scholarly journals Branch Point Identification and Sequence Requirements for Intron Splicing in Plasmodium falciparum

2011 ◽  
Vol 10 (11) ◽  
pp. 1422-1428 ◽  
Author(s):  
Xiaohong Zhang ◽  
Caitlin A. Tolzmann ◽  
Martin Melcher ◽  
Brian J. Haas ◽  
Malcolm J. Gardner ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Branch Point ◽  
Splice Site ◽  
Consensus Sequence ◽  
Nucleophilic Attack ◽  
Luciferase Reporter ◽  
Branch Points ◽  
Content Type ◽  
Evolutionary Forces

ABSTRACTSplicing of mRNA is an ancient and evolutionarily conserved process in eukaryotic organisms, but intron-exon structures vary.Plasmodium falciparumhas an extreme AT nucleotide bias (>80%), providing a unique opportunity to investigate how evolutionary forces have acted on intron structures. In this study, we developed anin vivoluciferase reporter splicing assay and employed it in combination with lariat isolation and sequencing to characterize 5′ and 3′ splicing requirements and experimentally determine the intron branch point inP. falciparum. This analysis indicates thatP. falciparummRNAs have canonical 5′ and 3′ splice sites. However, the 5′ consensus motif is weakly conserved and tolerates nucleotide substitution, including the fifth nucleotide in the intron, which is more typically a G nucleotide in most eukaryotes. In comparison, the 3′ splice site has a strong eukaryotic consensus sequence and adjacent polypyrimidine tract. In four differentP. falciparumpre-mRNAs, multiple branch points per intron were detected, with some at U instead of the typical A residue. A weak branch point consensus was detected among 18 identified branch points. This analysis indicates thatP. falciparumretains many consensus eukaryotic splice site features, despite having an extreme codon bias, and possesses flexibility in branch point nucleophilic attack.

scholarly journals Novel Two-Component System MacRS Is a Pleiotropic Regulator That Controls Multiple Morphogenic Membrane Protein Genes inStreptomyces coelicolor

2018 ◽  
Vol 85 (4) ◽  
Author(s):  
Meng Liu ◽  
Peipei Zhang ◽  
Yanping Zhu ◽  
Ting Lu ◽  
Yemin Wang ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Consensus Sequence ◽  
Aerial Mycelium ◽  
Dnase I ◽  
Inverted Repeats ◽  
Content Type ◽  
Dnase I Footprinting ◽  
Two Component

ABSTRACTAs with most annotated two-component systems (TCSs) ofStreptomyces coelicolor, the function of TCS SCO2120/2121 was unknown. Based on our findings, we have designated this TCS MacRS, formorphogenesis andactinorhodin regulator/sensor. Our study indicated that either single or double mutation of MacRS largely blocked production of actinorhodin but enhanced formation of aerial mycelium. Chromatin immunoprecipitation (ChIP) sequencing, using anS. coelicolorstrain expressing MacR-Flag fusion protein, identifiedin vivotargets of MacR, and DNase I footprinting of these targets revealed a consensus sequence for MacR binding, TGAGTACnnGTACTCA, containing two 7-bp inverted repeats. A genome-wide search revealed sites identical or highly similar to this consensus sequence upstream of six genes encoding putative membrane proteins or lipoproteins. These predicted sites were confirmed as MacR binding sites by DNase I footprinting and electrophoretic mobility shift assaysin vitroand by ChIP-quantitative PCRin vivo, and transcriptional analyses demonstrated that MacR significantly impacts expression of these target genes. Disruption of three of these genes,sco6728,sco4924, andsco4011, markedly accelerated aerial mycelium formation, indicating that their gene products are novel morphogenic factors. Two-hybrid assays indicated that these three proteins, which we have named morphogenic membrane protein A (MmpA; SCO6728), MmpB (SCO4924), and MmpC (SCO4011), interact with one another and with the putative membrane protein and MacR target SCO4225. Notably, SAV6081/82 and SVEN1780/81, homologs of MacRS TCS fromS. avermitilisandS. venezuelae, respectively, can substitute for MacRS, indicating functional conservation. Our findings reveal a role for MacRS in cellular morphogenesis and secondary metabolism inStreptomyces.IMPORTANCETCSs help bacteria adapt to environmental stresses by altering gene expression. However, the roles and corresponding regulatory mechanisms of most TCSs in theStreptomycesmodel strainS. coelicolorare unknown. We investigated the previously uncharacterized MacRS TCS and identified the core DNA recognition sequence, two seven-nucleotide inverted repeats, for the DNA-binding protein MacR. We further found that MacR directly controls a group of membrane proteins, including MmpA-C, which are novel morphogenic factors that delay formation of aerial mycelium. We also discovered that these membrane proteins interact with one another and that otherStreptomycesspecies have conserved MacRS homologs. Our findings suggest a conserved role for MacRS in morphogenesis and/or other membrane-associated activities. Additionally, our study showed that MacRS impacts, albeit indirectly, the production of the signature metabolite actinorhodin, further suggesting that MacRS and its homologs function as novel pleiotropic regulatory systems inStreptomyces.

scholarly journals In Vivo Efficacy and Pharmacokinetics of the 2-Aminomethylphenol Antimalarial JPC-3210 in the Aotus Monkey-Human Malaria Model

2019 ◽  
Vol 64 (3) ◽  
Author(s):  
Fiona J. McCallum ◽  
Geoffrey W. Birrell ◽  
Marina Chavchich ◽  
Ivor Harris ◽  
Nicanor Obaldia ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Oral Dose ◽  
In Vivo Efficacy ◽  
Content Type ◽  
Treatment And Prevention ◽  
Elimination Half ◽  
Long Acting ◽  
Further Development ◽  
Malaria Model

ABSTRACT Nonimmune Aotus monkeys infected with Plasmodium falciparum and Plasmodium vivax were cured of their infections when treated with a single oral dose of 5 mg/kg and 10 mg/kg of the 2-aminomethylphenol, JPC-3210, respectively. Corresponding mean blood elimination half-lives of JPC-3210 were lengthy at 19.1 days and 20.5 days, respectively. This in vivo potency and lengthy half-life supports the further development of JPC-3210 as a promising, long-acting blood schizontocidal antimalarial for malaria treatment and prevention.

scholarly journals Computational Chemogenomics Drug Repositioning Strategy Enables the Discovery of Epirubicin as a New Repurposed Hit for Plasmodium falciparum and P. vivax

2020 ◽  
Vol 64 (9) ◽  
Author(s):  
Letícia Tiburcio Ferreira ◽  
Juliana Rodrigues ◽  
Gustavo Capatti Cassiano ◽  
Tatyana Almeida Tavella ◽  
Kaira Cristina Peralis Tomaz ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
In Silico ◽  
Antimalarial Activity ◽  
Drug Repositioning ◽  
Dna Gyrase ◽  
Plasmodium Yoelii ◽  
Computer Assisted ◽  
Content Type

ABSTRACT Widespread resistance against antimalarial drugs thwarts current efforts for controlling the disease and urges the discovery of new effective treatments. Drug repositioning is increasingly becoming an attractive strategy since it can reduce costs, risks, and time-to-market. Herein, we have used this strategy to identify novel antimalarial hits. We used a comparative in silico chemogenomics approach to select Plasmodium falciparum and Plasmodium vivax proteins as potential drug targets and analyzed them using a computer-assisted drug repositioning pipeline to identify approved drugs with potential antimalarial activity. Among the seven drugs identified as promising antimalarial candidates, the anthracycline epirubicin was selected for further experimental validation. Epirubicin was shown to be potent in vitro against sensitive and multidrug-resistant P. falciparum strains and P. vivax field isolates in the nanomolar range, as well as being effective against an in vivo murine model of Plasmodium yoelii. Transmission-blocking activity was observed for epirubicin in vitro and in vivo. Finally, using yeast-based haploinsufficiency chemical genomic profiling, we aimed to get insights into the mechanism of action of epirubicin. Beyond the target predicted in silico (a DNA gyrase in the apicoplast), functional assays suggested a GlcNac-1-P-transferase (GPT) enzyme as a potential target. Docking calculations predicted the binding mode of epirubicin with DNA gyrase and GPT proteins. Epirubicin is originally an antitumoral agent and presents associated toxicity. However, its antiplasmodial activity against not only P. falciparum but also P. vivax in different stages of the parasite life cycle supports the use of this drug as a scaffold for hit-to-lead optimization in malaria drug discovery.

scholarly journals Pyrimidine tracts between the 5' splice site and branch point facilitate splicing and recognition of a small Drosophila intron.

1997 ◽  
Vol 17 (5) ◽  
pp. 2774-2780 ◽  
Author(s):  
C F Kennedy ◽  
S M Berget
Keyword(s):  
Drosophila Melanogaster ◽  
Branch Point ◽  
Splice Site ◽  
Minimum Size ◽  
Cross Linking ◽  
In Vitro Splicing ◽  
Precursor Rna ◽  
Minimal Region

The minimum size for splicing of a vertebrate intron is approximately 70 nucleotides. In Drosophila melanogaster, more than half of the introns are significantly below this minimum yet function well. Such short introns often lack the pyrimidine tract located between the branch point and 3' splice site common to metazoan introns. To investigate if small introns contain special sequences that facilitate their recognition, the sequences and factors required for the splicing of a 59-nucleotide intron from the D. melanogaster mle gene have been examined. This intron contains only a minimal region of interrupted pyrimidines downstream of the branch point. Instead, two longer, uninterrupted C-rich tracts are located between the 5' splice site and branch point. Both of these sequences are required for maximal in vivo and in vitro splicing. The upstream sequences are also required for maximal binding of factors to the 5' splice site, cross-linking of U2AF to precursor RNA, and assembly of the active spliceosome, suggesting that sequences upstream of the branch point influence events at both ends of the small mle intron. Thus, a very short intron lacking a classical pyrimidine tract between the branch point and 3' splice site requires accessory pyrimidine sequences in the short region between the 5' splice site and branch point.

scholarly journals Multiple cis-acting sequence elements are required for efficient splicing of simian virus 40 small-t antigen pre-mRNA.

1988 ◽  
Vol 8 (9) ◽  
pp. 3582-3590 ◽  
Author(s):  
X Y Fu ◽  
J D Colgan ◽  
J L Manley
Keyword(s):  
Alternative Splicing ◽  
Branch Point ◽  
Splice Site ◽  
Simian Virus 40 ◽  
Simian Virus ◽  
T Antigen ◽  
Specific Sequence ◽  
Small T Antigen

We have determined the effects of a number of mutations in the small-t antigen mRNA intron on the alternative splicing pattern of the simian virus 40 early transcript. Expansion of the distance separating the small-t pre-mRNA lariat branch point and the shared large T-small t 3' splice site from 18 to 29 nucleotides (nt) resulted in a relative enhancement of small-t splicing in vivo. This finding, coupled with the observation that large-T pre-RNA splicing in vitro was not affected by this expansion, suggests that small-t splicing is specifically constrained by a short branch point-3' splice site distance. Similarly, the distance separating the 5' splice site and branch point (48 nt) was found to be at or near a minimum for small-t splicing, because deletions in this region as small as 2 nt dramatically reduced the ratio of small-t to large-T mRNA that accumulated in transfected cells. Finally, a specific sequence within the small-t intron, encompassing the upstream branch sites used in large-T splicing, was found to be an important element in the cell-specific pattern of early alternative splicing. Substitutions within this region reduced the ratio of small-t to large-T mRNA produced in HeLa cells but had only minor effects in human 293 cells.

scholarly journals Interaction between the Negative Regulator of Splicing Element and a 3′ Splice Site: Requirement for U1 Small Nuclear Ribonucleoprotein and the 3′ Splice Site Branch Point/Pyrimidine Tract

1999 ◽  
Vol 73 (3) ◽  
pp. 2394-2400 ◽  
Author(s):  
Craig R. Cook ◽  
Mark T. McNally
Keyword(s):  
Branch Point ◽  
Splice Site ◽  
Rna Splicing ◽  
Nuclear Extract ◽  
Negative Regulator ◽  
Rous Sarcoma ◽  
Small Nuclear Ribonucleoprotein ◽  
A Minor

ABSTRACT The negative regulator of splicing (NRS) from Rous sarcoma virus suppresses viral RNA splicing and is one of several ciselements that account for the accumulation of large amounts of unspliced RNA for use as gag-pol mRNA and progeny virion genomic RNA. The NRS can also inhibit splicing of heterologous introns in vivo and in vitro. Previous data showed that the splicing factors SF2/ASF and U1, U2, and U11 small nuclear ribonucleoproteins (snRNPs) bind the NRS, and a correlation was established between SF2/ASF and U11 binding and activity, suggesting that these factors are important for function. These observations, and the finding that a large spliceosome-like complex (NRS-C) assembles on NRS RNA in nuclear extract, led to the proposal that the NRS is recognized as a minor-class 5′ splice site. One model to explain NRS splicing inhibition holds that the NRS interacts nonproductively with and sequesters U2-dependent 3′ splice sites. In this study, we provide evidence that the NRS interacts with an adenovirus 3′ splice site. The interaction was dependent on the integrity of the branch point and pyrimidine tract of the 3′ splice site, and it was sensitive to a mutation that was previously shown to abolish U11 snRNP binding and NRS function. However, further mutational analyses of NRS sequences have identified a U1 binding site that overlaps the U11 site, and the interaction with the 3′ splice site correlated with U1, not U11, binding. These results show that the NRS can interact with a 3′ splice site and suggest that U1 is of primary importance for NRS splicing inhibition.

scholarly journals The Mu Subunit of Plasmodium falciparum Clathrin-Associated Adaptor Protein 2 ModulatesIn VitroParasite Response to Artemisinin and Quinine

2015 ◽  
Vol 59 (5) ◽  
pp. 2540-2547 ◽  
Author(s):  
Gisela Henriques ◽  
Donelly A. van Schalkwyk ◽  
Rebekah Burrow ◽  
David C. Warhurst ◽  
Eloise Thompson ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Adaptor Protein ◽  
Content Type ◽  
Artemisinin Derivatives ◽  
Combination Treatments ◽  
Antimalarial Resistance ◽  
Transgenic Parasites ◽  
Multiple Drugs

ABSTRACTThe emergence of drug-resistant parasites is a serious threat faced by malaria control programs. Understanding the genetic basis of resistance is critical to the success of treatment and intervention strategies. A novel locus associated with antimalarial resistance,ap2-mu(encoding the mu chain of the adaptor protein 2 [AP2] complex), was recently identified in studies on the rodent malaria parasitePlasmodium chabaudi(pcap2-mu). Furthermore, analysis in Kenyan malaria patients of polymorphisms in thePlasmodium falciparumap2-muhomologue,pfap2-mu, found evidence that differences in the amino acid encoded by codon 160 are associated with enhanced parasite survivalin vivofollowing combination treatments which included artemisinin derivatives. Here, we characterize the role ofpfap2-muin mediating thein vitroantimalarial drug response ofP. falciparumby generating transgenic parasites constitutively expressing codon 160 encoding either the wild-type Ser (Ser160) or the Asn mutant (160Asn) form ofpfap2-mu. Transgenic parasites carrying thepfap2-mu160Asn allele were significantly less sensitive to dihydroartemisinin using a standard 48-hin vitrotest, providing direct evidence of an altered parasite response to artemisinin. Our data also provide evidence thatpfap2-muvariants can modulate parasite sensitivity to quinine. No evidence was found thatpfap2-muvariants contribute to the slow-clearance phenotype exhibited byP. falciparumin Cambodian patients treated with artesunate monotherapy. These findings provide compelling evidence thatpfap2-mucan modulateP. falciparumresponses to multiple drugs. We propose that this gene should be evaluated further as a potential molecular marker of antimalarial resistance.

scholarly journals Mapping of branch sites in trans-spliced pre-mRNAs of Trypanosoma brucei.

1989 ◽  
Vol 9 (10) ◽  
pp. 4291-4297 ◽  
Author(s):  
E Patzelt ◽  
K L Perry ◽  
N Agabian
Keyword(s):  
Trypanosoma Brucei ◽  
Branch Point ◽  
Splice Site ◽  
Mammalian Cells ◽  
Branch Points ◽  
Beta Tubulin ◽  
Alpha Tubulin ◽  
Phosphodiester Bond ◽  
Trans Splicing ◽  
Covalently Linked

The process of trans splicing is essential to the maturation of all mRNAs in the Trypanosomatidae, a family of protozoan parasites, and to specific mRNAs in several species of nematode. In Trypanosoma brucei, a 39-nucleotide (nt) leader sequence originating from a small, 139-nt donor RNA (the spliced leader [SL] RNA) is spliced to the 5' end of mRNAs. An intermediate in this trans-splicing process is a Y structure which contains the 3' 100 nt of the SL RNA covalently linked to the pre-mRNA via a 2'-5' phosphodiester bond at the branch point residue. We mapped the branch points in T. brucei alpha- and beta-tubulin pre-mRNAs. The primary branch acceptors for the alpha- and beta-tubulins are 44 and 56 nt upstream of the 3' splice sites, respectively, and are A residues. Minor branch acceptors were detected 42 and 49 nt upstream of the alpha-tubulin splice site and 58 nt upstream of the splice site in beta-tubulin. The regions surrounding these branch points lack homology to the consensus sequences determined for mammalian cells and yeasts; there is also no conservation among the sequences themselves. Thus, the identified sequences suggest that the mechanism of branch point recognition in T. brucei differs from the mechanism of recognition by U2 RNA that has been proposed for other eucaryotes.

scholarly journals In VitroandIn VivoAntimalarial Activities of T-2307, a Novel Arylamidine

2012 ◽  
Vol 56 (4) ◽  
pp. 2191-2193 ◽  
Author(s):  
Akiko Kimura ◽  
Hiroshi Nishikawa ◽  
Nobuhiko Nomura ◽  
Junichi Mitsuyama ◽  
Shinya Fukumoto ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Body Weight ◽  
Broad Spectrum ◽  
Antimalarial Activity ◽  
Liver Stage ◽  
Rodent Malaria ◽  
Content Type ◽  
Clinically Significant

ABSTRACTT-2307, a novel arylamidine, has been shown to exhibit broad-spectrum antifungal activities against clinically significant pathogens. Here, we evaluated thein vitroandin vivoantimalarial activity of T-2307. The 50% inhibitory concentrations (IC50s) of T-2307 againstPlasmodium falciparumFCR-3 and K-1 strains were 0.47 and 0.17 μM, respectively. T-2307 at 2.5 to 10 mg/kg of body weight/day exhibited activity against blood stage and liver stage parasites in rodent malaria models. In conclusion, T-2307 exhibitedin vitroandin vivoantimalarial activity.

scholarly journals The Plasmodium falciparum Cell-Traversal Protein for Ookinetes and Sporozoites as a Candidate for Preerythrocytic and Transmission-Blocking Vaccines

2016 ◽  
Vol 85 (2) ◽  
Author(s):  
Diego A. Espinosa ◽  
Joel Vega-Rodriguez ◽  
Yevel Flores-Garcia ◽  
Amy R. Noe ◽  
Christian Muñoz ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Monoclonal Antibodies ◽  
Immune Responses ◽  
Passive Immunization ◽  
Content Type ◽  
Adjuvant System ◽  
Neutralizing Capacity ◽  
Important Evidence ◽  
Transmission Blocking Vaccines

ABSTRACT Recent studies have shown that immune responses against the cell-traversal protein for Plasmodium ookinetes and sporozoites (CelTOS) can inhibit parasite infection. While these studies provide important evidence toward the development of vaccines targeting this protein, it remains unknown whether these responses could engage the Plasmodium falciparum CelTOS in vivo. Using a newly developed rodent malaria chimeric parasite expressing the P. falciparum CelTOS (PfCelTOS), we evaluated the protective effect of in vivo immune responses elicited by vaccination and assessed the neutralizing capacity of monoclonal antibodies specific against PfCelTOS. Mice immunized with recombinant P. falciparum CelTOS in combination with the glucopyranosyl lipid adjuvant-stable emulsion (GLA-SE) or glucopyranosyl lipid adjuvant-liposome-QS21 (GLA-LSQ) adjuvant system significantly inhibited sporozoite hepatocyte infection. Notably, monoclonal antibodies against PfCelTOS strongly inhibited oocyst development of P. falciparum and Plasmodium berghei expressing PfCelTOS in Anopheles gambiae mosquitoes. Taken together, our results demonstrate that anti-CelTOS responses elicited by vaccination or passive immunization can inhibit sporozoite and ookinete infection and impair vector transmission.

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