Genomic and Proteomic Study of Andreprevotia ripae Isolated from an Anthill Reveals an Extensive Repertoire of Chitinolytic Enzymes

Abstract

Chitin is an abundant natural polysaccharide that is hard to degrade because of its crystalline nature and because it is embedded in robust co-polymeric materials containing other polysaccharides, proteins, and minerals. Thus, it is of interest to study the enzymatic machineries of specialized microbes found in chitin-rich environments. We describe a genomic and proteomic analysis of Andreprevotia ripae , a chitinolytic Gram-negative bacterium isolated from an anthill. The genome of A. ripae encodes four secreted family GH19 chitinases of which two were detected and upregulated during growth on chitin. In addition, the genome encodes as many as 25 secreted GH18 chitinases, of which 17 were detected and 12 were upregulated during growth on chitin. Finally, the single lytic polysaccharide monooxygenase (LPMO) was strongly upregulated during growth on chitin. Whereas 66% of the 29 secreted chitinases contained two carbohydrate-binding modules (CBMs), this fraction was 93% (13 out of 14) for the upregulated chitinases, suggesting an important role for these CBMs. Next to an unprecedented multiplicity of upregulated chitinases, this study reveals several chitin-induced proteins that contain chitin-binding CBMs but lack a known catalytic function. These proteins are interesting targets for discovery of enzymes used by nature to convert chitin-rich biomass. The MS proteomic data have been deposited in the PRIDE database with accession number PXD025087.

Isolation, biochemical characterization, and genome sequencing of two high‐quality genomes of a novel chitinolytic Jeongeupia species

“…According to a study from 2016, which compared the chitinolytic systems of aquatic and terrestrial chitinolytic systems based on available genomes at that time, Jeongeupia exhibits an exceptionally rich enzyme toolkit (Bai et al, 2016 ), that reminds us of fungal Trichoderma species (Seidl et al, 2005 ). To our knowledge, few bacteria, among them Streptomyces coelicolor A3(2) (Saito et al, 2000 ) and Andreprevotia ripae (Lorentzen et al, 2021 ), are described with access to comparable chitinase gene copy numbers.…”

Proteomic and Transcriptomic Analyses to Decipher the Chitinolytic Response of Jeongeupia spp.

“…Lorentzen et al discovered a Gram-negative bacterium in an abandoned ant hill with an unprecedentedly rich chitinase arsenal [ 53 ]. During investigation of its secretome, they observed that an increased fraction (93%) of upregulated chitinases contained two carbohydrate-binding modules of the Pfam family 5/12 (CBM5/12).…”