The project EvoPlas had three main objectives. The three objectives proposed were the following:
Objective 1: To characterize the diversity and distribution of oriTs.
To fulfil this objective, we collected and characterized the largest database of experimentally validated oriTs so far. During the procedure of this WP, we run into a risk previously foreseen in the section 3.1 of the DoA (Risk and Contingency table, WP1, Medium Risk): most of the oriTs are unknown, limiting our study to a few species. To overcome this limitation: (1) we focused the first characterization on the model species in which most oriTs are already described; and (2) we developed a novel methodology to ab initio identify oriTs in any bacterial species without the need of having already described cases.
Objective 2: To unveil the mechanisms of mobility of the NT plasmids.
To answer this question, we helped ourselves with the outcome of the previous objective. We used the collection of oriTs, and remaining data on non-canonical mechanisms of mobility, to characterize the mobility of those plasmids that were previously considered non-mobile. This objective was key to answer the first biological question highlighted in the section 1.1 of the DoA: “Do ‘non-transmissible’ plasmids move between bacteria more than envisioned?”.
Objective 3: To identify the evolutionary origin of NT plasmids.
This objective was an ambitious section of the project, whose accomplishment would answer the second and last biological question proposed in the DoA: “What is the evolutionary origin and fate of ‘non-transmissible’ plasmids?”. To reach this objective, we used the data obtained from the previous two objectives to: (1) understand the evolutionary origin of these plasmids from the degradation of previously conjugative replicons; and (2) to propose the theory that some could have evolved de novo from non-mobile elements.
All these results have led to three different scientific publications:
Ares-Arroyo M, Coluzzi C, Rocha EPC. Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation. (2023) Nucleic Acids Res. Apr 24;51(7):3001-3016. doi: 10.1093/nar/gkac1079. PMID: 36442505; PMCID: PMC10123127.
Ares-Arroyo M, Nucci A, Rocha EPC. (2024). Identification of novel origins of transfer across bacterial plasmids. Doi: 10.1101/2024.01.30.577996 [Under review in Nature Microbiology]
Ares-Arroyo M, Coluzzi C, Moura de Sousa J, Rocha EPC. (2024). EcoEvoRxiv. Hijackers, hitchhikers, or co-drivers? The mysteries of microbial mobilizable genetic elements. Doi: 10.32942/X2R89M [Under review in PLOS Biology]
Additionally, this data gave rise to scientific collaboration:
Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, Bikard D, Hall AR, Sørensen SJ, Pinilla-Redondo R. (2024) Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans. Cell Host Microbe. Jun 12;32(6):875-886.e9. doi: 10.1016/j.chom.2024.04.016. Epub 2024 May 15. PMID: 38754416.
