In silico guided reconstruction and analysis of ICAM-1-binding var genes from Plasmodium falciparum

Carrington, Eilidh; Otto, Thomas D.; Szestak, Tadge; Lennartz, Frank; Higgins, Matthew K.; Newbold, Chris; Craig, Alister G.

doi:10.1038/s41598-018-21591-8

Cited by 4 publications

(11 citation statements)

References 60 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2 C ). This cluster complements a hydrophobic patch on ICAM-1 D1 which has previously been identified as important for ICAM-1 binding by B-type PfEMP1 (27, 35, 36).…”

Section: Resultsmentioning

confidence: 71%

“…We first performed an updated phylogenetic analysis of all DBLβ domains that have been tested for the ability to bind to ICAM-1 ( SI Appendix , Table S1). Since publication of similar analyses, in which the only available B- and C-type PfEMP1 sequences were from the IT4 strain of P. falciparum (22, 26, 28), 3 ICAM-1 binding DBLβ domains from non-IT4 group B and C PfEMP1 have been identified (27). Inclusion of these sequences confirmed the clustering of A-type ICAM-1 binding domains observed earlier and showed that ICAM-1 binding domains from group B and C PfEMP1 mostly form a separate, albeit less well-defined, cluster (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…4 A and B ). To test whether these residues are equivalent in function to the hydrophobic patch in IT4var13, we introduced mutations into the DBLβ domain of the C-type PfEMP1 J1a (27) and tested their effect on binding to ICAM-1 by SPR. With the exception of L1093D, these mutations reduced binding and affinity by 2- to 20-fold, which was not due to the disruption of the overall fold of the domain, as verified by CD spectroscopy and thermal melt experiments (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…However, finding a correlation between expression of PfEMP1 that bind to ICAM-1 and malaria outcome has been much more challenging, with conflicting results about whether ICAM-1 binding is linked to cerebral malaria (22–25). ICAM-1 binding is mediated by a subset of Duffy binding-like (DBL) domains, the DBLβ domains, which are found in either A-type or BC-type PfEMP1 (26–29). Recent studies showed that A-type PfEMP1 with an ICAM-1 binding DBLβ domain also contain a neighboring EPCR-binding CIDRα domain and that these dual-binding PfEMP1 are associated with cerebral malaria (22, 30, 31).…”

mentioning

confidence: 99%

See 3 more Smart Citations

Structural insights into diverse modes of ICAM-1 binding by Plasmodium falciparum -infected erythrocytes

Lennartz

Smith

Craig

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

A major determinant of pathogenicity in malaria caused by Plasmodium falciparum is the adhesion of parasite-infected erythrocytes to the vasculature or tissues of infected individuals. This occludes blood flow, leads to inflammation, and increases parasitemia by reducing spleen-mediated clearance of the parasite. This adhesion is mediated by PfEMP1, a multivariant family of around 60 proteins per parasite genome which interact with specific host receptors. One of the most common of these receptors is intracellular adhesion molecule-1 (ICAM-1), which is bound by 2 distinct groups of PfEMP1, A-type and B or C (BC)-type. Here, we present the structure of a domain from a B-type PfEMP1 bound to ICAM-1, revealing a complex binding site. Comparison with the existing structure of an A-type PfEMP1 bound to ICAM-1 shows that the 2 complexes share a globally similar architecture. However, while the A-type PfEMP1 bind ICAM-1 through a highly conserved binding surface, the BC-type PfEMP1 use a binding site that is more diverse in sequence, similar to how PfEMP1 interact with other human receptors. We also show that A- and BC-type PfEMP1 present ICAM-1 at different angles, perhaps influencing the ability of neighboring PfEMP1 domains to bind additional receptors. This illustrates the deep diversity of the PfEMP1 and demonstrates how variations in a single domain architecture can modulate binding to a specific ligand to control function and facilitate immune evasion.

show abstract

“…2 C ). This cluster complements a hydrophobic patch on ICAM-1 D1 which has previously been identified as important for ICAM-1 binding by B-type PfEMP1 (27, 35, 36).…”

Section: Resultsmentioning

confidence: 71%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Structural insights into diverse modes of ICAM-1 binding by Plasmodium falciparum -infected erythrocytes

Lennartz

Smith

Craig

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

show abstract

“…However, this strategy is currently limited to the already identified PfEMP1 domains and does not give proficiency of the expressed proteins. Recently, several strategies have been implemented to investigate the variability of full-length var genes using whole genome sequencing [6,26,27] or dedicated long range sequencing with a hybrid PCR approach [23]. In addition, Tonkin Hill et al performed de novo assembly of var genes issued from RNA sequencing (RNAseq) and identified transcripts up-regulated in severe malaria [28].…”

Section: Introductionmentioning

confidence: 99%

From genomic to LC-MS/MS evidence: Analysis of PfEMP1 in Benin malaria cases

Kamaliddin

Rombaut

Guillochon³

et al. 2019

PLoS ONE

View full text Add to dashboard Cite

Background PfEMP1 is the major protein from parasitic origin involved in the pathophysiology of severe malaria, and PfEMP1 domain subtypes are associated with the infection outcome. In addition, PfEMP1 variability is endless and current publicly available protein repositories do not reflect the high diversity of the sequences of PfEMP1 proteins. The identification of PfEMP1 protein sequences expressed with samples remains challenging. The aim of our study is to identify the different PfEMP1 proteins variants expressed within patient samples, and therefore identify PfEMP1 proteins domains expressed by patients presenting uncomplicated malaria or severe malaria in malaria endemic setting in Cotonou, Benin. Methods We performed a multi-omic approach to decipher PfEMP1 expression at the patient’s level in different clinical settings. Using a combination of whole genome sequencing approach and RNA sequencing, we were able to identify new PfEMP1 sequences and created a new custom protein database. This database was used for protein identification in mass spectrometry analysis. Results The differential expression analysis of RNAsequencing data shows an increased expression of the var domains transcripts DBLα1.7, DBLα1.1, DBLα2 and DBLβ12 in samples from patients suffering from Cerebral Malaria compared to Uncomplicated Malaria. Our approach allowed us to attribute PfEMP1 sequences to each sample and identify new peptides associated to PfEMP1 proteins in mass spectrometry. Conclusion We highlighted the diversity of the PfEMP1 sequences from field sample compared to reference sequences repositories and confirmed the validity of our approach. These findings should contribute to further vaccine development strategies based on PfEMP1 proteins.

show abstract

Varia: a tool for prediction, analysis and visualisation of variable genes

et al. 2022

Self Cite

View full text Add to dashboard Cite

Background Parasites use polymorphic gene families to evade the immune system or interact with the host. Assessing the diversity and expression of such gene families in pathogens can inform on the repertoire or host interaction phenotypes of clinical relevance. However, obtaining the sequences and quantifying their expression is a challenge. In Plasmodium falciparum, the highly polymorphic var genes encode the major virulence protein, PfEMP1, which bind a range of human receptors through varying combinations of DBL and CIDR domains. Here we present a tool, Varia, to predict near full-length gene sequences and domain compositions of query genes from database genes sharing short sequence tags. Varia generates output through two complementary pipelines. Varia_VIP returns all putative gene sequences and domain compositions of the query gene from any partial sequence provided, thereby enabling experimental validation of specific genes of interest and detailed assessment of their putative domain structure. Varia_GEM accommodates rapid profiling of var gene expression in complex patient samples from DBLα expression sequence tags (EST), by computing a sample overall transcript profile stratified by PfEMP1 domain types. Results Varia_VIP was tested querying sequence tags from all DBL domain types using different search criteria. On average 92% of query tags had one or more 99% identical database hits, resulting in the full-length query gene sequence being identified (> 99% identical DNA > 80% of query gene) among the five most prominent database hits, for ~ 33% of the query genes. Optimized Varia_GEM settings allowed correct prediction of > 90% of domains placed among the four most N-terminal domains, including the DBLα domain, and > 70% of C-terminal domains. With this accuracy, N-terminal domains could be predicted for > 80% of queries, whereas prediction rates of C-terminal domains dropped with the distance from the DBLα from 70 to 40%. Conclusion Prediction of var sequence and domain composition is possible from short sequence tags. Varia can be used to guide experimental validation of PfEMP1 sequences of interest and conduct high-throughput analysis of var type expression in patient samples.

show abstract

In silico guided reconstruction and analysis of ICAM-1-binding var genes from Plasmodium falciparum

Cited by 4 publications

References 60 publications

Structural insights into diverse modes of ICAM-1 binding by Plasmodium falciparum -infected erythrocytes

Structural insights into diverse modes of ICAM-1 binding by Plasmodium falciparum -infected erythrocytes

From genomic to LC-MS/MS evidence: Analysis of PfEMP1 in Benin malaria cases

Varia: a tool for prediction, analysis and visualisation of variable genes

Contact Info

Product

Resources

About