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J N Reeve

Publications and source records attributed to J N Reeve.

At least 55 records · Page 3Linked to original sources

Histones and chromatin structure in hyperthermophilic Archaea.

HMf is a histone from the hyperthermophile Methanothermus fervidus. It is the archetype and most studied member of a family of archaeal histones that have primary sequences and three-dimensional structures in common with the eukaryal nucleosome core histones and that bind and compact DNA molecules into nucleosome-like structures (NLS). HMf preparations are mixtures of two similar, small (approximately 7.5 kDa) polypeptides designated HMfA and HMfB that in vivo form both homodimers and heterodimers. HMfA synthesis predominates during exponential growth but the relative amount of HMfB increases as M. fervidus cells enter the stationary growth phase. Analyses of homogeneous preparations of recombinant (r) (HMfA)2 and (rHMfB)2 have demonstrated that these proteins have different DNA-binding and compaction properties in vitro, consistent with different roles in vivo for the (HMfA)2, (HMfB)2 and HMfA. HmfB dimers, and for the NLS that they form, in regulating gene expression and in genome compaction and stability.

Amino Acid Sequence↗

Characterization of a 45-kDa flavoprotein and evidence for a rubredoxin, two proteins that could participate in electron transport from H2 to CO2 in methanogenesis in Methanobacterium thermoautotrophicum.

Methanobacterium thermoautotrophicum strains contain a flavoprotein (flavoprotein A) that copurifies with the H2:heterodisulfide oxidoreductase complex. In this study, we report the iron-dependent synthesis and biochemical properties of flavoprotein A, cloning and sequencing of the flavoprotein-A-encoding gene (fpaA) and the co-transcription of fpaA with two downstream open reading frames, one of which (rdxA) appears to encode a rubredoxin. Native flavoprotein A has been shown to be a homodimer of a 45-kDa polypeptide that contains 1.3 mol FMN/45-kDa subunit but no iron or acid-labile sulfur. Catalytic amounts of the H2:heterodisulfide oxidoreductase complex or of the F420-reducing hydrogenase reduced flavoprotein A with H2, at specific rates of 0.3-0.4 U/mg enzyme, generating up to 70% flavin semiquinone before reduction to the flavin hydroquinone was observed. This intermediate accumulation of the semiquinone species had a kinetic rather than a thermodynamic basis, because the semiquinone form of flavoprotein A, generated by photoreduction, disproportionated quantitatively to the quinone and hydroquinone species. The midpoint potential of the quinone/hydroquinone couple was estimated to be 230 +/- 15 mV, at pH 7.6, versus the normal hydrogen electrode. Quantitation of Western blots demonstrated that flavoprotein A constituted approximately 1.5% of the soluble protein in cells grown in an iron-sufficient medium but that this increased to about 6% of the cellular protein when the iron the medium was depleted. The increase in the flavoprotein A content of cells grown under iron-limiting conditions was mirrored by a decrease in the content of the iron-rich polyferredoxin that also copurified with the H2:heterodisulfide oxidoreductase complex. The fpaA gene, cloned and sequenced from M. thermoautotrophicum strain delta H, encodes 404 amino acids in a sequence that has a C-terminal domain (approximately 130 amino acid residues) with features consistent with a flavodoxin structure. The remainder of flavoprotein A has sequences that are also predicted to be present in the N-terminal region of the orf14 gene product, which also appears to be an enlarged flavodoxin, encoded in the nif region of Rhodobacter capsulatus. Immediately downstream from fpaA, two open reading frames designated orfX and rdxA, have been located and shown by Northern-blot analyses to be co-transcribed with fpaA, although approximately 50% of fpaA-orfX-rdxA transcripts terminated or were cleaved within rdxA. Primer extension studies revealed that transcription of this transcriptional unit (the fpa operon) was initiated 32 nucleotides upstream of fpaA, at a site 25 nucleotides downstream from a sequence consistent with an archaeal TATA-box promoter element.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

Structure and stability of histone HMf from the hyperthermophilic archaeon Methanothermus fervidus.

The secondary and quaternary structures and stabilities of recombinant (r) forms of the HMfA and HMfB histones from Methanothermus fervidus have been investigated by CD spectroscopy and formaldehyde-mediated protein-protein cross-linking. Both proteins were shown to be dimers in solutions containing 5-1300 mM KCl, at pH 6-10 and 25-83 degrees C, and specifically in 1 M KCl, at pH 7.5 and 83 degrees C, conditions which approximate those in vivo in M. fervidus cells. Heat treatment of a mixture of rHMfA and rHMfB homodimers resulted in the formation of rHMfA.rHMfB heterodimers, as demonstrated by two-dimensional PAGE. Heterodimer formation did not result in a CD-detectable conformational change from the homodimer states, indicating that homogeneous (rHMfA)2 and (rHMfB)2 preparations may be considered as structural models of heterodimers. At pH 2, both rHMfA and rHMfB were denatured under low-salt (< 0.2 M KCl) conditions, and their conformations were stabilized in a cooperative manner by increasing KCl concentration, with cooperativity constants for KCl uptake of 2.7 and 3.1, respectively. The alpha-helical conformations of rHMfA and rHMfB were salt-dependent, at both pH 2 and pH 7.5, with maximal helicities in 1 M KCl of 84% and 63% at pH 2, and 72% and 65% at pH 7.5, respectively. The data obtained indicate that the structures of HMfA and HMfB, in 100-200 mM KCl at pH 7.5 and 25 degrees C, are likely to be very similar to their in vivo structures, even though these conditions are far removed from those found in vivo.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

Cloning, sequencing, and transcriptional analysis of the coenzyme F420-dependent methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase gene from Methanobacterium thermoautotrophicum strain Marburg and functional expression in Escherichia coli.

Two methylenetetrahydromethanopterin dehydrogenases have been purified from Methanobacterium thermoautotrophicum strain Marburg: one (MTD) is coenzyme F420-dependent and oxygen-stable (Mukhopadhyay, B., and Daniels, L. (1989) Can. J. Microbiol. 35, 499-507), and the other (MTH) is coenzyme F420-independent (or hydrogenase-type) and oxygen-sensitive (Zirngibl, C., Hedderich, R., and Thauer, R. K. (1990) FEBS Lett. 261, 112-116). Based on the NH2-terminal sequence of MTD, a 36-mer oligonucleotide was designed and used to identify and clone a 6.1-kilobase pair EcoRI fragment of M. thermoautotrophicum DNA. Sequencing of this fragment revealed an 825-base pair (bp) MTD encoding gene (mtd), which was expressed in Escherichia coli yielding an enzyme that, like the native enzyme, was oxygen-stable, strictly dependent on coenzyme F420, thermostable, thermophilic, and exhibited maximum activity at an acidic pH. The amino acid sequence predicts that MTD is a hydrophobic and acidic protein with no identifiable homology to MTH (von Bunau, R., Zirngibl, C., Thauer, R. K., and Klein, A. (1991) Eur. J. Biochem. 202, 1205-1208), but comparisons with coenzyme F420 utilizing enzymes revealed a conserved region at the NH2 terminus of MTD that could correspond to the ability to interact with coenzyme F420. The mtd transcript was approximately 900 nucleotides long and initiated 8 bp upstream of the translation initiation codon and 22 bp downstream from an archaeal promoter sequence. The mtd coding sequence was followed by several poly(dT) sequences and an inverted repeat that could be transcription termination signals.

Amino Acid Sequence↗

Improved N-terminal processing of recombinant proteins synthesized in Escherichia coli.

Preparations of rHMfA (recombinant histone A from Methanothermus fervidus) synthesized in E. coli by the heterologous expression of the hmfA gene were found to contain a mixture of rHMfA molecules, approximately 40% that retained the N-terminal formyl-methionyl residue (f-met-rHMfA), approximately 50% that lacked the formyl moiety but retained the methionyl residue (met-rHMfA), and only approximately 10% that had lost both components of the protein synthesis initiating amino acid residue and therefore had the same N-terminal sequence as native HMfA molecules synthesized in Mt. fervidus. Expression of the hmfA gene in E. coli cells grown in the presence of trimethoprim and thymidine, coupled with the concurrent over-expression of a methionine aminopeptidase-encoding map gene, has been shown to overcome this N-terminal heterogeneity problem and to result in rHMfA preparations in which > 85% of the molecules have the fully processed, native N-terminal sequence. This procedure should be generally useful for ensuring N-terminal processing of recombinant proteins synthesized in E. coli.

Archaea↗

Purification of the copper response extracellular proteins secreted by the copper-resistant methanogen Methanobacterium bryantii BKYH and cloning, sequencing, and transcription of the gene encoding these proteins.

When the copper-resistant methanogen Methanobacterium bryantii BKYH was exposed to 1 mM Cu(II), it secreted approximately fourfold increased levels of three proteins, copper response extracellular (CRX) proteins. The members of the CRX protein trio had apparent molecular masses of 40.8, 42.3, and 42.9 kDa and were purified together from the culture supernatant and separated from each other by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The N-terminal amino acid sequences of the three proteins were essentially identical, and antibodies raised against one of the trio reacted with all three proteins and with three other intracellular proteins with slightly higher molecular weights. The N-terminal amino acid sequence of one of these larger proteins was different from that of the secreted CRX proteins. The gene crx, which encodes the CRX proteins, was cloned and sequenced, and crx transcription was characterized. The crx sequence predicts that the encoded polypeptide is synthesized as a precursor with an N-terminal leader peptide, containing 28 amino acid residues, that is removed during the extracellular secretion of the CRX proteins. Transcription was initiated 274 bp upstream from the crx gene, producing an approximately 1.4-kb monocistronic transcript that was present in M. bryantii BKYH cells under all growth conditions but that increased approximately fourfold in vivo in response to Cu addition. The CRX proteins appear to be glycosylated, since they react with concanavalin A and neuraminidase, and to be the products of one gene that have different levels of posttranslational glycosylation. This is supported by very similar chromatographic and electrophoretic properties, identical N-terminal amino acid sequences, immunological cross-reactivities, and the detection of only one crx-related sequence by Southern blotting. Western blots (immunoblots) showed no evidence for CRX proteins in cell lysates of several other Methanobacterium strains.

Amino Acid Sequence↗

Cloning, sequencing, and growth phase-dependent transcription of the coenzyme F420-dependent N5,N10-methylenetetrahydromethanopterin reductase-encoding genes from Methanobacterium thermoautotrophicum delta H and Methanopyrus kandleri.

The mer genes, which encode the coenzyme F420-dependent N5,N10-methylenetetrahydromethanopterin reductases (CH2 = H4MPT reductases), and their flanking regions have been cloned from Methanobacterium thermoautotrophicum delta H and Methanopyrus kandleri and sequenced. The mer genes have DNA sequences that are 57% identical and encode polypeptides with amino acid sequences that are 57% identical and 71% similar, with calculated molecular masses of 33.6 and 37.5 kDa, respectively. In M. thermoautotrophicum, mer transcription has been shown to initiate 10 bp upstream from the ATG translation initiating codon and to generate a monocistronic transcript approximately 1 kb in length. This transcript was synthesized at all stages of M. thermoautotrophicum delta H growth in batch cultures but was found to increase in abundance from the earliest stages of exponential growth, reaching a maximum level at the mid-exponential growth phase. For comparison, transcription of the ftr gene from M. thermoautotrophicum delta H that encodes the formylmethanofuran:tetrahydromethanopterin formyltransferase (A. A. DiMarco, K. A. Sment, J. Konisky, and R. S. Wolfe, J. Biol. Chem. 265:472-476, 1990) was included in this study. The ftr transcript was found similarly to be monocistronic and to be approximately 1 kb in length, but, in contrast to the mer transcript, the ftr transcript was present at maximum levels at both the early and the mid-exponential growth stages.

Amino Acid Sequence↗

Methanobacterium formicicum, a mesophilic methanogen, contains three HFo histones.

The mesophilic methanogen Methanobacterium formicicum JF-1 has been shown to contain three members of the HMf family of archaeal histones, designated HFoA1, HFoA2, and HFoB, and their encodinig genes (hfoA1, hfoA2, and hfoB) have been cloned and sequenced. The HFo histones have primary sequences that are 75 to 82% identical to the HMf sequences and appear to share ancestry with the core histones that form the eukaryal nucleosome. The HFo proteins bind and compact DNA molecules into nucleosome-like structures apparently identical to those formed by the HMf proteins, but, in contrast to the HMf proteins, this activity of the HFo proteins is lost after incubation at 95 degrees C for 5 h.

Amino Acid Sequence↗

Organization and growth phase-dependent transcription of methane genes in two regions of the Methanobacterium thermoautotrophicum genome.

Two regions of the Methanobacterium thermoautotrophicum genome containing genes that encode enzymes involved in methanogenesis (methane genes) have been cloned and sequenced to determine the extent of methane gene clustering and conservation. One region from the M. thermoautotrophicum strains delta H and Winter, extending approximately 13.5 kb upstream from the adjacent mvhDGAB and mrtBDGA operons that encode the methyl-viologen-reducing hydrogenase (MVH) and the methyl coenzyme M reductase II (MRII), respectively, was sequenced, and 76% sequence identity and very similar gene organizations were demonstrated. Five closely linked open reading frames were located immediately upstream of the mvh operon and were designated flpECBDA. The flpCBD genes encode amino acid sequences that are 31, 47, and 65% identical to the primary sequences of the alpha and beta subunits of formate dehydrogenase and the delta subunit of MVH, respectively. Located immediately upstream of the flp genes was the mth gene, which encodes the H2-dependent methylene-tetrahydromethanopterin dehydrogenase (MTH). In contrast to this mth-flp-mvh-mrt cluster of methane genes, a separate approximately 5.4-kb genomic fragment cloned from M. thermoautotrophicum delta H contained only one methane gene, the mtd gene, which encodes the 8-hydroxy-5-deazaflavin (H2F420)-dependent methylene-tetrahydromethanopterin dehydrogenase (MTD). Northern (RNA) blot experiments demonstrated that mth was transcribed only at early growth stages in fermentor-grown cultures of M. thermoautotrophicum delta H, whereas mtd was transcribed at later growth stages and in the stationary phase. Very similar transcription patterns have been observed by T.D. Pihl, S. Sharma, and J. N. Reeve (J. Bacteriol. 176:6384-6391, 1994) for the MRI- and MRII-encoding operons, mrtBDGA and mcrBDCGA, im M. thermoautotrophicum deltaH, suggesting coordinated regulation of methane gene expression. In contrast to the growth phase-dependent transcription of the mth/mrt and mtd/mcr genes, transcription of the mvhDGAB and frhADGB operons, which encode the two (NiFe) hydrogenases in M. thermoautotrophicum deltaH, was found to occur at all growth stages.

Amino Acid Sequence↗

Growth-phase-dependent synthesis of histones in the archaeon Methanothermus fervidus.

Histone preparations from Methanothermus fervidus (HMf) contain two small polypeptides, HMfA and HMfB, which in solution are dimers and compact DNA to form nucleosome-like structures. These archaeal nucleosome-like structures constrain positive DNA supercoils, in contrast to the negatively supercoiled DNA in eukaryal nucleosomes. HMfA has been found to make up as much as 80% of HMf preparations synthesized by M. fervidus cells during the exponential growth phase of batch cultures but to decrease to approximately 50% as cultures enter the stationary phase. By using a nondenaturing polyacrylamide gel system at pH 6.1, we have demonstrated that HMf preparations contain HMfA homodimers, HMfB homodimers, and HMfA-HMfB heterodimers and that heating a mixture of recombinant HMfA and HMfB homodimers at 95 degrees C for 5 min generates HMfA-HMfB heterodimers. Circular dichroism spectroscopy indicates that HMfA and HMfB have very similar secondary structures, but based on agarose gel electrophoretic mobility shifts, DNA topology assays, and electron microscopy, they have different DNA binding properties. HMfA binding to DNA could be detected at lower protein/DNA ratios than HMfB, but HMfB binding resulted in more extensive DNA compaction. The increased HMfB synthesized in cells approaching the stationary phase and the highly compacted state of HMfB-bound DNA are consistent with preparations for the impending period of limited genome activity.

Archaea↗

Histone-encoding genes from Pyrococcus: evidence for members of the HMf family of archaeal histones in a non-methanogenic Archaeon.

Two genes, designated hpyA1 and hpyA2, have been cloned and sequenced from Pyrococcus strain GB-3a. They are predicted to encode proteins (HPyA1 and HPyA2, respectively) that are approx. 60% identical to the histones HMf and HMt, characterized from methanogenic Archaea. These archaeal histones also contain the amino-acid sequences, conserved in eukaryotic H4 histones, that are thought to interact directly with DNA.

Amino Acid Sequence↗

mRNAs in the methanogenic archaeon Methanococcus vannielii: numbers, half-lives and processing.

Cells from the early exponential growth phase of cultures of the methanogenic archaeon Methanococcus vannielii have been shown to contain c. 180 transcripts of the mcrBDCGA (mcr) operon, c. 100 transcripts of the MvaL1,L10,L12 (Mva) operon, c. 8 transcripts of the argG gene and c. 1 transcript of the secY gene. These values decreased to c. 50 mcr transcripts, c. 30 Mva transcripts, c. 3 argG transcripts and < 1 secY transcript per cell as the cultures entered the stationary phase of growth. Addition of bromo-ethanesulphonate (BES) or removal of H2 inhibited growth and RNA synthesis in vivo and, at 37 degrees C in the presence of BES, the half-lives of the mcr, Mva, argG and secY transcripts were found to be 15 min, 30 min, 57 min and 7 min, respectively. Addition of puromycin, pseudomonic acid or virginiamycin also inhibited growth but did not inhibit transcription. In the presence of puromycin the half-lives of the mcr and Mva transcripts increased c. 4.6-fold and c. 3.5-fold, respectively, and there was a net accumulation of the Mva transcript. Addition of pseudomonic acid or virginiamycin also increased the half-life of the Mva transcript and also resulted in the accumulation of a second, shorter Mva transcript but did not increase the half-life of the mcr transcript. Transcription of the mcr operon was not stimulated by partial inhibition of methanogenesis.

Argininosuccinate Synthase↗

Growth phase-dependent transcription of the genes that encode the two methyl coenzyme M reductase isoenzymes and N5-methyltetrahydromethanopterin:coenzyme M methyltransferase in Methanobacterium thermoautotrophicum delta H.

The genes encoding the two isoenzymes of methyl coenzyme M reductase (MRI and MRII) in Methanobacterium thermoautotrophicum delta H have been cloned and sequenced. The MRI-encoding mcr operon (mcrBDCGA) has been located immediately upstream from the mtr operon (mtrEDCBA) that encodes N5-methyltetrahydromethanopterin:coenzyme M methyltransferase, the enzyme that catalyzes the step preceding the MR-catalyzed reaction in methanogenesis. The MRII-encoding mrt operon (mrtBDGA) has been located between the operon that encodes the methyl viologen-reducing hydrogenase and an open reading frame (designated pyrC) predicted to encode dihydroorotase. Surprisingly, the mrt operon has been found to contain only four genes (mrtBDGA), lacking the equivalent of the mcrC gene that is present in all mcr operons. A protocol that isolates transcripts intact from M. thermoautotrophicum delta H cells has been developed and used, with primer extension and Northern (RNA) blot procedures, to identify the sites of transcription initiation upstream of the mcr, mrt, and mtr operons and to determine the relative numbers of these transcripts in cells at different growth stages. Transcription of the mrt operon was found to occur only at early times in batch cultures and was then replaced by transcription of the mcr operon. Transcripts of the mtr operon were detectable at all times; however, at early times, all mtr transcripts were initiated at the mtr promoter, whereas at later times, during mcr transcription, approximately 3% of mcr transcripts were extended to generate mcr plus mtr transcripts that constituted approximately 20% of all mtr transcripts present.

Amino Acid Sequence↗

Association of the mcrD gene product with methyl coenzyme M reductase in Methanococcus vannielii.

The mcrD gene, subcloned from the methyl coenzyme M reductase (MR) encoding mcrBDCGA operon in Methanococcus vannielii, has been expressed at a high level in Escherichia coli. Rabbit antibodies, raised against the product of this gene (rgpmcrD, recombinant gene product of mcrD) purified from E. coli, have been used to quantitate gpmcrD in M. vannielii and to follow its fate during MR purification. The molar ratio of gpmcrD to MR was found to be approx. 1:15 in cells of M. vannielii taken from batch cultures at all stages of growth. Sedimentation of lysates of M. vannielii cells through sucrose gradients and analyses of the fractions obtained by Western blotting and immunoprecipitation have demonstrated the presence of a macromolecular complex containing both gpmcrD and MR. Addition of mcrD antibodies or removal of gpmcrD from lysates of M. vannielii cells by immunoprecipitation decreased the rates of methanogenesis in vitro by approx. 20%. Addition of purified rgpmcrD to these lysates did not stimulate methanogenesis.

Blotting, Western↗

Identification of the mcrC gene product in Methanococcus vannielii.

The polypeptide encoded by the mcrC gene has been identified in Methanococcus vannielii by immunoblotting using rabbit antibodies raised against the product of a lacZ-mcrC gene fusion synthesized and purified from Escherichia coli. The mcrC gene product (gpmcrC) was located in both the supernatant and pellet fractions after centrifugation of Mc. vannielii cell extracts for 2 h at 100,000 x g. When anaerobic reducing conditions were maintained during purification, gpmcrC co-sedimented through sucrose gradients to the same position as molecules of the methyl coenzyme M reductase holoenzyme (approx. 300 kDa). This co-sedimentation was lost under aerobic, nonreducing conditions.

Amino Acid Sequence↗

Transcription in vitro and in vivo of the 7S RNA gene associated with the ribosomal RNA operon in the hyperthermophilic archaeon Methanothermus fervidus.

The gene encoding the archaeal 7S RNA in the hyperthermophile Methanothermus fervidus is linked to a tRNA(Ser) and rRNA operon in the arrangement 5'-7S RNA-14nt-tRNA(Ser)-196nt-16S rRNA and the promoter directing transcription of this 7S RNA gene has now been identified. Initiation of transcription of the 7S RNA gene has been shown to occur both in vivo in M. fervidus and in vitro, using a Methanococcus thermolithotrophicus derived cell-free transcription system, at the first G residue within the initiator sequence ATGG, located 6 bp upstream of the 5' end of the 7S RNA coding region. Cotranscription of the 7S RNA and tRNA(Ser) has been demonstrated in vitro.

Base Sequence↗

Transfer RNA genes from the hyperthermophilic Archaeon, Methanopyrus kandleri.

Genes encoding the Leu (GAG), Ser (UGA), Gln (UUG) and Lys (UUU) tRNAs have been cloned and sequenced from the deep sea hyperthermophilic Archaeon, Methanopyrus kandleri. Sequences conforming to the TATA box element established for methanogen promoters are located upstream of the tRNA(Gln) and tRNA(Lys) genes. All four of the tRNA genes appear to encode the 3' terminal CCA residues of the mature tRNA. These methanogen tRNAs are predicted to contain most, but not all, invariant residues and are characterized by a high level of G + C base pairing, consistent with the 98 degrees C optimum growth temperature of M. kandleri.

Base Sequence↗

Identification and isolation of the polyferredoxin from Methanobacterium thermoautotrophicum strain delta H.

Sequencing the genes encoding the methyl viologen-reducing hydrogenase, cloned from Methanobacterium thermoautotrophicum strain delta H and Methanothermus fervidus, revealed the presence of tightly linked genes, designated mvhB, which were predicted to encode proteins containing six tandemly arranged bacterial ferrodoxin-like domains. A lacZ-mvhB gene fusion has been constructed and expressed in Escherichia coli. Rabbit antibodies raised against the fusion polypeptide purified from E. coli have been used to identify and isolate the polyferrodoxin from Mb. thermoautotrophicum strain delta H. The polyferredoxin accumulates in cells of the methanogen during exponential growth but decreases rapidly on entry into stationary phase. It is not processed into monoferredoxins and is located primarily in the soluble fraction of cell lysates of Mb. thermoautotrophicum. Metronidazole reduction by crude extracts of Mb. thermoautotrophicum strain delta H cells, dependent on the presence of hydrogen and the heterodisulfide CoM-S-S-HTP [formed from the two coenzymes 2-mercaptoethanesulfonic acid (coenzyme M, HS-CoM) and N-(7-mercaptoheptanoyl)threonine O3-phosphate (HS-HTP)], was not inhibited by the antibodies raised against the LacZ-MvhB fusion polypeptide.

Base Sequence↗