Complete conservation of an immunogenic gene (lcr1) in Leishmania infantum and Leishmania chagasi isolated from Iran, Spain and Brazil.
The leishmaniasis is a spectrum of diseases of humans and other mammals. The disease is caused by kinetoplastid flagellates of genus Leishmania (L.). Kala-azar is the visceral and most severe form of these diseases that leads to death if untreated. The yearly incidence of visceral leishmaniasis (VL) is 0.5 million cases (1,2). VL is currently sporadic in all 30 provinces of Iran and endemic in at least threee provinces of the country (3,4). In a year prospective survey in north-west Iran, the average incidence rate of infection was 2.8% per year with all ages equally at risk. One in 13 infections in children led to VL, and this ratio decreased significantly with age (5). The causative agents of VL are members of L. donovani complex, classified into four species: L. archibaldi, L. chagasi, L. donovani and L. infantum, distinguished by the vectors, reservoir host and in pathology (6). Leishmania strains isolated from kala-azar patients in Iran have been identified as L. infantum (3,7) which is the principal agent of the disease in animal reservoir hosts in different parts of Iran (8). L. chagasi is the usual causative agent of kala-azar in the Americas (9,10). The New World species Leishmania chagasi is now widely accepted to be a synonym of L. infantum; however, in recent work Latin American authors still consider these species to be distinct (11). Definitive proof that L. chagasi and L. infantum are synonymous is not yet established (12,13).
There is need for development of effective tools for detection, prevention and treatment of kala-azar (14). An important feature of a vaccine candidate, or component of a subunit vaccine against leishmaniasis is conservation of the molecule throughout different species and strains of the parasites. A molecule used as a diagnostic criterion either by serology or PCR, would have the same requirement. Thus, the question of whether L. infantum and L. chagasi are identical or distinct, and the degree of conservation of antigenic proteins across species and strains, has important implications for development of a new diagnostic test or vaccine. An important implication would be use of the results obtained from studies on one species to the other, if these two Leishmania species are identical. An example would be the possible use of LCR1 of L. chagasi as part of a protective vaccine against both L. chagasi and L. infantum. LCR1 was discovered from L. chagasi and has been shown to confer partial protection against L. chagasi in a mouse model15. An lcr1 homologue sequence has been reported from one strain of L. infantum (MCAN/ES/98/LLM-877), (GenBank Accession number: AM502245.1) from Spain. Whether LCR1 molecule is conserved in other strains of L. infantum remains to be studied. The aim of our study was to compare the sequence of /crl between an Iranian isolate of L. infantum and L. chagasi. For this purpose we determined lcr1 sequence in an Iranian isolate of L. infantum and compared it with homologous sequences from L. chagasi and L. infantum reported in GenBank.
Material & Methods
Parasite: Leishmania infantum MHOM/04/IR/IPI UN10 was isolated from a 1.5 yr old boy from Imam Khomeini Hospital in Tehran, Iran in 2004. Diagnosis of kala-azar was confirmed in this child by isolation of the parasite from bone marrow culture in NNN media. The isolate was stored in liquid nitrogen soon after isolation. The parasite was recovered from liquid nitrogen by thawing and culturing it in NNN media (16). Logarithmically growing parasites were harvested and washed by centrifugation in phosphate buffer saline (PBS) twice and were stored in aliquots of 100 x [10.sup.8] parasites (for DNA extraction) and 1 x [10.sup.9] parasites (for isoenzyme electrophoresis) in -70[degrees]C. The following reference strains were used in isoenzyme electrophoresis studies: L. major strain MRHO/IR/75/ER, L. tropica strain MHOM/SU/74/ K27, and L. infantum strain MHOM/TN/80/IPT1.
Isoenzyme e/ectrophoresis: Discontinuous vertical polyacrylamide gel electrophoresis (PAGE) and cellulose acetate were used for isoenzyme analysis of the isolate. About 1 x [10.sup.9] parasites were mixed with equal volumes of a hypotonic aqueous solution of enzyme stabilizer (1 mM EDTA, 1 mM [epsilon]-aminoncaproic acid, 1 mM dithiothreitol), frozen and thawed thrice. Soluble extract of lysed promastigotes was prepared by centrifugation at 30,000> g at 4[degrees]C for 30 min, and stored at -70[degrees]C until use. Four enzymes were used for analysis of isolates: malate dehydrogenase (MDH), malic enzyme (ME), glucose phosphate isomerase (GPI), superoxide dismutase (SOD) (17,18).
ITS1 sequencing: Genomic DNA was extracted by LiC1 extraction (19). The internal transcribed spacer 1 (ITS1) region was amplified using DNA extracted from parasite and ITS1 specific primers LITSR and L5.8S and analyzed by restriction fragment length polymorphism (RFLP) analysis using the restriction endonuclease HaeIII (20). PCR amplification of genomic DNA of L. infantum by ITS1 specific primers resulted in a sharp single band on agarose gel electrophoresis. The PCR product was directly sent for sequencing (Macrogene Company, Korea). Each PCR product was sequenced at least twice by ITS1 specific primers: once by forward primer (LITSR) and once by reverse primer (L5.8S). Nucleotide in each position was considered correct if two sequencing results (which were sequenced in opposite directions) confirmed each other.
Amplification of lcr1: Polymerase chain reaction (PCR) was performed in 200 [micro]1 thin wall tubes. Each reaction consists of 3 [micro]l genomic DNA (containing 6-8 ng DNA), 0.4 [micro]1 Taq DNA polymerase (5 units) (GenetBio Co., Korea), 1.5 [micro]1 of [MgCl.sub.2] (25 mM), 0.5 [micro]1 of dNTPs (10 mM) and 2.5 [micro]1 10 x PCR buffer (GenetBio Co., Korea), 0.125 [micro]1 of each forward and reverse primers (100 pmol/[micro]1). The primers flanked the reported antigenic fragment of lcr1 (21).
The sequences and names of forward and reverse primers were: 5'-TAGGGATCCCATGAGCTG GCCAAA-3' (named LCR1-F1) and 5' GTCGACAAGCTTACTCGAGGTCCT CGATGG 3' (named LCR1-R1), respectively. The primers included restriction sites (underlined) for BamHI (in lcr1-F1) and HindIII (in lcr1-R1). PCR was performed in thermocycler (Mastercycler gradient, Eppendorf Co., Hamburg, Germany) under the following program: 95[degrees]C for 2 min, 35 cycles of 95[degrees]C for 20 sec, 65.1[degrees]C for 30 sec, and 72[degrees]C for 1 min, and 72[degrees]C for 25 min. Great cares were taken to prevent contamination including using disposable tips and tubes and performance of the procedure under laminar air flow. Template negative tube was included in all runs and results were disregarded if template negative control showed any band (even faint) in agarose gel electrophoresis. All the PCR products were electrophoresed in 1% agarose gel.
Restriction fragment length polymorphism (RFLP): PCR product obtained by using primers specific for lcr1 was digested by restriction enzyme HaeIII (BsuRI) (Fermentas Co., Ontario, Canada) at concentration of10 unit/[micro]1 for 4 h at 37[degrees]C. The reaction was terminated on dry plate at 80[degrees]C for 20 min. The digested and undigested PCR products were electrophoresed in 1% agarose gel and their molecular weight were approximately determined using 1 Kb molecular weight marker (Fermentas Co., Ontario, Canada).
Sequencing of lcr1 through T/A cloning: Amplification of the lcr1 gene from L. infantum genomic DNA by lcr1 specific primers resulted in a major band of the expected molecular size (785 bp). The band was extracted from agarose gel using Silica Bead DNA Gel Extraction kit (Fermentas Co., Ontario, Canada). The gel extracted DNA fragments were cloned using the InsTA cloning kit (Fermentas Co., Ontario, Canada) according to the manufacturer's instructions. Briefly, gel extracted DNA fragment was ligated into pTZ57R plasmid and transformed into DH5[alpha] strain of Escherichia coli. Plasmids were prepared using the Accu Prep Plasmid Mini Extraction plasmid purification kit (Bioneer Co., Korea) according to the manufacturer's instructions. The DNA inserts were sequenced (Macrogene Company, Korea) at least twice using the forward and reverse plasmid specific primers. Nucleotide in each position was considered correct if the two sequencing results confirmed each other.
Cloning and sequencing of lcr1 by Pfu DNA polymerase: To determine whether the sequence variants were created during PCR due to Taq polymerase error, lcr1 was amplified from the parasite genomic DNA by Pfu DNA polymerase (Fermentas Co., Ontario, Canada) which exhibits 3'[right arrow]5' exonuclease (proof reading) activity according to manufacturer's instructions. PCR product of lcr1 was extracted from gel as mentioned above for T/A cloning. The PCR product was inserted into pRSET A plasmid (Invitrogen Co., Carlsbad, USA) by double digestion of both lcr1 PCR product and the plasmid, extraction of digested products from gel, and ligation of lcr1 into the plasmid by ligase (Fermentas Co., Ontario, Canada) according to manufacturer's instructions. The insert containing plasmid was transformed into TOP10F' E. coli (Invitrogen Co. Carlsbad, USA). The plasmid was purified from transformed bacteria, screened by colony PCR method (22) followed by digestion by HaeIII (Fermentas Co., Ontario, Canada) for finding plasmids with correct insert. Two plasmids containing lcr1 were sequenced by plasmid specific primers (Macrogen Company, Korea).
Species identification by isoenzyme electrophoresis: The Leishmania isolate studied in the present report (MHOM/04/IR/IPI-UN10) was identified as L. infantum by isoenzyme electrophoresis. The isoenzyme profiles of this isolate were consistent with the profile of L. infantum strain MHOM/TN/80/IPT1. This conclusion was based on the isoenzyme profiles of four enzymes: malate dehydrogenase (MDH) (Fig. 1), malic enzyme (ME), glucose phosphate isomerase (GPI), and superoxide dismutase (SOD).
Species identification by ITS1 sequencing: The ITS1 of the Leishmania isolate studied in the present report was sequenced and submitted to GenBank (accession number GQ444144) (Fig. 2). The species of this isolate was confirmed to be L. infantum as its ITS1 is completely identical to ITS1 sequence located in chromosome 27 of L. infantum strain MCAN/ES/98/LLM-877 reported in GenBank (Accession No. AM502245.1). The ITS1 sequence of L. infantum MHOM/04/IR/IPI-UN10 (studied in the present study) was completely identical to ITS1 sequence of many L. chagasi strains, e.g. strain MHOM/BR/85/M9702 (Accession No. AJ000306).
RFLP of lcr1 sequence: PCR amplification of lcr1 fragment from L. infantum MHOM/04/IR/IPI-UN10 resulted in an amplicon with size of the expected 785 bp (Fig. 3). Digestion of lcr1 with HaeIII resulted in two bands of 631 and 142 bp long (and a 12 bp band that cannot be seen, due to its too short length in agarose gel) (Fig. 3). This restriction digestion pattern is consistent with the published lcr1 sequence of L. chagasi (23).
[FIGURE 1 OMITTED]
Lcr1 sequence: Plasmids containing lcr1 sequence obtained by T/A cloning method (PCR amplification was performed by taq DNA polymerase) were extracted from three different clones of the recombinant bacteria and sequenced using plasmid specific primers. These three lcr1 sequences were compared with the published sequence from lcr1 of L. chagasi (Fig. 4). Each of these three lcr1 sequences had 1-2 different nucleotides in comparison to lcr1 of L. chagasi. The difference in the nucleotides present in these clones was attributed to lack of proof reading of Taq DNA polymerase used for amplification. This conclusion is valid because each discordant nucleotide is only present in one clone and is absent in the other two clones. This is true for all nucleotide discrepancies observed between the three clones. In addition, sequences of two clones obtained by Pfu DNA polymerase confirmed the sequence concluded from the Taq-amplified sequences (Fig. 4). These data show that the sequence of lcr1 of the Iranian L. infantum is completely identical to lcr1 sequences of L. chagasi. The concluded sequence of lcr1 from L. infantum MHOM/04/IR/UN-10 was submitted to GenBank (Accession No. GQ850521.1) (Fig. 5), and was compared with lcr1 reported for L. chagasi and L. infantum in GenBank. Lcr1 sequence of our Iranian isolate is identical to lcr1 sequence ofL. chagasi and lcr1 sequence of L. infantum (Accession Nos. U23437.1 and AM502245.1 respectively).
[FIGURE 3 OMITTED]
Sequence analysis of the Leishmania spp. genomes is leading to the conclusion that two Leishmania species causing visceral leishmaniasis, L. chagasi isolated from subjects in the New World and L. infantum derived from patient in the Old World, may be one and the same13. This implies that new diagnostic assays or vaccine candidates may exhibit identical efficacy for each of these species. Nonetheless, in advance of full agreement that these are indeed identical species, it is important to compare the nucleotide and protein sequences of genes and gene products chosen for clinical assay development. The purpose of this study was to assess the potential utility of the LCR1 protein for diagnosis of or immunization against visceral leishmaniasis caused by L. infantum in Iran. We, therefore, compared the sequence of lcr1 fragment in an Iranian isolate of L. infantum with the homologous regions from a Brazilian L. chagasi isolate (strain MHOM/BR/00/1669) and a Spanish L. infantum (MCAN/ES/98/LLM-877).
The data presented in this paper are novel; the first report about lcr1 from an Iranian L. infantum isolate. Our results showed that the ITS1 and the lcr1 sequences were identical among all three genomes (Iranian L. infantum, Spanish L. infantum, and Brazilian L. chagasi). This finding is in agreement with reports that L. infantum and L. chagasi are synonymous (12, 24-27).
Complete identity of the antigenic region of the LCR1 protein in isolates of L. infantum from different regions of the Old World (Iran and Spain) and with that of L. chagasi from Brazil (New World) is an important step in evaluation of this molecule for potential clinical use. The complete conservation of LCR1 indicates that LCR1 could be evaluated as a potential component of a subunit vaccine against VL. The next step will be to study immune response to LCR1 protein in human individuals exposed to L. infantum or L. chagasi in different countries. We propose that similar sequence evaluation in strains from diverse geographic regions be performed prior to testing antigenic peptides for their potential as protective vaccines.
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H. Mahmoudzadeh-Niknam [a], F. Abrishami [a], M. Doroudian [a], M. Moradi [a], M.H. Alimohammadian [a] & P. Parvizi [b]
[a] Department of Immunology; [b] Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
Corresponding author: Dr Hamid Mahmoudzadeh-Niknam, Department of Immunology, Pasteur Institute of Iran, Tehran 13164, Iran.
E-mail: email@example.com; firstname.lastname@example.org
Received: 30 May 2010
Accepted in revised form : 23 October 2010
Fig. 2: ITS1 containing sequences in L. infantum isolate MHOM/IR/04/IPI-UN10 (GenBank Accession: GQ444144.1). Genomic DNA of L. infantum was amplified by ITS1 specific primers and the PCR product was directly sequenced. Each PCR product was sequenced at least twice (from opposite directions). 1 ctggatcatt ttccgatgat tacacccaaa 61 tatatatgta ggcctttccc acatacacag 121 aaaaaggccg atcgacgtta taacgcaccg 181 caaaaaatat acggcgtttc ggtttttggc 241 cataacgtgt cgcgatggat gacttggctt 301 gataagtggt atca 1 aaacatatac aactcgggga gacctatgta 61 caaagttttg tactcaaaat ttgcagtaaa 121 cctatacaaa agcaaaaatg tccgtttata 181 ggggtgggtg cgtgtgtgga taacggctca 241 cctatttcgt tgaagaacgc agtaaagtgc 301 Fig. 4: Lcr1 nucleotide differences between 5 clones obtained from the Iranian L. infantum and the reported L. chagasi in GenBank. PCR amplification was performed by Taq or Pfu DNA polymerases for the indicated clones. The rest of nucleotides in the 785 nucleotide span of lcr1 were identical in all five clones of the Iranian L. infantum and L. chagasi. Enzyme used for Position Sequence origin amplification 254 Clone No. 4 Taq DNA polymerase A Clone No. 6 Taq DNA polymerase G Clone No. 3 Taq DNA polymerase G Clone No. 2 Pfu DNA polymerase G Clone No. 16 Pfu DNA polymerase G L. chagasi (GenBank Accession No. U23437.1) -- G Position Position Position Sequence origin 312 396 691 Clone No. 4 G A C Clone No. 6 A A T Clone No. 3 G G T Clone No. 2 G A T Clone No. 16 G A T L. chagasi (GenBank Accession No. U23437.1) G A T Fig. 5: Lcr1 sequence of L. infantum isolate MHOM/IR/04/IPI-UN10 (GenBank Accession: GQ850521.1). 1 cccatgagct ggccaaagtc gaactggcga 61 agggcgtgcc actggcggac ctcccgctca 121 agcagcgtca ggcgctgaag aacaccagga 181 aggagaggat gaacgaccgt gtccacgaca 241 gctacctgaa cccggagccg cagaatgtac 301 cgatcttccg cgaaatggag aacgagctgt 361 cgggcaagat tgcagagctg caggacgacc 421 acctacggcg caaggagctt gctaatcagg 481 agctgccact caactacgac ccgatcctca 541 agaaaaaccc gaagcggaat gccgatgtgc 601 gcatcgatga catcgcgcgc gactttctgg 661 cggagggggt gcaattggag cgcctgccgc 721 agagggacct gcgcgcgctg aagaagcaac 781 tcgag 1 aggaccgtgc cttcctcgac cctgagccgg 61 gcgacgaccc ggagttcaac gtactggcga 121 ggggccgcga ccccgaaatg aaggacctgg 181 tcgcaaggga gttcctcagc aagcaccgcg 241 ccattgccga catccccctc aaccgcgacc 301 tgaaggctat gaaggacccc cgcagcaatg 361 tcaacaaccg cgcagacgac ctcgcgaagg 421 agcaggagcc tctcggcgtg ccgctggaag 481 atccactgga acgcaagcgc cgcgacatca 541 tgcgcaacct cgagcgggag atcgccgcgc 601 cgaaggagcg tgctttcctg gaccaggaac 661 tgtcagatga cagggagttt cacgaaatgg 721 cagcaaagaa cagggacgcc atcgaggacc 781
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|Author:||Mahmoudzadeh-Niknam, H.; Abrishami, F.; Doroudian, M.; Moradi, M.; Alimohammadian, M.H.; Parvizi, P.|
|Publication:||Journal of Vector Borne Diseases|
|Date:||Dec 1, 2010|
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