scholarly journals Identification of Hypoxia-Inducible Target Genes of Aspergillus fumigatus by Transcriptome Analysis Reveals Cellular Respiration as an Important Contributor to Hypoxic Survival

2014 ◽  
Vol 13 (9) ◽  
pp. 1241-1253 ◽  
Author(s):  
Kristin Kroll ◽  
Vera Pähtz ◽  
Falk Hillmann ◽  
Yakir Vaknin ◽  
Wolfgang Schmidt-Heck ◽  
...  
Keyword(s):  
Aspergillus Fumigatus ◽  
Nitrogen Metabolism ◽  
Transcriptome Analysis ◽  
Metal Ion ◽  
Target Genes ◽  
Cellular Respiration ◽  
Cell Wall Polysaccharide ◽  
Content Type ◽  
Nitrite Reductase Gene ◽  
Reductase Gene

ABSTRACT Aspergillus fumigatus is an opportunistic, airborne pathogen that causes invasive aspergillosis in immunocompromised patients. During the infection process, A. fumigatus is challenged by hypoxic microenvironments occurring in inflammatory, necrotic tissue. To gain further insights into the adaptation mechanism, A. fumigatus was cultivated in an oxygen-controlled chemostat under hypoxic and normoxic conditions. Transcriptome analysis revealed a significant increase in transcripts associated with cell wall polysaccharide metabolism, amino acid and metal ion transport, nitrogen metabolism, and glycolysis. A concomitant reduction in transcript levels was observed with cellular trafficking and G-protein-coupled signaling. To learn more about the functional roles of hypoxia-induced transcripts, we deleted A. fumigatus genes putatively involved in reactive nitrogen species detoxification ( fhpA ), NAD + regeneration ( frdA and osmA ), nitrogen metabolism ( niaD and niiA ), and respiration ( rcfB ). We show that the nitric oxygen (NO)-detoxifying flavohemoprotein gene fhpA is strongly induced by hypoxia independent of the nitrogen source but is dispensable for hypoxic survival. By deleting the nitrate reductase gene niaD , the nitrite reductase gene niiA , and the two fumarate reductase genes frdA and osmA , we found that alternative electron acceptors, such as nitrate and fumarate, do not have a significant impact on growth of A. fumigatus during hypoxia, but functional mitochondrial respiratory chain complexes are essential under these conditions. Inhibition studies indicated that primarily complexes III and IV play a crucial role in the hypoxic growth of A. fumigatus .

scholarly journals Genomic Characterization of Urethritis-Associated Neisseria meningitidis Shows that a Wide Range of N. meningitidis Strains Can Cause Urethritis

2017 ◽  
Vol 55 (12) ◽  
pp. 3374-3383 ◽  
Author(s):  
Kevin C. Ma ◽  
Magnus Unemo ◽  
Samo Jeverica ◽  
Robert D. Kirkcaldy ◽  
Hideyuki Takahashi ◽  
...  
Keyword(s):  
Neisseria Meningitidis ◽  
Etiologic Agent ◽  
Factor H ◽  
Urogenital Tract ◽  
Genetic Characteristics ◽  
Content Type ◽  
Nitrite Reductase Gene ◽  
Reductase Gene ◽  
Wide Range ◽  
Genomic Characterization

ABSTRACTNeisseria meningitidis, typically a resident of the oro- or nasopharynx and the causative agent of meningococcal meningitis and meningococcemia, is capable of invading and colonizing the urogenital tract. This can result in urethritis, akin to the syndrome caused by its sister species,N. gonorrhoeae, the etiologic agent of gonorrhea. Recently, meningococcal strains associated with outbreaks of urethritis were reported to share genetic characteristics with the gonococcus, raising the question of the extent to which these strains contain features that promote adaptation to the genitourinary niche, making them gonococcus-like and distinguishing them from otherN. meningitidisstrains. Here, we analyzed the genomes of 39 diverseN. meningitidisisolates associated with urethritis, collected independently over a decade and across three continents. In particular, we characterized the diversity of the nitrite reductase gene (aniA), the factor H-binding protein gene (fHbp), and the capsule biosynthetic locus, all of which are loci previously suggested to be associated with urogenital colonization. We observed notable diversity, including frameshift variants, inaniAandfHbpand the presence of intact, disrupted, and absent capsule biosynthetic genes, indicating that urogenital colonization and urethritis caused byN. meningitidisare possible across a range of meningococcal genotypes. Previously identified allelic patterns in urethritis-associatedN. meningitidisstrains may reflect genetic diversity in the underlying meningococcal population rather than novel adaptation to the urogenital tract.

scholarly journals Potentially Mobile Denitrification Genes Identified inAzospirillumsp. Strain TSH58

2018 ◽  
Vol 85 (2) ◽  
Author(s):  
Jeonghwan Jang ◽  
Yoriko Sakai ◽  
Keishi Senoo ◽  
Satoshi Ishii
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Nitrite Reductase ◽  
Rrna Gene ◽  
Content Type ◽  
Denitrification Gene ◽  
Nitrite Reductase Gene ◽  
Reductase Gene ◽  
Denitrification Genes ◽  
The 16S Rrna Gene

ABSTRACTDenitrification ability is sporadically distributed among diverse bacteria, archaea, and fungi. In addition, disagreement has been found between denitrification gene phylogenies and the 16S rRNA gene phylogeny. These facts have suggested potential occurrences of horizontal gene transfer (HGT) for the denitrification genes. However, evidence of HGT has not been clearly presented thus far. In this study, we identified the sequences and the localization of the nitrite reductase genes in the genomes of 41 denitrifyingAzospirillumsp. strains and searched for mobile genetic elements that contain denitrification genes. AllAzospirillumsp. strains examined in this study possessed multiple replicons (4 to 11 replicons), with their sizes ranging from 7 to 1,031 kbp. Among those, the nitrite reductase genenirKwas located on large replicons (549 to 941 kbp). Genome sequencing showed thatAzospirillumstrains that had similarnirKsequences also shared similarnir-norgene arrangements, especially between the TSH58, Sp7T, and Sp245 strains. In addition to the high similarity betweennir-norgene clusters among the threeAzospirillumstrains, a composite transposon structure was identified in the genome of strain TSH58, which contains thenir-norgene cluster and the novel IS6family insertion sequences (ISAz581and ISAz582). ThenirKgene within the composite transposon system was actively transcribed under denitrification-inducing conditions. Although not experimentally verified in this study, the composite transposon system containing thenir-norgene cluster could be transferred to other cells if it is moved to a prophage region and the phage becomes activated and released outside the cells. Taken together, strain TSH58 most likely acquired its denitrification ability by HGT from closely relatedAzospirillumsp. denitrifiers.IMPORTANCEThe evolutionary history of denitrification is complex. While the occurrence of horizontal gene transfer has been suggested for denitrification genes, most studies report circumstantial evidences, such as disagreement between denitrification gene phylogenies and the 16S rRNA gene phylogeny. Based on the comparative genome analyses ofAzospirillumsp. denitrifiers, we identified denitrification genes, includingnirKandnorCBQD, located on a mobile genetic element in the genome ofAzospirillumsp. strain TSH58. ThenirKwas actively transcribed under denitrification-inducing conditions. Since this gene was the sole nitrite reductase gene in strain TSH58, this strain most likely benefitted by acquiring denitrification genes via horizontal gene transfer. This finding will significantly advance our scientific knowledge regarding the ecology and evolution of denitrification.

scholarly journals mSphere of Influence: the Importance of Metabolism for Pathogen Adaptation to Host-Imposed Stresses

mSphere ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Jorge Amich
Keyword(s):  
Gene Expression ◽  
Invasive Aspergillosis ◽  
Aspergillus Fumigatus ◽  
Nitrogen Metabolism ◽  
Content Type

ABSTRACT Jorge Amich studies several aspects of sulfur and nitrogen metabolism in Aspergillus fumigatus, with the ultimate aim of identifying targets for the development of novel antifungals. In this mSphere of Influence article, he reflects on how “Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis” (A. McDonagh, N. D. Fedorova, J. Crabtree, Y. Yu, S. Kim, et al., PLoS Pathog 4:e1000154, 2008, https://doi.org/10.1371/journal.ppat.1000154) impacted his thinking about in vivo metabolism and how to investigate it.

scholarly journals Divergent Targets of Aspergillus fumigatus AcuK and AcuM Transcription Factors during GrowthIn Vitroversus Invasive Disease

2014 ◽  
Vol 83 (3) ◽  
pp. 923-933 ◽  
Author(s):  
Monsicha Pongpom ◽  
Hong Liu ◽  
Wenjie Xu ◽  
Brendan D. Snarr ◽  
Donald C. Sheppard ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Aspergillus Fumigatus ◽  
Target Genes ◽  
Iron Acquisition ◽  
Altered Expression ◽  
Content Type ◽  
Regulatory Pathways ◽  
Transcriptional Profiles

InAspergillus nidulans, the AcuK and AcuM transcription factors form a complex that regulates gluconeogenesis. InAspergillus fumigatus, AcuM governs gluconeogenesis and iron acquisitionin vitroand virulence in immunosuppressed mice. However, the function of AcuK was previously unknown. Throughin vitrostudies, we found thatA. fumigatusΔacuKsingle and ΔacuKΔacuMdouble mutants had impaired gluconeogenesis and iron acquisition, similar to the ΔacuMmutant. Also, the ΔacuK, ΔacuM, and ΔacuKΔacuMmutants had similar virulence defects in mice. However, the ΔacuKmutant had a milder defect in extracellular siderophore activity and induction of epithelial cell damagein vitrothan did the ΔacuMmutant. Moreover, overexpression ofacuMin the ΔacuKmutant altered expression of 3 genes and partially restored growth under iron-limited conditions, suggesting that AcuM can govern some genes independently of AcuK. Although the ΔacuKand ΔacuMmutants had very similar transcriptional profilesin vitro, their transcriptional profiles during murine pulmonary infection differed both from theirin vitroprofiles and from each other. While AcuK and AcuM governed the expression of only a few iron-responsive genesin vivo, they influenced the expression of other virulence-related genes, such ashexAanddvrA. Therefore, inA. fumigatus, while AcuK and AcuM likely function as part of the same complex, they can also function independently of each other. Furthermore, AcuK and AcuM have different target genesin vivothanin vitro, suggesting thatin vivoinfection stimulates unique transcriptional regulatory pathways inA. fumigatus.

scholarly journals AtrR Is an Essential Determinant of Azole Resistance in Aspergillus fumigatus

mBio ◽  
2019 ◽  
Vol 10 (2) ◽  
Author(s):  
Sanjoy Paul ◽  
Mark Stamnes ◽  
Grace Heredge Thomas ◽  
Hong Liu ◽  
Daisuke Hagiwara ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Aspergillus Fumigatus ◽  
High Throughput ◽  
Transcriptional Control ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Azole Resistance ◽  
Promoter Regions ◽  
Mobility Shift ◽  
Content Type

ABSTRACT Aspergillosis associated with azole-resistant Aspergillus fumigatus has a mortality rate that can approach 90% in certain patient populations. The best-understood avenue for azole resistance involves changes in the cyp51A gene that encodes the target of azole drugs, lanosterol α-14 demethylase. The most common azole resistance allele currently described is a linked change corresponding to a change in the coding sequence of cyp51A and a duplication of a 34-bp region in the promoter leading to a tandem repeat (TR). Our previous studies identified a positively acting transcription factor called AtrR that binds to the promoter of cyp51A as well as that of an important membrane transporter protein gene called abcG1. In this work, we characterize two different mutant alleles of atrR, either an overproducing or an epitope-tagged form, causing constitutive activation of this factor. Using an epitope-tagged allele of atrR for chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq), the genomic binding sites for AtrR were determined. Close to 900 genes were found to have an AtrR response element (ATRE) in their promoter regions. Transcriptome evaluation by RNA sequencing (RNA-seq) indicated that both alleles led to elevated transcription of a subset of target genes. An electrophoretic mobility shift assay and DNase I protection mapping localized the ATREs in both the abcG1 and cyp51A promoters. The ATRE in cyp51A was located within the 34-bp repeat element. Virulence in a murine model was compromised when AtrR was either deleted or overproduced, indicating that the proper dosage of this factor is key for pathogenesis. IMPORTANCE Aspergillus fumigatus is the major filamentous fungal pathogen in humans. Infections associated with A. fumigatus are often treated with azole drugs, but resistance to these antifungal agents is increasing. Mortality from aspergillosis associated with azole-resistant fungi is extremely high. Previous work has identified transcriptional control of the azole drug target-encoding gene cyp51A as an important contributor to resistance in A. fumigatus. Here, we demonstrate that the transcription factor AtrR binds to a region in the cyp51A promoter that is associated with alleles of this gene conferring clinically important azole resistance. Using high-throughput genomic technologies, we also uncover a large suite of target genes controlled by AtrR. These data indicate that AtrR coordinately regulates many different processes involved in drug resistance, metabolism, and virulence. Our new understanding of AtrR function provides important new insight into the pathogenesis of A. fumigatus.

scholarly journals Fungal Extracellular Vesicles Are Involved in Intraspecies Intracellular Communication

mBio ◽  
2022 ◽  
Author(s):  
Tamires A. Bitencourt ◽  
Otavio Hatanaka ◽  
Andre M. Pessoni ◽  
Mateus S. Freitas ◽  
Gabriel Trentin ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Aspergillus Fumigatus ◽  
Extracellular Vesicles ◽  
Target Genes ◽  
Paracoccidioides Brasiliensis ◽  
Content Type ◽  
Intracellular Communication

Here, we report a study about extracellular vesicles (EVs) as communication mediators in fungi. Our results demonstrated the role of EVs from Candida albicans , Aspergillus fumigatus , and Paracoccidioides brasiliensis regulating the expression of target genes and phenotype features.

New dosimetric approach for multidimensional dose evaluation in gamma knife radiosurgery

2000 ◽  
Vol 93 (supplement_3) ◽  
pp. 239-242 ◽  
Author(s):  
R. Foroni ◽  
G. Gambraini ◽  
U. Danesi ◽  
M. Mauri ◽  
E. Pompilio ◽  
...  
Keyword(s):  
Gamma Knife ◽  
Metal Ion ◽  
Light Transmission ◽  
Xylenol Orange ◽  
Ferrous Sulphate ◽  
Gamma Knife Radiosurgery ◽  
Absorbed Dose ◽  
Content Type ◽  
3D Representation ◽  
Fine Print

✓ During the past two decades, the progress in computerized treatment planning systems has led to more accurate imaging and therapy by using the gamma knife, especially with the smallest collimators (4 mm). However, the ionization chambers that have been used to calibrate the gamma knife are not useful with the smallest collimators because the chambers are too big compared with the irradiated volume. Therefore, it is important to develop more suitable dosimeters. This study proposes a new dosimeter method. The FriXyGel method proposed here is based on a phantom dosimeter, an acquisition chain, and dedicated software. This dosimeter uses an agarose gel into which a ferrous sulphate solution (Fricke solution) and a metal ion indicator (xylenol orange) are incorporated. The absorbed dose is detected through measurements of visible light transmission, imaged by means of a charge-coupled device camera provided with a suitable optical filter. Gel layers are imaged before and after irradiation, and the differences in light absorption are related to the absorbed dose. By choosing convenient thickness of gel layers and by building up a phantom with different gel slices, it is possible to obtain a three-dimensional (3D) representation of the absorbed dose. The final 3D representation is reached after several mathematical processes have been applied to the images. The first step identifies and reduces all factors that could alter the original data, such as nonuniformity in illumination. Then, after calibration procedures, it is possible to obtain absorbed dose values and to discover their 3D representation. This goal has been reached by developing appropriate software that performs all the calculations necessary for spatial representation routines and prompt comparison with theoretical calculations.

Molecular Cloning and Characterization of Nitrite Reductase Gene from Sugarbeet

2011 ◽  
Vol 37 (8) ◽  
pp. 1406-1414
Author(s):  
Xiao-Yan SHI ◽  
Yan-Da ZENG ◽  
Shi-Long LI ◽  
Yu-Bo WANG ◽  
Feng-Ming MA ◽  
...  
Keyword(s):  
Molecular Cloning ◽  
Nitrite Reductase ◽  
Nitrite Reductase Gene ◽  
Reductase Gene

scholarly journals Transcriptome Analysis Reveals a Promotion of Carotenoid Production by Copper Ions in Recombinant Saccharomyces cerevisiae

2021 ◽  
Vol 9 (2) ◽  
pp. 233
Author(s):  
Buli Su ◽  
Anzhang Li ◽  
Ming-Rong Deng ◽  
Honghui Zhu
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcriptome Analysis ◽  
Gene Expression Analysis ◽  
Target Genes ◽  
Copper Ions ◽  
Carotenoid Production ◽  
Carotenoid Accumulation ◽  
Nutritional Components ◽  
Differential Gene ◽  
First Time

We previously constructed a Saccharomyces cerevisiae carotenoid producer BL03-D-4 which produced much more carotenoid in YPM (modified YPD) media than YPD media. In this study, the impacts of nutritional components on carotenoid accumulation of BL03-D-4 were investigated. When using YPM media, the carotenoid yield was increased 10-fold compared to using the YPD media. To elucidate the hidden mechanism, a transcriptome analysis was performed and showed that 464 genes changed significantly in YPM media. Furthermore, inspired by the differential gene expression analysis which indicated that ADY2, HES1, and CUP1 showed the most remarkable changes, we found that the improvement of carotenoid accumulation in YPM media was mainly due to the copper ions, since supplementation of 0.08 mM CuSO4 in YPD media could increase carotenoid yield 9.2-fold. Reverse engineering of target genes was performed and carotenoid yield could be increased 6.4-fold in YPD media through overexpression of ACE1. The present study revealed for the first time the prominent promotion of carotenoid yield by copper ions in engineered S. cerevisiae and provided a new target ACE1 for genetic engineering of S. cerevisiae for the bioproduction of carotenoids.

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