Advances in Applied Microbiology (eBook)

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2015 | 1. Auflage
204 Seiten
Elsevier Science (Verlag)
978-0-12-802515-4 (ISBN)

Published since 1959, Advances in Applied Microbiology continues to be one of the most widely read and authoritative review sources in microbiology.

The series contains comprehensive reviews of the most current research in applied microbiology. Recent areas covered include bacterial diversity in the human gut, protozoan grazing of freshwater biofilms, metals in yeast fermentation processes and the interpretation of host-pathogen dialogue through microarrays.

Eclectic volumes are supplemented by thematic volumes on various topics, including Archaea and sick building syndrome. Impact factor for 2013: 2.243

Contributions from leading authorities
Informs and updates on all the latest developments in the field

Published since 1959, Advances in Applied Microbiology continues to be one of the most widely read and authoritative review sources in microbiology. The series contains comprehensive reviews of the most current research in applied microbiology. Recent areas covered include bacterial diversity in the human gut, protozoan grazing of freshwater biofilms, metals in yeast fermentation processes and the interpretation of host-pathogen dialogue through microarrays. Eclectic volumes are supplemented by thematic volumes on various topics, including Archaea and sick building syndrome. Impact factor for 2013: 2.243 Contributions from leading authorities Informs and updates on all the latest developments in the field

4. Catabolism

4.1. Polysaccharide and Oligosaccharide Hydrolysis

4.1.1. Hemicellulose

In a recent analysis, De Maayer, Brumm, Mead, and Cowan (2014) have shown that most of the sequenced and partially sequenced strains of Geobacillus spp. have a range of hemicellulose utilization genes present in a genomic island, typically although not exclusively located between echD, an enoyl coenzyme A (CoA) hydratase-encoding gene, and npd, a nitropropane dioxygenase-encoding gene. Comparison of the G + C content between the genes in the island and the rest of the chromosome suggests that the island was acquired from an organism with lower G + C content, and this has occurred in at least two independent events in different strains. Based on the extensive work characterizing hemicellulose utilization in G. stearothermophilus T6 (Alalouf et al., 2011; Salama et al., 2012; Shulami et al., 2011; Tabachnikov & Shoham, 2013), identification of orthologous genes in other strains shows that both the gene complement and arrangement of clusters in the genomic island are highly variable. A pattern emerges that suggests that Geobacillus spp. fully secrete only a small number of glycoside hydrolases, but these degrade noncrystalline polymeric substrates to short oligomers that can be transported inside the cell. These are then further hydrolyzed to monomers by nonsecreted glycoside hydrolases and glycosidases inside the cell. This catabolic strategy reveals a notable metabolic efficiency, employing a minimal set of secreted enzymes together with enhanced energy gain through transporting (then internally hydrolyzing) oligomers rather than monomers.

There is no evidence for true cellulolytic activity (ability to degrade crystalline cellulose) in Geobacillus spp., although extracellular enzymes showing endoglucanase activity (probably low specificity GH5; Aspeborg, Coutinho, Wang, Brumer, & Henrissat, 2012) have been detected. However, GH10 xylanases are secreted by many strains (Balazs et al., 2013; Liu et al., 2012) and GH43 endo α-1,5-arabinanases (pectin-derived arabinan degrading) by a few (De Maayer et al., 2014; Shulami et al., 2011).

In G. stearothermophilus, T6 the island encodes 13 gene clusters covering 76.1 kb (De Maayer et al., 2014). One “cluster” comprises the single extracellular xylanase gene, which is functionally complemented by a cluster encoding xylooligosaccharide transport, two clusters encoding intracellular xylooligosaccharide degradation, and a cluster encoding xylose utilization. This strain is also capable of pectin degradation, with a gene cluster encoding arabinan utilization that includes abnA, encoding the GH43 endo α-1,5-arabinanase, and abnEFG, which encodes an arabinosaccharide transporter. This is functionally complemented by clusters encoding intracellular arabinofuranose metabolism (a single “cluster” of abnF encoding arabinofuranosidase), arabinose transport, and arabinose metabolism. For metabolism of the glucuronic acid-rich backbone of pectin, the T6 genomic island also has clusters that encode aldotetrauronic acid transport, intracellular aldotetrauronic acid degradation, and glucuronic acid metabolism. Some strains that express a GH5 endoglucanase also encode an oligosaccharide transporter, although its substrate specificity is not known and an intracellular β-glucosidase, which is consistent with the extracellular breakdown of amorphous cellulose, transport of β-glucan oligosaccharides, and subsequent intracellular hydrolysis.

4.1.2. Starch

The main commercial α-amylases derive from Bacillus amyloliquefaciens and Bacillus licheniformis and are particularly thermostable (Termamyl, a modified version of the B. licheniformis enzyme is active at 110 °C; Nielsen & Borchert, 2000). It is therefore not surprising to find that many Geobacillus spp. also produce α-amylases with excellent thermostability (Offen, Viksoe-Nielsen, Borchert, Wilson, & Davies, 2015; Suvd, Fujimoto, Takase, Matsumura, & Mizuno, 2001). As α-amylases tend to be specific for cleavage of the α1-4 linkage, the complete breakdown of starch requires a debranching enzyme to cleave the 1-6 linked side chains. In commercial starch breakdown, this is normally done after high-temperature (to aid liquefaction) α-amylase treatment, using a fungal glucoamylase. Bacteria tend to use a 1-6 specific pullulanase for this step, and a few Geobacillus spp. also express this activity (Kuriki, Okada, & Imanaka, 1988), although accumulating evidence suggests that the enzyme involved might actually belong to a novel class of enzyme known as a neopullulanase, which cleaves both 1-4 and 1-6 linkages and also have high activity against cyclodextrin (Lee et al., 2002; Takata et al., 1992).

4.2. Hydrocarbons

4.2.1. Alkanes

The ability of Geobacillus spp. to use aliphatic and aromatic hydrocarbons as carbon substrates and transform hydrocarbon substrates such as steroids has been frequently reported, but has only been systematically studied in a few cases. A conventional alkane-degrading alkBFGHJKL operon has been elucidated (Wentzel, Ellingsen, Kotlar, Zotchev, & Throne-Holst, 2007), with the first ORF encoding a membrane-bound alkane monooxygenase (AlkB), which is functional against midchain length (C6–C18) alkanes. An alkB homolog has been amplified from G. thermoleovorans strain T70, and demonstrated to be induced in a temperature-dependent manner in the presence of 1% n-hexadecane (Marchant, Sharkey, Banat, Rahman, & Perfumo, 2006). To date, alkB homologs have been found in Geobacillus sp. MH-1 (Liu et al., 2009) and G. subterraneus K (Korshunova et al., 2011), as well as in 11 alkane-degrading Geobacillus isolates in a single study (Tourova et al., 2008).

Geobacillus denitrificans NG80-2 has also been shown to grow on long chain (C15–C36) alkanes employing a novel, plasmid-encoded monooxygenase, LadA. Clearly, the ability to metabolize very long chain hydrocarbons is assisted by high temperatures, which should keep the substrate liquid and improve solubility Although LadA was originally thought to be extracellular and function without cofactors, it is now known to contain Flavin Mononucleotide (FMN) and require an NADPH-dependent FMN reductase for activity. The crystal structure of G. thermodenitrificans NG80-2 LadA has since been elucidated in complex with FMN, which suggests that hydroxylation occurs via a C4a-hydroperoxyflavin intermediate, rather than the classic heme or nonheme iron mechanisms (Feng et al., 2007; Li et al., 2008; Wang et al., 2006). LadA orthologs have subsequently been described in G. thermoleovorans B23, Geobacillus sp. GHH01, G11MC16, Y4.1MC1, and G. thermoglucosidasius C56-YS93 (Boonmak, Takahashi, & Morikawa, 2014). In these strains, the ladA orthologs are present on a genomic island, which also includes the gene encoding the FMN reductase; however, in G. thermoleovorans B23 at least one of these genes is more similar to an alkanesulphonate monooxygenase from the same SsuD bacterial luciferase family.

4.2.2. Aromatics

The capacity of Geobacillus strains to metabolize aromatic compounds has been studied since the mid-1970s, when they were generally referred to as thermophilic Bacillus spp. (Buswell & Twomey, 1975). Since then, several phenol-degrading Geobacillus spp. have been isolated and characterized, including G. stearothermophilus DSM 6285 (Omokoko, Jäntges, Zimmermann, Reiss, & Hartmeier, 2008) and G. thermoglucosidasius A7 (Duffner, Kirchner, Bauer, & Müller, 2000).

The phenol degradation pathway in G. stearothermophilus DSM 6285, encoded by 20.2 kb of DNA, has been elucidated as 15 ORFs residing on a low-copy megaplasmid (Omokoko et al., 2008). Ten genes encode proteins that are directly linked with the meta-cleavage pathway, including a phenol hydroxylase (PheA), a catechol 2,3-dioxygenase, a 4-oxalocrotonate tautomerase, a 2-oxopent-4-dienoate hydratase, a 4-oxalocrotonate decarboxylase, a 4-hydroxy-2-oxovalerate aldolase, and an acetaldehyde dehydrogenase (Duffner et al., 2000; Omokoko et al., 2008). The largest ORF, pheR, displays a strong similarity to transcriptional regulators associated with phenol metabolism in Geobacter lovleyi SZ, and is thought to be the first example of a transcriptional regulator of phenol metabolism identified in Gram-positive bacteria (Omokoko et al., 2008).

Notable work has been done on the characterization of the first enzyme in the degradation pathway, PheA, which catalyzes the ortho-hydroxylation of phenol to catechol. PheA, a two-component enzyme encoded by the pheA1 and pheA2 genes, is strictly FAD dependent (Kirchner, Westphal, Müller, & van Berkel, 2003). Intriguingly, a function of PheA2 is in the catalysis of the NADH-dependent...

Erscheint lt. Verlag	1.6.2015
Mitarbeit	Herausgeber (Serie): Geoffrey Michael Gadd, Sima Sariaslani
Sprache	englisch
Themenwelt	Medizin / Pharmazie ► Allgemeines / Lexika
	Medizin / Pharmazie ► Medizinische Fachgebiete ► Mikrobiologie / Infektologie / Reisemedizin
	Studium ► Querschnittsbereiche ► Infektiologie / Immunologie
	Naturwissenschaften ► Biologie ► Zellbiologie
ISBN-10	0-12-802515-8 / 0128025158
ISBN-13	978-0-12-802515-4 / 9780128025154

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