scholarly journals Integrative analysis of proteome and transcriptome dynamics duringBacillus subtilisspore revival

2019 ◽  
Author(s):  
Bhagyashree Swarge ◽  
Martijs Jonker ◽  
Wishwas Abhyankar ◽  
Huub Hoefsloot ◽  
Chris G. de Koster ◽  
...  
Keyword(s):  
Spore Germination ◽  
Differentially Expressed ◽  
Protein Loss ◽  
Active Protein ◽  
Vegetative Cells ◽  
Genes Encoding ◽  
Molecular Machinery ◽  
Spore Outgrowth ◽  
Reference Proteome ◽  
Time Point

AbstractBacillus subtilisforms highly resistant, metabolically inactive dormant spores upon nutrient limitation. These endospores pose challenges to the food and medical sectors. Spores reactivate their metabolism upon contact with germinants and develop into vegetative cells. The activation of the molecular machinery that triggers the progress of germination and spore outgrowth is still unsettled. To gain further insight in spore germination and outgrowth processes, the transcriptome and proteome changeover during spore germination and outgrowth to vegetative cells, was analysed.B. subtilistranscriptome analysis allow us to trace the different functional groups of genes expressed. For each time-point sample, the change in the spore proteome was quantitatively monitored relative to the reference proteome of15N metabolically labelled vegetative cells. We observed until the phase transition, i.e. completion of germination, no significant change in the proteome. We have identified 36 transcripts present abundantly in the dormant spores. This number is in close agreement with the previous findings. These transcripts mainly belong to the genes encoding small acid soluble proteins (sspE, sspO, sspI, sspK, sspF) and proteins with uncharacterized functions. We observed in total 3152 differentially expressed genes, but ‘only’ 323 differentially expressed proteins (total 451 proteins identified and quantified). Our data shows that 173 proteins from dormant spores, both spore unique proteins and protein shared with vegetative cells, are lost during the phase transitioning period. This loss is in addition to the active protein degradation, undertaken by the spore proteases such as Gpr, as germination and outgrowth proceeds. Further analysis is required to functionally interpret the observed protein loss. The observed diverse timing of the synthesis of different protein sets reveals a putative core-strategy of the revival of ‘life’ starting from theB. subtilisspore.

scholarly journals Teicoplanin Suppresses Vegetative Clostridioides Difficile and Spore Outgrowth

Antibiotics ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 984
Author(s):  
Suvash Chandra Ojha ◽  
Matthew Phanchana ◽  
Phurt Harnvoravongchai ◽  
Surang Chankhamhaengdecha ◽  
Sombat Singhakaew ◽  
...  
Keyword(s):  
Health Care ◽  
Spore Germination ◽  
Antimicrobial Agents ◽  
Vegetative Cells ◽  
Health Care Settings ◽  
Minimal Inhibitory Concentrations ◽  
Clostridioides Difficile ◽  
Global Priority ◽  
Clostridioides Difficile Infection ◽  
Spore Outgrowth

In recent decades, the incidence of Clostridioides difficile infection (CDI) has remained high in both community and health-care settings. With the increasing rate of treatment failures and its ability to form spores, an alternative treatment for CDI has become a global priority. We used the microdilution assay to determine minimal inhibitory concentrations (MICs) of vancomycin and teicoplanin against 30 distinct C. difficile strains isolated from various host origins. We also examined the effect of drugs on spore germination and outgrowth by following the development of OD600. Finally, we confirmed the spore germination and cell stages by microscopy. We showed that teicoplanin exhibited lower MICs compared to vancomycin in all tested isolates. MICs of teicoplanin ranged from 0.03–0.25 µg/mL, while vancomycin ranged from 0.5–4 µg/mL. Exposure of C. difficile spores to broth supplemented with various concentrations of antimicrobial agents did not affect the initiation of germination, but the outgrowth to vegetative cells was inhibited by all test compounds. This finding was concordant with aberrant vegetative cells after antibiotic treatment observed by light microscopy. This work highlights the efficiency of teicoplanin for treatment of C. difficile through prevention of vegetative cell outgrowth.

scholarly journals Dynamic alteration in miRNA and mRNA expression profiles at different stages of chronic arsenic exposure-induced carcinogenesis in a human cell culture model of skin cancer

2021 ◽  
Author(s):  
Mayukh Banerjee ◽  
Ana Ferragut Cardoso ◽  
Laila Al-Eryani ◽  
Jianmin Pan ◽  
Theodore S. Kalbfleisch ◽  
...  
Keyword(s):  
Skin Cancer ◽  
Mrna Expression ◽  
Hacat Cell ◽  
Arsenic Exposure ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Mesenchymal Transition ◽  
Chronic Arsenic Exposure ◽  
Pathway Analyses ◽  
Time Point

AbstractChronic arsenic exposure causes skin cancer, although the underlying molecular mechanisms are not well defined. Altered microRNA and mRNA expression likely play a pivotal role in carcinogenesis. Changes in genome-wide differential expression of miRNA and mRNA at 3 strategic time points upon chronic sodium arsenite (As3+) exposure were investigated in a well-validated HaCaT cell line model of arsenic-induced cutaneous squamous cell carcinoma (cSCC). Quadruplicate independent HaCaT cell cultures were exposed to 0 or 100 nM As3+ for up to 28-weeks (wk). Cell growth was monitored throughout the course of exposure and epithelial-mesenchymal transition (EMT) was examined employing immunoblot. Differentially expressed miRNA and mRNA profiles were generated at 7, 19, and 28-wk by RNA-seq, followed by identification of differentially expressed mRNA targets of differentially expressed miRNAs through expression pairing at each time point. Pathway analyses were performed for total differentially expressed mRNAs and for the miRNA targeted mRNAs at each time point. RNA-seq predictions were validated by immunoblot of selected target proteins. While the As3+-exposed cells grew slower initially, growth was equal to that of unexposed cells by 19-wk (transformation initiation), and exposed cells subsequently grew faster than passage-matched unexposed cells. As3+-exposed cells had undergone EMT at 28-wk. Pathway analyses demonstrate dysregulation of carcinogenesis-related pathways and networks in a complex coordinated manner at each time point. Immunoblot data largely corroborate RNA-seq predictions in the endoplasmic reticulum stress (ER stress) pathway. This study provides a detailed molecular picture of changes occurring during the arsenic-induced transformation of human keratinocytes.

scholarly journals Genes Encoding Transcription Factors TaDREB5 and TaNFYC-A7 Are Differentially Expressed in Leaves of Bread Wheat in Response to Drought, Dehydration and ABA

2018 ◽  
Vol 9 ◽  
Author(s):  
Lyudmila Zotova ◽  
Akhylbek Kurishbayev ◽  
Satyvaldy Jatayev ◽  
Gulmira Khassanova ◽  
Askar Zhubatkanov ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Bread Wheat ◽  
Differentially Expressed ◽  
Genes Encoding

Long-Living Budding Yeast Cell Subpopulation Induced by Ethanol/Acetate and Respiration

2019 ◽  
Vol 75 (8) ◽  
pp. 1448-1456 ◽  
Author(s):  
Young-Yon Kwon ◽  
Seung-Soo Kim ◽  
Han-Jun Lee ◽  
Seo-Hyeong Sheen ◽  
Kyoung Heon Kim ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Budding Yeast ◽  
Gradient Centrifugation ◽  
Carbon Sources ◽  
Cell Types ◽  
Glucose Sensing ◽  
Differentially Expressed ◽  
Cell Subpopulation ◽  
Genes Encoding ◽  
Cell Transcriptome

Abstract Budding yeast generate heterogeneous cells that can be separated into two distinctive cell types: short-living low-density and long-living high-density (HD) cells by density gradient centrifugation. We found that ethanol and acetate induce formation of HD cells, and mitochondrial respiration is required. From their transcriptomes and metabolomes, we found upregulated differentially expressed genes in HD cells involved in the RGT2/RGT1 glucose sensing pathway and its downstream genes encoding hexose transporters. For HD cells, we determined an abundance of various carbon sources including glucose, lactate, pyruvate, trehalose, mannitol, mannose, and galactose. Other upregulated differentially expressed genes in HD cells were involved in the TORC1–SCH9 signaling pathway and its downstream genes involved in cytoplasmic translation. We also measured an abundance of free amino acids in HD cells including valine, proline, isoleucine, and glutamine. These characteristics of the HD cell transcriptome and metabolome may be important conditions for maintaining a long-living phenotype.

scholarly journals RNA-Seq Transcriptome Analysis of Peripheral Blood From Cattle Infected With Mycobacterium bovis Across an Experimental Time Course

2021 ◽  
Vol 8 ◽  
Author(s):  
Kirsten E. McLoughlin ◽  
Carolina N. Correia ◽  
John A. Browne ◽  
David A. Magee ◽  
Nicolas C. Nalpas ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Mycobacterium Bovis ◽  
Peripheral Blood ◽  
Post Infection ◽  
Time Course ◽  
De Novo ◽  
Differentially Expressed Gene ◽  
Differentially Expressed ◽  
Infection Time ◽  
Time Point

Bovine tuberculosis, caused by infection with members of the Mycobacterium tuberculosis complex, particularly Mycobacterium bovis, is a major endemic disease affecting cattle populations worldwide, despite the implementation of stringent surveillance and control programs in many countries. The development of high-throughput functional genomics technologies, including RNA sequencing, has enabled detailed analysis of the host transcriptome to M. bovis infection, particularly at the macrophage and peripheral blood level. In the present study, we have analysed the transcriptome of bovine whole peripheral blood samples collected at −1 week pre-infection and +1, +2, +6, +10, and +12 weeks post-infection time points. Differentially expressed genes were catalogued and evaluated at each post-infection time point relative to the −1 week pre-infection time point and used for the identification of putative candidate host transcriptional biomarkers for M. bovis infection. Differentially expressed gene sets were also used for examination of cellular pathways associated with the host response to M. bovis infection, construction of de novo gene interaction networks enriched for host differentially expressed genes, and time-series analyses to identify functionally important groups of genes displaying similar patterns of expression across the infection time course. A notable outcome of these analyses was identification of a 19-gene transcriptional biosignature of infection consisting of genes increased in expression across the time course from +1 week to +12 weeks post-infection.

scholarly journals Tyrosine kinases Tie1 and Tie2 are differentially expressed in non-small cell lung cancer.

2020 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Tyrosine Kinases ◽  
The United States ◽  
Small Cell ◽  
Differentially Expressed ◽  
Small Cell Lung ◽  
Genes Encoding ◽  
Epidermal Growth

Non-small cell lung cancer (NSCLC) is the leading cause of cancer death in the United States (1). We mined published microarray data (2, 3, 4) to identify differentially expressed genes in NSCLC. We found that the genes encoding the tyrosine kinase with immunoglobulin and epidermal growth factor homology domains 1 - Tie1, and its counterpart Tie2 - were both among the genes whose expression was most quantitatively different in tumors from patients with NSCLC as compared to the lung. Tie1 and Tie2 may be important for initiation or progression of non-small cell lung cancer in humans.

scholarly journals Expression of Bovine F1-ATPase with Functional Complementation in Yeast Saccharomyces cerevisiae

2005 ◽  
Vol 280 (23) ◽  
pp. 22418-22424 ◽  
Author(s):  
Neeti Puri ◽  
Jie Lai-Zhang ◽  
Scott Meier ◽  
David M. Mueller
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Molecular Mass ◽  
Atp Synthase ◽  
Specific Activity ◽  
Functional Complementation ◽  
Yeast Saccharomyces Cerevisiae ◽  
F1 Atpase ◽  
Mitochondrial Atp Synthase ◽  
Genes Encoding ◽  
Molecular Machinery

The mitochondrial F1F0-ATP synthase is a multimeric enzyme complex composed of at least 16 unique peptides with an overall molecular mass of ∼600 kDa. F1-ATPase is composed of α3β3γδϵ with an overall molecular mass of 370 kDa. The genes encoding bovine F1-ATPase have been expressed in a quintuple yeast Saccharomyces cerevisiae deletion mutant (ΔαΔβΔγΔδΔϵ). This strain expressing bovine F1 is unable to grow on medium containing a non-fermentable carbon source (YPG), indicating that the enzyme is non-functional. However, daughter strains were easily selected for growth on YPG medium and these were evolved for improved growth on YPG medium. The evolution of the strains was presumably due to mutations, but mutations in the genes encoding the subunits of the bovine F1-ATPase were not required for the ability of the cell to grow on YPG medium. The bovine enzyme expressed in yeast was partially purified to a specific activity of about half of that of the enzyme purified from bovine heart mitochondria. These results indicate that the molecular machinery required for the assembly of the mitochondrial ATP synthase is conserved from bovine and yeast and suggest that yeast may be useful for the expression, mutagenesis, and analysis of the mammalian F1- or F1F0-ATP synthase.

scholarly journals Suboptimal Bacillus licheniformis and Bacillus weihenstephanensis Spore Incubation Conditions Increase Heterogeneity of Spore Outgrowth Time

2020 ◽  
Vol 86 (6) ◽  
Author(s):  
C. Trunet ◽  
N. Mtimet ◽  
A.-G. Mathot ◽  
F. Postollec ◽  
I. Leguerinel ◽  
...  
Keyword(s):  
Heat Treatment ◽  
Flow Cytometry ◽  
Bacillus Licheniformis ◽  
Model Parameters ◽  
Vegetative Cells ◽  
Content Type ◽  
Bacillus Weihenstephanensis ◽  
Spore Outgrowth ◽  
Growth Limits ◽  
Kinetics Of

ABSTRACT Changes with time of a population of Bacillus weihenstephanensis KBAB4 and Bacillus licheniformis AD978 dormant spores into germinated spores and vegetative cells were followed by flow cytometry, at pH ranges of 4.7 to 7.4 and temperatures of 10°C to 37°C for B. weihenstephanensis and 18°C to 59°C for B. licheniformis. Incubation conditions lower than optimal temperatures or pH led to lower proportions of dormant spores able to germinate and extended time of germination, a lower proportion of germinated spores able to outgrow, an extension of their times of outgrowth, and an increase of the heterogeneity of spore outgrowth time. A model based on the strain growth limits was proposed to quantify the impact of incubation temperature and pH on the passage through each physiological stage. The heat treatment temperature or time acted independently on spore recovery. Indeed, a treatment at 85°C for 12 min or at 95°C for 2 min did not have the same impact on spore germination and outgrowth kinetics of B. weihenstephanensis despite the fact that they both led to a 10-fold reduction of the population. Moreover, acidic sporulation pH increased the time of outgrowth 1.2-fold and lowered the proportion of spores able to germinate and outgrow 1.4-fold. Interestingly, we showed by proteomic analysis that some proteins involved in germination and outgrowth were detected at a lower abundance in spores produced at pH 5.5 than in those produced at pH 7.0, maybe at the origin of germination and outgrowth behavior of spores produced at suboptimal pH. IMPORTANCE Sporulation and incubation conditions have an impact on the numbers of spores able to recover after exposure to sublethal heat treatment. Using flow cytometry, we were able to follow at a single-cell level the changes in the physiological states of heat-stressed spores of Bacillus spp. and to discriminate between dormant spores, germinated spores, and outgrowing vegetative cells. We developed original mathematical models that describe (i) the changes with time of the proportion of cells in their different states during germination and outgrowth and (ii) the influence of temperature and pH on the kinetics of spore recovery using the growth limits of the tested strains as model parameters. We think that these models better predict spore recovery after a sublethal heat treatment, a common situation in food processing and a concern for food preservation and safety.

Antibotulinal Properties of Selected Aromatic and Aliphatic Ketones

1993 ◽  
Vol 56 (9) ◽  
pp. 795-800 ◽  
Author(s):  
BOBBY L. BOWLES ◽  
ARTHUR J. MILLER
Keyword(s):  
Spore Germination ◽  
Inhibitory Activity ◽  
Antimicrobial Agents ◽  
Dipicolinic Acid ◽  
Carbon Chain ◽  
Maximum Activity ◽  
Carbon Chain Length ◽  
Vegetative Cells ◽  
Aliphatic Ketones ◽  
Acid Release

Several aromatic and aliphatic ketones were tested for inhibitory activity against Clostridium botulinum spores and cells. Six-tenths mM 3-heptanone, 3-hexanone, or benzophenone delayed spore germination in botulinal assay medium (BAM) broth at 32°C. Sporicidal activity was observed for 1,250 mM 2,3-pentanedione, while 2-octanone, 3-octanone, or benzophenone were effective at 2,500 mM. In general, higher concentrations were required to inhibit vegetative cells than to prevent spore germination. Maximum activity against vegetative cells was observed at 25 mM acetanisole (4′-methoxyacetophenone), 2,3-butanedione, 2,3-pentanedione, 2-pentanone, or benzophenone, and inhibition was independent of pH. Five-tenths mM acetanisole inhibited dipicolinic acid release, 100 mM reduced 20 min 80°C thermal resistance, and 5.0 mM delayed toxigenesis in BAM broth at 32°C. Furthermore, inhibitory activity of acetanisole was comparable to that observed in BAM broth when tested in commercially prepared chicken and beef broths. The spectrum of antibotulinal activity was dependent upon carbon chain length, carbonyl position, number of carbonyls, and aromaticity. The inhibitions observed suggest that aliphatic and aromatic ketones might have potential as novel antimicrobial agents.

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