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

Abstract

Chitin is the second most abundant polysaccharide worldwide as part of arthropods' exoskeletons and fungal cell walls. Low concentrations in soils and sediments indicate rapid decomposition through chitinolytic organisms in terrestrial and aquatic ecosystems. The enacting enzymes, so‐called chitinases, and their products, chitooligosaccharides, exhibit promising characteristics with applications ranging from crop protection to cosmetics, medical, textile, and wastewater industries. Exploring novel chitinolytic organisms is crucial to expand the enzymatical toolkit for biotechnological chitin utilization and to deepen our understanding of diverse catalytic mechanisms. In this study, we present two long‐read sequencing‐based genomes of highly similar Jeongeupia species, which have been screened, isolated, and biochemically characterized from chitin‐amended soil samples. Through metabolic characterization, whole‐genome alignments, and phylogenetic analysis, we could demonstrate how the investigated strains differ from the taxonomically closest strain Jeongeupia naejangsanensis BIO‐TAS4‐2T (DSM 24253). In silico analysis and sequence alignment revealed a multitude of highly conserved chitinolytic enzymes in the investigated Jeongeupia genomes. Based on these results, we suggest that the two strains represent a novel species within the genus of Jeongeupia, which may be useful for environmentally friendly N‐acetylglucosamine production from crustacean shell or fungal biomass waste or as a crop protection agent.

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

“…Although this strategy is well described in both fungi and bacteria [ 21 , 22 ], a multitude of export pathways have been identified for the latter, with the Sec and Tat systems noted as major facilitators [ 23 , 24 , 25 ]. As previously demonstrated [ 19 ], the investigated strain’s genome contains 13 glycoside hydrolases of family 18 (GH18) [ 26 , 27 ], which imply not only chitinases (EC 3.2.1.14) of classes III and V but also non-catalytic, accessory proteins. Furthermore, six β-N-acetyl-hexosaminidases, three of which could be attributed to either the GH3 or GH20 family, three GH19 chitinases, and a single lytic polysaccharide monooxygenase (LPMO, AA10; formerly CBM33) are present on a genetic level.…”

“…In total, 600 transcripts were upregulated at least 20% or 1.2-fold and with an adjusted p -value of <0.1 with chitin in contrast to 468 with glucose as the carbon source. The increased gene recruitment, paired with the extraordinarily abundant chitinolytic machinery of the investigated organism [ 19 ], leaves room for speculation regarding whether the Jeongeupia genus specializes in chitin as a primary carbon source. In contrast to D-glucose, chitin exhibits a more rigid, less accessible and acetylated structure, which plainly requires more enzymes for degradation, deacetylation, and finally, assimilation.…”

“…The FtsX-like permease family are predicted transmembrane proteins that can release, for example, lipoproteins from the cytosol to the periplasm in an ATP-dependent manner (refer to UniProt accession P57382). Nonetheless, six out of the thirteen genome-encoded GH18 [ 19 ] were upregulated during exposure to colloidal chitin, albeit on surprisingly low ranks, underpinning the intra- and extracellular proteomic results. In addition, two of the three GH19 type chitinases and one of the three GH20 hexosaminidases exhibited increased transcript rates.…”

“…In a follow-up study, Saito et al elaborated that the multiplicity of chitinases in Streptomyces spp. has developed through domain deletion and gene duplication [ 75 ], which might be extrapolated to other chitinase-rich genera like Jeongeupia [ 19 , 76 ].…”

“…In this study, we used our previously isolated and genome-sequenced bacterium Jeongeupia wiesaeckerbachi [ 19 ], which is closely related to Jeongeupia naejangsanensis [ 20 ]. Due to the high-resolution genome data available in our group, we chose this microorganism as a model to investigate and characterize its extensive chitinolytic machinery for the first time, using a three-way systems biology approach: First, the most abundant extracellular chitin-active (interacting with chitin or COS molecules) enzymes were identified through LC-MS/MS analysis of the average secretome with colloidal chitin and crab shell chitin as inducers of the chitinolytic enzyme machinery, respectively.…”