bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of signalling in the sporulation phosphorelay
Authors: Stephenson Keith , Hoch James A. 
Published: March 2003

SummaryTwo‐component and phosphorelay signal transduction systems are believed to function as environ‐mental sensors that programme gene expression to the composition of the ecological niche in which a microbe normally resides. The question of how evolutionarily related bacteria that occupy different environments change their signal transduction pathways to adapt to such environments was asked of the sporulation phosphorelay of Bacillus subtilis, Bacillus halodurans, Bacillus anthracis and Bacillus stearothermophilus. Comparison of the primary amino acid sequence of phosphorelay proteins with the known structural and interactive properties of the B. subtilis proteins revealed that the amino acid residues of interaction surfaces between phosphorelay proteins and between a phosphorelay protein and DNA resist evolutionary change. The absolute conservation of interaction surfaces allowed the identification of sporulation sensor kinases in B. halodurans, B. anthracis and B. stearothermophilus. In these sensor kinases, the signal‐sensing domains are vastly different in size and subdomain composition, with little apparent conservation between species, whereas the catalytic domains of these sensor kinases retain the high level of homology observed for the other phosphorelay proteins. Adaptation to new environments appears to result in rapid evolution of signalling domains to maximize environmental impact while maintaining identical protein–protein and protein–DNA contacts in the entire phosphorelay. In Clostridial genomes, only the Spo0A protein was found, suggesting that the anaerobic relatives of the Bacilli do not use a phosphorelay and phosphorylate Spo0A directly with sensor kinases.
Conjugative transposons: the tip of the iceberg
Authors: Burrus Vincent , Pavlovic Guillaume , Decaris Bernard , Guédon Gérard 
Published: March 2003

SummaryElements that excise and integrate, such as prophages, and transfer by conjugation, such as plasmids, have been found in various bacteria. These elements appear to have a diversified set of characteristics including cell‐to‐cell contact using pili or cell aggregation, transfer of single‐stranded or double‐stranded DNA, low or high specificity of integration and serine or tyrosine recombinases. This has led to a highly heterogeneous nomenclature, including conjugative transposons, integrative ‘plasmids’, genomic islands and numerous unclassified elements. However, all these elements excise by site‐specific recombination, transfer the resulting circular form by conjugation and integrate by recombination between a specific site of this circular form and a site in the genome of their host. Whereas replication of the circular form probably occurs during conjugation, this replication is not involved in the maintenance of the element. In this review, we show that these elements share very similar characteristics and, therefore, we propose to classify them as integrative and conjugative elements (ICEs). These elements evolve by acquisition or exchanges of modules with various transferable elements including at least ICEs and plasmids. The ICEs are probably widespread among the bacteria.
Primary and secondary metabolism, and post‐translational protein modifications, as portrayed by proteomic analysis of Streptomyces coelicolor
Authors: Hesketh A. R. , Chandra G. , Shaw A. D. , Rowland J. J. , Kell D. B. , Bibb M. J. , Chater K. F. 
Published: March 2003

SummaryThe newly sequenced genome of Streptomyces coelicolor is estimated to encode 7825 theoretical proteins. We have mapped approximately 10% of the theoretical proteome experimentally using two‐dimensional gel electrophoresis and matrix‐assisted laser desorption ionization time‐of‐flight (MALDI‐TOF) mass spectrometry. Products from 770 different genes were identified, and the types of proteins represented are discussed in terms of their anno‐tated functional classes. An average of 1.2 proteins per gene was observed, indicating extensive post‐translational regulation. Examples of modification by N‐acetylation, adenylylation and proteolytic processing were characterized using mass spectrometry. Proteins from both primary and certain secondary metabolic pathways are strongly represented on the map, and a number of these enzymes were identified at more than one two‐dimensional gel location. Post‐translational modification mechanisms may therefore play a significant role in the regulation of these pathways. Unexpectedly, one of the enzymes for synthesis of the actinorhodin polyketide antibiotic appears to be located outside the cytoplasmic compartment, within the cell wall matrix. Of 20 gene clusters encoding enzymes characteristic of secondary metabolism, eight are represented on the proteome map, including three that specify the production of novel metabolites. This information will be valuable in the characterization of the new metabolites.
A novel repressor of nif and glnA expression in the methanogenic archaeon Methanococcus maripaludis
Authors: Lie Thomas J. , Leigh John A. 
Published: March 2003

SummaryNitrogen assimilation in the methanogenic archaeon Methanococcus maripaludis is regulated by transcriptional repression involving a palindromic ‘nitrogen operator’ repressor binding sequence. Here we report the isolation of the nitrogen repressor, NrpR, from M. maripaludis using DNA affinity purification. Deletion of the nrpR gene resulted in loss of nitrogen operator binding activity in cell extracts and loss of repression of nif (nitrogen‐fixation) and glnA (glutamine synthetase) gene expression in vivo. Genetic complementation of the nrpR mutation restored all functions. NrpR contained a putative N‐terminal winged helix–turn–helix motif followed by two mutually homologous domains of unknown function. Comparison of the migration of NrpR in gel‐filtration chromatography with its subunit molecular weight (60 kDa) suggested that NrpR was a tetramer. Several lines of evidence suggested that the level of NrpR itself is not regulated, and the binding affinity of NrpR to the nitrogen operator is controlled by an unknown mechanism. Homologues of NrpR were found only in certain species in the kingdom Euryarchaeota. Full length homologues were found in Methanocaldococcus jannaschii and Methanothermobacter thermoautotrophicus, and homologues lacking one or more of the three polypeptide domains were found in Archaeoglobus fulgidus, Methanopyrus kandleri, Methanosarcina acetivorans, and Methanosarcina mazei. NrpR represents a new family of regulators unique to the Euryarchaeota.
A conserved sequence at the C‐terminus of MinD is required for binding to the membrane and targeting MinC to the septum
Authors: Hu Zonglin , Lutkenhaus Joe 
Published: March 2003

SummaryMinD is a key component of an oscillatory system that spatially regulates cell division in Escherichia coli. It is a peripheral membrane ATPase that recruits MinC and oscillates between the two halves of the cell in a MinE dependent manner. In vitro MinD binds to phospholipid vesicles in an ATP‐dependent manner and is released through MinE‐stimulated ATP hydrolysis. In this study we examined the function of the conserved C‐terminus of MinD. Short truncations of three and ten amino acids dramatically decreased the ability of MinD to localize to the membrane and spatially regulate division. These truncations bound MinC but were deficient in targeting MinC to the septum. In vitro they dimerized, but were deficient in binding to phospholipid vesicles and undergoing MinE stimulation. We suggest a model in which the ATP‐dependent dimerization of MinD affects the conformation of the C‐terminal region, a potential amphipathic helix, triggering membrane binding.
AREA directly mediates nitrogen regulation of gibberellin biosynthesis in Gibberella fujikuroi, but its activity is not affected by NMR
Authors: Mihlan Martina , Homann Veronika , Liu Ta‐Wei D. , Tudzynski Bettina 
Published: March 2003

SummaryAREA (NIT2) is a general transcription factor involved in derepression of numerous genes responsible for nitrogen utilization in Gibberella fujikuroi and many other fungi. We have previously shown that the deletion of areA‐GF resulted in mutants with significantly reduced gibberellin (GA) production. Here we demonstrate that the expression level of six of the seven GA biosynthesis genes is drastically reduced in mutants lacking areA. Furthermore, we show that, despite the fact that GAs are nitrogen‐free diterpenoid compounds, which are not obviously involved in nitrogen metabolism, AREA binds directly to the promoters of the six N‐regulated genes. The binding of AREA was analysed in more detail using the promoter of one of the GA‐biosynthesis genes encoding the ent‐kaurene oxidase (P450‐4). Deletion/mutation analysis of the P450‐4 promoter fused to the Escherichia coli uidA gene, which encodes β‐glucuronidase, allowed the in vivo identification of functional GATA motifs. We have also analysed the nmr gene of G. fujikuroi (nmr‐GF) which has high similarity to the Neurospora crassa nmr‐1 and Aspergillus nidulans nmrA genes, both involved in nitrogen metabolite repression. In contrast to our expectation, deletion of nmr‐GF did not result in significant derepression of the GA biosynthesis genes in the presence of ammonium, glutamine or glutamate. Overexpression of the nmr‐GF gene fused to the strong promoter of the G. fujikuroi glutamine synthetase (gs) gene revealed only a very slight repression of the nitrate reductase (niaD) gene, resulting in weak resistance to chlorate. Surprisingly, this effect was only observed in the presence of high amounts of glutamate; cultivation on ammonium failed to induce any resistance to chlorate. Despite the limited effect of gene replacement and overexpression of nmr‐GF on the nitrogen metabolism of G. fujikuroi itself, the gene fully restored nitrogen metabolite repression in A. nidulans and N. crassa nmr mutants. Therefore, we postulate that, in contrast to A. nidulans and N. crassa, NMR does not function independently as the main modulator of AREA in G. fujikuroi.
Acyl‐homoserine lactone acylase from Ralstonia strain XJ12B represents a novel and potent class of quorum‐quenching enzymes
Authors: Lin Yi‐Han , Xu Jin‐Ling , Hu Jiangyong , Wang Lian‐Hui , Ong Say Leong , Leadbetter Jared Renton , Zhang Lian‐Hui 
Published: March 2003

Summary N
‐acylhomoserine lactones (AHLs) are used as signal molecules by many quorum‐sensing Proteobacteria. Diverse plant and animal pathogens use AHLs to regulate infection and virulence functions. These signals are subject to biological inactivation by AHL‐lactonases and AHL‐acylases. Previously, little was known about the molecular details underlying the latter mechanism. An AHL signal‐inactivating bacterium, identified as a
Ralstonia
sp., was isolated from a mixed‐species biofilm. The signal inactivation encoding gene from this organism, which we call
aiiD
, was cloned and successfully expressed in
Escherichia coli
and inactivated three AHLs tested. The predicted 794‐amino‐acid polypeptide was most similar to the aculeacin A acylase (AAC) from
Actinoplanes utahensis
and also shared significant similarities with cephalosporin acylases and other N‐terminal (Ntn) hydrolases. However, the most similar homologues of AiiD are deduced proteins of undemonstrated function from available
Ralstonia
,
Deinococcus
and
Pseudomonas
genomes. LC‐MS analyses demonstrated that AiiD hydrolyses the AHL amide, releasing homoserine lactone and the corresponding fatty acid. Expression of AiiD in
Pseudomonas aeruginosa PAO1 quenched quorum sensing by this bacterium, decreasing its ability to swarm, produce elastase and pyocyanin and to paralyse nematodes. Thus, AHL‐acylases have fundamental implications and hold biotechnological promise in quenching quorum sensing.
Regulation of the central glycolytic genes in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose‐1,6‐bisphosphate
Authors: Doan Thierry , Aymerich Stéphane 
Published: March 2003

SummaryGlycolysis is one of the best and widely conserved general metabolic pathways. Bacillus subtilis enzymes catalysing the central part of glycolysis, gathering the steps of interconversion of the triose phosphates from dihydroxyacetone‐phosphate to phosphoenolpyruvate, are encoded by five genes, gapA, pgk, tpi, pgm and eno. They are transcribed in a hexacistronic operon together with cggR, the first cistron, encoding the repressor of this gapA operon. Using deletion analysis, we have localized the CggR operator between the promoter and the first gene of the operon. CggR was purified and used in gel mobility shift assays and DNase I footprinting experiments to delimit its target sequence. Site‐directed mutagenesis and in vivo tests demonstrated that it consists of two direct‐repeats (CGGGACN6TGTCN4CGGGACN6TG TC). Sequence analysis and transcriptome comparison of a wild‐type and a cggR mutant strain strongly suggested that CggR regulates only the gapA operon. The presence of glycolytic carbon sources induces expression of the gapA operon. Genetic experiments allowed us to identify the metabolic steps required for the formation of the CggR effector. In vitro experiments with the suggested candidates allowed us to demonstrate that fructose‐1,6‐biphosphate (FBP) acts as an inhibitor of CggR DNA‐binding activity (10 mM for full inhibition). FBP is thus the major signal for both CcpA‐dependent catabolite repression (or activation) and activation of the central glycolytic genes. Genomic sequence comparisons suggest that these results can apply to numerous low‐G+C, Gram‐positive bacterial species.
Enteric nerve stimulation evokes a premature colonic migrating motor complex in mouse
Authors: Spencer N. J. , Bywater R. A. 
Published: March 2003

Abstract The effects of enteric nerve stimuli were investigated on spontaneously occurring colonic migrating motor complexes (CMMCs) in isolated mouse colon. Changes in circular smooth muscle tension were recorded simultaneously from the proximal, mid and distal regions of an in vitro preparation of whole mouse colon at 36 ± 1 °C. The CMMCs were recorded from all preparations with a mean interval between contractions ranging from 135.2 ± 9.3 to 163.3 ± 22.4 s. The CMMCs migrated spontaneously from the proximal to distal colon and were abolished by tetrodotoxin (1 μmol L−1). In approximately half of all trials (57 of 103, n = 31), trains of stimuli (20 Hz, 2–5 s, 1 ms, 40–70 V) delivered to the mid or distal regions of colon, during the intervals between CMMCs, elicited a premature CMMC. However, similar trains of stimuli delivered to the proximal colon were without similar effects (33 trials, n = 13). It is suggested that in isolated whole mouse colon, CMMCs can be evoked prematurely by trains of electrical stimuli applied to the enteric nerves. The observation that nerve stimuli failed to evoke a premature CMMC from the proximal colon suggests that selective activation of functional ascending pathways may be required to initiate a premature CMMC.
Degeneration of the cerebellar granule cell layer in transgenic mice expressing genes of human foamy virus
Authors: Lampe  , Marino  , Rethwilm  , Aguzzi  
Published: March 2003

J. Lampe, S. Marino, A. Rethwilm and A. Aguzzi (1998) Neuropathology and Applied Neurobiology24, 36–43Degeneration of the cerebellar granule cell layer in transgenic mice expressing genes of human foamy virusTransgenic mice expressing various combinations of structural and regulatory genes of human foamy virus (HFV) develop a neurodegenerative syndrome. Δgpe transgenic mice (which express the auxiliary bel‐1 and bet genes along with truncated forms of gag, pol, and env) develop a severe neurological syndrome consisting mainly of spastic tetraparesis and blindness, and show neuronal loss in the hippocampus and cerebral cortex. In addition, mice in two of eight Δgpe lines developed an ataxic gait. Here we studied the phenotype of these two lines, and show that these mice exhibit progressive degeneration of their cerebellar granule cells beginning at 4–8 weeks of age. Transgenic mRNA and HFV proteins accumulate in cerebellar granule cells immediately before the onset of degeneration. The Purkinje cell layer is largely unaffected by this pathological process. Probably due to the loss of granule cell processes, the cerebellar molecular layer is narrowed in the late stages of the disease. These findings indicate that HFV gene products can be neurotoxic for cerebellar granule cells.
Changes in neuron size in cynomolgus macaques infected with various immunodeficiency viruses and poliovirus
Authors: Montgomery  , Wood  , Stott  , Sharp  , Luthert  
Published: March 2003

gabctgChanges in neuron size in cynomolgus macaques infected with various immunodeficiency viruses and poliovirusHuman immunodeficiency virus (HIV) infection leads to clinically significant neuronal pathology, but the underlying mechanism remains unclear. Infection of rhesus macaques with the simian immunodeficiency virus SIVmac251has been shown to cause atrophy of hippocampal pyramidal cells. The aim of the current investigation was to determine whether SIVmac251and other viruses with differing abilities to cause immune suppression or encephalitis could cause neuronal atrophy in cynomolgus macaques. Animals infected with SIVmac251(n=22), HIV‐2 (n=6), SIVmac239(n=7) and poliovirus (n=10) were investigated, together with 16 controls. Hippocampal pyramidal cell diameter, averaged across the four CA subfields, was reduced by 16.6% in the SIVmac251group (P<0.0001) and by 13.3% in the HIV‐2 group (P<0.001), even though the latter virus does not generally cause immunosuppression. Conversely, SIVmac239 , which does cause immunosuppression, caused an average neuronal hypertrophy of 6.8% (P=0.033). Of possible relevance to the different behaviour of the two SIVs is that SIVmac239is lymphocyte tropic and does not infect CNS microgliain vivowhereas SIVmac251does. Animals inoculated with poliovirus into the lumbar spinal cord for polio vaccine neurovirulence testing acted as positive controls for CNS inflammation and they also showed an increase in neuronal diameter (4.1%,P=0.025). The atrophy seen with SIVmac251and HIV‐2 involved all CA subfields but the hypertrophy following SIVmac239or poliovirus infection was restricted to CA1 and CA2. These observations show a dissociation between the ability of immunodeficiency viruses to cause immune suppression and neuronal pathology and demonstrate that CNS inflammation per se may cause neuronal hypertrophy.
Evidence for an ischaemic origin of deep white matter lesions in the ageing brain
Authors: Ince P. G. , Fernando M. ,   on behalf of the MRC Cognitive Function and Ageing Neuropathology Study
Published: March 2003

Introduction:  The pathogenesis of white matter lesions (WMLs) is not established. Evidence from clinical,. pathological and pathophysiological studies favours a vascular mechanism for subcortical WMLs (DWML) and a nonischaemic origin for periventricular (PV) hyperintensities. Small vessel degeneration giving rise to ischaemia is the hypothetical origin for subcortical WMLs.Methods:  PV lesions (PVL) and deep subcortical lesions (DWML) demonstrated in MRI scans of fixed coronal brain slices, from elderly postmortem brain donors to the MRC CFAS(N) cohort, were sampled together with nonlesional WM from the same brains. Immunohistochemistry was performed to detect activated microglia (CD68), endothelial activation (ICAM‐1), capillary basement membrane (Collagen IV), and hypoxia‐inducible factor‐1α (HIF‐1α) expression. Quantitative analysis of microvasculature was performed with digital images using Image Pro Plus software. The sample consisted of 18 PV (seven nonlesional) and 23 DWML (11 nonlesional) regions from 15 subjects. Statistical analysis was performed using SPSS software.Results:  Vascular changes in arterioles were related to ML and not to dementia. DWML arterioles had thicker walls (P < 0.001; 95%CI = 5.6–8.4), bigger external diameters (P < 0.001; 95%CI = 7.7–17.8) and larger perivascular spaces (P < 0.05; 95%CI = 13.3–19.4) than nonlesional areas. Vascular lumen diameters remained the same. The ICAM‐1/Collagen 4 ratio was significantly elevated in lesional DWML (P = 0.001) but not in the periventricular regions (P = 0.85) reflecting capillary endothelial activation. HIF‐1α expression (P = 0.004) and presence of activated microglia (P = 0.001) were more frequent in DWML. The prevalence (χ2 = 0.053; P = 0.82) and absolute counts (P = 0.07) of HIF‐1α expression, and the presence of activated microglia (P = 0.95) in PVL were not increased over control WM.Discussion:  DWML show vascular degenerative changes in arterioles, reactive changes in capillaries and persistent HIF expression, all consistent with chronic ischaemia. The study raises the possibility that an age‐related impairment of the neovascular response to ischaemia results in WM lesions.
Cerebral palsy, low birthweight and socio‐economic deprivation: inequalities in a major cause of childhood disability
Authors: Dolk Helen , Pattenden Sam , Johnson Ann 
Published: March 2003

SummaryThere is currently little and conflicting evidence concerning the existence of socio‐economic inequalities in cerebral palsy prevalence, or the extent to which this is influenced by socio‐economic inequalities in low birthweight, a strong risk factor for cerebral palsy. The study is based on 753 children registered with cerebral palsy, resident in the former Oxford Regional Health Authority area and born in the years 1984–90. Two population definitions were used: 1. Children with cerebral palsy resident at birth in the area, with resident births as denominator, 2. Children with cerebral palsy resident at age 5 in the area, with children of ages 1–7 resident in the area in the 1991 census as denominator. Children with cerebral palsy and all births/children were classified according to the Carstairs area deprivation index (grouped into quintiles) of their ward of residence. The prevalence among residents at birth varied from 2.08 per 1000 births in the most affluent quintile to 3.33 in the most deprived quintile (trend P < 0.001). Although there was a tendency for children to move to more affluent areas during early childhood, the socio‐economic gradient was similar at age 5. A greater proportion of births in the more deprived quintiles were of low or very low birthweight, the proportion rising from 5.6% in the most affluent quintile to 8.2% in the most deprived. Within the normal birthweight category there was a trend for higher prevalence of cerebral palsy in more deprived quintiles, from 1.29 per 1000 in the most affluent quintile to 2.42 in the most deprived quintile (trend P < 0.001). Within the low birthweight and very low birthweight groups, separately or combined, there was no evidence of any relationship between cerebral palsy prevalence and deprivation. We estimate that up to 17% of cerebral palsy cases might be ‘preventable’ in terms of the reduction to be expected if the whole population had the rate of cerebral palsy of the most affluent quintile. Although the strong socio‐economic gradient for cerebral palsy was restricted to the normal birthweight category, we estimate that two‐thirds of the excess cases in the population associated with greater socio‐economic deprivation were normal birthweight cases, and one‐third were low birthweight cases owing to the greater prevalence of low birthweight in more deprived populations. The pattern of socio‐economic inequalities should be further explored in other regions, and should be taken into account in aetiological research, and in the effective delivery and evaluation of services.