Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Abstract

We present here the complete 2.4-Mb genome of the cellulolytic actinobacterial thermophile Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized and elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls, and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. Several of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and noncoding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs-dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and the presence of three laterally acquired genomic islands of likely ecophysiological value.

Figure 1.

Schematic of the A. cellulolyticus 11B genome. The outermost circle gives the genome coordinates. The next two inner rings show the predicted genes on the leading (outer circle) and the lagging (inner circle) strands. Color scheme is as follows: dark gray, hypothetical proteins; light gray, conserved hypothetical and unknown function; brown, general function prediction; red, replication and repair; green, energy metabolism; blue, carbon and carbohydrate metabolism; cyan, lipid metabolism; magenta, transcription; yellow, translation; orange, amino acid metabolism; pink, metabolism of cofactors and vitamins; light red, purine and pyrimidine metabolism; lavender, signal transduction; sky blue, cellular processes; pale green, structural RNAs. Ring 4 displays the positions of the glycoside hydrolases (black bars), the three GIs (triangles), the flagellar biosynthetic genes (red star) , and the rRNA operon (blue star). Ring 5 shows the G+C content along the genome. The innermost ring, ring 6, displays the GC skew.

Figure 2.

Genomic signature plot. A sliding window plot of the percent G+C content (top line, y-axis on the left) as well as the deviation in genomic signature (ΔGS; bottom line, secondary y-axis on right) along the chromosome. Regions 1, 2, and 3 on the plot indicate the location of the three GIs: GI1, GI2, and GI3, respectively. Arrow indicates the location of the flagellar and motility genes.

Figure 3.

Synteny and gene organization of the flagellar biosynthetic genes in actinobacteria. The A. cellulolyticus locus Acel_0827-Acel_0864 is displayed; the syntenic region ranges from Acel_0829 to Acel_0861. Ace, Kra, Lxy, and Noc denote A. cellulolyticus, K. radiotolerans, L. xyli, and Nocardioides sp. JS614, respectively. Chromosomal gene organization from each of the completely assembled genomes is shown, except in the case of K. radiotolerans, for which genes from two different contigs are shown. Therefore, the true order of the whole region in K. radiotolerans remains unclear. Synteny between the different chromosomal regions is indicated by green lines (for genes on the same strand) and red lines (for genes on opposite strands). The gene sizes in the different organisms are not drawn to scale. Also, the K. radiotolerans genes are colored differently than the genes in the other three organisms.

Figure 4.

Plot of the G+C content of noncoding RNAs (rRNA + tRNAs) versus the G+C of genome in prokaryotes. The following shapes and shades are used for distinguishing the organisms: black circles, hyperthermophiles; dark gray circles, thermophiles; open circles, mesophiles; filled squares, psychrophiles; inverted gray triangle, A. cellulolyticus; gray triangle, T. fusca; inverted open triangles, two Frankia sp. (ACN14a, CcI3), and open triangles, two Streptomyces sp. (S. avermitilis, S. coelicolor). Black lines represent the regression line and 95% confidence intervals, computed for the mesophiles.

Figure 5.

Reduced dimensionality plot of PCA of amino acid usage in ribosomal proteins in 409 prokaryotes. The following shapes and shades are used for distinguishing the organisms: black circles, hyperthermophiles; dark gray circles, thermophiles; open circles, mesophiles; black squares, psychrophiles; inverted gray triangle, A. cellulolyticus; gray triangle, T. fusca; inverted open triangles, two Frankia sp. (ACN14a, CcI3), and open triangles, two Streptomyces sp. (S. avermitilis, S. coelicolor).