bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catabolite repression in Bacillus subtilis: a global regulatory mechanism for the Gram‐positive bacteria?
Authors: Hueck Christoph J. , Hillen Wolfgang 
Published: October 2006

SummaryThree components involved in catabolite repression (CR) of gene expression in Bacillus have been identified. The cis‐acting catabolite responsive element (CRE), which is present in many genes encoding carbon catabolic enzymes in various species of the Gram‐positive bacteria, mediates CR of several genes in Bacillus subtilis, Bacillus megaterium, and Staphylococcus xylosus. CR of most genes regulated via CRE is also affected by the trans‐acting factors CcpA and HPr. Similarities between CcpA and Lac and Gal repressors suggest binding of CcpA to CRE. HPr, a component of the phosphoenol pyruvate:sugar phosphotransferase system, undergoes regulatory phosphorylation at a serine residue by a fcuctose‐1,6‐diphosphate‐activated kinase. A mutant of HPr, which is not phosphorylatable at this position because of an exchange of serine to alanine, lacks CR of several catabolic activities. This mutant phenotype is similar to the one exhibited by a ccpA mutant. Direct protein‐protein interaction between CcpA and HPr(Ser‐P) was recently demonstrated and constitutes a link between metabolic activity and CR.
Alkaliphiles:‘basic’molecular problems of pH tolerance and bioenergetics
Authors: Krulwich Terry Ann 
Published: October 2006

SummaryAlkaliphilic Bacillus species provide experimental opportunities for examination of physiological processes under conditions in which the stress of the extreme environment brings issues of general biological importance into special focus. The alkaliphile, like many other cells, uses Na+/H+ antiporters in pH regulation, but its array of these porters, and other ion‐flux pathways that energize and support their activity, result in an extraordinary capacity for pH homeostasis; this process nonetheless becomes the factor that limits growth at the upper edge of the pH range. Above pH 9.5, aerobic alkaliphiles maintain a cytoplasmic pH that is two or more units below the external pH. This chemiosmotically adverse δpH is bypassed by use of an electrochemical gradient of Na+ rather than of protons to energize solute uptake and motility. By contrast, ATP synthesis occurs via completely proton‐coupled oxidative phosphorylation that proceeds just as well, or better, at pH10 and above as it does in the same bacteria growing at lower pH, without the adverse pH gradient. Various mechanisms that might explain this conundrum are described, and the current state of the evidence supporting them is summarized.
Regulation of gene expression by trans‐encoded antisense RNAs
Authors: Delihas Nicholas 
Published: October 2006

SummaryMembers of a class of antisense RNAs are encoded by genes that are located at loci other than those of their target genes. Three examples of antisense RNA genes are discussed here. micF is found in Escherichia coli and other bacteria and functions to control outer membrane protein F levels in response to environmental stimuli. dicF is also found in E. coli and is involved in the regulation of cell division, lin‐4 is found in the nematode Caenorhabditis elegans and functions during larval development. Nucleotide sequences of at least two of these genes appear to be phylogenetically conserved. The trans‐encoded antisense RNAs are small RNAs which display only partial complementarity to their target RNAs. Models for RNA/RNA interactions have been proposed. It is possible that currently known unlinked antisense RNA genes are part of a larger class of heretofore undiscovered regulatory RNA genes. Possible ways of detecting other unlinked antisense RNA genes are discussed.
Identification of a novel cellulose‐binding domain the multidomain 120 kDa xylanase XynA of the hyperthermophilic bacterium Thermotoga maritima
Authors: Winterhalter Christoph , Heinrich Peter , Candussio Anton , Wich Günther , Liebl Wolfgang 
Published: October 2006

SummaryA segment of Thermotoga maritima strain MSB8 chromosomal DNA was isolated which encodes an endo‐1,4‐β‐D‐xylanase, and the nucleotide sequence of the xylanase gene, designated xynA, was determined. With a half‐life of about 40 min at 90°C at the optimal pH of 6.2, purified recombinant XynA is one of the most thermostable xylanases known. XynA is a 1059‐amino‐acid (˜120 kDa) modular enzyme composed of an N‐terminal signal peptide and five domains, in the order A1‐A2‐B‐C1‐C2. By comparison with other xylanases of family 10 of glycosyl hydrolases, the central ˜340‐amino‐acid part (domain B) of XynA represents the catalytic domain. The N terminal ˜150‐amino‐acid repeated domains (A1‐A2) have no significant similarity to the C‐terminal ˜170‐amino‐acid repeated domains (C1‐C2). Cellulose‐binding studies with truncated XynA derivatives and hybrid proteins indicated that the C‐terminal repeated domains mediate the binding of XynA to microcrystalline cellulose and that C2 alone can also promote cellulose binding. C1 and C2 did not share amino acid sequence similarity with any other known cellulose‐binding domain (CBD) and thus are CBDS of a novel type. Structurally related protein segments which are probably also CBDs were found in other multi‐domain xylanolytic enzymes. Deletion of the N‐terminal repeated domains or of all the non‐catalytic domains resulted In substantially reduced tbermostability while a truncated xylanase derivative lacking the C‐terminal tandem repeat was as thermostable as the full‐length enzyme. It is argued that the multidomain organization of some enzymes may be one of the strategies adopted by thermophiles to protect their proteins against thermal denaturation.
Induction of phospholipase‐ and flagellar synthesis in Serratia liquefaciens is controlled by expression of the flagellar master operon flhD
Authors: Givskov Michael , Eberl Leo , Christiansen Gunna , Benedik Michael J. , Molin Søren 
Published: October 2006

SummaryWhen a liquid culture of Serratia spp. reaches the last part of the logarithmic phase of growth it induces the synthesis of several extracellular hydrolytic enzymes. In this communication we show that synthesis and secretion of the extracellular phospholipase is coupled to expression of flagella. Expression of flagella is demonstrated to follow a growth‐phase‐dependent pattern. Cloning, complementation studies and DNA‐sequencing analysis has identified a genetic region in Serratia liquefaciens which exhibits extensive homology to the Escherichia coli flhD flagellar master operon. Interruption of the chromosomal flhD operon in S. liquefaciens results in non‐flagellated and phospholipase‐negative cells, but the synthesis of other exoenzymes is not affected. By placing the flhD operon under the control of a foreign inducible promoter we have shown that increased transcription through the flhD operon leads to induction of flagellar synthesis and phospholipase expression.
Plasmodium falciparum protein associated with the invasion junction contains a conserved oxidoreductase domain
Authors: Hudson‐Taylor Diana E. , Dolan Stephen A. , Klotz Francis W. , Fujioka Hisashi , Aikawa Masamichi , Koonin Eugene V. , Miller Louis H. 
Published: October 2006

SummaryThe merozoite cap protein‐1 (MCP‐1) of Plasmodium falciparum follows the distribution of the moving Junction during invasion of erythrocytes. We have cloned the gene encoding this protein from a cDNA library using a monoclonal antibody. The protein lacks a signal sequence and has no predicted trans‐membrane domains; none of the antisera reacts with the surfaces of intact merozoites, indicating that the cap distribution is submembranous. MCP‐1 is divided into three domains. The N‐terminal domain includes a 52‐amino‐acid region that is highly conserved in a large family of bacterial and eukaryotic proteins. Based on the known functions of two proteins of this family and the pattern of amino acid conservation, it is predicted that this domain may possess oxido‐reductase activity, since the active cysteine residue of this domain is invariant in all proteins of the family. The other two domains of MCP‐1 are not found in any other members of this protein family and may reflect the specific function of MCP‐1 in invasion. The middle domain is negatively charged and enriched in glutamate; the C‐terminal domain is positively charged and enriched in lysine. By virtue of its positive charge, the C‐terminal domain resembles domains in some cytoskeleton‐associated proteins and may mediate the interaction of MCP‐1 with cytoskeleton in Plasmodium.
Genetic suppression and phenotypic masking of a Myxococcus xanthus frzF‐ defect
Authors: Kashefi Kazem , Hartzell Patricia L. 
Published: October 2006

SummaryAn insertion of transposon Tn5‐lac, ω4519, generates a lacZ fusion with a Myxococcus xanthus promoter expressed during both vegetative growth and development. Sequence analysis of the junction of ω4519 with M. xanthus DNA shows that the insertion is in frzF, a homologue of cheR from Salmonella typhimurium. When frzF‐ (or frzCD‐) cells are starved for nutrients at modest densities, they aggregate to form a radial pattern and produce fewer than 1% of the wild‐type complement of spores. At higher densities, frzF::ω519 cells form‘frizzy’aggregates and produce 80–90% of the wild‐type complement of spores. In contrast, when cells with both a frzF‐ (or frzCD‐) and an sgtA1 mutation are allowed to develop at either low or high cell densities, they produce frizzy aggregates containing a near wild‐type complement of heat‐resistant spores. In addition to suppressing the density dependence of fruiting‐body morphogenesis, the sglA1 mutation also suppresses the sporulation defect caused by two different frzF‐ mutations and a frzCD‐ mutation. In contrast, a mutation in a different S motility gene, sglG1, does not suppress the frz‐ mutations. Thus, the suppression of frz‐ mutations by sgl‐ mutations is allele‐specific, and depends on the sgl allele, but not the frz allele. Because the phenotypes of frz‐ mutations have been determined in a (suppressing) sglA1 genetic background, the frz genes may play more central roles in development than initially recognized.
The Neisseria meningitidis haemoglobin receptor: its role in iron utilization and virulence
Authors: Stojijkovic Igor , Hwa Vivian , de Saint Martin Luc , O'Gaora Peadar , Nassif Xavier , Heffron Fred , So Magdalene 
Published: October 2006

SummaryThe Neisseris meningitidis haemoglobin receptor gene, hmbR, was cloned by complementation in a porphyrin‐requiring Escherichia coli mutant. hmbR encodes an 89.5 kDa outer membrane protein which shares amino acid homology with the TonB‐dependent receptors of Gram‐negative bacteria. HmbR had the highest similarity to Neisseria transferrin and lactoferrin receptors. The utilization of haemoglobin as an iron source required internalization of the haemin moiety by the cell. The mechanism of haemin internalization via the haemoglobin receptor was TonB‐dependent in E. coli. A N. meningitidis hmbR mutant was unable to use haemoglobin but could still use haemin as a sole iron source. The existence of a second N. meningitidis receptor gene, specific for haemin, was shown by the isolation of cosmids which did not hybridize with the hmbR probe, but which were able to complement an E. coli hemA aroB mutant on haemin‐supplemented plates. The N. meningitidis hmbR mutant was attenuated in an infant rat model for meningococcal infection, indicating that haemoglobin utilization is important for N. meningitidis virulence.
ComC is required for the processing and translocation of ComGC, a pilin‐like competence protein of Bacillus subtilis
Authors: Chung Y. S. , Dubnau D. 
Published: October 2006

SummaryComGC is a cell surface‐localized protein required for DNA binding during transformation in Bacillus subtilis. It resembles type IV prepilins in its N‐terminal domain, particularly in the amino acid sequence surrounding the processing cleavage sites of these proteins. ComC is another protein required for DNA binding, which resembles the processing proteases that cleave type IV prepilins. We show here that ComGC is processed in competent cells and that this processing requires ComC. We also demonstrate that the PilD protein of Neisseria gonorrhoeae, a ComC homologue, can process ComGC in Escherichia coli, and that the ComC protein itself is the only B. subtilis protein needed to accomplish cleavage of ComGC in the latter organism. Based on NaOH‐solubility studies, we have shown that in the absence of ComC, but in the presence of all other competence proteins, B. subtilis is incapable of correctly translocating ComGC to the outer face of the cell membrane. Finally, we show that ComGC can be cross‐linked to yield a form with higher molecular mass, possibly a dimer, and present evidence suggesting that formation of the higher mass complex takes place in the membrane, prior to translocation. Formation of this complex does not require ComC or any of the comG products, other than ComGC itself.
AmpD, essential for both β‐lactamase regulation and cell wall recycling, is a novel cytosolic N‐acetylmuramyl‐L‐alanine amidase
Authors: Jacobs Christine , Joris Bernard , Jamin Marc , Klarsov Klaus , van Beeumen Jozef , Mengin‐Lecreulx Dominique , van Heijenoort Jean , Park James T. , Normark Staffan , Frère Jean‐Marie 
Published: October 2006

SummaryIn enterobacteria, the ampD gene encodes a cytosolic protein which acts as a negative regulator of β‐lactamase expression. It is shown here that the AmpD protein is a novel N‐acetylmuramyl‐L‐alanine amidase (E.C.3.5.1.28) participating in the intracellular recycling of peptido‐glycan fragments. Surprisingly, AmpD exhibits an exclusive specificity for substrates containing anhydro muramic acid. This anhydro bond is mainly found in the peptidoglycan degradation products formed by the periplasmic lytic transglycosylases and thus might behave as a‘recycling tag’allowing the enzyme to distinguish these fragments from the newly synthesized peptidoglycan precursors. The AmpD substrate (or substrates) which accumulates in the absence of the corresponding enzymatic activity acts as an intracellular positive effector for β‐lactamase expression and might represent an element of a communication network between the chromosome and the cell wall peptidoglycan.
Identification of cellular proteins involved in nikkomycin production in Steptomyces tendae Tü901
Authors: Möhrle V. , Roos U. , Bormann C. 
Published: October 2006

SummaryExpression of genes involved in nikkomycin production in Streptomyces tendae was investigated by two‐dimensional gel electrophoresis of cellular proteins. Ten gene products (P1–P10) were identified that were synthesized when nikkomycin was produced; these proteins were not detected in non‐producing mutants. N‐terminal sequences of six of the 10 proteins were obtained by microsequencing of protein spots excised from preparative two‐dimensional gels. Protein P8 was identified as l‐histidine amino‐transferase (HisAT), which has been previously correlated with nikkomycin production. By using oligo‐nucleotide probes deduced from the N‐terminal sequences of protein P2 and P6, we isolated an 8 kb Bam HI fragment and a 6.5 kb Pvu II fragment, respectively, from the genome of Streptomyces tendae Tü901. Restriction analyses revealed that both fragments overlapped within a region of 1.5 kb. Mapping of the oligonucleotide probe hybridizing sites indicated that the genes encoding protein P2 and P6 are closely spaced on the 8 kb Bam HI fragment, and the latter is located on the overlapping region. DNA sequence analysis revealed that proteins P1 and P2 are encoded by a single gene, orfP1, that is translated at two initiation codons. The orfP1 gene was interrupted by homologous recombination using the integrating vector pWHM3. The gene‐disrupted transformants did not produce nikkomycin, indicating that proteins P1 and P2 are essential for nikkomycin production. The data presented show that reverse genetics was successfully used to isolate genes Involved in nikkomycin production.
Identification of phosphoproteins in Escherichia coli
Authors: Freestone P. , Grant S. , Toth I. , Norris V. 
Published: October 2006

SummaryThe substrates of ion‐ and lipld‐stimulated protein kinase activity in extracts of Escherichia coli were purified by chromatography. Subsequent N‐terminal sequencing suggests that these substrates include the following: a novel 80kDa protein co‐purifying with RNA polymerase but partially homologous to elongation factor G; a protein with an apparent molecular weight of 65kDa identified as the ribosomal protein S1; and a 32 kDa protein identified as succinyl CoA synthetase, a key enzyme in the tricarboxylic acid cycle. The phosphorylation of these three proteins was markedly stimulated by the addition of manganese, and occurred on threonine, serine or tyrosine residues as indicated by the stability of the phosphoresidues during acid treatment. In addition, a calcium‐stimulated protein of 70kDa was identified as the heat‐shook protein DnaK, and a 17kDa lipid‐stimulated phosphoprotein as nucleotide diphosphate kinase.
Group B streptococci adhere to a variant of fibronectin attached to a solid phase
Authors: Tamura Glen S. , Rubens Craig E. 
Published: October 2006

SummaryGroup B streptococci (GBS) are the leading cause of neonatal pneumonia and meningitis. Adherence of GBS to host tissues may play an important role in the pathogenesis of infection. The host molecules which mediate GBS adherence to host tissues are unknown. Many bacterial pathogens adhere to fibronectin, an important component of the extracellular matrix (ECM). Some pathogens adhere to both immobilized and soluble fibronectin, while others adhere to immobilized fibronectin, but not to soluble fibronectin. Previous data indicated that GBS do not adhere to soluble fibronectin. We studied the ability of GBS to adhere to immobilized fibronectin. Forty‐five per cent of the input inoculum of COH1, a virulent GBS isolate, adhered to fibronectin immobilized on polystyrene. COH1 did not adhere to the other ECM proteins tested (laminin, type I collagen, vitronectin, and tenascin). Nine out of nine GBS strains from human sources tested adhered specifically to fibronectin at levels varying from 4–60%. We considered the possibility that GBS were adherent to a contaminant in the fibronectin preparation. Properties of fibronectin, including the presence of an immunologic epitope of fibronectin and binding to collagen, were verified to be properties of the molecule to which GBS adhere. COH1 adhered to fibronectin captured by a monoclonal antibody to fibronectin (FN‐15), confirming that the molecule to which GBS adhere bears immunologic determinants of fibronectin. Adherence of COH1 to fibronectin was inhibited by collagen, confirming that the molecule to which GBS adhere binds to collagen. These data strongly suggest that GBS adhere to fibronectin, and not to a contaminant. Protein blot analysis revealed that GBS were adherent to a high‐molecular‐weight variant of non‐reduced fibronectin monomers and dimers. GBS did not adhere to reduced fibronectin monomers. We conclude that GBS adhere to a variant of plasma fibronectin when attached to a solid phase.
Analysis of a chemotaxis operon in Rhizobium meliloti*
Authors: Greek Michaela , Platzer Josef , Sourjik Victor , Schmitt Rüdiger 
Published: October 2006

SummaryGenes controlling chemotaxis towards L‐amino acids and d‐mannitol in Rhizobium meliloti have been identified by Tn5 insertions that lead to chemotaxis‐deficient mutants. The tagged genes span an 8.7 kbp region that has been sequenced. These genes are part of a large operon containing three novel open reading frames, orf1, orf2 and orf9, and six familiar chemotaxis (che) genes, cheY1‐cheA‐cheW‐cheR‐cheB‐cheY2, that have been assigned by their similarity to known Escherichia coli genes. The second copy of cheY may be part of a second signalling chain; orf1 and orf2 encode sequence motifs that resemble the signalling domain of E. coli MCPs (methyl‐accepting chemotaxis proteins), while the product of orf9 may contain a transmembrane domain. No protein methylation has been observed in Rhizobium meliloti in response to l‐amino acids. However, the presence of cheR (methyltransferase gene) and cheB (methyl‐esterase gene) suggested that MCPs are likely components of the chemotactic response in R. meliloti. Therefore, it is postulated that two chemotaxis pathways are functional in R meliloti: one responds to l‐amino acids via ORF1‐ORF2, whereas the other (probably responding to specific plant exudates) acts via MCP‐like receptors, and both interact with the central components CheW‐CheA‐CheY1 and/or CheY2.
Interspecies recombination In nature: a meningococcus that has acquired a gonococcal PIB porin
Authors: Vázquez Julio A‐ , Berron Sonsoles , O'Rourke Maria , Carpenter Gill , Feil Edward , Smith Noel H. , Spratt Brian G. 
Published: October 2006

SummaryA. vaginal isolate of Neisseria has been reported to resemble Neisseria meningitidis in biochemical characteristics but to react with serological reagents that are specific to the PI porin from Neisseria gonorrhoeae. We have confirmed that this isolate has the biochemical attributes of a meningococcus and have shown that it clusters among meningococcal Isolates on a dendrogram based on isoenzyme variation within housekeeping enzymes from populations of N. meningitidis and N. gonorrhoeae. Furthermore, the sequences of the fbp and adk genes were typical of those of N. meningitidis and were distinct from those of N. gonorrhoeae. However, the porB gene was very similar to the por genes of N. gonorrhoeae isolates that express the PIB class of outer‐membrane porin (differing from one gonococcal por allele at only a single nucleotide site), and was clearly distinct from the porB genes of N. meningitidis. The isolate therefore appears to be a typical meningococcus, except that its porB gene has been replaced with the por gene from a gonococcus.
Effect of inhA and katG on isoniazid resistance and virulence of Mycobacterium bovis
Authors: Wilson Theresa M. , de Lisle Geoffrey W. , Collins Desmond M. 
Published: October 2006

SummaryIsoniazid (INH) resistance of the Mycobacterium tuberculosis Complex (MtbC) is associated with both loss of catalase activity and mutation of the inhA gene. However, the relative contributions of these changes to resistance and to the loss of virulence for guinea‐pigs is unknown. In this study, a virulent strain of Mycobacterium bovis, a member of the MtbC., was exposed to increasing concentrations of INH. Two INH‐resistant strains were produced which had lost catalase activity. Strain WAg405, which had a higher resistance to INH, also had a mutation in the inhA gene. This demonstrated that loss of catalase activity and mutation of inhA had a cumulative effect on INH resistance. When a functional katG gene was integrated into the genome of WAg405 the INH resistance was greatly reduced. This indicated that most of the resistance had been caused by loss of catalase activity. While the parent INH‐sensitive strain was virulent for guinea‐pigs, the INH‐resistant strains were significantly less virulent. Integration of a functional katG gene into the most resistant strain restored full virulence. This clearly established that katG is a virulence factor for M. bovis and that mutation of the inhA gene has no effect on virulence.