1. Introduction
Nematodes (phylum Nematoda) diverged from other animals between 600–1,200 million years ago [1] and have become one of the most diverse animal phyla on earth, second only to arthropods. Many nematodes are parasites of plants, animals, and humans, posing major global ecological and economic challenges. Close to 30,000 species have been identified [1], with an estimated one million species thought to exist [2]. An astounding 16,000+ species are parasites of plants and animals, causing diseases worldwide of major socio-economic importance. In agriculture, the current financial losses caused by parasites to domesticated animals and crops greatly affect farm profitability and exacerbate challenges to global food production and distribution. Root-knot nematodes alone infect more than 3,000 plant species and cause an estimated $100 billion annual loss worldwide [3].
Nematode genomes encode for proteins specific to the phylum Nematoda, and are critically important for understanding nematode biology [4-6]. Proteins specific to the phylum Nematoda are ideal targets for drugs with low toxicity to the host and the environment. Despite the importance of nematode-specific proteins and protein families, few have been identified and very little information regarding them is available on public databases [7].
Recent studies have investigated a novel, nematode-specific family of proteins, the fatty acid and retinol binding (FAR) proteins of the phylum Nematoda. The limited information available regarding this family of proteins, as well as the areas that are poorly understood concerning their
The nematode model organism,
It was recently discovered that parasitic nematodes of plants, animals and humans secrete these structurally novel FAR proteins into the tissues they occupy [11].This family of proteins has been shown to be highly conserved across animal parasitic nematodes. The lipid-binding characteristics of FAR proteins across multiple families of parasitic nematodes, and their presence at the host-parasite interface, lends support to the idea that this nematode-restricted family of proteins may play a crucial role in the life cycle of the roundworms, providing essential lipids they cannot synthesize themselves [12], and possibly directly in the parasitism of their animal hosts. It is speculated by researchers that these proteins may interfere with intercellular lipid signaling to manipulate the defense reactions of the host or acquire essential lipids for the nematodes [10,13,14].
The highly conserved nematode-specific FAR proteins are thought to play a critical role in lipid sequestration and delivery from the host to the nematode of a broad range of essential fatty acids, retinoids and other nutrients. Hydrophobic lipophilic molecules such as fatty acids, eicosanoids, retinoids and steroids have important functions both as energy sources and in metabolic signaling [15]. They affect fundamental processes such as gene transcription, cell development, inflammation and the immune response [16-18].
2. Previous research on parasitic FAR proteins
To support the growing evidence that FAR proteins play an active role in nematode development and survival when in contact with host tissue, researchers have performed RT-PCR to determine the developmental stage specificity of
Based on secondary structure analysis, the structure of FAR proteins are clearly unlike that of any family of lipid-binding proteins, and also structurally distinct from proteins known from any organisms- from bacteria to plants to humans, increasing the possibility that they may present useful targets for drug development [20].
Below is an example of an abbreviated, ClustalW alignment demonstrating the conservation of amino acids from human parasitic FAR proteins across the phylum Nematode (Figure 1):
There is not three-dimensional structural information available for parasitic FAR proteins and there is little information available regarding key amino acids involved in the function of parasitic FARs. The empirical structural information that exists for FAR proteins is a circular dichroism analysis showing that the Ov-FAR-1 protein from
A study conducted in 2009 reported the X-ray crystallographic structure of Ce-FAR-7 from
In addition, a previous study investigating key amino acids in FAR ligand binding was performed on the FAR protein from the plant parasitic nematode
Thus, as it stands, there is a significant dearth of information available detailing amino acids that play a key role in ligand binding and protein function for FARs. Future work is likely to provide information on the key amino acids involved in fatty acid and lipid binding, which is essential to a basic understanding of FAR function and evolution, and the ability to utilize FAR proteins as a target for nematode-control measures.
To date, several FAR proteins, from a multitude of different nematode species, have been identified, recombinantly produced, isolated, and characterized [10,11,13,14].
FAR proteins discovered have been analyzed for fatty acid and retinol binding capabilities using spectrofluorimetry and fluorescence-based ligand-binding assays. Most commonly, fluorescence emission spectra were recorded at 20°C with the fluorescent fatty acid analog DAUDA or retinol diluted in PBS, as well as oleic acid diluted in PBS for competitive binding studies [10,11,13,14].
Image from Bath et al. 2009 Identification of an Immunogenic, Secreted Fatty Acid and Retinol-Binding Protein (Hp-FAR-1) from Heligmosomoides polygyrus. J. Nemat. 41(3):228-233.Figure 2.Example of an SDS-PAGE of recombinant His-tagged FAR protein (in this case, Hp-FAR-1), produced by nickel-affinity chromatography.Figures 3-5 demonstrate the specific results obtained for the FAR protein from
Figure 3 shows Hp-FAR-1 binding characteristics, which are typical for parasitic FAR proteins, demonstrating the FAR protein bound to the fluorophore-tagged fatty acid DAUDA to produce a significant blue shift in its peak emission from 543 nm to 484 nm, which is unusually large for lipid transporter proteins but typical for FAR proteins [11,13,14,21], and indicative of a highly apolar binding site. Figure 4 shows that the addition of oleic acid to Hp-FAR-1:DAUDA complexes displaced DAUDA from the protein’s binding site very efficiently, and complete replacement was observed at a ligand:competitor ratio of approximately 1:9. Figure 5 shows binding of retinol by Hp-FAR-1 which is indicated by a substantial increase in fluorescence emission intensity when retinol is added to a solution of Hp-FAR-1 in buffer [10].
Phosphorylation is one of the most common post-translational modifications that occurs on cellular proteins [22]. This process causes changes in the function, activity, localization, and/or stability in about 30 percent of cellular proteins [23]. A preliminary paper investigating the more distantly related Ce-FAR-7 protein presents evidence to suggest that retinol binding is positively regulated by CKII phosphorylation at a conserved site located near the binding pocket associated with retinol binding [15]. Previous research has also demonstrated that this is 100% conserved across all plant, animal and human parasitic nematode FAR proteins known to date [10,14,15,19].
Given this high conservation of the CKII phosphorylation site, and the overall high identity of the orthologs involved, it is reasonable to assume that CKII phosphorylation may also play a role in parasitic FAR:retinol binding. However, such studies have not yet been conducted, and basic questions regarding the role of the phosphorylation in parasitic nematodes, the impact of phosphorylation of Kds of ligand binding, and possible shifts in preference for ligands have not been analyzed.
Ligand binding by Hp-FAR-1. Protein was mixed with environment-sensitive fluorescent ligands DAUDA (panel A), oleic acid (panel B) or retinol (panel C).
Analysis of the impact of phosphorylation on parasitic FAR proteins is of great interest for future studies because the initial binding capabilities of the analyzed Ce-FAR-7 are distinctly different than those of the distantly human and animal parasitic FARs, and thus one cannot make the assumption that CKII phosphorylation has the same role in parasitic FARs. While the results from Ce-FAR-7 suggest that the retinol binding site (P2) is probably regulated by CKII, the fatty acid binding pocket (P1) was not affected by phosphorylation. However, Ce-FAR-7’s affinity for retinol is an order of magnitude lower than that for fatty acids, implying that, in contrast to the other FAR family members, transport of retinoids is not the major function of Ce-FAR-7 [15]. Thus, it is still unknown if the FAR protein affinity for signaling lipids, such as retinoids, is regulated in parasitic FARs, and if it is, how phosphorylation impacts the Kds of the bound ligands.
Nematode FARs may function in scavenging, transport and metabolism of hydrophobic lipophilic molecules such as fatty acids, eicosanoids, retinoids, and steroids. These molecules have important functions as energy sources and are used in metabolic and developmental processes of embryogenesis, glycoprotein synthesis, growth and cellular differentiation [24,25]. Parasites cannot synthesize all of the lipids required for metabolism, but instead rely on a ready-made supply from their host. FAR proteins might facilitate uptake, transport and distribution of these molecules to specific target tissues [24].
Secretion of FARs into host tissues by parasites may, however, have significance beyond mere resource acquisition, in particular as depletion of these substances can significantly alter the tissue environment. For example, retinol has intrinsic importance in collagen synthesis and tissue repair mechanisms in a variety of tissues including the skin and the gut [26]. Retinol also prevents the decline in IgA and Th2 cytokine levels [27].
Cellular responses to
3. Future directions and parasitic FARs as targets in drug development
There is an increasing interest by laboratories in investigating FAR proteins [11,14-15,30]. Continued studies will provide invaluable information as to exactly which amino acids are key in the binding of fatty acids and retinol, as well as the possible
A fuller appreciation of the function of FAR protein secretion will require a more detailed analysis and understanding of what parasitic FARs bind. Do they, for example, preferentially bind inflammatory mediators, their metabolic products or other potential pharmacologically active lipid mediators? Interference with such binding activities would likely have significant effects on the survival of nematodes and the impact of FARs on tissue dwelling and disease processes, and would further justify the relevance of targeting these molecules for drug targeting and/or vaccine development.
It is speculated, based on bioinformatic analyses, phylogenic studies, and the high conservation of FAR proteins amongst parasitic nematodes, that the evolution of FAR proteins may have been a precursor to nematode parasitism [13]. As such, it is also of interest to explore naturally occurring sequence variations, to determine which conserved regions or amino acids are imperative for ligand binding. Results from such studies are likely to shed more light on the role of FAR proteins in parasitism, with implications for their possible role(s) in the adaptation of free-living to parasitic lifestyles, by combining our knowledge of protein function with our information about sequence conservation from species to species.
Of particular interest for investigating the potential role of FARs in human parasitic diseases are the FAR affinities for the many vitamin A derivatives and fatty acids that are known to regulate expression of genes through the retinoic acid receptors (RARs) and retinoid X receptors (RXRs). These include RA in both of its stereoisomeric forms, all-trans retinoic acid (ATRA, binds RARs) and 13-cis-retinoic acid (binds RAR). In addition, 9-cis-retinoic acid, which is converted from 13-cis-retinoic acid (binds RARs and RXRs) [31]. Two other RAR-interacting retinoids have been identified in tissue: all-trans 13,14-dihydroretinoic acid and beta –apoands-14’-carotenal [32,33]. Phytanic acid [34], docosahexaenoic acid [35] and other unsaturated fatty acids [36] have been proposed as additional/alternative ligands for RXRs. Future research may investigate the binding abilities FARs to leukotrienes and prostaglandins, both of which are compounds involved in the inflammatory response [18].
As the screening of potential FAR ligands broadens, it will provide researchers with a much fuller appreciation of the potential function of FAR protein secretion. The information gained with respect to ligands bound would be useful in the design and analysis of FAR studies aiming to target FARs in parasites, by demonstrating the potential pathways that interference with FAR binding activities are likely to effect.
Investigating the potential role(s) of FAR proteins in parasitic nematodes at a range of physiologically relevant temperatures is an area of research that should not be overlooked, in the event that ligand binding dissociation constants (Kds) are temperature sensitive. Such an expansion of the analysis to include additional temperatures may be quite relevant, as previous research has demonstrated significant variation in the binding affinities of various proteins to their ligands with regard to environmental temperature [37], and nematode-specific FAR proteins have been shown to be heat-stable [13,20]. Given that plant-parasitic nematodes are much more prevalent during warmer seasons and in tropical climates [38-40] and that animal parasites would, by their nature, inhabit warmer environments, it seems possible that FAR studies conducted to date, at 20°C, may not accurately reflect the binding properties of this family of protein
The investigation of the role of phosphorylation by comparing the Kds for the most commonly tested ligands (DAUDA, oleic acid and RA) will likely be expanded by subjecting phosphorylated FAR proteins to a broader panel of ligands, to determine if the binding preferences and Kds for a broader range of ligands are altered upon phosphorylation. This knowledge would shed light on our basic understanding of nematode development and biology, by investigating the role of the conserved CKII phosphorylation site on FAR proteins with respect to ligand binding capabilities and respective Kds. The function of the N-terminal conserved CKII phosphorylation site on FARs may be important for ligand-binding. When phosphorylated, it may increase or decrease the affinity of the binding pockets for the binding of any number of essential fatty acids, retinoids and other nutrients that nematodes are not able to synthesize on their own [12]. Such knowledge sheds light on the possible
The ability of FAR proteins to bind fatty acids and retinoids is a characteristic of particular interest to parasitologists, due to the proteins potential function in nutrient acquisition, manipulation of the parasite’s environment, and countering host defense reactions [24,41,42]. Retinoids, in particular, have the potential to regulate the expression of multiple genes by various mechanisms [43], through the binding of either RARs or RXRs [28]. When bound with ligand, the receptors transactivate specific cis-elements of target genes, known as Retinoic Acid Response Elements (RAREs). It is through this mechanism that retinol acts to positively regulate the T cell-derived cytokine interleukin 4 (IL-4). This is a key finding with respect to animal and human parasitism, in that localized host IL-4 levels are directly correlated to host protection [9,28,29], and thus a parasites’ ability to regulate local IL-4 levels through an E/S protein may, in fact, be key to their survival.
Continued research in this area of FAR protein function will likely provide invaluable information regarding the possible
Our growing understanding of the nematode-specific family of protein continues to provide invaluable information regarding the possible
Acknowledgement
The authors would like to thank Kelsey Swagger (William Mitchell College of Law, St. Paul, MN) and Tyler Chase (Concordia College, Moorhead, MN) for their production of the ClustalW alignment of the parasitic FAR protein sequences.
References
- 1.
Caenorhabditis elegans is a nematode. ScienceBlaxter M. 1998 282 5396 2041 2046 - 2.
Biodiversity of nematode assemblages from the region of the Clarion-Clipperton Fracture Zone, an area of commercial mining interest. BMC EcologyLambshead P. J. Brown C. J. Ferrero T. J. Hawkins L. E. Smith C. R. Mitchell N. J. 2003 1 EOF - 3.
Analysis of Gene expression in soybean (Glycine max) roots in response to the root knot nematode Meloidogyne incognita using microarrays and KEGG pathways. BMC GenomicsIbrahim H. M. Hosseini P. Alkharouf N. W. Hussein E. H. Gamal-Din El Ael. K. Aly M. A. Matthews B. F. 2001 220 EOF - 4.
Plant parasitic nematode proteins and the host parasite interaction. Briefings in Functional Genomics & ProteomicsCurtis R. H. 2007 6 1 50 58 - 5.
Getting to the roots of parasitism by nematodes. Trends ParasitolDavis E. L. Hussey R. S. Baum T. J. 2004 20 3 134 141 - 6.
Characterization of plant nematode genes: identifying targets for a transgenic defence. ParasitologyLilley C. J. Urwin P. E. Atkinson H. J. 1999 Suppl) S63 72 - 7.
Molecular determinants archetypical to phylum Nematoda. BCM GenomicsYin Y. Martin J. Abubucker S. Wang Z. Wyrwicz L. Rychlewshi L. Mc Carter J. P. Wilson R. K. Mitreva M. 2009 114 EOF - 8.
Understanding chronic nematode infections: evolutionary considerations, current hypotheses and the way forward. Int. J. Parasitol.Behnke J. M. Barnard C. J. Wakelin D. 1999 22 7 861 907 - 9.
Paras. Immunol.Gustad T. Robinson M. Memory T. H. cells induce. alternatively activated. macrophages to. mediate protection. against nematode. parasites 1996 18 87 93 - 10.
Identification of an Immunogenic, Secreted Fatty Acid and Retinol-Binding Protein (Hp-FAR-1) from Heligmosomoides polygyrus. J. Nemat.Bath J. L. Robinson M. Kennedy M. W. Agbasi C. Linz L. Maetzold E. Scheidt M. Knox M. Ram D. Hein J. Clark C. Drees J. 2009 41 3 228 233 - 11.
Mol. Biochem. Parasitol.Garofalo A. Klager S. L. Rowlinson M. C. Nirmalan N. Klion A. Allen J. E. Kennedy M. W. Bradley J. E. The F. A. R. proteins of. filarial nematodes. secretion glycosylation. lipid binding. characteristics 2002 122 161 170 - 12.
Biochemistry of parasitic helminths. Baltimore, MD: University Park Press;Barrett J. 1981 - 13.
J.M., Kelly, S.M., Price, N.C., Cooper, A., Watson, D.G., Kennedy, M.W., Bradley, J.E. The FAR protein family of the nematode Caenorhabditis elegans- Differential lipid binding properties, structural characteristics, and developmental regulation. J. Biol. Chem.Garofalo A. Rowlinson M. C. Amambua N. A. Hughes J. M. Kelly S. M. Price N. C. Cooper A. Watson D. G. Kennedy M. W. Bradley J. E. The F. A. R. protein family. of the. nematode Caenorhabditis. elegans-Differential lipid. binding properties. structural characteristics. developmental regulation. 2003 278 8065 8074 - 14.
Biochem. J.Prior A. Jones J. T. Blok V. C. Beauchamp J. Mc Dermott L. Cooper A. Kennedy M. W. A. surface-associated retinol. fatty acid-binding. protein . Gp-F A. R- from the. potato cyst. nematode Globodera. pallida lipid. binding activities. structural analysis. expression pattern. 2001 356 387 394 - 15.
JBCJordanova R. Groves M. R. Kostova E. Woltersdorf C. Liebau E. Tucker P. A. Fatty acid. retinoid-binding proteins. have distinct. binding pockets. for the. two types. of cargo. J. B. 2009 284 51 35818 26 - 16.
Inflammation and Metabolic Disorders. NatureHotasmisligil G. S. 2006 444 1721 860 867 - 17.
Identification of a lipokine, a lipid hormone linking adipose tissue to systemic metabolism. CellCao H. Gerhold K. Mayrs J. R. Wiest M. M. Watkins S. M. Hotasmisligil G. S. 2008 134 6 933 944 - 18.
Funk, C.D. Prostaglandins and leukotrienes: advances in eicosanoid biology. Science2001 294 5548 1871 1875 - 19.
Basavaraju, S., Zhan, B., Kennedy, M.W., Liu, Y., Hawdon, J., Hotez, P.M. Ac-FAR-1, a 20 kDa fatty acid- and retinol-binding protein secreted by adult Ancylostoma caninum hookworms: gene transcription pattern, ligand binding properties and structural characterization. Mol Biochem Parasitol.2003 126 1 63 71 - 20.
Characterisation of a fatty acid and retinol binding protein orthologue from the hookworm Ancylostoma ceylanicum. Int. J. Parasit.Fairfax K. C. Vermeire J. J. Harrison L. M. Bungiro R. D. Grant W. Husain S. Z. Cappello M. 2009 39 1561 1571 - 21.
JBCKennedy M. W. Garside L. H. Goodrick L. E. Mc Dermott L. Brass A. Price N. C. Kelly S. M. Cooper A. Bradley J. E. The Ov. protein of. the parasitic. nematode Onchocerca. volvulus-A structurally. novel class. of small. helix-rich retinol-binding. proteins J. B. 1997 272 47 29443 48 - 22.
Dynamic interactions of proteins in complex networks: A more structured view. FEBS JournalStein A. Pache R. A. Bernad P. Pons M. Aloy P. 2009 276 19 5390 405 - 23.
Trends in GeneticsPtacek J. Snyder M. Charging it. up Global. analysis of. protein phosphorylation. 2006 22 10 545 54 - 24.
The polyprotein lipid binding proteins of nematodes. Biochem Biophys ActaKennedy M. W. 2000 1476 149 164 - 25.
Novel classes of fatty acid and retinol binding protein from nematodes. Molecular and Cellular BiochemistryMc Dermott L. Cooper A. Kennedy M. W. 1999 69 EOF 75 EOF - 26.
Nutrient antioxidants in gastrointestinal diseases. Gastroenterol Clin North AM.Bulger E. M. Helton W. S. 1998 27 2 403 19 - 27.
J. Nutr.Nikawa T. Odahara K. Koizumi H. Kido Y. Teshima S. Rokutan K. Kishi K. Vitamin A. prevents the. decline in. immunoglobin A. Th cytokine. levels in. small intestinal. mucosa of. protein-malnourished mice. 1999 129 5 934 941 - 28.
Requirements for the development of IL-4-producing T cells during intestinal nematode Infections: what it takes to make a Th2 cell in vivo. Immunol. Rev.Liu Z. Liu Q. Pesce J. Anthony R. M. Lamb E. Whitmire J. Hamed H. Morimoto M. Urban Jr J. F. Gause W. C. Anthony R. 2004 201 57 74 - 29.
Nature MedicineAnthony R. M. Urban Jr J. F. Alem F. Hamed H. A. Rozo C. T. Boucher J. Van Rooijen N. Gause W. C. Memory T. H. cells induce. alternatively activated. macrophages to. mediate protection. against nematode. parasites 2006 12 955 960 - 30.
How helminth lipid-binding proteins offload their ligands to membranes: differential mechanisms of fatty acid transfer by the ABA-1 polyprotein allergen and Ov-FAR-1 proteins of nematodes and Sj-FABPc of schistosomes. J. Biochem.Mc Dermott L. Kennedy M. W. Mc Manus D. P. Bradley J. E. Cooper A. 2002 41 21 6706 6713 - 31.
Faseb J.Chambon P. A. decade of. molecular biology. of retinoic. acid receptors. 1996 10 9 940 954 - 32.
Metabolism and transactivation activity of 13,14-dihydroretinoic acid. J. Biol. Chem.Moise A. R. Kuksa V. Blaner W. S. Baehr W. Palczewski K. 2005 280 27815 27825 - 33.
Asymmetric cleavage of {beta}-carotene yields a transcriptional repressor of RXR and PPAR responses. Mol. Endocrinol.Ziouzenkova O. Orashanu G. Sukhova G. Lau E. Berger J. P. Tang G. Krinsky N. I. Dolnikowski G. G. Plutzky J. 2007 21 1 77 88 - 34.
Phytanic acid is a retinoid X receptor ligand. Eur. J. Biochem.Lemotte P. K. Keidel S. Apfel C. M. 1996 236 328 333 - 35.
Sciencede Urquiza A. M. Liu S. Sjoberg M. Zetterstrom R. H. Griffiths W. Sjovall J. Perlmann T. Docosahexaenoic acid. a. ligand for. the retinoid. X. receptor in. mouse brain. 2000 290 2140 2144 - 36.
Isolation and characterization of unsaturated fatty acids as natural ligands for the retinoid-X receptor. Arch. Biochem. Biophys.Goldstein J. T. Dobrzyn A. Clagett-Dame M. Pike J. W. De Luca H. F. 2003 420 185 193 - 37.
Homologous proteins with different affinities for groEL- The refolding of the aspartate aminotransferase isozymes at varying temperatures. JBCMattingly Jr J. R. Iriarte A. Martinez-Carrion M. 1995 270 3 1138 48 - 38.
Stable virulence against the tomato resistance Mi gene in the parthenogenetic root-knot nematode Meloidogyne incognita. PhytopathologyCastagnone-Sereno P. Bongiovanni M. Dalmassto A. 1993 83 8 803 805 - 39.
The heat-stable root-knot nematode resistance gene Mi-9 from Lycopersicon peruvianum is localized on the short arm of chromosome 6. Theor. Appl. Genet.Ammiraju J. Veremis J. Huang X. Roberts P. Kaloshian I. 2003 106 3 478 84 - 40.
High-resolution mapping and chromosome landing at the root-knot nematode resistance locus Ma from Myrobalan plum using a large-insert BAC DNA library. Theor. Appl. Genet.Claverie M. Dirlewanger E. Cosson P. Bosselut N. Lecouls A. C. Voisin R. Kleinhentz M. Lafargue B. Caboche M. Calhoub B. Esmenjaud D. 2004 109 6 1318 27 - 41.
Wallingford and New York: CABI publishing;Kennedy M. W. Molecular Biology. Biochemistry Immunology In. Kennedy M. W. Harnett W. (eds Parasitic Nematodes. 2001 309 330 - 42.
Bradley J. E. Nirmalan N. Klager S. L. Faulkner H. Kennedy M. W. Trends Parasitol. 2001 17 471 475 - 43.
Gene expression regulation by retinol acid. J. Lipid Res.Balmer J. E. Blomhoff R. 2002 43 11 1773 1808