Eduardo Rocha - Selected Publications#

Ares-Arroyo M, Coluzzi C, Rocha EPC (2023) Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation. Nucleic Acids Research 51:3001–3016 https://doi.org/10.1093/nar/gkac1079

For more than a decade there was an outstanding mystery in the field of plasmid biology, in that most plasmids seemed to lack the genetic elements required for conjugation. In this article we show that majority of plasmids in Escherichia coli and Staphylococcus aureus have an origin of transfer by conjugation. Classed the NAR Breakthrough Article of the issue.

Moura de Sousa J, Fillol-Salom A, Penadés J, Rocha EPC (2023) Identification and characterization of thousands of bacteriophage satellites across bacteria. Nucleic Acids Research 51:2759-2777 https://doi.org/10.1093/nar/gkad123

Until we started working on phage satellites three years ago only a handful of elements were known. In this study we characterized the best-known types of phage satellites and thousands of novel elements. This article demonstrates for the first time that phage satellites are exceedingly common in bacterial genomes. It also provides the first software to identify phage satellites.

Rocha EPC, Bikard D (2022) Microbial defenses against mobile genetic elements and viruses: who defends whom from what? PLoS Biology 20: e3001514. https://doi.org/10.1371/journal.pbio.3001514

In this essay we’ve put forward the hypothesis that one should not study bacterial immune systems in the frame of the interaction between the bacterium and one mobile genetic element. Instead, to understand the frequency and evolution of microbial immune systems, one needs to consider them as the result of the interaction between multiple agents in the bacterial genome. Classed Highly cited paper (Web of Science)

Rousset F, Cabezas Caballero J, Piastra-Facon F, Fernández-Rodríguez J, Clermont O, Denamur E, Rocha EPC*, David Bikard* (2021) The impact of genetic diversity on gene essentiality within the E. coli species. Nature Microbiology 6:301–312 https://doi.org/10.1038/s41564-020-00839-y

This study uses a CRISPRi method to identify essential genes among core genes of E. coli in a diverse panel of strains representative of the species. It shows that many essential genes are only essential in a specific genetic background. This suggests extensive epistatic interactions in E. coli, even among core genes, that may result in genes becoming essential only in specific contexts.

Pfeifer E, Sousa JAM, Touchon M, Rocha EPC (2021) Bacteria have numerous well-related and highly-diverse groups of phage-plasmids with conserved phage and variable plasmid gene repertoires. Nucleic Acids Res 49: 2655-2673. https://doi.org/10.1093/nar/gkab064

In this study we show that contrary to common belief, a significant fraction of all plasmids (7%) are also phages and, conversely, more than 10% of the temperate phages remain in cells as plasmids instead of integrating the chromosome. We identified thousands of such elements and highlighted the existence of many old well conserved families of these elements. In a subsequent paper (Pfeifer, mBIO, 22) we show that phage-plasmids often carry antibiotic resistance genes and demonstrate for the first time the lysogenic conversion of a bacterium to antibiotic resistance by a natural phage (a phage-plasmid).

Haudiquet M, Buffet A, Rendueles O, Rocha EPC (2021) Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of a nosocomial pathogen. PLoS Biology 19(7): e3001276. https://doi.org/10.1371/journal.pbio.3001276

Demonstration that specific interactions between the Klebsiella capsule, phages, and conjugative elements shape gene flow. The rate and type of gene transfer depends on the vector (phage or plasmid) and on the structure of the envelope (capsule). Had a perspective accompanying paper in PLoS Biology.

Garcia-Garcera M, Rocha EPC (2020) Community diversity and habitat structure shape the repertoire of extracellular proteins in bacteria. Nature Communications 11:758. https://doi.org/10.1038/s41467-020-14572-x.

Secreted proteins are colonization and virulence factors, but also expensive due to production costs and impossibility of recycling its amino acids. We made an analysis of thousands of meta-genomes and revealed the ecological constraints acting on the repertoires of genes for secreted proteins.

Denise R, Abby SS, Rocha EPC (2019) Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PLoS Biology 17:e3000390. https://doi.org/10.1371/journal.pbio.3000390

First integrated analysis showing that type 4 filaments evolved through processes of horizontal transfer, duplication, deletion, and mutation to produce a wide range of functions involved in motility, protein secretion and natural transformation. Had a perspective accompanying paper in PLoS Biology.

Clerissi C, Touchon M, Capela D, Tang M, Cruveiller S, Parker MA, Moulin L, Masson-Boivin C, Rocha EPC (2018) Parallels between experimental and natural evolution of legume symbionts. Nature Communications 9:2264. https://doi.org/10.1038/s41467-018-04778-5

This study compared the evolution of a plant mutualist (rhizobia) from a soil bacterium in the laboratory and in natural populations. It revealed that the processes have clear parallels. Surprisingly, in both cases evolution occurred more in the genetic background than in the plasmid carrying the novel trait. Many of these mutations are involved in the rewiring of the cell's genetic networks.

Cury J, Oliveira P, de la Cruz F, Rocha EPC (2018) Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements. Mol Biol Evol 35:2230-2239. https://doi.org/10.1093/molbev/msy123

It has been known for decades that some mobile genetic elements are extra-chromosomal while others are integrated into the chromosome. But it was not known why. This study is the first to elucidate the relative benefits and costs of the two evolutionary strategies. Extra-chromosomal elements evolve faster in terms of gene repertoires, while those that integrate into the chromosome have a wider host spectrum. Prize for best paper of the year by a PhD student in MBE.