Conservation and Variation in Strategies for DNA Replication of Kinetoplastid Nuclear Genomes

Abstract

Introduction: Understanding how the nuclear genome of kinetoplastid parasites is replicated received experimental stimulus from sequencing of the Leishmania major, Trypanosoma brucei and Trypanosoma cruzi genomes around 10 years ago. Gene annotations suggested key players in DNA replication initiation could not be found in these organisms, despite considerable conservation amongst characterised eukaryotes. Initial studies that indicated trypanosomatids might possess an archaeal-like Origin Recognition Complex (ORC), composed of only a single factor termed ORC1/CDC6, have been supplanted by the more recent identification of an ORC in T. brucei. However, the constituent subunits of T. brucei ORC are highly diverged relative to other eukaryotic ORCs and the activity of the complex appears subject to novel, positive regulation. The availability of whole genome sequences has also allowed the deployment of genome-wide strategies to map DNA replication dynamics, to date in T. brucei and Leishmania. ORC1/CDC6 binding and function in T. brucei displays pronounced overlap with the unconventional organisation of gene expression in the genome. Moreover, mapping of sites of replication initiation suggests pronounced differences in replication dynamics in Leishmania relative to T. brucei.

Conclusion: Here we discuss what implications these emerging data may have for parasite and eukaryotic biology of DNA replication.

Keywords: DNA replication; Kinetoplastid parasites; Leishmania; Origin recognition complex (ORC); Origins of replication; Trypanosoma brucei.

Fig. (1)

The Origin Recognition Complex (ORC) of T. brucei. A) Evolution of our understanding of the origin-binding machinery of T. brucei in the last ten years, from a single factor like in archaea, to a highly divergent ORC-like complex resembling the system in model eukaryotes. B) Schematic representation of T. brucei ORC-like complex subunits and identified domains.

Fig. (2)

Origins of replication in T. brucei and Leishmania. Origins of replication in T. brucei chromosome 8 (orange) and L. major chromosome 36 (blue) mapped in early S phase cells by MFA-seq. The top track represents the gene coding sequences, and the graph below illustrates the read depth ratio between early S phase and G2 populations (y-axis), with each dot representing the median S/G2 ratio (y-axis) in 2.5 kbp windows across the chromosome (x-axis); adapted from Marques et al., 2015. In the L. major panel, the vertical blue lines represent origins of replication mapped by SNS-seq; adapted from Lombraña et al., 2016.