bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type Three Effector Gene Distribution and Sequence Analysis Provide New Insights into the Pathogenicity of Plant-Pathogenic Xanthomonas arboricola
Authors: Hajri Ahmed , Pothier Joël F. , Fischer-Le Saux Marion , Bonneau Sophie , Poussier Stéphane , Boureau Tristan , Duffy Brion , Manceau Charles 
Published: November 2011

ABSTRACT

Xanthomonas arboricola
is a complex bacterial species which mainly attacks fruit trees and is responsible for emerging diseases in Europe. It comprises seven pathovars (
X. arboricola
pv. pruni,
X. arboricola
pv. corylina,
X. arboricola
pv. juglandis,
X. arboricola
pv. populi,
X. arboricola
pv. poinsettiicola,
X. arboricola
pv. celebensis, and
X. arboricola
pv. fragariae), each exhibiting characteristic disease symptoms and distinct host specificities. To better understand the factors underlying this ecological trait, we first assessed the phylogenetic relationships among a worldwide collection of
X. arboricola
strains by sequencing the housekeeping gene
rpoD
. This analysis revealed that strains of
X. arboricola
pathovar populi are divergent from the main
X. arboricola
cluster formed by all other strains. Then, we investigated the distribution of 53 type III effector (T3E) genes in a collection of 57
X. arboricola
strains that are representative of the main
X. arboricola
cluster. Our results showed that T3E repertoires vary greatly between
X. arboricola
pathovars in terms of size. Indeed,
X. arboricola
pathovars pruni, corylina, and juglandis, which are responsible for economically important stone fruit and nut diseases in Europe, harbored the largest T3E repertoires, whereas pathovars poinsettiicola, celebensis, and fragariae harbored the smallest. We also identified several differences in T3E gene content between
X. arboricola
pathovars pruni, corylina, and juglandis which may account for their differing host specificities. Further, we examined the allelic diversity of eight T3E genes from
X. arboricola
pathovars. This analysis revealed very limited allelic variations at the different loci. Altogether, the data presented here provide new insights into the evolution of pathogenicity and host range of
X. arboricola
and are discussed in terms of emergence of new diseases within this bacterial species.
Casuarina Root Exudates Alter the Physiology, Surface Properties, and Plant Infectivity of Frankia sp. Strain CcI3
Authors: Beauchemin Nicholas J. , Furnholm Teal , Lavenus Julien , Svistoonoff Sergio , Doumas Patrick , Bogusz Didier , Laplaze Laurent , Tisa Louis S. 
Published: November 2011

ABSTRACT

The actinomycete genus
Frankia
forms nitrogen-fixing symbioses with 8 different families of actinorhizal plants, representing more than 200 different species. Very little is known about the initial molecular interactions between
Frankia
and host plants in the rhizosphere. Root exudates are important in
Rhizobium
-legume symbiosis, especially for initiating Nod factor synthesis. We measured differences in
Frankia
physiology after exposure to host aqueous root exudates to assess their effects on actinorhizal symbioses.
Casuarina cunninghamiana
root exudates were collected from plants under nitrogen-sufficient and -deficient conditions and tested on
Frankia
sp. strain CcI3. Root exudates increased the growth yield of
Frankia
in the presence of a carbon source, but
Frankia
was unable to use the root exudates as a sole carbon or energy source. Exposure to root exudates caused hyphal “curling” in
Frankia
cells, suggesting a chemotrophic response or surface property change. Exposure to root exudates altered Congo red dye binding, which indicated changes in the bacterial surface properties at the fatty acid level. Fourier transform infrared spectroscopy (FTIR) confirmed fatty acid changes and revealed further carbohydrate changes.
Frankia
cells preexposed to
C. cunninghamiana
root exudates for 6 days formed nodules on the host plant significantly earlier than control cells. These data support the hypothesis of early chemical signaling between actinorhizal host plants and
Frankia
in the rhizosphere.
Identification and Characterization of a Xyloglucan-Specific Family 74 Glycosyl Hydrolase from Streptomyces coelicolor A3(2)
Authors: Enkhbaatar Bolormaa , Temuujin Uyangaa , Lim Ju-Hyeon , Chi Won-Jae , Chang Yong-Keun , Hong Soon-Kwang 
Published: November 2011

ABSTRACT

The
sco6545
gene of
Streptomyces coelicolor
A3(2) was nominated as a putative cellulase with 863 mature-form amino acids (90.58 kDa). We overexpressed and purified Sco6545 and demonstrated that the protein is not a cellulase but a xyloglucan-specific glycosyl hydrolase which cleaves xyloglucan at unbranched glucose residues.
DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences
Authors: Wright Erik S. , Yilmaz L. Safak , Noguera Daniel R. 
Published: November 2011

ABSTRACT

DECIPHER is a new method for finding 16S rRNA chimeric sequences by the use of a search-based approach. The method is based upon detecting short fragments that are uncommon in the phylogenetic group where a query sequence is classified but frequently found in another phylogenetic group. The algorithm was calibrated for full sequences (fs_DECIPHER) and short sequences (ss_DECIPHER) and benchmarked against WigeoN (Pintail), ChimeraSlayer, and Uchime using artificially generated chimeras. Overall, ss_DECIPHER and Uchime provided the highest chimera detection for sequences 100 to 600 nucleotides long (79% and 81%, respectively), but Uchime's performance deteriorated for longer sequences, while ss_DECIPHER maintained a high detection rate (89%). Both methods had low false-positive rates (1.3% and 1.6%). The more conservative fs_DECIPHER, benchmarked only for sequences longer than 600 nucleotides, had an overall detection rate lower than that of ss_DECIPHER (75%) but higher than those of the other programs. In addition, fs_DECIPHER had the lowest false-positive rate among all the benchmarked programs (<0.20%). DECIPHER was outperformed only by ChimeraSlayer and Uchime when chimeras were formed from closely related parents (less than 10% divergence). Given the differences in the programs, it was possible to detect over 89% of all chimeras with just the combination of ss_DECIPHER and Uchime. Using fs_DECIPHER, we detected between 1% and 2% additional chimeras in the RDP, SILVA, and Greengenes databases from which chimeras had already been removed with Pintail or Bellerophon. DECIPHER was implemented in the R programming language and is directly accessible through a webpage or by downloading the program as an R package (
http://DECIPHER.cee.wisc.edu
).
Multiple Plastids Collected by the Dinoflagellate Dinophysis mitra through Kleptoplastidy
Authors: Nishitani Goh , Nagai Satoshi , Hayakawa Shiho , Kosaka Yuki , Sakurada Kiyonari , Kamiyama Takashi , Gojobori Takashi 
Published: November 2011

ABSTRACT

Kleptoplastidy is the retention of plastids obtained from ingested algal prey, which may remain temporarily functional and be used for photosynthesis by the predator. We showed that the marine dinoflagellate
Dinophysis mitra
has great kleptoplastid diversity. We obtained 308 plastid
rbc
L
sequences by gene cloning from 14
D. mitra
cells and 102 operational taxonomic units (OTUs). Most sequences were new in the genetic database and positioned within Haptophyceae (227 sequences [73.7%], 80 OTUs [78.4%]), particularly within the genus
Chrysochromulina
. Others were closely related to Prasinophyceae (16 sequences [5.2%], 5 OTUs [4.9%]), Dictyochophyceae (14 sequences [4.5%], 5 OTUs [4.9%]), Pelagophyceae (14 sequences [4.5%], 1 OTU [1.0%]), Bolidophyceae (3 sequences [1.0%], 1 OTU [1.0%]), and Bacillariophyceae (1 sequence [0.3%], 1 OTU [1.0%]); however, 33 sequences (10.8%) as 9 OTUs (8.8%) were not closely clustered with any particular group. Only six sequences were identical to those of
Chrysochromulina simplex
,
Chrysochromulina hirta
,
Chrysochromulina
sp. TKB8936,
Micromonas pusilla
NEPCC29,
Micromonas pusilla
CCMP491, and an unidentified diatom. Thus, we detected >100 different plastid sequences from 14
D. mitra
cells, strongly suggesting kleptoplastidy and the need for mixotrophic prey such as
Laboea
,
Tontonia
, and
Strombidium
-like ciliates, which retain numerous symbiotic plastids from different origins, for propagation and plastid sequestration.
Electron Donors Supporting Growth and Electroactivity of Geobacter sulfurreducens Anode Biofilms
Authors: Speers Allison M. , Reguera Gemma 
Published: November 2011

ABSTRACT

Geobacter
bacteria efficiently oxidize acetate into electricity in bioelectrochemical systems, yet the range of fermentation products that support the growth of anode biofilms and electricity production has not been thoroughly investigated. Here, we show that
Geobacter sulfurreducens
oxidized formate and lactate with electrodes and Fe(III) as terminal electron acceptors, though with reduced efficiency compared to acetate. The structure of the formate and lactate biofilms increased in roughness, and the substratum coverage decreased, to alleviate the metabolic constraints derived from the assimilation of carbon from the substrates. Low levels of acetate promoted formate carbon assimilation and biofilm growth and increased the system's performance to levels comparable to those with acetate only. Lactate carbon assimilation also limited biofilm growth and led to the partial oxidization of lactate to acetate. However, lactate was fully oxidized in the presence of fumarate, which redirected carbon fluxes into the tricarboxylic acid (TCA) cycle, and by acetate-grown biofilms. These results expand the known ranges of electron donors for
Geobacter
-driven fuel cells and identify microbial constraints that can be targeted to develop better-performing strains and increase the performance of bioelectrochemical systems.
Cultured Representatives of Two Major Phylogroups of Human Colonic Faecalibacterium prausnitzii Can Utilize Pectin, Uronic Acids, and Host-Derived Substrates for Growth
Authors: Lopez-Siles Mireia , Khan Tanweer M. , Duncan Sylvia H. , Harmsen Hermie J. M. , Garcia-Gil L. Jesús , Flint Harry J. 
Published: November 2011

ABSTRACT

Faecalibacterium prausnitzii
is one of the most abundant commensal bacteria in the healthy human large intestine, but information on genetic diversity and substrate utilization is limited. Here, we examine the phylogeny, phenotypic characteristics, and influence of gut environmental factors on growth of
F. prausnitzii
strains isolated from healthy subjects. Phylogenetic analysis based on the 16S rRNA sequences indicated that the cultured strains were representative of
F. prausnitzii
sequences detected by direct analysis of fecal DNA and separated the available isolates into two phylogroups. Most
F. prausnitzii
strains tested grew well under anaerobic conditions on apple pectin. Furthermore,
F. prausnitzii
strains competed successfully in coculture with two other abundant pectin-utilizing species,
Bacteroides thetaiotaomicron
and
Eubacterium eligens
, with apple pectin as substrate, suggesting that this species makes a contribution to pectin fermentation in the colon. Many
F. prausnitzii
isolates were able to utilize uronic acids for growth, an ability previously thought to be confined to
Bacteroides
spp. among human colonic anaerobes. Most strains grew on
N
-acetylglucosamine, demonstrating an ability to utilize host-derived substrates. All strains tested were bile sensitive, showing at least 80% growth inhibition in the presence of 0.5 μg/ml bile salts, while inhibition at mildly acidic pH was strain dependent. These attributes help to explain the abundance of
F. prausnitzii
in the colonic community but also suggest factors in the gut environment that may limit its distribution.
Responses of MethanogenmcrAGenes and Their Transcripts to an Alternate Dry/Wet Cycle of Paddy Field Soil
Authors: Ma Ke , Conrad Ralf , Lu Yahai 
Published: November 2011

ABSTRACTIntermittent drainage can substantially reduce methane emission from rice fields, but the microbial mechanisms remain poorly understood. In the present study, we determined the rates of methane production and emission, the dynamics of ferric iron and sulfate, and the abundance of methanogenmcrAgenes (encoding the alpha subunit of methyl coenzyme M reductase) and their transcripts in response to alternate dry/wet cycles in paddy field soil. We found that intermittent drainage did not affect the growth of rice plants but significantly reduced the rates of both methane production and emission. The dry/wet cycles also resulted in shifts of soil redox conditions, increasing the concentrations of ferric iron and sulfate in the soil. Quantitative PCR analysis revealed that bothmcrAgene copies andmcrAtranscripts significantly decreased after dry/wet alternation compared to continuous flooding. Correlation and regression analyses showed that the abundance ofmcrAgenes and transcripts positively correlated with methane production potential and soil water content and negatively correlated with the concentrations of ferric iron and sulfate in the soil. However, the transcription ofmcrAgenes was reduced to a greater extent than the abundance ofmcrAgenes, resulting in very lowmcrAtranscript/gene ratios after intermittent drainage. Furthermore, terminal restriction fragment length polymorphism analysis revealed that the composition of methanogenic community remained stable under dry/wet cycles, whereas that of metabolically active methanogens strongly changed. Collectively, our study demonstrated a stronger effect of intermittent drainage on the abundance ofmcrAtranscripts than ofmcrAgenes in rice field soil.
Development of a New Strategy for Production of Medium-Chain-Length Polyhydroxyalkanoates by Recombinant Escherichia coli via Inexpensive Non-Fatty Acid Feedstocks
Authors: Wang Qin , Tappel Ryan C. , Zhu Chengjun , Nomura Christopher T. 
Published: November 2011

ABSTRACTPseudomonas putidaKT2440 is capable of producing medium-chain-length polyhydroxyalkanoates (MCL-PHAs) when grown on unrelated carbon sources during nutrient limitation. Transcription levels of genes putatively involved in PHA biosynthesis were assessed by quantitative real-time PCR (qRT-PCR) inP. putidagrown on glycerol as a sole carbon source. The results showed that two genes,phaGand the PP0763 gene, were highly upregulated among genes potentially involved in the biosynthesis of MCL-PHAs from unrelated carbon sources. Previous studies have describedphaGas a 3-hydroxyacyl-acyl carrier protein (ACP)-coenzyme A (CoA) transferase, and based on homology, the PP0763 gene was predicted to encode a medium-chain-fatty-acid CoA ligase. High expression levels of these genes during PHA production inP. putidaled to the hypothesis that these two genes are involved in PHA biosynthesis from non-fatty acid carbon sources, such as glucose and glycerol. ThephaGppand PP0763 genes fromP. putidawere cloned and coexpressed with the engineeredPseudomonassp. 61-3 PHA synthase genephaCl(STQK)psin recombinantEscherichia coli. Up to 400 mg liter−1MCL-PHAs was successfully produced from glucose. This study has produced the largest amount of MCL-PHAs reported from non-fatty acid carbon sources in recombinantE. colito date and opens up the possibility of using inexpensive feedstocks to produce MCL-PHA polymers.
Effectiveness of a Simplified Method for Isolation of Burkholderia pseudomallei from Soil
Authors: Limmathurotsakul Direk , Wuthiekanun Vanaporn , Amornchai Premjit , Wongsuwan Gumphol , Day Nicholas P. J. , Peacock Sharon J. 
Published: November 2011

ABSTRACT

Detection of environmental
Burkholderia pseudomallei
indicates a risk for melioidosis and is important for the development of a global risk map. We describe a simple method for detecting
B. pseudomallei
using direct culture of soil in enrichment broth. This gives a rate of positivity comparable to that obtained with a standard method but is cheaper and labor saving.
Iron Storage Proteins Are Essential for the Survival and Pathogenesis of Mycobacterium tuberculosis in THP-1 Macrophages and the Guinea Pig Model of Infection
Authors: Reddy P. Vineel , Puri Rupangi Verma , Khera Aparna , Tyagi Anil K. 
Published: November 2011

ABSTRACTIron is one of the crucial elements required for the growth ofMycobacterium tuberculosis. However, excess free iron becomes toxic for the cells because it catalyzes the production of reactive oxygen radicals, leading to oxidative damage. Hence, it is essential for the pathogen to have the ability to store intracellular iron in an iron-rich environment and utilize it under iron depletion.M. tuberculosishas two iron storage proteins, namely BfrA (Rv1876; a bacterioferritin) and BfrB (Rv3841; a ferritin-like protein). However, the demonstration of biological significance requires the disruption of relevant genes and the evaluation of the resulting mutant for its ability to survive in the host and cause disease. In this study, we have disruptedbfrAandbfrBofM. tuberculosisand demonstrated that these genes are crucial for the storage and supply of iron for the growth of bacteria and to withstand oxidative stressin vitro. In addition, thebfrA bfrBdouble mutant (H37Rv ΔbfrAΔbfrB) exhibited a marked reduction in its ability to survive inside human macrophages. Guinea pigs infected with H37Rv ΔbfrAΔbfrBexhibited a marked diminution in the dissemination of the bacilli to spleen compared to that of the parental strain. Moreover, guinea pigs infected with H37Rv ΔbfrAΔbfrBexhibited significantly reduced pathological damage in spleen and lungs compared to that of animals infected with the parental strain. Our study clearly demonstrates the importance of these iron storage proteins in the survival and pathogenesis ofM. tuberculosisin the host and establishes them as attractive targets for the development of new inhibitors against mycobacterial infections.
Decreased Transport Restores Growth of a Salmonella enterica
apbC
Mutant on Tricarballylate
Authors: Boyd Jeffrey M. , Teoh Wei Ping , Downs Diana M. 
Published: November 2011

ABSTRACT

Mutants of
Salmonella enterica
lacking
apbC
have nutritional and biochemical properties indicative of defects in iron-sulfur ([Fe-S]) cluster metabolism. An
apbC
mutant is unable to grow on tricarballylate as a carbon source. Based on the ability of ApbC to transfer an [Fe-S] cluster to an apoprotein, this defect was attributed to poor loading of the [Fe-S] cluster-containing TcuB enzyme. Consistent with these observations, a previous study showed that overexpression of
iscU
, which encodes an [Fe-S] cluster molecular scaffold, suppressed the tricarballylate growth defect of an
apbC
mutant (J. M. Boyd, J. A. Lewis, J. C. Escalante-Semerena, and D. M. Downs, J. Bacteriol. 190:4596–4602, 2008). In this study,
tcuC
mutations that suppress the growth defect of an
apbC
mutant by decreasing the intracellular concentration of tricarballylate are described. Collectively, the suppressor analyses support a model in which reduced TcuB activity prevents growth on tricarballylate by (i) decreasing catabolism and (ii) allowing levels of tricarballylate that are toxic to the cell to accumulate. The
apbC tcuC
mutant strains described here reveal that the balance of the metabolic network can be altered by the accumulation of deleterious metabolites.
Substrate Recognition Mechanism and Substrate-Dependent Conformational Changes of an ROK Family Glucokinase from Streptomyces griseus
Authors: Miyazono Ken-ichi , Tabei Nobumitsu , Morita Sho , Ohnishi Yasuo , Horinouchi Sueharu , Tanokura Masaru 
Published: November 2011

ABSTRACT

Carbon catabolite repression (CCR) is a widespread phenomenon in many bacteria that is defined as the repression of catabolic enzyme activities for an unfavorable carbon source by the presence of a preferable carbon source. In
Streptomyces
, secondary metabolite production often is negatively affected by the carbon source, indicating the involvement of CCR in secondary metabolism. Although the CCR mechanism in
Streptomyces
still is unclear, glucokinase is presumably a central player in CCR. SgGlkA, a glucokinase from
S. griseus
, belongs to the ROK family glucokinases, which have two consensus sequence motifs (1 and 2). Here, we report the crystal structures of apo-SgGlkA, SgGlkA in complex with glucose, and SgGlkA in complex with glucose and adenylyl imidodiphosphate (AMPPNP), which are the first structures of an ROK family glucokinase. SgGlkA is divided into a small α/β domain and a large α+β domain, and it forms a dimer-of-dimer tetrameric configuration. SgGlkA binds a β-anomer of glucose between the two domains, and His157 in consensus sequence 1 plays an important role in the glucose-binding mechanism and anomer specificity of SgGlkA. In the structures of SgGlkA, His157 forms an HC3-type zinc finger motif with three cysteine residues in consensus sequence 2 to bind a zinc ion, and it forms two hydrogen bonds with the C1 and C2 hydroxyls of glucose. When the three structures are compared, the structure of SgGlkA is found to be modified by the binding of substrates. The substrate-dependent conformational changes of SgGlkA may be related to the CCR mechanism in
Streptomyces
.
Problems with a great idea: referral by prehospital emergency services to a community-based falls-prevention service
Authors: Comans Tracy A , Currin Michelle L , Quinn Jamie , Tippett Vivienne , Rogers Anthea , Haines Terry P 
Published: November 2011

Background and aimFalls are the leading cause of injury in older adults. Identifying people at risk before they experience a serious fall requiring hospitalisation allows an opportunity to intervene earlier and potentially reduce further falls and subsequent healthcare costs. The purpose of this project was to develop a referral pathway to a community falls-prevention team for older people who had experienced a fall attended by a paramedic service and who were not transported to hospital. It was also hypothesised that providing intervention to this group of clients would reduce future falls-related ambulance call-outs, emergency department presentations and hospital admissions.MethodsAn education package, referral pathway and follow-up procedures were developed. Both services had regular meetings, and work shadowing with the paramedics was also trialled to encourage more referrals. A range of demographic and other outcome measures were collected to compare people referred through the paramedic pathway and through traditional pathways.ResultsInternal data from the Queensland Ambulance Service indicated that there were approximately six falls per week by community-dwelling older persons in the eligible service catchment area (south west Brisbane metropolitan area) who were attended to by Queensland Ambulance Service paramedics, but not transported to hospital during the 2-year study period (2008–2009). Of the potential 638 eligible patients, only 17 (2.6%) were referred for a falls assessment.ConclusionAlthough this pilot programme had support from all levels of management as well as from the service providers, it did not translate into actual referrals. Several explanations are provided for these preliminary findings.