Author response for "Global distribution of single amino acid polymorphisms in Plasmodium vivax Duffy-binding-like domain and implications for vaccine development efforts"

Plasmodium vivax ( Pv ) malaria continues to be geographically widespread with approximately 15 million worldwide cases annually. Along with other proteins, Duffy-binding proteins (DBPs) are used by plasmodium for RBC invasion and the parasite-encoded receptor binding regions lie in their Duffy-binding-like (DBL) domains—thus making it a prime vaccine candidate. This study explores the sequence diversity in Pv DBL globally, with an emphasis on India as it remains a major contributor to the global Pv malaria burden. Based on 1358 Pv DBL protein sequences available in NCBI, we identified 140 polymorphic sites within 315 residues of Pv DBL. Alarmingly, country-wise mapping of SAAPs from field isolates revealed varied and distinct polymorphic profiles for different nations. We report here 31 polymorphic residue positions in the global SAAP profile, most of which map to the Pv DBL subdomain 2 ( α 1– α 6). A distinct clustering of SAAPs distal to the DARC-binding sites is indicative of immune evasive strategies by the parasite. Analyses of Pv DBL-neutralizing antibody complexes revealed that between 24% and 54% of interface residues are polymorphic. This work provides a framework to recce and expand the polymorphic space coverage in Pv DBLs as this has direct implications for vaccine development studies. It also emphasizes the significance of surveying global SAAP distributions before or alongside the identification of vaccine candidates.

Download Full-text

Maintenance of the Shigella sonnei virulence plasmid is dependent on its repertoire and amino acid sequence of toxin:antitoxin systems

Journal of Bacteriology ◽

10.1128/jb.00519-21 ◽

2022 ◽

Author(s):

Jessica E. Martyn ◽

Giulia Pilla ◽

Sarah Hollingshead ◽

Kristoffer S. Winther ◽

Susan Lea ◽

...

Keyword(s):

Amino Acid ◽

Vaccine Development ◽

Shigella Flexneri ◽

Amino Acid Sequences ◽

Shigella Sonnei ◽

Single Amino Acid ◽

Multi Drug Resistance ◽

Virulence Plasmid ◽

Closely Related Species ◽

Single Amino Acid Polymorphisms

Shigella sonnei is a major cause of bacillary dysentery, and of increasing concern due to the spread of multi-drug resistance. S. sonnei harbours pINV, a ∼ 210 kb plasmid that encodes a Type III secretion system (T3SS), which is essential for virulence. During growth in the laboratory, avirulence arises spontaneously in S. sonnei at high frequency, hampering studies on and vaccine development against this important pathogen. Here we investigated the molecular basis for the emergence of avirulence in S. sonnei , and show that avirulence mainly results from pINV loss, consistent with previous findings. Ancestral deletions have led to the loss from S. sonnei pINV of two toxin:antitoxin (TA) systems involved in plasmid maintenance, CcdAB and GmvAT, which are found on pINV in Shigella flexneri . We show that introduction of these TA systems into S. sonnei pINV reduced but did not eliminate pINV loss, while single amino acid polymorphisms found in the S. sonnei VapBC TA system compared with S. flexneri VapBC also contribute to pINV loss. Avirulence also results from deletions of T3SS-associated genes on pINV through recombination between insertion sequences (ISs) on the plasmid; these events differ from those observed in S. flexneri due to the different distribution and repertoire of ISs. Our findings demonstrate that TA systems and ISs influence plasmid dynamics and loss in S. sonnei , and could be exploited for the design and evaluation of vaccines. IMPORTANCE Shigella sonnei is the major cause of shigellosis in high-income and industrialising countries, and an emerging multi-drug resistant pathogen. A significant challenge when studying this bacterium is that it spontaneously becomes avirulent during growth in the laboratory, through loss of its virulence plasmid (pINV). Here we decipher the mechanisms leading to avirulence in S. sonnei and how the limited repertoire and amino acid sequences of plasmid-encoded toxin:antitoxin (TA) systems make the maintenance of pINV in this bacterium less efficient compared with Shigella flexneri . Our findings highlight how subtle differences in plasmids in closely-related species have marked effects and could be exploited to reduce plasmid loss in S. sonnei . This should facilitate research on this bacterium and vaccine development.

Download Full-text

Recent Advances in Predicting Functional Impact of Single Amino Acid Polymorphisms: A Review of Useful Features, Computational Methods and Available Tools

Current Bioinformatics ◽

10.2174/1574893611308020004 ◽

2013 ◽

Vol 8 (2) ◽

pp. 161-176 ◽

Cited By ~ 6

Author(s):

Mingjun Wang ◽

Zhongwei Sun ◽

Tatsuya Akutsu ◽

Jiangning Song

Keyword(s):

Amino Acid ◽

Computational Methods ◽

Single Amino Acid ◽

Functional Impact ◽

Recent Advances ◽

Single Amino Acid Polymorphisms

Download Full-text

Structures suggest an approach for converting weak self-peptide tumor antigens into superagonists for CD8 T cells in cancer

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2100588118 ◽

2021 ◽

Vol 118 (23) ◽

pp. e2100588118

Author(s):

Pengcheng Wei ◽

Kimberly R. Jordan ◽

Jonathan D. Buhrman ◽

Jun Lei ◽

Hexiang Deng ◽

...

Keyword(s):

T Cells ◽

Amino Acid ◽

T Cell ◽

Amino Acid Substitution ◽

Cd8 T Cells ◽

Tumor Antigens ◽

Vaccine Development ◽

Single Amino Acid ◽

Cell Repertoire ◽

Subtle Change

Tumors frequently express unmutated self-tumor–associated antigens (self-TAAs). However, trial results using self-TAAs as vaccine targets against cancer are mixed, often attributed to deletion of T cells with high-affinity receptors (TCRs) for self-TAAs during T cell development. Mutating these weak self-TAAs to produce higher affinity, effective vaccines is challenging, since the mutations may not benefit all members of the broad self-TAA–specific T cell repertoire. We previously identified a common weak murine self-TAA that we converted to a highly effective antitumor vaccine by a single amino acid substitution. In this case the modified and natural self-TAAs still raised very similar sets of CD8 T cells. Our structural studies herein show that the modification of the self-TAA resulted in a subtle change in the major histocompatibility complex I–TAA structure. This amino acid substitution allowed a dramatic conformational change in the peptide during subsequent TCR engagement, creating a large increase in TCR affinity and accounting for the efficacy of the modified self-TAA as a vaccine. These results show that carefully selected, well-characterized modifications to a poorly immunogenic self-TAA can rescue the immune response of the large repertoire of weakly responding natural self-TAA–specific CD8 T cells, driving them to proliferate and differentiate into functional effectors. Subsequently, the unmodified self-TAA on the tumor cells, while unable to drive this response, is nevertheless a sufficient target for the CD8 cytotoxic effectors. Our results suggest a pathway for more efficiently identifying variants of common self-TAAs, which could be useful in vaccine development, complementing other current nonantigen-specific immunotherapies.

Download Full-text

Effect of single amino acid substitutions on the formation of the PlA and Bak alloantigenic epitopes

Blood ◽

10.1182/blood.v78.3.681.681 ◽

1991 ◽

Vol 78 (3) ◽

pp. 681-687 ◽

Cited By ~ 51

Author(s):

A Goldberger ◽

M Kolodziej ◽

M Poncz ◽

JS Bennett ◽

PJ Newman

Keyword(s):

Amino Acid ◽

Expression System ◽

Single Amino Acid ◽

Expression Vectors ◽

Membrane Glycoproteins ◽

Amino Acid Polymorphism ◽

Specific Expression ◽

Mammalian Expression ◽

Single Amino Acid Polymorphisms ◽

Necessary And Sufficient

Abstract The subunits that comprise the platelet-specific integrin alpha IIb beta 3 are polymorphic in nature, with several allelic forms present in the human gene pool. Minor changes in the secondary and tertiary structures of platelet membrane glycoproteins (GP) IIb and IIIa encoded by these alleles can result in an alloimmune reaction after transfusion or during pregnancy. To better understand the molecular structure of the PlA alloantigen system, located on GPIIIa, and the Bak alloantigen on GPIIb, we used a heterologous mammalian expression system to express these integrin subunits in their known polymorphic forms. An expression vector containing the PlA1 form of a GPIIIa cDNA, which encodes a leucine at amino acid 33 (Leu33), was modified to express the PlA2- associated form encoding a proline at amino acid 33 (Pro33). Similarly, a Baka GPIIb cDNA expressing an isoleucine at amino acid 843 (IIe843) was modified to express the Bakb form containing a serine at the same position (Ser843). Transfection of these vectors into COS cells resulted in the synthesis of GPIIb and GPIIIa molecules that were identical in size to those present in platelet lysates. Immunoprecipitation of the GPIIIa-transfected COS lysates with PlA)- specific alloantisera indicated that the Leu33 form was recognized only by anti-PIA1 sera while the Pro33 form was bound only by anti-PlA2 sera, showing that single amino acid polymorphisms are necessary and sufficient to direct the formation of the PlA1 and PlA2 alloepitopes. Similar experiments with Bak allele-specific expression vectors indicated that while the amino acid polymorphism (IIe843 in equilibrium Ser843) was necessary, posttranslational processing of pro-IIb was required for efficient exposure of both the Baka and Bakb alloepitopes.

Download Full-text

Genotypic Differences in Dengue Virus Neutralization Are Explained by a Single Amino Acid Mutation That Modulates Virus Breathing

mBio ◽

10.1128/mbio.01559-15 ◽

2015 ◽

Vol 6 (6) ◽

Cited By ~ 35

Author(s):

Kimberly A. Dowd ◽

Christina R. DeMaso ◽

Theodore C. Pierson

Keyword(s):

Amino Acid ◽

Dengue Virus ◽

Vaccine Development ◽

Antibody Binding ◽

Single Amino Acid ◽

Genotypic Differences ◽

Conformational Ensembles ◽

Single Amino Acid Residue ◽

Virus Serotype ◽

Serotype 1

ABSTRACTFlaviviruses sample an ensemble of virion conformations resulting from the conformational flexibility of their structural proteins. To investigate how sequence variation among strains impacts virus breathing, we performed studies with the monoclonal antibody (MAb) E111, which binds an inaccessible domain III envelope (E) protein epitope of dengue virus serotype 1 (DENV1). Prior studies indicated that an observed ~200-fold difference in neutralization between the DENV1 strains Western Pacific-74 (West Pac-74) and 16007 could not be explained by differences in the affinity of MAb E111 for each strain. Through neutralization studies with wild-type and variant viruses carrying genes encoding reciprocal mutations at all 13 amino acid differences between the E proteins of West Pac-74 and 16007, we found that E111 neutralization susceptibility mapped solely to the presence of a lysine or arginine at E domain II residue 204, located distally from the E111 epitope. This same residue correlated with neutralization differences observed for MAbs specific for epitopes distinct from E111, suggesting that this amino acid dictates changes in the conformational ensembles sampled by the virus. Furthermore, an observed twofold difference in the stability of infectious West Pac-74 versus 16007 in solution also mapped to E residue 204. Our results demonstrate that neutralization susceptibility can be altered in an epitope-independent manner by natural strain variation that influences the structures sampled by DENV. That different conformational ensembles of flaviviruses may affect the landscape available for antibody binding, as well as virus stability, has important implications for functional studies of antibody potency, a critical aspect of vaccine development.IMPORTANCEThe global burden of dengue virus (DENV) is growing, with recent estimates of ~390 million human infections each year. Antibodies play a crucial role in protection from DENV infection, and vaccines that elicit a robust antibody response are being actively pursued. We report here the identification of a single amino acid residue in the envelope protein of DENV serotype 1 that results in global changes to virus structure and stability when it is changed. Our results indicate that naturally occurring variation at this particular site among virus strains impacts the ensemble of structures sampled by the virus, a process referred to as virus breathing. The finding that such limited and conservative sequence changes can modulate the landscape available for antibody binding has important implications for both vaccine development and the study of DENV-reactive antibodies.

Download Full-text