Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies.

Phillip J Brumm,Pieter De Maayer,David A Mead,Don A Cowan

doi:10.3389/fmicb.2015.00430

Abstract

In this work we report the whole genome sequences of six new Geobacillus xylanolytic strains along with the genomic analysis of their capability to degrade carbohydrates. The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus. We have identified a ~200 kb unique super-cluster in all six strains, containing five to eight distinct carbohydrate degradation clusters in a single genomic region, a feature not seen in other genera. The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. All six strains are able to utilize fructose, arabinose, xylose, mannitol, gluconate, xylan, and α-1,6-glucosides. The gene clusters for utilization of these seven substrates have identical organization and the individual proteins have a high percent identity to their homologs. The strains show significant differences in their ability to utilize inositol, sucrose, lactose, α-mannosides, α-1,4-glucosides and arabinan.

Highlights

Thermophiles have been a source of industrial enzymes for over 30 years (Vieille and Zeikus, 2001; Haki and Rakshit, 2003; de Miguel Bouzas et al, 2006)
The six sequenced Geobacillus strains described here have a range of GC contents from 43.9% to 52.5% and clade with named Geobacillus species throughout the entire genus
None of the six strains produced extracellular xylanase when grown on glucose, in agreement with reports of catabolite repression of G. stearothermophilus extracellular xylanase production (Cho and Choi, 1999)

Summary

Introduction

Thermophiles have been a source of industrial enzymes for over 30 years (Vieille and Zeikus, 2001; Haki and Rakshit, 2003; de Miguel Bouzas et al, 2006). While cellulose is a homopolymer of beta-1,4-linked glucose, xylans are heteropolymers containing a range of species-specific modifications to the backbone chain (Saha, 2003) These modifications include the attachment of neutral sugars such as arabinose, galactose, and glucose, attachment of charged sugars such as glucuronic acid, and acetylation, giving rise to unsubstituted xylans, arabinoxylans, glucuronoxylans, and arabinoglucuronoxylans (these will all be collectively called xylan). The result of these modifications is a bewildering diversity in Geobacillus carbohydrate degradation the chemical compositions and structures of xylans (recently reviewed in Girio et al, 2010), and the need for a wide range of enzymes and enzyme activities to degrade these structures. A range of other enzymes with potential industrial applications have been identified in Geobacillus species including α-galactosidases (Fridjonsson et al, 1999; Merceron et al, 2012) for use in soy processing, β-galactosidases (Goodman and Pederson, 1976; Hirata et al, 1984, 1986; Solomon et al, 2013) for use in milk processing, lipases (Jeong et al, 2001; Sinchaikul et al, 2002; Abdul Rahman et al, 2009; Ebrahimpour et al, 2011; Balan et al, 2012) and proteases (Nishiya and Imanaka, 1990; Jang et al, 1992; Hawumba et al, 2002; Chen et al, 2004; Itoi et al, 2006) for use in detergents, and amylases (Sen and Oriel, 1989; Brumm et al, 1991; Narang and Satyanarayana, 2001; Kamasaka et al, 2002; Ferner-Ortner-Bleckmann et al, 2009; Mok et al, 2013; Nasrollahi et al, 2013) for use in corn wet milling, baking and ethanol production

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