bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of an ethylene response factor in chlorophyll degradation during citrus fruit degreening
Authors: Yin Xue‐ren , Xie Xiu‐lan , Xia Xiao‐jian , Yu Jing‐quan , Ferguson Ian B. , Giovannoni James J. , Chen Kun‐song 
Published: April 2016

SummaryChlorophyll degradation naturally occurs during plant senescence. However, in fruit such as citrus, it is a positive characteristic, as degreening is an important colour development contributing to fruit quality. In the present work, Citrus sinensis Osbeck, cv. Newhall fruit was used as a model for chlorophyll degradation. An ethylene response factor, CitERF13, was isolated and its transcriptional changes were closely correlated with fruit peel degreening during development or in response to ethylene. Dual‐luciferase and yeast one‐hybrid assays, as well as motif mutation, indicated that CitERF13 directly binds to the CitPPH promoter and enhances its activity. Transient and stable over‐expression of CitERF13 resulted in rapid chlorophyll degradation in Nicotiana tabacum leaves and led to accumulation of pheophorbide (Pheide) a, a metabolite of pheophorbide hydrolase (PPH). Similar results were observed from transient transformation of CitERF13 in citrus fruit peel. Moreover, this function of CitERF13 was conserved within Arabidopsis and tomato, as the homologs AtERF17 and SlERF16 similarly acted as activators of PPH genes and accelerators of chlorophyll degradation.
PLURIPETALA mediates ROP2 localization and stability in parallel to SCN1 but synergistically with TIP1 in root hairs
Authors: Chai Sen , Ge Fu‐Rong , Feng Qiang‐Nan , Li Sha , Zhang Yan 
Published: April 2016

SummaryPrenylation, the post‐translational attachment of prenyl groups to substrate proteins, can affect their distribution and interactomes. Arabidopsis PLURIPETALA (PLP) encodes the shared α subunit of two heterodimeric protein isoprenyltransferases, whose functional loss provides a unique opportunity to study developmental and cellular processes mediated by its prenylated substrates, such as ROP GTPases. As molecular switches, the distribution and activation of ROPs are mediated by various factors, including guanine nucleotide exchange factors, GTPase activating proteins, guanine nucleotide dissociation inhibitors (RhoGDIs), prenylation, and S‐acylation. However, how these factors together ensure that dynamic ROP signalling is still obscure. We report here that a loss‐of‐function allele of PLP resulted in cytoplasmic accumulation of ROP2 in root hairs and reduced its stability. Consequently, two downstream events of ROP signalling, i.e. actin microfilament (MF) organization and the production of reactive oxygen species (ROS), were compromised. Genetic, cytological and biochemical evidence supports an additive interaction between prenylation and RhoGDI1/SCN1 in ROP2 distribution and stability whereas PLP acts synergistically with the protein S‐acyl transferase TIP GROWTH DEFECTIVE1 during root hair growth. By using root hair growth as a model system, we uncovered complex interactions among prenylation, RhoGDIs, and S‐acylation in dynamic ROP signalling.
Basset Hound thrombopathia in a 4‐month‐old female Ba‐Shar (Sharp Asset)
Authors: Christopherson Pete W. , Alexander Eric A. , King Kevin B. , Boudreaux Mary K. 
Published: April 2016

AbstractA 3‐month‐old female Basset Hound‐Shar Pei mix puppy (Ba‐Shar or Sharp Asset) presented with oral bleeding due to a cracked molar. On physical exam, an aural hematoma was also noted that the owner indicated was chronic. The puppy was hospitalized for over 24 h until the bleeding was brought under control. At 4 months of age, the puppy again presented with oral bleeding due to loss of deciduous teeth and was hospitalized until bleeding was controlled. Coagulation screening tests, platelet numbers, and von Willebrand Factor antigen levels were within reference limits. Based on the presence of platelet‐type bleeding in the face of normal screening test results, samples were submitted for DNA testing for Basset Hound thrombopathia. The puppy tested as affected for the calcium and diacylglycerol regulated guanine nucleotide exchange factor I (CalDAG‐GEFI) mutation causing this disorder. This is the first time thrombopathia has been diagnosed in a “designer” breed.
p21‐Activated kinase (Pak) regulates airway smooth muscle contraction by regulating paxillin complexes that mediate actin polymerization
Authors: Zhang Wenwu , Huang Youliang , Gunst Susan J. 
Published: April 2016

Key points
In airway smooth muscle, tension development caused by a contractile stimulus requires phosphorylation of the 20 kDa myosin light chain (MLC), which activates crossbridge cycling and the polymerization of a pool of submembraneous actin.
The p21‐activated kinases (Paks) can regulate the contractility of smooth muscle and non‐muscle cells, and there is evidence that this occurs through the regulation of MLC phosphorylation.
We show that Pak has no effect on MLC phosphorylation during the contraction of airway smooth muscle, and that it regulates contraction by mediating actin polymerization.
We find that Pak phosphorylates the adhesion junction protein, paxillin, on Ser273, which promotes the formation of a signalling complex that activates the small GTPase, cdc42, and the actin polymerization catalyst, neuronal Wiskott–Aldrich syndrome protein (N‐WASP).
These studies demonstrate a novel role for Pak in regulating the contractility of smooth muscle by regulating actin polymerization.
AbstractThe p21‐activated kinases (Pak) can regulate contractility in smooth muscle and other cell and tissue types, but the mechanisms by which Paks regulate cell contractility are unclear. In airway smooth muscle, stimulus‐induced contraction requires phosphorylation of the 20 kDa light chain of myosin, which activates crossbridge cycling, as well as the polymerization of a small pool of actin. The role of Pak in airway smooth muscle contraction was evaluated by inhibiting acetylcholine (ACh)‐induced Pak activation through the expression of a kinase inactive mutant, Pak1 K299R, or by treating tissues with the Pak inhibitor, IPA3. Pak inhibition suppressed actin polymerization and contraction in response to ACh, but it did not affect myosin light chain phosphorylation. Pak activation induced paxillin phosphorylation on Ser273; the paxillin mutant, paxillin S273A, inhibited paxillin Ser273 phosphorylation and inhibited actin polymerization and contraction. Immunoprecipitation analysis of tissue extracts and proximity ligation assays in dissociated cells showed that Pak activation and paxillin Ser273 phosphorylation triggered the formation of an adhesion junction signalling complex with paxillin that included G‐protein‐coupled receptor kinase‐interacting protein (GIT1) and the cdc42 guanine exchange factor, βPIX (Pak interactive exchange factor). Assembly of the Pak–GIT1–βPIX–paxillin complex was necessary for cdc42 and neuronal Wiskott–Aldrich syndrome protein (N‐WASP) activation, actin polymerization and contraction in response to ACh. RhoA activation was also required for the recruitment of Pak to adhesion junctions, Pak activation, paxillin Ser273 phosphorylation and paxillin complex assembly. These studies demonstrate a novel role for Pak in the regulation of N‐WASP activation, actin dynamics and cell contractility.
Short-Term Exposure to Coal Combustion Waste Has Little Impact on the Skin Microbiome of Adult Spring Peepers (Pseudacris crucifer)
Authors: Hughey Myra C. , Walke Jenifer B. , Becker Matthew H. , Umile Thomas P. , Burzynski Elizabeth A. , Minbiole Kevin P. C. , Iannetta Anthony A. , Santiago Celina N. , Hopkins William A. , Belden Lisa K. 
Published: April 2016

ABSTRACTDisruptions to the microbiome can impact host health as can exposure to environmental contaminants. However, few studies have addressed how environmental contaminants impact the microbiome. We explored this question for frogs that breed in wetlands contaminated with fly ash, a by-product of coal combustion that is enriched in trace elements. We found differences in the bacterial communities among a fly ash-contaminated site and several reference wetlands. We then experimentally assessed the impacts of fly ash on the skin microbiome of adult spring peepers (Pseudacris crucifer). Frogs were exposed to fly ash in the laboratory for 12 h, the duration of a typical breeding event, and the skin microbiome was assessed after 5 days (experiment 1) or after 5 and 15 days (experiment 2). We examined bacterial community structure using 16S rRNA gene amplicon sequencing and metabolite profiles using high-pressure liquid chromatography-mass spectrometry (HPLC-MS). We found little impact as the result of acute exposure to fly ash on the bacterial communities or metabolite profiles in either experiment, suggesting that the bacterial symbiont communities of adults may be relatively resistant to brief contaminant exposure. However, housing frogs in the laboratory altered bacterial community structure in the two experiments, which supports prior research suggesting that environmental source pools are important for maintaining the amphibian skin microbiome. Therefore, for contaminants like fly ash that may alter the potential source pool of symbionts, we think it may be important to explore how contaminants affect the initial assembly of the amphibian skin microbiome in larval amphibians that develop within contaminated sites.IMPORTANCEAnimals are hosts to many symbiotic microorganisms, collectively called the microbiome, that play critical roles in host health. Therefore, environmental contaminants that alter the microbiome may impact hosts. Some of the most widespread contaminants, produced worldwide, are derived from the mining, storage, and combustion of coal for energy. Fly ash, for example, is a by-product of coal combustion. It contains compounds such as arsenic, selenium, cadmium, and strontium and is a recognized source of ground and surface water contamination. Here, we experimentally investigated the impacts of short-term fly ash exposure on the skin microbiome of spring peepers, one of many species of amphibian that sometimes breed in open fly ash disposal ponds. This research provides a look into the potential impacts of fly ash on an animal's microbiome and suggests important future directions for research on the effects of environmental contaminants on the microbiome.
Effects of Polycyclic Aromatic Hydrocarbon Mixtures on Degradation, Gene Expression, and Metabolite Production in Four Mycobacterium Species
Authors: Hennessee Christiane T. , Li Qing X. 
Published: April 2016

ABSTRACT

Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental contaminants that are hazardous to human health. It has been demonstrated that members of the
Mycobacterium
genus are among the most effective degraders of PAHs, but few studies have focused on the degradation of PAH mixtures. In this study, single and mixed PAH metabolism was investigated in four phylogenetically distinct
Mycobacterium
species with respect to (i) parent compound degradation, (ii) bacterial growth, (iii) catabolic gene expression, and (iv) metabolite production. Synergistic and antagonistic effects on four model PAH compounds (benzo[
a
]pyrene, pyrene, fluoranthene, and phenanthrene) characterized degradation of mixtures in a strain- and mixture-dependent manner. The mixture of pyrene and phenanthrene, in particular, resulted in antagonized degradation by three out of four bacterial species, and further studies were narrowed to investigate the degradation of this mixture. Antagonistic effects persisted over time and were correlated with reduced bacterial growth. Antagonized degradation of PAH was not caused by preferential degradation of secondary PAHs, nor were mixture compounds or concentrations toxic to cells growing on sugars. Reverse transcription-PCR (RT-PCR) studies of the characterized catabolic pathway of phenanthrene showed that in one organism, antagonism of mixture degradation was associated with downregulated gene expression. Metabolite profiling revealed that antagonism in mixture degradation was associated with the shunting of substrate through alternative pathways not used during the degradation of single PAHs. The results of this study demonstrate metabolic differences between single and mixed PAH degradation with consequences for risk assessment and bioremediation of PAH-contaminated sites.

IMPORTANCE
Mycobacterium
species are promising organisms for environmental bioremediation because of their ubiquitous presence in soils and their ability to catabolize aromatic compounds. PAHs can be degraded effectively as single compounds, but mixed substrates often are subject to degradative inhibition, which may explain the persistence of these pollutants in soils. Single and mixed PAH degradation by diverse
Mycobacterium
species was compared, with associated bacterial growth, gene expression, and metabolite production. The results demonstrate that antagonism characterized degradation in a strain- and mixture-dependent manner. One strain that was versatile in its pathway use of single chemicals also efficiently degraded the mixture, whereas antagonism in other the strains was associated with altered metabolic profiles, indicating unusual pathway use. The impacts of this work on risk assessment and bioremediation modeling studies indicate the need to account for mixture-generated intermediates and to recognize mixture degradation as a property distinct from that of PAH substrate range.
Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea)
Authors: Delport Tiffany C. , Power Michelle L. , Harcourt Robert G. , Webster Koa N. , Tetu Sasha G. 
Published: April 2016

ABSTRACT

Gut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion (
Neophoca cinerea
), an endangered pinniped with localized distribution, were examined. A comparison of samples from individuals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla:
Firmicutes
,
Proteobacteria
,
Bacteroidetes
,
Actinobacteria
, and
Fusobacteria
. The phylum
Firmicutes
was dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), while
Proteobacteria
contributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial families
Clostridiaceae
and
Ruminococcaceae
were more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species.

IMPORTANCE
The Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study of the fecal microbiota of a large number of Australian sea lions from geographically diverse wild and captive populations. Colony location and captivity were found to influence the gut microbial community compositions of these animals. Our findings significantly extend the baseline knowledge of marine mammal gut microbiome composition and variability.
Constitutive Expression of a Nag-Like Dioxygenase Gene through an Internal Promoter in the 2-Chloronitrobenzene Catabolism Gene Cluster of Pseudomonas stutzeri ZWLR2-1
Authors: Gao Yi-Zhou , Liu Hong , Chao Hong-Jun , Zhou Ning-Yi 
Published: April 2016

ABSTRACT

The gene cluster encoding the 2-chloronitrobenzene (2CNB) catabolism pathway in
Pseudomonas stutzeri
ZWLR2-1 is a patchwork assembly of a Nag-like dioxygenase (dioxygenase belonging to the naphthalene dioxygenase NagAaAbAcAd family from
Ralstonia
sp. strain U2) gene cluster and a chlorocatechol catabolism cluster. However, the transcriptional regulator gene usually present in the Nag-like dioxygenase gene cluster is missing, leaving it unclear how this cluster is expressed. The pattern of expression of the 2CNB catabolism cluster was investigated here. The results demonstrate that the expression was constitutive and not induced by its substrate 2CNB or salicylate, the usual inducer of expression in the Nag-like dioxygenase family. Reverse transcription-PCR indicated the presence of at least one transcript containing all the structural genes for 2CNB degradation. Among the three promoters verified in the gene cluster, P1 served as the promoter for the entire catabolism operon, but the internal promoters P2 and P3 also enhanced the transcription of the genes downstream. The P3 promoter, which was not previously defined as a promoter sequence, was the strongest of these three promoters. It drove the expression of
cnbAcAd
encoding the dioxygenase that catalyzes the initial reaction in the 2CNB catabolism pathway. Bioinformatics and mutation analyses suggested that this P3 promoter evolved through the duplication of an 18-bp fragment and introduction of an extra 132-bp fragment.

IMPORTANCE
The release of many synthetic compounds into the environment places selective pressure on bacteria to develop their ability to utilize these chemicals to grow. One of the problems that a bacterium must surmount is to evolve a regulatory device for expression of the corresponding catabolism genes. Considering that 2CNB is a xenobiotic that has existed only since the onset of synthetic chemistry, it may be a good example for studying the molecular mechanisms underlying rapid evolution in regulatory networks for the catabolism of synthetic compounds. The 2CNB utilizer
Pseudomonas stutzeri
ZWLR2-1 in this study has adapted itself to the new pollutant by evolving the always-inducible Nag-like dioxygenase into a constitutively expressed enzyme, and its expression has escaped the influence of salicylate. This may facilitate an understanding of how bacteria can rapidly adapt to the new synthetic compounds by evolving its expression system for key enzymes involved in the degradation of a xenobiotic.
Calcineurin and Calcium Channel CchA Coordinate the Salt Stress Response by Regulating Cytoplasmic Ca
2+
Homeostasis in Aspergillus nidulans
Authors: Wang Sha , Liu Xiao , Qian Hui , Zhang Shizhu , Lu Ling 
Published: April 2016

ABSTRACT

The eukaryotic calcium/calmodulin-dependent protein phosphatase calcineurin is crucial for the environmental adaption of fungi. However, the mechanism of coordinate regulation of the response to salt stress by calcineurin and the high-affinity calcium channel CchA in fungi is not well understood. Here we show that the deletion of
cchA
suppresses the hyphal growth defects caused by the loss of calcineurin under salt stress in
Aspergillus nidulans
. Additionally, the hypersensitivity of the Δ
cnaA
strain to extracellular calcium and cell-wall-damaging agents can be suppressed by
cchA
deletion. Using the calcium-sensitive photoprotein aequorin to monitor the cytoplasmic Ca
2+
concentration ([Ca
2+
]
c
) in living cells, we found that calcineurin negatively regulates CchA on calcium uptake in response to external calcium in normally cultured cells. However, in salt-stress-pretreated cells, loss of either
cnaA
or
cchA
significantly decreased the [Ca
2+
]
c
, but a deficiency in both
cnaA
and
cchA
switches the [Ca
2+
]
c
to the reference strain level, indicating that calcineurin and CchA synergistically coordinate calcium influx under salt stress. Moreover, real-time PCR results showed that the dysfunction of
cchA
in the Δ
cnaA
strain dramatically restored the expression of
enaA
(a major determinant for sodium detoxification), which was abolished in the Δ
cnaA
strain under salt stress. These results suggest that double deficiencies of
cnaA
and
cchA
could bypass the requirement of calcineurin to induce
enaA
expression under salt stress. Finally, YvcA, a member of the transient receptor potential channel (TRPC) protein family of vacuolar Ca
2+
channels, was proven to compensate for calcineurin-CchA in fungal salt stress adaption.

IMPORTANCE
The feedback inhibition relationship between calcineurin and the calcium channel Cch1/Mid1 has been well recognized from yeast. Interestingly, our previous study (S. Wang et al., PLoS One
7:
e46564, 2012,
http://dx.doi.org/10.1371/journal.pone.0046564
) showed that the deletion of
cchA
could suppress the hyphal growth defects caused by the loss of calcineurin under salt stress in
Aspergillus nidulans
. In this study, our findings suggest that fungi are able to develop a unique mechanism for adapting to environmental salt stress. Compared to cells cultured normally, the NaCl-pretreated cells had a remarkable increase in transient [Ca
2+
]
c
. Furthermore, we show that calcineurin and CchA are required to modulate cellular calcium levels and synergistically coordinate calcium influx under salt stress. Finally, YvcA, a member of of the TRPC family of vacuolar Ca
2+
channels, was proven to compensate for calcineurin-CchA in fungal salt stress adaption. The findings in this study provide insights into the complex regulatory links between calcineurin and CchA to maintain cytoplasmic Ca
2+
homeostasis in response to different environments.
An Efficient Method To Generate Gene Deletion Mutants of the Rapamycin-Producing Bacterium Streptomyces iranensis HM 35
Authors: Netzker Tina , Schroeckh Volker , Gregory Matthew A. , Flak Michal , Krespach Mario K. C. , Leadlay Peter F. , Brakhage Axel A. 
Published: April 2016

ABSTRACTStreptomyces iranensisHM 35 is an alternative rapamycin producer toStreptomyces rapamycinicus. Targeted genetic modification of rapamycin-producing actinomycetes is a powerful tool for the directed production of rapamycin derivatives, and it has also revealed some key features of the molecular biology of rapamycin formation inS. rapamycinicus.The approach depends upon efficient conjugational plasmid transfer fromEscherichia colitoStreptomyces, and the failure of this step has frustrated its application toStreptomyces iranensisHM 35. Here, by systematically optimizing the process of conjugational plasmid transfer, including screening of various media, and by defining optimal temperatures and concentrations of antibiotics and Ca2+ions in the conjugation media, we have achieved exconjugant formation for each of a series of gene deletions inS. iranensisHM 35. Among them wererapK, which generates the starter unit for rapamycin biosynthesis, andhutF, encoding a histidine catabolizing enzyme. The protocol that we have developed may allow efficient generation of targeted gene knockout mutants ofStreptomycesspecies that are genetically difficult to manipulate.IMPORTANCEThe developed protocol of conjugational plasmid transfer fromEscherichia colitoStreptomyces iranensismay allow efficient generation of targeted gene knockout mutants of other genetically difficult to manipulate, but valuable,Streptomycesspecies.