Proteome and acylome analyses of the functional interaction network between the carbazole‐degradative plasmid pCAR1 and host Pseudomonas putida KT2440

Abstract

Understanding the interplay between a plasmid and its host system is a bottleneck towards prediction of the fate of plasmid-harbouring strains in the natural environments. Here, we studied the impact of the conjugative plasmid pCAR1, involved in carbazole degradation, on the proteome of Pseudomonas putida KT2440 using SILAC method. Furthermore, we investigated two acyl lysine modifications (acetylation and succinylation) that respond to the metabolic status of the cell and are implicated in regulation of various cellular processes. The total proteome analysis revealed that the abundance of key proteins involved in metabolism, signal transduction and motility was affected by pCAR1 carriage. In total, we identified 1359 unique acetylation sites on 637 proteins and 567 unique succinylation sites on 259 proteins. Changes in the acylation status of proteins involved in metabolism and translation by pCAR1 carriage were detected. Remarkably, acylation was identified on proteins involved in important plasmid functions, including partitioning and carbazole degradation, and on nucleoid-associated proteins that play a key role in the functional interaction with the chromosome. This study provides a novel insight on the functional consequences of plasmid carriage and improves our understanding of the plasmid-host cross-talk.

Post-translational Protein Acetylation: An Elegant Mechanism for Bacteria to Dynamically Regulate Metabolic Functions

“…It is now clear that the extent of acetylation, the mechanisms by which acetylation occurs, the identities of acetylated proteins, and the locations of acetylation on those proteins can vary between organisms; yet, in most cases, there is great conservation in core cellular processes (Nakayasu et al, 2017). Such approaches have shown that acetylation occurs on proteins involved in a wide diversity of cellular process, especially central metabolism and translation (Wang et al, 2010; Weinert et al, 2013a; Baeza et al, 2014; Kuhn et al, 2014; Kosono et al, 2015; Schilling et al, 2015; Kentache et al, 2016; Birhanu et al, 2017; Jers et al, 2017; Nagano-Shoji et al, 2017; Post et al, 2017; Bontemps-Gallo et al, 2018; Gaviard et al, 2018; Sun et al, 2018; Vasileva et al, 2018; Yoshida et al, 2019). As stated above, many of these acetylations are conserved.…”

A Novel Small RNA on the Pseudomonas putida KT2440 Chromosome Is Involved in the Fitness Cost Imposed by IncP-1 Plasmid RP4

“…When a plasmid is introduced into the host cell, transcriptional, proteomic, and metabolic profiles are altered greatly (San Millan et al, 2018;Vasileva et al, 2018) consequently, a fitness cost is imposed on the host cell by the plasmid. The molecular basis underlying fitness costs is incompletely known, although several important factors have been identified, such as plasmid replication protein (Sota et al, 2010), helicase (Loftie-Eaton et al, 2015San Millan et al, 2015) and global transcriptional regulators (Doyle et al, 2007;Harrison et al, 2015;Stalder et al, 2017).…”

“…Moreover, it was demonstrated that pCAR1 carriage affects the chromosomal transcriptional profile differently among hosts (Shintani et al, 2010), and modulates the primary cell functions of each host (Takahashi et al, 2015). Recently, we reported that pCAR1 carriage altered the proteome profile of strain KT2440; in particular, the acylation status of proteins involved in metabolism and translation was altered (Vasileva et al, 2018). These effects of pCAR1 carriage on the host cell may explain the fitness cost imposed by pCAR1.…”

Endogenous and Foreign Nucleoid-Associated Proteins of Bacteria: Occurrence, Interactions and Effects on Mobile Genetic Elements and Host's Biology

“…Comparative studies of the transcriptional profiles of the wild type strain with or without the pCAR1 plasmid, and a pmr mutant, showed that pmr disruption had far greater effects on the host transcriptome than did pCAR1 carriage [177]. Follow-up experiments using proteomic approaches and pCAR1-free versus pCAR1-harboring cells, further confirmed that plasmid carriage greatly affects many host related processes, including the utilization of several metabolites and amino acids, along with respiration [165].…”

“…Intrerstingly, the binding sites of the three NAPs are almost identical and all three proteins regulate the transcriptional networks in the plasmid-harboring cells cooperatively [178]. Recently, a comprehensive analysis of the post-translational modifications (PTMs) of the Pseudomonas proteome added an additional layer of information to our current understanding of the pCAR1 plasmid impact on its host [165], being this also the first report of PTM effects in plasmid-host interactions.…”