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M E Lidstrom

Publications and source records attributed to M E Lidstrom.

At least 37 records · Page 2Linked to original sources
PubMed1998

The NADP-dependent methylene tetrahydromethanopterin dehydrogenase in Methylobacterium extorquens AM1.

An NADP-dependent methylene tetrahydromethanopterin (H4MPT) dehydrogenase has recently been proposed to be involved in formaldehyde oxidation to CO2 in Methylobacterium extorquens AM1. We report here on the purification of this novel enzyme to apparent homogeneity. Via the N-terminal amino acid sequence, it was identified to be the mtdA gene product. The purified enzyme catalyzed the dehydrogenation of methylene H4MPT with NADP+ rather than with NAD+, with a specific activity of approximately 400 U/mg of protein. It also catalyzed the dehydrogenation of methylene tetrahydrofolate (methylene H4F) with NADP+. With methylene H4F as the substrate, however, the specific activity (26 U/mg) and the catalytic efficiency (Vmax/Km) were approximately 20-fold lower than with methylene H4MPT. Whereas the dehydrogenation of methylene H4MPT (E0 = -390 mV) with NADP+ (E0 = -320 mV) proceeded essentially irreversibly, the dehydrogenation of methylene H4F (E0 = -300 mV) was fully reversible. Comparison of the primary structure of the NADP-dependent dehydrogenase from M. extorquens AM1 with those of methylene H4F dehydrogenases from other bacteria and eucarya and with those of methylene H4MPT dehydrogenases from methanogenic archaea revealed only marginally significant similarity (<15%).

Amino Acid Sequence↗
PubMed1997

Cloning and characterization of corA, a gene encoding a copper-repressible polypeptide in the type I methanotroph, Methylomicrobium albus BG8.

In an attempt to identify proteins involved in copper transport in the type I methanotroph Methylomicrobium albus BG8, copper-regulated polypeptides were examined. One major copper-repressible membrane polypeptide of approx. 28,500 Da was identified and designated CorA. The gene encoding this polypeptide was isolated and sequenced, and it shared a low identity with a calcium channel protein. An insertion mutation in corA of M. albus BG8 grew very poorly, suggesting that CorA is important for growth of this methanotroph. CorA may be involved in transport of copper and/or other divalent metals ions in M. albus BG8.

Amino Acid Sequence↗
PubMed1997

Methane and trichloroethylene oxidation by an estuarine methanotroph, Methylobacter sp. strain BB5.1.

An estuarine methanotroph was isolated from sediment enrichments and designated Methylobacter sp. strain BB5.1. In cells grown on medium with added copper, oxidation of methane and trichloroethylene occurred with similar Ks values, but the Vmax for trichloroethylene oxidation was only 0.1% of the methane oxidation Vmax. Cells grown on low-copper medium did not oxidize trichloroethylene and showed a variable rate of methane oxidation.

Copper↗
PubMed1997

Identification and mutation of a gene required for glycerate kinase activity from a facultative methylotroph, Methylobacterium extorquens AM1.

A gene (gckA) responsible for the activity of glycerate kinase has been identified within a chromosomal fragment of the serine cycle methylotroph Methylobacterium extorquens AM1. A mutation in gckA leads to a specific C1-negative phenotype. The polypeptide sequence derived from gckA showed high similarity to a product of ttuD essential for tartrate metabolism in Agrobacterium vitis. Our data suggest that gckA and ttuD might be structural genes for glycerate kinase and that the serine cycle and the tartrate utilization pathway share a series of reactions.

Base Sequence↗
PubMed1996

Characterization and nucleotide sequence of pqqE and pqqF in Methylobacterium extorquens AM1.

Methylobacterium extorquens AM1 pqqEF are genes required for synthesis of pyrroloquinoline quinone (PQQ). The nucleotide sequence of these genes indicates PqqE belongs to an endopeptidase family, including PqqF of Klebsiella pneumoniae, and M. extorquens AM1 PqqF has low identity with the same endopeptidase family. M. extorquens AM1 pqqE complemented a K. pneumoniae pqqF mutant.

Amino Acid Sequence↗
PubMed1995

Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related.

Genes encoding particulate methane monooxygenase and ammonia monooxygenase share high sequence identity. Degenerate oligonucleotide primers were designed, based on regions of shared amino acid sequence between the 27-kDa polypeptides, which are believed to contain the active sites, of particulate methane monooxygenase and ammonia monooxygenase. A 525-bp internal DNA fragment of the genes encoding these polypeptides (pmoA and amoA) from a variety of methanotrophic and nitrifying bacteria was amplified by PCR, cloned and sequenced. Representatives of each of the phylogenetic groups of both methanotrophs (alpha- and gamma-Proteobacteria) and ammonia-oxidizing nitrifying bacteria (beta- and gamma-Proteobacteria) were included. Analysis of the predicted amino acid sequences of these genes revealed strong conservation of both primary and secondary structure. Nitrosococcus oceanus AmoA showed higher identity to PmoA sequences from other members of the gamma-Proteobacteria than to AmoA sequences. These results suggest that the particulate methane monooxygenase and ammonia monooxygenase are evolutionarily related enzymes despite their different physiological roles in these bacteria.

Amino Acid Sequence↗
PubMed1995

The role of copper in the pMMO of Methylococcus capsulatus bath: a structural vs. catalytic function.

Methanotrophs convert methane to methanol by the methane monooxygenase (MMO). It is well known that two forms of the MMO can be expressed: one form is found in the cytoplasm, or in the soluble fraction (sMMO); the other is associated with the membranes, or particulate fraction (pMMO). The sMMO has been extensively examined, and much is known about its structure and mechanism of dioxygen activation. The pMMO, however, is less well understood: the enzyme has proven difficult to purify as it loses activity once the membranes become solubilized. Furthermore, although copper is known to be important for the stability and activity of the pMMO, its role is still unclear. In a recent study, we reported the use of electron paramagnetic resonance (EPR) spectroscopy to probe the nature of the copper ions in these membranes. Two EPR signals were uncovered for the highly oxidized membranes: one set of signals arises from the type 2 Cu(II) centers, and the other has been assigned to trinuclear copper (Cu(II) clusters (H.-H. Nguyen, et al., J. Biol. Chem., 269, 14995 (1994). Here, we attempt to correlate the EPR spectra of the membrane fraction of Methylococcus capsulatus Bath with the amount of copper present in the membranes and to the activity of the pMMO as measured by the production of propylene oxide from propene by the pMMO. From these studies, we conclude that the primary role of copper is in the active site of the pMMO rather than simply a structural one.

Binding Sites↗
PubMed1995

Methanol oxidation mutants in Methylobacterium extorquens AM1: identification of new genetic complementation groups.

Two-hundred-and-eight new Methylobacterium extorquens AM1 methanol oxidation (Mox) mutants were isolated and placed into complementation groups. Complementation analyses identified new Mox groups in the Mxb and Mxc loci and at a new locus, Mxd. Thirty-seven mutants at the Mxb locus were divided into MxbM and MxbD complementation groups on the basis of their complementation pattern. Twenty-nine mutants at the Mxc locus fell into three complementation groups, MxcB, MxcQ and MxcE. The direction of transcription for genes at this locus could be inferred from the subclones. Eighteen of the new mutants were not complemented by previously isolated M. extorquens AM1 clones but were complemented by two new overlapping clones. This locus was called Mxd and the mutants fell into two complementation groups, MxdR and MxdS. Immunoblots from all these mutant classes showed that all of the Mxb and Mxc strains had substantially reduced levels of MxaF (large subunit of methanol dehydrogenase) and cytochrome cL, compared to the wild-type. These mutants, particularly the Mxb mutants, also had elevated levels of cytochrome c-553. These results are consistent with a role for the MxbMD and MxcBQE complementation groups in the regulation of expression of mxaF. The MxdR and MxdS mutants had normal levels of MxaF and both c-type cytochromes.

Genes, Bacterial↗
PubMed1995

The mxaAKL genes of Methylobacter albus BG8.

The facultative methanol utilizer Methylobacterium extorquens AM1 contains at least three genes (mxaA, K and L) that encode functions involved in providing calcium to the holoenzyme of methanol dehydrogenase, the enzyme that oxidizes methanol to formaldehyde in this strain. Methane-utilizing bacteria (methanotrophs) also contain methanol dehydrogenase, and evidence suggests that similar methanol oxidation (Mox) functions may be present in some of these strains. DNA fragments from Methylobacterium extorquens AM1 specific to mxaA, mxaK and mxaL were isolated for use as hybridization probes against genomic digests of a variety of methanotrophic bacteria. Only the mxaL probe showed substantial hybridization, and it was used to identify and isolate an 8.5 kb HindIII fragment from Methylobacter albus BG8 (a Type I methanotroph). Hybridization of restriction digests of this fragment to individual probes for Methylobacterium extorquens AM1 mxaA, K and L indicated that the relative mxa gene order in Methylobacter albus BG8 is A-K-L. A T7 dual promoter/polymerase protein expression system indicated that five polypeptides are expressed from a 4.5 kb region of Methylobacter albus BG8 DNA in Escherichia coli, all transcribed in the same direction, and they apparently correspond to mxaACKDL. The functions of mxaC and mxaD are currently not known, but the order of mxaDL is reversed in Methylobacter albus BG8 compared to Methylobacterium extorquens AM1. When subclones of the Methylobacter albus BG8 fragment containing these genes were used as hybridization probes to genomic digests of methanotrophic bacteria, specific bands were detected that suggested a similar gene order in most cases. These data indicate that the mxaAKL region is relatively highly conserved in methanotrophs, and that in most cases the mxaAKL genes are grouped together in the same order as in the facultative methanol utilizer Methylobacterium extorquens AM1.

Chromosome Mapping↗
PubMed1995

Transcriptional analysis of pqqD and study of the regulation of pyrroloquinoline quinone biosynthesis in Methylobacterium extorquens AM1.

Methanol dehydrogenase, the enzyme that oxidizes methanol to formaldehyde in gram-negative methylotrophs, contains the prosthetic group pyrroloquinoline quinone (PQQ). To begin to analyze how the synthesis of PQQ is coordinated with the production of other methanol dehydrogenase components, the transcription of one of the key PQQ synthesis genes has been studied. This gene (pqqD) encodes a 29-amino-acid peptide that is thought to be the precursor for PQQ biosynthesis. A unique transcription start site was mapped to a guanidine nucleotide 95 bp upstream of the pqqD initiator codon. RNA blot analysis identified two transcripts, a major one of 240 bases encoding pqqD and a minor one of 1,300 bases encoding pqqD and the gene immediately downstream, pqqG. Both transcripts are present at similar levels in cells grown on methanol and on succinate, but the levels of PQQ are about fivefold higher in cells grown on methanol than in cells grown on succinate. These results suggest that PQQ production is regulated at a level different from the transcription of pqqD. The genes mxbM, mxbD, mxcQ, mxcE, and mxaB are required for transcription of the genes encoding the methanol dehydrogenase subunits and were assessed for their role in PQQ production. PQQ levels were measured in mutants defective in each of these regulatory genes and compared with levels of pqqD transcription, measured with a transcriptional fusion between the pqqD promoter and xylE. The results showed that only a subset of these regulatory genes (mxbM, mxbD, and mxaB) is required for transcription of pqqD, and only mxbM and mxbD mutants affected the final levels of PQQ significantly.

Alcohol Oxidoreductases↗
PubMed1995

Particulate methane monooxygenase genes in methanotrophs.

A 45-kDa membrane polypeptide that is associated with activity of the particulate methane monooxygenase (pMMO) has been purified from three methanotrophic bacteria, and the N-terminal amino acid sequence was found to be identical in 17 of 20 positions for all three polypeptides and identical in 14 of 20 positions for the N terminus of AmoB, the 43-kDa subunit of ammonia monooxygenase. DNA from a variety of methanotrophs was screened with two probes, an oligonucleotide designed from the N-terminal sequence of the 45-kDa polypeptide from Methylococcus capsulatus Bath and an internal fragment of amoA, which encodes the 27-kDa subunit of ammonia monooxygenase. In most cases, two hybridizing fragments were identified with each probe. Three overlapping DNA fragments containing one of the copies of the gene encoding the 45-kDa pMMO polypeptide (pmoB) were cloned from Methylococcus capsulatus Bath. A 2.1-kb region was sequenced and found to contain both pmoB and a second gene, pmoA. The predicted amino acid sequences of these genes revealed high identity with those of the gene products of amoB and amoA, respectively. Further hybridization experiments with DNA from Methylococcus capsulatus Bath and Methylobacter albus BG8 confirmed the presence of two copies of pmoB in both strains. These results suggest that the 45- and 27-kDa pMMO-associated polypeptides of methanotrophs are subunits of the pMMO and are present in duplicate gene copies in methanotrophs.

Amino Acid Sequence↗
PubMed1995

Cloning, sequencing, and mutation of a gene for azurin in Methylobacillus flagellatum KT.

The gene cluster for methylamine utilization (mau genes) has been cloned from the obligate methylotrophic bacterium Methylobacillus flagellatum KT. Partial sequence data showed that the organization of these genes was similar to that found in Methylophilus methylotrophus W3A1-NS, including the lack of a gene for amicyanin, which had been thought to be the electron acceptor for methylamine dehydrogenase in M. flagellatum KT. However, a gene encoding azurin was discovered at the 3' end of the mau gene cluster, transcribed in the opposite orientation. A mutant with a defect in this gene showed impaired growth on methylamine, suggesting that azurin is involved in methylamine oxidation in M. flagellatum KT.

Amino Acid Sequence↗
PubMed1995

Identification and nucleotide sequences of mxaA, mxaC, mxaK, mxaL, and mxaD genes from Methylobacterium extorquens AM1.

The DNA sequence for a 4.4-kb HindIII-XhoI Methylobacterium extorquens AM1 DNA fragment that is known to contain three genes (mxaAKL) involved in incorporation of calcium into methanol dehydrogenase (I. W. Richardson and C. Anthony, Biochem. J. 287:709-7115, 1992) was determined. Five complete open reading frames and two partial open reading frames were found, suggesting that this region contains previously unidentified genes. A combination of sequence analysis, mutant complementation data, and gene expression studies showed that these genes correspond to mxaSACKLDorf1. Of the three previously unidentified genes (mxaC, mxaD, and orf1), mutant complementation studies showed that mxaC is required for methanol oxidation, while the function of the other two genes is still unknown.

Alcohol Oxidoreductases↗
PubMed1994

Identification of a promoter region for mxaF (moxF) from the type I methanotroph, Methylobacter albus BG8.

A fragment of Methylobacter albus BG8 DNA containing mxaF (moxF), the gene encoding the alpha subunit of methanol dehydrogenase, was previously cloned using a fragment of mxaF from Methylobacterium extorquens AM1 as a probe (Stephens et al., J. Bacteriol. (1988) 170, 2063-2069). In this study we identified the 5' portion of mxaF of M. albus BG8 and sequenced a 1.7-kb region containing the 5' portion of mxaF and 1.5 kb of upstream DNA. The deduced N-terminal amino acid sequence of mxaF was found to have very high similarity to the previously sequenced mxaF genes. The region directly upstream of mxaF was cloned into a promoter probe vector (pGD500), and promoter activity was demonstrated when the fragment was present in the correct orientation with relation to the reporter gene (lacZ). Using reverse transcriptase, the transcription initiation start site was determined, which was separated from the translation initiation site by 190 nucleotides.

Alcohol Oxidoreductases↗
PubMed1994

Sequence of the gene for a NAD(P)-dependent formaldehyde dehydrogenase (class III alcohol dehydrogenase) from a marine methanotroph Methylobacter marinus A45.

A fragment of Methylobacter marinus A45 DNA has been cloned and sequenced, and an open reading frame has been identified that could code for a 46-kDa polypeptide. Comparison of the deduced amino acid sequence of the polypeptide against the protein data bank has revealed strong similarity with a number of alcohol dehydrogenases, with highest similarity towards class III alcohol dehydrogenases, which recently have been shown to be identical to glutathione-dependent formaldehyde dehydrogenases. We were unable to measure appreciable levels of NAD(P)-dependent formaldehyde dehydrogenases or alcohol dehydrogenase activities using aldehydes or primary or secondary alcohols in cell-free extracts from batch cultures of M. marinus A45. However, formaldehyde dehydrogenases activity was detected on zymograms. Our data suggest that, although NAD(P)-linked formaldehyde dehydrogenase or alcohol dehydrogenase activities are undetectable in cell-free extracts of most methylotrophs employing the ribulose monophosphate pathway for formaldehyde assimilation and dissimilation, the gene encoding formaldehyde dehydrogenase is present in M. marinus A45 and may be present in more of these organisms as well.

Aldehyde Oxidoreductases↗
PubMed1994

The nature of the copper ions in the membranes containing the particulate methane monooxygenase from Methylococcus capsulatus (Bath).

It is shown that the particulate methane monooxygenase (pMMO) has an obligate requirement for copper. The MMO activity in the particulate fractions obtained from Methylococcus capsulatus (Bath) cells is found to increase with increasing copper content of the membranes. The enzyme activity from membranes obtained from cells grown at low copper levels can be stimulated further by the addition of Cu(II) ions to the assay medium. The membrane-bound copper ions can exist in both Cu(II) and Cu(I) forms. EPR and magnetic susceptibility characterizations of the membranes indicate the presence of an exchange-coupled trinuclear Cu(II) cluster when the bulk of the copper ions is oxidized. However, the functional form of the enzyme is the reduced or partially reduced form. The copper ions in the membrane fractions as isolated often exhibit a high level of reduction. An EPR spectrum with one unpaired electron spin delocalized over three copper nuclei has been observed for the two-electron reduced trinuclear copper cluster. The high correlation between the copper level in the membranes and enzymatic activity as well as the high reactivity of the reduced copper clusters toward dioxygen strongly indicate that the membrane-bound copper ions constitute the active sites of the pMMO.

Cell Membrane↗