Genome sequence of the plant growth promoting endophytic bacterium Enterobacter sp. 638

Abstract

Enterobacter sp. 638 is an endophytic plant growth promoting gamma-proteobacterium that was isolated from the stem of poplar (Populus trichocarpaxdeltoides cv. H11-11), a potentially important biofuel feed stock plant. The Enterobacter sp. 638 genome sequence reveals the presence of a 4,518,712 bp chromosome and a 157,749 bp plasmid (pENT638-1). Genome annotation and comparative genomics allowed the identification of an extended set of genes specific to the plant niche adaptation of this bacterium. This includes genes that code for putative proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion (pili, adhesion, hemagglutinin, cellulose biosynthesis), colonization/establishment inside the plant (chemiotaxis, flagella, cellobiose phosphorylase), plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol. Metabolite analysis confirmed by quantitative RT-PCR showed that, the production of acetoin and 2,3-butanediol is induced by the presence of sucrose in the growth medium. Interestingly, both the genetic determinants required for sucrose metabolism and the synthesis of acetoin and 2,3-butanediol are clustered on a genomic island. These findings point to a close interaction between Enterobacter sp. 638 and its poplar host, where the availability of sucrose, a major plant sugar, affects the synthesis of plant growth promoting phytohormones by the endophytic bacterium. The availability of the genome sequence, combined with metabolome and transcriptome analysis, will provide a better understanding of the synergistic interactions between poplar and its growth promoting endophyte Enterobacter sp. 638. This information can be further exploited to improve establishment and sustainable production of poplar as an energy feedstock on marginal, non-agricultural soils using endophytic bacteria as growth promoting agents.

Figure 1. Circular representation of the Enterobacter sp. 638 chromosome.

Circles displayed (from the outside): the GC percent deviation (GC window - mean GC) in a 1000-bp window, predicted CDSs transcribed in the clockwise direction, predicted CDSs transcribed in the counterclockwise direction, CDS in clockwise and counterclockwise direction colored according to their COG classes, the position of all the palindromic repeats, the position of the 100 palindromic repeats (CCCTCTCCCXX(X)GGGAGAGGG), GC skew (G+C/G−C) in a 1000-bp window, and coordinates in kilo bases pair. Syntenic regions compared with E. coli K12 are shown with genes displayed in orange, while genes displayed in purple correspond to non syntenic region. Arrows indicate to putative functions of genes located in region that are not in synteny with E. coli K12 (for further detail on gene content for each regions see Table 1). A syntenic region is defined by a minimum of three consecutive genes that are present in E. coli K12 genome sequence, and that show a similar genetic organization.

Figure 2. Circular representation of the Enterobacter sp. 638 plasmid pENT638-1.

Circles displayed from the outside): subdivision of pENT-01 group of function, gene annotation, the GC percent deviation (GC window - mean GC) in a 1000-bp window, predicted CDSs (red) transcribed in the clockwise direction, predicted CDSs (blue) transcribed in the counterclockwise direction, GC skew (G+C/G−C) in a 1000-bp window, transposable elements from IS elements (pink) and pseudogenes (grey). Toxin/anti T toxin (TA) systems are shown with an asterisk (*).

Figure 3. Overview of metabolism and transport in Enterobacter sp. 638.

Predicted pathways for the interaction between Enterobacter sp. 638 and the plant are shown. Export or import of solutes is designated by the direction of the arrow through the transporter. The dash arrows show the putative function of certain molecular biosynthesized by Enterobacter sp. 638 in regard to its plant host.

Figure 4. Schematic representation of Genomic Region 29 found on the chromosome of Enterobacter sp. 638.

Putative open reading frames are indicated by arrows, below which the Enterobacter sp. 638 gene number and gene annotation are shown. The genes involved in sucrose transport and utilization, acetoin and 2,3-butanediol synthesis, the toxin-antitoxin (TA system), as well as other putative functions are also indicated.