bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genetic consequences of extreme variation in sexual and clonal reproduction in an aquatic plant
Authors: Eckert Christopher G. , Lui Keiko , Bronson Kelly , Corradini Pierre , Bruneau Anne. 
Published: March 2003

AbstractMost plants combine sexual reproduction with asexual clonal reproduction in varying degrees, yet the genetic consequences of reproductive variation remain poorly understood. The aquatic plant Butomus umbellatus exhibits striking reproductive variation related to ploidy. Diploids produce abundant viable seed whereas triploids are sexually sterile. Diploids also produce hundreds of tiny clonal bulbils, whereas triploids exhibit only limited clonal multiplication through rhizome fragmentation. We investigated whether this marked difference in reproductive strategy influences the diversity of genotypes within populations and their movement between populations by performing two large‐scale population surveys (n = 58 populations) and assaying genotypic variation using random amplified polymorphic DNA (RAPDs). Contrary to expectations, sexually fertile populations did not exhibit higher genotypic diversity than sterile populations. For each cytotype, we detected one very common and widespread genotype. This would only occur with a very low probability (< 10−7) under regular sexual recombination. Compatibility analysis also indicated that the pattern of genotypic variation largely conformed to that expected with predominant clonal reproduction. The potential for recombination in diploids is not realized, possibly because seeds are outcompeted by bulbils for safe sites during establishment. We also failed to find evidence for more extensive movement of fertile than sterile genotypes. Aside from the few widespread genotypes, most were restricted to single populations. Genotypes in fertile populations were very strongly differentiated from those in sterile populations, suggesting that new triploids have not arisen during the colonization of North America. The colonization of North America involves two distinct forms of B. umbellatus that, despite striking reproductive differences, exhibit largely clonal population genetic structures.
Phylogeography of lemmings (Lemmus): no evidence for postglacial colonization of Arctic from the Beringian refugium
Authors: Fedorov V. B. , Goropashnaya A. V. , Jaarola M. , Cook J. A. 
Published: March 2003

AbstractBeringia is considered as an important glacial refugium that served as the main source for colonization of formerly glaciated Arctic regions. To obtain high resolution views of Arctic refugial history, we examined mitochondrial cytochromebphylogeography in the northern genus of rodents,Lemmus (true lemmings), sampled across its circumpolar distribution. Strong phylogeographical structure suggests vicariant separation over several glacial–interglacial periods and does not provide evidence supporting the importance of Beringia for extensive colonization of formerly glaciated regions. Rather than a source of postglacial colonization, Beringia represents an area of intraspecific endemism previously undetected by biogeographical analysis. Existing phylogeographical structure suggests that vicariant separation by glacial barriers was an important factor generating genetic divergence and, thus, increasing genetic diversity in lemmings on continental and circumpolar scales. However, there is little evidence for the direct effect of the last glaciation on the level of genetic variation and allele genealogy in lemmings on a regional geographical scale. This finding implies that the population genetic models of postglacial colonization suggested for temperate taxa might have limited applicability for Arctic species.
Phase variation of a β‐1,3 galactosyltransferase involved in generation of the ganglioside GM1‐like lipo‐oligosaccharide of Campylobacter jejuni
Authors: Linton Dennis , Gilbert Michel , Hitchen Paul G. , Dell Anne , Morris Howard R. , Wakarchuk Warren W. , Gregson Norman A. , Wren Brendan W. 
Published: March 2003

Ganglioside mimicry by Campylobacter jejuni lipo‐oligosaccharide (LOS) is thought to be a critical factor in the triggering of the Guillain–Barré and Miller–Fisher syndrome neuropathies after C. jejuni infection. The combination of a completed genome sequence and a ganglioside GM1‐like LOS structure makes C. jejuni NCTC 11168 a useful model strain for the identification and characterization of the genes involved in the biosynthesis of ganglioside‐mimicking LOS. Genome analysis identified a putative LOS biosynthetic cluster and, from this, we describe a putative gene (ORF Cj1139c), which we have termed wlaN, with a significant level of similarity to a number of bacterial glycosyltransferases. Mutation of this gene in C. jejuni NCTC 11168 resulted in a LOS molecule of increased electrophoretic mobility, which also failed to bind cholera toxin. Comparison of LOS structural data from wild type and the mutant strain indicated lack of a terminal β‐1,3‐linked galactose residue in the latter. The wlaN gene product was demonstrated unambiguously as a β‐1,3 galactosyltransferase responsible for converting GM2‐like LOS structures to GM1‐like by in vitro expression. We also show that the presence of an intragenic homopolymeric tract renders the expression of a functional wlaN gene product phase variable, resulting in distinct C. jejuni NCTC 11168 cell populations with alternate GM1 or GM2 ganglioside‐mimicking LOS structures. The distribution of wlaN among a number of C. jejuni strains with known LOS structure was determined and, for C. jejuni NCTC 12500, similar wlaN gene phase variation was shown to occur, so that this strain has the potential to synthesize a GM1‐like LOS structure as well as the ganglioside GM2‐like LOS structure proposed in the literature.
A protein with similarity to the human retinoblastoma binding protein 2 acts specifically as a repressor for genes regulated by the b mating type locus in Ustilago maydis
Authors: Quadbeck‐Seeger Claudia , Wanner Gerhard , Huber Sieglinde , Kahmann Regine , Kämper Jörg 
Published: March 2003

Pathogenic development in the corn smut fungus Ustilago maydis is controlled by a heterodimer of the two homeodomain proteins bE and bW which are encoded by the b mating type locus. The bE/bW heterodimer is thought to achieve its function as a transcriptional regulator of pathogenicity genes, either directly by binding to cis regulatory sequences or indirectly via a b‐dependent regulatory cascade.In a screen for components of the b‐dependent regulatory cascade we have isolated Rum1 (regulator U. maydis 1), a protein with similarities to the human retinoblastoma binding protein 2. Deletion of rum1 results in expression of several b regulated genes independently from their activation via the bE/bW heterodimer. rum1 mutant strains remain pathogenic, proliferate in planta, but fail to produce spores. The defect leads to an arrest in spore development at a defined stage before the spore wall is generated. Deduced from the highly conserved domain structure of Rum1 that includes a DNA‐binding motif and a region known to facilitate the interaction with histone deacetylases, we propose that Rum1 functions as a transcriptional repressor through the modulation of chromatin structure.
Evidence of recent lateral gene transfer among hyperthermophilic Archaea
Authors: DiRuggiero Jocelyne , Dunn Diane , Maeder Dennis L. , Holley‐Shanks Rhonda , Chatard Jerome , Horlacher Reinhold , Robb Frank T. , Boos Winfried , Weiss Robert B. 
Published: March 2003

A total of 153 nucleotide differences were found over a contiguous 16 kb region between two hyperthermophilic Archaea, Pyrococcus furiosus and Thermococcus litoralis. The 16 kb region in P. furiosus is flanked by insertion sequence (IS) elements with inverted and direct repeats. Both IS elements contain a single open reading frame (ORF) encoding a putative protein of 233 amino acids identified as a transposase. This 16 kb region has the features of a typical bacterial composite transposon and represents a possible mechanism for lateral gene transfer between Archaea or possibly between Archaea and Bacteria. A total of 23 homologous IS elements was found in the genome sequence of P. furiosus, whereas no full‐length IS elements were identified in the genomes of Pyrococcus abyssi and Pyrococcus horikoshii. Only one IS element was found in T. litoralis. In P. furiosus and T. litoralis, the 16 kb region contains an ABC transport system for maltose and trehalose that was characterized biochemically for T. litoralis. Regulation of expression studies showed that the malE gene, located on the transposon, and the encoded trehalose/maltose‐binding protein (TMBP) are induced in the presence of maltose and trehalose in both P. furiosus and T. litoralis. The implications of transposition as a mechanism for lateral gene transfer among Archaea are discussed.
G‐protein signalling mediates differential production of toxic secondary metabolites
Authors: Tag Andrew , Hicks Julie , Garifullina Gulnara , Ake Charles , Phillips T. D. , Beremand Marian , Keller Nancy 
Published: March 2003

Filamentous fungi elaborate a complex array of secondary metabolites, including antibiotics and mycotoxins. As many of these compounds pose significant economic and health concerns, elucidation of the underlying cellular mechanisms that control their production is essential. Previous work revealed that synthesis of the carcinogenic mycotoxins sterigmatocystin (ST) and aflatoxin (AF) in Aspergillus species is negatively controlled by FadA, the α‐subunit of a heterotrimeric G‐protein. In sharp contrast, we show here that the dominant activating fadA allele, fadAG42R, stimulates transcription of a gene from the A. nidulans penicillin (PN) gene cluster and elevates penicillin production. Thus, FadA has opposite roles in regulating the biosynthesis of a potent antibiotic (PN) and a lethal mycotoxin (ST) in A. nidulans. Furthermore, expression of fadAG42R in Fusarium sporotrichioides increases trichothecene (TR) mycotoxin production and alters TR gene expression. Our findings reveal that a G‐protein defines an important control point for differential expression of fungal secondary metabolites within and across fungal genera. These data provide critical evidence suggesting that targeting G‐protein signal transduction pathways as a means of controlling or preventing the production of a single mycotoxin could have serious undesirable consequences with regard to the production of other secondary metabolites.
The txtAB genes of the plant pathogen Streptomyces acidiscabies encode a peptide synthetase required for phytotoxin thaxtomin A production and pathogenicity
Authors: Healy Frank G. , Wach Michael , Krasnoff Stuart B. , Gibson Donna M. , Loria Rosemary 
Published: March 2003

Four Streptomyces species have been described as the causal agents of scab disease, which affects economically important root and tuber crops worldwide. These species produce a family of cyclic dipeptides, the thaxtomins, which alone mimic disease symptomatology. Structural considerations suggest that thaxtomins are synthesized non‐ribosomally. Degenerate oligonucleotide primers were used to amplify conserved portions of the acyladenylation module of peptide synthetase genes from genomic DNA of representatives of the four species. Pairwise Southern hybridizations identified a peptide synthetase acyladenylation module conserved among three species. The complete nucleotide sequences of two peptide synthetase genes (txtAB) were determined from S. acidiscabies 84.104 cosmid library clones. The organization of the deduced TxtA and TxtB peptide synthetase catalytic domains is consistent with the formation of N‐methylated cyclic dipeptides such as thaxtomins. Based on high‐performance liquid chromatography (HPLC) analysis, thaxtomin A production was abolished in txtA gene disruption mutants. Although the growth and morphological characteristics of the mutants were identical to those of the parent strain, txtA mutants were avirulent on potato tubers. Moreover, introduction of the thaxtomin synthetase cosmid into a txtA mutant restored both pathogenicity and thaxtomin A production, demonstrating a critical role for thaxtomins in pathogenesis.
Conserved amino acid motifs from the novel Piv/MooV family of transposases and site‐specific recombinases are required for catalysis of DNA inversion by Piv
Authors: Tobiason Deborah M. , Buchner John M. , Thiel William H. , Gernert Kim M. , Karls Anna C. Glasgow 
Published: March 2003

Piv, a site‐specific invertase from Moraxella lacunata, exhibits amino acid homology with the transposases of the IS110/IS492 family of insertion elements. The functions of conserved amino acid motifs that define this novel family of both transposases and site‐specific recombinases (Piv/MooV family) were examined by mutagenesis of fully conserved amino acids within each motif in Piv. All Piv mutants altered in conserved residues were defective for in vivo inversion of the M. lacunata invertible DNA segment, but competent for in vivo binding to Piv DNA recognition sequences. Although the primary amino acid sequences of the Piv/MooV recombinases do not contain a conserved DDE motif, which defines the retroviral integrase/transposase (IN/Tnps) family, the predicted secondary structural elements of Piv align well with those of the IN/Tnps for which crystal structures have been determined. Molecular modelling of Piv based on these alignments predicts that E59, conserved as either E or D in the Piv/MooV family, forms a catalytic pocket with the conserved D9 and D101 residues. Analysis of Piv E59G confirms a role for E59 in catalysis of inversion. These results suggest that Piv and the related IS110/IS492 transposases mediate DNA recombination by a common mechanism involving a catalytic DED or DDD motif.
Differential role of the Mu B protein in phage Mu integration vs. replication: mechanistic insights into two transposition pathways
Authors: Roldan Leslie Ann S. , Baker Tania A. 
Published: March 2003

The Mu B protein is an ATP‐dependent DNA‐binding protein and an allosteric activator of the Mu transposase. As a result of these activities, Mu B is instrumental in efficient transposition and target‐site choice. We analysed in vivo the role of Mu B in the two different recombination reactions performed by phage Mu: non‐replicative transposition, the pathway used during integration, and replicative transposition, the pathway used during lytic growth. Utilizing a sensitive PCR‐based assay for Mu transposition, we found that Mu B is not required for integration, but enhances the rate and extent of the process. Furthermore, three different mutant versions of Mu B, Mu BC99Y, Mu BK106A, and Mu B1−294, stimulate integration to a similar level as the wild‐type protein. In contrast, these mutant proteins fail to support Mu growth. This deficiency is attributable to a defect in formation of an essential intermediate for replicative transposition. Biochemical analysis of the Mu B mutant proteins reveals common features: the mutants retain the ability to stimulate transposase, but are defective in DNA binding and target DNA delivery. These data indicate that activation of transposase by Mu B is sufficient for robust non‐replicative transposition. Efficient replicative transposition, however, demands that the Mu B protein not only activate transposase, but also bind and deliver the target DNA.
Transposon mutagenesis of Campylobacter jejuni identifies a bipartite energy taxis system required for motility
Authors: Hendrixson David R. , Akerley Brian J. , DiRita Victor J. 
Published: March 2003

Campylobacter jejuni constitutes the leading cause of bacterial gastroenteritis in the United States and a major cause of diarrhoea worldwide. Little is known about virulence mechanisms in this organism because of the scarcity of suitable genetic tools. We have developed an efficient system of in vitro transposon mutagenesis using a mariner‐based transposon and purified mariner transposase. Through in vitro transposition of C. jejuni chromosomal DNA followed by natural transformation of the transposed DNA, large random transposon mutant libraries consisting of ≈ 16 000 individual mutants were generated. The first genetic screen of C. jejuni using a transposon‐generated mutant library identified 28 mutants defective for flagellar motility, one of the few known virulence determinants of this pathogen. We developed a second genetic system, which allows for the construction of defined chromosomal deletions in C. jejuni, and demonstrated the requirement of σ28 and σ54 for motility. In addition, we show that σ28 is involved in the transcription of flaA and that σ54 is required for transcription of three other flagellar genes, flaB and flgDE. We also identified two previously uncharacterized genes required for motility encoding proteins that we call CetA and CetB, which mediate energy taxis responses. Through our analysis of the Cet proteins, we propose a unique mechanism for sensing energy levels and mediating energy taxis in C. jejuni.
Regulation of catalase–peroxidase (KatG) expression, isoniazid sensitivity and virulence by furA of Mycobacterium tuberculosis
Authors: Pym Alexander S. , Domenech Pilar , Honoré Nadine , Song Jian , Deretic Vojo , Cole Stewart T. 
Published: March 2003

Mycobacterium tuberculosis has two genes for ferric uptake regulator orthologues, one of which, furA, is situated immediately upstream of katG encoding catalase–peroxidase, a major virulence factor that also activates the prodrug isoniazid. This association suggested that furA might regulate katG and other genes involved in pathogenesis. Transcript mapping showed katG to be expressed from a strong promoter, with consensus −10 and −35 elements, preceding furA. No promoter activity was demonstrated downstream of the furA start codon, using different gene reporter systems, indicating that furA and katG are co‐transcribed from a common regulatory region. The respective roles of these two genes in the isoniazid susceptibility and virulence of M. tuberculosis were assessed by combinatorial complementation of a Δ(furA–katG) strain that is heavily attenuated in a mouse model of tuberculosis. In the absence of furA, katG was upregulated, cells became hypersensitive to isoniazid, and full virulence was restored, indicating that furA regulates the transcription of both genes. When furA alone was introduced into the Δ(furA–katG) mutant, survival in mouse lungs was moderately increased, suggesting that FurA could regulate genes, other than katG, that are involved in pathogenesis. These do not include the oxidative stress genes ahpC and sodA, or those for siderophore production.
Mutational analysis of the high‐affinity BvgA binding site in the fha promoter of Bordetella pertussis
Authors: Boucher Philip E. , Yang Mei‐Shin , Stibitz Scott 
Published: March 2003

In order to define a consensus binding sequence for the response regulator BvgA, we have undertaken a systematic analysis of contributions made by each nucleotide within the heptad half‐sites that are present in an inverted orientation at the promoter for the fha operon. Using in vitro binding assays, we examined the full complement of 21 single point mutations symmetrically arranged in this heptad repeat. Both gel shift and nitrocellulose filter‐binding assays provided evidence that nucleotides at positions 3 (thymidine), 4 (cytosine) and 7 (adenine) in the binding heptad contribute substantially to sequence‐specific recognition by BvgA. Furthermore, a T to A conversion at position 6 reduced binding. Selected binding site mutations were introduced into a modified fha promoter and examined for their effects on BvgA activation of promoter activity in vivo. Only those substitutions most severely affecting binding in vitro affected promoter activity in vivo. The in vivo effects of substitutions that had a significant effect on binding in vitro but did not severely affect in vivo promoter activity under standard culture conditions could be detected in vivo either in combination with additional substitutions or from their effect on the sensitivity of the mutant promoters to modulation by magnesium sulphate.
A bacterial linear motor: cellular and molecular organization of the contractile cytoskeleton of the helical bacterium Spiroplasma melliferum BC3
Authors: Trachtenberg Shlomo , Gilad Rami 
Published: March 2003

The Mollicutes (Mycoplasma, Acholeplasma, and Spiroplasma) are the smallest, simplest and most primitive free‐living and self‐replicating known cells. These bacteria have evolved from Clostridia by regressive evolution and genome reduction to the range of 5.8 × 105−2.2 × 106 basepairs (bp). Structurally, the Mollicutes completely lack cell walls and are enveloped by only a cholesterol containing cell membrane. The Mollicutes contain what can be defined as a bacterial cytoskeleton. The Spiroplasmas are unique in having a well‐defined, dynamic, helical cell geometry and a flat, monolayered, membrane‐bound cytoskeleton, which follows, intracellularly, the shortest helical line on the cellular coil. By applying cryo‐electron‐microscopy to whole cells, isolated cytoskeletons and cytoskeletal fibrils and subunits, as well as by selective extraction of cellular components, we determined, at a resolution of ∼25 Å, the cellular and molecular organization of the cytoskeleton. The cytoskeleton is assembled from a 59 kDa protein. The 59 kDa protein, has an equivalent sphere diameter of ∼50 Å. Given the ∼100 Å axial and lateral spacings in the cytoskeletal ribbons and the near‐circular shape of the subunit, we suggest that the subunit is a tetramer of 59 kDa monomers; the tetramers assemble further into flat fibrils, seven of which form a flat, monolayered, well‐ordered ribbon. The cytoskeleton may function as a linear motor by differential and coordinated length‐changes of the fibrils driven by conformational changes of the tetrameric subunits, the shape of which changes from near circular to elliptical. The cytoskeleton controls both the dynamic helical shape and the consequent motility of the cell. A stable cluster of proteins co‐purifies with the cytoskeleton. These apparent membrane and membrane‐associated proteins may function as anchor proteins.
The integrative element pSAM2 from Streptomyces: kinetics and mode of conjugal transfer
Authors: Possoz Christophe , Ribard Carin , Gagnat Josette , Pernodet Jean‐Luc , Guérineau Michel 
Published: March 2003

pSAM2 is an 11 kb integrative element from Streptomyces ambofaciens that is capable of conjugal transfer. A system based on differential DNA modification by SalI methyltransferase was used to localize pSAM2 in the donor or recipient strain, and thus to determine the various steps associated with transfer. Initiation (i.e. excision and replication of pSAM2 in the donor) occurs a few hours after mating with a recipient strain. pSAM2 replicates in the recipient strain, spreads within the mycelium and then integrates into the chromosome. Transfer generally involves single‐stranded DNA. In Streptomyces, only a few genes, such as traSA for pSAM2, are required for conjugal transfer. Using the differential sensitivity to the SalI restriction–modification system of transfers involving single‐ and double‐stranded DNA, we found that pSAM2 was probably transferred to the recipient as double‐stranded DNA. This provides the first experimental evidence for the transfer of double‐stranded DNA during bacterial conjugation. Thus, TraSA, involved in pSAM2 transfer, and SpoIIIE, which is involved in chromosome partitioning in Bacillus subtilis, display similarities in both sequence and function: both seem to transport double‐stranded DNA actively, either from donor to recipient or from mother cell to prespore.