scholarly journals Chromosome-Wide Analysis of Gene Function by RNA Interference in the African Trypanosome

2006 ◽  
Vol 5 (9) ◽  
pp. 1539-1549 ◽  
Author(s):  
Chandra Subramaniam ◽  
Paul Veazey ◽  
Seth Redmond ◽  
Jamie Hayes-Sinclair ◽  
Emma Chambers ◽  
...  
Keyword(s):  
Rna Interference ◽  
Gene Function ◽  
Drug Targets ◽  
Cell Cycle Progression ◽  
In Silico Analysis ◽  
Phenotypic Analysis ◽  
Online Data ◽  
Systematic Analysis ◽  
Chromosome I

ABSTRACT Trypanosomatids of the order Kinetoplastida are major contributors to global disease and morbidity, and understanding their basic biology coupled with the development of new drug targets represents a critical need. Additionally, trypanosomes are among the more accessible divergent eukaryote experimental systems. The genome of Trypanosoma brucei contains 8,131 predicted open reading frames (ORFs), of which over half have no known homologues beyond the Kinetoplastida and a substantial number of others are poorly defined by in silico analysis. Thus, a major challenge following completion of the T. brucei genome sequence is to obtain functional data for all trypanosome ORFs. As T. brucei is more experimentally tractable than the related Trypanosoma cruzi and Leishmania spp. and shares >75% of their genes, functional analysis of T. brucei has the potential to inform a range of parasite biology. Here, we report methods for systematic mRNA ablation by RNA interference (RNAi) and for phenotypic analysis, together with online data dissemination. This represents the first systematic analysis of gene function in a parasitic organism. In total, 210 genes have been targeted in the bloodstream form parasite, representing an essentially complete phenotypic catalogue of chromosome I together with a validation set. Over 30% of the chromosome I genes generated a phenotype when targeted by RNAi; most commonly, this affected cell growth, viability, and/or cell cycle progression. RNAi against approximately 12% of ORFs was lethal, and an additional 11% had growth defects but retained short-term viability in culture. Although we found no evidence for clustering or a bias towards widely evolutionarily conserved genes within the essential ORF cohort, the putative chromosome I centromere is adjacent to a domain containing genes with no associated phenotype. Involvement of such a large proportion of genes in robust growth in vitro indicates that a high proportion of the expressed trypanosome genome is required for efficient propagation; many of these gene products represent potential drug targets.

Discerning novel drug targets for treating Mycobacterium avium ss. paratuberculosis-associated autoimmune disorders: an in silico approach

2020 ◽  
Author(s):  
Anjali Garg ◽  
Neelja Singhal ◽  
Manish Kumar
Keyword(s):  
Multiple Sclerosis ◽  
Autoimmune Diseases ◽  
Mycobacterium Avium ◽  
In Silico ◽  
Drug Targets ◽  
Molecular Mimicry ◽  
Mycobacterium Avium Subspecies Paratuberculosis ◽  
In Silico Analysis ◽  
Experimental Drugs

Abstract Mycobacterium avium subspecies paratuberculosis (MAP) exhibits ‘molecular mimicry’ with the human host resulting in several autoimmune diseases such as multiple sclerosis, type 1 diabetes mellitus (T1DM), Hashimoto’s thyroiditis, Crohn’s disease (CD), etc. The conventional therapy for autoimmune diseases includes immunosuppressants or immunomodulators that treat the symptoms rather than the etiology and/or causative mechanism(s). Eliminating MAP–the etiopathological agent might be a better strategy to treat MAP-associated autoimmune diseases. In this case study, we conducted a systematic in silico analysis to identify the metabolic chokepoints of MAP’s mimicry proteins and their interacting partners. The probable inhibitors of chokepoint proteins were identified using DrugBank. DrugBank molecules were stringently screened and molecular interactions were analyzed by molecular docking and ‘off-target’ binding. Thus, we identified 18 metabolic chokepoints of MAP mimicry proteins and 13 DrugBank molecules that could inhibit three chokepoint proteins viz. katG, rpoB and narH. On the basis of molecular interaction between drug and target proteins finally eight DrugBank molecules, viz. DB00609, DB00951, DB00615, DB01220, DB08638, DB08226, DB08266 and DB07349 were selected and are proposed for treatment of three MAP-associated autoimmune diseases namely, T1DM, CD and multiple sclerosis. Because these molecules are either approved by the Food and Drug Administration or these are experimental drugs that can be easily incorporated in clinical studies or tested in vitro. The proposed strategy may be used to repurpose drugs to treat autoimmune diseases induced by other pathogens.

scholarly journals Antisense RNA Modulation of Alkyl Hydroperoxide Reductase Levels in Helicobacter pylori Correlates with Organic Peroxide Toxicity but Not Infectivity

2007 ◽  
Vol 189 (9) ◽  
pp. 3359-3368 ◽  
Author(s):  
Matthew A. Croxen ◽  
Peter B. Ernst ◽  
Paul S. Hoffman
Keyword(s):  
Helicobacter Pylori ◽  
Rna Interference ◽  
Gene Function ◽  
Antisense Rna ◽  
In Vitro Growth ◽  
Protein Levels ◽  
Alkyl Hydroperoxide ◽  
Gastric Colonization ◽  
H Pylori

ABSTRACT Much of the gene content of the human gastric pathogen Helicobacter pylori (∼1.7-Mb genome) is considered essential. This view is based on the completeness of metabolic pathways, infrequency of nutritional auxotrophies, and paucity of pathway redundancies typically found in bacteria with larger genomes. Thus, genetic analysis of gene function is often hampered by lethality. In the absence of controllable promoters, often used to titrate gene function, we investigated the feasibility of an antisense RNA interference strategy. To test the antisense approach, we targeted alkyl hydroperoxide reductase (AhpC), one of the most abundant proteins expressed by H. pylori and one whose function is essential for both in vitro growth and gastric colonization. Here, we show that antisense ahpC (as-ahpC) RNA expression from shuttle vector pDH37::as-ahpC achieved an ∼72% knockdown of AhpC protein levels, which correlated with increased susceptibilities to hydrogen peroxide, cumene, and tert-butyl hydroperoxides but not with growth efficiency. Compensatory increases in catalase levels were not observed in the knockdowns. Expression of single-copy antisense constructs (expressed under the urease promoter and containing an fd phage terminator) from the rdxA locus of mouse-colonizing strain X47 achieved a 32% knockdown of AhpC protein levels (relative to wild-type X47 levels), which correlated with increased susceptibility to organic peroxides but not with mouse colonization efficiency. Our studies indicate that high levels of AhpC are not required for in vitro growth or for primary gastric colonization. Perhaps AhpC, like catalase, assumes a greater role in combating exogenous peroxides arising from lifelong chronic inflammation. These studies also demonstrate the utility of antisense RNA interference in the evaluation of gene function in H. pylori.

scholarly journals RNA interference and the use of small interfering RNA to study gene function in mammalian systems

2004 ◽  
Vol 33 (3) ◽  
pp. 545-557 ◽  
Author(s):  
I Bantounas ◽  
L A Phylactou ◽  
J B Uney
Keyword(s):  
Rna Interference ◽  
Gene Function ◽  
Viral Vector ◽  
Sirna Delivery ◽  
Interferon Response ◽  
Rnai Pathway ◽  
Small Interfering Rnas ◽  
Rnai Technology

In the past 2 years, extraordinary developments in RNA interference (RNAi)-based methodologies have seen small interfering RNAs (siRNA) become the method of choice for researchers wishing to target specific genes for silencing. In this review, an historic overview of the biochemistry of the RNAi pathway is described together with the latest advances in the RNAi field. Particular emphasis is given to strategies by which siRNAs are used to study mammalian gene function. In this regard, the use of plasmid-based and viral vector-based systems to mediate long-term RNAi in vitro and in vivo are described. However, recent work has shown that non-specific silencing effects and activation of the interferon response may occur following the use of some siRNA and delivery vector combinations. Future goals must therefore be to understand the mechanisms by which siRNA delivery leads to unwanted gene silencing effects in cells and, in this way, RNAi technology can reach its tremendous potential as a scientific tool and ultimately be used for therapeutic purposes.

scholarly journals Global assessment ofMycobacterium aviumsubspecieshominissuisgenetic requirement for growth and virulence

2019 ◽  
Author(s):  
Marte S. Dragset ◽  
Thomas R. Ioerger ◽  
Maja Loevenich ◽  
Markus Haug ◽  
Niruja Sivakumar ◽  
...  
Keyword(s):  
Mycobacterium Avium ◽  
Gene Function ◽  
Drug Targets ◽  
Virulence Genes ◽  
Genetic Manipulation ◽  
Specific Treatment ◽  
Hypothetical Protein ◽  
Transposon Mutagenesis ◽  
High Density

AbstractNontuberculous mycobacterial infections caused by the opportunistic pathogenMycobacterium aviumsubsp.hominissuis(MAH) are currently receiving renewed attention due to increased incidence combined with difficult treatment. Insights into the disease-causing mechanisms of this species have been hampered by difficulties in genetic manipulation of the bacteria. Here, we identified and sequenced a highly transformable, virulent MAH clinical isolate susceptible to high-density transposon mutagenesis, facilitating global gene disruption and subsequent investigation of MAH gene function. By transposon insertion sequencing (TnSeq) of this strain, we defined the MAH genome-wide genetic requirement for virulence andin vitrogrowth, and organized ~3500 identified transposon mutants for hypothesis-driven research. The majority (71 %) of the genes we identified as essential for MAHin vitrohad a growth-essential mutual ortholog in the related and highly virulentM. tuberculosis(Mtb). However, passaging our library through a mouse model of infection revealed a substantial number (54% of total hits) of novel virulence genes. Strikingly, > 97 % of the MAH virulence genes had a mutual ortholog inMtb. Two of the three virulence genes specific to MAH (i.e. noMtbmutual orthologs) were PPE proteins, a family of proteins unique to mycobacteria and highly associated with virulence. Finally, we validated novel genes as required for successful MAH infection; one encoding a probable MFS transporter and another a hypothetical protein located in immediate vicinity of six other identified virulence genes. In summary, we provide new, fundamental insights into the underlying genetic requirement of MAH for growth and host infection.Author summaryPulmonary disease caused by nontuberculous mycobacteria is increasing worldwide. The majority of these infections are caused by theM. aviumcomplex (MAC), whereof >90% arise fromMycobacterium aviumsubsp.hominissuis(MAH). Treatment of MAH infections is currently difficult, with a combination of antibiotics given for at least 12 months. To control MAH by improved therapy, prevention and diagnostics, we need to understand the underlying mechanisms of infection. While genetic manipulation of pathogens is crucial to study pathogenesis,M. avium(Mav) has been found notoriously hard to engineer. Here, we identify an MAH strain highly susceptible to high-density transposon mutagenesis and transformation, facilitating genetic engineering and analysis of gene function. We provide crucial insights into this strain’s global genetic requirements for growth and infection. Surprisingly, we find that the vast majority of genes required for MAH growth and virulence (96% and 97%, respectively) have mutual orthologs in the tuberculosis-causing pathogenM. tuberculosis(Mtb). However, we also find growth and virulence genes specific to MAC species. Finally, we validate novel mycobacterial virulence factors that might serve as future drug targets for MAH-specific treatment, or translate to broader treatment of related mycobacterial diseases.

scholarly journals Antimycobacterial, Enzyme Inhibition, and Molecular Interaction Studies of Psoromic Acid in Mycobacterium tuberculosis: Efficacy and Safety Investigations

2018 ◽  
Vol 7 (8) ◽  
pp. 226 ◽  
Author(s):  
Sherif Hassan ◽  
Miroslava Šudomová ◽  
Kateřina Berchová-Bímová ◽  
Shanmugaraj Gowrishankar ◽  
Kannan Rengasamy
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Active Sites ◽  
In Silico Analysis ◽  
Inhibitory Effect ◽  
In Vitro Assays ◽  
Standard Drug ◽  
Antituberculosis Therapy ◽  
Ic50 Value

The current study explores the antimycobacterial efficacy of lichen-derived psoromic acid (PA) against clinical strains of Mycobacterium tuberculosis (M.tb). Additionally, the inhibitory efficacy of PA against two critical enzymes associated with M.tb, namely, UDP-galactopyranose mutase (UGM) and arylamine-N-acetyltransferase (TBNAT), as drug targets for antituberculosis therapy were determined. PA showed a profound inhibitory effect towards all the M.tb strains tested, with minimum inhibitory concentrations (MICs) ranging between 3.2 and 4.1 µM, and selectivity indices (SIs) ranging between 18.3 and 23.4. On the other hand, the standard drug isoniazid (INH) displayed comparably high MIC values (varying from 5.4 to 5.8 µM) as well as low SI values (13.0–13.9). Interestingly, PA did not exhibit any cytotoxic effects on a human liver hepatocellular carcinoma cell line even at the highest concentration tested (75 µM). PA demonstrated remarkable suppressing propensity against UGM compared to standard uridine-5'-diphosphate (UDP), with 85.8 and 99.3% of inhibition, respectively. In addition, PA also exerted phenomenal inhibitory efficacy (half maximal inhibitory concentration (IC50) value = 8.7 µM, and 77.4% inhibition) against TBNAT compared with standard INH (IC50 value = 6.2 µM and 96.3% inhibition). Furthermore, in silico analysis validated the outcomes of in vitro assays, as the molecular interactions of PA with the active sites of UGM and TBNAT were unveiled using molecular docking and structure–activity relationship studies. Concomitantly, our findings present PA as an effective and safe natural drug plausible for use in controlling tuberculosis infections.

scholarly journals RNA Interference of Dual Oxidase in the Plant Nematode Meloidogyne incognita

2005 ◽  
Vol 18 (10) ◽  
pp. 1099-1106 ◽  
Author(s):  
Manjula Bakhetia ◽  
Wayne Charlton ◽  
Howard J. Atkinson ◽  
Michael J. McPherson
Keyword(s):  
Rna Interference ◽  
Gene Function ◽  
Meloidogyne Incognita ◽  
Feeding Strategy ◽  
Model Organisms ◽  
Parasitic Nematodes ◽  
In Planta ◽  
Oxidase Gene ◽  
Dual Oxidase

RNA interference (RNAi) is a powerful tool for the analysis of gene function in model organisms such as the nematode Caenorhabditis elegans. Recent demonstrations of RNAi in plant parasitic nematodes provide a stimulus to explore the potential of using RNAi to investigate disruption of gene function in Meloidogyne incognita, one of the most important nematode pests of global agriculture. We have used RNAi to examine the importance of dual oxidases (peroxidase and NADPH oxidase), a class of enzyme associated with extracellular matrix cross-linking in C. elegans. RNAi uptake by M. incognita juveniles is highly efficient. In planta infection data show that a single 4-h preinfection treatment with double-stranded RNA derived from the peroxidase region of a dual oxidase gene has effects on gene expression that are phenotypically observable 35 days postinfection. This RNAi effect results in a reduction in egg numbers at 35 days of up to 70%. The in vitro feeding strategy provides a powerful tool for identifying functionally important genes, including those that are potential targets for the development of new agrochemicals or transgenic resistance strategies.

RNA interference and its clinical applications

2007 ◽  
Vol 148 (47) ◽  
pp. 2235-2240 ◽  
Author(s):  
Gyöngyi Munkácsy ◽  
Zsolt Tulassay ◽  
Balázs Győrffy
Keyword(s):  
Rna Interference ◽  
Clinical Applications

Az RNS-interferencia a poszttranszkripciós génelcsendesítés olyan formája, amelynek során rövid, specifikusan RNS-molekulák elnyomják a gének kifejeződésében kulcsszerepet játszó hírvivő RNS-ek működését. A sejtbe juttatott dupla szálú vagy rövid interferáló RNS-molekulák aktiválják az RNS-indukált elcsendesítő komplexet, amely a célgén hírvivő RNS-ét lebontja. A sejtek saját szabályozó mikro-RNS-molekulákkal is rendelkeznek, amelyeknek hírvivő RNS-e képes önmagával hajtűt képezni, amit a sejt dupla szálú RNS-ként értelmez. Az RNS-interferencia élettani működései közé tartozik a vírusok és a transzpozonok elleni védekezés, valamint a génkifejeződés szabályozása. Az RNS-interferencia nemcsak in vitro alkalmazható az egyes gének működésének vizsgálatára, hanem klinikai alkalmazásainak lehetőségei is megjelentek. Eddig vírusfertőzésekben, az időskori makuladegeneráció gátlására, a vér koleszterinszint-csökkentésére, daganatellenes és neurodegeneratív betegségek kezelésében alkalmazták. Az RNS-interferencia alkalmazását azonban nehezíti, hogy a megfelelő rövid interferáló RNS-molekulák tervezéséhez szükséges bioinformatikai algoritmusok nem tökéletesek; a szervezet szöveteibe való bejuttatásuk nehéz; illetve csak olyan esetekben alkalmazható, amelyekben átmeneti antagonista génelcsendesítő hatás és nem hosszú távú kezelés szükséges. Az alkalmazás legnagyobb előnye a jelentős specificitás, ami miatt mellékhatása is kevés. Az RNS-interferencia alapú kezelések megjelenése már a közeli jövőben várható.

Current Status and Future Perspective for Research on Medicinal Plants with Anticancerous Activity and Minimum Cytotoxic Value

2019 ◽  
Vol 20 (12) ◽  
pp. 1227-1243
Author(s):  
Hina Qamar ◽  
Sumbul Rehman ◽  
D.K. Chauhan
Keyword(s):  
Side Effects ◽  
Medicinal Plants ◽  
Anticancer Agents ◽  
Drug Targets ◽  
Psidium Guajava ◽  
Current Status ◽  
Future Perspective ◽  
Wide Range

Cancer is the second leading cause of morbidity and mortality worldwide. Although chemotherapy and radiotherapy enhance the survival rate of cancerous patients but they have several acute toxic effects. Therefore, there is a need to search for new anticancer agents having better efficacy and lesser side effects. In this regard, herbal treatment is found to be a safe method for treating and preventing cancer. Here, an attempt has been made to screen some less explored medicinal plants like Ammania baccifera, Asclepias curassavica, Azadarichta indica, Butea monosperma, Croton tiglium, Hedera nepalensis, Jatropha curcas, Momordica charantia, Moringa oleifera, Psidium guajava, etc. having potent anticancer activity with minimum cytotoxic value (IC50 >3μM) and lesser or negligible toxicity. They are rich in active phytochemicals with a wide range of drug targets. In this study, these medicinal plants were evaluated for dose-dependent cytotoxicological studies via in vitro MTT assay and in vivo tumor models along with some more plants which are reported to have IC50 value in the range of 0.019-0.528 mg/ml. The findings indicate that these plants inhibit tumor growth by their antiproliferative, pro-apoptotic, anti-metastatic and anti-angiogenic molecular targets. They are widely used because of their easy availability, affordable price and having no or sometimes minimal side effects. This review provides a baseline for the discovery of anticancer drugs from medicinal plants having minimum cytotoxic value with minimal side effects and establishment of their analogues for the welfare of mankind.

Small Molecules Effective Against Liver and Blood Stage Malarial Infection

2019 ◽  
Vol 18 (23) ◽  
pp. 2008-2021 ◽  
Author(s):  
Snigdha Singh ◽  
Neha Sharma ◽  
Charu Upadhyay ◽  
Sumit Kumar ◽  
Brijesh Rathi ◽  
...  
Keyword(s):  
Drug Targets ◽  
Malaria Parasite ◽  
Blood Stage ◽  
Culture Methods ◽  
Liver Stage ◽  
Malarial Infection ◽  
Dual Stage ◽  
New Treatment ◽  
Global Threat

Malaria is a lethal disease causing devastating global impact by killing more than 8,00,000 individuals yearly. A noticeable decline in malaria related deaths can be attributed to the most reliable treatment, ACTs against P. falciparum. However, the cumulative resistance of the malaria parasite against ACTs is a global threat to control the disease and, therefore the new effective therapeutics are urgently needed, including new treatment approaches. Majority of the antimalarial drugs target BS malarial infection. Currently, scientists are eager to explore the drugs with potency against not only BS but other life stages such as sexual and asexual stages of the malaria parasite. Liver Stage is considered as one of the important drug targets as it always leads to BS and the infection can be cured at this stage before it enters into the Blood Stage. However, a limited number of compounds are reported effective against LS malaria infection probably due to scarcity of in vitro LS culture methods and clinical possibilities. This mini review covers a range of chemical compounds showing efficacy against BS and LS of the malaria parasite’s life cycle collectively (i.e. dual stage activity). These scaffolds targeting dual stages are essential for the eradication of malaria and to evade resistance.

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