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Biomedical subjects

R Haselkorn

Publications and source records attributed to R Haselkorn.

At least 73 records · Page 4Linked to original sources
PubMed1990

Expression, nucleotide sequence and mutational analysis of two open reading frames in the nif gene region of Anabaena sp. strain PCC7120.

A 1.8 kb transcript corresponding to a region of the Anabaena 7120 chromosome 4 kb downstream of the nifHDK operon appears 12-18 h after heterocyst induction. The DNA corresponding to this transcript was sequenced and found to contain two open reading frames, designated ORF 1 and ORF 2. Two polypeptides, of 30 kDa and 13 kDa, encoded by these ORFs were expressed in Escherichia coli. An apparent start site for the transcript, detected by S1 nuclease protection, was located 42 bp upstream of the ATG start codon of ORF 1. ORF 2 shows strong sequence similarity to ORF 6 in the nif gene region of Azotobacter vinelandii. ORF 1 was interrupted using a 1.4 kb neomycin resistance cassette and the resulting mutant grew very slowly on medium lacking combined nitrogen. The mutant had 45% of wild-type acetylene reduction activity, which could be complemented by a 2.8 kb EcoRI fragment of wild-type Anabaena DNA containing only ORF 1 and ORF 2. Thus, one or both of these ORFs is required for efficient nitrogen fixation in Anabaena.

Amino Acid Sequence↗
PubMed1989

Nitrogen fixation (nif) genes of the cyanobacterium Anabaena species strain PCC 7120. The nifB-fdxN-nifS-nifU operon.

A second nitrogen fixation (nif) operon in the cyanobacterium (blue-green alga) Anabaena (Nostoc) sp. strain PCC 7120 has been identified and sequenced. It is located just upstream of the nifHDK operon and consists of four genes in the order nifB, fdxN, nifS, and nifU. The three nif genes were identified on the basis of their similarity with the corresponding genes from other diazotrophs. The fourth gene, fdxN, codes for a bacterial type ferredoxin (Mulligan, M. E., Buikema, W. J., and Haselkorn, R. (1988) J. Bacteriol. 167, 4406-4410). The four genes are probably transcribed as a single operon, but are expressed at a lower level than the nifHDK operon, and only after a developmentally induced DNA rearrangement occurs that excises a 55-kilobase pair element from within the fdxN gene (Golden, J. W., Mulligan, M. E., and Haselkorn, R. (1987) Nature 327, 526-529; Golden, J. W., Carrasco, C. D., Mulligan, M. E., Schneider, G. J., and Haselkorn, R. (1988) J. Bacteriol. 170, 5034-5041). The promoter for the nifB operon was located by primer extension. Comparison of the nifB 5'-flanking sequence with the nifH 5'-flanking sequence did not reveal any consensus base pairs that would define a nif promoter for Anabaena. The operon contains two instances of 7-base pair directly repeated sequences: seven copies of the repeated sequence are found between the nifB and fdxN genes and six copies are found between the nifS and nifU genes. The function of these repeats is unknown.

Amino Acid Sequence↗
PubMed1989

Resistance to the photosystem II herbicide diuron is dominant to sensitivity in the cyanobacterium Synechococcus sp. PCC7942.

The transformable cyanobacterium, Synechococcus sp. PCC7942, was used to study the genetics of resistance to the herbicide diuron. In wild-type cells, diuron binds to one of the core proteins, called D1, of photosystem II reaction centres. This binding prevents the transfer of electrons from Q(A), the primary quinone acceptor, to Q(B), which is necessary to create the charge separation that drives ATP synthesis. A single amino acid substitution in the D1 protein reduces diuron binding and confers herbicide resistance to reaction centres containing the substituted D1 protein. In Synechococcus 7942, the D1 protein is encoded by three functional genes called psbAI, psbAII and psbAIII. By selectively altering one member at a time of the three-member psbA gene family, we have demonstrated that diuron-resistant alleles are dominant to diuron-sensitive alleles. The relative abundance of the different psbA gene transcripts is correlated with the fraction of diuron-resistant reaction centres and with the degree of diuron resistance. Growth in sublethal diuron selectively increases the steady-state levels of transcripts of genes (psbA and psbD) encoding the core proteins of photosystem II. We have also found that turnover of the D1 protein can be uncoupled from electron transport through photosystem II.

Journal Article↗
PubMed1989

Nucleotide sequence of the gene encoding the 33 kDa water oxidizing polypeptide in Anabaena sp. strain PCC 7120 and its expression in Escherichia coli.

The 33 kDa extrinsic polypeptide of photosystem II, also known as the manganese-stabilizing polypeptide (MSP), is located on the lumen side of the thylakoid and is involved in water oxidation. The gene for MSP, designated woxA, has been cloned from the nitrogen-fixing filamentous cyanobacterium Anabaena and sequenced. The woxA open reading frame was found to be 819 bp. The deduced amino acid sequence was 63% and 59% homologous with that of Synechococcus and Synechocystis, respectively, and 44% conserved when compared to the MSP of spinach or pea. Two cysteine residues at positions 48 and 73 were found to be conserved in cyanobacteria and plants. The first 29 amino acids are hydrophobic and may represent the transit peptide. woxA: :phoA translational fusion products, in which the body of Escherichia coli alkaline phosphatase was fused to the amino terminal portion of woxA between residues 35 and 130, yielded active alkaline phosphatase in E. coli. Thus the transit peptide of woxA functions in E. coli to transport phosphatase across the cytoplasmic membrane. S1 mapping and primer extension experiments showed that the woxA transcription initiation site is located 220 bp upstream from the translational start. The woxA promoter has some resemblance to the E. coli consensus and other known Anabaena vegetative cell promoters.

Amino Acid Sequence↗
PubMed1989

Isolation, sequence and transcription of the gene encoding the photosystem II chlorophyll-binding protein, CP-47, in the cyanobacterium Anabaena 7120.

The psbB gene from the cyanobacterium Anabaena 7120 was cloned and its nucleotide sequence determined. This gene codes for the photosystem II chlorophyll-binding protein CP-47. We identified an open reading frame of 1527 bases that can code for a polypeptide with a predicted molecular weight of 56,254. Expression of the psbB gene in Anabaena 7120 results in two transcripts that begin 302 or 238 bp upstream of the open reading frame and both end 288 bp downstream following a 21 bp inverted repeat. We also show that the levels of these psbB gene transcripts as well as those of the glnA, rbcLS, and psbA genes, in RNA prepared from whole filaments, remain constant during heterocyst differentiation.

Amino Acid Sequence↗
PubMed1989

The DNA sequence of the Rhodobacter capsulatus ntrA, ntrB and ntrC gene analogues required for nitrogen fixation.

We have determined the DNA sequence for the genes nifR1, nifR2 and nifR4 in the photosynthetic bacterium Rhodobacter capsulatus. These genes regulate transcription of the nifHDK operon and so limit the expression of nitrogen fixation activity to periods of low environmental concentrations of both oxygen and fixed nitrogen. The sequences of these three genes are similar to components of the ntr regulation system in Escherichia coli and Klebsiella pneumoniae. The two-component regulatory system of ntrB and ntrC in E. coli is represented by nifR2 and nifR1 in R. capsulatus and nifR4 in R. capsulatus is the equivalent of the E. coli ntr-related sigma factor ntrA.

Amino Acid Sequence↗
PubMed1989

Comparison of DNA restriction fragment length polymorphisms of Nostoc strains in and from cycads.

DNA was prepared from cyanobacteria freshly isolated from coralloid roots of natural populations of five cycad species: Ceratozamia mexicana mexicana (Mexico), C. mexicana robusta (Mexico), Dioon spinulosum (Mexico), Zamia furfuraceae (Mexico) and Z. skinneri (Costa Rica). Using the Southern blot technique and cloned Anabaena PCC 7120 nifK and glnA genes as probes, restriction fragment length polymorphisms of these cyanobacterial symbionts were compared. The five cyanobacterial preparations showed differences in the sizes of their DNA fragments hybridizing with both probes, indicating that different cyanobacterial species and/or strains were in the symbiotic associations. On the other hand, a similar comparison of cyanobacteria freshly collected from a single Encephalartos altensteinii coralloid root and from three independently subcultured isolates from the same coralloid root revealed that these were likely to be one and the same organism. Moreover, the complexity of restriction patterns shows that a mixture of Nostoc strains can associate with a single cycad species although a single cyanobacterial strain can predominate in the root of a single cycad plant. Thus, a wide range of Nostoc strains appear to associate with the coralloid roots of cycads.

Blotting, Southern↗
PubMed1989

Tn5 mutagenesis of Anabaena sp. strain PCC 7120: isolation of a new mutant unable to grow without combined nitrogen.

Methylation by Ava methylases in Escherichia coli increases the efficiency to transfer of Tn5 in pBR322bla:: Tn5 from E. coli to Anabaena sp. strain PCC 7120 by conjugation. Following conjugation, Tn5 but not pBR322 sequences were found at many different positions in the Anabaena chromosome. This procedure was used to mutagenize, tag, and clone a previously unrecognized gene required for nitrogen fixation in this Anabaena sp.

Blotting, Southern↗
PubMed1988

Ammonia-constitutive nitrogen fixation mutants of Rhodobacter capsulatus.

Mutants of R. capsulatus that express nif genes constitutively with respect to ammonia were studied in order to define better the circuit that regulates nif gene transcription. One mutant class could be complemented in trans by a cosmid clone containing a wild-type gene (nifR5) defined by Tn5 inserts as being no longer than 1.6 kb. The nifR5 gene is unlinked to previously described nif genes. A second mutant class could not be complemented by the wild-type cosmid library. For one mutant in this class, a nifH::lac fusion was used to select further mutants that were Lac-. Only two of these could be complemented in trans to Lac+; the complementing gene was nifR4, which is analogous to the ntrA gene of enterobacteria. Both complemented strains were Nifc. Therefore these mutations do not bypass the need for the nifR4 gene product. A third class of constitutive mutant was found by selecting Nif+ revertants of a Nif- strain deleted for the nifR1 and nifR2 genes. The nifR1 and nifR2 genes are homologues of enterobacterial ntrC and ntrB genes, respectively. Not all of the Nif+ revertants were constitutive; some were regulated normally by ammonia. We suspect that the latter revertants use alternate Ntr systems to activate nif gene transcription, a suggestion consistent with the observation that numerous bands in Southern blots of total DNA of R. capsulatus are identified by Escherichia coli ntr gene probes.

Ammonia↗
PubMed1988

Molecular cloning and nucleotide sequence analysis of the gene coding for heterocyst ferredoxin from the cyanobacterium Anabaena sp. strain PCC 7120.

In heterocysts of the filamentous cyanobacterium Anabaena 7120 a specific [2Fe-2S] ferredoxin is synthesized, serving as immediate electron donor to nitrogenase. The structural gene for this heterocyst ferredoxin, fdxH, was isolated from a recombinant lambda library, using an oligonucleotide probe derived from a unique segment of the N-terminal amino acid sequence of the purified protein. The sequence of the entire fdxH coding region was determined including 3' and 5' flanking sequences. Assuming proteolytic cleavage of the first methionine residue, the molecular weight of Anabaena 7120 heterocyst ferredoxin is 10,806. Compared with the ferredoxin from vegetative cells, 47 out of 98 amino acid residues are different, including conversions within a highly conserved region responsible for binding of the iron-sulfur cluster. Northern hybridization with a 0.64 kb EcoRI DNA fragment containing the entire fdxH gene indicated two major transcripts of 0.59 and 1.85 kb, which are expressed at a late stage of heterocyst differentiation. By S1 nuclease digestion and primer extension a possible start site of transcription was mapped, 132 bp upstream of fdxH; however, neither a typical Escherichia coli nor nif-type promoter sequence was apparent. Southern hybridization detected only one copy of the fdxH gene in the Anabaena 7120 genome. FdxH is located approximately 7 kb downstream from the nifHDK gene cluster.

Amino Acid Sequence↗
PubMed1988

Organization of the nif genes in cyanobacteria in symbiotic association with Azolla and Anthoceros.

The sizes of endonuclease digestion fragments of DNA from cyanobacteria in symbiotic association with Azolla caroliniana or Anthoceros punctatus, or in free-living culture, were compared by Southern hybridization using cloned nitrogenase (nif) genes from Anabaena sp. PCC 7120 as probes. The restriction fragment pattern produced by cyanobacteria isolated from A. caroliniana by culture through symbiotic association with Anthoceros differed from that of the major symbiotic cyanobacterium freshly separated from A. caroliniana. The results indicate that minor cyanobacterial symbionts occur in association with Azolla and that the dominant symbiont was not cultured in the free-living state. Both the absence of hybridization to an xisA gene probe and the mapping of restriction fragments indicated a contiguous nifHDK organization in all cells of the symbiont in association with Azolla. On the other hand, in the cultured isolate from Azolla and in Nostoc sp. 7801, the nifD and nifK genes are nominally separated by an interval of unknown length, compatible with the interruption of the nifHDK operon by a DNA element as observed in Anabaena sp. PCC 7120. In the above cultured strains, restriction fragments consistent with a contiguous nifHDK operon were also present at varying hybridization intensities, especially in Nostoc sp. 7801 grown in association with Anthoceros, presumably due to gene rearrangement in a fraction of the cells.

Autoradiography↗
PubMed1988

Characterization of two early promoters of cyanophage N-1.

Restriction fragments of cyanophage N-1 DNA, containing genes transcribed early in infection of Anabaena, were identified by hybridization with RNA prepared from infected cells. Two of these fragments were isolated by binding to Anabaena RNA polymerase on filters and were subsequently cloned. The start sites for transcription by Anabaena RNA polymerase were determined by run-off assays. The sequences of the two promoter regions thus localized were similar to each other in the -35 and -10 regions and nearly identical to the consensus sequence for promoters in Escherichia coli.

Base Sequence↗
PubMed1988

Deletion of a 55-kilobase-pair DNA element from the chromosome during heterocyst differentiation of Anabaena sp. strain PCC 7120.

The filamentous cyanobacterium Anabaena sp. strain PCC 7120 produces terminally differentiated heterocysts in response to a lack of combined nitrogen. Heterocysts are found approximately every 10th cell along the filament and are morphologically and biochemically specialized for nitrogen fixation. At least two DNA rearrangements occur during heterocyst differentiation in Anabaena sp. strain PCC 7120, both the result of developmentally regulated site-specific recombination. The first is an 11-kilobase-pair (kb) deletion from within the 3' end of the nifD gene. The second rearrangement occurs near the nifS gene but has not been completely characterized. The DNA sequences found at the recombination sites for each of the two rearrangements show no similarity to each other. To determine the topology of the rearrangement near the nifS gene, cosmid libraries of vegetative-cell genomic DNA were constructed and used to clone the region of the chromosome involved in the rearrangement. Cosmid clones which spanned the DNA separating the two recombination sites that define the ends of the element were obtained. The restriction map of this region of the chromosome showed that the rearrangement was the deletion of a 55-kb DNA element from the heterocyst chromosome. The excised DNA was neither degraded nor amplified, and its function, if any, is unknown. The 55-kb element was not detectably transcribed in either vegetative cells or heterocysts. The deletion resulted in placement of the rbcLS operon about 10 kb from the nifS gene on the chromosome. Although the nifD 11-kb and nifS 55-kb rearrangements both occurred under normal aerobic heterocyst-inducing conditions, only the 55-kb excision occurred in argon-bubbled cultures, indicating that the two DNA rearrangements can be regulated differently.

Chromosome Deletion↗
PubMed1988

Bacterial-type ferredoxin genes in the nitrogen fixation regions of the cyanobacterium Anabaena sp. strain PCC 7120 and Rhizobium meliloti.

The nucleotide sequence of a region located downstream of the nifB gene, both in the cyanobacterium Anabaena sp. strain PCC 7120 and in Rhizobium meliloti, has been determined. This region contains a gene (fdxN) whose predicted polypeptide product strongly resembles typical bacterial ferredoxins. Cyanobacteria have not previously been shown to contain bacterial-type ferredoxins. The presence of this gene suggests that nitrogen-fixing cyanobacteria have at least four distinct ferredoxins.

Amino Acid Sequence↗
PubMed1987

Purification and characterization of RNA polymerase from the cyanobacterium Anabaena 7120.

A procedure for the purification of RNA polymerase from vegetative cells of the filamentous cyanobacterium Anabaena 7120 is described. Polyethyleneimine precipitation followed by gel filtration and affinity chromatography steps results in greater than 99% purification with 46% yield. The enzyme has a novel core component of Mr = 66,000, designated gamma, in addition to the typical prokaryotic beta'beta alpha 2 core enzyme. The sigma subunit has been identified by reconstitution of specific transcriptional activity from core enzyme and gel-purified sigma. In transcription assays, this RNA polymerase initiates at a number of Anabaena vegetative cell promoters, as well as from a bacteriophage T4 early promoter, but does not initiate at nitrogen fixation (nif) promoters used in heterocysts. The promoter specificity of Anabaena RNA polymerase is compared with that of Escherichia coli RNA polymerase.

Base Sequence↗
PubMed1987

Cloning and light regulation of expression of the phycocyanin operon of the cyanobacterium Anabaena.

The biliprotein phycocyanin (PC) is a major constituent of the light-harvesting apparatus of cyanobacteria and red algae. A DNA fragment encoding the beta and alpha subunits of PC was isolated from a genomic library of the cyanobacterium Anabaena 7120 DNA. The single-copy PC genes are part of a larger operon which consists of five open reading frames (ORFs) encoding, in order, the beta and alpha subunits of PC, two linker polypeptides associated with PC in phycobilisome rods, and a fifth ORF, which may encode a linker polypeptide involved in attachment of the phycobilisome rod to the core of the structure. The operon yields three major transcripts, the first of which (1.4 kb) encodes only the PC subunits. A second (3.6 kb) encodes all five ORFs, and appears to arise from partial read-through of a terminator following the PC subunit genes. The third transcript (1.4 kb) encodes the last two ORFs. The relative levels of the three transcripts in vivo are modulated by light intensity, but they are not altered by the removal of fixed nitrogen from the growth medium. The site of light regulation appears to be the terminator following the PC genes, rather than a promoter.

Amino Acid Sequence↗