bluuebunny/crossref_metadata_2025_split huggingface dataset:
The biosynthesis and biological role of 6‐deoxyheptose in the lipopolysaccharide O‐antigen of Yersinia pseudotuberculosis
Authors: Ho Nathan , Kondakova Anna N. , Knirel Yuriy A. , Creuzenet Carole 
Published: February 2008

Summary Yersinia pseudotuberculosis O:2a harbours 6‐deoxy‐d‐manno‐heptose in its O‐antigen. The biological function of 6‐deoxyheptose and its role in virulence is unknown and its biosynthetic pathway has not been demonstrated experimentally. Here, we show that dmhA and dmhB are necessary for 6‐deoxyheptose biosynthesis in Y. pseudotuberculosis. Their disruption resulted in the lack of 6‐deoxyheptose in the O‐unit and its replacement by d‐glycero‐d‐manno‐heptose, thus indicating relaxed specificity of the glycosyltransferases, polymerase and ligase involved in lipopolysaccharide synthesis. The dmhB mutant exhibited a lower content in ketooctonic acid (Ko)‐containing core molecules and reduced ligation and polymerization of the O‐unit. We also show that Tyr128 is essential for activity of DmhB, and that DmhB functions as an oligomer, based on the dominant negative effect of overexpression of DmhB Y128F in dmhA. Moreover, we demonstrate that 6‐deoxyheptose is important for virulence‐related functions of the outer membrane and its appendages in vitro, such as barrier function against bile salts, polymyxin and novobiocin, and flagella‐mediated motility. Although both mutants colonized the mouse ceacum as well as the wild type, the dmhB mutant was impaired for colonization of the liver, suggesting that DmhB represents a potential therapeutic target.
Cleavage of mRNAs and role of tmRNA system under amino acid starvation in Escherichia coli
Authors: Li Xia , Yagi Mieko , Morita Teppei , Aiba Hiroji 
Published: February 2008

SummaryWe have shown previously that ribosome stalling during translation caused by various reasons leads to mRNA cleavage, resulting in non‐stop mRNAs that are eliminated in a tmRNA‐dependent manner. Amino acid starvation is a physiological condition in which ribosome stalling is expected to occur more frequently. Here we demonstrate that mRNA cleavage is induced by amino acid starvation, resulting in accumulation of truncated mRNAs in cells lacking tmRNA. The truncated mRNAs are eliminated in wild‐type cells, indicating that the tmRNA system rapidly degrade the truncated mRNAs. The cleavage pattern of model mRNAs in which serine codons were replaced with threonine codons indicated that mRNA cleavage occurs near serine codons in response to serine starvation. Cells lacking all of the five known toxin loci were proficient in mRNA cleavage, showing that toxin–antitoxin systems are not responsible for the cleavage. A mild serine starvation caused a significant growth inhibition in cells lacking tmRNA but not in wild‐type cells. The ribosome‐mediated mRNA cleavage along with the tmRNA system is an important mechanism that enables cells to adapt to amino acid starvation conditions.
FliL is essential for swarming: motor rotation in absence of FliL fractures the flagellar rod in swarmer cells of Salmonella enterica
Authors: Attmannspacher Ursula , Scharf Birgit E. , Harshey Rasika M. 
Published: February 2008

Summary fliL is the first gene in a flagellar operon that specifies members of the switch complex and type III export system in Salmonella enterica and Escherichia coli, but no function has been ascribed to this gene thus far. Here we report that a fliL mutant is slightly impaired for swimming but completely defective in swarming in both organisms, and have studied this phenotype further in S. enterica. We have found that on swarm agar, mutant cells release or ‘eject’ their flagellar filaments. The released filaments are attached to the hook and part of the rod structure; we have identified the distal rod protein FlgG but not the proximal rod protein FlgF in these filaments. Rod fracture was not observed if flagellar rotation was prevented by removal of proteins that supply proton flow through the motor. Based on these and other results, we propose that motors experience a higher torque on swarm agar owing to an increased proton motive force, and that FliL allows the rod to withstand the increased torsional stress. The flagella‐release phenotype of the S. enterica fliL mutant has a bearing on FliL‐dependent flagellar ejection during the swimmer‐ to stalk‐cell transition in the developmental cycle of Caulobacter crescentus.
Bicarbonate‐mediated transcriptional activation of divergent operons by the virulence regulatory protein, RegA, from Citrobacter rodentium
Authors: Yang Ji , Hart Emily , Tauschek Marija , Price G. Dean , Hartland Elizabeth L. , Strugnell Richard A. , Robins‐Browne Roy M. 
Published: February 2008

SummaryRegulation of virulence gene expression plays a central role in the pathogenesis of enteric bacteria as they encounter diverse environmental conditions in the gastrointestinal tract of their hosts. In this study, we investigated environmental regulation of two putative virulence determinants adcA and kfc by RegA, an AraC/XylS‐like regulator, from Citrobacter rodentium, and identified bicarbonate as the environmental signal which induced transcription of adcA and kfc through RegA. Primer extension experiments showed that adcA and kfc were divergently transcribed from σ70 promoters. In vivo and in vitro experiments demonstrated that bicarbonate facilitated and stabilized the binding of RegA to an operator located between the two promoters. The interaction of RegA with its DNA target resulted in the formation of a nucleosome‐like structure, which evidently displaced the histone‐like proteins, H‐NS and StpA, from the adcA and kfc promoter regions, leading to transcriptional derepression. In addition, our results indicated that RegA also behaved as a Class I activator by directly stimulating transcription initiation by RNA polymerase. This is the first report to describe the molecular mechanism by which an environmental chemical stimulates transcription of virulence‐associated genes of an enteric pathogen through an AraC/XlyS‐like activator.
The disturbance of small RNA pathways enhanced abscisic acid response and multiple stress responses in Arabidopsis
Authors: ZHANG JIAN‐FENG , YUAN LI‐JIE , SHAO YI , DU WEI , YAN DA‐WEI , LU YING‐TANG 
Published: February 2008

ABSTRACTThe phytohormone abscisic acid (ABA) regulates plant growth and development as well as stress tolerance. To gain more insights into ABA signalling, a population of chemical‐inducible activation‐tagged Arabidopsis mutants was screened on the basis of the ABA effect on the inhibition of seed germination. Two novel ABA supersensitive mutants ABA supersensitive during germination1 (absg1) and absg2 were characterized as alleles of Dicer‐like1 (DCL1) and HEN1, respectively, as microRNA biogenesis genes, and accordingly, these two mutants were renamed dcl1‐11 and hen1‐16. The dcl1‐11 mutant was an ABA hypersensitive mutant for seed germination and root growth. Reverse transcriptase polymerase chain reaction assays revealed that the expression of ABA‐ and stress‐responsive genes was increased in dcl1‐11, as compared with the wild type (WT). Furthermore, the germination assay showed that dcl1‐11 was also more sensitive to salt and osmotic stress. The hen1‐16 mutant also showed supersensitive to ABA during seed germination. Further analysis showed that, among the microRNA biogenesis genes, all the other mutants were not only enhanced in sensitivity to ABA, salt and osmotic stress, but also enhanced the expression of ABA‐responsive genes. In addition to the mutants in the microRNA biogenesis, the interruption of the production of crucial components of other small RNA pathways such as dcl2, dcl3 and dcl4 also caused ABA supersensitive during germination.
Lutein epoxide cycle, light harvesting and photoprotection in species of the tropical tree genusInga
Authors: MATSUBARA SHIZUE , KRAUSE G. HEINRICH , SELTMANN MARTIN , VIRGO AURELIO , KURSAR THOMAS A. , JAHNS PETER , WINTER KLAUS 
Published: February 2008

ABSTRACTDynamics and possible function of the lutein epoxide (Lx) cycle, that is, the reversible conversion of Lx to lutein (L) in the light‐harvesting antennae, were investigated in leaves of tropical tree species. Photosynthetic pigments were quantified in nineIngaspecies and species from three other genera. InInga, Lx levels were high in shade leaves (mostly above 20 mmol mol−1chlorophyll) and low in sun leaves. InVirola surinamensis, both sun and shade leaves exhibited very high Lx contents (about 60 mmol mol−1chlorophyll). InInga marginatagrown under high irradiance, Lx slowly accumulated within several days upon transfer to deep shade. When shade leaves ofI. marginatawere briefly exposed to the sunlight, both violaxanthin and Lx were quickly de‐epoxidized. Subsequently, overnight recovery occurred only for violaxanthin, not for Lx. In such leaves, containing reduced levels of Lx and increased levels of L, chlorophyll fluorescence induction showed significantly slower reduction of the photosystem II electron acceptor,QA, and faster formation as well as a higher level of non‐photochemical quenching. The results indicate that slow Lx accumulation inIngaleaves may improve light harvesting under limiting light, while quick de‐epoxidation of Lx to L in response to excess light may enhance photoprotection.
Immune‐challenged house wren broods differ in the relative strengths of their responses among different axes of the immune system
Authors: FORSMAN A. M. , VOGEL L. A. , SAKALUK S. K. , GRINDSTAFF J. L. , THOMPSON C. F. 
Published: February 2008

AbstractSingle components of the immune system are widely used to assess immune function in free‐living vertebrates. However, as different immunological components are triggered by different types of threats and may be regulated independently, there is little reason to assume that they should respond similarly if challenged. We investigated whether three commonly assayed immune responses, cutaneous immune activity (phytohaemagglutinin assay), antibody response (tetanus toxoid immunization), and plasma bactericidal activity (Escherichia colikilling) are positively related in nestling house wrens (Troglodytes aedon). Multivariate analysis revealed significant differences in overall immune responsiveness among broods (i.e. nests), primarily attributable to differences in plasma bactericidal activity. Among broods, humoral immune response was negatively related to cutaneous immune activity and positively related to plasma bactericidal activity. We found no significant relationships among these measures of immunity among individual nestlings within broods. Our results suggest that different broods (i.e. families) invest differentially in the various branches of the immune system. Further study is needed to characterize the roles of maternal, genetic and environmental effects on the expression of this physiological bias.
Suppression of Root Rotting Fungi and Root Knot Nematode of Chili by Seaweed and Pseudomonas aeruginosa
Authors: Sultana V. , Ara J. , Ehteshamul‐Haque S. 
Published: February 2008

AbstractSolvent fractions (i.e. n‐hexane, chloroform and methanol) of the ethanol extracts of the seaweeds Codium iyengarii, Jania capillacea, Stokeyia indica and Solieria robusta caused more than 50% mortality of Meloidogyne javanica juveniles within 24 h at 10 mg/ml. Nematode mortality increased with an increase in fraction concentration or exposure time. The n‐hexane fractions from S. indica, J. capillacea and C. iyengarii and the chloroform fraction from S. robusta also resulted in more than 50% mortality within 48 h at 1.0 mg/ml. In a screen‐house experiment application of S. indica and S. robusta as soil amendments alone or with Pseudomonas aeruginosa, a plant growth promoting rhizobacterium (PGPR), significantly suppressed infection of chili roots by root‐infecting fungi Macrophomina phaseolina, Rhizoctonia solani, Fusarium solani and the root knot nematode Meloidogyne javanica. Seaweed alone or with PGPR also increased plant growth. Suppressive effect on root pathogens and growth enhancement potential of seaweeds and P. aeruginosa were also effective in field plots.
Complete Genome Sequences of Two Chinese Beet soil‐borne virus Isolates Provide Evidence that the Genome is Highly Conserved
Authors: Wang B. , Li M. , Han C. , Li D. , Yu J. 
Published: February 2008

AbstractThe complete nucleotide sequences of two Chinese isolates of Beet soil‐borne virus (BSBV) from the Inner Mongolia and Xinjiang provinces (designated BSBV‐IM and BSBV‐XJ, respectively) were found to share around 99% sequence identity with that of a previously reported German isolate (BSBV‐G). The genome organization of the three isolates was identical. A diversity index (Pi) analysis indicated that the overall nucleotide variability of all RNAs among the three isolates was <7%, only for the 5′ part of the first triple gene block gene on RNA3 was it >6%. Although the 3′ end of BSBV RNA 3 was previously reported to be highly variable, the results of this study show that the total BSBV genomes are considerably conserved, especially RNAs 1 and 2.
Molecular and Biological Diversities ofCucumber green mottle mosaic virusfrom Cucurbitaceous Crops in Korea
Authors: Yoon J. Y. , Choi G. S. , Choi S. K. , Hong J. S. , Choi J. K. , Kim W. , Lee G. P. , Ryu K. H. 
Published: February 2008

AbstractCucumber green mottle mosaic virus(CGMMV) is the first‐known cucurbit‐infecting tobamovirus. To analyse its biological and molecular diversities, 36 isolates of CGMMV were collected from watermelon (Citrullus vulgaris) and cucumber (Cucumis sativus) plants in Korea. The cDNAs of coat protein (CP) and partial movement protein genes of the isolates were synthesized by reverse transcription and polymerase chain reaction (RT‐PCR) and subjected to single‐strand conformation polymorphism (SSCP) analysis with 530 bp‐synthesized RT‐PCR products. CGMMV isolates were categorized into three subgroups by SSCP analysis, designated types I, II and III. All watermelon isolates of CGMMV belonged to types I and II, whereas cucumber isolates were subgrouped into types II and III. These three type isolates of CGMMV were divided by RT‐PCR‐restriction fragment length polymorphism (RFLP) using full‐length cDNAs of three types of CGMMV. Biological properties of each subgroup‐type of CGMMV isolates were determined by mechanical inoculation of common host plants of CGMMV. Among the virus isolates, isolate NW‐1, belonging to type I, did not infect cucumber (cv. Baegbong), whereas all CGMMV isolates (types II and III) infected the same host species. In addition, all isolates of CGMMV types could infectNicotiana debneyii, except that isolate KC1‐2, subgrouped into type III, failed to infect. Nucleotide and predicted amino acid sequences ofCPgene of CGMMV isolates were compared to those of reported CGMMVs and other cucurbit‐infecting tobamoviruses. In phylogenetic tree analyses between CGMMV isolates and other cucurbit‐infecting tobamoviruses, CGMMV was subgrouped as a cluster and no remarkable molecular diversity was found among the CGMMV isolates.
Whole Genome Sequence and Characterization of a Novel Isolate of PVY Inducing Tuber Necrotic Ringspot in Potato and Leaf Mosaic in Tobacco
Authors: Chikh Ali M. , Maoka T. , Natsuaki K. T. 
Published: February 2008

AbstractIn a previous study on a Syrian isolate of Potato virus Y (PVY), namely PVY‐12, a point mutation in the coat protein (CP) was detected. This mutation caused the double reactivity of this isolate to monoclonal antibodies specific to O and N serotypes. We report here the biological and molecular characteristics of PVY‐12. In potato, PVY‐12 behaved like a PVYNTN isolate inducing potato tuber necrotic ringspot disease although it induced mosaic in tobacco like PVYO. The genomic analysis grouped PVY‐12 with the recombinant PVYNTN isolates, which is consistent with the phenotype in potato. PVY‐12 HC‐Pro had the two amino acids K400 and E419 that were previously reported as determinant keys of the tobacco necrotic response. This indicates the involvement of other determinants in this phenotype yet to be determined. This is the first report on a PVYNTN isolate that induces mosaic in tobacco, implying that the induction of potato tuber necrosis does not require the ability to induce the tobacco necrosis. PVY‐12 genome had four recombinant points in the P1, HC‐Pro/P3, 6K2/NIa and C terminal region of the CP gene identical to those of PVYNTN isolates 12–94 and 34/01. The PVY‐12 central genomic part flanked by nucleotide positions 2414 and 8604 had highest similarity with that of the Syrian isolate SYR‐NB‐16 suggesting a common origin of these isolates. This common origin was supported using the phylogenetic analysis of this region. In addition, the phylogenetic analysis of the whole genome of the reported North American PVYN:O and the European PVYNW along with other PVY isolates suggests that PVYN:O might have descended from PVYNW with the isolate SASA‐207 as a nearest‐known relative.
Effects of Membrane Filtering of Tomato Root Exudates on Conidial Germination of Fusarium oxysporum f. sp. lycopersici
Authors: Steinkellner S. , Mammerler R. , Vierheilig H. 
Published: February 2008

AbstractThe effect of different membrane filters on the bioactivity of tomato root exudates was tested in an in vitro assay addressing the germination of microconidia of the soil‐borne fungus Fusarium oxysporum f. sp. lycopersici. Membrane filtration of unsterile root exudates with filters of different membrane materials and filter brands resulted in an increased microconidia germination. This effect varied depending on the used membrane filter but was lacking when sterile root exudates were used. The alteration of the bioactivity of unsterile root exudates therefore seems to be due to the presence of microbial contaminants. The varying effects of different filter brands may be due to their differential potential of retaining inhibitory compounds. When working with root exudates, such effects of membrane filtration have to be taken into account.
Allelic relationship between spontaneous and induced mutant genes for stem fasciation in chickpea
Authors: Srinivasan S. , Gaur P. M. , Rao B. V. 
Published: February 2008

AbstractStem fasciation is a morphological abnormality observed in plants where the stem is widened and leaves and flowers or pods are clustered at the apex. Several spontaneous mutants and one induced mutant for stem fasciation are found in chickpea (Cicer arietinum L.). This study was aimed at determining allelic relationship between spontaneous and induced mutant genes controlling stem fasciation and effects of stem fasciation on grain yield. Two spontaneous (ICC 2042 and ICC 5645) and one induced (JGM 2) stem fasciation mutants were crossed in all combinations, excluding reciprocals. The F1 and F2 plants from a cross between the two spontaneous mutants had fasciated stem. This indicated the presence of a common gene (designated fas1) for stem fasciation in the two spontaneous mutants. The F1s of the crosses of the induced mutant JGM 2 with both spontaneous mutants had normal plants and segregated in a ratio of 9 normal : 7 fasciated plants in F2. Thus, the gene for stem fasciation in the induced mutant JGM 2 (designated fas2) is not allelic to the common gene for stem fasciation in spontaneous mutants. The two genes in dominant condition produced normal non‐fasciated stem. The fasciated and the non‐fasciated F2 plants did not differ significantly for number of pods per plant, number of seeds per plant, grain yield per plant and seed size, suggesting that it is possible to exploit the fasciated trait in chickpea breeding without compromising on yield.
Integrated regulation involving quorum sensing, a two‐component system, a GGDEF/EAL domain protein and a post‐transcriptional regulator controls swarming and RhlA‐dependent surfactant biosynthesis in Serratia
Authors: Williamson Neil R. , Fineran Peter C. , Ogawa Wakano , Woodley Louise R. , Salmond George P. C. 
Published: February 2008

Summary Serratia sp. ATCC 39006 (Serratia 39006) is a Gram‐negative bacterium which produces the secondary metabolite antibiotics, prodigiosin and 1‐carbapen‐2‐em‐3‐carboxylic acid and secretes plant cell wall degrading enzymes. In this study we have identified mutations in the genes, pigX, rap and rsmA, which caused increased production of a previously unidentified surfactant and flagella‐dependent swarming phenotype in Serratia 39006. Analysis of both the biosynthesis and regulation of surfactant production and swarming, revealed FlhC, quorum sensing, a GGDEF/EAL domain protein (PigX), a GacAS two‐component system, an Rsm system and Rap as key regulators. In addition, surfactant biosynthesis required a protein similar to RhlA, involved in rhamnolipid synthesis in Pseudomonas aeruginosa. Homologues of RhlA have not previously been identified in members of the Enterobacteriaceae. Furthermore, we provide evidence that the surfactant may be responsible for dispersal of the antimicrobial pigment, prodigiosin. This study demonstrates the complex regulatory inputs into the coordinated multicellular swarming phenotype in Serratia.
Recent evolutionary diversification of a protist lineage
Authors: Logares Ramiro , Daugbjerg Niels , Boltovskoy Andrés , Kremp Anke , Laybourn‐Parry Johanna , Rengefors Karin 
Published: February 2008

SummaryHere, we have identified a protist (dinoflagellate) lineage that has diversified recently in evolutionary terms. The species members of this lineage inhabit cold‐water marine and lacustrine habitats, which are distributed along a broad range of salinities (0–32) and geographic distances (0–18 000 km). Moreover, the species present different degrees of morphological and sometimes physiological variability. Altogether, we analysed 30 strains, generating 55 new DNA sequences. The nuclear ribosomal DNA (nrDNA) sequences (including rapidly evolving introns) were very similar or identical among all the analysed isolates. This very low nrDNA differentiation was contrasted by a relatively high cytochrome b (COB) mitochondrial DNA (mtDNA) polymorphism, even though the COB evolves very slowly in dinoflagellates. The 16 Maximum Likelihood and Bayesian phylogenies constructed using nr/mtDNA indicated that the studied cold‐water dinoflagellates constitute a monophyletic group (supported also by the morphological analyses), which appears to be evolutionary related to marine‐brackish and sometimes toxic Pfiesteria species. We conclude that the studied dinoflagellates belong to a lineage which has diversified recently and spread, sometimes over long distances, across low‐temperature environments which differ markedly in ecology (marine versus lacustrine communities) and salinity. Probably, this evolutionary diversification was promoted by the variety of natural selection regimes encountered in the different environments.