bluuebunny/crossref_metadata_2025 huggingface dataset:
Aboriginal fire management in south‐eastern Australia: aims and frequency
Authors: Gott Beth
Published: June 2005

Aim  To examine the purpose of burning by Aborigines of south‐eastern Australia.

Location  South‐eastern Australia.

Methods  A survey of the ethnography and ecology relating to Aboriginal fire.

Results  Ecologists have only recently acknowledged the past history of Aboriginal burning. Its purpose was to maximise plant and animal food resources.

Main Conclusions  The seasonal timing and frequency of Aboriginal burning is embedded in various ecosystems.
Environmental determinants of vascular plant species richness in the Austrian Alps
Authors: Moser Dietmar , Dullinger Stefan , Englisch Thorsten , Niklfeld Harald , Plutzar Christoph , Sauberer Norbert , Zechmeister Harald Gustav , Grabherr Georg
Published: June 2005

Aim  To test predictions of different large‐scale biodiversity hypotheses by analysing species richness patterns of vascular plants in the Austrian Alps.

Location  The Austrian part of the Alps (c. 53,500 km2).

Methods  Within the floristic inventory of Central Europe the Austrian part of the Alps were systematically mapped for vascular plants. Data collection was based on a rectangular grid of 5 × 3 arc minutes (34–35 km2). Emerging species richness patterns were correlated with several environmental factors using generalized linear models. Primary environmental variables like temperature, precipitation and evapotranspiration were used to test climate‐related hypotheses of species richness. Additionally, spatial and temporal variations in climatic conditions were considered. Bedrock geology, particularly the amount of calcareous substrates, the proximity to rivers and lakes and secondary variables like topographic, edaphic and land‐use heterogeneity were used as additional predictors. Model results were evaluated by correlating modelled and observed species numbers.

Results  Our final multiple regression model explains c. 50% of the variance in species richness patterns. Model evaluation results in a correlation coefficient of 0.64 between modelled and observed species numbers in an independent test data set. Climatic variables like temperature and potential evapotranspiration (PET) proved to be by far the most important predictors. In general, variables indicating climatic favourableness like the maxima of temperature and PET performed better than those indicating stress, like the respective minima. Bedrock mineralogy, especially the amount of calcareous substrate, had some additional explanatory power but was less influential than suggested by comparable studies. The amount of precipitation does not have any effect on species richness regionally. Among the descriptors of heterogeneity, edaphic and land‐use heterogeneity are more closely correlated with species numbers than topographic heterogeneity.

Main conclusions  The results support energy‐driven processes as primary determinants of vascular plant species richness in temperate mountains. Stressful conditions obviously decrease species numbers, but presence of favourable habitats has higher predictive power in the context of species richness modelling. The importance of precipitation for driving global species diversity patterns is not necessarily reflected regionally. Annual range of temperature, an indicator of short‐term climatic stability, proved to be of minor importance for the determination of regional species richness patterns. In general, our study suggests environmental heterogeneity to be of rather low predictive value for species richness patterns regionally. However, it may gain importance at more local scales.
Global distribution of the European species of the lichen genus Melanelia Essl.
Authors: Otte Volker , Esslinger Theodore L. , Litterski Birgit
Published: June 2005

Aim  The global distribution of the European species of Melanelia Essl. (Lichenes: Parmeliaceae) was investigated in order to understand their distribution patterns against the background of ecogeographical and historical factors.

Location  The location of the study is global, with a local emphasis on Europe.

Methods  Geographical distribution and ecology of the species were investigated on the basis of herbarium studies and data from the literature as well as field observations. Distribution maps were created with ArcView GIS. The distribution patterns are expressed as three‐dimensional ‘areal formulas’, regarding zonal distribution, altitudinal range and oceanicity, using a previously described method. The observed distribution patterns are discussed on the basis of their analogies with vascular plants and with respect to the ecogeographical vs. historical factors reflected by them.

Results  With the exception of one species that is endemic to Europe, all species studied occur in both northern continents. A number of species have tropical‐alpine outposts, and two species occur also in extratropical zones of the southern hemisphere. Arctic and boreal distributions are circumpolar, while in the southern holarctic zones an affinity to the western sides of both northern continents is frequent.

Main conclusions  The distribution patterns appear to be mainly determined by contemporary ecogeographical factors. Most species probably have largely filled their potential distribution, at least within the Holarctic. Thus, the geographical origin and dispersal history of a species cannot reliably be reconstructed; they can be dissimilar in different species with similar distributions.
Body size, biomic specialization and range size of African large mammals
Authors: Fernández Manuel Hernández , Vrba Elisabeth S.
Published: June 2005

Aim The goal of this paper is to examine the relationships between body size, biomic specialization and range size in the African large mammals, which are defined as all the African species corresponding to the orders Primates, Carnivora, Proboscidea, Perissodactyla, Hyracoidea, Tubulidentata, Artiodactyla and Pholidota.

Location The study used the large mammal assemblage from Africa.

Methods The degree of biomic specialization of African large mammals is investigated using the biomic specialization index (BSI) for each mammal species, based on the number of biomes it inhabits. Range size for each species is measured as the latitudinal extent of the geographical distribution of the species. We have analysed our data using both conventional cross‐species analyses and phylogenetically independent contrasts.

Results There is a polygonal relationship between species biomic specialization and body size. While small and large species are biomic specialists, medium‐sized species are distributed along the whole range of biomic specialization. The latitudinal extent–body size relationship is approximately triangular. Small‐bodied species may have either large or small ranges, whereas large‐bodied ones have only large ranges. A positive correlation between latitudinal extent and biomic specialization is evident, although their relationship is better described as triangular.

Main conclusions We found a polygonal relationship between species biomic specialization and body size, which agrees with previous arguments that small‐bodied species have more limited dispersal and, therefore, they may come to occupy a lesser proportion of their potential inhabitable biomes. On the other hand, large‐bodied species are constrained to inhabit biomes with a high productivity. A polygonal relationship between species latitudinal extent and body size in African large mammals agrees with previous studies of the relationship between range size and body size in other continents. The independent study of the macroecological pattern in biomic specialization highlights different factors that influence the body size–range size relationship. Although body size is usually implicated as a correlate of both specialization and geographical range size in large mammals, much of the variation in these variables cannot be attributed to size differences but to biome specific factors such as productivity, area, history, etc.
Global patterns of plant diversity and floristic knowledge
Authors: Kier Gerold , Mutke Jens , Dinerstein Eric , Ricketts Taylor H. , Küper Wolfgang , Kreft Holger , Barthlott Wilhelm
Published: June 2005

Aims  We present the first global map of vascular plant species richness by ecoregion and compare these results with the published literature on global priorities for plant conservation. In so doing, we assess the state of floristic knowledge across ecoregions as described in floras, checklists, and other published documents and pinpoint geographical gaps in our understanding of the global vascular plant flora. Finally, we explore the relationships between plant species richness by ecoregion and our knowledge of the flora, and between plant richness and the human footprint – a spatially explicit measure of the loss and degradation of natural habitats and ecosystems as a result of human activities.

Location  Global.

Methods  Richness estimates for the 867 terrestrial ecoregions of the world were derived from published richness data of c. 1800 geographical units. We applied one of four methods to assess richness, depending on data quality. These included collation and interpretation of published data, use of species–area curves to extrapolate richness, use of taxon‐based data, and estimates derived from other ecoregions within the same biome.

Results  The highest estimate of plant species richness is in the Borneo lowlands ecoregion (10,000 species) followed by nine ecoregions located in Central and South America with ≥ 8000 species; all are found within the Tropical and Subtropical Moist Broadleaf Forests biome. Among the 51 ecoregions with ≥ 5000 species, only five are located in temperate regions. For 43% of the 867 ecoregions, data quality was considered good or moderate. Among biomes, adequate data are especially lacking for flooded grasslands and flooded savannas. We found a significant correlation between species richness and data quality for only a few biomes, and, in all of these cases, our results indicated that species‐rich ecoregions are better studied than those poor in vascular plants. Similarly, only in a few biomes did we find significant correlations between species richness and the human footprint, all of which were positive.

Main conclusions  The work presented here sets the stage for comparisons of degree of concordance of plant species richness with plant endemism and vertebrate species richness: important analyses for a comprehensive global biodiversity strategy. We suggest: (1) that current global plant conservation strategies be reviewed to check if they cover the most outstanding examples of regions from each of the world's major biomes, even if these examples are species‐poor compared with other biomes; (2) that flooded grasslands and flooded savannas should become a global priority in collecting and compiling richness data for vascular plants; and (3) that future studies which rely upon species–area calculations do not use a uniform parameter value but instead use values derived separately for subregions.
Historical biogeography and phylogeny of monachine seals (Pinnipedia: Phocidae) based on mitochondrial and nuclear DNA data
Authors: Fyler C. A. , Reeder T. W. , Berta A. , Antonelis G. , Aguilar A. , Androukaki E.
Published: June 2005

Aim To determine the origin and diversification of monachine seals using a phylogenetic framework.

Methods Molecular sequence data from three mitochondrial genes (cytb, ND1 and 12S), and one nuclear marker (an intron from theα‐lactalbumin gene) were examined from all extant species of monachine seals. Maximum likelihood and partitioned Bayesian inference were used to analyse separate and combined (mitochondrial + nuclear) data sets. Divergence times were estimated from the resultant phylogeny using nonparametric rate smoothing as implemented by the program r8s.

Results Mirounga,Monachusand the Lobodontini form three well‐supported clades within a monophyletic Monachinae. Lobodontini + Miroungaform a clade sister toMonachus. Molecular divergence dates indicate that the first split within the Monachinae (Lobodontini + Miroungaclade andMonachus) occurred between 11.8 and 13.8 Ma andMirounga,Monachusand the Lobodontini originated 2.7–3.4, 9.1–10.8 and 10.0–11.6 Ma, respectively.

Main conclusions Two main clades exist within Monachinae,Monachusand Lobodontini + Mirounga.Monachus, a warm water clade, originated in the North Atlantic and maintained the temperate water affinities of their ancestors as they diversified in the subtropic regions of the Northern Hemisphere. The cold‐water clade, Lobodontini + Mirounga, dispersed southward to the cooler climates of the Southern Hemisphere. The Lobodontini continued south until reaching the Antarctic region where they diversified into the present‐day fauna.Miroungashows an anti‐tropical distribution either reflective of a once cosmopolitan range that was separated by warming waters in the tropics or of transequatorial dispersal.
Lichenological evidence for the recognition of inland rain forests in western North America
Authors: Goward Trevor , Spribille Toby
Published: June 2005

Aim  The coastal temperate rain forests of north‐western North America are internationally renowned as the archetypal expression of the temperate rain forest biome. Less well documented is the existence of somewhat similar forests 500–700 km inland on the windward slopes of the Columbia and Rocky Mountains. Here we attempt to show that these inland ‘wetbelt’ forests warrant rain forest status.

Location  North‐western North America.

Methods  We use tree‐dwelling macrolichens to assess the degree of environmental congruence between the coastal temperate rain forests and their inland counterparts.

Results  We report three key findings: (1) 40% of oceanic, epiphytic macrolichens found in Pacific coastal rain forests occur also in inland regions; (2) epiphytic species richness decreases with decreasing latitude, such that roughly 70% of disjunct oceanic species are restricted to regions north of 51° N; and (3) the southward decline in lichen diversity is correlated with a parallel decrease in summer precipitation, but not with mean annual precipitation.

Main conclusions  These observations are consistent with the recognition of an inland rain forest formation between 50 and 54° N. Inland rain forests represent a small, biologically significant ecosystem whose continued fragmentation and conversion to tree plantations warrant close scrutiny.
Functional genomics of bacterial pathogens: from post‐genomics to therapeutic targets
Authors: Polissi Alessandra , Soria Marco R.
Published: June 2005

A wealth of new data have become available to the scientific community as a result of the sequencing of many pathogen genomes. A recent meeting devoted to functional genomics of pathogenic microorganisms confirmed the notion that bacterial genomes are not static, because large blocks of genes can be acquired or deleted. Less complex environments usually result in reduction in genome size, while genome expansion is usually associated with environmental change and complexity. During the meeting, pathogenicity and evolutionary aspects were illustrated for enteric pathogens, as well as the microevolution of the plague bacillus Yersinia pestis. New clues for evolution and pathogenicity were derived from comparative genomics of Listeria species. The genomic organization of Bartonellae, an emerging human pathogen, was also discussed in an evolutionary context. Population and functional genomics of Anthrax‐causing bacteria highlighted current scientific interest in this potential biothreat.
Direct binding of the quorum sensing regulator CepR of Burkholderia cenocepacia to two target promoters in vitro
Authors: Weingart Christine L. , White Catharine E. , Liu Suping , Chai Yunrong , Cho Hongbaek , Tsai Ching‐Sung , Wei Yuping , Delay Nicholas R. , Gronquist Matthew R. , Eberhard Anatol , Winans Stephen C.
Published: June 2005

Burkholderia cenocepacia is an opportunistic human pathogen that can aggressively colonize the cystic fibrosis lung. This organism has a LuxR/LuxI‐type quorum sensing system that enables cell–cell communication via exchange of acyl homoserine lactones (AHLs). The CepR and CepI proteins constitute a global regulatory system, controlling expression of at least 40 genes, including those controlling swarming motility and biofilm formation. In this study, we isolated seven lacZ fusions in a clinical isolate of B. cenocepacia that are inducible by octanoyl‐HSL. Induction of all of these genes requires CepR. The cepI promoter was tested for induction by a set of 33 synthetic autoinducers and analogues, and was most strongly induced by long‐chain AHLs lacking 3‐oxo substitutions. Expression of this promoter was inhibited by high concentrations of three different autoinducers, each having six‐carbon acyl chains. When CepR protein was overproduced in Escherichia coli, it accumulated in a soluble form in the presence of octanoyl‐HSL, but accumulated only as insoluble inclusion bodies in its absence. Purified CepR‐OHL complexes bound to specific DNA sequences at the cepI and aidA promoters with high specificity. These binding sites included a 16‐nucleotide imperfect dyad symmetry. Both CepR binding sites are centred approximately 44 nucleotides upstream of the respective transcription start sites.
A genetic screen identifies genes and sites involved in pilin antigenic variation in Neisseria gonorrhoeae
Authors: Sechman Eric V. , Rohrer Melissa S. , Seifert H. Steven
Published: June 2005

It has previously been shown that the frequency of pilin antigenic variation in Neisseria gonorrhoeae (the gonococcus, Gc) is regulated by iron availability. To identify factors involved in pilin variation in an iron‐dependent or an iron‐independent manner, we conducted a genetic screen of transposon‐mutated gonococci using a pilus‐dependent colony morphology phenotype to detect antigenic variation deficient mutants. Forty‐six total mutants representing insertions in 30 different genes were shown to have reduced colony morphology changes resulting from impaired pilin variation. Five mutants exhibited an iron‐dependent decrease in pilin variation, while the remaining 41 displayed an iron‐independent decrease in pilin variation. Based on the levels of antigenic variation impairment, we defined the genes as being essential for, important for, or involved in antigenic variation. DNA repair and DNA transformation frequencies of each mutant were measured to determine whether other recombination‐based processes were also affected in the mutants. Each mutant was placed into one of six classes based on their pilin variation, DNA repair and DNA transformation phenotypes. Among the many genes identified, recR is shown to be an additional member of the gonococcal RecF‐like recombination pathway. In addition, recG and ruvA represent the first evidence that the processing of Holliday junctions is required for pilin antigenic variation. Moreover, two independent insertions in a non‐coding region upstream of the pilE gene suggest that cis‐acting sequences important for pilin variation are found in that region. Finally, insertions that effect expression of the thrB and thrC genes suggest that molecules in the threonine biosynthetic pathway are important for pilin variation. Many of the other genes identified in this genetic screen do not have an obvious role in pilin variation, DNA repair, or DNA transformation.
Bacterial ribosomal RNA in pieces
Authors: Evguenieva‐Hackenberg Elena
Published: June 2005

The exact knowledge on the ribosomal RNA (rRNA) structure is an important prerequisite for work  with rRNA sequences in bioinformatic analyses and in experimental research. Most available rRNA sequences of bacteria are based on gene sequences and on similarity analyses using Escherichia coli rRNA as a standard. Therefore, it is often overlooked that many bacteria harbour mature rRNA ‘in pieces’. In some cases, the processing steps during the fragmentation lead to the removal of rRNA segments that are usually found in the ribosome. In this review, the current knowledge on the mechanisms of rRNA fragmentation and on the occurrence of fragmented rRNA in bacteria is summarized, and the physiological implications of this phenomenon are discussed.
Interactions between folding factors and bacterial outer membrane proteins
Authors: Mogensen Jesper E. , Otzen Daniel E.
Published: June 2005

The outer membrane is the first line of contact between Gram‐negative bacteria and their external environment. Embedded in the outer membrane are integral outer membrane proteins (OMPs) that perform a diverse range of tasks. OMPs are synthesized in the cytoplasm and are translocated across the inner membrane and probably diffuse through the periplasm before they are inserted into the outer membrane in a folded and biologically active form. Passage through the periplasm presents a number of challenges, due to the hydrophobic nature of the OMPs and the choice of membranes into which they can insert. Recently, a number of periplasmic proteins and one OMP have been shown to play a role in OMP biogenesis. In this review, we describe what is known about these folding factors and how they function in a biological context. In particular, we focus on how they interact with the OMPs at the molecular level and present a comprehensive overview of data relating to a possible effect on OMP folding yield and kinetics. Furthermore, we discuss the role of lipo‐chaperones, i.e. lipopolysaccharide and phospholipids, in OMP folding. Important advances have clearly been made in the field, but much work remains to be done, particularly in terms of describing the biophysical basis for the chaperone–OMP interactions which so intricately regulate OMP biogenesis.
CTXφ and Vibrio cholerae: exploring a newly recognized type of phage–host cell relationship
Authors: McLeod Sarah M. , Kimsey Harvey H. , Davis Brigid M. , Waldor Matthew K.
Published: June 2005

The genes encoding cholera toxin, one of the principal virulence factors of the diarrhoeal pathogen Vibrio cholerae, are part of the genome of CTXφ, a filamentous bacteriophage. Thus, CTXφ has played a critical role in the evolution of the pathogenicity of V. cholerae. Unlike the well‐studied F pilus‐specific filamentous coliphages, CTXφ integrates site‐specifically into its host chromosome and forms stable lysogens. Here we focus on the CTXφ life cycle and, in particular, on recent studies of the mechanism of CTXφ integration and the factors that govern lysogeny. These and other processes illustrate the remarkable dependence of CTXφ on host‐encoded factors.
Effect of 5′‐proximal elements on decay of a model mRNA in Bacillus subtilis
Authors: Sharp Josh S. , Bechhofer David H.
Published: June 2005

Previous work showed that a 42‐nucleotide sequence from an SP82 bacteriophage early RNA functions as a 5′ mRNA stabilizer in Bacillus subtilis. Real‐time reverse transcriptase polymerase chain reaction (RT‐PCR) analysis of decay of a model mRNA with alterations at the 5′‐end was used to elucidate the mechanism of SP82‐mediated stability. A predicted 5′‐terminal stem–loop structure was essential for stabilization. Increasing the strength of the 5′‐terminal structure above a minimum level did not result in increased stability. A thorough analysis of the context in which the stabilizing structure occurred included the effects of distance from 5′‐end, translation of downstream coding sequence, and distance between the secondary structure and the ribosome binding site. Our data are consistent with the dominant mRNA decay pathway in B. subtilis being 5′‐end dependent.
Dissecting functional similarities of ribosome‐associated chaperones from Saccharomyces cerevisiae and Escherichia coli
Authors: Rauch Thomas , Hundley Heather A. , Pfund Chris , Wegrzyn Renee D. , Walter William , Kramer Günter , Kim So‐Young , Craig Elizabeth A. , Deuerling Elke
Published: June 2005

Ribosome‐tethered chaperones that interact with nascent polypeptide chains have been identified in both prokaryotic and eukaryotic systems. However, these ribosome‐associated chaperones share no sequence similarity: bacterial trigger factors (TF) form an independent protein family while the yeast machinery is Hsp70‐based. The absence of any component of the yeast machinery results in slow growth at low temperatures and sensitivity to aminoglycoside protein synthesis inhibitors. After establishing that yeast ribosomal protein Rpl25 is able to recruit TF to ribosomes when expressed in place of its Escherichia coli homologue L23, the ribosomal TF tether, we tested whether such divergent ribosome‐associated chaperones are functionally interchangeable. E. coli TF was expressed in yeast cells that lacked the endogenous ribosome‐bound machinery. TF associated with yeast ribosomes, cross‐linked to yeast nascent polypeptides and partially complemented the aminoglycoside sensitivity, demonstrating that ribosome‐associated chaperones from divergent organisms share common functions, despite their lack of sequence similarity.
The Escherichia coli baby cell column: a novel cell synchronization method provides new insight into the bacterial cell cycle
Authors: Bates David , Epstein Jessica , Boye Erik , Fahrner Karen , Berg Howard , Kleckner Nancy
Published: June 2005

We describe a new method for synchronizing bacterial cells. Cells that have transiently expressed an inducible mutant ‘sticky’ flagellin are adhered to a volume of glass beads suspended in a chromatography column though which growth medium is pumped. Following repression of flagellin synthesis, newborn cells are eluted from the column in large quantities exceeding that of current baby machine techniques by approximately 10‐fold. Eluted cultures of ‘baby cells’ are highly synchronous as determined by analysis of DNA replication, cell division and other events, over time after elution from the column. We also show that use of ‘minutes after elution’ as a time metric permits much greater temporal resolution among sequential chromosomal events than the commonly used metric of cell size (length). The former approach reveals the existence of transient intermediate stages that are missed by the latter approach. This finding has two important implications. First, at a practical level, the baby cell column is a particularly powerful method for temporal analysis. Second, at a conceptual level, replication‐related events are more tightly linked to cell birth (i.e. cell division) than to absolute cell mass.
Co‐ordinated bacteriocin production and competence development: a possible mechanism for taking up DNA from neighbouring species
Authors: Kreth Jens , Merritt Justin , Shi Wenyuan , Qi Fengxia
Published: June 2005

It is important to ensure DNA availability when bacterial cells develop competence. Previous studies in Streptococcus pneumoniae demonstrated that the competence‐stimulating peptide (CSP) induced autolysin production and cell lysis of its own non‐competent cells, suggesting a possible active mechanism to secure a homologous DNA pool for uptake and recombination. In this study, we found that in Streptococcus mutans CSP induced co‐ordinated expression of competence and mutacin production genes. This mutacin (mutacin IV) is a non‐lantibiotic bacteriocin which kills closely related Streptococcal species such as S. gordonii. In mixed cultures of S. mutans and S. gordonii harbouring a shuttle plasmid, plasmid DNA transfer from S. gordonii to S. mutans was observed in a CSP and mutacin IV‐dependent manner. Further analysis demonstrated an increased DNA release from S. gordonii upon addition of the partially purified mutacin IV extract. On the basis of these findings, we propose that Streptococcus mutans, which resides in a multispecies oral biofilm, may utilize the competence‐induced bacteriocin production to acquire transforming DNA from other species living in the same ecological niche. This hypothesis is also consistent with a well‐known phenomenon that a large genomic diversity exists among different S. mutans strains. This diversity may have resulted from extensive horizontal gene transfer.
Ribosome‐based protein folding systems are structurally divergent but functionally universal across biological kingdoms
Authors: Ito Koreaki
Published: June 2005

In bacteria, Trigger factor (TF) is the first chaperone that interacts with nascent polypeptides as soon as they emerge from the exit tunnel of the ribosome. TF binds to the ribosomal protein L23 located next to the tunnel exit of the large subunit, with which it forms a cradle‐like space embracing the polypeptide exit region. It cooperates with the DnaK Hsp70 chaperone system to ensure correct folding of a number of newly translated cytosolic proteins in Escherichia coli. Whereas TF is exclusively found in prokaryotes and chloroplasts, Saccharomyces cerevisiae, a eukaryotic microorganism, has a three‐member Hsp70‐J protein complex, Ssb–Ssz–Zuo, which could act as a ribosome‐associated folding facilitator. In the work reported in this volume of Molecular Microbiology, Rauch et al. (2005, Mol Microbiol, doi:10.1111/j.1365‐2958.2005.04690.x) examined the functional similarity of the ribosome‐associated chaperones in prokaryotes and eukaryotes. In spite of the fact that TF and the Hsp70‐based triad are structurally unrelated, TF can bind to the yeast ribosome via Rpl25 (the L23 counterpart) and can substitute for some, but not all, of the functions assigned to Ssb–Ssz–Zuo in yeast. The functional conservation of the ribosome‐associated chaperones without structural similarity is remarkable and suggests that during evolution nature has employed a common design but divergent components to facilitate folding of polypeptides as they emerge from the ribosomal exit, a fundamental process required for the efficient expression of genetic information.
Development of the endoplasmic reticulum, mitochondrion and apicoplast during the asexual life cycle of Plasmodium falciparum
Authors: van Dooren Giel G. , Marti Matthias , Tonkin Christopher J. , Stimmler Luciana M. , Cowman Alan F. , McFadden Geoffrey I.
Published: June 2005

Plasmodium parasites are unicellular eukaryotes that undergo a series of remarkable morphological transformations during the course of a multistage life cycle spanning two hosts (mosquito and human). Relatively little is known about the dynamics of cellular organelles throughout the course of these transformations. Here we describe the morphology of three organelles (endoplasmic reticulum, apicoplast and mitochondrion) through the human blood stages of the parasite life cycle using fluorescent reporter proteins fused to organelle targeting sequences. The endoplasmic reticulum begins as a simple crescent‐shaped organelle that develops into a perinuclear ring with two small protrusions, followed by transformation into an extensive reticulated network as the parasite enlarges. Similarly, the apicoplast and the mitochondrion grow from single, small, discrete organelles into highly branched structures in later‐stage parasites. These branched structures undergo an ordered fission – apicoplast followed by mitochondrion – to create multiple daughter organelles that are apparently linked as pairs for packaging into daughter cells. This is the first in‐depth examination of intracellular organelles in live parasites during the asexual life cycle of this important human pathogen.
Dual regulation of genes involved in acetoin biosynthesis and motility/biofilm formation by the virulence activator AphA and the acetate‐responsive LysR‐type regulator AlsR in Vibrio cholerae
Authors: Kovacikova Gabriela , Lin Wei , Skorupski Karen
Published: June 2005

AphA is a quorum sensing‐regulated activator that initiates the virulence cascade in Vibrio cholerae by cooperating with the LysR‐type regulator AphB at the tcpPH promoter on the Vibrio pathogenicity island (VPI). To identify the ancestral chromosomal genes in V. cholerae regulated by AphA, we carried out a microarray analysis and show here that AphA influences the expression of 15 genes not associated with the VPI. One set of genes strongly repressed by AphA is involved in the biosynthesis of acetoin, a product synthesized by a variety of bacteria that plays a role in preventing intracellular acidification and which is essential for the viability of V. cholerae in the presence of glucose. Also present in this operon are two putative signal transduction proteins with EAL and GGDEF domains that oppositely influence motility and biofilm formation. Gel mobility shift assays show that AphA binds to a site upstream of the first gene in the acetoin operon. Transcriptional lacZ fusions indicate that at low cell density AphA represses the expression of the acetoin genes up to 15‐fold. Voges Proskauer tests confirm that deletion of AphA increases the production of acetoin under non‐inducing conditions and also that the LysR‐type regulator AlsR divergently transcribed from the operon is required for its production. This is the first report of a specific repressor protein involved in the transcriptional control of acetoin production as well as the co‐regulation of these genes with those that influence motility and biofilm formation. The results here provide a model for the dual regulation of these processes by acetate and quorum sensing through AlsR and AphA.
Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression
Authors: Browning Douglas F. , Grainger David C. , Beatty Christine M. , Wolfe Alan J. , Cole Jeffrey A. , Busby Stephen J. W.
Published: June 2005

Expression from the Escherichia coli nrf operon promoter is activated by the anaerobically triggered transcription factor, FNR, and by the nitrate/nitrite ion‐controlled response regulators, NarL or NarP, but is repressed by the IHF and Fis proteins. Here, we present in vitro studies on the nrf promoter, using permanganate footprinting to measure open complex formation, and DNase I footprinting to monitor binding of the different regulators and the interactions between them. Our results show that open complex formation is completely dependent on FNR and is enhanced by NarL, but is repressed by IHF or Fis. NarL counteracts repression by IHF but is unable to alter repression by Fis. These results suggest mechanisms by which nrf promoter activity is modulated by the different factors. Expression from the nrf promoter is known to be repressed in rich media, especially in the presence of glucose, but the molecular basis of this is not understood. Here, we show that this catabolite repression is relieved by mutations that weaken the DNA site for Fis, improve the DNA site for FNR or improve the promoter −10 or −35 elements. Hence, Fis protein is a major factor responsible for catabolite repression at the nrf promoter, and Fis can override activation by FNR and NarL or NarP.
HxlR, a member of the DUF24 protein family, is a DNA‐binding protein that acts as a positive regulator of the formaldehyde‐inducible hxlAB operon in Bacillus subtilis
Authors: Yurimoto Hiroya , Hirai Reiko , Matsuno Norimichi , Yasueda Hisashi , Kato Nobuo , Sakai Yasuyoshi
Published: June 2005

The HxlR protein from Bacillus subtilis belongs to the DUF24 protein family (InterPro No. IPR002577) of unknown function. The hxlR gene that encodes this protein is located upstream of the hxlAB operon. This operon encodes two key enzymes in the ribulose monophosphate pathway that are involved in formaldehyde fixation, 3‐hexulose‐6‐phosphate synthase and 6‐phospho‐3‐hexuloisomerase. Expression of the hxlAB operon is induced by the presence of formaldehyde. Recombinant HxlR prepared from Escherichia coli showed specific binding to a region of DNA upstream of the hxlAB operon. Using gel‐retardation and DNase I footprinting assays, we identified two 25 bp binding regions for HxlR within the upstream DNA. Surface plasmon resonance analyses suggested that two HxlR dimers sequentially bound to the DNA. Finally, we demonstrated that each of the two binding regions for HxlR was necessary for formaldehyde‐induced expression of the hxlAB operon in B. subtilis. Thus, we have shown that HxlR is a DNA‐binding protein that is necessary for formaldehyde‐induced expression of hxlAB in B. subtilis.
A chaperone‐like HrpG protein acts as a suppressor of HrpV in regulation of the Pseudomonas syringae pv. syringae type III secretion system
Authors: Wei Chia‐Fong , Deng Wen‐Ling , Huang Hsiou‐Chen
Published: June 2005

The cloned hrp/hrc cluster of Pseudomonas syringae pv. syringae 61 (Pss61) contains 28 proteins, and many of those are assembled into a type III secretion system (TTSS) that is responsible for eliciting the hypersensitive response (HR) in non‐host plants and causing diseases on host plants (Huang et al., 1995). hrpG, the second gene in the hrpC operon, encodes a 15.4 kDa cytoplasmic protein whose predicted structure is similar to SicP (E‐value: 0.19), a TTSS chaperone of Salmonella typhimurium. Two non‐polar hrpG mutants, Pss61‐N826 and Pss61‐N674, were produced to investigate the biological function of hrpG gene. Pss61‐N826, generated by replacing the coding sequence of hrpG with an nptII gene lacking both the promoter and the terminator, was found to be capable of eliciting the wild‐type HR; whereas Pss61‐N674 generated by replacement of a terminatorless nptII gene in the hrpG coding sequence showed the delayed HR phenotype. Northern and Western blotting analyses showed that the expression of hrpZ, hrcJ and hrcQb genes residing on two different operons in Pss61‐N674 was reduced due to the nptII promoter‐driven constitutive expression of hrpV that codes for a negative regulator. Interestingly, a plasmid‐borne hrpG can derepress the hrp expression in Pss61‐N674 and in Pss61 overexpressing HrpV without decreasing the hrpV transcript. Moreover, results of yeast two‐hybrid assay, pull‐down assay and far Western analysis show that HrpG and HrpV interact with each other in vivo and in vitro. Additionally, HrpV interacts with a positive regulator HrpS according to analysis of a yeast two‐hybrid system. Based on the results presented in this study, we propose that HrpG acts as a suppressor of the negative regulator HrpV mediated via protein–protein interaction, leading to modulation of hrp/hrc expression subsequently freeing HrpS to promote the activation of other downstream hrp/hrc genes.
A single gene directs both production and immunity of halocin C8 in a haloarchaeal strain AS7092
Authors: Sun Chaomin , Li Yun , Mei Shuangshuang , Lu Qiuhe , Zhou Ligang , Xiang Hua
Published: June 2005

Halocin C8 (HalC8) is an extremely stable and hydrophobic microhalocin with 76 amino acids, and has a wide inhibitory spectrum against the haloarchaea. It is derived from the C‐terminus of a 283‐amino‐acid prepro‐protein (ProC8), which was demonstrated by molecular cloning of the halC8 gene, and verified by the N‐terminal amino acid sequencing as well as MALDI‐TOF‐MS analysis of the purified HalC8. The production of this halocin is controlled through both transcription regulation and protein processing: the halC8 transcripts and HalC8 activity rapidly increased to maximal levels upon transition from exponential to stationary phase. However, while halC8 transcripts remained abundant, the HalC8 processing was inhibited during stationary phase. Remarkably, agar‐diffusion test revealed the unprocessed ProC8 and its 207‐amino‐acid N‐terminal peptide (HalI), with or without the putative Tat signal sequence, were capable to block the halocin activity of HalC8 in vitro. In addition, heterologous expression of HalI in Haloarcula hispanica rendered this sensitive strain remarkable resistance to HalC8, indicating that HalI encodes the immunity property of the producer. In accordance with this immunity function, HalI and ProC8 were both found localized on the cellular membrane. Protein interaction assay revealed that HalI likely sequestrated the HalC8 activity by specific binding. To our knowledge, this is the first report on halocin immunity, and our results that a single gene encodes both peptide antibiotic and immunity protein also provide a novel immune mechanism for peptide antibiotics.
Binding sites of VanRB and σ70 RNA polymerase in the vanB vancomycin resistance operon of Enterococcus faecium BM4524
Authors: Depardieu Florence , Courvalin Patrice , Kolb Annie
Published: June 2005

The vanB operon of Enterococcus faecium BM4524 which confers inducible resistance to vancomycin is composed of the vanRBSB gene encoding a two‐component regulatory system and the vanYBWHBBXB resistance genes that are transcribed from promoters PRB and PYB respectively. In this study, primer extension revealed transcription start sites at 13 and 48 bp upstream from the start codon of vanRB and vanYB, respectively, that allowed identification of −10 and −35 promoter motifs. The VanRB protein was overproduced in Escherichia coli, purified and phosphorylated (VanRB‐P) non‐enzymically with acetylphosphate. VanRB‐P and VanRB specifically bound to PRB and PYB promoters. VanRB bound at a single site at position −32.5 upstream from the PRB transcriptional start site and at two sites at positions −33.5 and −55.5 upstream from that of PYB. The proximal VanRB binding site overlapped the −35 region of both promoters. VanRB was converted from a monomer to a dimer upon acetylphosphate treatment. VanRB‐P had higher affinity than VanRB for its targets and appeared more efficient than VanRB in promoting open complex formation with PRB and PYB. In the absence of regulator, E. coli RNA polymerase was able to interact with PRB but not with PYB. Phosphorylation of VanRB significantly increased promoter interaction with RNA polymerase and led to an extended and modified footprint. In vitro transcription assays showed that VanRB‐P activates PYB more strongly than PRB. Analysis of the protected regions revealed one copy of a 21 bp sequence in the PRB promoter and two copies in the PYB promoter which may serve as recognition sites for VanRB and VanRB‐P binding that are required for transcriptional activation and expression of vancomycin resistance.
Cell cycle‐regulated degradation of tmRNA is controlled by RNase R and SmpB
Authors: Hong Sue‐Jean , Tran Quyen‐Anh , Keiler Kenneth C.
Published: June 2005

The  production  and  removal  of  regulatory  RNAs must be controlled to ensure proper physiological responses. SsrA RNA (tmRNA), a regulatory RNA conserved in all bacteria, is cell cycle regulated and is important for control of cell cycle progression in Caulobacter crescentus. We report that RNase R, a highly conserved 3′ to 5′ exoribonuclease, is required for the selective degradation of SsrA RNA in stalked cells. Purified RNase R degrades SsrA RNA in vitro, and is kinetically competent to account for all SsrA RNA turnover. SmpB, a tmRNA‐binding protein, protects SsrA RNA from RNase R degradation in vitro, and the levels of SmpB protein during the cell cycle correlate with SsrA RNA stability. These results suggest that SmpB binding controls the timing of SsrA RNA degradation by RNase R. We propose a model for the regulated degradation of SsrA RNA in which RNase R degrades SsrA RNA from a non‐tRNA‐like 3′ end, and SmpB specifically protects SsrA RNA from RNase R. This model explains the regulation of SsrA RNA in other bacteria, and suggests that a highly conserved regulatory mechanism controls SsrA activity.
The transcriptional activator ClgR controls transcription of genes involved in proteolysis and DNA repair in Corynebacterium glutamicum
Authors: Engels Sabine , Ludwig Carsten , Schweitzer Jens‐Eric , Mack Christina , Bott Michael , Schaffer Steffen
Published: June 2005

Expression of the structural genes encoding the ATP‐dependent proteases ClpCP and Lon in Corynebacterium glutamicum and Streptomyces lividans is activated by the transcriptional regulator ClgR in response to yet unknown environmental stimuli. As it was not known whether ClgR controls expression of additional genes we used DNA microarrays in order to comprehensively define the ClgR regulon in C. glutamicum. The mRNA levels of 16 genes decreased ≥ 2‐fold in a ΔclgRΔclpC mutant (ClgR absent) compared with a ΔclpC mutant (ClgR present). For five genes in four operons (NCgl0748, ptrB, hflX and NCgl0240‐recR) regulation by ClgR could be independently verified by primer extension analyses and confirmation of binding of purified ClgR to the regulatory regions of these operons. ptrB encodes an endopeptidase, which is consistent with the proteolytic functions of the genes already known to be under ClgR control. However, RecR is unrelated to proteolysis but required for recombinational repair of UV‐induced DNA damage. Possibly ClgR‐dependent activation of gene expression is triggered by environmental stresses damaging both proteins and nucleic acids, although DNA damage induced by UV radiation and mitomycin C treatment did not result in ClgR‐dependent transcriptional activation of any of the newly identified ClgR regulon members. In order to functionally analyse the NCgl0748 and hflX genes we have constructed C. glutamicum strains with deletions in these genes. The ΔNCgl0748 mutant displayed reduced growth rates in minimal and rich media. The NCgl0748 protein was shown to be localized in the cytoplasm only, while the HflX pool is equally distributed between cytoplasm and plasma membrane. In order to study the proposed degradation of ClgR by ClpCP we have constructed a conditional clpP1P2 mutant. Depletion of ClpP1 and ClpP2 in that strain resulted in the accumulation of ClgR, indicating that ClgR is in fact a substrate of the ClpCP1 and/or ClpCP2 protease in C. glutamicum.
Contributions of protein structure and gene position to the compartmentalization of the regulatory proteins σE and SpoIIE in sporulating Bacillus subtilis
Authors: McBride Shonna M. , Rubio Aileen , Wang Lei , Haldenwang William G.
Published: June 2005

At an early stage in endospore formation Bacillus subtilis partitions itself into two dissimilar compartments with unique developmental fates. Transcription appropriate to each compartment is initiated by the activation of compartment‐specific RNA polymerase sigma subunits, σE in the mother cell and σF in the forespore. Among the possible factors contributing to the compartment specificity of σE and σF is the selective accumulation of the σE protein in the mother cell and that of SpoIIE, a regulatory phosphatase essential to the activation of σF, in the forespore. In the current work, fluorescent microscopy is used to investigate the contributions of σE and SpoIIE's protein structures, expression and the genetic asymmetry that develops during chromosome translocation into the forespore on their abundance in each compartment. Time of entry of the spoIIE and sigE genes into the forespore was found to have a significant effect on the enrichment of their products in one or the other compartment. In contrast, the structures of the proteins themselves do not appear to promote their transfer to a particular compartment, but nonetheless contribute to compartmentalization by facilitating degradation in the compartment where each protein's activity would be inappropriate.