Biology subjects

Cui, P.

Publications and source records attributed to Cui, P..

29 records · Page 2Linked to original sources

bioRxiv2019

microRNA seedless sites attenuate strong-seed-site-mediated target repression

MicroRNAs (miRNAs) regulate protein-coding gene expression primarily through cognitive binding sites in the 3 untranslated regions (3' UTRs). Seed sites are sequences in messenger RNAs (mRNAs) that form perfect Watson-Crick base-paring with a miRNAs seed region, which can effectively reduce mRNA abundance and/or repress protein translation. Some seedless sites, which do no form perfect seed-pairing with a miRNA, can also lead to target repression, often with lower efficacy. Here we report the surprising finding that when seedless sites and seed sites are co-present in the same 3UTR, seedless sites attenuate strong-seed-site-mediated target suppression, independent of 3' UTR length. This attenuation effect is detectable in >70% of transcriptomic datasets examined, in which specific miRNAs are experimentally increased or decreased. The attenuation effect is confirmed by 3UTR reporter assays and mediated through base-pairing between miRNA and seedless sites. Furthermore, this seedless-site-based attenuation effect could affect seed sites of the same miRNA or another miRNA, thus partially explaining the variability in target suppression and miRNA-mediated gene upregulation. Our findings reveal an unexpected principle of miRNA-mediated gene regulation, and could impact the understanding of many miRNA-regulated biological processes.

bioinformatics↗

bioRxiv2019

Promoter scanning during transcription initiation in Saccharomyces cerevisiae: Pol II in the \"shooting gallery\"

BackgroundThe majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In S. cerevisiae, a preinitiation complex comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the preinitiation complex (PIC) scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function. ResultsTo determine extent of promoter scanning across promoter classes in S. cerevisiae, we perturbed Pol II catalytic activity and GTF function and analyzed their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model. ConclusionsOur observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast - which we term the "shooting gallery". In this model, Pol II catalytic activity, and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.

molecular biology↗

bioRxiv2019

Identification of essential oils with activity against stationary phase Staphylococcus aureus

Staphylococcus aureus is the most dominant human pathogen, responsible for a variety of chronic and severe infections. There is mounting evidence that persisters are associated with treatment failure and relapse of persistent infections. While some essential oils were reported to have antimicrobial activity against growing S. aureus, activity of essential oils against the non-growing stationary phase S. aureus enriched in persisters has not been investigated. In this study, we evaluated the activity of 143 essential oils against stationary phase S. aureus and identified 39 essential oils (Cinnamon bark, Oregano, Thyme white, Bandit \"Thieves\", Lemongrass (Cymbopogon flexuosus), Sandalwood oil, Health shield, Allspice, Amyris, Palmarosa, Cinnamon leaf, Clove bud, Citronella, Geranium bourbon, Marjoram, Peppermint, Lemongrass (Cymbopogon citratus), Cornmint, Elemi, Ho wood, Head ease, Lemon eucalyptus, Litsea cubeba, Myrrh, Parsley seed, Coriander oil, Dillweed, Hyssop, Neroli, Rosewood oil, Tea tree, Cajeput, Glove bud, Lavender, Sleep tight, Vetiver, Palo santo, Sage oil, Yarrow) at 0.5% concentration, 10 essential oils (Cinnamon bark, Oregano, Thyme white, Bandit \"Thieves\", Lemongrass (Cymbopogon flexuosus), Sandalwood oil, Health shield, Allspice, Amyris, Palmarosa) at 0.25% concentration, and 7 essential oils (Cinnamon bark, Oregano, Thyme white, Lemongrass (Cymbopogon flexuosus), Allspice, Amyris, Palmarosa) at 0.125% concentration to have high activity against stationary phase S. aureus with no visible growth on agar plates after five-day exposure. Among the 10 essential oils which showed high activity at 0.25% concentration, 9 (Cinnamon bark, Oregano, Thyme white, Bandit \"Thieves\", Lemongrass (Cymbopogon flexuosus), Health shield, Allspice, Palmarosa, Amyris) showed higher activity than the known persister drug tosufloxacin, while the other one (Sandalwood oil) was found to be active at a higher concentration. In Oregano essential oil drug combination studies with clinical antibiotics, Oregano plus quinolone drugs (tosufloxacin, levofloxacin, ciprofloxacin) and rifampin completely eradicated all stationary phase S. aureus cells, but had no apparent enhancement for linezolid, vancomycin, sulfamethoxazole, trimethoprim, azithromycin and gentamicin. Our findings may facilitate development of more effective treatment for persistent S. aureus infections.

microbiology↗

bioRxiv2019

Identification of essential oils with strong activity against stationary phase uropathogenic Escherichia coli

Escherichia coli is the most dominant pathogen causing urinary tract infections (UTIs), but the current most frequently prescribed antibiotics do not always effectively cure the infection due to quiescent persister bacteria. While it has been reported that some essential oils have antimicrobial activity against growing E. coli, the activity of essential oils against the non-growing stationary phase E. coli which is enriched in persisters has not been investigated. We evaluated the activity of 140 essential oils against stationary phase uropathogenic E. coli UTI89 and identified 39, 8 and 3 essential oils at 0.5%, 0.25% and 0.125% concentrations to have high activity against stationary phase E. coli. Among the top eight essential oils, Oregano showed higher activity than the known persister drug tosufloxacin. The other top seven hits included Allspice, Bandit \"Thieves\", Cinnamon bark, Syzygium aromaticum, Health shield, Cinnamon leaf and Clove bud. In Oregano essential oil drug combination studies with common UTI antibiotics, Oregano plus quinolone drugs (tosufloxacin, levofloxacin, ciprofloxacin) completely eradicated all stationary phase E. coli cells, partially enhanced the activity of nitrofurantoin, but had no apparent enhancement for fosfomycin, meropenem and cefdinir. Our findings may facilitate development of more effective treatments for persistent UTIs.

microbiology↗

bioRxiv2019

Introducing RpsA Point Mutation Δ438A or D123A into the Chromosome of M. tuberculosis Confirms its Role in Causing Resistance to Pyrazinamide

Pyrazinamide (PZA) is a unique frontiline drug for shortening tuberculosis treatment, but its mechanisms of action are elusive. We previously identified RpsA as a target of PZA and found an alanine deletion at position 438 ({Delta}438A) in RpsA associated with PZA resistance, but its role in PZA resistance is controversial. Here, we introduced RpsA mutation {Delta}438A or D123A into M. tuberculosis chromosome and demonstrated that the introduced RspA mutations are indeed responsible for PZA resistance.

microbiology↗

bioRxiv2018

Identification of Polynucleotide Phosphorylase (PNPase) in Escherichia coli Involved in Persister Formation

Despite the identification of many genes and pathways involved in the persistence phenomenon of bacteria, the mechanisms of persistence are not well understood. Here, using Escherichia coli as a model, we identified polynucleotide phosphorylase (PNPase) as a key regulator in persister formation. We successfully constructed pnp knockout mutant strain and its complemented strain, and exposed the pnp knockout mutant and complemented strain to antibiotics and stress conditions. The results showed that, compared with the wild-type W3110, the pnp knockout strain had defect in persistence to antibiotics and stress conditions, and the persistence to antibiotics and stresses was restored upon complementation. RNA-Seq was performed to identify the transcriptome profile in the pnp knockout strain compared with wild-type strain W3110, and the data revealed that 242 (166 up-regulated, and 76 down-regulated) genes were differentially expressed in the pnp knockout mutant strain. KEGG pathway analysis of the up-regulated genes showed that they were mostly mapped to metabolism and virulence pathways, most of which are positively regulated by the global regulator cyclic AMP receptor protein (CRP). Similarly, the transcription level of the crp gene in the pnp-deletion strain increased 3.22-fold in the early stationary phase. We further explored the indicators of cellular metabolism of the pnp-deletion strain, the persistence phenotype of the pnp and crp double-deletion mutant, and the transcriptional activity of crp gene. Our results indicate that PNPase controls cellular metabolism by negatively regulating the crp operon at the post-transcriptional level by targeting the 5- Untranslated Region (UTR) of the crp transcript. This study offers new insight about the persister mechanisms and provides new targets for development of new drugs against persisters for more effective treatment of persistent bacterial infections.

microbiology↗

bioRxiv2017

Uterine progesterone signaling is a target for metformin therapy in polycystic ovary syndrome

Impaired progesterone (P4) signaling is linked to endometrial dysfunction and infertility in women with polycystic ovary syndrome (PCOS). Here we report for the first time that elevated expression of progesterone receptor (PGR) isoforms A and B parallels increased estrogen receptor (ER) expression in PCOS-like rat uteri. The aberrant PGR-targeted gene expression in PCOS-like rats before and after implantation overlaps with dysregulated expression of Fkbp52 and Ncoa2, two genes that contribute to the development of uterine P4 resistance. In vivo and in vitro studies of the effects of metformin on the regulation of the uterine P4 signaling pathway under PCOS conditions showed that metformin directly inhibits the expression of PGR and ER along with the regulation of several genes that are targeted dependently or independently of PGR-mediated uterine implantation. Functionally, metformin treatment corrected the abnormal expression of cell-specific PGR and ER and some PGR-target genes in PCOS-like rats with implantation. Additionally, we documented how metformin contributes to the regulation of the PGR-associated MAPK/ERK/p38 signaling pathway in the PCOS-like rat uterus. Our data provide novel insights into how metformin therapy regulates uterine P4 signaling molecules under PCOS conditions.

physiology↗

bioRxiv2017

Clofazimine targets essential nucleoid associated protein, mycobacterial integration host factor (mIHF), in Mycobacterium tuberculosis

Clofazimine (CFZ) is a phenazine derivative used for treatment of leprosy, MDR-TB and XDR-TB. There is recent interest in understanding how CFZ works following the demonstration of its unique ability to shorten the treatment of MDR-TB. However, the target of CFZ in mycobacteria has remained elusive. Here, we show that CFZ binds to mycobacterial integration host factor (mIHF), which is an essential nucleoid associated protein in mycobacteria involved in DNA protection, chromosome organization and global gene regulation. We demonstrate that CFZ inhibits mIHF binding to DNA and interferes with mycobacterial gene expression. This mode of action is unique among all antibiotics including antimycibacterial agents and may help to explain its unusual action against Mycobacterium tuberculosis. Our study provides new insight about the mechanism of action of this intriguing drug and has implications for developing more effective treatment of TB.

microbiology↗

bioRxiv2017

Identification of a Novel Gene argJ involved in Arginine Biosynthesis Critical for Persister Formation in Staphylococcus aureus

Staphylococcus aureus can cause both acute and recurrent persistent infections such as peritonitis, endocarditis, abscess, osteomyelitis, and chronic wound infections. An effective treatment to eradicate the persistent disease is still lacking as the mechanisms of S. aureus persistence are poorly understood. In this study, we performed a comprehensive and unbiased high-throughput mutant screen using S. aureus USA300 and identified argJ, encoding an acetyltransferase in the arginine biosynthesis pathway, whose mutation produced a significant defect in persister formation in multiple drugs and stresses. Genetic complementation and arginine supplementation restored persistence in the ArgJ mutant. Quantitative real-time PCR analysis showed that the arg genes were over-expressed under drug stressed conditions and in stationary phase cultures. In addition, the ArgJ mutant had attenuated virulence in both C. elegans and mouse models of infection. Our studies identify a novel mechanism of persistence mediated by arginine metabolism in S. aureus. These findings will not only provide new insights about the mechanisms of S. aureus persistence but also offer novel therapeutic targets that may help to develop more effective treatment of persistent S. aureus infections.

microbiology↗

bioRxiv2017

Identification of novel mutations associated with cycloserine resistance in Mycobacterium tuberculosis

ObjectivesD-cycloserine (DCS) is an important second-line drug used to treat multi-drug resistant (MDR) and extensively drug-resistant (XDR) tuberculosis. However, the mechanisms of resistance to DCS are not well understood. Here we investigated the molecular basis of DCS resistance using in vitro isolated resistant mutants of Mycobacterium tuberculosis.\n\nMethodsM. tuberculosis H37Rv was subjected to mutant selection on 7H11 agar plates containing varying concentrations of DCS. A total of 35 DCS-resistant mutants were isolated and 18 mutants were subjected to whole genome sequencing. The identified mutations associated with DCS resistance were confirmed by PCR-Sanger sequencing.\n\nResultsWe identified mutations in 17 genes that are associated with DCS resistance. Except mutations in alr (rv3423c) which is known to be involved in DCS resistance, 16 new genes rv0059, betP (rv0917), rv0221, rv1403c, rv1683, rv1726, gabD2 (rv1731), rv2749, sugI (rv3331), hisC2 (rv3 772), single mutation in 5 intergenic region of rv3345c and rv1435c, and insertion in 3 region of rv0759c were identified as solo mutations in their respective DCS-resistant mutants. Our findings indicate that the mechanisms of DCS resistance are more complex than previously thought and involve genes participating in different cellular functions such as lipid metabolism, methyltransferase, stress response, and transport proteins.\n\nConclusionsNew mutations in diverse genes associated with DCS are identified, which shed new light on the mechanisms of action and resistance of DCS. Future studies are needed to verify these findings in clinical strains so that molecular detection of DCS resistance for improved treatment of MDR-TB can be developed.

microbiology↗

bioRxiv2017

Identification of drug candidates that enhance pyrazinamide activity from a clinical drug library

Tuberculosis (TB) remains a leading cause of morbidity and mortality globally despite the availability of the TB therapy. 1 The current TB therapy is lengthy and suboptimal, requiring a treatment time of at least 6 months for drug susceptible TB and 9-12 months (shorter Bangladesh regimen) or 18-24 months (regular regimen) for multi-drug-resistant tuberculosis (MDR-TB). 1 The lengthy therapy makes patient compliance difficult, which frequently leads to emergence of drug-resistant strains. The requirement for the prolonged treatment is thought to be due to dormant persister bacteria which are not effectively killed by the current TB drugs, except rifampin and pyrazinamide (PZA) which have higher activity against persisters. 2, 3 Therefore new therapies should address the problem of insufficient efficacy against M. tuberculosis persisters, which could cause relapse of clinical disease. 4 PZA is a critical frontline TB drug that kills persister bacteria 5 and shortens the TB treatment from 9-12 months to 6 months. 6, 7 Although several new TB drugs are showing promise in clinical studies, none can replace PZA as they all have to be used together with PZA. 7 Because of the essentiality of PZA and the high cost of developing new drugs, in this study, we explored the idea of identifying drugs that enhance the anti-persister activity of PZA as an economic alternative approach to developing new drugs for improved treatment by screening an clinical drug library against old M. tuberculosis cultures enriched with persisters.

microbiology↗