scholarly journals Exposure to Solute Stress Affects Genome-Wide Expression but Not the Polycyclic Aromatic Hydrocarbon-Degrading Activity of Sphingomonas sp. Strain LH128 in Biofilms

2012 ◽  
Vol 78 (23) ◽  
pp. 8311-8320 ◽  
Author(s):  
Tekle Tafese Fida ◽  
Philip Breugelmans ◽  
Rob Lavigne ◽  
Edith Coronado ◽  
David R. Johnson ◽  
...  
Keyword(s):  
Chronic Stress ◽  
Nacl Stress ◽  
Stress Factors ◽  
Content Type ◽  
Transcriptomic Data ◽  
Acute And Chronic Stress ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Polycyclic Aromatic ◽  
Genome Wide Expression

ABSTRACTMembers of the genusSphingomonasare important catalysts for removal of polycyclic aromatic hydrocarbons (PAHs) in soil, but their activity can be affected by various stress factors. This study examines the physiological and genome-wide transcription response of the phenanthrene-degradingSphingomonassp. strain LH128 in biofilms to solute stress (invoked by 450 mM NaCl solution), either as an acute (4-h) or a chronic (3-day) exposure. The degree of membrane fatty acid saturation was increased as a response to chronic stress. Oxygen consumption in the biofilms and phenanthrene mineralization activities of biofilm cells were, however, not significantly affected after imposing either acute or chronic stress. This finding was in agreement with the transcriptomic data, since genes involved in PAH degradation were not differentially expressed in stressed conditions compared to nonstressed conditions. The transcriptomic data suggest that LH128 adapts to NaCl stress by (i) increasing the expression of genes coping with osmolytic and ionic stress such as biosynthesis of compatible solutes and regulation of ion homeostasis, (ii) increasing the expression of genes involved in general stress response, (iii) changing the expression of general and specific regulatory functions, and (iv) decreasing the expression of protein synthesis such as proteins involved in motility. Differences in gene expression between cells under acute and chronic stress suggest that LH128 goes through changes in genome-wide expression to fully adapt to NaCl stress, without significantly changing phenanthrene degrading activity.

scholarly journals Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis

2015 ◽  
Vol 81 (7) ◽  
pp. 2554-2561 ◽  
Author(s):  
Onur Ercan ◽  
Michiel Wels ◽  
Eddy J. Smid ◽  
Michiel Kleerebezem
Keyword(s):  
Lactococcus Lactis ◽  
Natural Transformation ◽  
Recovery Period ◽  
Transcriptional Responses ◽  
Content Type ◽  
Gene Set ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Elevated Expression ◽  
Branched Chain

ABSTRACTThis paper describes the transcriptional adaptations of nongrowing, retentostat cultures ofLactococcus lactisto starvation. Near-zero-growth cultures (μ = 0.0001 h−1) obtained by extended retentostat cultivation were exposed to starvation by termination of the medium supply for 24 h, followed by a recovery period of another 24 h by reinitiating the medium supply to the retentostat culture. During starvation, the viability of the culture was largely retained, and the expression of genes involved in transcription and translational machineries, cell division, and cell membrane energy metabolism was strongly repressed. Expression of these genes was largely recovered following the reinitiation of the medium supply. Starvation triggered the elevated expression of genes associated with synthesis of branched-chain amino acids, histidine, purine, and riboflavin. The expression of these biosynthesis genes was found to remain at an elevated level after reinitiation of the medium supply. In addition, starvation induced the complete gene set predicted to be involved in natural competence inL. lactisKF147, and the elevated expression of these genes was sustained during the subsequent recovery period, but our attempts to experimentally demonstrate natural transformation in these cells failed. Mining the starvation response gene set identified a conservedcis-acting element that resembles the lactococcal CodY motif in the upstream regions of genes associated with transcription and translational machineries, purine biosynthesis, and natural transformation inL. lactis, suggesting a role for CodY in the observed transcriptome adaptations to starvation in nongrowing cells.

Stress Factors in Affective Diseases

1984 ◽  
Vol 144 (2) ◽  
pp. 161-166 ◽  
Author(s):  
Elisabeth J. Bidzińska
Keyword(s):  
Chronic Stress ◽  
Affective Disorders ◽  
Stress Factors ◽  
Control Group ◽  
Family Conflicts ◽  
Similar Time ◽  
Bipolar Illness ◽  
Acute And Chronic Stress ◽  
Time Period ◽  
Healthy Control

An investigation carried out on 97 patients with affective disorders and on 100 healthy control subjects, revealed that acute and chronic stress factors occurred more in the group of patients with affective disorders than among healthy control over a similar time period. The frequency of stressful life situations was the same before the first affective episode in patients with unipolar and bipolar illness. The possible participation of such factors in triggering the first phase of illness is discussed. Similar factors appeared in both types of affective disorders. Significantly more frequent among patients than in the control group were: marital and family conflicts, health problems, emotional and ambitional failures, lack of success and work overload.

scholarly journals A conserved regulator controls asexual sporulation in the fungal pathogen Candida albicans

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Arturo Hernández-Cervantes ◽  
Sadri Znaidi ◽  
Lasse van Wijlick ◽  
Iryna Denega ◽  
Virginia Basso ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Chromatin Immunoprecipitation ◽  
Fungal Pathogen ◽  
Hyphal Growth ◽  
Second Phase ◽  
Asexual Sporulation ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Genome Wide Expression

AbstractTranscription factor Rme1 is conserved among ascomycetes and regulates meiosis and pseudohyphal growth in Saccharomyces cerevisiae. The genome of the meiosis-defective pathogen Candida albicans encodes an Rme1 homolog that is part of a transcriptional circuitry controlling hyphal growth. Here, we use chromatin immunoprecipitation and genome-wide expression analyses to study a possible role of Rme1 in C. albicans morphogenesis. We find that Rme1 binds upstream and activates the expression of genes that are upregulated during chlamydosporulation, an asexual process leading to formation of large, spherical, thick-walled cells during nutrient starvation. RME1 deletion abolishes chlamydosporulation in three Candida species, whereas its overexpression bypasses the requirement for chlamydosporulation cues and regulators. RME1 expression levels correlate with chlamydosporulation efficiency across clinical isolates. Interestingly, RME1 displays a biphasic pattern of expression, with a first phase independent of Rme1 function and dependent on chlamydospore-inducing cues, and a second phase dependent on Rme1 function and independent of chlamydospore-inducing cues. Our results indicate that Rme1 plays a central role in chlamydospore development in Candida species.

scholarly journals Antifungal Agent 4-AN Changes the Genome-Wide Expression Profile, Downregulates Virulence-Associated Genes and Induces Necrosis in Candida albicans Cells

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2928
Author(s):  
Aleksandra Martyna ◽  
Maciej Masłyk ◽  
Monika Janeczko ◽  
Elżbieta Kochanowicz ◽  
Bartłomiej Gielniewski ◽  
...  
Keyword(s):  
Candida Albicans ◽  
Expression Profile ◽  
Transcriptional Analysis ◽  
Pcr Analysis ◽  
Fungal Virulence ◽  
Sugar Transporters ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Genome Wide Expression

In the light of the increasing occurrence of antifungal resistance, there is an urgent need to search for new therapeutic strategies to overcome this phenomenon. One of the applied approaches is the synthesis of small-molecule compounds showing antifungal properties. Here we present a continuation of the research on the recently discovered anti-Candida albicans agent 4-AN. Using next generation sequencing and transcriptional analysis, we revealed that the treatment of C. albicans with 4-AN can change the expression profile of a large number of genes. The highest upregulation was observed in the case of genes involved in cell stress, while the highest downregulation was shown for genes coding sugar transporters. Real-time PCR analysis revealed 4-AN mediated reduction of the relative expression of genes engaged in fungal virulence (ALS1, ALS3, BCR1, CPH1, ECE1, EFG1, HWP1, HYR1 and SAP1). The determination of the fractional inhibitory concentration index (FICI) showed that the combination of 4-AN with amphotericin B is synergistic. Finally, flow cytometry analysis revealed that the compound induces mainly necrosis in C. albicans cells.

scholarly journals The Role of Fnr Paralogs in Controlling Anaerobic Metabolism in the Diazotroph Paenibacillus polymyxa WLY78

2020 ◽  
Vol 86 (10) ◽  
Author(s):  
Haowen Shi ◽  
Yongbin Li ◽  
Tianyi Hao ◽  
Xiaomeng Liu ◽  
Xiyun Zhao ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogenase Activity ◽  
Paenibacillus Polymyxa ◽  
Transcription Analysis ◽  
Content Type ◽  
Double Deletion ◽  
Expression Of Genes ◽  
Genome Wide ◽  
Promoter Deletion Analysis ◽  
Single Deletion

ABSTRACT Fnr is a transcriptional regulator that controls the expression of a variety of genes in response to oxygen limitation in bacteria. Genome sequencing revealed four genes (fnr1, fnr3, fnr5, and fnr7) coding for Fnr proteins in Paenibacillus polymyxa WLY78. Fnr1 and Fnr3 showed more similarity to each other than to Fnr5 and Fnr7. Also, Fnr1 and Fnr3 exhibited high similarity with Bacillus cereus Fnr and Bacillus subtilis Fnr in sequence and structures. Both the aerobically purified His-tagged Fnr1 and His-tagged Fnr3 in Escherichia coli could bind to the specific DNA promoter. Deletion analysis showed that the four fnr genes, especially fnr1 and fnr3, have significant impacts on growth and nitrogenase activity. Single deletion of fnr1 or fnr3 led to a 50% reduction in nitrogenase activity, and double deletion of fnr1 and fnr3 resulted to a 90% reduction in activity. Genome-wide transcription analysis showed that Fnr1 and Fnr3 indirectly activated expression of nif (nitrogen fixation) genes and Fe transport genes under anaerobic conditions. Fnr1 and Fnr3 inhibited expression of the genes involved in the aerobic respiratory chain and activated expression of genes responsible for anaerobic electron acceptor genes. IMPORTANCE The members of the nitrogen-fixing Paenibacillus spp. have great potential to be used as a bacterial fertilizer in agriculture. However, the functions of the fnr gene(s) in nitrogen fixation and other metabolisms in Paenibacillus spp. are not known. Here, we found that in P. polymyxa WLY78, Fnr1 and Fnr3 were responsible for regulation of numerous genes in response to changes in oxygen levels, but Fnr5 and Fnr7 exhibited little effect. Fnr1 and Fnr3 indirectly or directly regulated many types of important metabolism, such as nitrogen fixation, Fe uptake, respiration, and electron transport. This study not only reveals the function of the fnr genes of P. polymyxa WLY78 in nitrogen fixation and other metabolisms but also will provide insight into the evolution and regulatory mechanisms of fnr in Paenibacillus.

scholarly journals Meta-analysis of liver and heart transcriptomic data for functional annotation transfer in mammalian orthologs

2017 ◽  
Author(s):  
Pía Francesca Loren Reyes ◽  
Tom Michoel ◽  
Anagha Joshi ◽  
Guillaume Devailly
Keyword(s):  
Functional Annotation ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Gene Families ◽  
Homologous Gene ◽  
Orthologous Genes ◽  
Transcriptomic Data ◽  
Genome Wide ◽  
Genome Wide Expression ◽  
Functional Orthologs

AbstractFunctional annotation transfer across multi-gene family orthologs can lead to functional misannotations. We hypothesised that co-expression network will help predict functional orthologs amongst complex homologous gene families. To explore the use of transcriptomic data available in public domain to identify functionally equivalent ones from all predicted orthologs, we collected genome wide expression data in mouse and rat liver from over 1500 experiments with varied treatments. We used a hyper-graph clustering method to identify clusters of orthologous genes co-expressed in both mouse and rat. We validated these clusters by analysing expression profiles in each species separately, and demonstrating a high overlap. We then focused on genes in 18 homology groups with one-to-many or many-to-many relationships between two species, to discriminate between functionally equivalent and non-equivalent orthologs. Finally, we further applied our method by collecting heart transcriptomic data (over 1400 experiments) in rat and mouse to validate the method in an independent tissue.

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