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.

Figure 1

Distribution of orthologous genes present in Lentzea genomes.

Figure 2

Functional classification of protein-coding genes present in Lentzea genomes by the abundance of Clusters of Orthologous Groups (COGs). The colour code represents the level of abundance.

Figure 3

Circular map of the complete genome of L. guizhouensis DHS C013 along with the comparative genome maps of rest of the available Lentzea genome sequences. The figure was designed using BRIG. The gaps in the circles represent regions of low or no similarity.

Figure 4

Neighbor-joining phylogenetic relationship based on core proteome of Lentzea species. Numbers at nodes refer to bootstrap values based on 1000 replicates. Bar, 0.01 means amino acid substitutions per 100 amino acid position.

Figure 5

Heat map showing the abundance of BGCs distributed in Lentzea genome as predicted by antiSMASH database. Color keys represent variation of copy numbers of individual cluster among Lentzea genome.

Figure 6

Principal component analysis (PCA) among Lentzea species based on BGCs recovered through antiSMASH for their relationship.

Figure 7

Highly similar antimicrobial gene clusters of Lentzea species compared with known clusters in the antiSMASH database. Gene clusters for Nystatin (a), Nystatin A1 (b), Butyrolactol A (c), Indigoidine (d); and the putative compounds produced by these clusters Nystatin (e), Nystatin A1 (f), Butyrolactol A (g), and Indigoidine (h).

Figure 8

Highly similar antitumor gene clusters of Lentzea species compared with known clusters in the antiSMASH database. (a) alkylresorcinol, (b) BE-54017, (c) staurosporine.

Figure 9

Highly similar siderophores gene clusters of Lentzea species compared with known clusters in the antiSMASH database. Gene clusters for coelichelin (a), amychelin (b), mirubactin (c); and the putative compounds produced by these clusters coelichelin (d), amychelin (e), and mirubactin (f).

Figure 10

Species specific clusters and their putative products of Lentzea compared to the known clusters and their product from the antiSMASH database. (a) Biosynthetic cluster of anabaenopeptin NZ857/nostamide A of Nostoc punctiforme PCC 73102; (b) tomaymycin cluster of Streptomyces achromogenes compared with 88% similar genetic cluster of L. fradiae CGMCC 4.3506 and (c) genetic cluster for a macrolide group of antibiotics virginiamycin S1 of L. flava JCM 3296 having 83% similarity with that of Streptomyces virginiae.

Figure 11

Phylogenetic analysis of (a) condensation and (b) ketosynthase domains of NRPS and PKS genes in Lentzea genomes by Neighbor-joining method against NaPDoS database domains. Leaves are coloured to represent different Lentzea species, while coloured branches display domain class of database domains (A) NRPS C domain: Yellow = DCL, Red = LCL, Green = cyc, Blue = modAA, Light Brown = start, Purple = C. (B) PKS KS domain: Yellow = enediyne, Red = modular, Green = FAS, Blue = hybrid KS, Brown = trans, Purple = KS1, Pink = typeII, Light pink = iterative.

Figure 12

Heat map represents the abundance of the CAZymes present in Lentzea genome. The red color intensity is proportional to the abundance of the genes for CAZymes. Red box = unique enzymes.

Figure 13

Principal component analysis (PCA) among the different Lentzea based on CAZY enzymes recovered from dbCN2 for their relationship.

Figure 14

Schematic representation of the summarized work flow for Lentzea genome analysis to demarcate the gene clusters responsible for the production of CAZymes and pharmaceutically relevant secondary metabolites.