Reactivity-Based Screening for Citrulline-Containing Natural Products Reveals a Family of Bacterial Peptidyl Arginine Deiminases

Ribosomally
synthesized and post-translationally modified peptides
(RiPPs) are a family of natural products defined by a genetically
encoded precursor peptide that is processed by associated biosynthetic
enzymes to form the mature product. Lasso peptides are a class of
RiPP defined by an isopeptide linkage between the N-terminal amine
and an internal Asp/Glu residue with the C-terminal sequence threaded
through the macrocycle. This unique lariat topology, which typically
provides considerable stability toward heat and proteases, has stimulated
interest in lasso peptides as potential therapeutics. Post-translational
modifications beyond the class-defining, threaded macrolactam have
been reported, including one example of Arg deimination to yield citrulline
(Cit). Although a Cit-containing lasso peptide (i.e., citrulassin)
was serendipitously discovered during a genome-guided campaign, the
gene(s) responsible for Arg deimination has remained unknown. Herein,
we describe the use of reactivity-based screening to discriminate
bacterial strains that produce Arg- versus Cit-bearing citrulassins,
yielding 13 new lasso peptide variants. Partial phylogenetic profiling
identified a distally encoded peptidyl arginine deiminase (PAD) gene
ubiquitous to the Cit-containing variants. Absence of this gene correlated
strongly with lasso peptide variants only containing Arg (i.e., des-citrulassin). Heterologous expression of the PAD gene
in a des-citrulassin producer resulted in the production
of the deiminated analog, confirming PAD involvement in Arg deimination.
The PADs were then bioinformatically surveyed to provide a deeper
understanding of their taxonomic distribution and genomic contexts
and to facilitate future studies that will evaluate any additional
biochemical roles for the superfamily.