bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lotus japonicusNodulation Requires Two GRAS Domain Regulators, One of Which Is Functionally Conserved in a Non-Legume
Authors: Heckmann Anne B. , Lombardo Fabien , Miwa Hiroki , Perry Jillian A. , Bunnewell Sue , Parniske Martin , Wang Trevor L. , Downie J. Allan 
Published: October 2006

AbstractA new nodulation-defective mutant of Lotus japonicus does not initiate nodule cortical cell division in response to Mesorhizobium loti, but induces root hair deformation, Nod factor-induced calcium spiking, and mycorrhization. This phenotype, together with mapping data, suggested that the mutation could be in the ortholog of the Medicago truncatula NSP1 gene (MtNSP1). The sequence of the orthologous gene (LjNSP1) in the L. japonicus mutant (Ljnsp1-1) revealed a mutation causing a premature stop resulting in loss of the C-terminal 23 amino acids. We also sequenced the NSP2 gene from L. japonicus (LjNSP2). A mutant (Ljnsp2-3) with a premature stop codon was identified by TILLING showing a similar phenotype to Ljnsp1-1. Both LjNSP1 and LjNSP2 are predicted GRAS (GAI, RGA, SCR) domain transcriptional regulators. Transcript steady-state levels of LjNSP1 and LjNSP2 initially decreased and then increased following infection by M. loti. In hairy root transformations, LjNSP1 and MtNSP1 complemented both Mtnsp1-1 and Ljnsp1-1 mutants, demonstrating that these orthologous proteins have a conserved biochemical function. A Nicotiana benthamiana NSP1-like gene (NbNSP1) was shown to restore nodule formation in both Ljnsp1-1 and Mtnsp1-1 mutants, indicating that NSP1 regulators from legumes and non-legumes can propagate the Nod factor-induced signal, activating appropriate downstream targets. The L. japonicus nodules complemented with NbNSP1 contained some cells with abnormal bacteroids and could fix nitrogen. However, the NbNSP1-complemented M. truncatula nodules did not fix nitrogen and contained very few bacteria released from infection threads. These observations suggest that NSP1 is also involved in infection, bacterial release, and normal bacteroid formation in nodule cells.
Systemin in Solanum nigrum. The Tomato-Homologous Polypeptide Does Not Mediate Direct Defense Responses
Authors: Schmidt Silvia , Baldwin Ian T. 
Published: October 2006

Abstract
We extend Ryan's seminal work on the 18-amino acid polypeptide systemin in tomato's (Solanum lycopersicum) systemic wound response to the closely related solanaceous species Solanum nigrum. We compared wild-type plants to plants transformed with an inverted repeat prosystemin construct (IRSys) to silence the expression of the endogenous S. nigrum prosystemin gene. In wild-type plants elicited with wounding + oral secretions from Manduca sexta larvae, trypsin-proteinase inhibitors (TPIs) accumulated even though prosystemin transcripts were down-regulated. Neither reducing the endogenous systemin levels by RNAi nor complementing the plants with systemin by exogenously supplying the polypeptide through excised stems significantly increased TPI activity, indicating that systemin and TPIs are not correlated in S. nigrum. The performance of two herbivore species from two feeding guilds, M. sexta larvae and Myzus persicae nicotianae, did not differ between wild-type and IRSys plants, demonstrating that varying endogenous systemin levels do not alter the direct defenses of S. nigrum. Field experiments with wild-type and IRSys plants and the flea beetle Epitrix pubescens supported these glasshouse data. That levels of oral secretion-elicited jasmonic acid did not differ between wild-type and IRSys plants suggests that systemin is unlikely to mediate jasmonate signaling in S. nigrum as it does in tomato. We conclude that the tomato-homologous polypeptide does not mediate direct defense responses in S. nigrum.
Molecular analysis of the Corynebacterium glutamicum gdh gene encoding glutamate dehydrogenase
Authors: Börmann E. R. , Eikmanns B. J. , Sahm H. 
Published: October 2006

SummaryThe Corynebacterium glutamicum gdh gene encoding NADP‐dependent glutamate dehydrogenase (GDH) has been isolated by complementation of the Escherichia coli gdh mutant PA340. The gdh gene was subcloned into the E. coli/C. glutamicum shuttle vector pEK0 and introduced into C. glutamicum. Recombinant strains showed approximately eightfold higher specific GDH activity (15U mg protein‐1) relative to the wild type (1.8U mg protein ‐1). Physiological studies with wild‐type and recombinant C. glutamicum strains revealed no indication of significant regulation of gdh expression. The DNA sequence of 2082 bp, including the gdh gene, 5′‐, and 3′‐flanking regions, was determined. The structural gene consists of 1344 bp and codes for a polypeptide of 448 amino acid residues (Mr 49152) showing up to 53.6% identity with reported amino acid sequences of glutamate dehydrogenases from other organisms. Northern blot hybridization revealed a 1.65 kb mRNA transcript, indicating that the gdh gene of C. glutamicum is monocistronic. Transcription occurred from a G residue located 284bp upstream of the AUG considered to be the translational initiation codon.
The gene for the S7 ribosomal protein of Chlamydia trachomatis: characterization within the chlamydial sfr operon
Authors: Wagar E. A. , Pang M. 
Published: October 2006

SummaryThe prokaryotic ribosomal operon, str, contains open reading frames for the two elongation factors, elongation factor G (EF‐G) and elongation factor Tu (EF‐Tu), and ribosomal proteins 57 and S12. The DNA sequence and predicted amino acid sequence for S7 from Chlamydia trachomatis are presented and compared with homologues from other prokaryotes. Also, the relationship of the S7 gene to the open reading frames for ribosomal protein S12 and EF‐G is described. Significant amino acid homology is also noted when the amino‐terminal sequence of chlamydial EF‐G is compared with the cytoplasmic tetra‐cycline resistance factors, tetM and tetO, from streptococci and Campylobacter jejuni. Related findings and possible resistance mechanisms for the newly recognized tetracycline‐resistant clinical isolates of C. trachomatis are discussed.
Sequence diversity of the 1.3 kb retron (retron‐Ec107) among three distinct phylogenetic groups of Escherichia coli
Authors: Kawaguchi T. , Herzer P. J. , Inouye M. , Inouye S. 
Published: October 2006

SummaryIn the preceding paper, we showed that a new 1.3kb retron (retron‐Ec 107) in Escherichia coli is responsible for the biosynthesis of a branched‐RNA‐linked multicopy single‐stranded DNA (msDNA‐Ec107). Here, we show that this retron occurs in strains from different branches. A, B1, and D of a well‐defined phylogenetic tree of a collection of wild E. coli. Sequence comparisons of the retrons from these three branches were carried out. Sequence homology was well conserved among the strains within the same branch and the retron sequence from branch A was exactly the same with that from branch D, while there were 18 base substitutions between the retrons from branch B1 and A or D, resulting in seven amino acid substitutions in reverse transcriptase. No substitutions were found in the msDNA‐ and msdRNA‐coding regions, and there was no difference in the ability of msDNA production between them. These results suggest that the retron has probably been integrated into at least one of the three branches at an early stage of evolution and subsequently transferred to the other two branches, and also that the msDNA‐producing system has been conserved during evolution with some mutations in the retron.
Functional expression of the rat brown adipose tissue uncoupling protein in Saccharomyces cerevisiae
Authors: Bathgate B. , Freebairn E. M. , Greenland A. J. , Reid G. A. 
Published: October 2006

SummaryThe uncoupling protein (UCP) from mammalian brown adipose tissue is an integral component of the mitochondrial inner membrane where it dissipates the proton electrochemical gradient. UCP is transported into mitochondria from the cytosol but lacks a cleavable targeting peptide. We have expressed the rat UCP in Saccharomyces cerevisiae and shown that this protein, which is not normally found in yeast, is targeted to the mitochondria where it disrupts mitochondrial function, probably by uncoupling oxidative phosphorylation.The observed growth defect is dependent upon the level of expression of UCP. When the unmodified UCP cDNA is expressed in yeast under the control of the GAL10 promoter no defect in growth is observed. We have inserted the UCP coding sequence behind the strong phosphoglycerate kinase promoter under the control of the GAL1‐10 upstream activation site and introduced a yeast consensus sequence (ATAATG) at the translation start site. We have found that UCP expressed in S. cerevisiae is targeted to mitochondria and that its expression induces a marked growth defect on non‐fermentable carbon sources in a manner dependent on induction with galactose.
Molecular cloning, iron‐regulation and mutagenesis of the irp2 gene encoding HMWP2, a protein specific for the highly pathogenic Yersinia
Authors: Carniel E. , Guiyoule A. , Guilvout I. , Mercereau‐Puijalon O. 
Published: October 2006

SummaryUnder iron‐starvation, the highly pathogenic Yersinia synthesize several iron‐regulated proteins including two high‐molecular‐weight polypeptides (HMWP1 and HMWP2). From the chromosome of Yersinia enterocolitica serovar O:8 (strain Ye 8081), the genes coding for the HMWP2 (irp2) and its promoter were cloned into plasmid pUC18 (plR2) and used as a probe. We show here that the irp2 gene is present only in the highly pathogenic strains and that its promoter is iron‐regulated in Escherichia coli. After introduction of the plR2 plasmid into a fur mutant of E. coli, both the iron‐starved and the iron‐replete bacteria expressed the HMWP2. Repressibility of irp2 by iron was restored by introduction of a plasmid carrying the fur gene. These results demonstrate that the irp2 promoter is controlled by the Fur repressor in E. coli. Mutagenesis of the chromosomal irp2 gene of Yersinia pseudotuberculosis was obtained by homologous recombination with a 1 kb fragment of this gene cloned on the suicide plasmid pJM703.1. Inactivation of irp2 resulted in the non‐expression of both HMWPs, while introduction of plasmid plR2 into the mutant strain led to the synthesis of the HMWP2 only. Therefore, It is probable that the genes coding for the HMWPs constitute an operon where irp2 is upstream of irp1. When comparing the virulence of the wild‐type strain and of its irp2 mutant derivative, we found that the 50% lethality (LD50) for mice of the mutant strain was increased, whatever the route of infection, but more markedly when injected parenterally. Accordingly, these data demonstrate that a mutation in the irp2 gene alters the pathogenicity of Y. pseudotuberculosis. Since the introduction of the irp2 gene into the mutant strain did not restore its virulence, it is likely that both HMWPs are required for the expression of the high‐pathogenicity phenotype.
Porins and specific channels of bacterial outer membranes
Authors: Nikaido H. 
Published: October 2006

SummaryPorins and specific channels both produce water‐filled pores that allow the transmembrane diffusion of small solutes, but the latter contain specific ligandbinding sites within the channels. Recent structural studies show that many or most of these proteins exist as βbarrels with the βstrands traversing the thickness of the outer membrane. The channels often have diameters in the range of 1 nm, and thus the penetration rates of solutes through porin channels are likely to be affected strongly by what appear to be minor differences in the size, shape, hydrophobicity or charge of the solute molecule. With the specific channels, the presence of binding sites can accelerate very significantly the diffusion of some ligands when they are present at low concentrations. Thus these simple channels can sometimes achieve a surprising degree of real or apparent specificity. Recent data tend to favour the idea that these proteins are first exported into the periplasm, and then inserted into the outer membrane. Although lipopolysaccharides seem to play a significant role in the final assembly of the trimeric porins, the details of the targeting process still remain to be elucidated.
Evolutionary origins of bacterial bioluminescence
Authors: O'Kane Dennis J. , Prasher Douglas C. 
Published: October 2006

SummaryIn bacteria, most genes required for the bioluminescence phenotype are contained in lux operons. Sequence alignments of several lux gene products show the existence of at least two groups of paralogous products. The α‐ and β‐subunits of bacterial luciferase and the non‐fluorescent flavoprotein are paralogous, and two antennae proteins (lumazine protein and yellow fluorescence protein) are paralogous with riboflavin synthetase. Models describing the evolution of these paralogous proteins are suggested, as well as a postulate for the identity of the gene encoding a protobioluminescent luciferase.
Role of horizontal genetic exchange in the antigenic variation of the class 1 outer membrane protein of Neisseria meningitidis
Authors: Feavers I. M. , Heath A. B. , Bygraves J. A. , Maiden M. C. J. 
Published: October 2006

SummaryThe nucleotide sequences of the genes encoding the class 1 outer membrane protein of Neisseria meningitidis (PorA) from 15 meningococcal isolates have been examined. These strains, isolated over a number of years, represented a variety of serological types, clonal groups, and geographical locations. Analysis of the aligned nucleotide sequences showed that the known serological relationships between these proteins were not necessarily reflected throughout the nucleotide sequences of their genes. The uneven distribution of base substitutions, revealed by a comparison of the informative bases, suggested that these genes possessed a mosaic structure. This structure probably resulted from the horizontal transfer of DNA between strains and would have contributed to both the generation and the spread of novel antigenic variants of the protein. In addition, the nucleotide differences between porA genes from different strains were not consistent with the nucleotide sequence divergence of the whole chromosome, as indicated by pulsed‐field get electrophoresis (PFGE) fingerprinting techniques: some strains with divergent PFGE fingerprints shared porA genes with extensive regions of nucleotide sequence identity and, conversely, some strains with similar chromosome structures possessed porA genes with different nucleotide sequences and serological properties. This suggested that entire genes had been exchanged between strains. Given that the meningococcal class 1 OMP is a major component in novel vaccines, some of which are currently undergoing field trials, the potential of horizontal genetic exchange to generate antigenic diversity has implications for the design of such vaccines.
Expression of chitin synthase genes during yeast and hyphal growth phases of Candida albicans
Authors: Chen‐Wu J. L. , Zwicker J. , Bowen A. R. , Robbins P. W. 
Published: October 2006

SummaryChitin, the β1,4‐linked polymer of N‐acetylglucosamine, is a fibrous polysaccharide that in many yeasts helps to maintain the structure of the mother‐bud junction and in filamentous fungi is often the major supporting component of the cell wall. We have previously described a Candida albicans chitin synthase, CHS1. The DNA and derived protein sequences of a second gene, CHS2, are presented and compared with previously published gene sequences. Northern blot analysis shows that strikingly different levels of synthase 1 and 2 expression occur during yeast and hyphal phases of Candida growth.
Molecular analysis and expression of a Borrelia burgdorferi gene encoding a 22kDa protein (pC) in Escherichia coli
Authors: Fuchs R. , Jauris S. , Lottspeich F. , Preac‐Mursic V. , Wilske B. , Soutschek E. 
Published: October 2006

SummaryWe describe the cloning and expression of the pc gene which encodes a major immunodominant protein of Borrelia burgdorferi, the causative agent of Lyme borreliosis. The pC protein was purified from lysates of B. burgdorferi strain PKo. After tryptic digestion of the pC protein the resulting oligopeptides were applied to a gas‐phase sequenator. Thus partial amino acid sequences were obtained. The deduced oligonucleotides were used as hybridization probes. After Southern blotting a reactive band in the 3 kb range of PstI‐digested genomic DNA was detected. The insertion of these fragments into pUC vectors finally resulted in pc‐positive Escherichia coli clones. The gene (encoding a protein with 212 amino acids) was expressed in E. coli with varying deletions at the 5′ end. A sequence comparison with other outer membrane proteins of B. burgdorferi indicates a processing of pC that is similar to that of lipoproteins.
Protein‐specific features of the general secretion pathway in yeast: the secretion of acid phosphatase
Authors: Haguenauer‐Tsapis Rosine 
Published: October 2006

SummaryThe major phosphate‐repressible acid phosphatase (APase) of Saccharomyces cerevisiae, a cell wall glycoprotein, has been extensively used as a reporter protein to analyse successive steps in the yeast secretory pathway. In contrast to other yeast secretory proteins, APase can still be translocated into the endoplasmic reticulum (ER) even when it is made without its signal peptide. This property illustrates the permissiveness of targeting to the ER in yeast. Studies on APase‐containing hybrid proteins have provided some of the evidence that specific soluble factors must interact with secretory proteins prior to their translocation across the ER membrane. A systematic analysis of mutations affecting the sequence of the APase signal peptide cleavage site demonstrated that cleavage occurs only when the last amino acid of the signal sequence is small and neutral. This was one of the first studies to verify the requirements for signal peptidase cleavage that had previously only been predicted from statistical analysis. Studies performed either with inhibitors of glycosylation or with mutant APases demonstrated the critical role of core glycosylation for APase folding, which is essential for efficient transport beyond the ER. Following the fate of particular modified APases along the secretory pathway provided insights into some general properties of the secretory apparatus and illustrated the specific requirements for a given protein during its intracellular traffic.
Zygotic induction of plasmid ssb and psiB genes following conjugative transfer of Incl1 plasmid Collb‐P9
Authors: Jones A. Louise , Barth Peter T. , Wilkins Brian M. 
Published: October 2006

SummaryThe Incl1 conjugative plasmid Collb‐P9 carries a psiB gene that prevents induction of the SOS response in host bacteria. This locus is located 2.5 kb downstream of the ssb (single‐stranded DNA‐binding protein) gene in the leading region. This portion of Collb is strikingly similar to part of the leading region of the otherwise distinct F plasmid. Expression of psiB and ssb is increased when the host cell is exposed to an SOS‐inducing treatment or the Collb transfer system is derepressed. Moreover, expression of both genes on a derepressed plasmid is strongly enhanced in conjugatively infected recipient cells. Carriage of the psiB gene by Collb is shown to prevent a low level of SOS induction following conjugation. Plasmid ssb and psiB genes may function to promote installation of the replicon in the new cell.
Involvement of FtsZ in coupling of nucleoid separation with septation
Authors: Tétart Françoise , Albigot Renaud , Confer Annie , Mulder Egbert , Bouché Jean‐Pierre 
Published: October 2006

SummaryThe cell‐cycle parameters of an Escherichia coli strain expressing essential division gene ftsZ at one‐fifth of its normal level, because of antisense regulation by DicF RNA, have been analysed. Inhibition of FtsZ expression affects neither the generation time nor the replication initiation mass, the C period, or the constriction period, but it does dramatically retard the initiation of constriction relative to replication termination. Separation of the nucleoids is equally postponed, indicating that division is not coupled to termination of replication, but to partitioning. The severe inhibition of nucleoid separation by DicF RNA, and its suppression by overproduction of FtsZ, suggest a role for FtsZ in the control of separation, and consequently in the coupling of separation and division. We suggest that the normal pattern of nucleoid separation previously found in cells deficient in ftsZ function was a consequence of the loss of a negative effect exerted by FtsZ on separation. In agreement with this view, we find that nucleoid separation is temporarily inhibited after arrest of FtsZ synthesis, but is later resumed as FtsZ is further diluted into the elongating filaments.
Identification of replication and stability functions in the complete nucleotide sequence of plasmid pUH24 from the cyanobacterium Synechococcus sp. PCC 7942
Authors: Van der Plas Jan , Oosterhoff‐Teertstra Renske , Borrias Mies , Weisbeek Peter 
Published: October 2006

SummaryThe complete nucleotide sequence is presented for pUH24, the small plasmid of Synechococcus sp. PCC 7942. pUH24 consists of 7835bp and has a G+C content of 59%. The distribution of translation start and stop codons in the sequence allows 36 open reading frames that potentially encode polypeptides of 50 or more amino acids. We postulate that eight of these open reading frames are actual coding sequences. A region has been identified, by experiment, that contains two functions, designated pmaA and pmaB, involved in the segregational stability of the plasmid. The minimal region of pUH24 fully capable of supporting autonomous replication consists of a 3.6kb DNA fragment, which is almost entirely occupied by two overlapping genes most likely coding for essential replication proteins (repA and repB).
Protein A–calmodulin fusions: a novel approach for investigating calmodulin function in yeast
Authors: Stirling Douglas A. , Petrie Alison , Pulford David J. , Paterson David T. W. , Stark Michael J. R. 
Published: October 2006

SummaryA novel gene fusion approach which may be of more general use has been developed for investigating the function of calmodulin in the budding yeast Saccharomyces cerevisiae. By fusing a portion of the Staphylococcus aureus spa gene (encoding protein A) to CMD1, the S. cerevisiae gene encoding calmodulin, we have generated a yeast calmodulin with an affinity tag able to bind immunoglobulins. The chimaeric protein A–calmodulin (ProtA–CaM) polypeptide functions in vivo and shows Ca2+‐dependent binding to calmodulin target proteins. The spa–CMD1 fusion has been used (i) to prepare (by affinity chromatography) a fraction of yeast proteins which interact with calmodulin, (ii) to isolate genes encoding calmodulin target proteins by direct screening of an expression library, and (iii) to visualize calmodulin‐binding proteins in crude extracts by Western blot analysis.
Characterization of naturally elaborated blebs from serum‐susceptible and serum‐resistant strains of Neisseria gonorrhoeae
Authors: Pettit Robin K. , Judd Ralph C. 
Published: October 2006

SummaryOuter‐membrane blebs from two serum‐susceptible and two serum‐resistant strains of Neisseria gonorrhoeae were characterized. In general, bleb surfaces resembled cell surfaces, but there were qualitative and quantitative protein differences in blebs released by serum‐susceptible and serum‐resistant strains. Relative to blebs from serum‐resistant strains, blebs from serum‐susceptible strains expressed reduced amounts of major outer‐membrane proteins I and III, and little if any 68 000 Dalton outer‐membrane protein.