Marisa Farber

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5′ ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct.

Genetic diversity of Anaplasma marginale in Argentina.

Bovine anaplasmosis caused by Anaplasma marginale is a worldwide major constraint to cattle production. The A. marginale major surface protein 1 alpha (msp1alpha) gene contains a variable number of tandem repeats in the amino terminal region and has been used for the characterization of pathogen genetic diversity. This study reports the first characterization of A. marginale genetic diversity in Argentina based on msp1alpha genotypes and its putative relationship with Rhipicephalus (Boophilus) microplus infestations. Herein, we analyzed whole blood bovine samples from anaplasmosis outbreaks in R. microplus infested (9 samples) and eradicated/free (14 samples) regions. Sequence analysis revealed the existence of 15 different msp1alpha genotypes with 31 different repeat units. Six new repeat sequences were discovered in this study and 13/31 (42%) repeats were unique to Argentinean strains. The analysis of msp1alpha repeat sequences according to R. microplus infestations resulted in three repeat groups: (i) found in tick-infested regions (20 repeats), (ii) found in tick free regions (6 repeats) and (iii) randomly distributed (5 repeats). Moreover, A. marginale msp1alpha genetic diversity was higher in tick-infested regions than in tick free areas. These results, together with previous evidence suggesting that A. marginale msp1alpha repeat units co-evolved with the tick vector, might represent an evidence of the role of tick-mediated transmission for the generation of pathogen genetic diversity.

Detection of “Candidatus Rickettsia sp. strain Argentina”and Rickettsia bellii in Amblyomma ticks (Acari: Ixodidae) from Northern Argentina

Ixodid ticks were collected from vegetation and from humans, wild and domestic mammals in a rural area in the semi-arid Argentine Chaco in late spring 2006 to evaluate their potential role as vectors of Spotted Fever Group (SFG) rickettsiae. A total of 233 adult ticks, identified as Amblyomma parvum, Amblyomma tigrinum and Amblyomma pseudoconcolor, was examined for Rickettsia spp. We identified an SFG rickettsia of unknown pathogenicity, “Candidatus Rickettsia sp. strain Argentina”, in A. parvum and A. pseudoconcolor by PCR assays targeting gltA, ompA, ompB and 17-kDa outer membrane antigen rickettsial genes. Rickettsia bellii was detected in a host-seeking male of A. tigrinum. Amblyomma parvum is widespread in the study area and is a potential threat to human health.

Natural Selection for Operons Depends on Genome Size

In prokaryotes, genome size is associated with metabolic versatility, regulatory complexity, effective population size, and horizontal transfer rates. We therefore analyzed the covariation of genome size and operon conservation to assess the evolutionary models of operon formation and maintenance. In agreement with previous results, intraoperonic pairs of essential and of highly expressed genes are more conserved. Interestingly, intraoperonic pairs of genes are also more conserved when they encode proteins at similar cell concentrations, suggesting a role of cotranscription in diminishing the cost of waste and shortfall in gene expression. Larger genomes have fewer and smaller operons that are also less conserved. Importantly, lower conservation in larger genomes was observed for all classes of operons in terms of gene expression, essentiality, and balanced protein concentration. We reached very similar conclusions in independent analyses of three major bacterial clades (α- and β-Proteobacteria and Firmicutes). Operon conservation is inversely correlated to the abundance of transcription factors in the genome when controlled for genome size. This suggests a negative association between the complexity of genetic networks and operon conservation. These results show that genome size and/or its proxies are key determinants of the intensity of natural selection for operon organization. Our data fit better the evolutionary models based on the advantage of coregulation than those based on genetic linkage or stochastic gene expression. We suggest that larger genomes with highly complex genetic networks and many transcription factors endure weaker selection for operons than smaller genomes with fewer alternative tools for genetic regulation.

Efficiency of a recombinant MSA-2c-based ELISA to establish the persistence of antibodies in cattle vaccinated with Babesia bovis

Bovine babesiosis is caused by Babesia bovis and B. bigemina in Argentina. These protozoans are prevalent north of parallel 30 degrees S, where their natural vector Rhipicephalus (Boophilus) microplus is widespread. To prevent babesiosis outbreaks in endemic areas, an increasing population of 4-10-month-old calves are vaccinated with low virulence B. bovis R1A (BboR1A) and B. bigemina S1A (BbiS1A) strains. In non-endemic areas, an additional calf population is also vaccinated and boostered as adults, before they are relocated to R. microplus-endemic areas of the country. Serological tests are currently utilized not only to determine the status of natural Babesia spp. infections, but also to confirm the infection caused by vaccine strains. For this purpose, an indirect enzyme immunoassay (ELISA) based on the recombinant major surface antigen-2c (rMSA-2c) of B. bovis expressed in Escherichia coli, was standardized using sera from Babesia spp. experimentally infected cattle. ELISA(rMSA-2c) was validated using sera obtained weekly during 336 days from steers primed and boostered with BboR1A and/or BbiS1A on days 0 and 154, then compared with the immunofluorescent-antibody test (IFAT). Western blot (WB) protein analysis was used to confirm the specificity of the immune response to rMSA-2c. The sensitivity and specificity for ELISA(rMSA-2c) were 92 and 96% after the Babesia spp. priming and 88 and 73% after the boostering immunization, respectively. The sensitivity and specificity for IFAT were 99 and 90% after priming and 92 and 98% after boostering, respectively. Unlike IFAT, ELISA(rMSA-2c) detected a remarkable delayed booster response and a significant drop in specificity between 35 and 84 days after the booster immunization. Simultaneously, 87.5% of cattle boostered with B. bigemina showed cross-reactions in the ELISA(rMSA-2c), particularly between 63 and 77 days after the inoculation. A reaction against E. coli was observed, since bands of approximately 40 and/or 42kDa were detected using sera from cattle before and after Babesia spp. inoculations. ELISA(rMSA-2c) showed to be useful between 42 and 98 days after priming with Babesia spp. live vaccine to evaluate the success of infecting cattle. However, after boostering the test showed low specificity.

The twin-arginine translocation pathway in α-proteobacteria is functionally preserved irrespective of genomic and regulatory divergence.

The twin-arginine translocation (Tat) pathway exports fully folded proteins out of the cytoplasm of Gram-negative and Gram-positive bacteria. Although much progress has been made in unraveling the molecular mechanism and biochemical characterization of the Tat system, little is known concerning its functionality and biological role to confer adaptive skills, symbiosis or pathogenesis in the α-proteobacteria class. A comparative genomic analysis in the α-proteobacteria class confirmed the presence of tatA, tatB, and tatC genes in almost all genomes, but significant variations in gene synteny and rearrangements were found in the order Rickettsiales with respect to the typically described operon organization. Transcription of tat genes was confirmed for Anaplasma marginale str. St. Maries and Brucella abortus 2308, two α-proteobacteria with full and partial intracellular lifestyles, respectively. The tat genes of A. marginale are scattered throughout the genome, in contrast to the more generalized operon organization. Particularly, tatA showed an approximately 20-fold increase in mRNA levels relative to tatB and tatC. We showed Tat functionality in B. abortus 2308 for the first time, and confirmed conservation of functionality in A. marginale. We present the first experimental description of the Tat system in the Anaplasmataceae and Brucellaceae families. In particular, in A. marginale Tat functionality is conserved despite operon splitting as a consequence of genome rearrangements. Further studies will be required to understand how the proper stoichiometry of the Tat protein complex and its biological role are achieved. In addition, the predicted substrates might be the evidence of role of the Tat translocation system in the transition process from a free-living to a parasitic lifestyle in these α-proteobacteria.

Molecular Characterization of Babesia bovis Strains Using PCR Restriction Fragment Length Polymorphism Analysis of the msa2‐a/b Genes

The merozoite surface antigen‐2 (msa‐2) family of Babesia bovis is a group of variable genes that share conserved 5′ and 3′ ends and encode for membrane‐anchored glycoproteins that have been postulated as vaccine candidates. In this work, we analyzed the sequences of three of these genes (msa‐2a1, a2, and 2b) from two geographically distant strains and detected a certain degree of genotypic diversity that could be exploited to work out new molecular tools for the discrimination of B. bovis field samples. Here we describe a PCR restriction assay that was developed based on this observation and tested on several B. bovis strains and isolates. The results show a strain‐specific band pattern in geographically distant isolates, indicating the presence of differentially located BspMI restriction sites. This approach provides a simple method for the differentiation of American B. bovis strains.

Improved Molecular Tools for Detection of Babesia bigemina

Molecular detection of Babesia bigemina involves a nested PCR protocol and reverse line blot hybridization (RLBH) assay based on the 18S gene. In this study, we report the development of molecular tools for improving B. bigemina detection in bovine blood—a one‐step PCR assay based on the amplification of rap‐1a paralogous and a new RLBH Babesia spp. 18S probe. The one‐step PCR assay is highly specific, with an estimated analytical sensitivity corresponding to 0.00002% parasitemia. The RLBH assay, with a new B. bigemina probe, allows the detection of all tested B. bigemina isolates showing no cross‐hybridization with B. bovis 18S gene. By developing this highly specific and sensitive one‐step PCR and upgrading the RLBH assay for B. bigemina, we have improved molecular assays which, together with serologic methods, provide valuable tools for epidemiologic studies of bovine babesiosis.

Multi-locus typing scheme for Babesia bovis and Babesia bigemina reveals high levels of genetic variability in strains from Northern Argentina.

Bovine babesiosis, caused by the protozoa Babesia bovis and Babesia bigemina, is a tick-borne disease distributed in tropical regions worldwide. Current control measures are based on the use of acaricides and live attenuated vaccines. The major economic impact of babesiosis lies in the cattle industry. In order to gain insight into the extent of genetic diversity in populations of parasites in the field, we developed two MLST schemes for the molecular genotyping of B. bigemina and B. bovis. We have also developed a custom-designed bioinformatic pipeline to facilitate the automated processing of raw sequences and further diversity and phylogenetic analysis. The overall MLST scheme exhibited the maximum discriminatory power (Simpson Index=1) for B. bovis and a high level of discrimination for B. bigemina (Simpson Index=0.9545). Genetic diversity was very high and infections with multiple genotypes were frequently found for both parasites in outbreak samples from the Northeast and Northwest of Argentina. Recombination events, which could have arisen from these multiple infections, were suggested by intra-loci linkage disequilibrium analysis and the lack of congruence in phylogenetic trees from individual genes. The two MLST schemes developed here are a robust, objective and easily adoptable technology to analyze the genetic diversity and population structure of parasites of the genus Babesia.

A new set of molecular markers for the genotyping of Babesia bovis isolates.

Babesia bovis is a tick-borne apicomplexan pathogen that remains an important constraint for the development of cattle industries worldwide. The existence of different strains and subpopulations has long been described in this hemoparasite. However, few molecular markers have been reported for strain genotyping and characterization. Minisatellite sequences show high levels of variation and therefore provide excellent tools for both the genotyping and population genetic analysis. In this work we report a set of five molecular markers containing minisatellites that showed a variable degree of polymorphism in several American strains. We have used a bioinformatics approach to search for marker sequences contained in open reading frames. Five genes were chosen and primers were designed in conserved regions flanking the repeat region. Two of the genes were the previously described Bv80/Bb-1 and TRAP. The other three genes were named p200, Antigen 3 and Desmoyokin. Amplification by PCR, sequencing and comparative analysis of 11 strains from Argentina, Brazil, Uruguay, Mexico and USA determined that the tandem repeats varied in number and sequence among the isolates. Genome analysis of the five markers revealed that they were single copy and distributed across the four B. bovis chromosomes. When the new markers were analyzed in an experimental infection, absolute sequence conservation was found, indicating the stability of these markers during the course of infection. These markers were also stable during three syringe passages through calves. The application of this panel of molecular markers could provide new molecular tools for the genotyping of B. bovis isolates and analysis of changes in parasite populations following vaccination.