bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity
Authors: Bansal Kanika , Midha Samriti , Kumar Sanjeet , Patil Prabhu B. 
Published: March 2017

ABSTRACT

Citrus canker, caused by
Xanthomonas citri
pv. citri, is a serious disease of citrus plants worldwide. Earlier phylogenetic studies using housekeeping genes revealed that
X. citri
pv. citri is related to many other pathovars, which can be collectively referred as
Xanthomonas citri
pathovars (XCPs). From the present study, we report the genome sequences of 18 XCPs and compared them with four XCPs available in the public domain. In a tree based on phylogenomic marker genes, all the XCPs form a monophyletic cluster, suggesting their origin from a common ancestor. Phylogenomic analysis using the type strain further established that all the XCPs belong to one species. Clonal analysis of the core genome revealed the presence of two major lineages within this monophyletic cluster consisting of some clonal variants. Incidentally, the majority of these XCPs were first noticed in India, corroborating their clonal relationship and their common origin. Comparative analysis revealed an open pan-genome and the role of interstrain genomic flux of these XCPs since their diversification from a common ancestor. Even though there are wide variations in type III gene effectomes, we identified three core effectors which can be valuable in resistance-breeding programs. Overall, genomic examination of ecological relatives allowed us to dissect the tremendous genomic potential of
X. citri
species to rapidly evolve into specialized strains infecting diverse crop plants.

IMPORTANCE
Host specialization is one of the characteristic features of highly evolved pathogens such as the
Xanthomonas
group of phytopathogenic bacteria. Since the hosts involve staple crops and economically important fruits such as citrus, detailed understanding of the diversity and evolution of such strains infecting diverse plants is important for quarantine purposes. In the present study, we carried out genomic investigation of members of a phylogenetically and ecologically defined group of
Xanthomonas
strains pathogenic to diverse plants, including citrus. This group includes the oldest
Xanthomonas
pathovars and also recently emerged pathovars in a particular country where they are endemic. Our high-throughput genomic study has provided novel insights into the evolution of a unique lineage consisting of serious pathogens and their ecological relatives, suggesting the nature, scope, and pattern of rapid and recent diversification. Further, from the level of species to that of clonal variants, the study revealed interesting genomic patterns in diversification of a
Xanthomonas
lineage and perhaps will inspire careful study of the host range of the included pathovars.
The Azoarcus anaerobius 1,3-Dihydroxybenzene (Resorcinol) Anaerobic Degradation Pathway Is Controlled by the Coordinated Activity of Two Enhancer-Binding Proteins
Authors: Pacheco-Sánchez Daniel , Molina-Fuentes Águeda , Marín Patricia , Medina-Bellver Javier-I. , González-López Óscar , Marqués Silvia 
Published: March 2017

ABSTRACT

The anaerobic resorcinol degradation pathway in
Azoarcus anaerobius
is unique in that it uses an oxidative rather than a reductive strategy to overcome the aromatic ring stability in degradation of this compound, in a process that is dependent on nitrate respiration. We show that the pathway is organized in five transcriptional units, three of which are inducible by the presence of the substrate. Three σ
54
-dependent promoters located upstream from the three operons coding for the main pathway enzymes were identified, which shared a similar structure with conserved upstream activating sequences (UASs) located at 103 to 111 bp from the transcription start site. Expression of the pathway is controlled by the bacterial enhancer-binding proteins (bEBPs) RedR1 and RedR2, two homologous regulators that, despite their high sequence identity (97%), have nonredundant functions: RedR2, the master regulator which also controls RedR1 expression, is itself able to promote transcription from two of the promoters, while RedR1 activity is strictly dependent on the presence of RedR2. The two regulators were shown to interact with each other, suggesting that the natural mode of activation is by forming heterodimers, which become active in the presence of the substrate after its metabolization to hydroxybenzoquinone through the pathway enzymes. The model structure of the N-terminal domain of the proteins is composed of tandem GAF and PAS motifs; the possible mechanisms controlling the activity of the regulators are discussed.

IMPORTANCE
Azoarcus anaerobius
is a strict anaerobe that is able to use 1,3-dihydroxybenzene as the sole carbon source in a process that is dependent on nitrate respiration. We have shown that expression of the pathway is controlled by two regulators of almost identical sequences: the bEBPs RedR1 and RedR2, which share 97% identity. These regulators control three promoters with similar structure. Despite their sequence identity, the two bEBPs are not redundant and are both required for maximum pathway expression. In fact, the two proteins function as heterodimers and require activation by the pathway intermediate hydroxyhydroquinone. The structure of the domain sensing the activation signal resembles that of regulators that are known to interact with other proteins.
TM0416, a Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C
5
and C
6
Epimerization Reactions
Authors: Shin Sun-Mi , Cao Thinh-Phat , Choi Jin Myung , Kim Seong-Bo , Lee Sang-Jae , Lee Sung Haeng , Lee Dong-Woo 
Published: March 2017

ABSTRACT

There is currently little information on nonphosphorylated sugar epimerases, which are of potential interest for producing rare sugars. We found a gene (the TM0416 gene) encoding a putative
d
-tagatose-3-epimerase-related protein from the hyperthermophilic bacterium
Thermotoga maritima
. We overexpressed the TM0416 gene in
Escherichia coli
and purified the resulting recombinant protein for detailed characterization. Amino acid sequence alignment and a structural similarity search revealed that TM0416 is a putative nonphosphorylated sugar epimerase. The recombinant enzyme exhibited maximal C-3 epimerization of
l
-ribulose to
l
-xylulose at ∼80°C and pH 7 in the presence of 1 mM Mn
2+
. In addition, this enzyme showed unusually high activity for the epimerization of
d
-tagatose to
d
-sorbose, with a conversion yield of 20% after 6 h at 80°C. Remarkably, the enzyme catalyzed the isomerization of
d
-erythrose or
d
-threose to
d
-erythrulose significantly, with conversion yields of 71% and 54.5%, respectively, after 6 h at 80°C at pH 7. To further investigate the substrate specificity of TM0416, we determined its crystal structures in complex with divalent metal ions and
l
-erythrulose at resolutions of 1.5 and 1.6 Å. Detailed inspection of the structural features and biochemical data clearly demonstrated that this metalloenzyme, with a freely accessible substrate-binding site and neighboring hydrophobic residues, exhibits different and promiscuous substrate preferences, compared with its mesophilic counterparts. Therefore, this study suggests that TM0416 can be functionally classified as a novel type of
l
-ribulose 3-epimerase (R3E) with
d
-erythrose isomerase activity.

IMPORTANCE
Rare sugars, which occur naturally in small amounts, have attracted considerable attention in the food and drug industries. However, there is little information on nonphosphorylated sugar epimerases, which might potentially be applied for the production of rare sugars. This study describes the characterization and functional annotation of a putative nonphosphorylated sugar 3-epimerase from a hyperthermophilic bacterium. Furthermore, we determined its crystal structures in complex with divalent metal ions and
l
-erythrulose, highlighting its metal-dependent, bifunctional, sugar-isomerizing activity. This hyperthermophilic R3E exhibited
d
-erythrose/
d
-threose isomerase activity, with structural features near the substrate-binding site distinct from those of its mesophilic counterparts. Moreover, this metalloenzyme showed unusually high activity for the epimerization of
d
-tagatose to
d
-sorbose at 70°C. Therefore, TM0416 can be functionally classified as a novel type of promiscuous R3E with a potential for the production of rare sugars for the food and pharmaceutical industries.
Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem
Authors: Wang Yuanqi , Hatt Janet K. , Tsementzi Despina , Rodriguez-R Luis M. , Ruiz-Pérez Carlos A. , Weigand Michael R. , Kizer Heidi , Maresca Gina , Krishnan Raj , Poretsky Rachel , Spain Jim C. , Konstantinidis Konstantinos T. 
Published: March 2017

ABSTRACTA single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called “rare biosphere.” How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species.IMPORTANCEA single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants.
Unusual Versatility of the Filamentous, Diazotrophic Cyanobacterium Anabaena torulosa Revealed for Its Survival during Prolonged Uranium Exposure
Authors: Acharya Celin , Chandwadkar Pallavi , Nayak Chandrani 
Published: March 2017

ABSTRACT

Reports on interactions between cyanobacteria and uranyl carbonate are rare. Here, we present an interesting succession of the metabolic responses employed by a marine, filamentous, diazotrophic cyanobacterium,
Anabaena torulosa
for its survival following prolonged exposure to uranyl carbonate extending up to 384 h at pH 7.8 under phosphate-limited conditions. The cells sequestered uranium (U) within polyphosphates on initial exposure to 100 μM uranyl carbonate for 24 to 28 h. Further incubation until 120 h resulted in (i) significant degradation of cellular polyphosphates causing extensive chlorosis and cell lysis, (ii) akinete differentiation followed by (iii) extracellular uranyl precipitation. X-ray diffraction (XRD) analysis, fluorescence spectroscopy, X-ray absorption near edge structure (XANES), and extended X-ray absorption fine structure (EXAFS) spectroscopy established the identity of the bioprecipitated uranium as a U(VI) autunite-type mineral, which settled at the bottom of the vessel. Surprisingly,
A. torulosa
cells resurfaced as small green flakes typical of actively growing colonies on top of the test solutions within 192 to 240 h of U exposure. A consolidated investigation using kinetics, microscopy, and physiological and biochemical analyses suggested a role of inducible alkaline phosphatase activity of cell aggregates/akinetes in facilitating the germination of akinetes leading to substantial regeneration of
A. torulosa
by 384 h of uranyl incubation. The biomineralized uranium appeared to be stable following cell regeneration. Altogether, our results reveal novel insights into the survival mechanism adopted by
A. torulosa
to resist sustained uranium toxicity under phosphate-limited oxic conditions.

IMPORTANCE
Long-term effects of uranyl exposure in cyanobacteria under oxic phosphate-limited conditions have been inadequately explored. We conducted a comprehensive examination of the metabolic responses displayed by a marine cyanobacterium,
Anabaena torulosa
, to cope with prolonged exposure to uranyl carbonate at pH 7.8 under phosphate limitation. Our results highlight distinct adaptive mechanisms harbored by this cyanobacterium that enabled its natural regeneration following extensive cell lysis and uranium biomineralization under sustained uranium exposure. Such complex interactions between environmental microbes such as
Anabaena torulosa
and uranium over a broader time range advance our understanding on the impact of microbial processes on uranium biogeochemistry.
Adaptation of Salmonella enterica Serovar Senftenberg to Linalool and Its Association with Antibiotic Resistance and Environmental Persistence
Authors: Kalily Emmanuel , Hollander Amit , Korin Ben , Cymerman Itamar , Yaron Sima 
Published: March 2017

ABSTRACT

A clinical isolate of
Salmonella enterica
serovar Senftenberg, isolated from an outbreak linked to the herb
Ocimum basilicum
L. (basil), has been shown to be resistant to basil oil and to the terpene alcohol linalool. To better understand how human pathogens might develop resistance to linalool and to investigate the association of this resistance with resistance to different antimicrobial agents, selective pressure was applied to the wild-type strain by sequential exposure to increasing concentrations of linalool. The results demonstrated that
S
. Senftenberg adapted to linalool with a MIC increment of at least 8-fold, which also resulted in better resistance to basil oil and better survival on harvested basil leaves. Adaptation to linalool was shown to confer cross protection against the antibiotics trimethoprim, sulfamethoxazole, piperacillin, chloramphenicol, and tetracycline, increasing their MICs by 2- to 32-fold. The improved resistance was shown to correlate with multiple phenotypes that included changes in membrane fatty acid composition, induced efflux, reduced influx, controlled motility, and the ability to form larger aggregates in the presence of linalool. The adaptation to linalool obtained
in vitro
did not affect survival on the basil phyllosphere
in planta
and even diminished survival in soil, suggesting that development of extreme resistance to linalool may be accompanied by a loss of fitness. Altogether, this report notes the concern regarding the ability of human pathogens to develop resistance to commercial essential oils, a resistance that is also associated with cross-resistance to antibiotics and may endanger public health.

IMPORTANCE
Greater consumer awareness and concern regarding synthetic chemical additives have led producers to control microbial spoilage and hazards by the use of natural preservatives, such as plant essential oils with antimicrobial activity. This report establishes, however, that these compounds may provoke the emergence of resistant human pathogens. Herein, we demonstrate the acquisition of resistance to basil oil by
Salmonella
Senftenberg. Exposure to linalool, a component of basil oil, resulted in adaptation to the basil oil mixture, as well as cross protection against several antibiotics and better survival on harvested basil leaves. Collectively, this work highlights the hazard to public health while using plant essential oils without sufficient knowledge about their influence on pathogens at subinhibitory concentrations.
A Broad-Host-Range Tailocin from Burkholderia cenocepacia
Authors: Yao Guichun W. , Duarte Iris , Le Tram T. , Carmody Lisa , LiPuma John J. , Young Ry , Gonzalez Carlos F. 
Published: March 2017

ABSTRACT

The
Burkholderia cepacia
complex (Bcc) consists of 20 closely related Gram-negative bacterial species that are significant pathogens for persons with cystic fibrosis (CF). Some Bcc strains are highly transmissible and resistant to multiple antibiotics, making infection difficult to treat. A tailocin (phage tail-like bacteriocin), designated BceTMilo, with a broad host range against members of the Bcc, was identified in
B. cenocepacia
strain BC0425. Sixty-eight percent of Bcc representing 10 species and 90% of non-Bcc
Burkholderia
strains tested were sensitive to BceTMilo. BceTMilo also showed killing activity against
Pseudomonas aeruginosa
PAO1 and derivatives. Liquid chromatography-mass spectrometry analysis of the major BceTMilo proteins was used to identify a 23-kb tailocin locus in a draft BC0425 genome. The BceTMilo locus was syntenic and highly similar to a 24.6-kb region on chromosome 1 of
B. cenocepacia
J2315 (BCAL0081 to BCAL0107). A close relationship and synteny were observed between BceTMilo and
Burkholderia
phage KL3 and, by extension, with paradigm temperate myophage P2. Deletion mutants in the gene cluster encoding enzymes for biosynthesis of lipopolysaccharide (LPS) in the indicator strain
B. cenocepacia
K56-2 conferred resistance to BceTMilo. Analysis of the defined mutants in LPS biosynthetic genes indicated that an α-
d
-glucose residue in the core oligosaccharide is the receptor for BceTMilo.

IMPORTANCE
BceTMilo, presented in this study, is a broad-host-range tailocin active against
Burkholderia
spp. As such, BceTMilo and related or modified tailocins have potential as bactericidal therapeutic agents against plant- and human-pathogenic
Burkholderia
.
The patellofemoral pain and osteoarthritis subscale of the KOOS (KOOS-PF): development and validation using the COSMIN checklist
Authors: Crossley Kay M , Macri Erin M , Cowan Sallie M , Collins Natalie J , Roos Ewa M 
Published: March 2017

BackgroundPatellofemoral pain and osteoarthritis are prevalent and associated with substantial pain and functional impairments. Patient-reported outcome measures (PROMs) are recommended for research and clinical use, but no PROMs are specific for patellofemoral osteoarthritis, and existing PROMs for patellofemoral pain have methodological limitations. This study aimed to develop a new subscale of the Knee injury and Osteoarthritis Outcome Score for patellofemoral pain and osteoarthritis (KOOS-PF), and evaluate its measurement properties.MethodsItems were generated using input from 50 patients with patellofemoral pain and/or osteoarthritis and 14 health and medical clinicians. Item reduction was performed using data from patellofemoral cohorts (n=138). We used the COnsesus-based Standards for the selection of health Measurements INstruments guidelines to evaluate reliability, validity, responsiveness and interpretability of the final version of KOOS-PF and other KOOS subscales.ResultsFrom an initial 80 generated items, the final subscale included 11 items. KOOS-PF items loaded predominantly on one factor, pain during activities that load the patellofemoral joint. KOOS-PF had good internal consistency (Cronbach’s α 0.86) and adequate test–retest reliability (intraclass correlation coefficient 0.86). Hypothesis testing supported convergent, divergent and known-groups validity. Responsiveness was confirmed, with KOOS-PF demonstrating a moderate correlation with Global Rating of Change scores (r 0.52) and large effect size (Cohen’s d 0.89). Minimal detectable change was 2.3 (groups) and 16 (individuals), while minimal important change was 16.4. There were no floor or ceiling effects.ConclusionsThe 11-item KOOS-PF, developed in consultation with patients and clinicians, demonstrated adequate measurement properties, and is recommended for clinical and research use in patients with patellofemoral pain and osteoarthritis.
Stem cell injections in knee osteoarthritis: a systematic review of the literature
Authors: Pas Haiko IMFL , Winters Marinus , Haisma Hidde J , Koenis Martinus JJ , Tol Johannes L , Moen Maarten H 
Published: March 2017

ObjectiveStem cell injection for knee osteoarthritis (KOA) is an emerging new therapy, and we aimed to review its evidence of efficacy.DesignSystematic review.Eligibility criteriaCriteria for eligibility were randomised controlled trials (RCTs) and non-RCT on the efficacy of stem cell injections in KOA. All references were checked for missed articles.Data sourcesMEDLINE, EMBASE, CINAHL, Web of Science, Cochrane Library, PEDro and SPORTDiscus were searched. A grey literature search was performed. No restrictions were imposed to our search strategy.Risk of bias and data synthesisRisk of bias was assessed using the Cochrane risk of bias tool. Descriptive synthesis was performed using the levels of evidence according to the Oxford Levels of Evidence.ResultsFive RCTs and one non-RCT were found. Bone-marrow-derived stem cells, adipose-derived mesenchymal stem cells and peripheral blood stem cells were used. All trials were at high risk of bias, resulting in level-3 evidence. All five RCTs reported superior efficacy for patient-reported outcomes (Visual Analogue Scale, Western Ontario and McMaster Universities Arthritis Index, Tegner, Lysolm, International Knee Documentation Committee, Knee Injury and Osteoarthritis Outcome Score, Lequesne) compared with controls at final follow-up (range 24–48 months). Superior radiological outcomes were found favouring stem cell injection. Superior histological outcomes and/or improved arthroscopically scored healing rates were reported in two trials. No serious adverse events were reported.ConclusionSix trials with high risk of bias showed level-3 or level-4 evidence in favour of stem cell injections in KOA. In the absence of high-level evidence, we do not recommend stem cell therapy for KOA.