Abstract
Our previous study identified a new β-galactosidase in Erwinia sp. E602. To further understand the lactose metabolism in this strain, de novo genome assembly was conducted by using a strategy combining Illumina and PacBio sequencing technology. The whole genome of Erwinia sp. E602 includes a 4.8 Mb chromosome and a 326 kb large plasmid. A total of 4,739 genes, including 4,543 protein-coding genes, 25 rRNAs, 82 tRNAs and 7 other ncRNAs genes were annotated. The plasmid was the largest one characterized in genus Erwinia by far, and it contained a number of genes and pathways responsible for lactose metabolism and regulation. Moreover, a new plasmid-borne lac operon that lacked a typical β-galactoside transacetylase (lacA) gene was identified in the strain. Phylogenetic analysis showed that the genes lacY and lacZ in the operon were under positive selection, indicating the adaptation of lactose metabolism to the environment in Erwinia sp. E602. Our current study demonstrated that the hybrid de novo genome assembly using Illumina and PacBio sequencing technologies, as well as the metabolic pathway analysis, provided a useful strategy for better understanding of the evolution of undiscovered microbial species or strains.
Highlights
Erwinia is a group of the straight rod-shaped, facultative anaerobic, gram-negative bacterium of the Erwiniaceae family of Enterobacteriaceae
E602 genome, we identified a large plasmid and a new plasmid-borne lac operon containing a lacZ gene encoding the β-galactosidase with low-temperature activity, as well as evidence supporting positive selection pressure of the lac operon
4,472 genes including 4,296 protein-coding, 25 rRNAs, 82 tRNAs, and 7 other ncRNAs genes were located on the chromosome, while 277 protein-coding genes were located on the large plasmid
Summary
Erwinia is a group of the straight rod-shaped, facultative anaerobic, gram-negative bacterium of the Erwiniaceae family of Enterobacteriaceae. Most of the Erwinia species identified by far are pathogens, saprophytes, or epiphytes of plants. It has been reported that some Erwinia species ferment lactose as a carbon source. Our previous study characterized a β-galactosidase with relatively high activity at low temperature in the Erwinia sp. The lac operons typically involve three genes encoding the enzymes that enable bacteria to utilize lactose (Diaz-Hernandez and Santillan, 2010). The gene lacZ encodes the β-galactosidase, an enzyme that degrades lactose into monosaccharides glucose and galactose.
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