bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental and landscape effects on cross‐pollination rates observed at long distance among French oilseed rape Brassica napus commercial fields
Authors: Devaux C. , Klein E. K. , Lavigne C. , Sausse C. , Messéan A. 
Published: October 2007

Summary

Evaluation of our ability to predict cross‐pollination rates (CPR) at long distance using dispersal functions estimated in experimental set‐ups differing by either their scale or their environmental conditions is crucial to establish appropriate management rules following the release of genetically modified (GM) crops.
From 1998 to 2004 we measured oilseed rape CPR in commercial fields for 44 donor‐recipient couples separated by 220 up to 2000 m, from up to three different pollen donor cultivars in two French oilseed rape production areas. We followed the same sampling and screening designs and tested the effect of region, year, size, cultivar and distance on the observed CPR.
We then compared observed CPR to predictions from six empirical pollen dispersal models based on dispersal kernels that were fitted previously at the local and landscape scales. These predictions allowed us to test the possibility to extrapolate and up‐scale dispersal kernels.
The observed CPR varied from 0% to 0·092%. They were higher in Champagne‐Ardennes, where they depended negatively on distance, than in Bourgogne where they did not depend on distance. CPR also differed among years, being nil for the last 3 successive years, partly because of different environmental conditions and detection issues. CPR depended further on the source cultivars due to differences in pollen production. Dispersal kernels fitted at the local scale lead to systematic and huge underestimation of CPR, when observed. The power‐law kernel fitted at the landscape scale under‐estimated CPR by two orders of magnitude above 400 m but followed the rate of decrease of the observed pollination with distance.
Synthesis and applications. Caution should be taken when extrapolating and up‐scaling dispersal kernels and models because predictions may differ greatly from observations. Models should rely at least upon dispersal kernels estimated from landscape‐scale data obtained in different regions. Models should also integrate several phenomena at the agro‐ecosystem scale including the dispersal by insects and become more mechanistic to account for variations observed among years, environments and distance to borders.
The AraC/XylS regulator TxtR modulates thaxtomin biosynthesis and virulence in Streptomyces scabies
Authors: Joshi Madhumita V. , Bignell Dawn R. D. , Johnson Evan G. , Sparks Jed P. , Gibson Donna M. , Loria Rosemary 
Published: October 2007

Summary Streptomyces scabies is the best studied of those streptomycetes that cause an economically important disease known as potato scab. The phytotoxin thaxtomin is made exclusively by these pathogens and is required for virulence. Here we describe regulation of thaxtomin biosynthesis by TxtR, a member of the AraC/XylS family of transcriptional regulators. The txtR gene is imbedded in the thaxtomin biosynthetic pathway and is located on a conserved pathogenicity island in S. scabies, S. turgidiscabies and S. acidiscabies. Thaxtomin biosynthesis was abolished and virulence was almost eliminated in the txtR deletion mutant of S. scabies 87.22. Accumulation of thaxtomin biosynthetic gene (txtA, txtB, txtC, nos) transcripts was reduced compared with the wild‐type S. scabies 87.22. NOS‐dependent nitric oxide production by S. scabies was also reduced in the mutant. The TxtR protein bound cellobiose, an inducer of thaxtomin production, and transcription of txtR and thaxtomin biosynthetic genes was upregulated in response to cellobiose. TxtR is the first example of an AraC/XylS family protein regulated by cellobiose. Together, these data suggest that cellobiose, the smallest oligomer of cellulose, may signal the availability of expanding plant tissue, which is the site of action of thaxtomin.
A partner for the resuscitation‐promoting factors of Mycobacterium tuberculosis
Authors: Hett Erik C. , Chao Michael C. , Steyn Adrie J. , Fortune Sarah M. , Deng Lynn L. , Rubin Eric J. 
Published: October 2007

SummaryMany cases of active tuberculosis are thought to result from the reactivation of dormant Mycobacterium tuberculosis from a prior infection, yet remarkably little is known about the mechanism by which these non‐sporulating bacteria reactivate. A family of extracellular bacterial proteins, known as resuscitation‐promoting factors (Rpfs), has previously been shown to stimulate growth of dormant mycobacteria. While Rpf proteins are clearly peptidoglycan glycosidases, the mechanism and role of Rpf in mediating reactivation remains unclear. Here we use a yeast two‐hybrid screen to identify potential binding partners of RpfB and report the interaction between RpfB and a putative mycobacterial endopeptidase, which we named Rpf‐interacting protein A (RipA). This interaction was confirmed by in vitro and in vivo co‐precipitation assays. The interacting domains map to the C‐termini of both proteins, near predicted enzymatic domains. We show that RipA is a secreted, cell‐associated protein, found in the same cellular compartment as RpfB. Both RipA and RpfB localize to the septa of actively growing bacteria by fluorescence microscopy. Finally, we demonstrate that RipA is capable of digesting cell wall material and is indeed a peptidoglycan hydrolase. The interaction between these two peptidoglycan hydrolases at the septum suggests a role for the complex in cell division, possibly during reactivation.
Glutathione and Gts1p drive beneficial variability in the cadmium resistances of individual yeast cells
Authors: Smith Matthew C. A. , Sumner Edward R. , Avery Simon V. 
Published: October 2007

SummaryPhenotypic heterogeneity among individual cells within isogenic populations is widely documented, but its consequences are not well understood. Here, cell‐to‐cell variation in the stress resistance of Saccharomyces cerevisiae, particularly to cadmium, was revealed to depend on the antioxidant glutathione. Heterogeneity was decreased strikingly in gsh1 mutants. Furthermore, cells sorted according to differing reduced‐glutathione (GSH) contents exhibited differing stress resistances. The vacuolar GSH‐conjugate pathway of detoxification was implicated in heterogeneous Cd resistance. Metabolic oscillations (ultradian rhythms) in yeast are known to modulate single‐cell redox and GSH status. Gts1p stabilizes these oscillations and was found to be required for heterogeneous Cd and hydrogen‐peroxide resistance, through the same pathway as Gsh1p. Expression of GTS1 from a constitutive tet‐regulated promoter suppressed oscillations and heterogeneity in GSH content, and resulted in decreased variation in stress resistance. This enabled manipulation of the degree of gene expression noise in cultures. It was shown that cells expressing Gts1p heterogeneously had a competitive advantage over more‐homogeneous cell populations (with the same mean Gts1p expression), under continuous and fluctuating stress conditions. The results establish a novel molecular mechanism for single‐cell heterogeneity, and demonstrate experimentally fitness advantages that depend on deterministic variation in gene expression within cell populations.
The initiation and pattern of spread of histone H4 acetylation parallel the order of transcriptional activation of genes in the aflatoxin cluster
Authors: Roze Ludmila V. , Arthur Anna E. , Hong Sung‐Yong , Chanda Anindya , Linz John E. 
Published: October 2007

SummaryThe 27 genes involved in aflatoxin biosynthesis are clustered within a 70 kb region in the Aspergillus parasiticus genome. Using chromatin immunoprecipitation, we demonstrated a positive correlation between the initiation and spread of histone H4 acetylation in aflatoxin promoters and the onset of accumulation of aflatoxin proteins and aflatoxin. Histone H4 acetylation in the pksA (encodes an ‘early’ biosynthetic pathway enzyme) promoter peaked at 30 h, prior to the increased acetylation in the omtA and ordA (encode ‘late’ enzymes) promoters detected at 40 h. The specific order in which pksA, ver‐1 (encodes a ‘middle’ enzyme) and omtA transcripts accumulated in cells paralleled the pattern of spread of histone H4 acetylation. Binding of AflR, a positive regulator of aflatoxin biosynthesis, to the ordA promoter showed a positive correlation with the spread of histone H4 acetylation. The data suggest that the order of genes within the aflatoxin cluster determines the timing and order of transcriptional activation, and that the site of initiation and spread of histone H4 acetylation mediate this process. Our data indicate that the aflatoxin and adjacent sugar utilization clusters are part of a larger ‘regulatory unit’.
RutR is the uracil/thymine‐sensing master regulator of a set of genes for synthesis and degradation of pyrimidines
Authors: Shimada Tomohiro , Hirao Kiyo , Kori Ayako , Yamamoto Kaneyoshi , Ishihama Akira 
Published: October 2007

SummaryUsing the genomic SELEX, a total of six Escherichia coli DNA fragments have been identified, which formed complexes with transcription factor RutR. The RutR regulon was found to include a large number of genes encoding components for not only degradation of pyrimidines but also transport of glutamate, synthesis of glutamine, synthesis of pyrimidine nucleotides and arginine, and degradation of purines. DNase I footprinting indicated that RutR recognizes a palindromic sequence of TTGACCAnnTGGTCAA. The RutR box in P1 promoter of carAB encoding carbamoyl phosphate synthetase, a key enzyme of pyrimidine synthesis, overlaps with the PepA (CarP) repressor binding site, implying competition between RutR and PepA. Adding either uracil or thymine abolished RutR binding in vitro to the carAB P1 promoter. Accordingly, in the rutR‐deletion mutant or in the presence of uracil, the activation in vivo of carAB P1 promoter was markedly reduced. Northern blot analysis of the RutR target genes indicated that RutR represses the Gad system genes involved in glutamate‐dependent acid resistance and allantoin degradation. Altogether we propose that RutR is the pyrimidine sensor and the master regulator for a large set of the genes involved in the synthesis and degradation of pyrimidines.
GolS controls the response to gold by the hierarchical induction of Salmonella‐specific genes that include a CBA efflux‐coding operon
Authors: Pontel Lucas B. , Audero María E. Pérez , Espariz Martín , Checa Susana K. , Soncini Fernando C. 
Published: October 2007

Summary Salmonella employs a specific set of proteins that allows it to detect the presence of gold salts in the environment and to mount the appropriate resistance response. This includes a P‐type ATPase, GolT, and a small cytoplasmic metal binding protein, GolB. Their expression is controlled by a MerR‐like sensor, GolS, which is highly selective for Au ions. Here, we identify a new GolS‐controlled operon named gesABC which codes for a CBA efflux system, and establish its role in Au resistance. GesABC can also mediate drug resistance when induced by Au in a GolS‐dependent manner, in a strain deleted in the main drug transporter acrAB. The GolS‐controlled transcription of gesABC differs from the other GolS‐regulated loci. It is activated by gold, but not induced by copper, even in a strain deleted of the main Cu transporter gene copA, which triggers a substantial GolS‐dependent induction of golTS and golB. We demonstrate that the Au‐dependent induction of gesABC transcription requires higher GolS levels than for the other members of the gol regulon. This correlates with a divergent GolS operator in the gesABC promoter. We propose that the hierarchical induction within the gol regulon allows Salmonella to cope with Au‐contaminated environments.
Nitrosative stress treatment of E. coli targets distinct set of thiol‐containing proteins
Authors: Brandes Nicolas , Rinck Andrea , Leichert Lars Ingo , Jakob Ursula 
Published: October 2007

SummaryReactive nitrogen species (RNS) function as powerful antimicrobials in host defence, but so far little is known about their bacterial targets. In this study, we set out to identify Escherichia coli proteins with RNS‐sensitive cysteines. We found that only a very select set of proteins contain cysteines that undergo reversible thiol modifications upon nitric oxide (NO) treatment in vivo. Of the 10 proteins that we identified, six (AtpA, AceF, FabB, GapA, IlvC, TufA) have been shown to harbour functionally important thiol groups and are encoded by genes that are considered essential under our growth conditions. Media supplementation studies suggested that inactivation of AceF and IlvC is, in part, responsible for the observed NO‐induced growth inhibition, indicating that RNS‐mediated modifications play important physiological roles. Interestingly, the majority of RNS‐sensitive E. coli proteins differ from E. coli proteins that harbour H2O2‐sensitive thiol groups, implying that reactive oxygen and nitrogen species affect distinct physiological processes in bacteria. We confirmed this specificity by analysing the activity of one of our target proteins, the small subunit of glutamate synthase. In vivo and in vitro activity studies confirmed that glutamate synthase rapidly inactivates upon NO treatment but is resistant towards other oxidative stressors.
Genetic basis for retention of a critical virulence plasmid of Borrelia burgdorferi
Authors: Jewett Mollie W. , Byram Rebecca , Bestor Aaron , Tilly Kit , Lawrence Kevin , Burtnick Mary N. , Gherardini Frank , Rosa Patricia A. 
Published: October 2007

SummaryThe genome of Borrelia burgdorferi is composed of one linear chromosome and approximately 20 linear and circular plasmids. Although some plasmids are required by B. burgdorferi in vivo, most plasmids are dispensable for growth in vitro. However, circular plasmid (cp) 26 is present in all natural isolates and has never been lost during in vitro growth. This plasmid carries ospC, which is critical for mammalian infection. We previously showed that cp26 encodes essential functions, including the telomere resolvase, ResT, and hence cannot be displaced. Here we identify two additional essential genes on cp26, bbb26 and bbb27, through a systematic attempt to inactivate each open reading frame (ORF). Furthermore, an incompatible plasmid carrying resT, bbb26 and bbb27 could displace cp26. Computational and experimental analyses suggested that both BBB26 and BBB27 are membrane‐associated, periplasmic proteins. These data indicate that bbb26 and bbb27 encode essential but possibly redundant functions and that one or the other of these cp26 genes, in addition to resT, is required for bacterial viability. We conclude that the genetic linkage of critical physiological and virulence functions on cp26 is pertinent to its stable maintenance throughout the evolution of B. burgdorferi.
TECHNICAL ADVANCE: LeafAnalyser: a computational method for rapid and large‐scale analyses of leaf shape variation
Authors: Weight Caroline , Parnham Daniel , Waites Richard 
Published: October 2007

SummaryA comprehensive understanding of leaf shape is important in many investigations in plant biology. Techniques to assess variation in leaf shape are often time‐consuming, labour‐intensive and prohibited by complex calculation of large data sets. We have developed LeafAnalyser, software that uses image‐processing techniques to greatly simplify the measurement of leaf shape variation. LeafAnalyser places a large number of evenly distributed landmarks along leaf margins and records the position of each automatically. We used LeafAnalyser to analyse the variation in 3000 leaves from 400 plants of Antirrhinum majus. We were able to summarise the major trends in leaf shape variation using a principal components (PC) analysis and assess the changes in size, width and tip‐to‐base asymmetry within our leaf library. We demonstrate how this information can be used to develop a model that describes the range and variation of leaf shape within standard wild‐type lines, and illustrate the shape transformations that occur between leaf nodes. We also show that information from LeafAnalyser can be used to identify novel trends in shape variation, as low‐variance PCs that only affect a subset of position landmarks. These results provide a high‐throughput method to calculate leaf shape variation that allows a large number of leaves to be visualised in higher‐dimensional phenotypic space. To illustrate the applicability of LeafAnalyser we also calculated the leaf shape variation in 300 leaves from Arabidopsis thaliana.
A transcriptional repression motif in the MADS factor AGL15 is involved in recruitment of histone deacetylase complex components
Authors: Hill Kristine , Wang Huai , Perry Sharyn E. 
Published: October 2007

Summary AGAMOUS‐like 15 (AGL15) encodes a MADS‐domain transcription factor that is preferentially expressed in the plant embryo. A number of direct downstream targets of AGL15 have been identified, and although some of these target genes are induced in response to AGL15, others are repressed. Additionally, direct target genes have been analyzed that exhibit strong association with AGL15 in vivo, yet in vitro AGL15 binds only weakly. These data suggest that AGL15 may form complexes with other proteins, thus modulating the specificity and function of AGL15 in planta. Here we report that AGL15 interacts with members of the SWI‐independent 3/histone deacetylase (SIN3/HDAC) complex, and that AGL15 target genes are also responsive to an AGL15 interacting protein that is also a member of this complex, SIN3‐associated polypeptide of 18 kDa (SAP18). AGL15 can repress transcription in vivo, and a region essential to this repressive function contains a motif that is conserved among putative orthologs of AGL15. This motif mediates the association of AGL15 with SAP18, thus providing a possible mechanism for the role of AGL15 in regulating gene expression via recruitment of an HDAC complex.
Application of carborundum abrasion for investigating the leaf epidermis: molecular cloning of Catharanthus roseus 16‐hydroxytabersonine‐16‐O‐methyltransferase
Authors: Levac Dylan , Murata Jun , Kim Won S. , De Luca Vincenzo 
Published: October 2007

SummaryThe Madagascar periwinkle (Catharanthus roseus) produces the well‐known and remarkably complex anti‐cancer dimeric alkaloids vinblastine and vincristine that are derived from the coupling of vindoline and catharanthine monomers. This study describes the novel application of a carborundum abrasion (CA) technique for large‐scale isolation of leaf epidermis‐enriched proteins in order to purify to apparent homogeneity 16‐hydroxytabersonine‐16‐O‐methyltransferase (16OMT), which catalyses the second of six steps in the conversion of tabersonine into vindoline, and to clone the gene. Functional expression and biochemical characterization of recombinant 16OMT demonstrated its very narrow substrate specificity and high affinity for 16‐hydroxytabersonine. In addition to allowing the cloning of this gene, the CA technique clearly showed that 16OMT is predominantly expressed in Catharanthus leaf epidermis. The results provide compelling evidence that most of the pathway for vindoline biosynthesis, including the O‐methylation of 16‐hydroxytabersonine, occurs exclusively in the leaf epidermis, with subsequent steps occurring in other leaf cell types.
Evidence for a sorting endosome in Arabidopsis root cells
Authors: Jaillais Yvon , Fobis‐Loisy Isabelle , Miège Christine , Gaude Thierry 
Published: October 2007

SummaryIn eukaryotic cells, the endocytic and secretory pathways are key players in several physiological processes. These pathways are largely inter‐connected in animal and yeast cells through organelles named sorting endosomes. Sorting endosomes are multi‐vesicular compartments that redirect proteins towards various destinations, such as the lysosomes or vacuoles for degradation, the trans‐Golgi network for retrograde transport and the plasma membrane for recycling. In contrast, cross‐talk between the endocytic and secretory pathways has not been clearly established in plants, especially in terms of cargo protein trafficking. Here we show by co‐localization analyses that endosomes labelled with the AtSORTING NEXIN1 (AtSNX1) protein overlap with the pre‐vacuolar compartment in Arabidopsis root cells. In addition, alteration of the routing functions of AtSNX1 endosomes by drug treatments leads to mis‐routing of endocytic and secretory cargo proteins. Based on these results, we propose that the AtSNX1 endosomal compartment represents a sorting endosome in root cells, and that this specialized organelle is conserved throughout eukaryotes.
Subcellular co‐localization of Arabidopsis RTE1 and ETR1 supports a regulatory role for RTE1 in ETR1 ethylene signaling
Authors: Dong Chun‐Hai , Rivarola Maximo , Resnick Josephine S. , Maggin Benjamin D. , Chang Caren 
Published: October 2007

SummaryEthylene is an important plant growth regulator perceived by membrane‐bound ethylene receptors. The ETR1 ethylene receptor is positively regulated by a predicted membrane protein, RTE1, based on genetic studies in Arabidopsis. RTE1 homologs exist in plants, animals and protists, but the molecular function of RTE1 is unknown. Here, we examine RTE1 expression and subcellular protein localization in order to gain a better understanding of RTE1 and its function in relation to ETR1. Arabidopsis plants transformed with the RTE1 promoter fused to the β‐glucuronidase (GUS) reporter gene revealed that RTE1 expression partly correlates with previously described sites of ETR1 expression or sites of ethylene response, such as the seedling root, root hairs and apical hook. RTE1 transcript levels are also enhanced by ethylene treatment, and reduced by the inhibition of ethylene signaling. For subcellular localization of RTE1, a functional RTE1 fusion to red fluorescent protein (RFP) was expressed under the control of the native RTE1 promoter. Using fluorescence microscopy, RTE1 was observed primarily at the Golgi apparatus and partially at the endoplasmic reticulum (ER) in stably transformed Arabidopsis protoplasts, roots and root hairs. Next, a functional ETR1 fusion to a 5xMyc epitope tag was expressed under the control of the native ETR1 promoter. Immunohistochemistry of root hairs not only showed ETR1 residing at the ER as previously reported, but revealed substantial localization of ETR1 at the Golgi apparatus. Lastly, we demonstrated the subcellular co‐localization of RTE1 and ETR1. These findings support and enhance the genetic model that RTE1 plays a role in regulating ETR1.