scholarly journals Transcriptomic Analysis Reveals That Rho GTPases Regulate Trap Development and Lifestyle Transition of the Nematode-Trapping Fungus Arthrobotrys oligospora

2022 ◽  
Author(s):  
Le Yang ◽  
Xuemei Li ◽  
Na Bai ◽  
Xuewei Yang ◽  
Ke-Qin Zhang ◽  
...  
Keyword(s):  
Rho Gtpases ◽  
Aquatic Ecosystems ◽  
Transcriptomic Analysis ◽  
Arthrobotrys Oligospora ◽  
Model Species ◽  
Content Type

Nematode-trapping (NT) fungi are widely distributed in terrestrial and aquatic ecosystems. Their broad adaptability and flexible lifestyles make them ideal agents for controlling pathogenic nematodes. Arthrobotrys oligospora is a model species employed for understanding the interaction between fungi and nematodes.

scholarly journals Draft Genome Sequence of the Strawberry Anthracnose Pathogen Colletotrichum fructicola

2020 ◽  
Vol 9 (12) ◽  
Author(s):  
Andrew D. Armitage ◽  
Charlotte F. Nellist ◽  
Helen J. Bates ◽  
Liqing Zhang ◽  
Xiaohua Zou ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Causal Agent ◽  
Transcriptomic Analysis ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Colletotrichum Fructicola ◽  
Strawberry Anthracnose ◽  
Ornamental Crops

Colletotrichum fructicola is a causal agent of strawberry anthracnose and a major economic pathogen of horticultural and ornamental crops worldwide. Here, we present an annotated draft genome sequence for a C. fructicola isolate previously used for transcriptomic analysis. The assembly totals 58.0 Mb in 477 contigs with 18,143 predicted genes.

scholarly journals Characterization of Planctomyces limnophilus and Development of Genetic Tools for Its Manipulation Establish It as a Model Species for the Phylum Planctomycetes

2011 ◽  
Vol 77 (16) ◽  
pp. 5826-5829 ◽  
Author(s):  
Christian Jogler ◽  
Frank Oliver Glöckner ◽  
Roberto Kolter
Keyword(s):  
Eukaryotic Cells ◽  
Cellular Structures ◽  
Model Species ◽  
Content Type ◽  
Genetic Tools ◽  
Carbon And Nitrogen ◽  
Nitrogen Cycles ◽  
Global Carbon ◽  
The Phylum Planctomycetes

ABSTRACTPlanctomycetesrepresent a remarkable clade in the domainBacteriabecause they play crucial roles in global carbon and nitrogen cycles and display cellular structures that closely parallel those of eukaryotic cells. Studies onPlanctomyceteshave been hampered by the lack of genetic tools, which we developed forPlanctomyces limnophilus.

scholarly journals Occurrence of Virulence Genes Associated with Diarrheagenic Pathotypes in Escherichia coli Isolates from Surface Water

2012 ◽  
Vol 79 (1) ◽  
pp. 328-335 ◽  
Author(s):  
Jatinder P. S. Sidhu ◽  
Warish Ahmed ◽  
Leonie Hodgers ◽  
Simon Toze
Keyword(s):  
Escherichia Coli ◽  
Health Risks ◽  
High Frequency ◽  
Aquatic Ecosystems ◽  
Virulence Genes ◽  
Storm Water ◽  
Storm Events ◽  
Widespread Occurrence ◽  
Content Type ◽  
E Coli

ABSTRACTEscherichia coliisolates (n= 300) collected from six sites in subtropical Brisbane, Australia, prior to and after storm events were tested for the presence of 11 virulence genes (VGs) specific to diarrheagenic pathotypes. The presence ofeaeA,stx1,stx2, andehxAgenes specific for the enterohemorrhagicE. coli(EHEC) pathotype was detected in 56%, 6%, 10%, and 13% of isolates, respectively. The VGsastA(69%) andaggR(29%), carried by enteroaggregative (EAEC) pathotypes, were frequently detected inE. coliisolates. The enteropathogenicE. coli(EPEC) genebfpwas detected in 24% of isolates. In addition, enteroinvasiveE. coli(EIEC) VGipaHwas also detected in 14% of isolates. During dry periods, isolates belonging to the EAEC pathotype were most commonly detected (23%), followed by EHEC (11%) and EPEC (11%). Conversely, a more uniform prevalence of pathotypes, EPEC (14%), EAEC (12%), EIEC (10%), EHEC (7%), and ETEC (7%), was observed after the storm events. The results of this study highlight the widespread occurrence of potentially diarrheagenic pathotypes in the urban aquatic ecosystems. While the presence of VGs inE. coliisolates alone is insufficient to determine pathogenicity, the presence of diarrheagenicE. colipathotypes in high frequency after the storm events could lead to increased health risks if untreated storm water were to be used for nonpotable purposes and recreational activities.

scholarly journals Transcriptomic analysis of cyanobacterial alkane overproduction reveals stress-related genes and inhibitors of lipid droplet formation

2020 ◽  
Vol 6 (10) ◽  
Author(s):  
Daisy B. Arias ◽  
Kevin A. Gomez Pinto ◽  
Kerry K. Cooper ◽  
Michael L. Summers
Keyword(s):  
Type Species ◽  
Transcriptomic Analysis ◽  
Lag Phase ◽  
Content Type ◽  
Link Type ◽  
Production Platform ◽  
Genes Encoding ◽  
Transcriptional Changes ◽  
Stress Related Genes ◽  
Upregulated Genes

The cyanobacterium Nostoc punctiforme can form lipid droplets (LDs), internal inclusions containing triacylglycerols, carotenoids and alkanes. LDs are enriched for a 17 carbon-long alkane in N. punctiforme , and it has been shown that the overexpression of the aar and ado genes results in increased LD and alkane production. To identify transcriptional adaptations associated with increased alkane production, we performed comparative transcriptomic analysis of an alkane overproduction strain. RNA-seq data identified a large number of highly upregulated genes in the overproduction strain, including genes potentially involved in rRNA processing, mycosporine-glycine production and synthesis of non-ribosomal peptides, including nostopeptolide A. Other genes encoding helical carotenoid proteins, stress-induced proteins and those for microviridin synthesis were also upregulated. Construction of N. punctiforme strains with several upregulated genes or operons on multi-copy plasmids resulted in reduced alkane accumulation, indicating possible negative regulators of alkane production. A strain containing four genes for microviridin biosynthesis completely lost the ability to synthesize LDs. This strain exhibited wild-type growth and lag phase recovery under standard conditions, and slightly faster growth under high light. The transcriptional changes associated with increased alkane production identified in this work will provide the basis for future experiments designed to use cyanobacteria as a production platform for biofuel or high-value hydrophobic products.

scholarly journals Draft Genome Sequences of Nine Cultivable Heterotrophic Proteobacteria Isolated from Phycosphere Microbiota of Toxic Alexandrium catenella LZT09

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Xiao-Ling Zhang ◽  
Xi Yang ◽  
Shu-Jun Wang ◽  
Zhi-Wei Jiang ◽  
Zhang-Xian Xie ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Aquatic Ecosystems ◽  
Draft Genome ◽  
Toxic Dinoflagellate ◽  
Genome Sequences ◽  
Alexandrium Catenella ◽  
Genomic Features ◽  
Content Type ◽  
Microscopic Interactions

ABSTRACT Microscopic interactions between phycosphere microbiota and host algae play crucial roles in aquatic ecosystems. Despite their significance, there is a scarcity of available genome sequences derived from the phycosphere microbiome. Here, we report the draft genome sequences of nine heterotrophic proteobacterial strains isolated from the toxic dinoflagellate Alexandrium catenella LZT09 during execution of our Phycosphere Microbiome Project. Further exploration of the genomic features of the alga-associated bacterial community will profoundly help in deeply deciphering the processes and mechanisms governing the host-microbe interactome within algal holobionts in the ocean.

scholarly journals Upregulation of the Host SLC11A1 Gene by Clostridium difficile Toxin B Facilitates Glucosylation of Rho GTPases and Enhances Toxin Lethality

2013 ◽  
Vol 81 (8) ◽  
pp. 2724-2732 ◽  
Author(s):  
Yanan Feng ◽  
Stanley N. Cohen
Keyword(s):  
Clostridium Difficile ◽  
Rho Gtpases ◽  
Rna Binding ◽  
Divalent Cations ◽  
Bacterial Toxin ◽  
Content Type ◽  
Small Rho Gtpases ◽  
Protein Toxins ◽  
Mechanistic Basis ◽  
Clostridium Difficile Toxin B

ABSTRACTPseudomembranous enterocolitis associated withClostridium difficileinfection is an important cause of morbidity and mortality in patients being treated with antibiotics. Two closely related large protein toxins produced byC. difficile, TcdA and TcdB, which act identically but at different efficiencies to glucosylate low-molecular-weight Rho GTPases, underlie the microbe's pathogenicity. Using antisense RNA encoded by a library of human expressed sequence tags (ESTs), we randomly inactivated host chromosomal genes in HeLa cells and isolated clones that survived exposure to ordinarily lethal doses of TcdB. This phenotypic screening and subsequent analysis identified solute carrier family 11 member 1 (SLC11A1; formerly NRAMP1), a divalent cation transporter crucial to host defense against certain microbes, as an enhancer of TcdB lethality. Whereas SLC11A1 normally is poorly expressed in human cells of nonmyeloid lineage, TcdB increased SLC11A1 mRNA abundance in such cells through the actions of the RNA-binding protein HuR. We show that short hairpin RNA (shRNA) directed against SLC11A1 reduced TcdB glucosylation of small Rho GTPases and, consequently, toxin lethality. Consistent with the previously known role of SLC11A1 in cation transport, these effects were enhanced by elevation of Mn2+in media; conversely, they were decreased by treatment with a chelator of divalent cations. Our findings reveal an unsuspected role for SLC11A1 in determiningC. difficilepathogenicity, demonstrate the novel ability of a bacterial toxin to increase its cytotoxicity, establish a mechanistic basis for these effects, and suggest a therapeutic approach to mitigate cell killing byC. difficiletoxins A and B.

scholarly journals Genome-Wide Evaluation of the Interplay between Caenorhabditis elegans and Yersinia pseudotuberculosis duringIn VivoBiofilm Formation

2014 ◽  
Vol 83 (1) ◽  
pp. 17-27 ◽  
Author(s):  
George W. P. Joshua ◽  
Steve Atkinson ◽  
Robert J. Goldstone ◽  
Hannah L. Patrick ◽  
Richard A. Stabler ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Biofilm Formation ◽  
Yersinia Pseudotuberculosis ◽  
Regulatory Gene ◽  
Transcriptomic Analysis ◽  
Wild Type ◽  
Content Type ◽  
C Elegans ◽  
Regulatory Cascade ◽  
Genome Wide

The formation of an incapacitating biofilm onCaenorhabditis elegansbyYersinia pseudotuberculosisrepresents a tractable model for investigating the genetic basis for host-pathogen interplay during the biofilm-mediated infection of a living surface. Previously we established a role for quorum sensing (QS) and the master motility regulator, FlhDC, in biofilm formation byY. pseudotuberculosisonC. elegans. To obtain further genome-wide insights, we used transcriptomic analysis to obtain comparative information onC. elegansin the presence and absence of biofilm and on wild-typeY. pseudotuberculosisandY. pseudotuberculosisQS mutants. Infection ofC. eleganswith the wild-typeY. pseudotuberculosisresulted in the differential regulation of numerous genes, including a distinct subset of nematode C-lectin (clec) and fatty acid desaturase (fat) genes. Evaluation of the correspondingC. elegansclec-49andfat-3deletion mutants showed delayed biofilm formation and abolished biofilm formation, respectively. Transcriptomic analysis ofY. pseudotuberculosisrevealed that genes located in both of the histidine utilization (hut) operons were upregulated in both QS andflhDCmutants. In addition, mutation of the regulatory genehutCresulted in the loss of biofilm, increased expression offlhDC, and enhanced swimming motility. These data are consistent with the existence of a regulatory cascade in which the Hut pathway links QS andflhDC. This work also indicates that biofilm formation byY. pseudotuberculosisonC. elegansis an interactive process during which the initial attachment/recognition ofYersiniato/byC. elegansis followed by bacterial growth and biofilm formation.

scholarly journals Clostridium difficile Toxin A Attenuates Wnt/β-Catenin Signaling in Intestinal Epithelial Cells

2014 ◽  
Vol 82 (7) ◽  
pp. 2680-2687 ◽  
Author(s):  
Bruno Bezerra Lima ◽  
Bárbara Faria Fonseca ◽  
Nathália da Graça Amado ◽  
Débora Moreira Lima ◽  
Ronaldo Albuquerque Ribeiro ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Epithelial Cells ◽  
Wnt Signaling ◽  
Rho Gtpases ◽  
Small Gtpases ◽  
Host Cells ◽  
Reporter Assay ◽  
Content Type ◽  
Protein Levels ◽  
Dependent Inhibition

ABSTRACTClostridium difficiletoxins A and B (TcdA and TcdB) are homologous glycosyltransferases that inhibit a group of small GTPases within host cells, but several mechanisms underlying their pathogenic activity remain unclear. In this study, we evaluated the effects of TcdA on the Wnt/β-catenin pathway, the major driving force behind the proliferation of epithelial cells in colonic crypts. IEC-6 and RKO cells stimulated with Wnt3a-conditioned medium were incubated with 10, 50, and 100 ng/ml of TcdA for 24 h, resulting in a dose-dependent inhibition of the Wnt signaling, as demonstrated by a T-cell factor (TCF) reporter assay. This was further confirmed by immunofluorescence staining for nuclear localization of β-catenin and Western blotting for β-catenin and c-Myc (encoded by a Wnt target gene). Moreover, our Western blot analysis showed a decrease in the β-catenin protein levels, which was reversed by z-VAD-fmk, a pan-caspase inhibitor. Nonetheless, TcdA was still able to inhibit the Wnt/β-catenin pathway even in the presence of z-VAD-fmk, lithium chloride (a GSK3β inhibitor), or constitutively active β-catenin, as determined by a TCF reporter assay. Furthermore, preincubation of RKO cells with TcdA for 12 h also attenuated Wnt3a-mediated activation of Wnt signaling, suggesting that inactivation of Rho GTPases plays a significant role in that inhibition. Taken together, these findings suggest that attenuation of the Wnt signaling by TcdA is important for TcdA antiproliferative effects.

scholarly journals Bacterial Community Response to Petroleum Hydrocarbon Amendments in Freshwater, Marine, and Hypersaline Water-Containing Microcosms

2013 ◽  
Vol 79 (19) ◽  
pp. 5927-5935 ◽  
Author(s):  
Diogo Jurelevicius ◽  
Vanessa Marques Alvarez ◽  
Joana Montezano Marques ◽  
Laryssa Ribeiro Fonseca de Sousa Lima ◽  
Felipe de Almeida Dias ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Aquatic Ecosystems ◽  
Petroleum Hydrocarbon ◽  
Rna Extraction ◽  
Community Response ◽  
Hydrocarbon Contamination ◽  
Clone Libraries ◽  
Content Type ◽  
Hypersaline Water ◽  
General Response

ABSTRACTHydrocarbon-degrading bacterial communities from freshwater, marine, and hypersaline Brazilian aquatic ecosystems (with water salinities corresponding to 0.2%, 4%, and 5%, respectively) were enriched with different hydrocarbons (heptadecane, naphthalene, or crude oil). Changes within the different microcosms of bacterial communities were analyzed using cultivation approaches and molecular methods (DNA and RNA extraction, followed by genetic fingerprinting and analyses of clone libraries based on the 16S rRNA-coding gene). A redundancy analysis (RDA) of the genetic fingerprint data and a principal component analysis (PCA) of the clone libraries revealed hydrocarbon-enriched bacterial communities specific for each ecosystem studied. However, within the same ecosystem, different bacterial communities were selected according to the petroleum hydrocarbon used. In general, the results demonstrated thatAcinetobacterandCloacibacteriumwere the dominant genera in freshwater microcosms; theOceanospirillalesorder and theMarinobacter,Pseudomonas, andCycloclasticusgenera predominated in marine microcosms; and theOceanospirillalesorder and theMarinobactergenus were selected in the different hydrocarbon-containing microcosms in hypersaline water. Determination of total petroleum hydrocarbons (TPHs) in all microcosms after 32 days of incubation showed a decrease in the hydrocarbon concentration compared to that for the controls. A total of 50 (41.3%) isolates from the different hydrocarbon-contaminated microcosms were associated with the dominant operational taxonomic units (OTUs) obtained from the clone libraries, and their growth in the hydrocarbon contaminating the microcosm from which they were isolated as the sole carbon source was observed. These data provide insight into the general response of bacterial communities from freshwater, marine, and hypersaline aquatic ecosystems to petroleum hydrocarbon contamination.

scholarly journals Planctomycetes in Lakes: Poor or Strong Competitors for Phosphorus?

2013 ◽  
Vol 80 (3) ◽  
pp. 819-828 ◽  
Author(s):  
Thomas Pollet ◽  
Jean-François Humbert ◽  
Rémy D. Tadonléké
Keyword(s):  
Community Structure ◽  
Aquatic Ecosystems ◽  
Nutrient Supply ◽  
Alternative View ◽  
Content Type ◽  
Nutrient Additions ◽  
P Limitation ◽  
Limiting Nutrient ◽  
Perialpine Lakes ◽  
Nutrient Amendments

ABSTRACTExperiments were conducted with water samples from two perialpine lakes with differing eutrophication status in order to examine the effects of inorganic-nutrient amendments (nitrogen as NO3−or NH4+and phosphorus as PO43−) on the dynamics, structure, and composition ofPlanctomycetesand to test the hypothesis that the community structure ofPlanctomycetesmembers and that of the other bacteria (withoutPlanctomycetes, here referred to as bacteria-wP, the most represented groups within the community) would be similarly impacted by nutrient additions. Initial samples were characterized by high total nitrogen-to-total phosphorus ratios (range, 39 to 55), suggesting P rather than N was the limiting nutrient for microbial communities. Consistent with this, P additions stimulated phytoplankton growth and affected the community structure of bacteria-wP but, surprisingly, not that ofPlanctomycetes. N additions did not significantly affect the community structures of bacteria-wP andPlanctomycetesor thePlanctomycetesphylotype composition. The estimated generation time ofPlanctomyceteswas 123 h. These findings could suggest that the generally well-accepted statement that bacteria (as a whole) are superior to phytoplankton in the ability to obtain phosphorus under P limitation might actually not hold forPlanctomycetes.Planctomycetesmight be poor competitors for P that do not respond quickly to the nutrient supply, which may help explain why their abundance is low in aquatic systems. The alternative view thatPlanctomycetescould be strong competitors for P (storing it) is also discussed. Our findings highlight the need for further studies examiningPlanctomycetes-phosphorus relationships in aquatic ecosystems.

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