Dichloromethane metabolism and C1 utilization genes in Methylobacterium strains
               The GenBank accession numbers for the sequences determined in this work are AJ421476 and AJ421477.

Kayser, Martin; Ucurum, Zöhre; Vuilleumier, Stéphane

doi:10.1099/00221287-148-6-1915

Cited by 40 publications

(25 citation statements)

References 37 publications

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“…Conversely, however, hybridization analysis with probes corresponding to the mtdA, fae, and mchA genes of M. extorquens AM1 representing both branches of C 1 utilization described in M. extorquens AM1 (6,39,41) (Fig. 1) showed that these genes were also present in strain CM4 and in the dichloromethane-degrading strain Methylobacterium dichloromethanicum DM4 (13). In the latter strain, sequence analysis revealed very strong sequence conservation of these genes (Ͼ96% sequence identity at the DNA level) with their homologs of strain AM1 (13).…”

Section: Resultsmentioning

confidence: 99%

“…1) showed that these genes were also present in strain CM4 and in the dichloromethane-degrading strain Methylobacterium dichloromethanicum DM4 (13). In the latter strain, sequence analysis revealed very strong sequence conservation of these genes (Ͼ96% sequence identity at the DNA level) with their homologs of strain AM1 (13). This analysis was confirmed and extended by obtaining the expected PCR products for mtdA (454 bp; see Materials and Methods) and fchA (326 bp), which define the H 4 folate-dependent branch of C 1 characterized in M. extorquens AM1 (Fig.…”

Section: Resultsmentioning

confidence: 99%

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Chloromethane-Induced Genes Define a Third C ₁ Utilization Pathway in Methylobacterium chloromethanicum CM4

et al. 2002

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Methylobacterium chloromethanicum CM4 is an aerobic ␣-proteobacterium capable of growth with chloromethane as the sole carbon and energy source. Two proteins, CmuA and CmuB, were previously purified and shown to catalyze the dehalogenation of chloromethane and the vitamin B 12 -mediated transfer of the methyl group of chloromethane to tetrahydrofolate. Three genes located near cmuA and cmuB, designated metF, folD and purU and encoding homologs of methylene tetrahydrofolate (methylene-H 4 folate) reductase, methylene-H 4 folate dehydrogenase-methenyl-H 4 folate cyclohydrolase and formyl-H 4 folate hydrolase, respectively, suggested the existence of a chloromethane-specific oxidation pathway from methyl-tetrahydrofolate to formate in strain CM4. Hybridization and PCR analysis indicated that these genes were absent in Methylobacterium extorquens AM1, which is unable to grow with chloromethane. Studies with transcriptional xylE fusions demonstrated the chloromethane-dependent expression of these genes. Transcriptional start sites were mapped by primer extension and allowed to define three transcriptional units, each likely comprising several genes, that were specifically expressed during growth of strain CM4 with chloromethane. The DNA sequences of the deduced promoters display a high degree of sequence conservation but differ from the Methylobacterium promoters described thus far. As shown previously for purU, inactivation of the metF gene resulted in a CM4 mutant unable to grow with chloromethane. Methylene-H 4 folate reductase activity was detected in a cell extract of strain CM4 only in the presence of chloromethane but not in the metF mutant. Taken together, these data provide evidence that M. chloromethanicum CM4 requires a specific set of tetrahydrofolate-dependent enzymes for growth with chloromethane.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Chloromethane-Induced Genes Define a Third C ₁ Utilization Pathway in Methylobacterium chloromethanicum CM4

et al. 2002

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“…1). A partial cluster of nine genes has been sequenced from another Methylobacterium species closely related to M. extorquens (16), showing identical gene order and a high degree of sequence conservation at the DNA level, and thus is not shown in Fig. 1.…”

Section: Gene Islands Encoding H 4 Mpt-linked C 1 Transfer Reactions mentioning

confidence: 99%

Analysis of Gene Islands Involved in Methanopterin-Linked C ₁ Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Kalyuzhnaya¹,

Korotkova²,

Crowther³

et al. 2005

J Bacteriol

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In this study, the occurrence and chromosomal clustering of genes encoding C 1 transfer reactions linked to tetrahydromethanopterin (H 4 MPT) were analyzed in a variety of proteobacteria and in representatives of the Planctomycetes via genomic analysis or via partial sequencing by cosmid walking. Although a tendency for clustering was found common for the genes of interest, significant variations in gene order and the degree of clustering were uncovered both between and within different groups of Proteobacteria and between Proteobacteria and Planctomycetes. Phylogenetic analyses suggested that the evolution of genes encoding H 4 MPT-linked reactions in Proteobacteria involved lateral transfers within Proteobacteria and possibly between Proteobacteria and other phyla. Gene cluster comparisons revealed a number of novel genes potentially involved in the C 1 transfer reactions, and these were analyzed by mutation and expression analyses. Four genes, a homolog of pabB, and three genes conserved between methanogenic Archaea and Bacteria possessing H 4 MPT-linked functions, orfY, orf1, and afpA were shown to be involved in formaldehyde oxidation/detoxification, as judged by specific mutant phenotypes. In particular, pabB contributes to the biosynthesis of para-aminobenzoic acid, a precursor of both tetrahydrofolate and H 4 MPT, and afpA apparently encodes a novel dihydromethanopterin reductase, based on mutant complementation experiments.One of the major breakthroughs in the understanding of methylotrophy in Bacteria during the recent decade, the recognition of the tetrahydromethanopterin (H 4 MPT)-linked pathway for formaldehyde oxidation as a major C 1 oxidation pathway, was due to a serendipitous discovery of a cluster of genes in Methylobacterium extorquens AM1 that are homologous to the genes involved in methanogenesis in Archaea (7). It has since been demonstrated that this pathway is nearly ubiquitous in gram-negative methylotrophs (26). More recently, the pathway's presence has been expanded beyond methylotrophs (20), and even beyond Proteobacteria into the Planctomycetes (5, 10). Although phylogenetic analysis has argued against recent lateral transfer of the genes in question between methanogenic Archaea and Proteobacteria (5), the history of these genes in Bacteria remains poorly understood. Although some congruence has been observed between the phylogenetic positions of the respective species within Proteobacteria and phylogenies of genes involved in H 4 MPT-linked reactions (13, 15), the relationships of the latter are not always well resolved and sometimes are complicated by the presence of multiple gene copies. In the present study we attempted a more comprehensive analysis of gene islands in Bacteria involved in H 4 MPTlinked C 1 transfers via analysis of available genomic sequences, via expanding gene databases by cosmid walking, and via mutagenesis and phylogenetic analysis. The following major objectives were pursued: (i) to determine whether gene clustering patterns are conserved within specific gr...

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“…This four-gene dcm islet is conserved within most DCM-degrading strains (18). However, a strain of M. extorquens DM4 with a deletion of the genomic island, known as DM4-2cr (20), requires only the dcmA gene to recover growth on DCM (21). While the other genes in the genomic island may influence growth on DCM, they are not essential.…”

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“…Finally, the cell must quickly channel the formaldehyde product into its native one-carbon metabolic pathways to minimize any resulting toxicity (28). Given these challenges, it is not surprising that deliberate transfer of the dcmA gene to two other strains of M. extorquens, AM1 and CM4, was sufficient to enable growth on DCM only in strain CM4 (21). However, it remains unclear why strain AM1 was unable to grow on DCM, or how prevalent is the ability among methylotrophic bacteria to grow on DCM using dcmA.…”

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confidence: 99%

Phylogeny Poorly Predicts the Utility of a Challenging Horizontally Transferred Gene in Methylobacterium Strains

Vuilleumier¹,

Bringel²,

Marx³

2014

Journal of Bacteriology

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cHorizontal gene transfer plays a crucial role in microbial evolution. While much is known about the mechanisms that determine whether physical DNA can be transferred into a new host, the factors determining the utility of the transferred genes are less clear. We have explored this issue using dichloromethane consumption in Methylobacterium strains. Methylobacterium extorquens DM4 expresses a dichloromethane dehalogenase (DcmA) that has been acquired through horizontal gene transfer and allows the strain to grow on dichloromethane as the sole carbon and energy source. We transferred the dcmA gene into six Methylobacterium strains that include both close and distant evolutionary relatives. The transconjugants varied in their ability to grow on dichloromethane, but their fitness on dichloromethane did not correlate with the phylogeny of the parental strains or with any single tested physiological factor. This work highlights an important limiting factor in horizontal gene transfer, namely, the capacity of the recipient strain to accommodate the stress and metabolic disruption resulting from the acquisition of a new enzyme or pathway. Understanding these limitations may help to rationalize historical examples of horizontal transfer and aid deliberate genetic transfers in biotechnology for metabolic engineering.

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Dichloromethane metabolism and C1 utilization genes in Methylobacterium strains The GenBank accession numbers for the sequences determined in this work are AJ421476 and AJ421477.

Cited by 40 publications

References 37 publications

Chloromethane-Induced Genes Define a Third C ₁ Utilization Pathway in Methylobacterium chloromethanicum CM4

Chloromethane-Induced Genes Define a Third C ₁ Utilization Pathway in Methylobacterium chloromethanicum CM4

Analysis of Gene Islands Involved in Methanopterin-Linked C ₁ Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Phylogeny Poorly Predicts the Utility of a Challenging Horizontally Transferred Gene in Methylobacterium Strains

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Dichloromethane metabolism and C1 utilization genes in Methylobacterium strains The GenBank accession numbers for the sequences determined in this work are AJ421476 and AJ421477.

Cited by 40 publications

References 37 publications

Chloromethane-Induced Genes Define a Third C 1 Utilization Pathway in Methylobacterium chloromethanicum CM4

Chloromethane-Induced Genes Define a Third C 1 Utilization Pathway in Methylobacterium chloromethanicum CM4

Analysis of Gene Islands Involved in Methanopterin-Linked C 1 Transfer Reactions Reveals New Functions and Provides Evolutionary Insights

Phylogeny Poorly Predicts the Utility of a Challenging Horizontally Transferred Gene in Methylobacterium Strains

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Chloromethane-Induced Genes Define a Third C ₁ Utilization Pathway in Methylobacterium chloromethanicum CM4

Chloromethane-Induced Genes Define a Third C ₁ Utilization Pathway in Methylobacterium chloromethanicum CM4

Analysis of Gene Islands Involved in Methanopterin-Linked C ₁ Transfer Reactions Reveals New Functions and Provides Evolutionary Insights