Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice

Abstract

We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K. pneumoniae 342 is a member of the enteric bacteria, it serves as a model for studies of endophytic, plant-bacterial associations due to its efficient colonization of plant tissues (including maize and wheat, two of the most important crops in the world), while maintaining a mutualistic relationship that encompasses supplying organic nitrogen to the host plant. Genomic analysis examined K. pneumoniae 342 for the presence of previously identified genes from other bacteria involved in colonization of, or growth in, plants. From this set, approximately one-third were identified in K. pneumoniae 342, suggesting additional factors most likely contribute to its endophytic lifestyle. Comparative genome analyses were used to provide new insights into this question. Results included the identification of metabolic pathways and other features devoted to processing plant-derived cellulosic and aromatic compounds, and a robust complement of transport genes (15.4%), one of the highest percentages in bacterial genomes sequenced. Although virulence and antibiotic resistance genes were predicted, experiments conducted using mouse models showed pathogenicity to be attenuated in this strain. Comparative genomic analyses with the presumed human pathogen K. pneumoniae MGH78578 revealed that MGH78578 apparently cannot fix nitrogen, and the distribution of genes essential to surface attachment, secretion, transport, and regulation and signaling varied between each genome, which may indicate critical divergences between the strains that influence their preferred host ranges and lifestyles (endophytic plant associations for K. pneumoniae 342 and presumably human pathogenesis for MGH78578). Little genome information is available concerning endophytic bacteria. The K. pneumoniae 342 genome will drive new research into this less-understood, but important category of bacterial-plant host relationships, which could ultimately enhance growth and nutrition of important agricultural crops and development of plant-derived products and biofuels.

Figure 1. Circular Representation of the Closed Genome of Kp342.

The chromosome (A) is illustrated as a circle where each concentric circle represents genomic data and is numbered from the outermost to the innermost circle. Refer to the key for details on color representations and circle number. The comparisons to E. coli K12 (circle 5) and MGH78578 (circle 4) are noted as follows. The color indicates the position of the matching Kp342 region (circle 2) using NUCMER. The height of the tick indicates the percent identity of the NUCMER match. Plasmids pKP187 (B) and pKP91 (C) are likewise depicted circular, but each concentric circle from 4 to the innermost circle shows the NUCMER match to previously sequenced plasmids from NCBI, colored by the percent identity of the matching region. See key for color conversion.

Figure 2. Whole-Genome Comparison of Kp342 to K. pneumoniae MGH78578 and E. coli K12.

Line figures depict the results of NUCMER analysis. Colored lines denote nucleotide percent identity and are plotted according to the location in the reference Kp342 genome (x-axis) and the query genomes K. pneumoniae MGH78578 (A) and E. coli K12 (B).

Figure 3. Whole Genome Comparison of K. pneumoniae 342, K. pneumoniae MGH78578, and E. coli K12 Proteins.

The Venn diagram shows the number of proteins shared (black) or unique (red) within a particular relationship for all three organisms compared.