Summary: acidic terminal segments, variant surface antigen of PfEMP1
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Plasmodium falciparum erythrocyte membrane protein 1 Edit Wikipedia article
|PfEMP1, N-terminal segment|
|PfEMP DBL domain|
|PfEMP1, acidic terminal segment|
Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a family of proteins present on the membrane surface of red blood cells (RBCs or erythrocytes) that are infected by the malarial parasite Plasmodium falciparum. PfEMP1 is synthesized during the parasite's blood stage (erythrocytic schizogony) inside the RBC, during which the clinical symptoms of falciparum malaria are manifested. Acting as both an antigen and adhesion protein, it is thought to play a key role in the high level of virulence associated with P. falciparum. It was discovered in 1984 when it was reported that infected RBCs had unusually large-sized cell membrane proteins, and these proteins had antibody-binding (antigenic) properties. An elusive protein, its chemical structure and molecular properties were revealed only after a decade, in 1995. It is now established that there is not one but a large family of PfEMP1 proteins, genetically regulated (encoded) by a group of about 60 genes called var. Each P. falciparum is able to switch on and off specific var genes to produce a functionally different protein, thereby evading the host's immune system. RBCs carrying PfEMP1 on their surface stick to endothelial cells, which facilitates further binding with uninfected RBCs (through the processes of sequestration and rosetting), ultimately helping the parasite to both spread to other RBCs as well as bringing about the fatal symptoms of P. falciparum malaria.
Malaria is the deadliest among infectious diseases, accounting for approximately 429,000 human deaths in 2015 as of the latest estimate by the World Health Organization. In humans, malaria can be caused by five Plasmodium parasites, namely P. falciparum, P. vivax, P. malariae, P. ovale and P. knowlesi. P. falciparum is the most dangerous species, attributed to >99% of malaria's death toll, with 70% of these deaths occurring in children under the age of five years. The parasites are transmitted through the bites of female mosquitos (of the species of Anopheles). Before invading the RBCs and causing the symptoms of malaria, the parasites first multiply in the liver. The daughter parasites called merozoites then only infect the RBCs. They undergo structural development inside the RBCs, becoming trophozoites and schizonts. It is during this period that malarial symptoms are produced.
Unlike RBCs infected by other Plasmodium species, P. falciparum-infected RBCs had been known to spontaneously stick together. By the early 1980s, it was established that when the parasite (both the trophozoite and schizont forms) enters the blood stream and infects RBCs, the infected cells form knobs on their surface. Then they become sticky, and get attached to the walls (endothelium) of the blood vessels through a process called cytoadhesion, or cytoadherence. Such attachment favours binding with and accumulation of other RBCs. This process is known as sequestration. It is during this condition that the parasites induce an immune response (antigen-antibody reaction) and evade destruction in the spleen. Although the process and significance of sequestration were described in detail by two Italian physicians Amico Bignami and Ettore Marchiafava in the early 1890s, it took a century to discover the actual factor for the stickiness and virulence.
PfEMP1 was discovered by Russell J. Howard and his colleagues at the US National Institutes of Health in 1984. Using the techniques of radioiodination and immunoprecipitation, they found a unique but yet unknown antigen from P. falciparum-infected RBCs that appeared to cause binding with other cells. Since the antigenic protein could only be detected in infected cells, they asserted that the protein was produced by the malarial parasite, and not by RBCs. The antigen was large and appeared to be different in size in different strains of P. falciparum obtained from night monkey (Aotus). In one strain, called Camp (from Malaysia), the antigen was found to have a molecular size of approximately 285 kDa; while in the other, called St. Lucia (from El Salvador), it was approximately 260 kDa. Both antigens bind to cultured skin cancer (melanoma) cells. But the researchers failed to confirm whether or not the protein actually was an adhesion molecule to the wall of blood vessels. Later in the same year, they found out that the unknown antigen was associated only with RBCs having small lumps called knobs on their surface. The first human RBC antigen was reported in 1986. Howard's team found that the antigens from Gambian children, who were suffering from falciparum malaria, were similar to those from the RBCs of night monkey. They determined that the molecular sizes of the proteins ranged from 250 to 300 kDa.
In 1987, they discovered another type of surface antigen from the same Camp and St. Lucia strains of malarial parasites. This was also a large-sized protein of about 300 kDa, but quite different from the antigens reported in 1984. The new protein was unable to bind to melanoma cells and present only inside the cell. Hence, they named the earlier protein Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), to distinguish it from the newly identified Plasmodium falciparum erythrocyte membrane protein 2 (PfEMP2). The distinction was confirmed the next year, with an additional information that PfEMP1 is relatively less in number.
Although some of the properties of PfEMP1 were firmly established, the protein was difficult to isolate due to its low occurrence. Five years after its discovery, one of the original researchers Irwin Sherman began to doubt the existence of PfEMP1 as a unique protein. He argued that the antigen could be merely a surface protein of RBCs that changes upon infection with malarial parasites. A consensus was achieved in 1995 following the identification (by cloning) of the gene for PfEMP1. The discovery of the genes was independently reported by Howard's team and two other teams at NIH. Howard's team identified two genes for PfEMP1, and recombinant protein products of these genes were shown to have antigenic and adhesive properties. They further affirmed that PfEMP1 is the key molecule in the ability of P. falciparum to evade the host's immune system. Joseph D. Smith and others showed that PfEMP1 is actually a large family of proteins encoded by a multigene family called var. The gene products can bind to a variety of receptors including those on endothelial cells. Xin-Zhuan Su and others showed that there could be more than 50 var genes which are distributed on different chromosomes of the malarial parasite.
PfEMP1 is a large family of proteins having high molecular weights ranging from 200 to 350 kDa. The wide range of molecular size reflects extreme variation in the amino acid composition of the proteins. But all the PfEMP1 proteins can be described as having three basic structural components, namely, an extracellular domain (ECD), a transmembrane domain (TMD) and an intracellular acidic terminal segment (ATS). The extracellular domain is fully exposed on the cell surface, and is the most variable region. It consists of a number of sub-domains, including a short and conserved N terminal segment (NTS) at the outermost region, followed by a highly variable Duffy-binding-like (DBL) domain, sometimes a Ca2+-binding C2 domain, and then one or two cysteine-rich interdomain regions (CIDRs).
Duffy-binding-like domains are so named because of their similarity to the Duffy binding proteins of P. vivax and P. knowlesi. There are six variant types of DBL, named DBLÎ±, DBLÎ², DBLÎ³, DBLÎ´, DBLÎµ and DBLÎ¶. CIDR is also divided into three classes: CIDRÎ±, CIDRÎ² and CIDRÎ³. Both DBL and CIDR have an additional type called PAM, so named because of their specific involvement in pregnancy-associated malaria (PAM). In spite of the diverse DBL and CIDR proteins, the extracellular amino terminal region is partly conserved, consisting of about 60 amino acids of NTS, one each of DBLÎ± and CIDR1 proteins in tandem. This semi-conserved DBLÎ±-CIDR1 region is called the head structure. The last CIDR region joins the TMD, which is embedded in the cell membrane. The TMD and ATS are highly conserved among different PfEMP1s, and their structures have been solved using solution NMR ( ).
The head structure is followed by a variable combination of diverse DBL and CIDR proteins, and in many cases along with C2. This variation gives rise to different types of PfEMP1. The DBL-CIDR combination in a particular type of PfEMP1 protein is never random, but organized into specific sequences known as domain cassettes. In some domain cassettes, there are only two or few DBL domains and CIDR domains, but in others they cover the entire length of the PfEMP1. These differences are responsible for different binding capacity among different PfEMP1s. For instance, among the most well-known types, VAR3 (earlier called type 3 PfEMP1) is the smallest, consisting of only NTS with DBL1Î± and DBL2Îµ domains in the ECD. Its molecular size is approximately 150 kDa. In domain cassette (DC) 4 type, the ECD is made up of three domains DBLÎ±1.1/1.4, CIDRÎ±1.6 and DBLÎ²3. The DBLÎ²3 domain contains a binding site for intercellular adhesion molecule 1 (ICAM1). This is particularly implicated with the development of brain infection. VAR2CSA is atypical in having a single domain cassette that consists of three N terminal DBLPAM domains followed by three DBLÎµ domains and one CIDRPAM. The seven domains always occur together. The usual NTS is absent. The protein specifically binds to chondroitin sulphate A (CSA); hence the name VAR2CSA.
Synthesis and transport
The PfEMP1 proteins are regulated and produced (encoded) by about 60 different var genes, but an individual P. falciparum would switch on only a single var gene at a time to produce only one type of PfEMP. The var genes are distributed in two exons. Exon 1 encodes amino acids of the highly variable ECD, while exon 2 encodes those of the conserved TMD and ATS. Based on their location in the chromosome and sequence, the var genes are generally classified into three major groups, A, B, and C, and two intermediate groups, B/A and B/C; or sometimes simply into five classes, upsA, upsB, upsC, upsD, and upsE respectively. Groups A and B are found towards the terminal end (subtelomeric) region of the chromosome, while group C is in the central (centromeric) region.
Once the PfEMP1 protein is fully synthesized (translated), it is carried to the cytoplasm towards the RBC membrane. The NTS is crucial for such directional movement. Within the cytoplasm, the newly synthesized protein is attached to a Golgi-like membranous vesicle called the Maurer's cleft. Inside the Maurerâ€™s clefts is a family of proteins called Plasmodium helical interspersed subtelomeric (PHIST) proteins. Of the PHIST proteins, PFI1780w and PFE1605w bind the intracellular ATS of PfEMP1 during transport to the RBC membrane.
The PfEMP1 molecule is deposited at the RBC membrane at the knobs. These knobs are easily identified as conspicuous bumps on the infected RBCs from the early trophozoite stage onward. The malarial parasite cannot induce its virulence on RBCs without knobs. As many as 10,000 knobs are distributed throughout the surface of a mature infected RBC, and each knob is 50-80 nm in diameter. The export of pfEMP1 from Maurer's cleft to RBC membrane is mediated by binding of another protein produced by the parasite called knob-associated histidine-rich protein (KAHRP). KAHRP enhances the structural rigidity of infected RBC and adhesion of PfEMP1 on the knobs. It is also directly responsible for forming knobs, as indicated by the fact that kahrp gene-deficient malarial parasites do not form knobs. To form a knob, KAHRP aggregates several membrane skeletal proteins of the host RBC, such as spectrin, actin, ankyrin R, and spectrinâ€“actin band 4.1 complex. Upon arrival at the knob, PfEMP1 is attached to the spectrin network using the PHIST proteins.
The primary function of PfEMP1 is to bind and attach RBCs to the wall of the blood vessels. The most important binding properties of P. falciparum known to date are mediated by the head structure of PfEMP1, consisting of DBL domains and CIDRs. DBL domains can bind to a variety of cell receptors including thrombospondin (TSP), complement receptor 1 (CR1), chondroitin sulfate A (CSA), P-selectin, endothelial protein C receptor (EPCR), and heparan sulfate. The DBL domain adjacent to the head structure binds to ICAM1. CIDRs mainly bind to a large variety of cluster determinant 36 (CD36). These bindings produce the pathogenic characteristics of the parasite, such as sequestration of infected cells in different tissues, invasion of RBCs, and clustering of infected cells by a process called rosetting.
CIDR1 protein in the semi-conserved head structure is the principal and best understood adhesion site of PfEMP1. It binds with CD36 on endothelial cells. Only group B and C proteins are able to bind, and that too with only those having CIDRÎ±2-6 sequence types. On the other hand, group A proteins have either CIDRÎ±1 or CIDRÎ²/Î³/Î´, and they are responsible for the most severe condition of malaria. Binding with ICAM1 is achieved through the DBLÎ² domain adjacent to the head structure. However, many PfEMP1s having DBLÎ² domain do not bind to ICAM1, and it appears that only the DBLÎ² paired with C2 domain can to bind to ICAM1. The DBLÎ±-CIDRÎ³ tandem pair is the main factor for rosetting, sticking together the infected RBC with the uninfected cells, and thereby clogging of the blood vessels. This activity is performed through binding with CR1.
The most dangerous malarial infection is in the brain and is called cerebral malaria. In cerebral malaria, the PfEMP1 proteins involved are DC8 and DC13. They are named after the number of domain cassettes they contain, and are capable of binding not only endothelial cells of the brain, but also in different organs including brain, lung, heart, and bone marrow. Initially, it was assumed that PfEMP1 binds to ICAM1 in the brain, but DC8 and DC13 were found incompatible with ICAM1. Instead DC8 and DC13 specifically bind to EPCR using CIDRÎ± sub-types such as CIDRÎ±1.1, CIDRÎ±1.4, CIDRÎ±1.5 and CIDRÎ±1.7. However, it was later shown that DC13 can bind to both ICAM1 and EPCR. EPCR is thus a potential vaccine and drug target in cerebral malaria.
VAR2CSA is unique in that it is mostly produced by the placenta during pregnancy (the condition called pregnancy-associated malaria, PAM, or placental malaria). The majority of PAM is therefore due to VAR2SCA. Unlike other PfEMP1, VAR2CSA binds to chondroitin sulphate A present on the vascular endothelium of placenta. Although its individual domains can bind to CSA, its entire structure is used for complete binding. The major complication in PAM is low-birth-weight babies. However, women who survived the first infection generally develop an effective immune response. In P. falciparum-prevalent regions in Africa, pregnant women are found to contain high levels of antibody (immunoglobulin G, or IgG) against VAR2CSA, which protect them the placenta-attacking malarial parasite. They are noted for giving birth to heavier babies.
In a normal human immune system, malarial parasite binding to RBCs stimulates the production of antibodies that attack the PfEMP1 molecules. Binding of antibody with PfEMP1 disables the binding properties of DBL domains, causing loss of cell adhesion, and the infected RBC is destroyed. In this scenario, malaria is avoided. However, to evade the host's immune response, different P. falciparum switch on and off different var genes to produce functionally different (antigenically distinct) PfEMP1s. Each variant type of PfEMP1 has different binding property, and thus, is not always recognized by antibodies.
By default, all the var genes in the malarial parasite are inactivated. Activation (gene expression) of var is initiated upon infection of the organs. Further, in each organ only specific var genes are activated. The severity of the infection is determined by the type of organ in which infection occurs, hence, the type of var gene activated. For examples, in the most severe cases of malaria, such as cerebral malaria, only the var genes for the PfEMP1 proteins DC8 and DC13 are switched on. Upon the synthesis of DC8 and DC13, their CIDRÎ±1 domains bind to EPCR, which brings about the onset of severe malaria. The abundance of the gene products (transcripts) of these PfEMP1 proteins (specifically the CIDRÎ±1 subtype transcripts) directly relates to the severity of the disease. This further indicates that preventing the interaction between CIDRÎ±1 and EPCR would be good target for a potential vaccine. In pregnancy-associated malaria, another severe type of falciparum malaria, the gene for VAR2CSA (named var2csa) is activated in the placenta. Binding of VAR2CSA to CSA is the primary cause of premature delivery, death of the foetus and severe anaemia in the mother. This indicates that drugs targeting VAR2CSA will be able to prevent the effects of malaria, and for this reason VAR2CSA is the leading candidate for development of a PAM vaccine.
The 2017 version of this article has passed academic peer review (here) and was published in WikiJournal of Medicine.
It can be cited as: Lalchhandama K (2017). "Plasmodium falciparum erythrocyte membrane protein 1". WikiJournal of Medicine. 4 (1). doi:10.15347/wjm/2017.004.
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- Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B (October 2002). "Genome sequence of the human malaria parasite Plasmodium falciparum". Nature. 419 (6906): 498â€“511. doi:10.1038/nature01097. PMC 3836256. PMID 12368864.
- Chen Q, Fernandez V, SundstrÃ¶m A, Schlichtherle M, Datta S, Hagblom P, Wahlgren M (July 1998). "Developmental selection of var gene expression in Plasmodium falciparum". Nature. 394 (6691): 392â€“5. doi:10.1038/28660. PMID 9690477.
- Scherf A, Lopez-Rubio JJ, Riviere L (2008). "Antigenic variation in Plasmodium falciparum". Annual Review of Microbiology. 62 (1): 445â€“70. doi:10.1146/annurev.micro.61.080706.093134. PMID 18785843.
- Kyes SA, Kraemer SM, Smith JD (September 2007). "Antigenic variation in Plasmodium falciparum: gene organization and regulation of the var multigene family". Eukaryotic Cell. 6 (9): 1511â€“20. doi:10.1128/EC.00173-07. PMC 2043368. PMID 17644655.
- Kyes SA, Christodoulou Z, Raza A, Horrocks P, Pinches R, Rowe JA, Newbold CI (June 2003). "A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern". Molecular Microbiology. 48 (5): 1339â€“48. doi:10.1046/j.1365-2958.2003.03505.x. PMC 2869446. PMID 12787360.
- Kyriacou HM, Stone GN, Challis RJ, Raza A, Lyke KE, Thera MA, KonÃ© AK, Doumbo OK, Plowe CV, Rowe JA (December 2006). "Differential var gene transcription in Plasmodium falciparum isolates from patients with cerebral malaria compared to hyperparasitaemia". Molecular and Biochemical Parasitology. 150 (2): 211â€“8. doi:10.1016/j.molbiopara.2006.08.005. PMC 2176080. PMID 16996149.
- Kirchner S, Power BJ, Waters AP (September 2016). "Recent advances in malaria genomics and epigenomics". Genome Medicine. 8 (1): 92. doi:10.1186/s13073-016-0343-7. PMC 5015228. PMID 27605022.
- Rask TS, Hansen DA, Theander TG, Gorm Pedersen A, Lavstsen T (September 2010). "Plasmodium falciparum erythrocyte membrane protein 1 diversity in seven genomes--divide and conquer". PLoS Computational Biology. 6 (9): e1000933. doi:10.1371/journal.pcbi.1000933. PMC 2940729. PMID 20862303.
- Smith JD (July 2014). "The role of PfEMP1 adhesion domain classification in Plasmodium falciparum pathogenesis research". Molecular and Biochemical Parasitology. 195 (2): 82â€“7. doi:10.1016/j.molbiopara.2014.07.006. PMC 4159067. PMID 25064606.
- Mundwiler-Pachlatko E, Beck HP (December 2013). "Maurer's clefts, the enigma of Plasmodium falciparum". Proceedings of the National Academy of Sciences of the United States of America. 110 (50): 19987â€“94. doi:10.1073/pnas.1309247110. PMC 3864307. PMID 24284172.
- Warncke JD, Vakonakis I, Beck HP (December 2016). "Plasmodium Helical Interspersed Subtelomeric (PHIST) Proteins, at the Center of Host Cell Remodeling". Microbiology and Molecular Biology Reviews. 80 (4): 905â€“27. doi:10.1128/MMBR.00014-16. PMC 5116875. PMID 27582258.
- Cooke B, Coppel R, Wahlgren M (October 2000). "Falciparum malaria: sticking up, standing out and out-standing". Parasitology Today. 16 (10): 416â€“20. doi:10.1016/S0169-4758(00)01753-1. PMID 11006472.
- Nagao E, Kaneko O, Dvorak JA (May 2000). "Plasmodium falciparum-infected erythrocytes: qualitative and quantitative analyses of parasite-induced knobs by atomic force microscopy". Journal of Structural Biology. 130 (1): 34â€“44. doi:10.1006/jsbi.2000.4236. PMID 10806089.
- Maier AG, Rug M, O'Neill MT, Brown M, Chakravorty S, Szestak T, Chesson J, Wu Y, Hughes K, Coppel RL, Newbold C, Beeson JG, Craig A, Crabb BS, Cowman AF (July 2008). "Exported proteins required for virulence and rigidity of Plasmodium falciparum-infected human erythrocytes". Cell. 134 (1): 48â€“61. doi:10.1016/j.cell.2008.04.051. PMC 2568870. PMID 18614010.
- Watermeyer JM, Hale VL, Hackett F, Clare DK, Cutts EE, Vakonakis I, Fleck RA, Blackman MJ, Saibil HR (January 2016). "A spiral scaffold underlies cytoadherent knobs in Plasmodium falciparum-infected erythrocytes". Blood. 127 (3): 343â€“51. doi:10.1182/blood-2015-10-674002. PMC 4797390. PMID 26637786.
- Crabb BS, Cooke BM, Reeder JC, Waller RF, Caruana SR, Davern KM, Wickham ME, Brown GV, Coppel RL, Cowman AF (April 1997). "Targeted gene disruption shows that knobs enable malaria-infected red cells to cytoadhere under physiological shear stress". Cell. 89 (2): 287â€“96. doi:10.1016/S0092-8674(00)80207-X. PMID 9108483.
- Rug M, Prescott SW, Fernandez KM, Cooke BM, Cowman AF (July 2006). "The role of KAHRP domains in knob formation and cytoadherence of P falciparum-infected human erythrocytes". Blood. 108 (1): 370â€“8. doi:10.1182/blood-2005-11-4624. PMC 1895844. PMID 16507777.
- Oberli A, Slater LM, Cutts E, Brand F, Mundwiler-Pachlatko E, Rusch S, Masik MF, Erat MC, Beck HP, Vakonakis I (October 2014). "A Plasmodium falciparum PHIST protein binds the virulence factor PfEMP1 and comigrates to knobs on the host cell surface". FASEB Journal. 28 (10): 4420â€“33. doi:10.1096/fj.14-256057. PMC 4202109. PMID 24983468.
- Crabb BS, Cowman AF (October 2002). "Plasmodium falciparum virulence determinants unveiled". Genome Biology. 3 (11): REVIEWS1031. doi:10.1186/gb-2002-3-11-reviews1031. PMC 244921. PMID 12441004.
- Senczuk AM, Reeder JC, Kosmala MM, Ho M (November 2001). "Plasmodium falciparum erythrocyte membrane protein 1 functions as a ligand for P-selectin". Blood. 98 (10): 3132â€“5. doi:10.1182/blood.V98.10.3132. PMID 11698301.
- Turner L, Lavstsen T, Berger SS, Wang CW, Petersen JE, Avril M, Brazier AJ, Freeth J, Jespersen JS, Nielsen MA, Magistrado P, Lusingu J, Smith JD, Higgins MK, Theander TG (June 2013). "Severe malaria is associated with parasite binding to endothelial protein C receptor". Nature. 498 (7455): 502â€“5. doi:10.1038/nature12216. PMC 3870021. PMID 23739325.
- Angeletti D, Sandalova T, Wahlgren M, Achour A (2015). "Binding of subdomains 1/2 of PfEMP1-DBL1Î± to heparan sulfate or heparin mediates Plasmodium falciparum rosetting". PLOS ONE. 10 (3): e0118898. doi:10.1371/journal.pone.0118898. PMC 4351205. PMID 25742651.
- Smith JD, Craig AG, Kriek N, Hudson-Taylor D, Kyes S, Fagan T, Fagen T, Pinches R, Baruch DI, Newbold CI, Miller LH (February 2000). "Identification of a Plasmodium falciparum intercellular adhesion molecule-1 binding domain: a parasite adhesion trait implicated in cerebral malaria". Proceedings of the National Academy of Sciences of the United States of America. 97 (4): 1766â€“71. doi:10.1073/pnas.040545897. PMC 26510. PMID 10677532.
- Kraemer SM, Smith JD (August 2006). "A family affair: var genes, PfEMP1 binding, and malaria disease". Current Opinion in Microbiology. 9 (4): 374â€“80. doi:10.1016/j.mib.2006.06.006. PMID 16814594.
- Howell DP, Levin EA, Springer AL, Kraemer SM, Phippard DJ, Schief WR, Smith JD (January 2008). "Mapping a common interaction site used by Plasmodium falciparum Duffy binding-like domains to bind diverse host receptors". Molecular Microbiology. 67 (1): 78â€“87. doi:10.1111/j.1365-2958.2007.06019.x. PMID 18047571.
- Cowman AF, Crabb BS (February 2006). "Invasion of red blood cells by malaria parasites". Cell. 124 (4): 755â€“66. doi:10.1016/j.cell.2006.02.006. PMID 16497586.
- Rowe JA, Moulds JM, Newbold CI, Miller LH (July 1997). "P. falciparum rosetting mediated by a parasite-variant erythrocyte membrane protein and complement-receptor 1". Nature. 388 (6639): 292â€“5. doi:10.1038/40888. PMID 9230440.
- Vigan-Womas I, Guillotte M, Juillerat A, Hessel A, Raynal B, England P, Cohen JH, Bertrand O, Peyrard T, Bentley GA, Lewit-Bentley A, Mercereau-Puijalon O (2012). "Structural basis for the ABO blood-group dependence of Plasmodium falciparum rosetting". PLoS Pathogens. 8 (7): e1002781. doi:10.1371/journal.ppat.1002781. PMC 3395597. PMID 22807674.
- Baruch DI, Ma XC, Singh HB, Bi X, Pasloske BL, Howard RJ (November 1997). "Identification of a region of PfEMP1 that mediates adherence of Plasmodium falciparum infected erythrocytes to CD36: conserved function with variant sequence". Blood. 90 (9): 3766â€“75. doi:10.1182/blood.V90.9.3766. PMID 9345064.
- Hsieh FL, Turner L, Bolla JR, Robinson CV, Lavstsen T, Higgins MK (September 2016). "The structural basis for CD36 binding by the malaria parasite". Nature Communications. 7: 12837. doi:10.1038/ncomms12837. PMC 5052687. PMID 27667267.
- Howell DP, Samudrala R, Smith JD (July 2006). "Disguising itself--insights into Plasmodium falciparum binding and immune evasion from the DBL crystal structure". Molecular and Biochemical Parasitology. 148 (1): 1â€“9. doi:10.1016/j.molbiopara.2006.03.004. PMID 16621067.
- Stoute JA (October 2011). "Complement receptor 1 and malaria". Cellular Microbiology. 13 (10): 1441â€“50. doi:10.1111/j.1462-5822.2011.01648.x. PMID 21790941.
- Avril M, Brazier AJ, Melcher M, Sampath S, Smith JD (2013). "DC8 and DC13 var genes associated with severe malaria bind avidly to diverse endothelial cells". PLoS Pathogens. 9 (6): e1003430. doi:10.1371/journal.ppat.1003430. PMC 3694856. PMID 23825944.
- Avril M, Bernabeu M, Benjamin M, Brazier AJ, Smith JD (July 2016). "Interaction between Endothelial Protein C Receptor and Intercellular Adhesion Molecule 1 to Mediate Binding of Plasmodium falciparum-Infected Erythrocytes to Endothelial Cells". mBio. 7 (4): e00615â€“16. doi:10.1128/mBio.00615-16. PMC 4958245. PMID 27406562.
- Lau CK, Turner L, Jespersen JS, Lowe ED, Petersen B, Wang CW, Petersen JE, Lusingu J, Theander TG, Lavstsen T, Higgins MK (January 2015). "Structural conservation despite huge sequence diversity allows EPCR binding by the PfEMP1 family implicated in severe childhood malaria". Cell Host & Microbe. 17 (1): 118â€“29. doi:10.1016/j.chom.2014.11.007. PMC 4297295. PMID 25482433.
- Khunrae P, DahlbÃ¤ck M, Nielsen MA, Andersen G, Ditlev SB, Resende M, Pinto VV, Theander TG, Higgins MK, Salanti A (April 2010). "Full-length recombinant Plasmodium falciparum VAR2CSA binds specifically to CSPG and induces potent parasite adhesion-blocking antibodies". Journal of Molecular Biology. 397 (3): 826â€“34. doi:10.1016/j.jmb.2010.01.040. PMC 3715698. PMID 20109466.
- Deitsch KW, Chitnis CE (June 2012). "Molecular basis of severe malaria". Proceedings of the National Academy of Sciences of the United States of America. 109 (26): 10130â€“1. doi:10.1073/pnas.1207174109. PMC 3387049. PMID 22679282.
- Deshmukh, A. S.; Srivastava, S.; Dhar, S. K. (2013). "Plasmodium falciparum: epigenetic control of var gene regulation and disease". In Kundu, T. K. (ed.). Epigenetics: Development and Disease. Sub-Cellular Biochemistry. 61. Dordrecht: Springer. pp. 659â€“682. doi:10.1007/978-94-007-4525-4_28. ISBN 978-94-007-4524-7. PMID 23150271.
- Avril M, Tripathi AK, Brazier AJ, Andisi C, Janes JH, Soma VL, Sullivan DJ, Bull PC, Stins MF, Smith JD (June 2012). "A restricted subset of var genes mediates adherence of Plasmodium falciparum-infected erythrocytes to brain endothelial cells". Proceedings of the National Academy of Sciences of the United States of America. 109 (26): E1782â€“90. doi:10.1073/pnas.1120534109. PMC 3387091. PMID 22619321.
- Claessens A, Adams Y, Ghumra A, Lindergard G, Buchan CC, Andisi C, Bull PC, Mok S, Gupta AP, Wang CW, Turner L, Arman M, Raza A, Bozdech Z, Rowe JA (June 2012). "A subset of group A-like var genes encodes the malaria parasite ligands for binding to human brain endothelial cells". Proceedings of the National Academy of Sciences of the United States of America. 109 (26): E1772â€“81. doi:10.1073/pnas.1120461109. PMC 3387129. PMID 22619330.
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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
acidic terminal segments, variant surface antigen of PfEMP1 Provide feedback
ATS is the intracellular and relatively conserved acidic terminal segment of the Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) . this domain appears to be present in all variants of the highly polymorphic PfEMP1 proteins.
Lavstsen T, Salanti A, Jensen AT, Arnot DE, Theander TG;, Malar J. 2003;2:27.: Sub-grouping of Plasmodium falciparum 3D7 var genes based on sequence analysis of coding and non-coding regions. PUBMED:14565852 EPMC:14565852
This tab holds annotation information from the InterPro database.
InterPro entry IPR029211
ATS is the intracellular and relatively conserved acidic terminal segment of the Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) [ PUBMED:14565852 ]. This domain appears to be present in all variants of the highly polymorphic PfEMP1 proteins.
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
Loading domain graphics...
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Seed source:||Rask T, |
|Author:||Rask T, Coggill P|
|Number in seed:||24|
|Number in full:||878|
|Average length of the domain:||292.80 aa|
|Average identity of full alignment:||43 %|
|Average coverage of the sequence by the domain:||22.53 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.