Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery

Abstract

Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been ‘domesticated’, that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.

The mating pilus of E. coli pED208 acts as a conduit for ssDNA during horizontal gene transfer

“…S5C) ( 1 ). All solved structures of conjugation pili, both bacterial and archaeal, show a tight association of lipids with TraA subunits, with a 1:1 stoichiometric ratio for bacterial pili ( 2 – 5 , 15 ). It was suggested that one of the functions of this pilin:lipid association would be to facilitate reinsertion of the pilus subunits within the membrane during retraction events ( 5 ).…”

“…This study clearly shows that the pED208 pilus is involved in DNA transfer between donor and recipient cells separated by small or large distances. A physiological basis for conjugation at a distance may be supported by the mechanical robustness of the pili as it forms a resilient protective casing (or shaft) for DNA transfer between cells ( 3 , 24 ). This still leads to many unanswered questions.…”

“…This was viewed as consistent with the role of the pilus in transferring DNA. However, the structure of the A. tumefaciens T-pilus revealed a positively charged lumen ( 2 , 3 , 15 ), seemingly in conflict with this notion of DNA transfer. An explanation was suggested that the properties of the T-pilus lumen may have evolved as a compromise between transferring negatively charged DNA and positively charged effector proteins ( 3 , 16 ).…”

The F-pilus biomechanical adaptability accelerates conjugative dissemination of antimicrobial resistance and biofilm formation

“…Although it is not possible to evaluate the contribution of PG phospholipids in vivo 36 , our sMD simulations clearly show their fundamental role in maintaining the integrity of the filament, including an effect on the Glu29-Lys41 salt bridge interaction, and how the filament more readily falls apart in the absence of the PG phospholipids under force, although secondary structure of individual pilin subunits is well-maintained regardless of the presence of absence of the PG phospholipids. Given the large sequence and structural conservation among F-pilin (TraA) encoded by IncF plasmids (Supplementary Figure 3 A and 3B ), their extensive interaction interface 10 , 11 , and the positive effect of phospholipid molecules on pilus structural stability, we postulate that other pili classes will also benefit from being structurally reinforced by the presence of phospholipids, as exemplified by the recent structures of minimised and archaeal conjugative pili 44 , 45 .…”

Cryo-EM Structure of the R388 plasmid conjugative pilus reveals a helical polymer characterised by an unusual pilin/phospholipid binary complex

“…It is made of a major component, VirB2, and a minor one, VirB5. Pili may serve either as devices mediating attachment of the donor cell to the recipient cell, or as a conduit for relaxase/ssDNA transport, or both (Beltran et al, 2023; Goldlust et al, 2023). Some conjugative pili are capable of retraction, which will bring donor and recipient cells together.…”