due to the nptII promoter‐driven constitutive expression of hrpV that codes for a negative regulator. Interestingly, a plasmid‐borne hrpG can derepress the hrp expression in Pss61‐N674 and in Pss61 overexpressing HrpV without decreasing the hrpV transcript. Moreover, results of yeast two‐hybrid assay, pull‐down assay and far Western analysis show that HrpG and HrpV interact with each other in vivo and in vitro. Additionally, HrpV interacts with a positive regulator HrpS according to analysis of a yeast two‐hybrid system. Based on the results presented in this study, we propose that HrpG acts as a suppressor of the negative regulator HrpV mediated via protein–protein interaction, leading to modulation of hrp/hrc expression subsequently freeing HrpS to promote the activation of other downstream hrp/hrc genes.