Comparative proteomic analysis of two pathogenic Tritrichomonas foetus genotypes: there is more to the proteome than meets the eye

Proteomics-The State of the Field: The Definition and Analysis of Proteomes Should Be Based in Reality, Not Convenience

With growing recognition and acknowledgement of the genuine complexity of proteomes, we are finally entering the post-proteogenomic era. Routine assessment of proteomes as inferred correlates of gene sequences (i.e., canonical 'proteins') cannot provide the necessary critical analysis of systems-level biology that is needed to understand underlying molecular mechanisms and pathways or identify the most selective biomarkers and therapeutic targets. These critical requirements demand the analysis of proteomes at the level of proteoforms/protein species, the actual active molecular players. Currently, only highly refined integrated or integrative top-down proteomics (iTDP) enables the analytical depth necessary to provide routine, comprehensive, and quantitative proteome assessments across the widest range of proteoforms inherent to native systems. Here we provide a broad perspective of the field, taking in historical and current realities, to establish a more balanced understanding of where the field has come from (in particular during the ten years since Proteomes was launched), current issues, and how things likely need to proceed if necessary deep proteome analyses are to succeed. We base this in our firm belief that the best proteomic analyses reflect, as closely as possible, the native sample at the moment of sampling. We also seek to emphasise that this and future analytical approaches are likely best based on the broad recognition and exploitation of the complementarity of currently successful approaches. This also emphasises the need to continuously evaluate and further optimize established approaches, to avoid complacency in thinking and expectations but also to promote the critical and careful development and introduction of new approaches, most notably those that address proteoforms. Above all, we wish to emphasise that a rigorous focus on analytical quality must override current thinking that largely values analytical speed; the latter would certainly be nice, if only proteoforms could thus be effectively, routinely, and quantitatively assessed. Alas, proteomes are composed of proteoforms, not molecular species that can be amplified or that directly mirror genes (i.e., 'canonical'). The problem is hard, and we must accept and address it as such, but the payoff in playing this longer game of rigorous deep proteome analyses is the promise of far more selective biomarkers, drug targets, and truly personalised or even individualised medicine.

Optimized Proteome Reduction for Integrative Top–Down Proteomics

Integrative top–down proteomics is an analytical approach that fully addresses the breadth and complexity needed for effective and routine assessment of proteomes. Nonetheless, any such assessments also require a rigorous review of methodology to ensure the deepest possible quantitative proteome analyses. Here, we establish an optimized general protocol for proteome extracts to improve the reduction of proteoforms and, thus, resolution in 2DE. Dithiothreitol (DTT), tributylphosphine (TBP), and 2-hydroxyethyldisulfide (HED), combined and alone, were tested in one-dimensional SDS-PAGE (1DE), prior to implementation into a full 2DE protocol. Prior to sample rehydration, reduction with 100 mM DTT + 5 mM TBP yielded increased spot counts, total signal, and spot circularity (i.e., decreased streaking) compared to other conditions and reduction protocols reported in the literature. The data indicate that many widely implemented reduction protocols are significantly ‘under-powered’ in terms of proteoform reduction and thus, limit the quality and depth of routine top–down proteomic analyses.

Molecular prevalence and phylogenetic confirmation of bovine trichomoniasis in aborted cows in Iraq

Background and Aim

Bovine trichomoniasis, caused by Tritrichomonas foetus, is a venereal disease that is distributed in many countries, including Iraq. Compared with other abortive infectious diseases, prevalence of T. foetus is expected to be relatively low in the field by veterinarians. This study aimed to estimate the prevalence of T. foetus in aborted cows by conventional polymerase chain reaction (PCR) and phylogenetic analysis of local T. foetus isolates was documented in the National Center for Biotechnology Information as the first sequenced isolates from Iraq.

Materials and Methods

Vaginal fluids were collected from 62 aborted cows and examined by PCR. Data were reported for the following parameters: Vital signs (body temperature and respiratory and pulse rates), age (<4, 4-8, and >8 years), reproductive health status (premature calving, embryonic death, pyometra, and healthy newborn), breed (pure or crossbred), type of breeding (natural or artificial), bull-to-cow ratio (1:<10, 1:10-20, and 1:>20), contact of cow with bull(s) from other farmers (yes or no), and contact with stray animals (dogs and cats).

Results

A total of 20.97% of aborted cows were positive for T. foetus. Phylogenetic analysis for 10 positive local T. foetus isolates demonstrated high identity with the Thai (MN560972.2) and Chinese (MH115435.1) isolates, with an identity range of 98.8%-99.5% and 98.6%-99.3%, respectively. Clinical data showed that the vital signs differed insignificantly between cows positive and negative for T. foetus. Prevalence and risk of infection increased significantly in <4-year-old, early calving, embryonic death, crossbred, and naturally inseminated cows that had direct contact with bulls from other farmers, and contact with stray animals. Fetal pneumonia and death of premature calves were significant among positive aborted fetuses.

Conclusion

Tritrichomonas foetus is highly prevalent in aborted cows in Iraq and phylogenetic analysis demonstrated an identity between the local and global isolates, that is, Thai and Chinese, of cats.

In-depth comparative analysis of Tritrichomonas foetus transcriptomics reveals novel genes linked with adaptation to feline host

Tritrichomonas foetus is a flagellated parasite able to infect cattle, cats, and pigs. Despite its prevalence, feline tritrichomonosis has received markedly less attention than venereal infection, and little information about the molecular mechanisms that participate in feline host infection is available. Through a bioinformatics approach, we integrated public transcriptomic data for three T. foetus isolates and explored the differences at transcript level with a focus on pathogenesis and adaptation processes, particularly for the feline isolate. Our analysis revealed higher abundance levels of predicted virulence factors, such as proteases and surface antigens. Additionally, by a comparative and expression analysis of T. foetus genes, we proposed putative virulence factors that could be involved in feline infection. Finally, we identified a great proportion of predicted transcription factors of the MYB protein family and, by a promoter analysis, we revealed that MYB-related proteins could participate in the regulation of gene transcription in T. foetus. In conclusion, this integrated approach is a valuable resource for future studies of host–pathogen interactions and identifying new gene targets for improved feline tritrichomonosis diagnosis and treatment.

What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World?

Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit.

Proteomic signatures of metronidazole-resistant Trichomonas vaginalis reveal novel proteins associated with drug resistance

BACKGROUND

Trichomoniasis is the most common non-viral sexually transmitted disease caused by the protozoan parasite Trichomonas vaginalis. Metronidazole (MTZ) is a widely used drug for the treatment of trichomoniasis; however, increased resistance of the parasite to MTZ has emerged as a highly problematic public health issue.

METHODS

We conducted iTRAQ-based analysis to profile the proteomes of MTZ-sensitive (MTZ-S) and MTZ-resistant (MTZ-R) parasites. STRING and gene set enrichment analysis (GESA) were utilized to explore the protein-protein interaction networks and enriched pathways of the differentially expressed proteins, respectively. Proteins potentially related to MTZ resistance were selected for functional validation.

RESULTS

A total of 3123 proteins were identified from the MTZ-S and MTZ-R proteomes in response to drug treatment. Among the identified proteins, 304 proteins were differentially expressed in the MTZ-R proteome, including 228 upregulated and 76 downregulated proteins. GSEA showed that the amino acid-related metabolism, including arginine, proline, alanine, aspartate, and glutamate are the most upregulated pathways in the MTZ-R proteome, whereas oxidative phosphorylation is the most downregulated pathway. Ten proteins categorized into the gene set of oxidative phosphorylation were ATP synthase subunit-related proteins. Drug resistance was further examined in MTZ-S parasites pretreated with the ATP synthase inhibitors oligomycin and bafilomycin A1, showing enhanced MTZ resistance and potential roles of ATP synthase in drug susceptibility.

CONCLUSIONS

We provide novel insights into previously unidentified proteins associated with MTZ resistance, paving the way for future development of new drugs against MTZ-refractory trichomoniasis.

Whole genome sequencing of a feline strain of Tritrichomonas foetus reveals massive genetic differences to bovine and porcine isolates

Tritrichomonas foetus is a protozoan parasite that colonizes the reproductive tract of cattle as well as the gastrointestinal tract of cats. Bovine tritrichomonosis is a sexually transmitted disease whereas feline tritrichomonosis is thought to be transmitted by the fecal-oral route. Furthermore, T. foetus is known as an essentially apathogenic commensal located in the nasal cavity of pigs. Transmission of T. foetus between the different hosts has to be considered a realistic scenario that may have important implications for the epidemiology of infections and disease. In our study, we generated whole genome sequencing (WGS) data from bovine, feline and porcine T. foetus strains to investigate the genetic (dis)similarities among these diverse strains. As a reference, we used a previously released draft assembly from a bovine T. foetus strain K isolated from an infected bull in Brazil. In particular, we identified single nucleotide polymorphisms (SNPs) and the insertion-deletion (indel) variations within the genomes of the different strains. Interestingly, only a low degree of polymorphism (68 SNPs and indels) was found between the bovine and the porcine strains in terms of variants with a predicted impact of moderate or high and where one species is homozygous for one allele and the other homozygous for the other allele. Conversely, however, a 964 times higher number of such differences was detected by comparing the feline with either the bovine (65,569) or the porcine (65,615) strain. These data clearly indicated a close phylogenetic relationship between bovine and porcine T. foetus but a remarkable genetic distinctness of these two strains from the feline strain. The latter observation was confirmed by PCR-based sequencing of 20 in silico-selected indel markers and five in silico-selected SNP markers that uniformly demonstrated a relatively distant phylogenetic relationship of three independent feline T. foetus isolates in comparison to the bovine and porcine strains investigated. In summary, our comparative genome sequencing approach provided further insights into the genetic diversity of T. foetus in relation to the different host origins of the parasite. Furthermore, our study identified a large number of SNP- and indel-containing sequences that may be useful molecular markers for future epidemiological studies aimed at the elucidation of the transmission patterns of T. foetus within different host species.

Tritrichomonas Foetus as a Causative Agent of Tritrichomonosis in Different Animal Hosts

Tritrichomonas foetus is a protozoan parasite that has been traditionally identified as a cause of reproductive tract disease in cattle and gastrointestinal tract infection in cats. Moreover, T. foetus is also well known as a commensal of the nasal cavity, intestines, and stomach in swine. In this review we describe T. foetus as a pathogen dangerous to more than one animal host, diagnostic and taxonomic aspects of this infection, and the extent to which isolates from different hosts share genetic identity.

Multilocus analysis reveals further genetic differences between Tritrichomonas foetus from cats and cattle

Tritrichomonas foetus isolates from feline and bovine origin has been previously shown to carry a certain degree of genetic heterogeneity. Here, novel candidate molecular markers were developed by means of multilocus sequence typing of the gap2 gene (encoding for T. foetus glyceraldehyde-3-phosphate dehydrogenase), ITS region, the TR7/TR8 variable-length repeat and microsatellite genotyping. These markers were used to characterize T. foetus field isolates from bulls and domestic cats and to compare phylogenetically with the following ATCC isolates: T. foetus isolated from cattle and pig (syn. Tritrichomonas suis), Tritrichomonas mobilensis, Tetratrichomonas gallinarum and Pentatrichomonas hominis. Among them, TFMS10 and TFMS7 were found to be the most polymorphic markers. Moreover, an 809 bp fragment of the gap2 gene was successfully amplified from all the trichomonads included in this study and the sequence analysis revealed differences between T. foetus porcine and feline genotypes and T. mobilensis in comparison to the bovine T. foetus ATCC isolate. The TR7/TR8 repeat pattern was not reproducible, being only consistent the fragments of approximately 110 and 217 bp. Sequence analysis of the latter revealed the existence of 3 SNPs resulting in 98.6 % homology between bovine and feline isolates. A search for similar sequences was carried out to develop a Restriction Length Fragment Polymorphism analysis. A 503 bp region, named TF1, revealed the existence of two BbvI restriction enzyme sites that were able to generate different length fragments for T. foetus feline and bovine isolates. Finally, the neighbour-joining analyses showed that T. foetus porcine genotype clusters together with bovine genotype, whereas T. mobilensis and the feline genotype form a separate cluster.

Suppression of the Peripheral Immune System Limits the Central Immune Response Following Cuprizone-Feeding: Relevance to Modelling Multiple Sclerosis

Cuprizone (CPZ) preferentially affects oligodendrocytes (OLG), resulting in demyelination. To investigate whether central oligodendrocytosis and gliosis triggered an adaptive immune response, the impact of combining a standard (0.2%) or low (0.1%) dose of ingested CPZ with disruption of the blood brain barrier (BBB), using pertussis toxin (PT), was assessed in mice. 0.2% CPZ(±PT) for 5 weeks produced oligodendrocytosis, demyelination and gliosis plus marked splenic atrophy (37%) and reduced levels of CD4 (44%) and CD8 (61%). Conversely, 0.1% CPZ(±PT) produced a similar oligodendrocytosis, demyelination and gliosis but a smaller reduction in splenic CD4 (11%) and CD8 (14%) levels and no splenic atrophy. Long-term feeding of 0.1% CPZ(±PT) for 12 weeks produced similar reductions in CD4 (27%) and CD8 (43%), as well as splenic atrophy (33%), as seen with 0.2% CPZ(±PT) for 5 weeks. Collectively, these results suggest that 0.1% CPZ for 5 weeks may be a more promising model to study the ‘inside-out’ theory of Multiple Sclerosis (MS). However, neither CD4 nor CD8 were detected in the brain in CPZ±PT groups, indicating that CPZ-mediated suppression of peripheral immune organs is a major impediment to studying the ‘inside-out’ role of the adaptive immune system in this model over long time periods. Notably, CPZ(±PT)-feeding induced changes in the brain proteome related to the suppression of immune function, cellular metabolism, synaptic function and cellular structure/organization, indicating that demyelinating conditions, such as MS, can be initiated in the absence of adaptive immune system involvement.

Failure to detect Tritrichomonas foetus in a cross-sectional survey in the populations of feral cats and owned outpatient cats on St Kitts, West Indies

OBJECTIVES

For over two decades, feline trichomonosis caused by Tritrichomonas foetus has been recognized as a large-bowel protozoan disease of the domestic cat. It has a wide distribution, but no reports exist in the Caribbean. The objectives of this study were to detect the presence of T foetus and its prevalence in the domestic cat on St Kitts, West Indies.

METHODS

A cross-sectional study was performed between September 2014 and December 2015. This study recruited 115 feral cats from a trap-neuter-return program and 37 owned cats treated as outpatients at the university veterinary clinic. Fresh feces were inoculated in InPouch culture medium, as per the manufacturer's instructions. In addition, PCR was performed using primers for T foetus. DNA extraction with amplification using primers of a Feliscatus NADH dehydrogenase subunit 6 was used as a housekeeping gene for quality control.

RESULTS

Only two owned cats had reported diarrhea in the preceding 6 months. None of the 152 samples were positive on InPouch culture microscopic examination. Only 35/69 feral cat fecal DNA samples were positive for the housekeeping gene, of which none tested PCR positive for T foetus.

CONCLUSIONS AND RELEVANCE

T foetus was not detected by culture and PCR in feral cats and owned cats on St Kitts. A high proportion of PCR inhibitors in the DNA samples using a commercial fecal DNA kit can lead to underestimating the prevalence, which should be taken into consideration when a survey on gastrointestinal pathogens depends exclusively on molecular detection.