29DNA replication, transcription and chromatin remodeling are coordinated to 30 ensure accurate duplication of genetic and epigenetic information. In regard to DNA 31 replication, trypanosomatid parasites such as Trypanosoma brucei display unusual 32 properties including significantly fewer origins of replication than model eukaryotes, a 33 highly divergent Origin Replication Complex (ORC), and an apparent lack of several 34 replication factor homologs. Although recent studies in T. brucei indicate functional links 35 among DNA replication, transcription, and antigenic variation, the underlying 36 mechanisms remain unknown. Here, we adapted an unbiased technology for the 37 identification of replication fork proteins called iPOND (isolation of proteins on nascent 38 DNA) to T. brucei, its first application to a parasite system. This led to the mass 39 spectrometric identification of core replication machinery and of proteins associated with 40 transcription, chromatin organization, and DNA repair that were enriched in the vicinity 41 of an unperturbed active replication fork. Of a total of 410 enriched proteins, among 42 which DNA polymerase and replication factor C were scoring in the top, around 25%43 of the proteins identified were of unknown function and, therefore, have the potential to 44 be essential trypanosome-specific replication proteins. Initial characterization of a 45 protein annotated as a Replication Factor C subunit (Tb927.10.7990), and a protein of 46 unknown function (Tb927.3.5370) revealed that both proteins retain nuclear localization 47 throughout the cell cycle. While Tb927.3.5370 appeared to be a dispensable gene, 48 Tb927.10.7990 proved to be essential since its silencing caused a growth defect in 49 procyclic cells, accumulation of zoids and impaired DNA replication. Future studies on 50 the generated proteins list can contribute to the understanding of DNA replication 51 dynamics in T. brucei and how replication is coordinated with other cellular processes to 52 maintain genome integrity. 53 54 Introduction 55 Eukaryotic DNA replication is strictly coordinated and regulated by numerous 56 molecular machines to ensure genomic stability for future cell generations. DNA 57 replication initiation is coordinated with cell cycle progression through the multiprotein 58 Origin Recognition Complex (ORC) that plays an essential role by recruiting proteins 59 that lead to the assembly of the replicative machinery with the assistance of regulatory 60 components Cdc6 and Cdt1. The key factors Cdc45, the MCM replicative helicase 61 complex, and GINS proteins form the CMG complex that further recruits other 62 replication factors such as the clamp loader Replication factor C (RFC), the clamp 63 proliferating cell nuclear antigen (PCNA) and the three replicative DNA polymerases 64 ( ) leading to processive DNA replication [1,2]. 65 Instead of the archetypical Origin Recognition Complex (Orc1-6) found in model 66 eukaryotes, trypanosomes contain ORC1 and four other highly divergent ORC subunits ...
Extensive remodeling of the host gene expression environment by coronaviruses nsp1 proteins is a well-documented and conserved piece of the coronavirus-host takeover battle. However, whether and how the underlying mechanism of regulation or the transcriptional target landscape differ amongst coronaviruses remains mostly uncharacterized. In this study we use comparative transcriptomics to investigate the diversity of transcriptional targets between four different coronavirus nsp1 proteins (from MERS, SARS1, SARS2 and 229E). In parallel, we performed Affinity Purification followed by Mass-Spectrometry to identify common and divergent interactors between these different nsp1. For all four nsp1 tested, we detected widespread RNA destabilization, confirming that both β- and α- Coronavirus nsp1 broadly affect the host transcriptome. Surprisingly, we observed that even closely related nsp1 showed little similarities in the clustering of genes targeted. Additionally, we show that the RNA targeted by nsp1 from the α-CoV 229E partially overlapped with MERS nsp1 targets. Given MERS nsp1 preferential targeting of nuclear transcripts, these results may indicate that these nsp1 proteins share a similar targeting mechanism. Finally, we show that the interactome of these nsp1 proteins differ widely. Intriguingly, our data indicate that the 229E nsp1, which is the smallest of the nsp1 proteins tested here, interacts with the most host proteins, while MERS nsp1 only engaged with a few host proteins. Collectively, our work highlights that while nsp1 is a rather well-conserved protein with conserved functions across different coronaviruses, its precise effects on the host cell is virus-specific.
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