bluuebunny/crossref_metadata_2025_split huggingface dataset:
A nuclear protein in Schizosaccharomyces pombe with homology to the human tumour suppressor Fhit has decapping activity
Authors: Salehi Zivar , Geffers Lars , Vilela Cristina , Birkenhäger Ralf , Ptushkina Marina , Berthelot Karine , Ferro Myriam , Gaskell Simon , Hagan Iain , Stapley Ben , McCarthy John E. G. 
Published: March 2003

SummaryA number of eukaryotic proteins are already known to orchestrate key steps of mRNA metabolism and translation via interactions with the 5′ m7GpppN cap. We have characterized a new type of histidine triad (HIT) motif protein (Nhm1) that co‐purifies with the cap‐binding complex eIF4F of Schizosaccharomyces pombe. Nhm1 is an RNA‐binding protein that binds to m7GTP‐Sepharose, albeit with lower specificity and affinity for methylated GTP than is typical for the cap‐binding protein known as eukaryotic initiation factor 4E. Sequence searches have revealed that proteins with strong sequence similarity over all regions of the new protein exist in a wide range of eukaryotes, yet none has been characterized up to now. However, other proteins that share specific motifs with Nhm1 include the human Fhit tumour suppressor protein and the diadenosine 5′, 5′′′‐P1, P4‐tetraphosphate asymmetrical hydrolase of S. pombe. Our experimental work also reveals that Nhm1 inhibits translation in a cell‐free extract prepared from S. pombe, and that it is therefore a putative translational modulator. On the other hand, purified Nhm1 manifests mRNA decapping activity, yet is physically distinct from the Saccharomyces cerevisiae decapping enzyme Dcp1. Moreover, fluorescence and immunofluorescence microscopy show that Nhm1 is predominantly, although not exclusively, nuclear. We conclude that Nhm1 has evolved as a special branch of the HIT motif superfamily that has the potential to influence both the metabolism and the translation of mRNA, and that its presence in S. pombe suggests the utilization of a novel decapping pathway.
Molecular and functional analysis of the type III secretion signal of the Salmonella enterica InvJ protein
Authors: Rüssmann Holger , Kubori Tomoko , Sauer Jeannette , Galán Jorge E. 
Published: March 2003

SummaryCentral to the pathogenicity of Salmonella enterica is the function of a type III secretion system (TTSS) encoded within a pathogenicity island at centisome 63 (SPI‐1). An essential component of this system is a supramolecular structure termed the needle complex. Proteins to be delivered into host cells possess specific signals that route them to the type III secretion pathway. In addition, some bacterial proteins have signals that deliver them to the secretion complex to either become their structural components or exert their function at that location. One of these proteins is InvJ, which controls the length of the needle substructure of the needle complex. In this study, we have analysed the signal that targets InvJ to the TTSS. We found that amino acid residues 4 to 7 of InvJ are necessary and sufficient to mediate secretion of InvJ or a reporter protein in a TTSS‐dependent manner. InvJ secretion was found to be essential for its function in needle length determination, effector protein secretion and bacterial invasion of epithelial cells. Frameshift mutagenesis analysis indicated that the InvJ type III secretion signal sequence tolerates significant alterations in its amino acid sequence without affecting InvJ secretion. Introduction of silent mutations in the secretion signal coding sequence that result in drastically different predicted mRNA folds had no effect on InvJ secretion or expression.
Requirement of spermidine for developmental transitions in Aspergillus nidulans
Authors: Jin Yuan , Bok Jin Woo , Guzman‐de‐Peña Doralinda , Keller Nancy P. 
Published: March 2003

SummaryDeletion of the spermidine synthase gene in the fungus Aspergillus nidulans results in a strain, ΔspdA, which requires spermidine for growth and accumulates putrescine as the sole polyamine. Vegetative growth but not sporulation or sterigmatocystin production is observed when ΔspdA is grown on media supplemented with 0.05–0.10 mM exogenous spermidine. Supplementation of ΔspdA with ≥ 0.10 mM spermidine restores sterigmatocystin production and ≥ 0.50 mM spermidine produces a phenotype with denser asexual spore production and decreased radial hyphal growth compared with the wild type. ΔspdA spores germinate in unsupplemented media but germ tube growth ceases after 8 h upon which time the spores swell to approximately three times their normal diameter. Hyphal growth is resumed upon addition of 1.0 mM spermidine. Suppression of a G protein signalling pathway could not force asexual sporulation and sterigmatocystin production in ΔspdA strains grown in media lacking spermidine but could force both processes in ΔspdA strains supplemented with 0.05 mM spermidine. These results show that increasing levels of spermidine are required for the transitions from (i) germ tube to hyphal growth and (ii) hyphal growth to tissue differentiation and secondary metabolism. Suppression of G protein signalling can over‐ride the spermidine requirement for the latter but not the former transition.
The histidine kinase Hik33 perceives osmotic stress and cold stress in Synechocystis sp. PCC 6803
Authors: Mikami Koji , Kanesaki Yu , Suzuki Iwane , Murata Norio 
Published: March 2003

SummaryThe stress imposed on living organisms by hyperosmotic conditions and low temperature appears to be perceived via changes in the physical state of membrane lipids. We compared genome‐wide patterns of transcription between wild‐type Synechocystis sp. PCC 6803 and cells with a mutation in the histidine kinase Hik33 using a DNA microarray. Our results indicated that Hik33 regulated the expression of both osmostress‐inducible and cold‐inducible genes. The respective genes that were regulated by Hik33 under hyperosmotic and low‐temperature conditions were, for the most part, different from one another. However, Hik33 also regulated the expression of a set of genes whose expression was induced both by osmotic stress and by cold stress. These results indicate that Hik33 is involved in responses to osmotic stress and low‐temperature stress but that the mechanisms of the responses differ.
Subcellular localization of the Bacillus subtilis structural maintenance of chromosomes (SMC) protein
Authors: Lindow Janet C. , Kuwano Masayoshi , Moriya Shigeki , Grossman Alan D. 
Published: March 2003

SummaryThe Bacillus subtilis structural maintenance of chromosomes (SMC) protein is a member of a large family of proteins involved in chromosome organization. We found that SMC is a moderately abundant protein (∼1000 dimers per cell). In vivo cross‐linking and immunoprecipitation assays revealed that SMC binds to many regions on the chromosome. Visualization of SMC in live cells using a fusion to the green fluorescent protein (GFP) and in fixed cells using immunofluorescence microscopy indicated that a portion of SMC localizes as discrete foci in positions similar to that of the DNA replication machinery (replisome). When visualized simultaneously, SMC and the replisome were often in similar regions of the cell but did not always co‐localize. Persistence of SMC foci did not depend on ongoing replication, but did depend on ScpA and ScpB, two proteins thought to interact with SMC. Our results indicate that SMC is bound to many sites on the chromosome and a concentration of SMC is localized near replication forks, perhaps there to bind and organize newly replicated DNA.
A central regulator of morphological differentiation in the multicellular bacterium Streptomyces coelicolor
Authors: Nguyen Kien T. , Willey Joanne M. , Nguyen Liem D. , Nguyen Lieu T. , Viollier Patrick H. , Thompson Charles J. 
Published: March 2003

SummaryIn the multicellular bacterium Streptomyces coelicolor, functions of developmental (bald) genes are required for the biosynthesis of SapB, a hydrophobic peptidic morphogen that facilitates aerial hyphae formation. Here, we show that aerial hyphal growth and SapB biosynthesis could be activated independently from the normal developmental cascade by providing unprogrammed expression of functionally interactive genes within the ram cluster. ramC, ramS and ramR were essential for normal growth of aerial hyphae, and ramR, a response regulator gene, was a key activator of development. The ramR gene restored growth of aerial hyphae and SapB formation in all bald strains tested (albeit only weakly in the bldC mutant), many of which are characterized by physiological defects. Disruption of the ramR gene abolished SapB biosynthesis and severely delayed growth of aerial hyphae. Transcription of ramR was developmentally controlled, and RamR function in vivo depended on its putative phosphorylation site (D53). We identified and mapped RamR targets immediately upstream of the region encoding ramC and ramS, a putative operon. Overexpression of ramR in the wild‐type strain increased SapB levels and caused a distinctive wrinkled surface topology. Based on these results, we propose that phenotypes of bald mutations reflect an early stage in the Streptomyces developmental programme similar to the spo0 mutations in the unicellular bacterium Bacillus subtilis, and that RamR has analogies to Spo0A, the Bacillus response regulator that integrates physiological signals before triggering endospore formation.
Impact of large chromosomal inversions on the adaptation and evolution of Pseudomonas aeruginosa chronically colonizing cystic fibrosis lungs
Authors: Kresse Andreas U. , Dinesh Sriramulu D. , Larbig Karen , Römling Ute 
Published: March 2003

Summary Pseudomonas aeruginosa chronically colonizing the lungs of cystic fibrosis (CF) patients undergoes fast evolution leading to clonal divergence. More than half of the genotypes of P. aeruginosa clone C isolates exclusively from CF lung infection exhibit large chromosomal inversions (LCIs). To analyse the impact of LCIs, as a novel mechanism of bacterial adaptation, the underlying molecular mechanism was examined. Analysis of inversion breakpoints suggested an IS6100‐induced coupled insertion‐inversion mechanism. A selective advantage was created by insertion of IS6100 into wbpM, pilB and mutS which leads to common CF phenotypes such as O‐antigen and type IV pili deficiency and hypermutability. Speciation in bacteria is accompanied by LCIs. Therefore adaptation by LCIs that allows persistence of P. aeruginosa in the CF lung and species diversification in that new ecological niche can serve as a model for bacterial genome evolution.
The identification of circular extrachromosomal DNA in the nuclear genome ofTrypanosoma brucei
Authors: Alsford N. S. , Navarro M. , Jamnadass H. R. , Dunbar H. , Ackroyd M. , Murphy N. B. , Gull K. , Ersfeld K. 
Published: March 2003

SummaryNuclear extrachromosomal DNA elements have been identified in several kinetoplastids such asLeishmaniaandTrypanosoma cruzi, but never inTrypanosoma brucei. They can occur naturally or arise spontaneously as the result of sublethal drug exposure of parasites. In most cases, they are represented as circular elements and are mitotically unstable. In this study we describe the presence of circular DNA in the nucleus ofTrypanosoma brucei. This novel type of DNA was termed NR‐element (NlaIIIrepeat element). In contrast to drug‐induced episomes in other kinetoplastids, theT. bruceiextrachromosomal NR‐element is not generated by drug selection. Furthermore, the element is stable during mitosis over many generations. Restriction analysis of tagged NR‐element DNA, unusual migration patterns during pulsed field gel electrophoresis (PFGE) and CsCl/ethidium bromide equilibrium centrifugation demonstrates that the NR‐element represents circular DNA. Whereas it has been found in all field isolates of the parasites we analysed, it is not detectable in some laboratory strains notably the genome reference strain 927. The DNA sequence of this element is related to a 29 bp repeat present in the subtelomeric region of VSG‐bearing chromosomes ofT. brucei. It has been suggested that this subtelomeric region is part of a transition zone on chromosomes separating the relatively stable telomeric repeats from the recombinationaly active region downstream of VSG genes. Therefore, we discuss a functional connection between the occurrence of this circular DNA and subtelomeric recombination events inT. brucei.
Class V chitin synthase determines pathogenesis in the vascular wilt fungus Fusarium oxysporum and mediates resistance to plant defence compounds
Authors: Madrid Martan P. , Di Pietro Antonio , Roncero M. Isabel G. 
Published: March 2003

SummaryChitin, a β‐1,4‐linked polysaccharide of N‐acetylglucosamine, is a major structural component of fungal cell walls. Fungi have multiple classes of chitin synthases that catalyse N‐acetylglucosamine polymerization. Here, we demonstrate the requirement for a class V chitin synthase during host infection by the vascular wilt pathogen Fusarium oxysporum. The chsV gene was identified in an insertional mutagenesis screen for pathogenicity mutants. ChsV has a putative myosin motor and a chitin synthase domain characteristic of class V chitin synthases. The chsV insertional mutant and a gene replacement mutant of F. oxysporum display morphological abnormalities such as hyphal swellings that are indicative of alterations in cell wall structure and can be partially restored by osmotic stabilizer. The mutants are unable to infect and colonize tomato plants or to grow invasively on tomato fruit tissue. They are also hypersensitive to plant antimicrobial defence compounds such as the tomato phytoanticipin α‐tomatine or H2O2. Reintroduction of a functional chsV copy into the mutant restored the growth phenotype of the wild‐type strain. These data suggest that F. oxysporum requires a specific class V chitin synthase for pathogenesis, most probably to protect itself against plant defence mechanisms.
DNA binding properties of the HrmR protein of Nostoc punctiforme responsible for transcriptional regulation of genes involved in the differentiation of hormogonia
Authors: Campbell Elsie L. , Wong Francis C. Y. , Meeks John C. 
Published: March 2003

Summary Nostoc punctiforme
is an example of a filamentous cyanobacterium that is capable of differentiating non‐growing cells that constitute gliding filaments termed hormogonia. These gliding filaments serve in short distance dispersal and as infective units in establishing a symbiosis with plants, such as the bryophyte
Anthoceros punctatus
. Mutants of
N
.
punctiforme
exist which show elevated levels of initial infection of
A
.
punctatus
as a consequence of repeated cycles of hormogonium differentiation. Such mutations occur within the
hrmA
and
hrmU
genes. Further characterization of the
hrm
locus revealed several genes with an organizational and predicted protein sequence similarity to genes of heterotrophic bacteria that are involved in hexuronic acid metabolism. Genes in the
N. punctiforme
locus are transcribed in response to the presence of a plant extract containing hormogonium‐repressing factors. A predicted transcriptional repressor encoded in the locus, HrmR
,
was shown herein to be a specific DNA binding protein that regulates the transcription of its own gene and that of
hrmE
, a nearby gene. The ability of HrmR to bind DNA was abolished upon addition of either galacturonate or lysate from specifically induced
N
.
punctiforme
cells, implying that the
in vivo HrmR binding activity is modulated via an internal compound, most likely a sugar molecule.
A missense mutation in ftsZ differentially affects vegetative and developmentally controlled cell division in Streptomyces coelicolor A3(2)
Authors: Grantcharova Nina , Ubhayasekera Wimal , Mowbray Sherry L. , McCormick Joseph R. , Flärdh Klas 
Published: March 2003

Summary Streptomyces coelicolor
A3(2) undergoes at least two kinds of cell division: vegetative septation leading to cross‐walls in the substrate mycelium; and developmentally regulated sporulation septation in aerial hyphae. By isolation and characterization of a non‐sporulating
ftsZ
mutant, we demonstrate a difference between the two types of septation. The
ftsZ17
(Spo) allele gave rise to a classical
white
phenotype. The mutant grew as well as the parent on plates, and formed apparently normal hyphal cross‐walls, although with a small reduction in frequency. In contrast, sporulation septation was almost completely abolished, resulting in a phenotype reminiscent of
whiH
and
ftsZΔ2p
mutants. The
ftsZ17
(Spo) allele was partially dominant and had no detectable effect on the cellular FtsZ content. As judged from both immunofluorescence microscopy of FtsZ and translational fusion of
ftsZ
to
egfp
, the mutation prevented correct temporal and spatial assembly of Z rings in sporulating hyphae. Homology modelling of
S. coelicolor
FtsZ indicated that the mutation, an A249T change in the C‐terminal domain, would be expected to alter the protein on the lateral face of FtsZ protofilaments. The results suggest that cytokinesis may be developmentally controlled at the level of Z‐ring assembly during sporulation of
S. coelicolor A3(2).
Architecture of a protein central to iron homeostasis: crystal structure and spectroscopic analysis of the ferric uptake regulator
Authors: Pohl Ehmke , Haller Jon C. , Mijovilovich Ana , Meyer‐Klaucke Wolfram , Garman Elspeth , Vasil Michael L. 
Published: March 2003

SummaryIron is an essential element for almost all organisms, although an overload of this element results in toxicity because of the formation of hydroxyl radicals. Consequently, most living entities have developed sophisticated mechanisms to control their intracellular iron concentration. In many bacteria, including the opportunistic pathogen Pseudomonas aeruginosa, this task is performed by the ferric uptake regulator (Fur). Fur controls a wide variety of basic physiological processes including iron uptake systems and the expression of exotoxin A. Here, we present the first crystal structure of Fur from P. aeruginosa in complex with Zn2+ determined at a resolution of 1.8 Å. Furthermore, X‐ray absorption spectroscopic measurements and microPIXE analysis were performed in order to characterize the distinct zinc and iron binding sites in solution. The combination of these complementary techniques enables us to present a model for the activation and DNA binding of the Fur protein.
Versatility of inner membrane protein biogenesis in Escherichia coli
Authors: Fröderberg Linda , Houben Edith , Samuelson James C. , Chen Minyong , Park Sei‐Kyoung , Phillips Gregory J. , Dalbey Ross , Luirink Joen , De Gier Jan‐Willem L. 
Published: March 2003

SummaryTo further our understanding of inner membrane protein (IMP) biogenesis in Escherichia coli, we have accomplished the widest in vivo IMP assembly screen so far. The biogenesis of a set of model IMPs covering most IMP structures possible has been studied in a variety of signal recognition particle (SRP), Sec and YidC mutant strains. We show that the assembly of the complete set of model IMPs is assisted (i.e. requires the aid of proteinaceous factors), and that the requirements for assembly of the model IMPs into the inner membrane differ significantly from each other. This indicates that IMP assembly is much more versatile than previously thought.
Functions of the CckA histidine kinase in Caulobacter cell cycle control
Authors: Jacobs Christine , Ausmees Nora , Cordwell Stuart J. , Shapiro Lucy , Laub Michael T. 
Published: March 2003

SummaryThe CtrA master transcriptional regulator is a central control element in Caulobacter cell cycle progression and polar morphogenesis. Because of its critical role, CtrA activity is temporally regulated by multiple mechanisms including phosphorylation and ClpXP‐dependent degradation of CtrA. The CckA histidine kinase is known to contribute to CtrA phosphorylation. We show here that genes differentially expressed in a ctrA temperature‐sensitive (ts) mutant are similarly affected in a cckA ts mutant, that the phosphorylation of CckA coincides temporally with CtrA phosphorylation during the cell cycle, and that CckA is essential for viability because it is required for CtrA phosphorylation. Thus, it is the signal transduction pathway mediated by CckA that culminates in CtrA activation, which is temporally regulated and essential for cell cycle progression. CckA also positively regulates CtrA activity by a mechanism that is independent of CtrA phosphorylation. CtrA is more stable in the presence of CckA than it is absence, suggesting that CckA may also be involved, directly or indirectly, in the regulation of CtrA proteolysis.
Small intestinal dysmotility following abdominal irradiation in the rat small intestine
Authors: FRASER  , FRISBY  , BLACKSHAW  , SCHIRMER  , HOWARTH  , YEOH  
Published: March 2003

Abdominal symptoms such as diarrhoea, abdominal cramps and vomiting are common during and after abdominal radiotherapy for gynaecological and pelvic malignancy. It has recently been recognized that small intestinal dysmotility may contribute to these symptoms but the underlying mechanisms are unclear in part because of the technical difficulties inherent in performing studies in irradiated small intestine. The aim of the current study was to evaluate small intestinal motor activity using perfused micromanometric techniques in 6–8‐cm segments of ileum during arterial perfusion with isotonic oxygenated fluorocarbon solution. Intestinal segments from six rats were studied 4 days after treatment with 10 Gy abdominal irradiation. Ileal segments from nine nonirradiated animals acted as controls. For each experiment the total number of pressure waves, high‐amplitude (>20 mmHg, long‐duration >6 sec) pressure waves, and long (>20 associated) bursts of pressure waves were determined.Irradiation had no effect on the overall number of pressure waves, but increased high‐amplitude long‐duration (HALD) pressure waves (248 vs 7, P < 0.01). In control animals HALD waves were localized to a single recording site but after radiotherapy 74% of HALD waves were temporally associated with similar pressure waves in other manometric channels. Forty‐seven per cent of associated HALD waves migrated aborally. Retrograde migration of HALD waves was seen in five segments following irradiation. Irradiation abolished bursts of >20 pressure waves.High‐amplitude contractions which migrate aborally are likely to contribute to diarrhoea after abdominal irradiation. The in vitro small animal model of radiation enteritis will permit interventions to provide further insights into the mediation of intestinal dysmotility.