Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae

BACKGROUND

Protists of the family Trypanosomatidae (phylum Euglenozoa) have gained notoriety as parasites affecting humans, domestic animals, and agricultural plants. However, the true extent of the group's diversity spreads far beyond the medically and veterinary relevant species. We address several knowledge gaps in trypanosomatid research by undertaking sequencing, assembly, and analysis of genomes from previously overlooked representatives of this protistan group.

RESULTS

We assembled genomes for twenty-one trypanosomatid species, with a primary focus on insect parasites and Trypanosoma spp. parasitizing non-human hosts. The assemblies exhibit sizes consistent with previously sequenced trypanosomatid genomes, ranging from approximately 18 Mb for Obscuromonas modryi to 35 Mb for Crithidia brevicula and Zelonia costaricensis. Despite being the smallest, the genome of O. modryi has the highest content of repetitive elements, contributing nearly half of its total size. Conversely, the highest proportion of unique DNA is found in the genomes of Wallacemonas spp., with repeats accounting for less than 8% of the assembly length. The majority of examined species exhibit varying degrees of aneuploidy, with trisomy being the most frequently observed condition after disomy.

CONCLUSIONS

The genome of Obscuromonas modryi represents a very unusual, if not unique, example of evolution driven by two antidromous forces: i) increasing dependence on the host leading to genomic shrinkage and ii) expansion of repeats causing genome enlargement. The observed variation in somy within and between trypanosomatid genera suggests that these flagellates are largely predisposed to aneuploidy and, apparently, exploit it to gain a fitness advantage. High heterogeneity in the genome size, repeat content, and variation in chromosome copy numbers in the newly-sequenced species highlight the remarkable genome plasticity exhibited by trypanosomatid flagellates. These new genome assemblies are a robust foundation for future research on the genetic basis of life cycle changes and adaptation to different hosts in the family Trypanosomatidae.

Ku80 is involved in telomere maintenance but dispensable for genomic stability in Leishmania mexicana

BACKGROUND

Telomeres are indispensable for genome stability maintenance. They are maintained by the telomere-associated protein complex, which include Ku proteins and a telomerase among others. Here, we investigated a role of Ku80 in Leishmania mexicana. Leishmania is a genus of parasitic protists of the family Trypanosomatidae causing a vector-born disease called leishmaniasis.

METHODOLOGY/PRINCIPAL FINDINGS

We used the previously established CRISPR/Cas9 system to mediate ablation of Ku80- and Ku70-encoding genes in L. mexicana. Complete knock-outs of both genes were confirmed by Southern blotting, whole-genome Illumina sequencing, and RT-qPCR. Resulting telomeric phenotypes were subsequently investigated using Southern blotting detection of terminal restriction fragments. The genome integrity in the Ku80- deficient cells was further investigated by whole-genome sequencing. Our work revealed that telomeres in the ΔKu80 L. mexicana are elongated compared to those of the wild type. This is a surprising finding considering that in another model trypanosomatid, Trypanosoma brucei, they are shortened upon ablation of the same gene. A telomere elongation phenotype has been documented in other species and associated with a presence of telomerase-independent alternative telomere lengthening pathway. Our results also showed that Ku80 appears to be not involved in genome stability maintenance in L. mexicana.

CONCLUSION/SIGNIFICANCE

Ablation of the Ku proteins in L. mexicana triggers telomere elongation, but does not have an adverse impact on genome integrity.

Depletion of m-type thioredoxin impairs photosynthesis, carbon fixation, and oxidative stress in cyanobacteria

Thioredoxins (Trxs) are disulfide oxidoreductases that regulate many biological processes. The m-type thioredoxin (TrxA) is the only Trx present in all oxygenic photosynthetic organisms. Extensive biochemical and proteomic analyses have identified many TrxA target proteins in different photosynthetic organisms. However, the precise function of this essential protein in vivo is still poorly known. In this study, we generated a conditional Synechocystis sp. PCC 6803 mutant strain (STXA2) using an on-off promoter that is able to survive with only 2% of the TrxA level of the wild-type (WT) strain. STXA2 characterization revealed that TrxA depletion results in growth arrest and pronounced impairment of photosynthesis and the Calvin-Benson-Bassham (CBB) cycle. Analysis of the in vivo redox state of the bifunctional enzyme fructose-1,6-bisphosphatase/sedoheptulose-1,7-bisphosphatase showed higher levels of oxidation that affected enzyme activity in STXA2. This result implies that TrxA-mediated redox regulation of the CBB cycle is conserved in both cyanobacteria and chloroplasts, although the targets have different evolutionary origins. The STXA2 strain also accumulated more reactive oxygen species and was more sensitive to oxidative stress than the WT. Analysis of the in vivo redox state of 2-Cys peroxiredoxin revealed full oxidation, corresponding with TrxA depletion. Overall, these results indicate that depletion of TrxA in STXA2 greatly alters the cellular redox state, interfering with essential processes such as photosynthetic machinery operativity, carbon assimilation, and oxidative stress response. The TrxA regulatory role appears to be conserved along the evolution of oxygenic photosynthetic organisms.

Morphological Characterization of the Antennal Sensilla of the Afrotropical Sand Fly, Phlebotomus duboscqi (Diptera: Psychodidae)

We investigated by scanning electron microscopy the morphology, distribution, and abundance of antennal sensilla of females Phlebotomus duboscqi sand fly, an important vector of zoonotic cutaneous leishmaniasis at Afrotropical region. Thirteen well-differentiated sensilla were identified, among six types of cuticular sensilla. The probable function of these sensillary types is discussed in relation to their external structure and distribution. Five sensillary types were classified as olfactory sensilla, as they have specific morphological characters of sensilla with this function. Number and distribution of sensilla significantly differed between antennal segments. The results of the present work, besides corroborating in the expansion of the morphological and ultrastructural knowledge of P. duboscqi, can foment future electrophysiological studies for the development of volatile semiochemicals, to be used as attractants in traps for monitoring and selective vector control of this sand fly.

Pyrene Coating Transition Metal Disulfides as Protection from Photooxidation and Environmental Aging

Environmental degradation of transition metal disulfides (TMDs) is a key stumbling block in a range of applications. We show that a simple one-pot non-covalent pyrene coating process protects TMDs from both photoinduced oxidation and environmental aging. Pyrene is immobilized non-covalently on the basal plane of exfoliated MoS2 and WS2. The optical properties of TMD/pyrene are assessed via electronic absorption and fluorescence emission spectroscopy. High-resolution scanning transmission electron microscopy coupled with electron energy loss spectroscopy confirms extensive pyrene surface coverage, with density functional theory calculations suggesting a strongly bound stable parallel-stacked pyrene coverage of ~2-3 layers on the TMD surfaces. Raman spectroscopy of exfoliated TMDs while irradiating at 0.9 mW/4 μm2 under ambient conditions shows new and strong Raman bands due to oxidized states of Mo and W. Yet remarkably, under the same exposure conditions TMD/pyrene remain unperturbed. The current findings demonstrate that pyrene physisorbed on MoS2 and WS2 acts as an environmental barrier, preventing oxidative surface reactions in the TMDs catalyzed by moisture, air, and assisted by laser irradiation. Raman spectroscopy confirms that the hybrid materials stored under ambient conditions for two years remained structurally unaltered, corroborating the beneficial role of pyrene for not only hindering oxidation but also inhibiting aging.