Complete genome sequence of Thermus brockianus GE-1 reveals key enzymes of xylan/xylose metabolism

Abstract

Thermus brockianus strain GE-1 is a thermophilic, Gram-negative, rod-shaped and non-motile bacterium that was isolated from the Geysir geothermal area, Iceland. Like other thermophiles, Thermus species are often used as model organisms to understand the mechanism of action of extremozymes, especially focusing on their heat-activity and thermostability. Genome-specific features of T. brockianus GE-1 and their properties further help to explain processes of the adaption of extremophiles at elevated temperatures. Here we analyze the first whole genome sequence of T. brockianus strain GE-1. Insights of the genome sequence and the methodologies that were applied during de novo assembly and annotation are given in detail. The finished genome shows a phred quality value of QV50. The complete genome size is 2.38 Mb, comprising the chromosome (2,035,182 bp), the megaplasmid pTB1 (342,792 bp) and the smaller plasmid pTB2 (10,299 bp). Gene prediction revealed 2,511 genes in total, including 2,458 protein-encoding genes, 53 RNA and 66 pseudo genes. A unique genomic region on megaplasmid pTB1 was identified encoding key enzymes for xylan depolymerization and xylose metabolism. This is in agreement with the growth experiments in which xylan is utilized as sole source of carbon. Accordingly, we identified sequences encoding the xylanase Xyn10, an endoglucanase, the membrane ABC sugar transporter XylH, the xylose-binding protein XylF, the xylose isomerase XylA catalyzing the first step of xylose metabolism and the xylulokinase XylB, responsible for the second step of xylose metabolism. Our data indicate that an ancestor of T. brockianus obtained the ability to use xylose as alternative carbon source by horizontal gene transfer.

Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures

“…T. thermophilus is also known to produce a variety of polyamines, the most common ones, spermidine and spermine, are synthesised using a distinct pathway from L-arginine via aminopropyl agmatine (Oshima 2007) . Analysis of complete thermophilic genomes is a widely used method of finding both novel metabolic pathway, as well as enzymes of potential biotechnological use (Henne et al 2004;Schäfers et al 2017;Wu et al 2009) . An alternative pathway of menaquinone (MK) synthesis was discovered when no genes from the classical pathway were found in genomes of some MK-producing microorganism (Hiratsuka et al 2008) .…”

Genomic Analysis of Actinomyces sp. Strain CtC72, a Novel Fibrolytic Anaerobic Bacterium Isolated from Cattle Rumen

“…A total of 37 genes encoding for enzymes involved in xylan metabolism were identified in strain CtC72, namely three endo-1,4-βxylanase A genes (FIG00475203), four β-xylosidase genes (FIG00003086), two α-xylosidase (FIG00003174), two acetyl xylan esterase (FIG01955910), five α-L-arabinofuranosidase (FIG00037240), one ABC alpha-xylosidase transporter genes (FIG00089781), three xylose ABC transporter (FIG01276112), a xylose isomerase gene (FIG00019456), three xylulose kinase genes (FIG00000793), three xyloside transporter XynT genes and three xylose responsive transcription regulation factor ROK family. Of these, the most important enzymes are β-xylosidase and xylose isomerase, which carries out the first and second step in xylan degradation [27]. The strain CtC72 contained all the essential enzymes required for efficient xylan utilization making it an efficient xylanolytic organism (Fig.…”

Three-dimensional structure and functional studies of neopullulanase from Thermus brockianus

“…They have been isolated from different environments with high temperatures such as deep-sea hot vents, hot springs, volcanic eruptions, deep-sea hot vents etcetera and produce thermozymes, enzymes with superior conformational structure and tools due to the presence of a small number of extra hydrogen bonds, hydrophobic interactions, and electrostatic interactions. These enzymes play a significant role in biotechnological, chemical, food, pharmaceutical, pulp, paper and waste-treatment industries (Bruins et al, 2001;Kumar et al, 2019;Sharma et al, 2019;Schäfers et al, 2017). Researchers have isolated and described the activities and structures of neopullulanases from thermophilic bacteria such as Geobacillus stearothermophilus TRS40 (Kuriki et al, 1992), Bacillus stearothermophilus (Ece et al, 2015;Hondoh et al, 2003;Kamasaka et al, 2002;Kuriki et al, 1988).…”