The DNA transporter ComEC has metal‐dependent nuclease activity that is important for natural transformation

Silale, Augustinas; Lea, Susan M.; Berks, Ben C.

doi:10.1111/mmi.14720

Cited by 15 publications

(5 citation statements)

References 75 publications

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“…The interactions of ComFA with ComFC and ComEC have already been reported (Kramer et al , 2007 ; Diallo et al , 2017 ). A ternary complex between these proteins suggests that the energy provided by ComFA‐mediated ATP hydrolysis fuels ComEC‐mediated uptake of single‐stranded DNA molecules (Silale et al , 2021 ).…”

Section: Resultsmentioning

confidence: 99%

Protein complexes in cells by AI‐assisted structural proteomics

O’Reilly

Graziadei

Forbrig

et al. 2023

Molecular Systems Biology

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Accurately modeling the structures of proteins and their complexes using artificial intelligence is revolutionizing molecular biology. Experimental data enable a candidate‐based approach to systematically model novel protein assemblies. Here, we use a combination of in‐cell crosslinking mass spectrometry and co‐fractionation mass spectrometry (CoFrac‐MS) to identify protein–protein interactions in the model Gram‐positive bacterium Bacillus subtilis . We show that crosslinking interactions prior to cell lysis reveals protein interactions that are often lost upon cell lysis. We predict the structures of these protein interactions and others in the Subti Wiki database with AlphaFold‐Multimer and, after controlling for the false‐positive rate of the predictions, we propose novel structural models of 153 dimeric and 14 trimeric protein assemblies. Crosslinking MS data independently validates the AlphaFold predictions and scoring. We report and validate novel interactors of central cellular machineries that include the ribosome, RNA polymerase, and pyruvate dehydrogenase, assigning function to several uncharacterized proteins. Our approach uncovers protein–protein interactions inside intact cells, provides structural insight into their interaction interfaces, and is applicable to genetically intractable organisms, including pathogenic bacteria.

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Section: Resultsmentioning

confidence: 99%

Protein complexes in cells by AI‐assisted structural proteomics

O’Reilly

Graziadei

Forbrig

et al. 2023

Molecular Systems Biology

View full text Add to dashboard Cite

show abstract

“…The interactions of ComFA with ComFC and ComEC have already been reported (Kramer et al , 2007; Diallo et al , 2017). A ternary complex between these proteins suggests that the energy provided by ComFA-mediated ATP hydrolysis fuels ComEC mediated uptake of single-stranded DNA molecules (Silale et al , 2021).…”

Section: Resultsmentioning

confidence: 99%

Protein complexes in cells by AI-assisted structural proteomics

O’Reilly

Graziadei

Forbrig

et al. 2022

Preprint

View full text Add to dashboard Cite

Accurately modeling the structures of proteins and their complexes using artificial intelligence is revolutionizing molecular biology. Experimental data enable a candidate-based approach to systematically model novel protein assemblies. Here, we use a combination of in-cell crosslinking mass spectrometry, co-fractionation mass spectrometry and the SubtiWiki database to identify protein-protein interactions in the model Gram-positive bacterium Bacillus subtilis. Pairing this with structure prediction by AIphaFold-Multimer, we identify novel interactors of central machineries that include the ribosome, RNA polymerase and pyruvate dehydrogenase, as well as interactions involving uncharacterized proteins, which we functionally validate. After controlling for the false-positive rate of the AlphaFold approach, we propose novel structural models of 153 dimeric and 14 trimeric protein assemblies. We show that crosslinking MS data can independently validate AlphaFold predictions in situ. Our approach uncovers protein-protein interactions inside cells, provides structural insight into their interaction interface, and is applicable to genetically intractable organisms, including pathogenic bacteria.

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“…In natural transformation, competence proteins are involved mainly in gene regulation, DNA uptake, and DNA processing ( 17 , 53 , 55 ). For sequence analysis, the genome sequences of 5 A. paragallinarum strains and H. influenzae KW20 were downloaded from GenBank ( https://www.ncbi.nlm.nih.gov/genbank/ ).…”

Section: Methodsmentioning

confidence: 99%