Complete Genome Sequences of Six Strains of the Genus Methylobacterium

Marx, Christopher J.; Bringel, Françoise; Chistoserdova, Ludmila; Moulin, Lionel; Haque, Muhammad Farhan Ul; Fleischman, Darrell; Gruffaz, Christelle; Jourand, Philippe; Knief, Claudia; Lee, Ming‐Chun; Muller, Emilie; Nadalig, Thierry; Peyraud, Rémi; Roselli, Sandro; Russ, Lina; Goodwin, Lynne; Ivanova, Natalia; Kyrpides, Nikos C.; Lajus, Aurélie; Land, Miriam; Médigue, Claudine; Mikhailova, Natalia; Nolan, Matt; Woyke, Tanja; Stolyar, Sergey; Vorholt, Julia A.; Vuilleumier, Stéphane

doi:10.1128/jb.01009-12

Cited by 94 publications

(103 citation statements)

References 16 publications

(14 reference statements)

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“…In M. silvestris BL2, gmaS is essential for MMA utilization as a C and energy source (1), whereas this gene is unexpectedly dispensable in M. universalis FAM5 (6). Intriguingly, M. universalis FAM5 and M. silvestris BL2 are bacteria that contain only one gmaS homolog (see Table S2 in the supplemental material), in contrast to all of the strains of M. extorquens sequenced so far (8,25), which contain two gmaS homologs (Fig. 5).…”

Section: Discussionmentioning

confidence: 99%

“…Still, the genetic organization of NMG pathway genes in M. extorquens DM4 is strongly conserved within the sequenced genomes of M. extorquens (8,25), suggesting that possession of this gene set would allow all Methylobacterium strains to grow with MMA. That is not the case, since inactivation of mau genes for MADH in the closely related strain AM1 completely abolished its ability to grow on MMA as the sole C source (4).…”

Section: Discussionmentioning

confidence: 99%

“…Unlike M. extorquens strains DM4, PA1, and BJ001 (8,25), M. extorquens strains such as AM1 and CM4 contain mau genes and grow much faster with MMA as the sole carbon, nitrogen, and energy source (approximately 3-fold growth rate difference; C. Gruffaz and F. Bringel, unpublished data). Moreover, M. extorquens DM4 grew less efficiently with MMA than with methanol (generation times of 18.3 and 3.4 h, respectively; Table 2) (10).…”

Section: Discussionmentioning

confidence: 99%

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Genes of the N -Methylglutamate Pathway Are Essential for Growth of Methylobacterium extorquens DM4 with Monomethylamine

Gruffaz

Muller

Louhichi-Jelail

et al. 2014

Appl Environ Microbiol

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bMonomethylamine (MMA, CH 3 NH 2 ) can be used as a carbon and nitrogen source by many methylotrophic bacteria. Methylobacterium extorquens DM4 lacks the MMA dehydrogenase encoded by mau genes, which in M. extorquens AM1 is essential for growth on MMA. Identification and characterization of minitransposon mutants with an MMA-dependent phenotype showed that strain DM4 grows with MMA as the sole source of carbon, energy, and nitrogen by the N-methylglutamate (NMG) pathway. Independent mutations were found in a chromosomal region containing the genes gmaS, mgsABC, and mgdABCD for the three enzymes of the pathway, ␥-glutamylmethylamide (GMA) synthetase, NMG synthase, and NMG dehydrogenase, respectively. Reverse transcription-PCR confirmed the operonic structure of the two divergent gene clusters mgsABC-gmaS and mgdABCD and their induction during growth with MMA. The genes mgdABCD and mgsABC were found to be essential for utilization of MMA as a carbon and nitrogen source. The gene gmaS was essential for MMA utilization as a carbon source, but residual growth of mutant DM4gmaS growing with succinate and MMA as a nitrogen source was observed. Plasmid copies of gmaS and the gmaS homolog METDI4690, which encodes a protein 39% identical to GMA synthetase, fully restored the ability of mutants DM4gmaS and DM4gmaS⌬metdi4690 to use MMA as a carbon and nitrogen source. Similarly, chemically synthesized GMA, the product of GMA synthetase, could be used as a nitrogen source for growth in the wild-type strain, as well as in DM4gmaS and DM4gmaS⌬metdi4690 mutants. The NADH:ubiquinone oxidoreductase respiratory complex component NuoG was also found to be essential for growth with MMA as a carbon source. M onomethylamine (MMA; methylamine) is a nitrogen-containing C 1 compound released by natural sources such as the breakdown of proteins and amine osmolytes, as well as by humanmade nitrogen-containing pesticides, pharmaceuticals, and herbicides (1). MMA is ubiquitous in the environment and can serve as the sole source of carbon and energy for methylotrophic bacteria, which grow on compounds with no C-C bonds (2) but also as a nitrogen source for a large variety of bacteria (3). MMA utilization by Gram-negative bacteria occurs either by oxidation of MMA into formaldehyde by MMA dehydrogenase (MADH) encoded by mau genes (4) found only in methylotrophic bacteria so far (5) or by the N-methylglutamate (NMG) pathway, the genes for which were first identified in the betaproteobacterium Methyloversatilis universalis FAM5 (6). This metabolism effects the condensation of MMA with glutamate to NMG, with ␥-glutamylmethylamide (GMA) a possible intermediate (Fig. 1). The genes gmaS, mgsABC, and mgdABCD encode GMA synthetase (GMAS), NMG synthase, and NMG dehydrogenase, respectively (6). Of these, only gmaS was found not to be required for MMA metabolism in M. universalis FAM5 (6). In contrast, gmaS was also required for MMA utilization in the facultative methane utilizer Methylocella silvestris BL2 (1). In addition, the NMG pathway was recently ...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genes of the N -Methylglutamate Pathway Are Essential for Growth of Methylobacterium extorquens DM4 with Monomethylamine

Gruffaz

Muller

Louhichi-Jelail

et al. 2014

Appl Environ Microbiol

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“…We chose to use the box plot technique since the technique is suitable to visually summarize and compare groups of data [27]. A finding from the box plot visual representation (Figure 3) is that methanol-oxidizing Methylobacterium nodulans ORS 2060, the legume (Crotalaria) root-nodule-forming and nitrogen-fixing bacteria [28], has at least 7 sequenced plasmids [29]. The possession of an intact 120kb megaplasmid correlated with ability of Methylobacterium extorquens DM4 to utilize dichloromethane as sole source of carbon and energy [30].…”

Section: Interactive Analytics For Sense Making On Protein-coding Genmentioning

confidence: 99%

Interactive Analytics for Complex Cognitive Activities on Information from Annotations of Prokaryotic Genomes

Isokpehi¹,

Wootson²,

Smith-McInnis³

et al. 2017

JOCSE

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Several microbial genome databases provide collections of thousands of genome annotation files in formats suitable for the performance of complex cognitive activities such as decision making, sense making and analytical reasoning. The goal of the research reported in this article was to develop interactive analytics resources to support the performance of complex cognitive activities on a collection of publicly available genome information spaces. A supercomputing infrastructure (Blue Waters Supercomputer) provided computational tools to construct information spaces while visual analytics software and online bioinformatics resources provided tools to interact with the constructed information spaces. The Rhizobiales order of bacteria that includes the Brucella genus was the use case for preforming the complex cognitive activities. An interesting finding among the genomes of the dolphin pathogen, Brucella ceti, was a cluster of genes with evidence for function in conditions of limited nitrogen availability.

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“…Therefore, the study was continued with the closely related strain, M. extorquens PA1, which was recently isolated from the phyllosphere of Arabidopsis thaliana (Knief et al, 2010). In contrast to the five replicons possessed by M. extorquens AM1 (Vuilleumier et al, 2009), the M. extorquens PA1 genome is less complex and consists of only one chromosome (Marx et al, 2012), which may alleviate unwanted recombination events.…”

Section: Design Of a Forward Genetic Screen To Identify Novel Regulatmentioning

confidence: 99%

Single-domain response regulator involved in the general stress response of Methylobacterium extorquens

2013

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Complete Genome Sequences of Six Strains of the Genus Methylobacterium

Abstract: The complete and assembled genome sequences were determined for six strains of the alphaproteobacterial genus Methylobacterium, chosen for their key adaptations to different plant-associated niches and environmental constraints.

Cited by 94 publications

References 16 publications

Genes of the N -Methylglutamate Pathway Are Essential for Growth of Methylobacterium extorquens DM4 with Monomethylamine

Genes of the N -Methylglutamate Pathway Are Essential for Growth of Methylobacterium extorquens DM4 with Monomethylamine

Interactive Analytics for Complex Cognitive Activities on Information from Annotations of Prokaryotic Genomes

Single-domain response regulator involved in the general stress response of Methylobacterium extorquens

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