bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic block at early stages of the glycolytic pathway activates the Rcs phosphorelay system via increased synthesis of dTDP‐glucose in Escherichia coli
Authors: El‐Kazzaz Waleed , Morita Teppei , Tagami Hideaki , Inada Toshifumi , Aiba Hiroji 
Published: December 2004

SummaryA mutational block in the early stages of the glycolytic pathway facilitates the degradation of the ptsG mRNA encoding the major glucose transporter IICBGlc in Escherichia coli. The degradation is RNase E dependent and is correlated with the accumulation of either glucose‐6‐P or fructose‐6‐P (Kimata et al., 2001, EMBO J 20: 3587–3595; Morita et al., 2003, J Biol Chem 278: 15608–15614). In this paper, we investigate additional physiological effects resulting from the accumulation of glucose‐6‐P caused by a mutation in pgi encoding phosphoglucose isomerase, focusing on changes in gene expression. The addition of glucose to the pgi strain caused significant growth inhibition, in particular in the mlc background. Cell growth then gradually resumed as the level of IICBGlc decreased. We found that the transcription of the cps operon, encoding a series of proteins responsible for the synthesis of colanic acid, was markedly but transiently induced under this metabolic stress. Both genetic and biochemical studies revealed that the metabolic stress induces cps transcription by activating the RcsC/YojN/RcsB signal transduction system. Overexpression of glucose‐6‐P dehydrogenase eliminated both growth inhibition and cps induction by reducing the glucose‐6‐P level. Mutations in genes responsible for the synthesis of glucose‐1‐P and/or dTDP‐glucose eliminated the activation of the Rcs system by the metabolic stress. Taken together, we conclude that an increased synthesis of dTDP‐glucose activates the Rcs phosphorelay system, presumably by affecting the synthesis of oligosaccharides for enterobacterial common antigen and O‐antigen.
Topological analysis of Hin‐catalysed DNA recombination in vivo and in vitro
Authors: Merickel Stacy K. , Johnson Reid C. 
Published: December 2004

Summary In vitro
studies have demonstrated that Hin‐catalysed site‐specific DNA inversion occurs within a tripartite invertasome complex assembled at a branch on a supercoiled DNA molecule. Multiple DNA exchanges within a recombination complex (processive recombination) have been found to occur with particular substrates or reaction conditions. To investigate the mechanistic properties of the Hin recombination reaction
in vivo
, we have analysed the topology of recombination products generated by Hin catalysis in growing cells. Recombination between wild‐type recombination sites
in vivo
is primarily limited to one exchange. However, processive recombination leading to knotted DNA products is efficient on substrates containing recombination sites with non‐identical core nucleotides. Multiple exchanges are limited by a short DNA segment between the Fis‐bound enhancer and closest recombination site and by the strength of Fis–Hin interactions, implying that the enhancer normally remains associated with the recombining complex throughout a single exchange reaction, but that release of the enhancer leads to multiple exchanges. This work confirms salient mechanistic aspects of the reaction
in vivo
and provides strong evidence for the propensity of plectonemically branched DNA in prokaryotic cells. We also demonstrated that a single DNA exchange resulting in inversion
in vitro is accompanied by a loss of four negative supercoils.
Divergent binding sites on intercellular adhesion molecule‐1 (ICAM‐1) for variant Plasmodium falciparum isolates
Authors: Tse Man Tsuey , Chakrabarti Kausik , Gray Carolyn , Chitnis Chetan E. , Craig Alister 
Published: December 2004

SummaryAdhesion of human erythrocytes infected with the malaria parasite Plasmodium falciparum to host endothelium has been associated with severe forms of this disease. A number of endothelial receptors have been identified, and there is evidence that one of these, intercellular adhesion molecule‐1 (ICAM‐1), may play an important role in the pathology of cerebral malaria. Mutagenesis of domain 1 of ICAM‐1, which is involved in parasite adhesion, shows that the binding sites for different parasite variants overlap to a large extent, but that there are subtle differences between them that correlate with their adhesive phenotypes. This suggests that the ability to bind to ICAM‐1 has arisen from a common variant, but that subsequent changes have led to differences in binding avidity, which may affect pathogenesis. The definition of common binding determinants and the elucidation of links between ICAM‐1 binding phenotype and disease will provide new leads in the design of therapeutic interventions.
Cellular engineering in a minimal microbe: structure and assembly of the terminal organelle of Mycoplasma pneumoniae
Authors: Krause Duncan C. , Balish Mitchell F. 
Published: December 2004

Summary Mycoplasma pneumoniae
is a minimal microbe with respect to cell envelope composition, biosynthetic and regulatory capabilities and genome size, yet it possesses a remarkably complex, multifunctional terminal organelle. This membrane‐bound extension of the mycoplasma cell is defined by the presence of an electron‐dense core that appears as paired, parallel bars oriented longitudinally and enlarging at the distal end to form a terminal button. Most non‐cytadhering mutants of
M. pneumoniae isolated to date exhibit defects in the architecture of the terminal organelle. Detailed characterization of those mutants has revealed the identities of many component proteins of the terminal organelle as well as the likely order in which some of those components are required. Additional questions regarding the composition of the electron‐dense core, the means by which the terminal organelle is duplicated during cell division and the manner in which this process is regulated remain to be answered. Thus, it seems that there is much to be learned about cellular engineering and spatial regulation in these ‘simple’ cell wall‐less bacteria.
Intein harbouring large tandem repeats in replicative DNA helicase of Trichodesmium erythraeum
Authors: Yang Jing , Meng Qing , Liu Xiang‐Qin 
Published: December 2004

SummaryProtein splicing inteins can be small as ∼130 aa or up to ∼600 aa when harbouring an endonuclease domain. Here we report the identification and characterization of an unusually large intein, 1650 aa long and the largest of known inteins, encoded by the replicative DNA helicase gene dnaB of the oceanic N2‐fixing cyanobacterium Trichodesmium erythraeum. This Ter DnaB‐1 intein co‐exists with a 177‐aa mini‐intein in the same host protein and harbours large tandem repeats in which an 84‐aa sequence is repeated 16 times. Comparison between this tandem repeats and the recently reported tandem repeats of Ter DnaE‐1 intein revealed differences and similarities. The two tandem repeats, residing in different inteins of different host proteins, differ by 50% in size and have little sequence similarity. Tandem repeats in the Ter DnaB‐1 intein were required for the protein splicing activity when tested in Escherichia coli, in contrast to tandem repeats of the Ter DnaE‐1 intein that inhibited protein splicing. On the other hand, tandem repeats of both inteins are located in the same corresponding region of the intein sequence and have the same number of repeating units. These suggest that the two tandem repeats could be related but have diverged greatly in size, sequence and effect on protein splicing. Alternatively, they could have independent origins but evolved certain similarities because of common constraints in structure and maintenance.
Differences in two Pseudomonas aeruginosa cbb3 cytochrome oxidases
Authors: Comolli James C. , Donohue Timothy J. 
Published: December 2004

SummaryBacterial cytochrome cbb3 oxidases are members of the haeme‐copper oxidase superfamily that are important for energy conservation by a variety of proteobacteria under oxygen‐limiting conditions. The opportunistic pathogen Pseudomonas aeruginosa is unusual in possessing two operons that each potentially encode a cbb3 oxidase (cbb3‐1 or cbb3‐2). Our results demonstrate that, unlike typical enzymes of this class, the cbb3‐1 oxidase has an important metabolic function at high oxygen tensions. In highly aerated cultures, cbb3‐1 abundance and expression were greater than that of cbb3‐2, and only loss of cbb3‐1 influenced growth. Also, the activity of cbb3‐1, not cbb3‐2, inhibited expression of the alternative oxidase CioAB and thus influenced a signal transduction pathway much like that found in the α‐proteobacterium Rhodobacter sphaeroides. Cbb3‐2 appeared to play a more significant role under oxygen limitation by nature of its increased abundance and expression compared to highly aerated cultures, and the regulation of the cbb3‐2 operon by the putative iron‐sulphur protein Anr. These results indicate that each of the two P. aeruginosa cbb3 isoforms have assumed specialized energetic and regulatory roles.
Identification and characterization of NleA, a non‐LEE‐encoded type III translocated virulence factor of enterohaemorrhagic Escherichia coli O157:H7
Authors: Gruenheid Samantha , Sekirov Inna , Thomas Nikhil A. , Deng Wanyin , O'Donnell Paul , Goode David , Li Yuling , Frey Elizabeth A. , Brown Nathaniel F. , Metalnikov Pavel , Pawson Tony , Ashman Keith , Finlay B. Brett 
Published: December 2004

SummaryEnterohaemorrhagic Escherichia coli (EHEC) O157:H7 uses a specialized protein translocation apparatus, the type III secretion system (TTSS), to deliver bacterial effector proteins into host cells. These effectors interfere with host cytoskeletal pathways and signalling cascades to facilitate bacterial survival and replication and promote disease. The genes encoding the TTSS and all known type III secreted effectors in EHEC are localized in a single pathogenicity island on the bacterial chromosome known as the locus for enterocyte effacement (LEE). In this study, we performed a proteomic analysis of proteins secreted by the LEE‐encoded TTSS of EHEC. In addition to known LEE‐encoded type III secreted proteins, such as EspA, EspB and Tir, a novel protein, NleA (non‐LEE‐encoded effector A), was identified. NleA is encoded in a prophage‐associated pathogenicity island within the EHEC genome, distinct from the LEE. The LEE‐encoded TTSS directs translocation of NleA into host cells, where it localizes to the Golgi apparatus. In a panel of strains examined by Southern blot and database analyses, nleA was found to be present in all other LEE‐containing pathogens examined, including enteropathogenic E. coli and Citrobacter rodentium, and was absent from non‐pathogenic strains of E. coli and non‐LEE‐containing pathogens. NleA was determined to play a key role in virulence of C. rodentium in a mouse infection model.
The anaerobic chytridiomycete fungus Piromyces sp. E2 produces ethanol via pyruvate:formate lyase and an alcohol dehydrogenase E
Authors: Boxma Brigitte , Voncken Frank , Jannink Sander , Van Alen Theo , Akhmanova Anna , Van Weelden Susanne W. H. , Van Hellemond Jaap J. , Ricard Guenola , Huynen Martijn , Tielens Aloysius G. M. , Hackstein Johannes H. P. 
Published: December 2004

SummaryAnaerobic chytridiomycete fungi possess hydrogenosomes, which generate hydrogen and ATP, but also acetate and formate as end‐products of a prokaryotic‐type mixed‐acid fermentation. Notably, the anaerobic chytrids Piromyces and Neocallimastix use pyruvate:formate lyase (PFL) for the catabolism of pyruvate, which is in marked contrast to the hydrogenosomal metabolism of the anaerobic parabasalian flagellates Trichomonas vaginalis and Tritrichomonas foetus, because these organisms decarboxylate pyruvate with the aid of pyruvate:ferredoxin oxidoreductase (PFO). Here, we show that the chytrids Piromyces sp. E2 and Neocallimastix sp. L2 also possess an alcohol dehydrogenase E (ADHE) that makes them unique among hydrogenosome‐bearing anaerobes. We demonstrate that Piromyces sp. E2 routes the final steps of its carbohydrate catabolism via PFL and ADHE: in axenic culture under standard conditions and in the presence of 0.3% fructose, 35% of the carbohydrates were degraded in the cytosol to the end‐products ethanol, formate, lactate and succinate, whereas 65% were degraded via the hydrogenosomes to acetate and formate. These observations require a refinement of the previously published metabolic schemes. In particular, the importance of the hydrogenase in this type of hydrogenosome has to be revisited.
Identification of the sequences required for chromosomal replicator function in Kluyveromyces lactis
Authors: Irene Carmela , Maciariello Clelia , Cioci Francesco , Camilloni Giorgio , Newlon Carol S. , Fabiani Lucia 
Published: December 2004

SummaryThe analysis of replication intermediates of a Kluyveromyces lactis chromosomal autonomous replicating sequence (ARS), KARS101, has shown that it is active as a chromosomal replicator. KARS101 contains a 50 bp sequence conserved in two other K. lactis ARS elements. The deletion of the conserved sequence in KARS101 completely abolished replicator activity, in both the plasmids and the chromosome. Gel shift assays indicated that this sequence binds proteins present in K. lactis nuclear extracts, and a 40 bp sequence, previously defined as the core essential for K. lactis ARS function, is required for efficient binding. Reminiscent of the origin replication complex (ORC), the binding appears to be ATP dependent. A similar pattern of protection of the core was seen with in vitro footprinting. KARS101 also functions as an ARS sequence in Saccharomyces cerevisiae. A comparative study using S. cerevisiae nuclear extracts revealed that the sequence required for binding is a dodecanucleotide related to the S. cerevisiae ARS consensus sequence and essential for S. cerevisiae ARS activity.
Overproduction of the Lon protease triggers inhibition of translation in Escherichia coli: involvement of the yefM‐yoeB toxin‐antitoxin system
Authors: Christensen Susanne K. , Maenhaut‐Michel Geneviève , Mine Natacha , Gottesman Susan , Gerdes Kenn , Van Melderen Laurence 
Published: December 2004

SummaryIn Escherichia coli, the Lon ATP‐dependent protease is responsible for degradation of several regulatory proteins and for the elimination of abnormal proteins. Previous studies have shown that the overproduction of Lon is lethal. Here, we showed that Lon overproduction specifically inhibits translation through at least two different pathways. We have identified one of the pathways as being the chromosomal yefM‐yoeB toxin‐antitoxin system. The existence of a second pathway is demonstrated by the observation that the deletion of the yefM‐yoeB system did not completely suppress lethality and translation inhibition. We also showed that the YoeB toxin induces cleavage of translated mRNAs and that Lon overproduction specifically activates YoeB‐dependent mRNAs cleavage. Indeed, none of the other identified chromosomal toxin‐antitoxin systems (relBE, mazEF, chpB and dinJ‐yafQ) was involved in Lon‐dependent lethality, translation inhibition and mRNA cleavage even though the RelB and MazE antitoxins are known to be Lon substrates. Based on our results and other studies, translation inhibition appears to be the key element that triggers chromosomal toxin‐antitoxin systems. We propose that under Lon overproduction conditions, translation inhibition is mediated by Lon degradation of a component of the YoeB‐independent pathway, in turn activating the YoeB toxin by preventing synthesis of its unstable YefM antidote.
Large‐scale identification of essential Salmonella genes by trapping lethal insertions
Authors: Knuth Karin , Niesalla Heide , Hueck Christoph J. , Fuchs Thilo M. 
Published: December 2004

SummaryA novel screening approach based on insertion‐duplication mutagenesis (IDM) was established to efficiently screen for essential genes of Salmonella enterica serovar Typhimurium under laboratory conditions. Small, randomly generated genomic fragments were cloned into a conditionally replicating vector, and the resulting library of single Salmonella clones was grown under permissive conditions. Upon switching to non‐permissive temperature, discrimination between lethal and non‐lethal insertions following homologous recombination allowed the trapping of genes with essential functions. Further characterization of a total of 498 fragments resulting in such lethal knockout revealed 145 known essential genes and 112 functionally characterized or hypothetical genes not yet shown to encode essential genes, among them three Salmonella‐specific genes. The essentiality was demonstrated for a prioritised set of 15 putative indispensable genes by creating conditional lethal phenotypes. The results of this large‐scale screening indicate that in rich media, the class of Salmonella genes indispensable for growth is composed of approximately 490 genes.
Females avoid manipulative males and live longer
Authors: Moore A. J. , Gowaty P. A. , Moore P. J. 
Published: December 2004

Abstract
Female mate choice has been demonstrated in a wide variety of species and is now accepted as an important factor in sexual selection. One of the remaining questions, however, is why females prefer specific males. Do females or their offspring benefit from their choice? Or do females choose mates to minimize costs of mating? Here we show that, in the ovoviviparous cockroach Nauphoeta cinerea, where sexual selection has been well documented, females chose mates to avoid costly male manipulation. Females were partnered with preferred or nonpreferred mates, and fitness of the females measured. We found that females lived longer when they mated with preferred males. Female lifespan depended on the rate at which offspring developed from egg to parturition: slower development led to longer life. We manipulated the male pheromone and showed that the component of the pheromone blend that makes males attractive to females also delayed parturition. Thus, like other aspects of sexual conflict in this species, offspring development and thereby the mother's lifespan depended on exposure of females to specific components of the male pheromone. Males benefit from manipulating offspring development because females with accelerated parturition remained unreceptive whereas females with slower developing offspring readily remated after giving birth to their offspring. Our results suggest a hormone-like role for the male pheromone in N. cinerea and provide the first direct evidence of mate choice to avoid male manipulation. This study shows that dominant males may not be preferred males if they are manipulating females, why multiple components with contrasting effects can exist in a sexual signal, and emphasizes the complex fitness relationships that can arise in species with sexual conflict.
Adaptive seasonal trend in brood sex ratio: test in two sister species with contrasting breeding systems
Authors: Andersson M. , Wallander J. , Oring L. , Akst E. , Reed J. M. , Fleischer R. C. 
Published: December 2004

Abstract
Evolutionary theory predicts adaptive adjustment in offspring sex ratio by females. Seasonal change in sex ratio is one possibility, tested here in two sister species, the Common sandpiper and the Spotted sandpiper Actitis hypoleucos and A. macularia. In the monogamous Common sandpiper, males are the most competitive sex. In each of 3 years, there was a change from mainly sons in early clutches to mainly daughters in late clutches. This seasonal adjustment of clutch sex ratio took place within the female before the eggs were laid, not by differential egg or chick survival. The sex of all eggs laid in the clutches used here was determined molecularly from chick blood taken at the time of hatching. The Spotted sandpiper in contrast is polyandrous, with partly reversed sex roles. There was no seasonal trend from sons to daughters in this species. When tested together, the two species differed significantly as predicted by the hypothesis of adaptive sex ratio adjustment by females.
Sexual conflict in Sepsis cynipsea: female reluctance, fertility and mate choice
Authors: Hosken D. J. , Martin O. Y. , Born J. , Huber F. 
Published: December 2004

Abstract
Sexual conflict can elevate mating costs via male inflicted damage to females. Possible selective advantages to males include decreasing the likelihood that females remate and/or increasing females' current reproductive investment in a manner analogous to terminal reproductive investment. We investigated female mating behaviour relative to their number of previous copulations in the fly Sepsis cynipsea, and whether males accepted as first mates were more likely to be accepted again. Females were more likely to remate with new rather than original males, although there was no associated fitness benefit, and in contrast to theoretical predictions, females became less reluctant to remate as the number of previous copulations increased. Additionally, females did not increase reproductive investment as would be expected if they were ensuring their final reproductive efforts were maximized by remating. This suggests that damaging females is a pleiotropic effect which inadvertently leads to increased, not decreased, polyandry.
The emergence of cetaceans: phylogenetic analysis of male social behaviour supports the Cetartiodactyla clade
Authors: Lusseau D. 
Published: December 2004

Abstract
The phylogeny of cetaceans is still unresolved. Two hypotheses prevail for the position of cetaceans among ungulates. The first hypothesis shows that Artiodactyla is monophyletic and is sister taxon to a clade composed of cetaceans and mesonychians. The second one shows that Artiodactyla is paraphyletic and contains Cetacea that is sister taxon of Hippopotamida. These hypotheses are based on fossil records and molecular studies. The behaviour of extant species can provide as much phylogenetic information as other classical parameters. I considered the behaviour observed during male agonistic interactions in placental mammals in order to determine which of these hypotheses was supported by the behaviour of extant species. Headbutting was only observed in ruminants, hippopotamids and cetaceans, supporting the paraphyletic nature of Artiodactyla. Primitive ruminants (tragulids) and two genera of ruminants (Moschus and Oreamnos) were not observed headbutting. These secondary losses were only present in 6.25% of the 48 surveyed ruminant genera. Head-to-head attacks emerged in pigs, which have developed dermal protusions. Yet, these confrontations are not based on mutual blow delivery. The behavioural evidence supports the inclusion of cetaceans in Artiodactyla.