bluuebunny/crossref_metadata_2025_split huggingface dataset:
The regulation of carotenoid formation in tomato fruit
Authors: Enfissi Eugenia M.A. , Nogueira Marilise , Bramley Peter M. , Fraser Paul D. 
Published: November 2016

SummaryCarotenoid biosynthesis in plants includes a complex series of desaturation/isomerisation reactions, catalyzed by four independent enzymes. In bacteria and fungi one desaturase/isomerase enzyme completes the same series of reactions. In the present study, a bacterial desaturase (crtI) from Pantoea ananatis has been overexpressed in the tangerine mutant of tomato (Solanum lycopersicon) which accumulates cis‐carotene isomers in the fruit due to a defective isomerase (CRTISO) and the old gold crimson (ogc) tomato mutant, which is defective in the fruit‐enhanced lycopene β‐cyclase (CYCB). Comprehensive molecular and biochemical characterization of the resulting lines expressing crtI has revealed negative feedback mechanisms, acting predominantly at the level of phytoene synthase‐1 (PSY1), and feed‐forward mechanisms inducing cyclisation. In both cases, altered transcription appears to be the progenitor, with subsequent post‐transcriptional modulation highlighting the complexity of the processes involved in modulating carotenoid homeostasis in plant tissues.
Microbial Nursery Production of High-Quality Biological Soil Crust Biomass for Restoration of Degraded Dryland Soils
Authors: Velasco Ayuso Sergio , Giraldo Silva Ana , Nelson Corey , Barger Nichole N. , Garcia-Pichel Ferran 
Published: November 2016

ABSTRACT

Biological soil crusts (biocrusts) are slow-growing, phototroph-based microbial assemblages that develop on the topsoils of drylands. Biocrusts help maintain soil fertility and reduce erosion. Because their loss through human activities has negative ecological and environmental health consequences, biocrust restoration is of interest. Active soil inoculation with biocrust microorganisms can be an important tool in this endeavor. We present a culture-independent, two-step process to grow multispecies biocrusts in open greenhouse nursery facilities, based on the inoculation of local soils with local biocrust remnants and incubation under seminatural conditions that maintain the essence of the habitat but lessen its harshness. In each of four U.S. Southwest sites, we tested and deployed combinations of factors that maximized growth (gauged as chlorophyll
a
content) while minimizing microbial community shifts (assessed by 16S rRNA sequencing and bioinformatics), particularly for crust-forming cyanobacteria. Generally, doubling the frequency of natural wetting events, a 60% reduction in sunlight, and inoculation by slurry were optimal. Nutrient addition effects were site specific. In 4 months, our approach yielded crusts of high inoculum quality reared on local soil exposed to locally matched climates, acclimated to desiccation, and containing communities minimally shifted in composition from local ones. Our inoculum contained abundant crust-forming cyanobacteria and no significant numbers of allochthonous phototrophs, and it was sufficient to treat ca. 6,000 m
2
of degraded dryland soils at 1 to 5% of the typical crust biomass concentration, having started from a natural crust remnant as small as 6 to 30 cm
2
.

IMPORTANCE
Soil surface crusts can protect dryland soils from erosion, but they are often negatively impacted by human activities. Their degradation causes a loss of fertility, increased production of fugitive dust and intensity of dust storms with associated traffic problems, and provokes general public health hazards. Our results constitute an advance in the quest to actively restore biological soil covers by providing a means to obtain high-quality inoculum within a reasonable time (a few months), thereby allowing land managers to recover essential, but damaged, ecosystem services in a sustainable, self-perpetuating way as provided by biocrust communities.
Biogeography of Oenococcus oeni Reveals Distinctive but Nonspecific Populations in Wine-Producing Regions
Authors: El Khoury Mariette , Campbell-Sills Hugo , Salin Franck , Guichoux Erwan , Claisse Olivier , Lucas Patrick M. 
Published: November 2016

ABSTRACT

Understanding the mechanisms behind the typicity of regional wines inevitably brings attention to microorganisms associated with their production.
Oenococcus oeni
is the main bacterial species involved in wine and cider making. It develops after the yeast-driven alcoholic fermentation and performs the malolactic fermentation, which improves the taste and aromatic complexity of most wines. Here, we have evaluated the diversity and specificity of
O. oeni
strains in six regions. A total of 235 wines and ciders were collected during spontaneous malolactic fermentations and used to isolate 3,212 bacterial colonies. They were typed by multilocus variable analysis, which disclosed a total of 514
O. oeni
strains. Their phylogenetic relationships were evaluated by a second typing method based on single nucleotide polymorphism (SNP) analysis. Taken together, the results indicate that each region holds a high diversity of strains that constitute a unique population. However, strains present in each region belong to diverse phylogenetic groups, and the same groups can be detected in different regions, indicating that strains are not genetically adapted to regions. In contrast, greater strain identity was seen for cider, white wine, or red wine of Burgundy, suggesting that genetic adaptation to these products occurred.

IMPORTANCE
This study reports the isolation, genotyping, and geographic distribution analysis of the largest collection of
O. oeni
strains performed to date. It reveals that there is very high diversity of strains in each region, the majority of them being detected in a single region. The study also reports the development of an SNP genotyping method that is useful for analyzing the distribution of
O. oeni
phylogroups. The results show that strains are not genetically adapted to regions but to specific types of wines. They reveal new phylogroups of strains, particularly two phylogroups associated with white wines and red wines of Burgundy. Taken together, the results shed light on the diversity and specificity of wild strains of
O. oeni
, which is crucial for understanding their real contribution to the unique properties of wines.
The EbpA-RpoN Regulatory Pathway of the Pathogen Leptospira interrogans Is Essential for Survival in the Environment
Authors: Hu Wei-Lin , Pappas Christopher J. , Zhang Jun-Jie , Yang You-Yun , Yan Jie , Picardeau Mathieu , Yang X. Frank 
Published: November 2016

ABSTRACT

Leptospira interrogans
is the agent of leptospirosis, a reemerging zoonotic disease. It is transmitted to humans through environmental surface waters contaminated by the urine of mammals chronically infected by pathogenic strains able to survive in water for long periods. Little is known about the regulatory pathways underlying environmental sensing and host adaptation of
L. interrogans
during its enzootic cycle. This study identifies the EbpA-RpoN regulatory pathway in
L. interrogans
. In this pathway, EbpA, a σ
54
activator and putative prokaryotic enhancer-binding protein (EBP), and the alternative sigma factor RpoN (σ
54
) control expression of at least three genes, encoding AmtB (an ammonium transport protein) and two proteins of unknown function. Electrophoresis mobility shift assay demonstrated that recombinant RpoN and EbpA bind to the promoter region and upstream of these three identified genes, respectively. Genetic disruption of
ebpA
in
L. interrogans
serovar Manilae virtually abolished expression of the three genes, including
amtB
in two independent
ebpA
mutants. Complementation of the
ebpA
mutant restored expression of these genes. Intraperitoneal inoculation of gerbils with the
ebpA
mutant did not affect mortality. However, the
ebpA
mutant had decreased cell length
in vitro
and had a significantly lowered cell density at stationary phase when grown with
l
-alanine as the sole nitrogen source. Furthermore, the
ebpA
mutant has dramatically reduced long-term survival ability in water. Together, these studies identify a regulatory pathway, the EbpA-RpoN pathway, that plays an important role in the zoonotic cycle of
L. interrogans
.

IMPORTANCE
Leptospirosis is a reemerging disease with global importance. However, our understanding of gene regulation of the spirochetal pathogen
Leptospira interrogans
is still in its infancy, largely due to the lack of robust tools for genetic manipulation of this spirochete. Little is known about how the pathogen achieves its long-term survival in the aquatic environment. By utilizing bioinformatic, genetic, and biochemical methods, we discovered a regulatory pathway in
L. interrogans
, the EbpA-RpoN pathway, and demonstrated that this pathway plays an important role in environmental survival of this pathogen.
Salad Leaf Juices Enhance Salmonella Growth, Colonization of Fresh Produce, and Virulence
Authors: Koukkidis Giannis , Haigh Richard , Allcock Natalie , Jordan Suzanne , Freestone Primrose 
Published: November 2016

ABSTRACT

We show in this report that traces of juices released from salad leaves as they become damaged can significantly enhance colonization of salad leaves by
Salmonella enterica
. Salad juices in water increased
Salmonella
growth by 110% over the level seen with the unsupplemented control and in host-like serum-based media by more than 2,400-fold over control levels. In serum-based media, salad juices induced growth of
Salmonella
via provision of Fe from transferrin, and siderophore production was found to be integral to the growth induction process. Other aspects relevant to salad leaf colonization and retention were enhanced, such as motility and biofilm formation, which were increased over control levels by >220% and 250%, respectively; direct attachment to salad leaves increased by >350% when a salad leaf juice was present. In terms of growth and biofilm formation, the endogenous salad leaf microbiota was largely unresponsive to leaf juice, suggesting that
Salmonella
gains a marked growth advantage from fluids released by salad leaf damage. Salad leaf juices also enhanced pathogen attachment to the salad bag plastic. Over 5 days of refrigeration (a typical storage time for bagged salad leaves), even traces of juice within the salad bag fluids increased
Salmonella
growth in water by up to 280-fold over control cultures, as well as enhancing salad bag colonization, which could be an unappreciated factor in retention of pathogens in fresh produce. Collectively, the study data show that exposure to salad leaf juice may contribute to the persistence of
Salmonella
on salad leaves and strongly emphasize the importance of ensuring the microbiological safety of fresh produce.

IMPORTANCE
Salad leaves are an important part of a healthy diet but have been associated in recent years with a growing risk of food poisoning from bacterial pathogens such as
Salmonella enterica
. Although this is considered a significant public health problem, very little is known about the behavior of
Salmonella
in the actual salad bag. We show that juices released from the cut ends of the salad leaves enabled the
Salmonella
cells to grow in water, even when it was refrigerated. Salad juice exposure also helped the
Salmonella
cells to attach to the salad leaves so strongly that washing could not remove them. Collectively, the results presented in this report show that exposure to even traces of salad leaf juice may contribute to the persistence of
Salmonella
on salad leaves as well as priming it for establishing an infection in the consumer.
Insights into the Biosynthesis of Duramycin
Authors: Huo Liujie , Ökesli Ayşe , Zhao Ming , van der Donk Wilfred A. 
Published: November 2016

ABSTRACT

Lantibiotics are ribosomally synthesized and posttranslationally modified antimicrobial peptides that are characterized by the thioether cross-linked bisamino acids lanthionine (Lan) and methyllanthionine (MeLan). Duramycin contains 19 amino acids, including one Lan and two MeLans, an unusual lysinoalanine (Lal) bridge formed from the ε-amino group of lysine 19 and a serine residue at position 6, and an
erythro
-3-hydroxy-
l
-aspartic acid at position 15. These modifications are important for the interactions of duramycin with its biological target, phosphatidylethanolamine (PE). Based on the binding affinity and specificity for PE, duramycin has been investigated as a potential therapeutic, as a molecular probe to investigate the role and localization of PE in biological systems, and to block viral entry into mammalian cells. In this study, we identified the duramycin biosynthetic gene cluster by genome sequencing of
Streptomyces cinnamoneus
ATCC 12686 and investigated the
dur
biosynthetic machinery by heterologous expression in
Escherichia coli
. In addition, the analog duramycin C, containing six amino acid changes compared to duramycin, was successfully generated in
E. coli
. The substrate recognition motif of DurX, an α-ketoglutarate/iron(II)-dependent hydroxylase that carries out the hydroxylation of aspartate 15 of the precursor peptide DurA, was also investigated using mutagenesis of the DurA peptide. Both
in vivo
and
in vitro
results demonstrated that Gly16 is important for DurX activity.

IMPORTANCE
Duramycin is a natural product produced by certain bacteria that binds to phosphatidylethanolamine (PE). Because PE is involved in many cellular processes, duramycin is an antibiotic that kills bacteria, but it has also been used as a molecular probe to detect PE and monitor its localization in mammalian cells and even whole organisms, and it was recently shown to display broad-spectrum inhibition of viral entry into host cells. In addition, the molecule has been evaluated as treatment for cystic fibrosis. We report here the genes that are involved in duramycin biosynthesis, and we produced duramycin by expressing those genes in
Escherichia coli
. We show that duramycin analogs can also be produced. The ability to access duramycin and analogs by production in
E. coli
opens opportunities to improve duramycin as an antibiotic, PE probe, antiviral, or cystic fibrosis therapeutic.
Mitochondrial Superoxide Dismutase and Yap1p Act as a Signaling Module Contributing to Ethanol Tolerance of the Yeast Saccharomyces cerevisiae
Authors: Zyrina Anna N. , Smirnova Ekaterina A. , Markova Olga V. , Severin Fedor F. , Knorre Dmitry A. 
Published: November 2016

ABSTRACT

There are two superoxide dismutases in the yeast
Saccharomyces cerevisiae
—cytoplasmic and mitochondrial enzymes. Inactivation of the cytoplasmic enzyme, Sod1p, renders the cells sensitive to a variety of stresses, while inactivation of the mitochondrial isoform, Sod2p, typically has a weaker effect. One exception is ethanol-induced stress. Here we studied the role of Sod2p in ethanol tolerance of yeast. First, we found that repression of
SOD2
prevents ethanol-induced relocalization of yeast hydrogen peroxide-sensing transcription factor Yap1p, one of the key stress resistance proteins. In agreement with this, the levels of Trx2p and Gsh1p, proteins encoded by Yap1 target genes, were decreased in the absence of Sod2p. Analysis of the ethanol sensitivities of the cells lacking Sod2p, Yap1p, or both indicated that the two proteins act in the same pathway. Moreover, preconditioning with hydrogen peroxide restored the ethanol resistance of yeast cells with repressed
SOD2
. Interestingly, we found that mitochondrion-to-nucleus signaling by Rtg proteins antagonizes Yap1p activation. Together, our data suggest that hydrogen peroxide produced by Sod2p activates Yap1p and thus plays a signaling role in ethanol tolerance.

IMPORTANCE
Baker's yeast harbors multiple systems that ensure tolerance to high concentrations of ethanol. Still, the role of mitochondria under severe ethanol stress in yeast is not completely clear. Our study revealed a signaling function of mitochondria which contributes significantly to the ethanol tolerance of yeast cells. We found that mitochondrial superoxide dismutase Sod2p and cytoplasmic hydrogen peroxide sensor Yap1p act together as a module of the mitochondrion-to-nucleus signaling pathway. We also report cross talk between this pathway and the conventional retrograde signaling cascade activated by dysfunctional mitochondria.
Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria
Authors: Duranti Sabrina , Lugli Gabriele Andrea , Mancabelli Leonardo , Turroni Francesca , Milani Christian , Mangifesta Marta , Ferrario Chiara , Anzalone Rosaria , Viappiani Alice , van Sinderen Douwe , Ventura Marco 
Published: November 2016

ABSTRACT

The microbiota of the human gastrointestinal tract (GIT) may regularly be exposed to antibiotics, which are used to prevent and treat infectious diseases caused by bacteria and fungi. Bacterial communities of the gut retain a reservoir of antibiotic resistance (AR) genes, and antibiotic therapy thus positively selects for those microorganisms that harbor such genetic features, causing microbiota modulation. During the first months following birth, bifidobacteria represent some of the most dominant components of the human gut microbiota, although little is known about their AR gene complement (or resistome). In the current study, we assessed the resistome of the
Bifidobacterium
genus based on phenotypic and genotypic data of members that represent all currently recognized bifidobacterial (sub)species. Moreover, a comparison between the bifidobacterial resistome and gut metagenome data sets from adults and infants shows that the bifidobacterial community present at the first week following birth possesses a reduced AR arsenal compared to that present in the infant bifidobacterial population in subsequent weeks of the first year of life. Our findings reinforce the concept that the early infant gut microbiota is more susceptible to disturbances by antibiotic treatment than the gut microbiota developed at a later life stage.

IMPORTANCE
The spread of resistance to antibiotics among bacterial communities has represented a major concern since their discovery in the last century. The risk of genetic transfer of resistance genes between microorganisms has been extensively investigated due to its relevance to human health. In contrast, there is only limited information available on antibiotic resistance among human gut commensal microorganisms such as bifidobacteria, which are widely exploited by the food industry as health-promoting microorganisms or probiotic ingredients. In the current study, we explored the occurrence of antibiotic resistance genes in the genomes of bifidobacteria and evaluated their genetic mobility to other human gut commensal microorganisms.
Histone Deacetylase HDA-2 Regulates Trichoderma atroviride Growth, Conidiation, Blue Light Perception, and Oxidative Stress Responses
Authors: Osorio-Concepción Macario , Cristóbal-Mondragón Gema Rosa , Gutiérrez-Medina Braulio , Casas-Flores Sergio 
Published: November 2016

ABSTRACT

Fungal blue-light photoreceptors have been proposed as integrators of light and oxidative stress. However, additional elements participating in the integrative pathway remain to be identified. In
Trichoderma
atroviride
, the blue-light regulator (BLR) proteins BLR-1 and -2 are known to regulate gene transcription, mycelial growth, and asexual development upon illumination, and recent global transcriptional analysis revealed that the histone deacetylase-encoding gene
hda-2
is induced by light. Here, by assessing responses to stimuli in wild-type and Δ
hda-2
backgrounds, we evaluate the role of HDA-2 in the regulation of genes responsive to light and oxidative stress. Δ
hda-2
strains present reduced growth, misregulation of the
con-1
gene, and absence of conidia in response to light and mechanical injury. We found that the expression of
hda-2
is BLR-1 dependent and HDA-2 in turn is essential for the transcription of early and late light-responsive genes that include
blr-1
, indicating a regulatory feedback loop. When subjected to reactive oxygen species (ROS), Δ
hda-2
mutants display high sensitivity whereas Δ
blr
strains exhibit the opposite phenotype. Consistently, in the presence of ROS, ROS-related genes show high transcription levels in wild-type and Δ
blr
strains but misregulation in Δ
hda-2
mutants. Finally, chromatin immunoprecipitations of histone H3 acetylated at Lys9/Lys14 on
cat-3
and
gst-1
promoters display low accumulation of H3K9K14ac in Δ
blr
and Δ
hda-2
strains, suggesting indirect regulation of ROS-related genes by HDA-2. Our results point to a mutual dependence between HDA-2 and BLR proteins and reveal the role of these proteins in an intricate gene regulation landscape in response to blue light and ROS.

IMPORTANCE
Trichoderma
atroviride
is a free-living fungus commonly found in soil or colonizing plant roots and is widely used as an agent in biocontrol as it parasitizes other fungi, stimulates plant growth, and induces the plant defense system. To survive in various environments, fungi constantly sense and respond to potentially threatening external factors, such as light. In particular, UV light can damage biomolecules by producing free-radical reactions, in most cases involving reactive oxygen species (ROS). In
T. atroviride
, conidiation is essential for its survival, which is induced by light and mechanical injury. Notably, conidia are typically used as the inoculum in the field during biocontrol. Therefore, understanding the linkages between responses to light and exposure to ROS in
T. atroviride
is of major basic and practical relevance. Here, the histone deacetylase-encoding gene
hda-2
is induced by light and ROS, and its product regulates growth, conidiation, blue light perception, and oxidative stress responses.