scholarly journals Functional characterization of 5′ UTR cis-acting sequence elements that modulate translational efficiency in Plasmodium falciparum and humans

2022 ◽  
Vol 21 (1) ◽  
Author(s):  
Valentina E. Garcia ◽  
Rebekah Dial ◽  
Joseph L. DeRisi
Keyword(s):  
Plasmodium Falciparum ◽  
Translational Regulation ◽  
Base Composition ◽  
Functional Characterization ◽  
In Vitro Translation ◽  
Untranslated Regions ◽  
Model Organisms ◽  
Translational Efficiency ◽  
Regulatory Sequences ◽  
The Impact

Abstract Background The eukaryotic parasite Plasmodium falciparum causes millions of malarial infections annually while drug resistance to common anti-malarials is further confounding eradication efforts. Translation is an attractive therapeutic target that will benefit from a deeper mechanistic understanding. As the rate limiting step of translation, initiation is a primary driver of translational efficiency. It is a complex process regulated by both cis and trans acting factors, providing numerous potential targets. Relative to model organisms and humans, P. falciparum mRNAs feature unusual 5′ untranslated regions suggesting cis-acting sequence complexity in this parasite may act to tune levels of protein synthesis through their effects on translational efficiency. Methods Here, in vitro translation is deployed to compare the role of cis-acting regulatory sequences in P. falciparum and humans. Using parasite mRNAs with high or low translational efficiency, the presence, position, and termination status of upstream “AUG”s, in addition to the base composition of the 5′ untranslated regions, were characterized. Results The density of upstream “AUG”s differed significantly among the most and least efficiently translated genes in P. falciparum, as did the average “GC” content of the 5′ untranslated regions. Using exemplars from highly translated and poorly translated mRNAs, multiple putative upstream elements were interrogated for impact on translational efficiency. Upstream “AUG”s were found to repress translation to varying degrees, depending on their position and context, while combinations of upstream “AUG”s had non-additive effects. The base composition of the 5′ untranslated regions also impacted translation, but to a lesser degree. Surprisingly, the effects of cis-acting sequences were remarkably conserved between P. falciparum and humans. Conclusions While translational regulation is inherently complex, this work contributes toward a more comprehensive understanding of parasite and human translational regulation by examining the impact of discrete cis-acting features, acting alone or in context.

scholarly journals ­ Functional Characterization of 5’ UTR Cis-Acting Sequence Elements That Modulate Translational Efficiency in P. Falciparum and Humans

2021 ◽  
Author(s):  
Valentina E. Garcia ◽  
Rebekah Dial ◽  
Joseph L DeRisi
Keyword(s):  
Translational Regulation ◽  
Base Composition ◽  
Functional Characterization ◽  
Gc Content ◽  
Untranslated Regions ◽  
Model Organisms ◽  
Translational Efficiency ◽  
Regulatory Sequences ◽  
The Impact

Abstract BackgroundThe eukaryotic parasite Plasmodium falciparum causes millions of malarial infections annually while drug resistance to common antimalarials is further confounding eradication efforts. Translation is an attractive therapeutic target that will benefit from a deeper mechanistic understanding. As the rate limiting step of translation, initiation is a primary driver of translational efficiency. It is a complex process regulated by both cis and trans acting factors, providing numerous potential targets. Relative to model organisms and humans, P. falciparum mRNAs feature unusual 5’ untranslated regions suggesting cis-acting sequence complexity in this parasite may act to tune levels of protein synthesis through their effects on translational efficiency. MethodsHere, we deployed in vitro translation to compare the role of cis-acting regulatory sequences in P. falciparum and humans. Using parasite mRNAs with high or low translational efficiency, the presence, position, and termination status of upstream “AUG”s, in addition to the base composition of the 5’ untranslated regions, were characterized. ResultsThe density of upstream “AUG”s differed significantly among the most and least efficiently translated genes in P. falciparum, as did the average “GC” content of the 5’ untranslated regions. Using exemplars from highly translated and poorly translated mRNAs, multiple putative upstream elements were interrogated for impact on translational efficiency. Upstream “AUG”s were found to repress translation to varying degrees, depending on their position and context, while combinations of upstream “AUG”s had nonadditive effects. The base composition of the 5’ untranslated regions also impacted translation, but to a lesser degree. Surprisingly, the effects of cis-acting sequences were remarkably conserved between P. falciparum and humans. ConclusionWhile translational regulation is inherently complex, this work contributes toward a more comprehensive understanding of parasite and human translational regulation by examining the impact of discrete cis-acting features, acting alone or in context.

scholarly journals Functional characterization of 5’ UTR cis-acting sequence elements that modulate translational efficiency in P. falciparum and humans

2021 ◽  
Author(s):  
Valentina E. Garcia ◽  
Rebekah Dial ◽  
Joseph L. DeRisi
Keyword(s):  
Translational Regulation ◽  
Base Composition ◽  
Functional Characterization ◽  
Protein Translation ◽  
Untranslated Regions ◽  
Translational Efficiency ◽  
Regulatory Sequences ◽  
Termination Status ◽  
The Impact

AbstractThe eukaryotic parasite Plasmodium falciparum causes millions of malarial infections annually and drug resistance to common antimalarials confounds eradication efforts. Protein translation is an attractive therapeutic target that will benefit from a deeper mechanistic understanding. Translation initiation drives translational efficiency and is regulated by both cis and trans acting factors. P. falciparum mRNAs feature unusual 5’ untranslated regions suggesting that cis-acting sequences could play a significant role in determining translational efficiency. Here, we deployed in vitro translation to compare the role of cis-acting regulatory sequences in P. falciparum and humans. Using parasite mRNAs with high or low translational efficiency, the presence, position, and termination status of upstream start site, in addition to the base composition of the 5’ untranslated regions, were characterized. Within 130 nucleotide 5’ untranslated regions, upstream start sites were generally repressive but exhibited a nonadditive effect when combined, while the base composition of the two mRNAs demonstrated a more subtle role in regulating translational efficacy. Surprisingly, the effects of cis-acting sequences were remarkably conserved between P. falciparum and humans. While translational regulation is inherently complex, this work contributes toward a more comprehensive understanding of parasite and human translational regulation by examining the impact of discreet cis-acting features.

scholarly journals Protein trafficking in Plasmodium falciparum-infected red cells and impact of the expansion of exported protein families

Parasitology ◽  
2014 ◽  
Vol 141 (12) ◽  
pp. 1533-1543 ◽  
Author(s):  
SURENDRA K. PRAJAPATI ◽  
RICHARD CULLETON ◽  
OM P. SINGH
Keyword(s):  
Plasmodium Falciparum ◽  
Host Cell ◽  
Protein Trafficking ◽  
Malaria Parasite ◽  
Functional Characterization ◽  
Gene Families ◽  
Red Cells ◽  
Protein Families ◽  
The Impact ◽  
Export Signal

SUMMARYErythrocytes are extensively remodelled by the malaria parasite following invasion of the cell. Plasmodium falciparum encodes numerous virulence-associated and host-cell remodelling proteins that are trafficked to the cytoplasm, the cell membrane and the surface of the infected erythrocyte. The export of soluble proteins relies on a sequence directing entry into the secretory pathways in addition to an export signal. The export signal consisting of five amino acids is termed the Plasmodium export element (PEXEL) or the vacuole transport signal (VTS). Genome mining studies have revealed that PEXEL/VTS carrying protein families have expanded dramatically in P. falciparum compared with other malaria parasite species, possibly due to lineage-specific expansion linked to the unique requirements of P. falciparum for host-cell remodelling. The functional characterization of such genes and gene families may reveal potential drug targets that could inhibit protein trafficking in infected erythrocytes. This review highlights some of the recent advances and key knowledge gaps in protein trafficking pathways in P. falciparum-infected red cells and speculates on the impact of exported gene families in the trafficking pathway.

scholarly journals Redesigned TetR-Aptamer System To Control Gene Expression in Plasmodium falciparum

mSphere ◽  
2020 ◽  
Vol 5 (4) ◽  
Author(s):  
Krithika Rajaram ◽  
Hans B. Liu ◽  
Sean T. Prigge
Keyword(s):  
Gene Expression ◽  
Plasmodium Falciparum ◽  
Target Gene ◽  
Essential Genes ◽  
Untranslated Regions ◽  
Dependent Manner ◽  
Control Of Gene Expression ◽  
Content Type ◽  
Target Gene Expression ◽  
The Impact

ABSTRACT One of the most powerful approaches to understanding gene function involves turning genes on and off at will and measuring the impact at the cellular or organismal level. This particularly applies to the cohort of essential genes where traditional gene knockouts are inviable. In Plasmodium falciparum, conditional control of gene expression has been achieved by using multicomponent systems in which individual modules interact with each other to regulate DNA recombination, transcription, or posttranscriptional processes. The recently devised TetR-DOZI aptamer system relies on the ligand-regulatable interaction of a protein module with synthetic RNA aptamers to control the translation of a target gene. This technique has been successfully employed to study essential genes in P. falciparum and involves the insertion of several aptamer copies into the 3′ untranslated regions (UTRs), which provide control over mRNA fate. However, aptamer repeats are prone to recombination and one or more copies can be lost from the system, resulting in a loss of control over target gene expression. We rectified this issue by redesigning the aptamer array to minimize recombination while preserving the control elements. As proof of concept, we compared the original and modified arrays for their ability to knock down the levels of a putative essential apicoplast protein (PF3D7_0815700) and demonstrated that the modified array is highly stable and efficient. This redesign will enhance the utility of a tool that is quickly becoming a favored strategy for genetic studies in P. falciparum. IMPORTANCE Malaria elimination efforts have been repeatedly hindered by the evolution and spread of multidrug-resistant strains of Plasmodium falciparum. The absence of a commercially available vaccine emphasizes the need for a better understanding of Plasmodium biology in order to further translational research. This has been partly facilitated by targeted gene deletion strategies for the functional analysis of parasite genes. However, genes that are essential for parasite replication in erythrocytes are refractory to such methods, and require conditional knockdown or knockout approaches to dissect their function. One such approach is the TetR-DOZI system that employs multiple synthetic aptamers in the untranslated regions of target genes to control their expression in a tetracycline-dependent manner. Maintaining modified parasites with intact aptamer copies has been challenging since these repeats can be lost by recombination. By interspacing the aptamers with unique sequences, we created a stable genetic system that remains effective at controlling target gene expression.

scholarly journals Translational regulation of the cell cycle: when, where, how and why?

2011 ◽  
Vol 366 (1584) ◽  
pp. 3638-3652 ◽  
Author(s):  
Iva Kronja ◽  
Terry L. Orr-Weaver
Keyword(s):  
Cell Cycle ◽  
Translational Control ◽  
Translational Regulation ◽  
Cell Cycle Progression ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Early Embryogenesis ◽  
Model Organisms ◽  
Translational Efficiency ◽  
Cell Cycle Regulators

Translational regulation contributes to the control of archetypal and specialized cell cycles, such as the meiotic and early embryonic cycles. Late meiosis and early embryogenesis unfold in the absence of transcription, so they particularly rely on translational repression and activation of stored maternal mRNAs. Here, we present examples of cell cycle regulators that are translationally controlled during different cell cycle and developmental transitions in model organisms ranging from yeast to mouse. Our focus also is on the RNA-binding proteins that affect cell cycle progression by recognizing special features in untranslated regions of mRNAs. Recent research highlights the significance of the cytoplasmic polyadenylation element-binding protein (CPEB). CPEB determines polyadenylation status, and consequently translational efficiency, of its target mRNAs in both transcriptionally active somatic cells as well as in transcriptionally silent mature Xenopus oocytes and early embryos. We discuss the role of CPEB in mediating the translational timing and in some cases spindle-localized translation of critical regulators of Xenopus oogenesis and early embryogenesis. We conclude by outlining potential directions and approaches that may provide further insights into the translational control of the cell cycle.

scholarly journals A redesigned TetR-aptamer system to control gene expression in Plasmodium falciparum

2020 ◽  
Author(s):  
Krithika Rajaram ◽  
Hans B. Liu ◽  
Sean T. Prigge
Keyword(s):  
Gene Expression ◽  
Plasmodium Falciparum ◽  
Target Gene ◽  
Dna Recombination ◽  
Essential Genes ◽  
Untranslated Regions ◽  
Dependent Manner ◽  
Control Of Gene Expression ◽  
Target Gene Expression ◽  
The Impact

AbstractOne of the most powerful approaches to understanding gene function involves turning genes on and off at will and measuring the impact at the cellular or organismal level. This particularly applies to the cohort of essential genes where traditional gene knockouts are inviable. In Plasmodium falciparum, conditional control of gene expression has been achieved by using multi-component systems in which individual modules interact with each other to regulate DNA recombination, transcription or posttranscriptional processes. The recently devised TetR-DOZI aptamer system relies on the ligand-regulatable interaction of a protein module with synthetic RNA aptamers to control the translation of a target gene. This technique has been successfully employed to study essential genes in P. falciparum and involves the insertion of several aptamer copies into their 3’ untranslated regions (UTRs) which provide control over mRNA fate. However, aptamer repeats are prone to recombination and one or more copies can be lost from the system, resulting in a loss of control over target gene expression. We rectified this issue by redesigning the aptamer array to minimize recombination while preserving the control elements. As proof of concept, we compared the original and modified arrays for their ability to knock down the levels of a putative essential apicoplast protein (PF3D7_0815700) and demonstrated that the modified array is highly stable and efficient. This redesign will enhance the utility of a tool that is quickly becoming a favored strategy for genetic studies in P. falciparum.ImportanceMalaria elimination efforts have been repeatedly hindered by the evolution and spread of multidrug-resistant strains of Plasmodium falciparum. The absence of a commercially available vaccine emphasizes the need for a better understanding of Plasmodium biology in order to further translational research. This has been partly facilitated by targeted gene deletion strategies for the functional analysis of parasite genes. However, genes that are essential for parasite replication in erythrocytes are refractory to such methods, and require conditional knockdown or knockout approaches to dissect their function. One such approach is the TetR-DOZI system that employs multiple synthetic aptamers in the untranslated regions of target genes to control their expression in a tetracycline-dependent manner. Maintaining modified parasites with intact aptamer copies has been challenging since these repeats are frequently lost by recombination. By interspacing the aptamers with unique sequences, we created a stable genetic system that remains effective at controlling target gene expression.

scholarly journals Impact of Environmental Stressors on Gene Expression in the Embryo of the Italian Wall Lizard

2021 ◽  
Vol 11 (11) ◽  
pp. 4723
Author(s):  
Rosaria Scudiero ◽  
Chiara Maria Motta ◽  
Palma Simoniello
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Membrane Trafficking ◽  
Translational Regulation ◽  
Cellular Protection ◽  
Terrestrial Vertebrate ◽  
Expression Of Genes ◽  
Stress Changes ◽  
Probable Consequence ◽  
The Impact

The cleidoic eggs of oviparous reptiles are protected from the external environment by membranes and a parchment shell permeable to water and dissolved molecules. As a consequence, not only physical but also chemical insults can reach the developing embryos, interfering with gene expression. This review provides information on the impact of the exposure to cadmium contamination or thermal stress on gene expression during the development of Italian wall lizards of the genus Podarcis. The results obtained by transcriptomic analysis, although not exhaustive, allowed to identify some stress-reactive genes and, consequently, the molecular pathways in which these genes are involved. Cadmium-responsive genes encode proteins involved in cellular protection, metabolism and proliferation, membrane trafficking, protein interactions, neuronal transmission and plasticity, immune response, and transcription regulatory factors. Cold stress changes the expression of genes involved in transcriptional/translational regulation and chromatin remodeling and inhibits the transcription of a histone methyltransferase with the probable consequence of modifying the epigenetic control of DNA. These findings provide transcriptome-level evidence of how terrestrial vertebrate embryos cope with stress, giving a key to use in population survival and environmental change studies. A better understanding of the genes contributing to stress tolerance in vertebrates would facilitate methodologies and applications aimed at improving resistance to unfavourable environments.

scholarly journals The malaria burden of Amerindian groups of three Venezuelan states: a descriptive study based on programmatic data

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Juan C. Gabaldón-Figueira ◽  
Carlos Chaccour ◽  
Jorge Moreno ◽  
Maria Villegas ◽  
Leopoldo Villegas
Keyword(s):  
Risk Factors ◽  
Plasmodium Falciparum ◽  
Malaria Incidence ◽  
Hot Spot ◽  
Public Health Problem ◽  
Epidemiological Data ◽  
Descriptive Study ◽  
Malaria Burden ◽  
Indigenous Groups ◽  
The Impact

Abstract Background Fifty-three percent of all cases of malaria in the Americas in 2019 came from Venezuela, where the epidemic is heavily focused south of the Orinoco river, and where most of the country’s Amerindian groups live. Although the disease is known to represent a significant public health problem among these populations, little epidemiological data exists on the subject. This study aims to provide information on malaria incidence, geospatial clustering, and risk factors associated to Plasmodium falciparum infection among these groups. Methods This is a descriptive study based on the analysis of published and unpublished programmatic data collected by Venezuelan health authorities and non-government organizations between 2014 and 2018. The Annual Parasite Index among indigenous groups (API-i) in municipalities of three states (Amazonas, Bolivar, and Sucre) were calculated and compared using the Kruskal Wallis test, risk factors for Plasmodium falciparum infection were identified via binomial logistic regression and maps were constructed to identify clusters of malaria cases among indigenous patients via Moran’s I and Getis-Ord’s hot spot analysis. Results 116,097 cases of malaria in Amerindian groups were registered during the study period. An increasing trend was observed between 2014 and 2016 but reverted in 2018. Malaria incidence remains higher than in 2014 and hot spots were identified in the three states, although more importantly in the south of Bolivar. Most cases (73.3%) were caused by Plasmodium vivax, but the Hoti, Yanomami, and Eñepa indigenous groups presented higher odds for infection with Plasmodium falciparum. Conclusion Malaria cases among Amerindian populations increased between 2014 and 2018 and seem to have a different geographic distribution than those among the general population. These findings suggest that tailored interventions will be necessary to curb the impact of malaria transmission in these groups.

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