The Family Sphingomonadaceae

Glaeser, Stefanie P.; Giessen, Justus-Liebig-University

doi:10.1007/978-3-642-30197-1_302

Cited by 98 publications

(72 citation statements)

References 369 publications

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“…A Pseudomonas/Pseudoalteromonaslike Gammaproteobacteria was previously shown to putatively catalyze iron(II) oxidation under micro-aerobic conditions, isolated from volcanic seamount (Sudek et al, 2009), which may contribute to the formation of iron mats in the deep marine subsurface. Other lineages captured at this potential included Patulibacteraceae, Saprospiraceae, Chitinophagaceae, Sphingomonadaceae, and Solimonas, each putatively containing aerobic respiratory metabolism among their members (Saddler and Bradbury, 2005;Takahashi et al, 2006;Glaeser and Kämpfer, 2014;Kim et al, 2014;McIlroy and Nielsen, 2014;Rosenberg, 2014). The potential +0.01 V vs. SHE (WE2), chosen to mimic iron oxidation, favored the colonization of members from bacterial families Rhodobacteraceae, Syntrophaceae, and many OTUs were identified as unclassified at the phyla level ( Figure 3B).…”

Section: In Situ Current Response and Active Microbial Community Compmentioning

confidence: 99%

In situ Electrochemical Studies of the Terrestrial Deep Subsurface Biosphere at the Sanford Underground Research Facility, South Dakota, USA

et al. 2019

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Section: In Situ Current Response and Active Microbial Community Compmentioning

confidence: 99%

In situ Electrochemical Studies of the Terrestrial Deep Subsurface Biosphere at the Sanford Underground Research Facility, South Dakota, USA

et al. 2019

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“…Because of its importance, a wide variety of aryl demethylase systems have been identified from aryl compound-using soil and marine bacteria. These organisms are uniquely capable of metabolizing aromatic waste and natural breakdown products such as those derived from lignin, an aromatic heteropolymer derived from plants (1,5). Aryl O-demethylation, the removal of a methyl moiety from an aryl methoxy functional group, is especially vital to degradation and aerobic metabolism of aromatics and is a prerequisite step to aromatic ring opening, priming the ring for downstream oxidative cleavage and assimilation into the tricarboxylic acid (TCA) cycle (1).…”

mentioning

confidence: 99%

Structure of arylO-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

Kohler

Mills

Adams

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, was previously available. LigM-catalyzed demethylation enables further modification and ring opening of the single-ring aromatics vanillate and 3-Omethylgallate, which are common byproducts of biofuel production. Here, we characterize aryl O-demethylation by LigM and report its 1.81-Å crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. These results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.demethylase | biocatalysis | aryl metabolism | tetrahydrofolate | lignin D emethylation reactions are found throughout biology, impacting a wide range of cellular processes from metabolism and energy generation to genetic imprinting and DNA repair (1-3). Reflective of such extensive application, there is an immense diversity in the mechanisms used by demethylases, the enzymes responsible for catalyzing methyl transfer reactions. Intriguingly, only roughly 1% of identified demethylases have been characterized at a structural level (4), and those that have vary substantially in protein fold, making it difficult to discern the structural basis and catalytic determinants for this key biocatalytic process based on function alone.Aryl demethylation is of particular interest because it is an essential first step in the modification, and ultimately metabolism, of aromatic compounds under aerobic conditions. Because of its importance, a wide variety of aryl demethylase systems have been identified from aryl compound-using soil and marine bacteria. These organisms are uniquely capable of metabolizing aromatic waste and natural breakdown products such as those derived f...

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“…2005). Due to their clinical relevance and applications in biotechnology and bioremediation, the genomes of several members of the order Sphingomonadales have been sequenced (Glaeser and Kämpfer 2014; Tonon et al. 2014).…”

Section: Introductionmentioning

confidence: 99%

“…Although several prophages have been identified among the genomes of Sphingomonadales (Aylward et al. 2013; Glaeser and Kämpfer 2014; Tonon et al. 2014; Zheng et al.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales

Viswanathan

Narjala

Ravichandran

et al. 2017

Genome Biology and Evolution

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The order Sphingomonadales, containing the families Erythrobacteraceae and Sphingomonadaceae, is a relatively less well-studied phylogenetic branch within the class Alphaproteobacteria. Prophage elements are present in most bacterial genomes and are important determinants of adaptive evolution. An “intact” prophage was predicted within the genome of Sphingomonas hengshuiensis strain WHSC-8 and was designated Prophage IWHSC-8. Loci homologous to the region containing the first 22 open reading frames (ORFs) of Prophage IWHSC-8 were discovered among the genomes of numerous Sphingomonadales. In 17 genomes, the homologous loci were co-located with an ORF encoding a putative superoxide dismutase. Several other lines of molecular evidence implied that these homologous loci represent an ancient temperate bacteriophage integration, and this horizontal transfer event pre-dated niche-based speciation within the order Sphingomonadales. The “stabilization” of prophages in the genomes of their hosts is an indicator of “fitness” conferred by these elements and natural selection. Among the various ORFs predicted within the conserved prophages, an ORF encoding a putative proline-rich outer membrane protein A was consistently present among the genomes of many Sphingomonadales. Furthermore, the conserved prophages in six Sphingomonas sp. contained an ORF encoding a putative spermidine synthase. It is possible that one or more of these ORFs bestow selective fitness, and thus the prophages continue to be vertically transferred within the host strains. Although conserved prophages have been identified previously among closely related genera and species, this is the first systematic and detailed description of orthologous prophages at the level of an order that contains two diverse families and many pigmented species.

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The Family Sphingomonadaceae

Cited by 98 publications

References 369 publications

In situ Electrochemical Studies of the Terrestrial Deep Subsurface Biosphere at the Sanford Underground Research Facility, South Dakota, USA

In situ Electrochemical Studies of the Terrestrial Deep Subsurface Biosphere at the Sanford Underground Research Facility, South Dakota, USA

Structure of arylO-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism

Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales

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