bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular genecology of temperature response in Lolium perenne: 2. association of AFLP markers with ecogeography
Authors: Skøt L. , Sackville Hamilton N. R. , Mizen S. , Chorlton K. H. , Thomas I. D. 
Published: March 2003

AbstractImproved winter hardiness is an important breeding objective in the forage grass Lolium perenne. This is a complex trait with several components, including the ability to survive and grow at low temperature, to acclimate to cold, tolerate wind, snow cover and ice encasement. Marker‐assisted selection has the potential to increase the efficiency of breeding for improved cold tolerance. Here we describe a genecological approach to identifying molecular markers that are associated with adaptation to low winter temperatures. AFLP was used to assess the genetic diversity in 29 wild populations of ryegrass (Lolium perenne) representing a pan‐European temperature cline in terms of their geographical origin. A further 18 populations from a temperature cline in Bulgaria were also analysed. In addition, two varieties and five populations representing parents of mapping families currently in use at IGER were included in the analysis. Principal coordinate (PCoA) and cluster analyses of the molecular marker data showed that the Bulgarian altitude cline populations could be distinguished clearly from the other populations. Two regression analyses were carried out; one to identify AFLP markers that correlated in frequency with low mean January temperature of the geographical origin of the population, and another to identify AFLP markers correlating in frequency with the cold tolerance phenotype of the populations, as determined by LT50 values in freezing tests. In the first analysis six AFLP markers showed significant type II trends with mean January temperature, and in the second analysis 28 bands had a significant univariate relationship with the LT50 value of the accessions. In steps 2 and 3 of the stepwise analysis a further 4 and 5 bands, respectively, improved the fit significantly. The results of the two types of regression analysis are discussed in relation to ecogeography and cold tolerance phenotype of the populations.
Chloroplast DNA variation, postglacial recolonization and hybridization in hazel, Corylus avellana
Authors: Palmé A. E. , G. G. Vendramin  
Published: March 2003

SummaryTo unravel the postglacial migration history of hazel, Corylus avellana, the genetic variation at two types of chloroplast DNA markers, polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) and microsatellites, was assessed in 26 natural hazel populations distributed across the range of C. avellana. In addition a sequence of 2468 base pairs, which contains the matK gene, was analysed in seven individuals. Very little variation was detected overall [hT:PCR‐RFLP= 0.091, hT:microsatellite= 0.423, π (nucleotide diversity) = 0.00093] but the microsatellite markers, which have the highest levels of variation, show a clear geographical structure that divides Europe into two areas: (i) Italy and the Balkans, on one hand and (ii) the rest of Europe, on the other hand. These data exclude Italy and the Balkans as possible origins of the postglacial recolonization but cannot unambiguously show which other area is the origin, since the genetic data does not indicate the direction of spread. If we take the pollen record into account, the most likely scenario would be an expansion from southwestern France into most of Europe except Italy and the Balkans, and then a local expansion in the latter area. The two main haplotypes identified with both PCR‐RFLP and sequencing, A and B, were found not only in C. avellana but also in other European Corylus species and cultivars. Haplotype A, which is dominating all investigated natural populations of C. avellana, is also found in the European tree hazel (C. colurna) and haplotype B, which is rare in C. avellana, has been identified in the filbert (C. maxima) and C. avellana cultivars. This pattern seems to indicate a history of past hybridization among the European Corylus species and cultivars.
Geographic patterns of population genetic structure inMytilocypris(Ostracoda: Cyprididae): interpreting breeding systems, gene flow and history in species with differing distributions
Authors: Finston Terrie 
Published: March 2003

AbstractSamples from 83 populations of salt lake Ostracods belonging to the genusMytilocypriswere collected from 74 saline lakes and ponds in the semi‐arid regions of Australia. These populations were examined for variation at six polymorphic enzyme loci to diagnose breeding systems and to measure population structure, to investigate relative levels of gene flow in species with differing distributions and hence different presumed dispersal capabilities. Despite the occurrence of some populations in disjunct, peripheral, and recent ephemeral habitats, all populations of each species were found to reproduce sexually. Gene flow does occur on a local basis and appears to be facilitated by occupation in the same drainage basin for some species. There was considerable gene pool fragmentation among peripheral populations of four of the five species. Only one species,M. mytiloides, was relatively homogeneous across its range. It may be that gene flow is non‐existent into peripheral populations because of poor dispersal abilities, or it may not be frequent enough to overcome local selective pressures. Regardless of these possibilities, the observed gene pool fragmentation has implications for allopatric speciation.
Genetic differentiation in the winter pine processionary moth (Thaumetopoea pityocampa — wilkinsoni complex), inferred by AFLP and mitochondrial DNA markers
Authors: Salvato Paola , Battisti Andrea , Concato Silvia , Masutti Luigi , Patarnello Tomaso , Zane Lorenzo 
Published: March 2003

AbstractThe winter pine processionary moth has become an important pine pest in the last century, as a consequence of the spread of pine cultivation in the Mediterranean region. The pattern of genetic differentiation of this group, that includes two sibling species (Thaumetopoea pityocampa and Th. wilkinsoni), has been studied in nine populations using amplified fragment length polymorphism (AFLP) and single strand conformation polymorphism‐sequence analysis (SSCP) of the mitochondrial cytochrome oxidase 1 (COI) and cytochrome oxydase 2 (COII). Results indicate the existence of strong genetic differentiation between the two species that became separated before the Quaternary ice ages. Moreover data indicate that Th. pityocampa has a strong geographical structure, particularly evident at the nuclear level, where all pairwise φST resulted to be highly significant and individuals from the same population resulted to be strongly clustered when an individual tree was reconstructed. The estimates of the absolute number of migrants between populations (Nm), obtained from mitochondrial and nuclear DNA markers, suggest that gene flow is low and that a gender‐related dispersal could occur in this species. The males appear to disperse more than females, contributing to the genetic diversity of populations on a relatively wide range, reducing the risks of inbreeding and the genetic loss associated with bottlenecks occurring in isolated populations.
Genetic and transcriptional analysis of absA, an antibiotic gene cluster‐linked two‐component system that regulates multiple antibiotics in Streptomyces coelicolor
Authors: Anderson Todd B. , Brian Paul , Champness Wendy C. 
Published: March 2003

In Streptomyces coelicolor, the AbsA1–AbsA2 two‐component system regulates the expression of multiple antibiotic gene clusters. Here, we show that the response regulator encoded by the absA2 gene is a negative regulator of these antibiotic gene clusters. A genetic analysis shows that the phosphorylated form of the AbsA2 response regulator (phospho‐AbsA2), generated by the cognate AbsA1 sensor histidine kinase, is required for normal growth phase regulation of antibiotic synthesis. In the absence of phospho‐AbsA2, antibiotics are produced earlier and more abundantly. Overexpression of AbsA1 also deregulates antibiotic synthesis, apparently shifting the AbsA1 protein from a kinase‐active to a phospho‐AbsA2 phosphatase‐active form. The absA1 and absA2 genes, which are adjacent, are located in one of the antibiotic gene clusters that they regulate, the cluster for the calcium‐dependent antibiotic (CDA). The absA genes themselves are growth phase regulated, with phospho‐AbsA2 responsible for growth phase‐related positive autoregulation. We discuss the possible role and mechanism of AbsA‐mediated regulation of antibiotic synthesis in the S. coelicolor life cycle.
Consequences of RNase E scarcity in Escherichia coli
Authors: Jain Chaitanya , Deana Atilio , Belasco Joel G. 
Published: March 2003

SummaryThe endoribonuclease RNase E plays an important role in RNA processing and degradation in Escherichia coli. The construction of an E. coli strain in which the cellular concentration of RNase E can be precisely controlled has made it possible to examine and quantify the effect of RNase E scarcity on RNA decay, gene regulation and cell growth. These studies show that RNase E participates in a step in the degradation of its RNA substrates that is partially or fully rate‐determining. Our data also indicate that E. coli growth requires a cellular RNase E concentration at least 10–20% of normal and that the feedback mecha‐nism that limits overproduction of RNase E is also able to increase its synthesis when its concentration drops below normal. The magnitude of the in‐crease in RNA longevity under conditions of RNase E scarcity may be limited by an alternative pathway for RNA degradation. Additional experiments show that RNase E is a stable protein in E. coli. No other E. coli gene product, when either mutated or cloned on a multicopy plasmid, seems to be capable of compensating for an inadequate supply of this essential protein.
Functional assembly of the foreign carotenoid lycopene into the photosynthetic apparatus of Rhodobacter sphaeroides, achieved by replacement of the native 3‐step phytoene desaturase with its 4‐step counterpart from Erwinia herbicola
Authors: Garcia‐Asua Guillermo , Cogdell Richard J. , Hunter C. Neil 
Published: March 2003

SummaryPhotosynthetic organisms synthesize a diverse range of carotenoids. These pigments are important for the assembly, function and stability of photosynthetic pigment–protein complexes, and they are used to quench harmful radicals. The photosynthetic bacterium Rhodobacter sphaeroides was used as a model system to explore the origin of
carotenoid diversity. Replacing the native 3‐step phytoene desaturase (CrtI) with
the 4‐step enzyme from Erwinia herbicola results in significant flux down
the spirilloxanthin pathway for the first time in Rb. sphaeroides. In Rb.
sphaeroides, the completion of four desaturations to lycopene by the Erwinia
CrtI appears to require the absence of CrtC and, in a crtC background, even
the native 3‐step enzyme can synthesize a significant amount (13%) of lycopene,
in addition to the expected neurosporene. We suggest that the CrtC hydroxylase can
intervene in the sequence of reactions catalyzed by phytoene desaturase. We investigated
the properties of the lycopene‐synthesizing strain of Rb. sphaeroides. In
the LH2 light‐harvesting complex, lycopene transfers absorbed light energy to the
bacteriochlorophylls with an efficiency of 54%, which compares favourably
with other LH2 complexes that contain carotenoids with 11 conjugated double bonds.
Thus, lycopene can join the assembly pathway for photosynthetic complexes in Rb.
sphaeroides, and can perform its role as an energy donor to bacteriochlorophylls.
Uptake and intracellular transportation of a bacterial surface protein in lymphoid cells
Authors: Frick Inga‐Maria , Axcrona Karol , Härdig Ylva , Tapper Hans , Gustafsson Lotta , Kellner Roland , Leanderson Tomas , Björck Lars 
Published: March 2003

SummarySome strains of the human pathogen Streptococcus pyogenes express a surface protein called protein H, which is released from the streptococcal surface by a cysteine proteinase produced by the bacteria. Here, we find that soluble protein H binds to the surface of lymphocytes and granulocytes, and that the molecule is taken up by lymphocytes and transported to the perinuclear region. The translocation over the cell membrane is rapid, and the uptake and intracellular transportation is not dependent on actin polymerization. Protein H could be immunoprecipitated from cell extracts and nuclear preparations of lymphocytes, and analysis of molecular interactions between pro‐tein H and proteins of different cellular compart‐ments demonstrated a binding to nucleophosmin/ B23, a protein known to shuttle between the cytoplasm and the nucleus, and to the nuclear proteins SET and hnRNP A2/B1. Nucleophosmin/B23 was co‐immunoprecipitated with protein H from cell and nuclear extracts, and binding experiments, including kinetic analyses, suggest that protein H dissociating from nucleophosmin/B23 complexes in the perinuclear region or in the nucleus binds to proteins SET and hnRNP A2/B1. Finally, the uptake and intracellular transportation of protein H was found to result in a cytostatic effect on B and T lymphocytes.
Protein engineering modulates the transport properties and ion selectivity of the pores formed by staphylococcal γ‐haemolysins in lipid membranes
Authors: Comai Massimiliano , Serra Mauro Dalla , Coraiola Manuela , Werner Sandra , Colin Didier A. , Monteil Henri , Prévost Gilles , Menestrina Gianfranco 
Published: March 2003

SummaryStaphylococcal γ‐haemolysins are bicomponent toxins in a family including other leucocidins and α‐toxin. Two active toxins are formed combining HlgA or HlgC with HlgB. Both open pores in lipid membranes with conductance, current voltage characteristics and stability similar to α‐toxin, but different selectivity (cation instead of anion). Structural analogies between γ‐haemolysins and α‐toxin indicate the presence, at the pore entry, of a conserved region containing four positive charges in α‐toxin, but either positive or negative in γ‐haemolysins. Four mutants were produced (HlgA D44K, HlgB D47K, HlgB D49K and HlgB D47K/D49K) converting those negative charges to positive in HlgA and HlgB. When all charges were positive, the pores had the same selectivity and conductance as α‐toxin, suggesting that the cluster may form an entrance electrostatic filter. As mutated HlgC‐HlgB pores were less affected, additional charges in the lumen of the pore were changed (HlgB E107Q, HlgB D121N, HlgB T136D and HlgA K108T). Removing a negative charge from the lumen made the selectivity of both HlgA‐HlgB D121N and HlgC‐HlgB D121N more anionic. Residue D121 of HlgB is compensated by a positive residue (HlgA K108) in the HlgA‐HlgB pore, but isolated in the more cation‐selective HlgC‐HlgB pore. Interestingly, the pore formed by HlgA K108T‐HlgB, in which the positive charge of HlgA was removed, was as cation selective as HlgC‐HlgB. Meanwhile, the pore formed by HlgA K108T‐HlgB D121N, in which the two charge changes compensated, retrieved the properties of wild‐type HlgA‐HlgB. We conclude that the conductance and selectivity of the γ‐haemolysin pores depend substantially on the presence and location of charged residues in the channel.
Both metal binding sites in the homodimer are required for metalloregulation by the CadC repressor
Authors: Sun Yan , Wong Marco D. , Rosen Barry P. 
Published: March 2003

SummaryThe cadCA operon of plasmid pI258, which confers resistance to the soft
metals Cd(II), Pb(II) and Zn(II), is regulated by CadC, a metal‐responsive transcriptional
repressor. CadC is a 27.6 kDa homodimer composed of two 122‐residue monomers. Three
cysteine residues, Cys‐7, Cys‐58 and Cys‐60, have been shown to be required for sensing
soft metals. Thus, the repressor has two potential inducer binding sites, one on
each monomer. However, it is not known whether both binding sites are required for
derepression or whether binding of metal to a single site would result in transcript.
In this study, heterodimers were purified in which one binding site was wild type
and the other had substitutions of the cysteine residues. The wild type–mutant
heterodimers retained the ability to bind to cad operator/promoter DNA but did not dissociate from the DNA upon addition of soft metal ions. The results indicate that both subunits in the dimer must have functional metal binding sites for metal sensing to lead to derepression.
CpeR is an activator required for expression of the phycoerythrin operon (cpeBA) in the cyanobacterium Fremyella diplosiphon and is encoded in the phycoerythrin linker‐polypeptide operon (cpeCDESTR)
Authors: Cobley John G. , Clark A. Clay , Weerasurya Siromi , Queseda F. Anne , Xiao Jimmy Y. , Bandrapali Nirmala , D’Silva Ian , Thounaojam Maya , Oda Jeffrey F. , Sumiyoshi Teiko , Chu Man‐Ho 
Published: March 2003

SummaryIn the cyanobacteria, phycobilisomes are assembled from (αβ)6
hexamers of the coloured phycobili‐ proteins, allophycocyanin, phycocyanin and phy‐coerythrin
(PE). The precise architecture of the phycobilisome is determined by the various
colourless linker proteins that bind to the biliprotein hexamers. Genes for β
and α subunits of PE make up one operon (cpeBA), whereas genes
for PE‐associated linker polypeptides are in a second operon. In the chromatically
adapting cyanobacterium Fremyella diplosiphon green light is required for
the transcription of both cpeBA and the operon encoding the PE‐associated
linkers (cpeCDE). From the genome of F. diplosiphon we have
identified an open reading frame, cpeR, which, when expressed from a shuttle
plasmid, is capable of suppressing various mutations that cause a decrease in PE
synthesis. The introduction of a shuttle plasmid bearing cpeR+
into wild‐ type F. diplosiphon caused PE expression in red light. Fremyella
diplosiphon cpeR−, created by in vitro mutagenesis and
in vivo homologous recombination, is fully PE and, in this strain, cpeCDE
is transcribed normally whereas the transcript from cpeBA is undetectable.
Polymerase chain reaction (PCR) amplification of cDNA showed that cpeR is
transcribed as part of the cpeCDE operon on an extended transcript. As CpeR
is an activator required for expression of the cpeBA operon, we propose that
at the onset of green light the operons cpeCDESTR and cpeBA are expressed in series as a genetic cascade.
Discovery of two novel families of proteins that are proposed to interact with prokaryotic SMC proteins, and characterization of the Bacillus subtilis family members ScpA and ScpB
Authors: Soppa Jörg , Kobayashi Kazuo , Noirot‐Gros Marie‐Françoise , Oesterhelt Dieter , Ehrlich S. Dusko , Dervyn Etienne , Ogasawara Naotake , Moriya Shigeki 
Published: March 2003

SummaryStructural maintenance of chromosomes (SMC) proteins are present in all eukaryotes and in many prokaryotes. Eukaryotic SMC proteins form complexes with various non‐SMC subunits, which affect their function, whereas the prokaryotic homologues had no known non‐SMC partners and were thought to act as simple homodimers. Here we describe two novel families of proteins, widespread in archaea and (Gram‐positive) bacteria, which we denote ‘segregation and condensation proteins’ (Scps). ScpA genes are localized next to smc genes in nearly all SMC‐ containing archaea, suggesting that they belong to the same operon and are thus involved in a common process in the cell. The function of ScpA was studied in Bacillus subtilis, which also harbours a well characterized smc gene. Here we show that scpA mutants display characteristic phenotypes nearly identical to those of smc mutants, including temperature‐ sensitive growth, production of anucleate cells, formation of aberrant nucleoids, and chromosome splitting by the so‐called guillotine effect. Thus, both SMC and ScpA are required for chromosome segregation and condensation. Interestingly, mutants of another B. subtilis gene, scpB, which is localized downstream from scpA, display the same phenotypes, which indicate that ScpB is also involved in these functions. ScpB is generally present in species that also encode ScpA. The physical interaction of ScpA and SMC was proven (i) by the use of the yeast two‐hybrid system and (ii) by the isolation of a complex containing both proteins from cell extracts of B. subtilis. By extension, we speculate that interaction of orthologues of the two proteins is important for chromosome segregation in many archaea and bacteria, and propose that SMC proteins generally have non‐SMC protein partners that affect their function not only in eukaryotes but also in prokaryotes.
Molecular dissection of Salmonella FliH, a regulator of the ATPase FliI and the type III flagellar protein export pathway
Authors: González‐Pedrajo Bertha , Fraser Gillian M. , Minamino Tohru , Macnab Robert M. 
Published: March 2003

SummaryFliH is a soluble component of the flagellar export apparatus that binds to the ATPase FliI, and negatively regulates its activity. The 235‐amino‐acid FliH dimerizes and interacts with FliI to form a hetero‐trimeric (FliH)2FliI complex. In the present work, the importance of different regions of FliH was examined. A set of 24 scanning deletions of 10 amino acids was constructed over the entire FliH sequence, along with several combined deletions of 40 amino acids and truncations of both N‐ and C‐termini. The mutant proteins were examined with respect to (i) complementation; (ii) dominance and multicopy effects; (iii) interaction with wild‐type FliH; (iv) interaction with FliI; (v) inhibition of the ATPase activity of FliI; and (vi) interaction with the putative general chaperone FliJ. Analysis of the deletion mutants revealed a clear functional demarcation between the FliH N‐ and C‐terminal regions. The 10‐amino‐acid deletions throughout most of the N‐terminal half of the sequence complemented and were not dominant, whereas those throughout most of the C‐terminal half did not complement and were dominant. FliI binding was disrupted by C‐terminal deletions from residue 101 onwards, indicating that the C‐terminal domain of FliH is essential for interaction with FliI. FliH dimerization was abolished by deletion of residues 101–140 in the centre of the sequence, as were complementation, dominance and interaction with FliI and FliJ. The importance of this region was confirmed by the fact that fragment FliHC2 (residues 99–235) interacted with FliH and FliI, whereas fragment FliHC1 (residues 119–235) did not. FliHC2 formed a relatively unstable complex with FliI and showed biphasic regulation of ATPase activity, suggesting that the FliH N‐terminus stabilizes the (FliH)2FliI complex. Several of the N‐terminal deletions tested permitted close to normal ATPase activity of FliI. Deletion of the last five residues of FliH caused a fivefold activation of ATPase activity, suggesting that this region of FliH governs a switch between repression and activation of FliI. Deletion of the first 10 residues of FliH abolished complementation, severely reduced its interaction with FliJ and uncoupled its role as a FliI repressor from its other export functions. Based on these data, a model is presented for the domain construction and function of FliH in complex with FliI and FliJ.