Mutants of the obligate methylothroph Methylobacillus flagellatum KT defective in genes of the ribulose monophosphate cycle of formaldehyde fixation

Genomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceae

The genomes of three representatives of the family Methylophilaceae, Methylotenera mobilis JLW8, Methylotenera versatilis 301, and Methylovorus glucosetrophus SIP3-4, all isolated from a single study site, Lake Washington in Seattle, WA, were completely sequenced. These were compared to each other and to the previously published genomes of Methylobacillus flagellatus KT and an unclassified Methylophilales strain, HTCC2181. Comparative analysis revealed that the core genome of Methylophilaceae may be as small as approximately 600 genes, while the pangenome may be as large as approximately 6,000 genes. Significant divergence between the genomes in terms of both gene content and gene and protein conservation was uncovered, including the varied presence of certain genes involved in methylotrophy. Overall, our data demonstrate that metabolic potentials can vary significantly between different species of Methylophilaceae, including organisms inhabiting the very same environment. These data suggest that genetic divergence among the members of this family may be responsible for their specialized and nonredundant functions in C₁ cycling, which in turn suggests means for their successful coexistence in their specific ecological niches.

Growth of the obligate methylotroph Methylobacillus flagellatum under stationary and nonstationary conditions during continuous cultivation

The growth characteristics of a chemostat culture of the obligate methylotrophic bacterium Methylobacillus flagellatum have been determined. Steady-state cultures growing at a rate of 0.73-0.74 h(-1), equal to the maximal growth rate, were obtained under oxyturbidostat cultivation conditions. The response of a chemostat culture to a pulse increase of methanol concentration was studied. It was shown that slow and rapidly growing cultures of M. flagellatum responded differently to pulse methanol addition. The growth characteristics of slow-growing cultures decreased after methanol addition compared to those of stationary chemostat cultures. The growth characteristics of rapidly growing cultures were practically unchanged with and without pulse methanol addition.

Biosynthetic uniform13C,15N-labelling of zervamicin IIB. Complete13C and15N NMR assignment

Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (> 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution.

Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph

The roles of cyclic formaldehyde oxidation via 6-phosphogluconate dehydrogenase and linear oxidation via the tetrahydromethanopterin (H4MPT)-linked pathway were assessed in an obligate methylotroph, Methylobacillus flagellatus KT, by cloning, sequencing and mutating two chromosomal regions containing genes encoding enzymes specifically involved in these pathways: 6-phosphogluconate dehydrogenase, glucose-6-phosphate dehydrogenase and methenyl H4MPT cyclohydrolase (gndA, zwf and mch). No null mutants were obtained in gndA or zwf, implying that the cyclic oxidation of formaldehyde is required for C1 metabolism in this obligate methylotroph, probably as the main energy-generating pathway. In contrast, null mutants were generated in mch, indicating that the H4MPT-linked pathway is dispensable. These mutants showed enhanced sensitivity to formaldehyde, suggesting that this pathway plays a secondary physiological role in this methylotroph. This function is in contrast to Methylobacterium extorquens AM1, in which the H4MPT-linked pathway is essential.

Organization of methylamine utilization genes (mau) in 'Methylobacillus flagellatum ' KT and analysis of mau mutants

The organization of genes involved in utilization of methylamine (mau genes) was studied in the obligate methylotroph 'Methylobacillus flagellatum' KT. Nine open reading frames were identified as corresponding to the genes mauFBEDAGLMN. In addition, an open reading frame (orf-1 encoding a polypeptide with unknown function was identified upstream of the mau gene cluster. Subclones of the 'M. flagellatum' KT gene cluster were used for complementation of a series of chemically induced mau mutants of 'M. flagellatum' KT. Mutants in mauF, mauB, mauE/D, mauA, mauG, mauL and mauM were identified. Two mutants (mau-18 and mau-19) were not complemented by the known mau genes. Since none of the chemically induced mutants studies had a defect of orf-1 or mauN, inserting mutants in these genes were constructed. Phenotypically the mutants fell into three groups. The mauF, mauB, mauE/D, mauA, mauG, mauL and mauM mutants do not grow on methylamine as a source of carbon and lack methylamine dehydrogenase activity, but they synthesize both the large and the small subunit polypeptides albeit at different ratios. The mau-18 and mau-19 mutants do not grow on methylamine as a source of carbon, and lack both methylamine dehydrogenase activity and the methylamine dehydrogenase subunits. The orf-1 and mauN mutants grow on methylamine as a source of carbon and synthesize wild-type levels of methylamine dehydrogenase. It has been shown earlier that the product of the mauM gene is not required for synthesis of active methylamine dehydrogenase in Methylobacterium extorquens AM1 and Paracoccus denitrificans. However, MauM is required for synthesis of functional methylamine dehydrogenase in 'M. flagellatum'.

Genetics of methane and methanol oxidation in gram-negative methylotrophic bacteria

Within the past few years, considerable progress has been made in the understanding of the molecular genetics of methane and methanol oxidation. In order to summarize this progress and to illustrate the important genetic methods employed, this review will focus on several well-studied organisms. These organisms include the gram-negative faculative methylotrophs Methylobacterium extorquens, Methylobacterium organophilum and Paracoccus denitrificans. In addition, the obligate methanotrophs Methylococcus capsulatus and Methylosinus trichosporium are discussed. We have chosen not to discuss the genetics of methanol oxidation in the yeasts or in gram-positive bacteria. Likewise, the genetics of related topics (for example, methylamine oxidation and carbon assimilation pathways) are not reviewed here. Broad host range conjugatable plasmids have enabled researchers to complement mutations and clone genes from gram-negative methylotrophic bacteria. More recently, 'promoter probe' derivative plasmids have been used to elucidate aspects of gene regulation. Also, alternative gene-cloning techniques are proving useful in circumventing problems in the genetic studies of the obligate methanotrophs, the group of bacteria that is the most refractory to traditional methods.

Genetic mapping of the obligate methylotroph Methylobacillus flagellatum: characteristics of prime plasmids and mapping of the chromosome in time-of-entry units

A pULB113 (RP4::mini-Mu cts) plasmid was used to generate a library of prime plasmids carrying fragments of the Methylobacillus flagellatum genome. The genes carried by these prime plasmids were identified by complementation after transfer to suitably marked Escherichia coli and Pseudomonas aeruginosa strains. The hybrid plasmids were used for complementation mapping with a range of E. coli, M. flagellatum, and P. aeruginosa mutants. A preliminary map of the M. flagellatum genome section with seven groups of linked markers was obtained. Three of seven groups contain an overlapping sequence of cloned genes and can be considered as one large group of linked genes. A high-frequency-of-recombination donor of M. flagellatum (strain MFK64) mobilized the chromosome in a polarized manner from a single transfer origin. The donor was used to construct a time-of-entry map of the M. flagellatum chromosome. This was achieved by determining the time of entry of six randomly dispersed markers, four of which are included in known groups of linked markers. The linear map of M. flagellatum reported here consists of 44 markers.

Physiology and genetics of methylotrophic bacteria

Methylotrophic bacteria comprise a broad range of obligate aerobic microorganisms, which are able to proliferate on (a number of) compounds lacking carbon-carbon bonds. This contribution will essentially be limited to those organisms that are able to utilize methanol and will cover the physiological, biochemical and genetic aspects of this still diverse group of organisms. In recent years much progress has been made in the biochemical and genetic characterization of pathways and the knowledge of specific reactions involved in methanol catabolism. Only a few of the genetic loci hitherto found have been matched by biochemical experiments through the isolation or demonstration of specific gene products. Conversely, several factors have been identified by biochemical means and were shown to be involved in the methanol dehydrogenase reaction or subsequent electron transfer. For the majority of these components, their genetic loci are unknown. A comprehensive treatise on the regulation and molecular mechanism of methanol oxidation is therefore presented, followed by the data that have become available through the use of genetic analysis. The assemblage of methanol dehydrogenase enzyme, the role of pyrrolo-quinoline quinone, the involvement of accessory factors, the evident translocation of all these components to the periplasm and the dedicated link to the electron transport chain are now accepted and well studied phenomena in a few selected facultative methylotrophs. Metabolic regulation of gene expression, efficiency of energy conservation and the question whether universal rules apply to methylotrophs in general, have so far been given less attention. In order to expand these studies to less well known methylotrophic species initial results concerning such area as genetic mapping, the molecular characterization of specific genes and extrachromosomal genetics will also pass in review.

Mapping of pgi and gpd genes involved in C-1 assimilation in the obligate methylotroph Methylobacillus flagellatum

Homologous matings with plasmids R68.45 and pULB113, and also with Hfr type donor were employed for mapping pgi and gpd genes involved in C-1 metabolism in the obligate methylotroph Methylobacillus flagellatum. A preliminary map of the late chromosomal region was constructed on the basis of these experimental results. The C-1 markers were linked to methionine and leucine auxotrophy and nalidixic acid resistance markers. The phenomenon of retrotransfer, or shuttle transfer of chromosomal markers by Inc P1 plasmids, revealed earlier, was demonstrated for M. flagellatum.