Molecular genetics of glycophorin MNS variants

The Research of a Large-Scale Analysis Platform for MNS Blood Group Identification Based on Long-Read Sequencing

The objective of this study was to devise a novel approach for determining MNS blood group utilizing long-read sequencing (LRS) and to identify intricate genome variations associated with this blood group system. In this study, a total of 60 blood samples were collected from randomly selected Chinese Han blood donors. The amplification of the full-length sequences of GYPA exon 2-7 (11 kb) and GYPB exon 2-6 (7 kb) was conducted on the blood samples obtained from these 60 donors. Subsequently, the sequencing of these amplified sequences was performed using the PacBio platform. The obtained sequencing data were then compared with the reference sequence of the human genome (GRCh38) utilizing the pbmm2 software, resulting in the acquisition of the haploid sequences of GYPA and GYPB. The serological typing prediction was conducted using the International Society of Blood Transfusion (ISBT) database, while the analysis of SNVs sites was performed using deepvariant v1.2.0 software and reference sequence alignment. A total of 60 samples yielded unambiguous high-quality haplotypes, which can serve as a standardized reference sequence for molecular biology typing of MNSs in the Chinese population. In a total of 60 serological samples, the LRS method successfully identified the M, N, S, and s blood group antigens by analyzing specific genetic variations (c.59, c.71, c.72 for GYPA, and c.143 for GYPB), which aligned with the results obtained through conventional serological techniques. 4 Mur samples that had been previously validated through serology and molecular biology were successfully confirmed, and complete haploid sequences were obtained. Notably, one of the Mur samples exhibited a novel breakpoint, GYP (B1-136-B ψ 137-212-A213-229-B230-366), thereby representing a newly identified subtype. Single molecule sequencing, which eliminates the necessity for PCR amplification, effectively encompasses GC and high repeat regions, enhancing accuracy in quantifying mutations with low abundance or frequency. By employing LRS analysis of the core region of GYPA and GYPB, diverse genotypes of MNS can be precisely and reliably identified in a single assay. This approach presents a comprehensive, expeditious, and precise novel method for the categorization and investigation of MNS blood group system.

Heteromeric Solute Carriers: Function, Structure, Pathology and Pharmacology

Solute carriers form one of three major superfamilies of membrane transporters in humans, and include uniporters, exchangers and symporters. Following several decades of molecular characterisation, multiple solute carriers that form obligatory heteromers with unrelated subunits are emerging as a distinctive principle of membrane transporter assembly. Here we comprehensively review experimentally established heteromeric solute carriers: SLC3-SLC7 amino acid exchangers, SLC16 monocarboxylate/H⁺ symporters and basigin/embigin, SLC4A1 (AE1) and glycophorin A exchanger, SLC51 heteromer Ost α-Ost β uniporter, and SLC6 heteromeric symporters. The review covers the history of the heteromer discovery, transporter physiology, structure, disease associations and pharmacology - all with a focus on the heteromeric assembly. The cellular locations, requirements for complex formation, and the functional role of dimerization are extensively detailed, including analysis of the first complete heteromer structures, the SLC7-SLC3 family transporters LAT1-4F2hc, b^0,+AT-rBAT and the SLC6 family heteromer B⁰AT1-ACE2. We present a systematic analysis of the structural and functional aspects of heteromeric solute carriers and conclude with common principles of their functional roles and structural architecture.

Human genetics and malaria resistance

Malaria has been the pre-eminent cause of early mortality in many parts of the world throughout much of the last five thousand years and, as a result, it is the strongest force for selective pressure on the human genome yet described. Around one third of the variability in the risk of severe and complicated malaria is now explained by additive host genetic effects. Many individual variants have been identified that are associated with malaria protection, but the most important all relate to the structure or function of red blood cells. They include the classical polymorphisms that cause sickle cell trait, α-thalassaemia, G6PD deficiency, and the major red cell blood group variants. More recently however, with improving technology and experimental design, others have been identified that include the Dantu blood group variant, polymorphisms in the red cell membrane protein ATP2B4, and several variants related to the immune response. Characterising how these genes confer their effects could eventually inform novel therapeutic approaches to combat malaria. Nevertheless, all together, only a small proportion of the heritable component of malaria resistance can be explained by the variants described so far, underscoring its complex genetic architecture and the need for continued research.

Resistance to malaria through structural variation of red blood cell invasion receptors

The malaria parasite Plasmodium falciparum invades human red blood cells by a series of interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy-number variants affecting the host invasion receptor genes GYPA and GYPB We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently increased in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.

Red cell receptors as access points for malaria infection

PURPOSE OF REVIEW

Red cell receptors provide unique entry points for Plasmodium parasites to initiate blood-stage malaria infection. Parasites encode distinct ligands that bind specifically to both highly abundant and low-copy receptors. Recent advances in the understanding of molecular and structural mechanisms of these interactions provide fundamental insights into receptor-ligand biology and molecular targets for intervention.

RECENT FINDINGS

The review focuses on the requirements for known interactions, insight derived from complex structures, and mechanisms of receptor/ligand engagement. Further, novel roles for established red cell membrane proteins, parasite ligands and associated interacting partners have recently been established in red cell invasion.

SUMMARY

The new knowledge underlines the intricacies involved in invasion by a eukaryotic parasite into a eukaryotic host cell demonstrated by expanded parasite ligand families, redundancy in red cell receptor engagement, multitiered temporal binding, and the breadth of receptors engaged.

Critical glycosylated residues in exon three of erythrocyte glycophorin A engage Plasmodium falciparum EBA-175 and define receptor specificity

Erythrocyte invasion is an essential step in the pathogenesis of malaria. The erythrocyte binding-like (EBL) family of Plasmodium falciparum proteins recognizes glycophorins (Gp) on erythrocytes and plays a critical role in attachment during invasion. However, the molecular basis for specific receptor recognition by each parasite ligand has remained elusive, as is the case with the ligand/receptor pair P. falciparum EBA-175 (PfEBA-175)/GpA. This is due largely to difficulties in producing properly glycosylated and functional receptors. Here, we developed an expression system to produce recombinant glycosylated and functional GpA, as well as mutations and truncations. We identified the essential binding region and determinants for PfEBA-175 engagement, demonstrated that these determinants are required for the inhibition of parasite growth, and identified the glycans important in mediating the PfEBA-175–GpA interaction. The results suggest that PfEBA-175 engages multiple glycans of GpA encoded by exon 3 and that the presentation of glycans is likely required for high-avidity binding. The absence of exon 3 in GpB and GpE due to a splice site mutation confers specific recognition of GpA by PfEBA-175. We speculate that GpB and GpE may have arisen due to selective pressure to lose the PfEBA-175 binding site in GpA. The expression system described here has wider application for examining other EBL members important in parasite invasion, as well as additional pathogens that recognize glycophorins. The ability to define critical binding determinants in receptor-ligand interactions, as well as a system to genetically manipulate glycosylated receptors, opens new avenues for the design of interventions that disrupt parasite invasion.

Plasmodium falciparum uses distinct ligands that bind host cell receptors for invasion of red blood cells (RBCs) during malaria infection. A key entry pathway involves P. falciparum EBA-175 (PfEBA-175) recognizing glycophorin A (GpA) on RBCs. Despite knowledge of this protein-protein interaction, the complete mechanism for specific receptor engagement is not known. PfEBA-175 recognizes GpA but is unable to engage the related RBC receptor GpB or GpE. Understanding the necessary elements that enable PfEBA-175 to specifically recognize GpA is critical in developing specific and potent inhibitors of PfEBA-175 that disrupt host cell invasion and aid in malaria control. Here, we describe a novel system to produce and manipulate the host receptor GpA. Using this system, we probed the elements in GpA necessary for engagement and thus for host cell invasion. These studies have important implications for understanding how ligands and receptors interact and for the future development of malaria interventions.

Population genetics of GYPB and association study between GYPB*S/s polymorphism and susceptibility to P. falciparum infection in the Brazilian Amazon

BACKGROUND

Merozoites of Plasmodium falciparum invade through several pathways using different RBC receptors. Field isolates appear to use a greater variability of these receptors than laboratory isolates. Brazilian field isolates were shown to mostly utilize glycophorin A-independent invasion pathways via glycophorin B (GPB) and/or other receptors. The Brazilian population exhibits extensive polymorphism in blood group antigens, however, no studies have been done to relate the prevalence of the antigens that function as receptors for P. falciparum and the ability of the parasite to invade. Our study aimed to establish whether variation in the GYPB*S/s alleles influences susceptibility to infection with P. falciparum in the admixed population of Brazil.

METHODS

Two groups of Brazilian Amazonians from Porto Velho were studied: P. falciparum infected individuals (cases); and uninfected individuals who were born and/or have lived in the same endemic region for over ten years, were exposed to infection but have not had malaria over the study period (controls). The GPB Ss phenotype and GYPB*S/s alleles were determined by standard methods. Sixty two Ancestry Informative Markers were genotyped on each individual to estimate admixture and control its potential effect on the association between frequency of GYPB*S and malaria infection.

RESULTS

GYPB*S is associated with host susceptibility to infection with P. falciparum; GYPB*S/GYPB*S and GYPB*S/GYPB*s were significantly more prevalent in the in the P. falciparum infected individuals than in the controls (69.87% vs. 49.75%; P<0.02). Moreover, population genetics tests applied on the GYPB exon sequencing data suggest that natural selection shaped the observed pattern of nucleotide diversity.

CONCLUSION

Epidemiological and evolutionary approaches suggest an important role for the GPB receptor in RBC invasion by P. falciparum in Brazilian Amazons. Moreover, an increased susceptibility to infection by this parasite is associated with the GPB S+ variant in this population.

Red blood cell (RBC) membrane proteomics--Part I: Proteomics and RBC physiology

Membrane proteomics is concerned with accurately and sensitively identifying molecules involved in cell compartmentalisation, including those controlling the interface between the cell and the outside world. The high lipid content of the environment in which these proteins are found often causes a particular set of problems that must be overcome when isolating the required material before effective HPLC-MS approaches can be performed. The membrane is an unusually dynamic cellular structure since it interacts with an ever changing environment. A full understanding of this critical cell component will ultimately require, in addition to proteomics, lipidomics, glycomics, interactomics and study of post-translational modifications. Devoid of nucleus and organelles in mammalian species other than camelids, and constantly in motion in the blood stream, red blood cells (RBCs) are the sole mammalian oxygen transporter. The fact that mature mammalian RBCs have no internal membrane-bound organelles, somewhat simplifies proteomics analysis of the plasma membrane and the fact that it has no nucleus disqualifies microarray based methods. Proteomics has the potential to provide a better understanding of this critical interface, and thereby assist in identifying new approaches to diseases.

Sec1-FUT2-Sec1 hybrid allele generated by interlocus gene conversion

BACKGROUND

Many single-nucleotide polymorphisms have been identified in the coding region of the FUT2 locus, which encodes secretor type alpha(1,2)fucosyltransferase. In addition, three recombination alleles have been reported. Of these recombination alleles, a fusion gene generated by an unequal crossing over between Sec1, a pseudogene that locates 23 kb upstream to and has high sequence homology with FUT2 and FUT2, was identified as a Japanese-specific nonsecretor allele (se(fus)).

STUDY DESIGN AND METHODS

During the screening of the se(fus) in Mongolians (n = 118), a hybrid allele of Sec1-FUT2-Sec1 was found.

RESULTS

The DNA sequence suggested that the Sec1-FUT2-Sec1 allele contains a 275-bp sequence (between positions 259 and 533) that is identical to the FUT2 sequence including a 54-bp FUT2-specific region (between positions 417 and 470) and that might have been generated by an interlocus gene conversion.

CONCLUSION

Because the recombination region of se(fus) and the upstream recombination region of Sec1-FUT2-Sec1 are almost identical, this sequence stretch is likely to be the breakpoint for different kinds of recombinations that occur in this family of genes.

Genetic basis of blood group diversity

In the last 18 years the genes that encode all but one of the 29 blood group systems present on red blood cells (RBCs) have been identified. This body of knowledge has permitted the application of molecular techniques to characterize the common blood group antigens and to elucidate the background for some of the variant phenotypes. Just as the RBC was used as a model for the biochemical characterization of cell membranes, so the genes encoding blood groups provide a readily accessible model for the study of gene expression and diversity. The application of genotyping techniques to identify fetuses at risk of haemolytic disease of the newborn is now the standard of care, and the expansion of nucleic acid testing platforms to include both disease testing and blood typing in the blood centre is on the horizon. This review summarizes the molecular basis of blood groups and illustrates the mechanisms that generate diversity through specific examples.

Molecular evolution of alleles of the glycophorin A gene

Highly-homologous Glycophorin A (GPA), B and E genes are triplicate genes, and involve many subtypes and minor antigens constructing the Miltenberger subsystem. These genes and most of the variants are hypothesized to arise by recombination, because hot spots are located in the gene sequences. By sequencing exons 1-7 and introns 1-3 of standard alleles of GPA gene, M and N alleles were classified into six variations: provisionally called MN*M101, M102, M201, M202, N101 and N102 in our previous study. Here we further investigated the sequences of introns 4-6 using GPA gene-specific primers and by DNA sequencing, and found eight, five and nine new nucleotide substitutions or deletions in introns 4, 5 and 6, respectively. Using the computer program PHYLIP 3.5, the phylogenetic trees were reconstructed. Phylogenetic analysis of the allele sequences revealed that M200s alleles arose from M101 after the separation of M101 and N101 and branched to M201 and M202 via the accumulation of point mutations. M102 and N102 alleles were estimated to generate via recombination between M101 and N101 occurred around the hot spot. The findings also suggested the existence of other GPA variants with normal antigenicity, and are quite useful in the forensic and anthropological fields.

Glycophorin as a receptor for Escherichia coli alpha-hemolysin in erythrocytes

Escherichia coli alpha-hemolysin (HlyA) can lyse both red blood cells (RBC) and liposomes. However, the cells are lysed at HlyA concentrations 1-2 orders of magnitude lower than liposomes (large unilamellar vesicles). Treatment of RBC with trypsin, but not with chymotrypsin, reduces the sensitivity of RBC toward HlyA to the level of the liposomes. Since glycophorin, one of the main proteins in the RBC surface, can be hydrolyzed by trypsin much more readily than by chymotrypsin, the possibility was tested of a specific binding of HlyA to glycophorin. With this purpose, a number of experiments were performed. (a) HlyA was preincubated with purified glycophorin, after which it was found to be inactive against both RBC and liposomes. (b) Treatment of RBC with an anti-glycophorin antibody protected the cells against HlyA lysis. (c) Immobilized HlyA was able to bind glycophorin present in a detergent lysate of RBC ghosts. (d) Incorporation of glycophorin into pure phosphatidylcholine liposomes increased notoriously the sensitivity of the vesicles toward HlyA. (e) Treatment of the glycophorin-containing liposomes with trypsin reverted the vesicles to their original low sensitivity. The above results are interpreted in terms of glycophorin acting as a receptor for HlyA in RBC. The binding constant of HlyA for glycophorin was estimated, in RBC at sublytic HlyA concentrations, to be 1.5 x 10(-9) m.

A new h allele detected in Europe has a missense mutationin alpha(1,2)-fucosyltransferase motif II

BACKGROUND

The FUT1 gene encodes an alpha(1,2)-fucosyltransferase (H transferase), which determines the blood group H. Nonfunctional alleles of this gene, called h alleles and carrying loss-of-function mutations, are observed in the exceedingly rare Bombay phenotype. Twenty-three distinct h alleles have been characterized at the molecular level in various populations. The FUT2 (SE) gene is highly homologous to FUT1 (H:).

STUDY DESIGN AND METHODS

The FUT1 gene of an Austrian proband with the Bombay phenotype was characterized by nucleotide sequencing of the full-length coding sequence. A PCR method using sequence-specific primers for FUT2 genotyping in whites was developed. The plasma alpha(1,2)-fucosyltransferase activity was determined. The distribution of the mutations underlying 24 h alleles and 7 se alleles was analyzed.

RESULTS

The proband carried a new h allele. Two nucleotide changes, G785A and C786A, in codon 262 of the FUT1 gene resulted in the replacement of serine by lysine. No alpha(1,2)-fucosyltransferase activity was detected in the proband's plasma. The proband was homozygous for the seG428A allele. Six of 17 missense mutations in nonfunctional h and se alleles occurred in highly conserved fucosyltransferase motifs. No loss-of-function mutation was observed in the aminoterminal section encompassing the transmembraneous helix.

CONCLUSION

The missense mutation S262K in the FUT1 gene caused the loss of H transferase activity. The analysis of the distribution of mutations in nonfunctional FUT1 and FUT2 genes can point to functionally important domains in the H transferase.

[Blood groups and structure-activity relations]

In the recent years, advances in biochemistry and molecular genetics have contributed to establish the structure of the genes and proteins from most of the 23 blood group systems presently known. From these findings, five functional classes of molecules can be schematically distinguished: (i) transporters and channels, (ii) receptors for ligands, viruses, bacteria and parasites, (iii) adhesion molecules, (iv) enzymes, and (v) structural proteins. Recent advances on these molecules will be reviewed, particularly by illustrating available structure-function relationships.