- Volume 145, Issue 7, 1999

In cultures of the unicellular cyanobacterium Gloeothece sp. ATCC 27152 growing under alternating 12 h light and 12 h darkness, nitrogenase activity appears as cultures enter the dark phase. Synthesis of both component proteins of nitrogenase commences immediately prior to the appearance of activity and continues until about 8 h into the period of darkness. The two components (Fe-protein and MoFe-protein) are synthesized in a molar ratio of about 3:1. Degradation of the nitrogenase proteins starts as early as 4 h into the dark period and increases markedly as cultures enter the light phase. As a result, both nitrogenase proteins are completely absent from cultures during most of the light phase. In contrast, all of the other proteins investigated appeared to be present throughout the cycle of alternating light and darkness. Degradation of nitrogenase depends upon protein synthesis during the last 6 h of darkness and is prevented by addition of protease inhibitors. Two proteins, of M r 47000 and 29000, are specifically synthesized during this period and it is possible that they have a role in nitrogenase degradation. Proteolytic activity of extracts of Gloeothece, measured as the ability to degrade azocasein, increased markedly during the early part of the light period, but this increase did not depend on protein synthesis. This activity does not therefore correspond to that specifically involved in nitrogenase catabolism, though it may act on initial breakdown products generated by a nitrogenase-specific degradative system. A phycobiliprotein appears to act as a temporary store of the degradation products of nitrogenase.

A novel Erwinia carotovora subsp. carotovora mutant designated RexZ, (regulator of exoenzymes) showed reduced production of the degradative exoenzymes. The rexZ gene product shows similarity to the KdgR regulatory protein from Erwinia chrysanthemi, described as the major repressor of the pectin catabolism pathway genes in the latter species. In vitro DNA—protein interaction experiments demonstrated that the synthesis of the RexZ protein is controlled by the cAMP—CRP (cAMP—receptor protein) complex. Western blot analysis also revealed the presence of a second KdgR homologue (distinct from RexZ) which, like RexZ, was present in all species of the genus Erwinia tested. The corresponding KdgR proteins from both E. carotovora subsp. carotovora and E. carotovora subsp. atroseptica share a high level of sequence identity with the KdgR homologues from E. chrysanthemi and Escherichia coli. Although the E. carotovora subsp. carotovora rexZ regulatory region displayed specific interactions with both the purified E. chrysanthemi KdgR repressor and the partially purified E. carotovora subsp. carotovora KdgR, in vivo quantification revealed that the cellular level of RexZ protein was unaffected by the presence of pectic compounds. This study shows that the complex regulatory network governing virulence in the erwinias involves two totally distinct, but highly conserved, members of the IcIR class of DNA binding proteins: RexZ and KdgR.

Ribonucleotide reductases (RNRs) encoded by nrd (nucleotide reduction) genes are unique enzymes providing the DNA precursors in all living organisms and several viruses. The designation of four classes of RNRs reflects their use of diverse metallo-cofactors. Using oligonucleotide primers derived from conserved domains of the primary structure of known NrdA and NrdE proteins, an internal 938 bp fragment of the nrdE gene was amplified from genomic DNA of Corynebacterium glutamicum. With this PCR product a 4·36 kb fragment was identified and cloned containing the nrdHIE genes of C. glutamicum. A probe derived from nrdF2 of Mycobacterium tuberculosis allowed the cloning and sequencing of the nrdF gene located 3·1 kb further downstream, encoding the small subunit of the C. glutamicum RNR. Conjugative introduction of nrdE from C. glutamicum complemented thermosensitive mutants of Corynebacterium ammoniagenes which had a defective catalytic subunit of the Mn-RNR. The authors provide arguments for allocation of the C. glutamicum NrdEF proteins to class IV in the RNR classification scheme of Stubbe & van der Donk (1995) [Chem Biol 2, 793-801].

The nuclear rDNA intergenic spacer (IGS) of the ectomycorrhizal basidiomycete Laccaria bicolor was amplified and sequenced to identify the source of its intraspecific polymorphism. The IGS was amplified by PCR in several L. bicolor strains and shown to exhibit multiple bands and length polymorphism. The IGS loci were shown to segregate in a 1:1 ratio within haploid progenies in three dikaryotic strains, suggesting that divergent IGS haplotypes were present in the two nuclei of these strains. The two haplotypes of L. bicolor S238N were sequenced: the β-haplotype was 4160 bp in length, whereas the size of the α-haplotype was estimated to be about 4700 bp. These represent the largest published fungal IGS sequences to date. These sequences can be subdivided into three main regions, IGS1, 5S rDNA and IGS2. The IGS sequences are AT-rich and contain numerous occurrences of three types of subrepeats (e.g. T2AC3). The length polymorphism, observed between the IGS sequence of the α- and β-haplotypes, results from the insertion of various numbers of a 71 bp subrepeat, called B, occurring in IGS2. This variation in subrepeat number suggests that the two haplotypes resulted from unequal cross-overs. The L. bicolor IGS was aligned with IGS sequences of two other Tricholomataceae (i.e. Tricholoma matsutake and Collybia fusipes). No sequence similarity was observed between these IGSs, but homologous subrepeats were found in L. bicolor and T. matsutake. Analysis of IGS length polymorphism is therefore an efficient tool for investigating genetic relationships between genets and within progenies in natural fungal populations.

The Candida albicans CHS4 gene encoding chitin synthase 4 has been isolated using the Saccharomyces cerevisiae CHS4/SKT5 gene as a probe. The gene contains a 2061 bp open reading frame capable of encoding a protein of 687 amino acids (76053 Da). No intron was observed in the gene. Disruption of CHS4 in C. albicans yielded a Calcofluor-resistant phenotype, indicating that Chs4p contributes to chitin biosynthesis. Consistent with this, overexpression of Chs4p under the regulation of the ScGAL1 promoter enhanced chitin synthase 3 activity in S. cerevisiae 7- to 38-fold. In addition, chs3 and chs4 null mutants were significantly defective in Calcofluor white staining and their chitin content was 10% of that of the parental strain. Chs4p of C. albicans and S. cerevisiae showed 61 % identity in the C-terminal half of the proteins and that region of C. albicans Chs4p complemented the Chs4p function of a mutant of S. cerevisiae resistant to Calcofluor white. Therefore, it appears that Chs4p is involved in chitin synthase 3 activity by combining with Chs3p to interact synergistically in chitin biosynthesis.

Molecular evidence is provided in this paper to elucidate a long-standing intriguing phenomenon in fungal genetics: that many natural isolates of the constitutive diploid organism Candida albicans yield strain-specific, recessive mutants at a reproducible frequency that is as high as a few percent of the surviving cells after exposure to UV irradiation or other mutagens. Southern hybridization analysis and DNA sequence data indicated that C. albicans CA12, a clinical isolate, is heterozygous for the ADE2 gene, carrying one functional and one null allele. Sequence analysis of the null allele revealed the presence of a 1·3 kb deletion, which locates between two AATC repeats and spans the promoter and coding regions of the gene. The adenine auxotrophic mutants, which were readily isolated after UV irradiation of C. albicans CA12, were proved to be the segregants of mitotic recombination as they remained as diploid, not hemizygous or haploid, cells and were homozygous for ade2. Analysis of reciprocal products of the mitotic recombination detected that the process of loss of heterozygosity was mediated by mitotic crossing over (reciprocal exchange of genetic information) as well as gene conversion (non-reciprocal exchange of genetic information).

The temperate bacteriophage Sf6 infects Shigella flexneri strains of serotype X or Y, converting them into serotypes 3a or 3b, respectively. The tailspike protein (TSP) of Sf6 possesses endo-1,3-α-l-rhamnosidase (endorhamnosidase) activity which results in cleavage of the lipopolysaccharide O-antigen receptor during the adsorption of the phage to the cell surface. When used in Southern hybridization, a P22 gene 9 (encoding P22 TSP) DNA probe hybridized with restriction fragment Pst1-7 of Sf6. DNA sequencing and analysis of Pstl-7 and the adjacent Psrl-8 fragment revealed an open reading frame (ORF1) of 1872 bp (624 amino acids) bearing amino acid sequence homology to the bacteriophage P22 TSP N-terminal head-binding domain. High conservation of key residues was suggestive of similar secondary and tertiary N-terminal protein structure and a similar function of the Sf6 TSP in this region. In addition, an amino acid sequence motif (DFGX3DGX6AX3A) was identified between residues 164 and 184 which was also found to exist in various prokaryotic and eukaryotic exo-/endoglycanases, C-5 epimerases and bacteriophage proteins. Expression of ORF1 from a T7 promoter produced a 67 kDa protein (detected by l-[35S]methionine labelling and SDS-PAGE). Assay of heat-treated cytoplasmic extracts containing the ORF1-encoded protein by incubation with whole Sh. flexneri Y cells demonstrated that O-antigen hydrolysis activity was present; ORF1 therefore encodes Sf6 TSP. Sf6 TSP exhibited specific and preferential activity for long-chain Sh. flexneri serotype X or Y O-antigen, cleavage of which resulted in the release of oligosaccharide fragments, consistent with octasaccharides in size, as detected by fluorophore-assisted carbohydrate electrophoresis (FACE).

Genes from the eubacterium Chlamydia typically do not share promoter consensus sequences with those of Escherichia coli and are not expressed when cloned in E. coli; nevertheless, the major σ-subunit identified from Chlamydia trachomatis has nearly identical amino acid sequence to E. coli σ70 in regions that contact DNA. Following expression of the chlamydial σ-subunit gene in E. coli, expression was specifically initiated from chlamydial promoter regions. Selective recognition of chlamydial promoters by holoenzyme was dependent upon the structure of the promoter DNA coupled with novel amino-and carboxyl-terminal extensions of the chlamydial σ-subunit.

PomA and PomB are integral membrane proteins and are essential for the rotation of the Na+-driven polar flagellar motor of Vibrio alginolyticus. On the basis of their similarity to MotA and MotB, which are the proton-conducting components of the H+-driven motor, they are thought to form the Na+-channel complex and to be essential for mechanochemical coupling in the motor. To investigate PomA function, random mutagenesis of the pomA gene by using hydroxylamine was carried out. We isolated 37 non-motile mutants (26 independent mutations) and most of the mutations were dominant; these mutant alleles are able to inhibit the motility of wild-type cells when greatly overexpressed. The mutant PomA proteins could be detected by immunoblotting, except for those with deletions or truncations. Many of the dominant mutations were mapped to the putative third or fourth transmembrane segments, which are the most conserved regions. Some mutations that showed strong dominance were in highly conserved residues. T186I is the mutation of a polar residue located in a transmembrane segment that might be involved in ion translocation. P199L occurred in a residue that is thought to mediate conformational changes essential for torque generation in MotA. These results suggest that PomA and MotA have very similar structures and roles, and the basic mechanism for torque generation will be similar in the proton and sodium motors.

It has previously been shown that the PAN promoter from Mycobacterium paratuberculosis can be used as a DNA probe to identify an RFLP between wild-type Mycobacterium bovis and the vaccine strain Mycobacterium bovis BCG. To investigate the genetic basis of this phenomenon, DNA fragments from a New Zealand M. bovis cattle strain and M. bovis BCG Pasteur, containing the PAN-binding region, were isolated from gene libraries, sequenced and characterized. Sequence analysis and comparison with database sequences showed that the PAN region in M. bovis, M. bovis BCG and Mycobacterium tuberculosis is identical and shares 70% similarity to the PAN sequence from M. paratuberculosis. The Shine-Dalgarno sequence and the −10 and −35 promoter regions are conserved between the different species. Analysis of the flanking sequences of the PAN region revealed that less than 1 kb downstream of PAN is a 2405 bp fragment that is present in M. bovis BCG but absent in the M. bovis wild-type strain. The distribution of the 2405 bp fragment in members of the M. tuberculosis complex was investigated and found to be present in 70 out of 70 M. tuberculosis strains, and 7 out of 7 M. bovis BCG daughter strains, 2 out of 2 Mycobacterium africanum strains, 2 out of 2 Mycobacterium microti strains and 7 out of 25 M. bovis strains. This is the first report of a genetic region of M. bovis BCG that is not universally present in M. bovis strains. The fragment does not appear to be present in any mycobacterial species outside the M. tuberculosis complex. It does not possess any characteristics of known transposable elements and the flanking sequences do not have any obvious features to suggest a deletion mechanism. The genetic location of this region is close to the 3′ end of the RD1 region of M. bovis and M. tuberculosis. The polymorphic nature of this locus in M. bovis will provide an additional genetic marker for strain differentiation.

The in vitro effect of nitric oxide (NO) and nitrite on blastoconidia and hyphae of Candida albicans was studied. Sodium nitroprusside (SNP) and S-nitroso-N-acetylpenicillamine (SNAP) were used as NO donors. Both minimal and complex media at two pH values, 7·0 and 4·5, were used for the assays. Blastoconidia were more susceptible than hyphae to NO. The NO effect on blastoconidia was greater at acidic pH. Nitrite affected the viability of blastoconidia in complex medium. The percentage germination and the relative rate of elongation of hyphae were both enhanced when NO was present in acidic conditions.