bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell differentiation of Proteus mirabilis is initiated by glutamine, a specific chemoattractant for swarming cells
Authors: Allison Clive , Lai Hsin‐Chih , Gygi Daniel , Hughes Colin 
Published: October 2006

SummarySwarming by Proteus mirabilis involves differentiation of typical short vegetative rods into filamentous hyper‐flagellated swarm cells which undergo cycles of rapid and co‐ordinated population migration across surfaces and exhibit high levels of virulence gene expression. By supplementing a minimal growth medium (MGM) unable to support swarming migration we identified a single amino acid, glutamine, as sufficient to signal initiation of cell differentiation and migration. Bacteria isolated from the migrating edge of colonies grown for 8h with glutamine as the only amino acid were filamentous and synthesized the characteristic high levels of flagellin and haemolysin. In contrast, addition of the other 19 common amino acids (excluding glutamine) individually or in combination did not initiate differentiation even after 24 h, cells remaining typical vegetative rods with basal levels of haemolysin and flagellin. The glutamine analogue γ‐glutamyl hydroxamate (GH) inhibited swarming but not growth of P. mirabilis on glutamine MGM and transposon mutants defective in glutamine uptake retained their response to glutamine signalling and its inhibition by GH, suggesting that differentiation signalling by glutamine may be transduced independently of the cellular glutamine transport system. Levels of mRNA transcribed from the haemolysin (hpmA) and flagellin (fliC) genes were low in vegetative cells grown on MGM without glutamine or with glutamine and GH, but were specifically increased c. 40‐fold during glutamine‐dependent differentiation. In liquid glutamine—MGM cultures, differentiation to filamentous hyper‐flagellated hyper‐haemorytic swarm cells occurred early in the exponential phase of growth, and increased concomitantly with the concentration of glutamine from a 0.1 mM threshold up to 10 mM. Differentiation in liquid culture was completely inhibited by GH but was further stimulated c. 30% in the absence of GH by the viscosity agent polyvinylpy‐rollidone (PVP). Chemotaxis assays of bacterial cells in which the viscosity of liquid media was varied by PVP to allow either swimming or swarming motility demonstrated that glutamine was chemoattractive specifically to differentiated swarming cells.
Sensor and regulator proteins from the cyanobacterium Synechococcus species PCC7942 that belong to the bacterial signal‐transduction protein families: implication in the adaptive response to phosphate limitation
Authors: Aiba Hirofumi , Nagaya Masahiro , Mizuno Takeshi 
Published: October 2006

SummaryA 1.2kb DNA fragment was cloned from Synechococcus sp. PCC7942, which is able phenotypicalty to complement a phoRcreC Escherichia coli mutant for the expression of alkaline phosphatase. A 2.5kb DNA fragment encompassing the putative gene was then cloned and its complete nucleotide sequence determined. Nucleotide sequencing revealed that the intact gene encodes a protein of 46389 Da, and that the deduced amino acid sequence shows a high degree of homology to those of the bacterial sensory kinase family. In the determined nucleotide sequence, another gene was adjacently located, which encodes a protein of 29012Da. This protein shows a high degree of homology to those of the response regulator family. Thus, we succeeded in the cloning of a pair of genes encoding the sensory kinase and response regulator, respectively, in a cyanobacterium. Mutant strains that lack these genes were constructed, and demonstrated to be defective in their ability to produce alkaline phosphatase and some inducible proteins in response to phosphate‐limitation in the medium. These results imply that the gene products identified in this study are probably involved, either directly or indirectly, in the signal‐transduction mechanism underlying regulation of the phosphate regulon in Synechococcus sp. PCC7942. Hence, the genes encoding the sensory kinase and response regulator were designated as sphS and sphR, respectively (Synechococcusphosphate regulon). The SphS protein was demonstrated in vitro to undergo phosphorylation in the presence of ATP.
High‐resolution mapping of genetic loci of Anabaena PCC 7120 required for photosynthesis and nitrogen fixation
Authors: Kuritz Tanya , Ernst Anneliese , Black Todd A. , Wolk C. Peter 
Published: October 2006

SummaryA physical map of the Anabaena genome permitted the localization of its genes to chromosomal fragments generated by rarely cutting restriction endonucleases and separated by pulsed‐field gel electrophoresis. We introduce a novel means of mapping more precisely to c. 20 kb by use of rare restriction sites within vectors bearing cloned sequences that undergo homologous recombination with the genome. We thereby localize and orient genes encoding principal photosynthetic pigments. The relative spacing of loci within a single restriction fragment was determined with even higher resolution, as illustrated for genes required for heterocyst development and nitrogen fixation that were marked with transposons. Small, newly visualized restriction fragments of the chromosome were also mapped.
Iron‐hydroxamate uptake systems in Bacillus subtilis: identification of a lipoprotein as part of a binding protein‐dependent transport system
Authors: Schneider Richard , Hantke Klaus 
Published: October 2006

Summary Bacillus subtilis was shown to utilize three types of hydroxamate siderophores, ferrichromes, ferrioxamines and shizokinen, each of which is taken up by different transport systems. Mutants deficient in the uptake of ferrichrome and/or ferrioxamine B were isolated. The gene fhuD, which was able to complement a mutant defective in ferrichrome uptake, was cloned. The deduced sequence of FhuD showed low but significant homology to the binding proteins FepB, FecB and FhuD of Escherichia coli, which are all components of binding protein‐dependent, ferric siderophore transport systems. The first 23 amino acids of FhuD of B. subtilis possessed all characteristics of a lipoprotein signal sequence. The processing of FhuD in E. coli was inhibited by globomycin. Inhibition by globomycin indicated a lipid modification at the N‐terminal cysteine in E. coli. It is highly likely that this step may also take place in B. subtilis. As in other binding protein‐dependent transport systems of Gram‐positive organisms it is proposed that the lack of a periplasm is compensated for by the lipid through which the binding protein is anchored to the cytoplasmic membrane.
Rhizobium phaseoli cytochrome c‐deficient mutant induces empty nodules on Phaseolus vulgaris L.
Authors: Soberón Mario , Aguilar Germán R. , Sánchez Federico 
Published: October 2006

SummaryA Rhizobium phaseoli cytochrome mutant, unable to oxidize N,N,N′,N′ ‐tetramethyl‐p‐phenylend(amine (TMPD), was isolated after Mu‐dl (Kan lac) mutagenesis of the wild‐type strain CE‐3. Mutant strain CFN4202 had sixfold less haem‐c but similar levels of b type, o and aa3 cytochromes than the wild‐type strain. CFN402 strain also showed reduced NADH‐ and TMPD‐oxidase activity than the wild‐type strain. Succinate‐oxidase activities were very similar. Western blot experiments, using antiserum against bovine c1 and c cytochromes, revealed that both proteins were present in CFN4202 membranes, suggesting a defect of haem binding to cytochrome c. Nodules formed by this strain in Phaseolus vulgaris did not contain bacteroids. These data suggest that the cytochrome c‐aa3 chain or some other respiratory chain, containing c‐type cytochromes in R. phaseoli, is essential for bacterial division during the early steps of the symbiotic interaction with the legume‐host.
AUA1, a gene involved in ammonia regulation of amino acid transport in Saccharomyces cerevisiae
Authors: Sophianopoulou Vicky , Diallinas George 
Published: October 2006

SummaryIn Saccharomyces cerevisiae the general amino acid (GAP1) permease catalyses active transport of apparently all amino acids across the plasma membrane. GAP1 activity is regulated by control of synthesis and control of activity in response to the nitrogen source supplied; ammonia and giutamine Inactivate GAP1 function while proline and urea allow its maximum expression. We have isolated and characterized a gene. AUA1, involved in ammonia regulation of GAP1 activity. AUA1 is not essential for growth but over‐expression of the AUA1 transcript in a high‐copy vector or due to a regulatory mutation. aua1‐1, present ∼10 bp upstream from the start of AUA1 transcription, releases GAP1 activity from ammonia‐inactivation without affecting GAP1 transcription. The aua1‐1 mutation has no phenotype when ammonia is replaced by proline or glutamate as the nitrogen source or when it is present in a gap1 background. AUA1 expression is itself ammonia repressible in a wild‐type strain but not in the aua1‐1 mutant. The AUA1 gene sequence contains a unique short open reading frame of 94 codons corresponding to a polypeptide of 11 714 Da. This polypeptide is highly hydrophilic and extremely basic. The AUA1 product shows no significant similarity with any previously known protein sequence. Interestingly, a 10‐amino acid segment of AUA1 is directly repeated in the most basic segment of the protein. Possible roles of AUA1 are discussed.
Sequence requirements for target activity in site‐specific recombination mediated by the Int protein of transposon Tn 1545
Authors: Trieu‐Cuot P. , Poyart‐Salmeron C. , Carlier C. , Courvalin P. 
Published: October 2006

SummaryExcision and integration of Tn 1545 occur by reciprocal site‐specific recombination between 6 (or 7)bp variable sequences present in the recombining attachment (atf) sites and designated overlap regions. We devised an assay for Tn1545 transposition in which derivatives containing the cis‐acting transposition sequences (atfTn 1545) integrate into a target replicon when complemented in trans by the transposon‐encoded integrase Int‐Tn. This assay was used to determine the characteristics of the DNA sequence that influence target site selection. Characterization of several integration sites indicated that a 20 bp segment, designated attB, contains the sequences required for target activity. It also appeared that (i) the target activity depends upon the extent of homology between the 7bp segments flanking the overlap regions in attB and attTn1545, and (ii) the degree of homology between the two recombining overlap regions does not affect the level of target activity and has no influence on integration orientation.
Identification of a nitrogen‐regulated promoter controlling expression of Klebsiella pneumoniae urease genes
Authors: Collins Carleen M. , Gutman Delia M. , Laman Heike 
Published: October 2006

SummarySynthesis of urease by Klebsiella species is known to be induced when the nitrogen source of the growth medium is limiting, suggesting that urease gene expression is controlled by the nitrogen regulatory (ntr) system. This study showed that K. pneumoniae with mutations in either ntrA or ntrC, two integral components of the ntr system, were phenotypically urease‐negative. These mutants could be complemented back to a urease positive phenotype with recombinant plasmids encoding the corresponding ntr gene. A series of ure–lacZYA transcriptional fusions, in conjunction with primer extension analysis, identified a DNA region that encoded a nitrogen‐regulated promoter. This promoter region controlled transcription of ureD, the first gene in the Klebsiella pneumoniae urease gene cluster, and ureA, a gene that resides immediately downstream of ureD. A high level of transcription from the ureD promoter required NAC, a recently characterized member of the nitrogen regulatory cascade. NAC is a Lys R‐like transcriptional regulator that can act at σ;70 promoters; expression from nac itself is dependent upon NTRA. Therefore, expression of K. pneumoniae urease was dependent upon the nitrogen regulatory cascade, and transcription of at least two urease genes was from a promoter that was positively regulated by NAC.
The sialidase superfamily and its spread by horizontal gene transfer
Authors: Roggentin Peter , Schauer Roland , Hoyer Lois L. , Vimr Eric R. 
Published: October 2006

SummarySialidases (neuraminidases, EC 3.2.1.18) belong to a class of glycosyl hydrolases that release terminal N‐acylneuraminate (slalic acid) residues from glycoproteins, glycolipids, and polysaccharides. These enzymes are common in animals of the deuterostomate lineage (Echinodermata through Mammalia) and also in diverse microorganisms that mostly exist as animal commensals or pathogens. Sialidases, and their sialyl substrates, appear to be absent from plants and most other metazoans. Even among bacteria, sialidase is found irregularly so that related species or even strains of one species differ in this property. This unusual phylogenetic distribution makes sialidases interesting for evolutionary studies. The biochemical diversity among bacterial sialidases does not indicate close relationships. However, at the molecular level, homologies are detectable, supporting the hypothesis of a common sialidase origin and thus of a sialidase super family. Some findings indicate that sialidase genes were recently transferred via phages among bacteria. The proposal of a sialidase origin in higher animals is suggested by the presence of apparently homologous enzymes in this kingdom, supporting the idea that some microbes may have acquired the genetic information during association with their animal hosts.
Transcriptional control of the Pseudomonas putida TOL plasmid catabolic pathways
Authors: Marqués Silvia , Ramos Juan L. 
Published: October 2006

SummaryTOL plasmid pWWO of Pseudomonas putida contains two operons that specify a pathway for the degradation of aromatic hydrocarbons. The upper pathway operon encodes the enzymes for the oxidation of toluene/xylenes to benzoate/toluates, and the meta‐cleavage pathway operon encodes the enzymes for the further oxidation of these compounds to Krebs cycle intermediates. Their expression is controlled by the gene products of two divergently transcribed regulatory genes, xylR and xylS. The XylR protein, which belongs to the NtrC family of regulators, is expressed from two tandem promoters and autoregulates its synthesis. XylR stimulates transcription from the xylS gene promoter (Ps) and the upper pathway operon promoter (Pu) in the presence of pathway substrates. Both promoters are a54 dependent, and Pu also requires the presence of integration host factor (IHF) for activation of transcription. Binding sites for XylR and IHF in the Pu promoter and for XylR in the Ps promoters have been defined. The XylS protein, which belongs to the AraC family of regulators, stimulates transcription from the mefa‐cleavage pathway operon promoter (Pm) in the presence of benzoates. The effector binding pocket and ONA‐binding region of XylS have been defined through the isolation of mutants that exhibit altered effector specificity and modified transcriptional patterns, respectively. Expression of the mefa‐cleavage pathway operon is also induced by xylene‐activated XylR protein via a cascade regulatory system in which this protein, in combination with σ;54, stimulates the expression from the xylS promoter. The increased concentration of XylS in turn leads to high level expression of the
Internalin‐mediated invasion of epithelial cells by Listeria monocytogenes is regulated by the bacterial growth state, temperature and the pleiotropic activator prfA
Authors: Dramsi S. , Kocks C. , Forestier C. , Cossart P. 
Published: October 2006

SummaryEntry of Listeria monocytogenes into epithelial cells requires expression of inlA, the first gene of an operon comprising two genes: inlA, which encodes internalin, a 800‐amino‐acid protein, and inlB, which encodes a 630‐amino‐acid protein. We report here that the inl locus is transcribed on two transcripts in constant relative ratio: a 5 kb transcript spanning inlA and inlB, and a 2.9 kb transcript that covers only inlA. The promoter is located 397 bp from the GTG initiator of inlA and displays in its ‐35 region a palindrome similar to that found in promoters controlled by the pleiotropic activator prfA. Transcription of the inl locus is, as are several other L. monocytogenes virulence genes, activated by prfA and regulated by temperature—with higher expression at 37°C versus 25°C — and bacterial growth state. It is maximal during exponential growth and correlates with maximal invasivity of the bacteria in the human epithelial cell line Caco‐2. It also correlates with maximum amounts of internalin present on the bacterial surface. Internalin is also detected in substantial amounts in culture supernatants. Taken together, these data suggest that surface‐bound internalin plays an important role in bacterial entry but do not exclude a role for the released form.
A C‐terminal truncation results in high‐level expression of the functional photoreceptor sensory rhodopsin I in the archaeon Halobacterium salinarium
Authors: Ferrando‐May Elisa , Brustmann Bettina , Oesterhelt Dieter 
Published: October 2006

SummaryExpression of the gene encoding the halobacterial photoreceptor sensory rhodopsin I (SRI), sopl, was studied by means of homologous gene targeting. A sopr− Halobacterium salinarium mutant strain was constructed by homologous replacement of sopl with a novobiocin‐resistant gyrB from Haloferax Aa 2.2. Cells bearing gyrB were resistant to novobiocin, indicating that the Haloferax gene is functional in H. salinarium. Complementation of this deletion strain with sopl fused to the bacterio‐opsin promoter resulted in the recovery of all phenotypical attributes of SRI. This establishes the first direct correlation between sopl and the function of its gene product, in the complemented deletion strain, functional expression of sopl occurred from the bop locus, where sopl had Integrated by homologous recombination. This shows that cotranscription of sopl and the gene encoding the SRI signal transducer, htrl, which is found in the wild type, is not a prerequisite for photosensory activity. Deletion of the last 43 bp at the 3′ end of sopl resulted in a 10‐fold increase in the amount of SRI, without affecting the activity of the pigment. The mRNA level of the truncated gene was not affected as compared to that of the wild type. We propose that regulation occurs at the protein level, probably through a negative determinant of protein stability located in the C‐terminus of SRI. Replacement of the last 26 amino acids of bacteriorhodopsin by the last 29 amino acids of SRI results in a decrease of the bacteriorhodopsin, supporting our observations. The C‐terminus of SRI is the first domain with a downregulating influence on protein levels thus far identified in H. salinarium. The system for SRI overexpression we present here greatly facilitates biochemical and biophysical studies on the photoreceptor and allows
Roles in inhibitor recognition and quinol oxidation of the amino acid side chains at positions of cytb providing resistance to Qo‐inhibitors of the bc1 complex from Rhodobacter capsulatus
Authors: Tokito Mariko K. , Daldal Fevzi 
Published: October 2006

SummaryThe substitutions M140I, F144S and L, G152S, T163A and V333A in cytochrome b of the ubiquinol‐cytochrome c oxidoreductase (bc1 complex) from Rhodobacter capsulatus provide resistance to the quinol oxidation (Qo inhibitors myxothiazol, mucidin and stigmatellin. Site‐directed mutagenesis with degenerate primers was used to define the role of these positions in inhibitor recognition and quinol oxidation, and a collection of various substitutions at each of these positions was obtained. The effects of these mutations on quinol oxidation, nature and level of inhibitor resistance, prosthetic group incorporation and assembly of the complex were analysed. Most of these mutations, unlike those at position 158 reported earlier, yielded functional bc1, complexes able to support the photosynthetic growth of R. capsulatus. However, they perturbed steady‐state quinol oxidation and inhibitor recognition indicating that they are important for the function of the Qo site. In particular, the presence of a methyl group on the β‐carbon (He and Val residues) at position 140, the absence of an aromatic ring (Phe, Tyr and Trp residues) at position 144 and the loss of residues with small side chains (Gly and Ala) at position 152 correlated with resistance to myxothiazol. On the other hand, no myxothiazol resistance was observed with the substitutions at positions 163 and 333 suggesting that they affected solely the recognition of stigmatellin. Five substitutions, M140R, F144H and R, G152P and T163R, yielded photosynthesis‐deficient mutants with assembled but impaired bc1 complexes. Unexpectedly, two substitutions at position 163 (T to F or P) yielded mutants lacking the three subunits of
The catR gene encoding a catalase from Aspergillus niger primary structure and elevated expression through increased gene copy number and use of a strong promoter
Authors: Fowler Timothy , Rey Michael W. , Vähä‐Vahe Peka , Power Scott D. , Berka Randy M. 
Published: October 2006

SummarySynthetic oligonucleotide probes based on amino acid sequence data were used to identify and clone cDNA sequences encoding a catalase (catalase‐R) of Aspergillus niger. One cDNA clone was subsequently used to isolate the corresponding genomic DNA sequences (designated catR). Nucleotide sequence analysis of both genomic and cDNA clones suggested that the catR coding region consists of five exons interrupted by four small introns. The deduced amino acid sequence of catalase‐R spans 730 residues which show significant homology to both prokaryotic and eukaryotic catalases, particularly in regions involved in catalytic activity and binding of the haem prosthetic group. Increased expression of the catR gene was obtained by transformation of an A. niger host strain with an integrative vector carrying the cloned genomic DNA segment. Several of these transformants produced three‐ to fivefold higher levels of catalase than the untransformed parent strain. Hybridization analyses indicated that these strains contained multiple copies of catR integrated into the genome. A second expression vector was constructed in which the catR coding region was functionally joined to the promoter and terminator elements of the A. niger glucoamylase (glaA) gene. A. niger transformants containing this vector produced from three‐ to 10‐fold higher levels of catalase‐R than the untransformed parent strain.
Nucleotide sequence and expression of the Pseudomonas aeruginosa algF gene controlling acetylation of alginate
Authors: Shinabarger Dean , May Thomas B. , Boyd Aoife , Ghosh Mita , Chakrabarty A. M. 
Published: October 2006

SummaryColonization of the cystic fibrosis lung by Pseudomonas aeruginosa is greatly facilitated by the production of an exopolysaccharide called alginate. In this study we determined the nucleotide sequence of an alginate modification gene, algF, which controls the addition of acetyl groups to alginate. Expression of algF using a T7 promoter‐expression system showed that algF codes for a 24.5 kDa polypeptide (predicted size 22 832 Da) that is processed to 19.5 kDa. The N‐terminus of the processed polypeptide matched the predicted amino acid sequence of AlgF starting at Asp‐29. An algF mutant failed to produce alginate owing to a polar effect on the downstream algA gene. Although the algA gene, provided in trans, restored synthesis of alginate, the alginate was non‐acetylated. We show that a plasmid containing both the algF and algA gene complements the alginate acetylation defect of the algF mutant strain.