Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities

Abstract

Rhodothermaceae bacterium RA is a halo-thermophile isolated from a saline hot spring. Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. In this report, we report on the resequencing of its complete genome using a PacBio RSII platform. The genome has a GC content of 68.3%, is 4,653,222 bp in size, and encodes 3711 genes. We are interested in understanding the carbohydrate metabolic pathway, in particular the lignocellulosic biomass degradation pathway. Strain RA harbors 57 glycosyl hydrolase (GH) genes that are affiliated with 30 families. The bacterium consists of cellulose-acting (GH 3, 5, 9, and 44) and hemicellulose-acting enzymes (GH 3, 10, and 43). A crude cell-free extract of the bacterium exhibited endoglucanase, xylanase, β-glucosidase, and β-xylosidase activities. The complete genome information coupled with biochemical assays confirms that strain RA is able to degrade cellulose and xylan. Therefore, strain RA is another excellent member of family Rhodothermaceae as a repository of novel and thermostable cellulolytic and hemicellulolytic enzymes.Electronic supplementary materialThe online version of this article (10.1007/s13205-018-1391-z) contains supplementary material, which is available to authorized users.

Characterizing a Halo-Tolerant GH10 Xylanase from Roseithermus sacchariphilus Strain RA and Its CBM-Truncated Variant

“…We previously isolated R. sacchariphilus RA from a saline hot spring (45 °C, pH 7.1, 13,000 mg/L for Cl − ion, and 7900 mg/L for Na + ) [26]. A complete genome sequencing elucidated that strain RA harbors 57 GHs affiliated to 30 families [21]. Two non-homologous xylanases were identified and designated as XynRA1 and XynRA2 respectively.…”

“…The gene sequence of putative xylanase (GenBank: ARA92359.1) was extracted from the complete genome of R. sacchariphilus RA (GenBank: CP020382.1) [20,21]. The mature xylanase gene was designated as xynRA2 .…”

“…The bacterium exhibited a low identity of 16S rRNA (89.3%) and ANI value (79.3) to the closest strain Rhodothermus marinus DSM 4252 T . This information indicates that Rhodothermaceae bacterium RA might represent a new genus in the family Rhodothermaceae [20,21]. In 2019, Park et al reported a strain MEBiC09517 T isolated from a port in South Korea [22].…”

Global Transcriptomic Responses of Roseithermus sacchariphilus Strain RA in Media Supplemented with Beechwood Xylan

“…Roseithermus sacchariphilus strain RA studied in this work was isolated in 2014 from the Ayer Hangat hot spring located in Langkawi Island, Malaysia [30,37]. The complete genome of strain RA was sequenced earlier [30,38]. When this bacterium was initially isolated, it was not assigned to any genera due to low 16S rRNA sequence similarity (<90%).…”

“…Both proteins exhibit slightly different in vitro biochemical characteristics [31,32]. Additionally, strain RA expresses up to four non-homologous cellulases, two β-glucosidases, and four α-l-rhamnosidases [38]. The biological functions of these non-homologous glycosyl hydrolases are divergent.…”