Conserved bacterial de novo guanine biosynthesis pathway enables microbial survival and colonization in the environmental niche of the urinary tract

ABSTRACT: Tuberculosis inflammation of vertebral column (spondylitis) can lead to neurogenic lower urinary tract dysfunction. There is lack of available publications for neurogenic lower urinary tract dysfunction in spinal tuberculosis. OBJECTIVE: To evaluate urodynamic disturbances in spinal tuberculosis before and after surgery for spondylitis. MATERIALS AND METHODS: We observed 19 patients with spinal tuberculosis, who had symptoms of micturitions impairment. 14 patients (73,6%) were male and 5 (26,4%) were female, average age was 43,7 7,9 years (2766). Control evaluation was performed after surgery on day 2128. RESULTS: Before surgery we found detrusor overactivity in 11 (57,9%) patients and 2 of those with detrusor overactivity had detrusor-sphincter dyssynergia. Detrusor hypo-/acontractility was diagnosed in 8 (42,1%). After surgery 5 patients (26,3%) exhibited improvement, in one case urodynamic disturbances were resolved. One patient developed detrusor overactivity and incontinence de novo and one patient had worsening neurological status, loss of sensitivity and acontractile bladder. CONCLUSION: Variable lower urinary tract dysfunction can be diagnosed in spinal tuberculosis. Only 26,3% of patients have improvement after surgery. New conditions or worsening of previous neurogenic lower urinary tract dysfunctions can be observed.

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Whole exome sequencing identifies FOXL2, FOXA2 and FOXA3 as candidate genes for monogenic congenital anomalies of the kidneys and urinary tract

Nephrology Dialysis Transplantation ◽

10.1093/ndt/gfab253 ◽

2021 ◽

Author(s):

Bixia Zheng ◽

Steve Seltzsam ◽

Chunyan Wang ◽

Luca Schierbaum ◽

Sophia Schneider ◽

...

Keyword(s):

Urinary Tract ◽

Exome Sequencing ◽

Candidate Genes ◽

Whole Exome Sequencing ◽

Congenital Anomalies ◽

De Novo ◽

Horseshoe Kidney ◽

Missense Variant ◽

Whole Exome ◽

Fox Genes

Abstract Background Congenital anomalies of the kidneys and urinary tract (CAKUT) constitute the most common cause of chronic kidney disease in the first three decades of life. Variants in four Forkhead box (FOX) transcription factors have been associated with CAKUT. We hypothesized that other FOX genes, if highly expressed in developing kidney, may also represent monogenic causes of CAKUT. Methods We here performed whole exome sequencing (WES) in 541 families with CAKUT and generated 4 lists of CAKUT candidate genes: A) 36 FOX genes showing high expression during renal development, B) 4 FOX genes known to cause CAKUT to validate list A; C) 80 genes that we identified as unique potential novel CAKUT candidate genes when performing WES in 541 CAKUT families, and D) 175 genes identified from WES as multiple potential novel CAKUT candidate genes. Results To prioritize potential novel CAKUT candidates in FOX gene family, we overlapped 36 FOX genes (list A) with list C and D of WES-derived CAKUT candidates. Intersection with list C, identified a de novo FOXL2 in-frame deletion in a patient with eyelid abnormalities and ureteropelvic junction obstruction, and a homozygous FOXA2 missense variant in a patient with horseshoe kidney. Intersection with list D, identified a heterozygous FOXA3 missense variant in a CAKUT family with multiple affected individuals. Conclusion We hereby identified FOXL2, FOXA2 and FOXA3 as novel monogenic candidate genes of CAKUT, supporting the utility of a paralog-based approach to discover mutated genes associated with human disease.

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De novo transcriptome and tissue specific expression analysis of genes associated with biosynthesis of secondary metabolites in Operculina turpethum (L.)

Scientific Reports ◽

10.1038/s41598-021-01906-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bhagyashree Biswal ◽

Biswajit Jena ◽

Alok Kumar Giri ◽

Laxmikanta Acharya

Keyword(s):

Secondary Metabolite ◽

De Novo ◽

Differentially Expressed Gene ◽

Homology Search ◽

Biosynthesis Pathway ◽

Terpenoid Biosynthesis ◽

De Novo Transcriptome ◽

Illumina Hiseq ◽

Secondary Metabolite Biosynthesis ◽

Root Tissues

AbstractThis study reported the first-ever de novo transcriptome analysis of Operculina turpethum, a high valued endangered medicinal plant, using the Illumina HiSeq 2500 platform. The de novo assembly generated a total of 64,259 unigenes and 20,870 CDS (coding sequence) with a mean length of 449 bp and 571 bp respectively. Further, 20,218 and 16,458 unigenes showed significant similarity with identified proteins of NR (non-redundant) and UniProt database respectively. The homology search carried out against publicly available database found the best match with Ipomoea nil sequences (82.6%). The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified 6538 unigenes functionally assigned to 378 modules with phenylpropanoid biosynthesis pathway as the most enriched among the secondary metabolite biosynthesis pathway followed by terpenoid biosynthesis. A total of 17,444 DEGs were identified among which majority of the DEGs (Differentially Expressed Gene) involved in secondary metabolite biosynthesis were found to be significantly upregulated in stem as compared to root tissues. The qRT-PCR validation of 9 unigenes involved in phenylpropanoid and terpenoid biosynthesis also showed a similar expression pattern. This finding suggests that stem tissues, rather than root tissues, could be used to prevent uprooting of O. turpethum in the wild, paving the way for the plant's effective conservation. Moreover, the study formed a valuable repository of genetic information which will provide a baseline for further molecular research.

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Genome-Wide Survey for Microdeletions or -Duplications in 155 Patients with Lower Urinary Tract Obstructions (LUTO)

Genes ◽

10.3390/genes12091449 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1449

Author(s):

Luca M. Schierbaum ◽

Sophia Schneider ◽

Stefan Herms ◽

Sugirthan Sivalingam ◽

Julia Fabian ◽

...

Keyword(s):

Urinary Tract ◽

Lower Urinary Tract ◽

De Novo ◽

Urinary Tract Obstruction ◽

Posterior Urethral Valves ◽

Rare Cnvs ◽

Genome Wide ◽

Lower Urinary Tract Obstruction ◽

Human Specific ◽

Lower Urinary

Lower urinary tract obstruction (LUTO) is, in most cases, caused by anatomical blockage of the bladder outlet. The most common form are posterior urethral valves (PUVs), a male-limited phenotype. Here, we surveyed the genome of 155 LUTO patients to identify disease-causing CNVs. Raw intensity data were collected for CNVs detected in LUTO patients and 4.392 healthy controls using CNVPartition, QuantiSNP and PennCNV. Overlapping CNVs between patients and controls were discarded. Additional filtering implicated CNV frequency in the database of genomic variants, gene content and final visual inspection detecting 37 ultra-rare CNVs. After, prioritization qPCR analysis confirmed 3 microduplications, all detected in PUV patients. One microduplication (5q23.2) occurred de novo in the two remaining microduplications found on chromosome 1p36.21 and 10q23.31. Parental DNA was not available for segregation analysis. All three duplications comprised 11 coding genes: four human specific lncRNA and one microRNA. Three coding genes (FBLIM1, SLC16A12, SNCAIP) and the microRNA MIR107 have previously been shown to be expressed in the developing urinary tract of mouse embryos. We propose that duplications, rare or de novo, contribute to PUV formation, a male-limited phenotype.

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Arginine-deprivation–induced oxidative damage sterilizes Mycobacterium tuberculosis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1808874115 ◽

2018 ◽

Vol 115 (39) ◽

pp. 9779-9784 ◽

Cited By ~ 22

Author(s):

Sangeeta Tiwari ◽

Andries J. van Tonder ◽

Catherine Vilchèze ◽

Vitor Mendes ◽

Sherine E. Thomas ◽

...

Keyword(s):

Oxidative Stress ◽

Dna Damage ◽

Mycobacterium Tuberculosis ◽

De Novo ◽

Target Space ◽

Biosynthesis Pathway ◽

Arginine Biosynthesis ◽

Arginine Deprivation

Reactive oxygen species (ROS)-mediated oxidative stress and DNA damage have recently been recognized as contributing to the efficacy of most bactericidal antibiotics, irrespective of their primary macromolecular targets. Inhibitors of targets involved in both combating oxidative stress as well as being required for in vivo survival may exhibit powerful synergistic action. This study demonstrates that the de novo arginine biosynthetic pathway in Mycobacterium tuberculosis (Mtb) is up-regulated in the early response to the oxidative stress-elevating agent isoniazid or vitamin C. Arginine deprivation rapidly sterilizes the Mtb de novo arginine biosynthesis pathway mutants ΔargB and ΔargF without the emergence of suppressor mutants in vitro as well as in vivo. Transcriptomic and flow cytometry studies of arginine-deprived Mtb have indicated accumulation of ROS and extensive DNA damage. Metabolomics studies following arginine deprivation have revealed that these cells experienced depletion of antioxidant thiols and accumulation of the upstream metabolite substrate of ArgB or ArgF enzymes. ΔargB and ΔargF were unable to scavenge host arginine and were quickly cleared from both immunocompetent and immunocompromised mice. In summary, our investigation revealed in vivo essentiality of the de novo arginine biosynthesis pathway for Mtb and a promising drug target space for combating tuberculosis.

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De novo transcriptome analysis of the critically endangered alpine Himalayan herb Nardostachys jatamansi reveals the biosynthesis pathway genes of tissue-specific secondary metabolites

Scientific Reports ◽

10.1038/s41598-020-74049-1 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Nisha Dhiman ◽

Anil Kumar ◽

Dinesh Kumar ◽

Amita Bhattacharya

Keyword(s):

Secondary Metabolites ◽

Transcriptome Analysis ◽

Vegetative Growth ◽

De Novo ◽

Biosynthesis Pathway ◽

De Novo Transcriptome ◽

Tissue Specific ◽

Nardostachys Jatamansi ◽

Secondary Metabolite Biosynthesis

Abstract The study is the first report on de novo transcriptome analysis of Nardostachys jatamansi, a critically endangered medicinal plant of alpine Himalayas. Illumina GAIIx sequencing of plants collected during end of vegetative growth (August) yielded 48,411 unigenes. 74.45% of these were annotated using UNIPROT. GO enrichment analysis, KEGG pathways and PPI network indicated simultaneous utilization of leaf photosynthates for flowering, rhizome fortification, stress response and tissue-specific secondary metabolites biosynthesis. Among the secondary metabolite biosynthesis genes, terpenoids were predominant. UPLC-PDA analysis of in vitro plants revealed temperature-dependent, tissue-specific differential distribution of various phenolics. Thus, as compared to 25 °C, the phenolic contents of both leaves (gallic acid and rutin) and roots (p-coumaric acid and cinnamic acid) were higher at 15 °C. These phenolics accounted for the therapeutic properties reported in the plant. In qRT-PCR of in vitro plants, secondary metabolite biosynthesis pathway genes showed higher expression at 15 °C and 14 h/10 h photoperiod (conditions representing end of vegetative growth period). This provided cues for in vitro modulation of identified secondary metabolites. Such modulation of secondary metabolites in in vitro systems can eliminate the need for uprooting N. jatamansi from wild. Hence, the study is a step towards effective conservation of the plant.

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Ceramide Suppresses Influenza A Virus Replication In Vitro

Journal of Virology ◽

10.1128/jvi.00053-19 ◽

2019 ◽

Vol 93 (7) ◽

Cited By ~ 8

Author(s):

Nadia Soudani ◽

Rouba Hage-Sleiman ◽

Walid Karam ◽

Ghassan Dbaibo ◽

Hassan Zaraket

Keyword(s):

Influenza A Virus ◽

Virus Replication ◽

Influenza A ◽

De Novo ◽

Dependent Manner ◽

Biosynthesis Pathway ◽

Influenza A H1n1 ◽

Ceramide Accumulation ◽

Antiviral Role

ABSTRACT Annual influenza outbreaks are associated with significant morbidity and mortality worldwide despite the availability of seasonal vaccines. Influenza pathogenesis depends on the manipulation of host cell signaling to promote virus replication. Ceramide is a sphingosine-derived lipid that regulates diverse cellular processes. Studies highlighted the differential role of ceramide de novo biosynthesis on the propagation of various viruses. Whether ceramide plays, a role in influenza virus replication is not known. In this study, we assessed the potential interplay between the influenza A (IAV) and ceramide biosynthesis pathways. The accumulation of ceramide in human lung epithelial cells infected with influenza A/H1N1 virus strains was evaluated using thin-layer chromatography and/or confocal microscopy. Virus replication was assessed upon the regulation of the de novo ceramide biosynthesis pathway. A significant increase in ceramide accumulation was observed in cells infected with IAV in a dose- and time-dependent manner. Inoculating the cells with UV-inactivated IAV did not result in ceramide accumulation in the cells, suggesting that the induction of ceramide required an active virus replication. Inhibiting de novo ceramide significantly decreased ceramide accumulation and enhanced virus replication. The addition of exogenous C6-ceramide prior to infection mediated an increase in cellular ceramide levels and significantly attenuated IAV replication and reduced viral titers (≈1 log10 PFU/ml unit). Therefore, our data demonstrate that ceramide accumulation through de novo biosynthesis pathway plays a protective and antiviral role against IAV infection. These findings propose new avenues for development of antiviral molecules and strategies. IMPORTANCE Understanding the effect of sphingolipid metabolism on viral pathogenesis provide important insights into the development of therapeutic strategies against microbial infections. In this study, we demonstrate a critical role of ceramide during influenza A virus infection. We demonstrate that ceramide produced through de novo biosynthesis possess an antiviral role. These observations unlock new opportunities for the development of novel antiviral therapies against influenza.

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Reconstruction of the Fatty Acid Biosynthetic Pathway ofExiguobacterium antarcticumB7 Based on Genomic and Bibliomic Data

BioMed Research International ◽

10.1155/2016/7863706 ◽

2016 ◽

Vol 2016 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Regiane Kawasaki ◽

Rafael A. Baraúna ◽

Artur Silva ◽

Marta S. P. Carepo ◽

Rui Oliveira ◽

...

Keyword(s):

Fatty Acids ◽

Fatty Acid ◽

Fatty Acid Biosynthesis ◽

De Novo ◽

Short Chain Fatty Acids ◽

Hexadecenoic Acid ◽

Biosynthesis Pathway ◽

Acid Biosynthesis ◽

Cold Environments ◽

Fatty Acid Biosynthesis Pathway

Exiguobacterium antarcticumB7 is extremophile Gram-positive bacteria able to survive in cold environments. A key factor to understanding cold adaptation processes is related to the modification of fatty acids composing the cell membranes of psychrotrophic bacteria. In our study we show thein silicoreconstruction of the fatty acid biosynthesis pathway ofE. antarcticumB7. To build the stoichiometric model, a semiautomatic procedure was applied, which integrates genome information using KEGG and RAST/SEED. Constraint-based methods, namely, Flux Balance Analysis (FBA) and elementary modes (EM), were applied. FBA was implemented in the sense of hexadecenoic acid production maximization. To evaluate the influence of the gene expression in the fluxome analysis, FBA was also calculated using thelog2⁡FCvalues obtained in the transcriptome analysis at 0°C and 37°C. The fatty acid biosynthesis pathway showed a total of 13 elementary flux modes, four of which showed routes for the production of hexadecenoic acid. The reconstructed pathway demonstrated the capacity ofE. antarcticumB7 tode novoproduce fatty acid molecules. Under the influence of the transcriptome, the fluxome was altered, promoting the production of short-chain fatty acids. The calculated models contribute to better understanding of the bacterial adaptation at cold environments.

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