Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes

Abstract

Fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. Although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within Bacteria. In this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and four metagenomic datasets, using the custom profile Hidden Markov Models for two- and three-domain laccases. More than 1,200 putative genes for laccase-like enzymes were retrieved from chromosomes and plasmids of diverse bacteria. In 76% of the genes, signal peptides were predicted, indicating that these bacterial laccases may be exported from the cytoplasm, which contrasts with the current belief. Moreover, several examples of putatively horizontally transferred bacterial laccase genes were described. Many metagenomic sequences encoding fragments of laccase-like enzymes could not be phylogenetically assigned, indicating considerable novelty. Laccase-like genes were also found in anaerobic bacteria, autotrophs and alkaliphiles, thus opening new hypotheses regarding their ecological functions. Bacteria identified as carrying laccase genes represent potential sources for future biotechnological applications.

Figure 1. A two-step approach for the construction of laccase-specific profile Hidden Markov Models (pHMM).

An initial set of known protein sequences was used to search for similar proteins that served for initial pHMMs building. These were refined with additional sequences and rebuilt from improved alignments. NCBI proteins – a database of all the proteins from the finished microbial genomes as described Methods.

Figure 2. Proportions of two-domain (black) and three-domain (grey) laccases in different phyla (left) and classes of Proteobacteria (right).

The numbers in brackets represent the total number of laccase genes found in each taxon.

Figure 3. List of species encoding laccase genes and possessing plasmids in their genomes.

The bars represent the number of laccase genes in the genome (black) and the number of laccase genes on plasmids (gray). The length of the bar shows the total number of genes for each organism.

Figure 4. Taxonomic affiliation of sequences encoding laccases-like proteins in the Global Ocean Survey data.

Proportions are shown for the total of 847, 245 and 32 sequences aligning well to the pHMMs of the three-domain laccases, type B two-domain laccases and type C two-domain laccases, respectively.