bluuebunny/crossref_metadata_2025_split huggingface dataset:
The leatherback turtle, Dermochelys coriacea, exhibits both polyandry and polygyny
Authors: Crim J. L. , Spotila L. D. , Spotila J. R. , O'Connor M. , Reina R. , Williams C. J. , Paladino F. V. 
Published: March 2003

AbstractThe leatherback turtle (Dermochelys coriacea) is an endangered species, and world‐wide populations are declining. To understand better the mating structure of this pelagic and fragile species, we investigated paternity in nearly 1000 hatchlings from Playa Grande in Parque Marino Nacional Las Baulas, Costa Rica. We collected DNA samples from 36 adult female leatherbacks and assessed allele frequency distributions for three microsatellite loci. For 20 of these 36 females, we examined DNA from hatchlings representing multiple clutches, and in some cases assessed up to four successive clutches from the same female. We inferred paternal alleles by comparing maternal and hatchling genotypes. We could not reject the null hypothesis of single paternity in 12 of 20 families (31 of 50 clutches), but we did reject the null hypothesis in two families (eight of 50 clutches). In the remaining six families, the null hypothesis could not be accepted or rejected with certainty because the number of hatchlings exhibiting extra nonmaternal alleles was small, and could thus be a result of mutation or sample error. Successive clutches laid by the same female had the same paternal allelic contribution, indicating sperm storage or possibly monogamy. None of 20 females shared the same three‐locus genotype whereas there were two instances of shared genotypes among 17 inferred paternal three‐locus genotypes. We conclude that both polyandry and polygyny are part of the mating structure of this leatherback sea turtle population.
Phylogeny, taxonomy, genetics and global heritage ranks of an imperilled, freshwater snail genus Lithasia (Pleuroceridae)
Authors: Minton Russell L. , Lydeard Charles 
Published: March 2003

AbstractNumerous aquatic species are threatened with extinction from habitat elimination or modification. One particularly imperilled group is the freshwater gastropod family Pleuroceridae. Pleurocerids reach their greatest diversity in the southeastern United States, and many species are currently considered extinct, endangered or threatened. One issue hindering efforts to implement conservation management plans for imperilled pleurocerid species is that the taxonomy is in an abysmal state. The taxonomy of pleurocerids is currently based on late 19th‐ and early 20th‐century studies, which used a typological or morphospecies concept. Most biologists today doubt the validity of many of the currently recognized species; however, this does not stop them from assigning conservation ranks in an attempt to determine which species are imperilled or currently stable. We conducted a phylogenetic analysis of the pleurocerid genus Lithasia using morphological and mitochondrial DNA sequence (mtDNA) data in an attempt to delimit species boundaries and test previous taxonomic schemes. We found that the current taxonomy of Lithasia does not reflect species diversity adequately within the genus, with two new undescribed species being discovered. The conservation status ranks of the new, undescribed species are imperilled and would have been overlooked had we relied on the conventional taxonomy. Additionally, the undescribed species’ conservation ranks that were previously apparently secure became vulnerable due to being inappropriately assigned as members of formerly widely distributed species instead of the imperilled status they warrant and vice versa, as some taxa that were considered imperilled are now thought to be modestly stable. Our study suggests that conservation ranks should be considered suspect at best in taxonomically poorly known groups until the taxa are reviewed using modern systematic methods.
Lack of genetic and plumage differentiation in the red‐billed quelea Quelea quelea across a migratory divide in southern Africa
Authors: Dallimer M. , Jones P. J. , Pemberton J. M. , Cheke R. A. 
Published: March 2003

AbstractA migratory divide usually signals the presence of a geographical region over which other traits, such as morphology and genotypes, also undergo rapid change. A migratory divide has been hypothesized in central southern Africa for the abundant migratory weaver, the red‐billed quelea Quelea quelea. The positioning of the divide in the region is based on the patterns of rainfall in the region that stimulate the annual migrations of queleas. Evidence indicates that premigratory queleas near the divide show two distinct preferred directions for migration. We used eight polymorphic microsatellite loci and a range of plumage characters to determine whether there was population structure among red‐billed queleas in southern Africa, and specifically whether this structure coincided with the location of the migratory divide. There was no evidence of population genetic structure. An amova revealed no significant differences between samples taken either side of the migratory divide. Similarly, there was no geographical variation in plumage patterns across southern Africa. For both microsatellites and plumage characteristics, the variation that does exist occurs within each sampled site, with little differentiation between sites. We were therefore unable to find any evidence that either plumage or microsatellite genotypes varied in a similar way to migratory direction preference in red‐billed queleas in southern Africa. This is perhaps because the migratory divide does not act to separate individuals into populations within which genetic and plumage differentiation can be maintained.
A collagen‐like surface glycoprotein is a structural component of the Bacillus anthracis exosporium
Authors: Sylvestre Patricia , Couture‐Tosi Evelyne , Mock Michèle 
Published: March 2003

Summary Bacillus anthracis
, the aetiological agent of anthrax, is a Gram‐positive spore‐forming bacterium. The exosporium is the outermost integument surrounding the mature spore. Here, we describe the purification and the characterization of an immunodominant protein of the spore surface. This protein was abundant, glycosylated and part of the exosporium. The amino‐terminal sequence was determined and the corresponding gene was identified. It encodes a protein of 382 amino acid residues, the central part of which contains a region of GXX motifs presenting similarity to mammalian collagen proteins. Thus, this collagen‐like surface protein was named BclA (for
Bacillus
c
ollagen‐
l
ike protein of
anthracis
). BclA was absent from vegetative cells; it was detected only in spores and sporulating cells. A potential promoter, dependent on the sigma factor
σ
K
, which is required for a variety of events late in sporulation, was found upstream from the
bclA
gene. A
bclA deletion mutant was constructed and analysed. Electron microscopy studies showed that BclA is a structural component of the filaments covering the outer layer of the exosporium.
Mycobacterium smegmatis laminin‐binding glycoprotein shares epitopes with Mycobacterium tuberculosis heparin‐binding haemagglutinin
Authors: Pethe Kevin , Puech Virginie , Daffé Mamadou , Josenhans Christine , Drobecq Hervé , Locht Camille , Menozzi Franco D. 
Published: March 2003

Mycobacterium tuberculosis, the causative agent of tuberculosis, produces a heparin‐binding haemagglutinin adhesin (HBHA), which is involved in its epithelial adherence. To ascertain whether HBHA is also present in fast‐growing mycobacteria, Mycobacterium smegmatis was studied using anti‐HBHA monoclonal antibodies (mAbs). A cross‐reactive protein was detected by immunoblotting of M. smegmatis whole‐cell lysates. However, the M. tuberculosis HBHA‐encoding gene failed to hybridize with M. smegmatis chromosomal DNA in Southern blot analyses. The M. smegmatis protein recognized by the anti‐HBHA mAbs was purified by heparin–Sepharose chromatography, and its amino‐terminal sequence was found to be identical to that of the previously described histone‐like protein, indicating that M. smegmatis does not produce HBHA. Biochemical analysis of the M. smegmatis histone‐like protein shows that it is glycosylated like HBHA. Immunoelectron microscopy demonstrated that the M. smegmatis protein is present on the mycobacterial surface, a cellular localization inconsistent with a histone‐like function, but compatible with an adhesin activity. In vitro protein interaction assays showed that this glycoprotein binds to laminin, a major component of basement membranes. Therefore, the protein was called M. smegmatis laminin‐binding protein (MS‐LBP). MS‐LBP does not appear to be involved in adherence in the absence of laminin but is responsible for the laminin‐mediated mycobacterial adherence to human pneumocytes and macrophages. Homologous laminin‐binding adhesins are also produced by virulent mycobacteria such as M. tuberculosis and Mycobacterium leprae, suggesting that this adherence mechanism may contribute to the pathogenesis of mycobacterial diseases.
Iron‐free pyoverdin binds to its outer membrane receptor FpvA in Pseudomonas aeruginosa: a new mechanism for membrane iron transport
Authors: Schalk Isabelle J. , Hennard Christophe , Dugave Christophe , Poole Keith , Abdallah Mohamed A. , Pattus Franc 
Published: March 2003

Under iron limitation, Pseudomonas aeruginosa secretes a fluorescent siderophore called pyoverdin, which, after complexing iron, is transported back into the cell via its outer membrane receptor FpvA. Previous studies demonstrated co‐purification of FpvA with iron‐free PaA and reported similar binding affinities of iron‐free pyoverdin and ferric‐pyoverdin to purified FpvA. The fluorescence resonance energy transfer between iron‐free PaA and the FpvA receptor here reveals the existence of an FpvA–pyoverdin complex in P. aeruginosa in vivo, suggesting that the pyoverdin‐loaded FpvA is the normal state of the receptor in the absence of iron. Using tritiated ferric‐pyoverdin, it is shown that iron‐free PaA binds to the outer membrane but is not taken up into the cell, and that in vitro and, presumably, in vivo ferric‐pyoverdin displaces the bound iron‐free pyoverdin on FpvA–PaA to form FpvA–PaA‐Fe complexes. In vivo, the kinetics of formation of this FpvA–PaA‐Fe complex are more than two orders of magnitude faster than in vitro and depend on the presence of TonB. In P. aeruginosa, two tonB genes have been identified (tonB1 and tonB2). TonB1 is directly involved in ferric‐pyoverdin uptake, and TonB2 seems to be able partially to replace TonB1 in its role in iron acquisition. However, no effect of TonB1 or TonB2 on the apparent affinity of free pyoverdin to FpvA was observed, and a 17‐fold difference was measured between the affinities of the two forms of pyoverdin (PaA and PaA‐Fe) to FpvA in the absence of TonB1 or TonB2. The mechanism of iron uptake in P. aeruginosa via the pyoverdin pathway is discussed in view of these new findings.
The relationship between visible intracellular aggregates that appear after overexpression of Sup35 and the yeast prion‐like elements [PSI+] and [PIN+]
Authors: Zhou Ping , Derkatch Irina L. , Liebman Susan W. 
Published: March 2003

Overproduced fusions of Sup35 or its prion domain with green fluorescent protein (GFP) have previously been shown to form frequent dots in [PSI+] cells. Rare foci seen in [psi−] cells were hypothesized to indicate the de novo induction of [PSI+] caused by the overproduced prion domain. Here, we describe novel ring‐type aggregates that also appear in [psi−] cultures upon Sup35 overproduction and show directly that dot and ring aggregates only appear in cells that have become [PSI+]. The formation of either type of aggregate requires [PIN+], an element needed for the induction of [PSI+]. Although aggregates are visible predominantly in stationary‐phase cultures, [PSI+] induction starts in exponential phase, suggesting that much smaller aggregates can also propagate [PSI+]. Such small aggregates are probably present in [PSI+] cells and, upon Sup35–GFP overproduction, facilitate the frequent formation of dot aggregates, but only the occasional appearance of ring aggregates. In contrast, rings are very frequent when [PSI+] cultures, including those lacking [PIN+], are grown in the presence of GuHCl or excess Hsp104 while overexpressing Sup35–GFP. Thus, intermediates formed during [PSI+] curing seem to facilitate ring formation. Surprisingly, GuHCl and excess Hsp104, which are known to promote loss of [PSI+], did not prevent the de novo induction of [PSI+] by excess Sup35 in [psi−][PIN+] strains.
Lipid A and O‐chain modifications cause Rhizobium lipopolysaccharides to become hydrophobic during bacteroid development
Authors: Kannenberg Elmar L. , Carlson Russell W. 
Published: March 2003

Modifications to the lipopolysaccharide (LPS) structure caused by three different growth conditions were investigated in the pea‐nodulating strain Rhizobium leguminosarum 3841. The LPSs extracted by hot phenol–water from cultured cells fractionated into hydrophilic water and/or hydrophobic phenol phases. Most of the LPSs from cells grown under standard conditions extracted into the water phase, but a greater proportion of LPSs were extracted into the phenol phase from cells grown under acidic or reduced‐oxygen conditions, or when isolated from root nodules as bacteroids. Compared with the water‐extracted LPSs, the phenol‐extracted LPSs contained greater degrees of glycosyl methylation and O‐acetylation, increased levels of xylose, glucose and mannose and increased amounts of long‐chain fatty acids attached to the lipid A moiety. The water‐ and phenol‐phase LPSs also differed in their reactivity with monoclonal antibodies and in their polyacrylamide gel electrophoretic banding patterns. Phenol‐extracted LPSs from rhizobia grown under reduced‐oxygen conditions closely resembled the bulk of LPSs isolated from pea nodule bacteria (i.e. mainly bacteroids) in their chemical properties, reactivities with monoclonal antibodies and extraction behaviour. This finding suggests that, during symbiotic bacteroid development, reduced oxygen tension induces structural modifications in LPSs that cause a switch from predominantly hydrophilic to predominantly hydrophobic molecular forms. Increased hydrophobicity of LPSs was also positively correlated with an increase in the surface hydrophobicity of whole cells, as shown by the high degree of adhesion to hydrocarbons of bacterial cells isolated from nodules or from cultures grown under low‐oxygen conditions. The implications of these LPS modifications are discussed for rhizobial survival and function in different soil and in planta habitats.
Crystal structure of the global regulator FlhD from Escherichia coli at 1.8 Å resolution
Authors: Campos Andrés , Zhang RongGuang , Alkire Randal W. , Matsumura Philip , Westbrook Edwin M. 
Published: March 2003

FlhD is a 13.3 kDa transcriptional activator protein of flagellar genes and a global regulator. FlhD activates the transcription of class II operons in the flagellar regulon when complexed with a second protein FlhC (21.5 kDa). FlhD also regulates other expression systems in Escherichia coli. We are seeking to understand this plasticity of FlhD's DNA‐binding specificity and, to this end, we have determined the crystal structure of the isolated FlhD protein. The structure was solved by substituting seleno‐methionine for natural sulphur‐methionine in FlhD, crystallizing the protein and determining the structure factor phases by the method of multiple‐energy anomalous dispersion (MAD). The FlhD protein is dimeric. The dimer is tightly coupled, with an intimate contact surface, implying that the dimer does not easily dissociate. The FlhD monomer is predominantly α‐helical. The C‐termini of both FlhD monomers (residues 83–116) are completely disrupted by crystal packing, implying that this region of FlhD is highly flexible. However, part of the C‐terminus structure in chain A (residues 83–98) was modelled using a native FlhD crystal. What is seen in chain A suggests a classic DNA‐binding, helix–turn–helix (HTH) motif. FlhD does not bind DNA by itself, so it may be that the DNA‐binding HTH motif becomes rigidly defined only when FlhD forms a complex with some other protein, such as FlhC. If this were true, it might explain how FlhD exhibits plasticity in its DNA‐binding specificity, as each partner protein with which it forms a complex could allosterically affect the binding specificity of its HTH motif. A disulphide bridge is seen between the unique cysteine residues (Cys‐65) of FlhD native homodimers. Alanine substitution at Cys‐65 does not affect FlhD transcription activator activity, suggesting that the disulphide bond is not necessary for either dimer stability or this function of FlhD. Electrostatic potential analysis indicates that dimeric FlhD has a negatively charged surface.
Secretion of predicted Inc proteins of Chlamydia pneumoniae by a heterologous type III machinery
Authors: Subtil Agathe , Parsot Claude , Dautry‐Varsat Alice 
Published: March 2003

Chlamydia spp. are strictly intracellular pathogens that grow inside a vacuole, called an inclusion. They possess genes encoding proteins homologous to components of type III secretion machineries, which, in other bacterial pathogens, are involved in delivery of bacterial proteins within or through the membrane of eukaryotic host cells. Inc proteins are chlamydial proteins that are associated with the inclusion membrane and are characterized by the presence of a large hydrophobic domain in their amino acid sequence. To investigate whether Inc proteins and other proteins exhibiting a similar hydropathic profile might be secreted by a type III system, we used a heterologous secretion system. Chimeras were constructed by fusing the N‐terminal part of these proteins with a reporter, the Cya protein of Bordetella pertussis, and these were expressed in various strains of Shigella flexneri. We demonstrate that these hybrid proteins are secreted by the type III secretion system of S. flexneri, thereby providing evidence that IncA, IncB and IncC are secreted by a type III mechanism in chlamydiae. Moreover, we show that three other proteins from Chlamydia pneumoniae, all of which have in common the presence of a large hydrophobic domain, are also secreted by S. flexneri type III secretion machinery.
Type III export: new uses for an old pathway
Authors: Plano Gregory V. , Day James B. , Ferracci Franco 
Published: March 2003

Gram‐negative bacteria use type III secretion (TTS) systems to translocate proteins into the extracellular environment or directly into eukaryotic cells. These complex secretory systems are assembled from over 20 different structural proteins, including 10 that have counterparts in the flagellar export pathway. Secretion substrates are directed to the TTS machinery via mRNA and/or amino acid secretion signals. TTS chaperones bind to select secretion substrates and assist in the export process. Recent progress in the understanding of TTS is reviewed.
The switch from inorganic to organic sulphur assimilation in Escherichia coli: adenosine 5′‐phosphosulphate (APS) as a signalling molecule for sulphate excess
Authors: Bykowski Tomasz , Ploeg Jan R. van der , Iwanicka‐Nowicka Roksana , Hryniewicz Monika M. 
Published: March 2003

SummaryThe utilization of organosulphur compounds as sources of sulphur by Escherichia
coli is strongly repressed by sulphate. To search for the signal enabling E.
coli to alternate gene expression according to the sulphur source, we investigated
the transcriptional control of the ssuEADCB operon, required for the transport
and desulphonation of aliphatic sulphonates. We demonstrate that, of the two LysR‐type
regulators involved in expression from the ssu promoter, Cbl acts as a direct
and sufficient activator of transcription in vivo and in vitro, whereas
CysB downregulates the promoter efficiency. Most importantly, the Cbl‐mediated transcription
initiation at the ssu promoter in vitro is abolished in the presence
of an early metabolite of the sulphate assimilatory pathway, adenosine 5′‐phosphosulphate
(APS). This role for APS was confirmed in vivo by measuring the expression
of β‐galactosidase from a transcriptional ssu–lacZ fusion in strains containing different mutations blocking the synthesis and consumption of APS. Our data comprise the first evidence that APS may act as the negative cofactor of the transcriptional regulator Cbl, and that APS, and not sulphate itself, serves as the signalling molecule for sulphate excess.
Mapping the DNA‐binding domain and target sequences of the Streptomyces peucetius daunorubicin biosynthesis regulatory protein, DnrI
Authors: Sheldon Paul J. , Busarow Sara B. , Hutchinson C. Richard 
Published: March 2003

Summary Streptomyces antibiotic regulatory proteins (SARPs) constitute a novel family of transcriptional activators that control the expression of several diverse anti‐biotic biosynthetic gene clusters. The Streptomyces peucetius DnrI protein, one of only a handful of these proteins yet discovered, controls the biosynthesis of the polyketide antitumour antibiotics daunorubicin and doxorubicin. Recently, comparative analyses have revealed significant similarities among the predicted DNA‐binding domains of the SARPs and the C‐terminal DNA‐binding domain of the OmpR family of regulatory proteins. Using the crystal structure of the OmpR‐binding domain as a template, DnrI was mapped by truncation and site‐directed mutagenesis. Several highly conserved residues within the N‐terminus are crucial for DNA binding and protein function. Tandemly arranged heptameric imperfect repeat sequences are found within the −35 promoter regions of target genes. Substitutions for each nucleotide within the repeats of the dnrG–dpsABCD promoter were performed by site‐directed mutage‐nesis. The mutant promoter fragments were found to have modified binding characteristics in gel mobility shift assays. The spacing between the repeat target sequences is also critical for successful occupation by DnrI and, therefore, competent transcriptional activation of the dnrG–dpsABCD operon.
ClpP‐dependent degradation of PopR allows tightly regulated expression of the clpP3 clpP4 operon in Streptomyces lividans
Authors: Viala Julie , Mazodier Philippe 
Published: March 2003

SummaryFive clpP genes have been identified in Streptomyces coelicolor.

The clpP1 and clpP2 genes form one operon, the clpP3 and clpP4

genes form another, and clpP5 is monocistronic. Previous studies in Streptomyces

lividans have shown that the first operon (clpP1 clpP2) is required for

a normal cell cycle. Expression of the second operon (clpP3 clpP4) is activated

by PopR if the first operon is nonfunctional. We show here that PopR degradation

is primarily dependent on ClpP1 and ClpP2, but can also be achieved by ClpP3 and

ClpP4. The carboxy‐terminus of PopR plays an essential part in the degradation process.

Indeed, replacement of the last two alanine residues by aspartate residues greatly

increased PopR stability. These substitutions did not impair PopR activity and, as

expected, accumulation of the mutant form of PopR led to very strong expression of

the clpP3 clpP4 operon. Increased PopR levels led to delayed sporulation. The results obtained in this study support the notion of cross‐processing between ClpP1 and ClpP2.