Comparative Analysis of the Minimum Number of Replication Origins in Trypanosomatids and Yeasts

Abstract

Single-celled eukaryote genomes predominantly replicate through multiple origins. Although origin usage during the S-phase has been elucidated in some of these organisms, few studies have comparatively approached this dynamic. Here, we developed a user-friendly website able to calculate the length of the cell cycle phases for any organism. Next, using a formula developed by our group, we showed a comparative analysis among the minimum number of replication origins (MO) required to duplicate an entire chromosome within the S-phase duration in trypanosomatids (Trypanosoma cruzi, Leishmania major, and Trypanosoma brucei) and yeasts (Saccharomyces cerevisiae and Schizosaccharomyces pombe). Using the data obtained by our analysis, it was possible to predict the MO required in a situation of replication stress. Also, our findings allow establishing a threshold for the number of origins, which serves as a parameter for genome approaches that map origins. Moreover, our data suggest that when compared to yeasts, trypanosomatids use much more origins than the minimum needed. This is the first time a comparative analysis of the minimum number of origins has been successfully applied. These data may provide new insight into the understanding of the replication mechanism and a new methodological framework for studying single-celled eukaryote genomes.

How much (ATP) does it cost to build a trypanosome? A theoretical study on the quantity of ATP needed to maintain and duplicate a bloodstream-formTrypanosoma bruceicell

“…It has been estimated as being at least 20 ATPs per ORI (Lynch and Marinov, 2015). In T. brucei , there is a minimum number of 33 ORIs necessary to replicate the 11 megabase chromosomes (da Silva et al, 2020), which adds at least 1,320 ATP molecules per S-phase of the cell cycle. Additionally , T. brucei has at least 6 intermediate-sized chromosomes and about 50-100 minichromosomes (Melville et al, 2000).…”

Life in plastic, it’s fantastic! How Leishmania exploit genome instability to shape gene expression

“…DNA replication in Leishmania (reviewed by da Silva et al, 2017;Damasceno et al, 2021) could contribute to aneuploidy in several ways. A unanimous model for Leishmania DNA replication has yet to be reached (Lombraña et al, 2016;Stanojcic et al, 2016;Damasceno et al, 2020a;da Silva et al, 2020), though current data supports replication preferentially initiates from a single site (an 'origin') per chromosome during early S-phase. Generally, the origin site is positioned at a transcription unit boundary (or strand-switch region: SSR), however why replication initiates here is still unknown.…”

Cell Cycle, Telomeres, and Telomerase in Leishmania spp.: What Do We Know So Far?

“…Six years ago, Marques et al, (2015) [46] used a marker frequency analysis coupled with deep sequencing (MFA-seq) to evidence that L. major replicates each of its chromosomes during the S phase using a single replication origin. However, in a more recent study, da Silva et al, (2020) [47] used mathematical equations to reveal that it is improbable that L. major uses only a single origin per chromosome during the S phase. The explanation for these discrepancies is that the MFA-seq approach is not sensitive enough to identify all replication origins [47].…”

“…However, in a more recent study, da Silva et al, (2020) [47] used mathematical equations to reveal that it is improbable that L. major uses only a single origin per chromosome during the S phase. The explanation for these discrepancies is that the MFA-seq approach is not sensitive enough to identify all replication origins [47]. Nevertheless, further sensitive assays are needed to establish how many origins are used per chromosome during the S phase in Leishmania spp.…”