Comprehensive genome analysis of Lentzea reveals repertoire of polymer-degrading enzymes and bioactive compounds with clinical relevance

Abstract

The genus Lentzea is a rare group of actinobacteria having potential for the exploration of bioactive compounds. Despite its proven ability to produce compounds with medical relevance, Lentzea genome analysis remains unexplored. Here we show a detailed understanding of the genetic features, biosynthetic gene clusters (BGCs), and genetic clusters for carbohydrate-active enzymes present in the Lentzea genome. Our analysis determines the genes for core proteins, non-ribosomal peptide synthetase condensation domain, and polyketide synthases-ketide synthase domain. The antiSMASH-based sequence analysis identifies 692 BGCs among which 8% are identical to the BGCs that produce geosmin, citrulassin, achromosin (lassopeptide), vancosamine, anabaenopeptin NZ857/nostamide A, alkylresorcinol, BE-54017, and bezastatin. The remaining BGCs code for advanced category antimicrobials like calcium-dependent, glycosylated, terpenoids, lipopeptides, thiopeptide, lanthipeptide, lassopeptide, lingual antimicrobial peptide and lantibiotics together with antiviral, antibacterial, antifungal, antiparasitic, anticancer agents. About 28% of the BGCs, that codes for bioactive secondary metabolites, are exclusive in Lentzea and could lead to new compound discoveries. We also find 7121 genes that code for carbohydrate-degrading enzymes which could essentially convert a wide range of polymeric carbohydrates. Genome mining of such genus is very much useful to give scientific leads for experimental validation in the discovery of new-generation bioactive molecules of biotechnological importance.

Lentzea sokolovensis sp. nov., Lentzea kristufekii sp. nov. and Lentzea miocenica sp. nov., rare actinobacteria from Miocene lacustrine sediment of the Sokolov Coal Basin, Czech Republic

“…S1). These results are consistent with the tree previously presented by [5, 29], who also constructed their phylogenetic tree using the core protein-coding genes of the available genomes.…”

“…The genus Lentzea has recently attracted a great deal interest due to its underestimated genetic diversity [ 3 4 ], including its genetic potential for biosynthesis of natural products that are in high demand in the pharmaceutical field [ 5 ]. For instance, lentzeosides with anti-HIV-1 integrase activity were isolated from the extremotolerant Lentzea sp.…”

“…from various oligotrophic or extreme environments could be a good source of novel natural products. However, to date (May 2023), only 21 good-quality genomes of the 27 species validly published under the International Code of Nomenclature of Prokaryotes (ICNP) are publicly available, with the reference genomes of Lentzea deserti and Lentzea atacamensis being identical [ 8 ], and the sole exception of Lentzea indica , which is not validly published under the ICNP but has a very complete genome in comparison with the other strains [ 5 ].…”

Diversity and Antimicrobial Activities of Actinobacteria Isolated from Mining Soils in Midelt Region, Morocco

“…Antimicrobial activities in Lentzea indicate that rare Actinobacteria strains are appropriate sources of bioactive compounds. The recent analysis of the Lentzea genome reveals a repertoire of biosynthetic gene clusters (BGCs) among which more than 90% code for antimicrobial molecules including mainly terpenoids, lipopeptides, and thiopeptides [ 66 ].…”

Luteibacter sahniisp. nov., a novel yellow-pigmented probiotic bacterium from rice seed microbiome

“…In particular, the presence of RiPP-like, NRPS, and T1PKS clusters suggests the potential biosynthesis of bioactive molecules with diverse antimicrobial properties (Maiti and Mandal, 2022). These metabolites could play a pivotal role in mediating interactions between the novel Luteibacter species and its environment, including potential plant pathogens.…”