Principal sigma subunit of the Caulobacter crescentus RNA polymerase

We have identified the gene encoding the Caulobacter crescentus principal sigma subunit, RpoD. The rpoD gene codes for a polypeptide of 653 amino acids with a predicted molecular mass of 72,623 Da (sigma 73). The C. crescentus sigma subunit has extensive amino acid sequence homology with the principal sigma factors of a number of divergent procaryotes. In particular, the segments designated region 2 that are involved in core polymerase binding and promoter recognition were identical among these bacteria despite the fact that the -10 region recognized by the C. crescentus sigma 73 differs significantly from that of the other bacteria. Thus, it appears that additional sigma factor regions must be involved in -10 region recognition. This conclusion was strengthened by a heterologous complementation assay in which C. crescentus sigma 73 was capable of complementing the Escherichia coli rpoD285 temperature-sensitive mutant. Furthermore, C. crescentus sigma 73 conferred new specificity on the E. coli RNA polymerase, allowing the expression of C. crescentus promoters in E. coli. Thus, the C. crescentus sigma 73 appears to have a broader specificity than does the sigma 70 of the enteric bacteria.

A consensus promoter sequence for Caulobacter crescentus genes involved in biosynthetic and housekeeping functions

Caulobacter crescentus differentiates prior to each cell division to form two different daughter cells: a monoflagellated swarmer cell and a nonmotile stalked cell. Thus, one might expect that developmentally expressed genes would be regulated by mechanisms different from those used to regulate the expression of the biosynthetic genes. To determine a consensus promoter sequence for genes involved in biosynthetic or housekeeping functions, DNA fragments containing the regulatory regions of the ilvD, ilvR, cysC, pleC, and fdxA genes were cloned. S1 nuclease protection mapping and primer extension techniques were used to identify the transcription initiation sites. Comparison of the regulatory regions of these genes with those of the published sequences of the ilvBN, rrnA, trpFBA, dnaA, dnaK, hemE, and rsaA genes has resulted in the identification of a putative promoter consensus sequence. The -35 region contains the sequence TTGACGS, which is similar to the Escherichia coli -35 region, while the -10 region, GCTANAWC, has a more balanced GC content than the corresponding region in E. coli. Oligonucleotide-directed site-specific mutagenesis of both the ilvBN and pleC promoters indicates that mutations that make a promoter more like the consensus result in increased promoter activity, while mutations decreasing similarity to the consensus result in decreased promoter activity.

A ferredoxin, designated FdxP, stimulates p-hydroxybenzoate hydroxylase activity in Caulobacter crescentus

A gene, fdxP, was identified upstream of the rrnA gene in Caulobacter crescentus and shown to encode ferredoxin II (FdII) by insertional inactivation. FdII is homologous to a class of [2Fe-2S] ferredoxins typified by putidaredoxin. Furthermore, reconstitution assays demonstrated that FdII was able to promote p-hydroxybenzoate hydroxylase activity in ferredoxin-depleted extracts. Thus, biodegradation of p-hydroxybenzoate may be ferredoxin dependent in C. crescentus.

Synthesis of the Caulobacter ferredoxin protein, FdxA, is cell cycle controlled

The fdxA gene was identified upstream of and in the opposite direction from the Caulobacter crescentus cysC gene. Analyses of the nucleotide sequence and the deduced amino acid sequence of the fdxA gene demonstrated that it encodes a ferredoxin with a molecular mass of 12,080 Da. This ferredoxin has common structural features with ferredoxins that contain a [3Fe-4S] and a [4Fe-4S] cluster, including seven conserved cysteines responsible for the binding of the two clusters. A mutation in the fdxA gene was obtained, and the resulting strain did not produce one of the two ferredoxins (FdI) found in C. crescentus. Further experiments demonstrated that the fdxA gene is temporally expressed in C. crescentus and that FdI is required for completion of the cell cycle at 37 degrees C.

Regulation of Caulobacter crescentus ilvBN gene expression

As part of an effort to determine the mechanisms employed by Caulobacter crescentus to regulate gene expression, the ilvBN genes encoding the two subunits of an acetohydroxy acid synthase (AHAS) have been characterized. Analysis of the DNA sequences indicated that the C. crescentus AHAS was highly homologous to AHAS isozymes from other organisms. S1 nuclease and primer extension studies demonstrated that transcription initiation occurred 172 bp upstream of the AHAS coding region. The region between the AHAS coding region and the transcription initiation site was shown to have the properties of a transcription attenuator. Deletion analysis of the region containing the stem-loop structure of the proposed attenuator resulted in the derepression of ilvBN expression. Thus, it appears that C. crescentus uses attenuation to regulate the expression of the ilvBN operon.

Identification and characterization of the ilvR gene encoding a LysR-type regulator of Caulobacter crescentus

The ilvR gene was located upstream of and transcribed divergently from the ilvD gene of Caulobacter crescentus. DNA nucleotide analysis determined that the ilvR and ilvD translation initiation codons are 98 bp apart. The promoter activity of the DNA region containing the divergent promoters was analyzed by using transcriptional fusions to promoterless reporter genes and immunoblot assays. The results indicate that the ilvR gene product positively regulates the expression of the ilvD gene while negatively autoregulating its own expression. The ilvR gene codes for a protein of 296 amino acid residues (M(r), 37,212). The N-terminal amino acid sequence of the IlvR protein contains a helix-turn-helix motif, suggesting that it is involved in protein-DNA interactions. Protein extracts from both wild-type and merodiploid strains showed specific DNA binding to a 227-bp DNA fragment spanning the ilvD-ilvR promoter region, while no protein-DNA complexes were observed in cell extracts from an ilvR mutant strain. Amino acid sequence comparison revealed that the IlvR protein is a member of the LysR family of transcriptional regulators.

Identification of genes affecting production of the adhesive holdfast of a marine caulobacter

Caulobacters are stalked bacteria that produce a structure termed a holdfast which enables firm attachment to surfaces. Tn5 insertion mutagenesis was used to identify genes affecting holdfast production or function in the marine strain MCS6. Twelve thousand Tn5 insertion mutants were screened for adhesion defects by an assay involving the attachment of cells to polystyrene microtiter dish wells. Among adhesion-defective mutants, those with multiple polar (pleiotropic) defects were excluded and the remainder were examined for the presence of holdfast. Forty-one mutants that produced no detectable holdfast or a significantly reduced amount were found. Southern blot and pulsed-field gel electrophoresis analyses indicated that 11 unique Tn5 insertions were clustered in three regions of the genome. In addition, 71 mutants that adhered poorly or not at all to polystyrene, yet still produced a holdfast, were found. Southern blot and pulsed-field gel electrophoresis analyses of 15 of these mutants showed eight unique Tn5 insertion sites clustered in two additional regions of the genome. An assay involving attachment to glass treated with siloxane chemicals (producing surfaces with varying degrees of hydrophobicity or hydrophilicity) was used to attempt characterization of this phenotype. Unexpectedly, no simple pattern of differences in binding between the mutants and wild-type caulobacters was found. In particular, no reduction in the ability of the mutants to bind to hydrophobic surfaces was noted. Complementation with cosmid clones was successful in nearly all cases and confirmed the designation of five genomic regions of holdfast-related genes. No detectable cross-hybridization was observed with several holdfast-related gene regions from a freshwater caulobacter, providing further evidence that the marine and freshwater caulobacters are genetically distinct.

Molecular characterization, nucleotide sequence, and expression of the fliO, fliP, fliQ, and fliR genes of Escherichia coli

The fliL operon of Escherichia coli contains seven genes that are involved in the biosynthesis and functioning of the flagellar organelle. DNA sequences for the first three genes of this operon have been reported previously. A 2.2-kb PstI restriction fragment was shown to complement known mutant alleles of the fliO, fliP, fliQ, and fliR genes, the four remaining genes of the fliL operon. Four open reading frames were identified by DNA sequence analysis and correlated to their corresponding genes by complementation analysis. These genes were found to encode very hydrophobic polypeptides with molecular masses of 11.1, 26.9, 9.6, and 28.5 kDa for FliO, FliP, FliQ, and FliR, respectively. Analysis of recombinant plasmids in a T7 promoter-polymerase expression system enabled us to identify three of the four gene products. On the basis of DNA sequence analysis and in vivo protein expression, it appears that the fliP gene product is synthesized as a precursor protein with an N-terminal signal peptide of 21 amino acids. The FliP protein was homologous to proteins encoded by a DNA sequence upstream of the flaA gene of Rhizobium meliloti, to a gene involved in pathogenicity in Xanthomonas campestris pv. glycines, and to the spa24 gene of the Shigella flexneri. The latter two genes encode proteins that appear to be involved in protein translocation, suggesting that the FliP protein may have a similar function.

A histidine protein kinase is involved in polar organelle development in Caulobacter crescentus

Mutations having pleiotropic effects on polar organelle development (pod) in Caulobacter crescentus have been identified and shown to occur in at least 13 genes scattered throughout the genome. Mutations at each locus affect a unique combination of polar traits, suggesting that complex interactions occur among these genes. The DNA sequence of one of these genes, pleC, indicates that it is homologous to members of the family of histidine protein kinase genes. Membes of this family include the senor components of the bacterial two-component regulatory systems. Furthermore, in vitro experiments demonstrated that the PleC protein was capable of autophosphorylation. These results suggest that the PleC protein (and perhaps the proteins encoded by the other pod genes as well) regulates the expression of genes involved in polar organelle development through the phosphorylation of key regulatory proteins. The use of a phosphorelay system cued to internal changes in the cell would provide a mechanism for coordinating major changes in gene expression with the completion of specific cell cycle events.

The Caulobacter crescentus flaFG region regulates synthesis and assembly of flagellin proteins encoded by two genetically unlinked gene clusters

At a specific time in the Caulobacter crescentus cell cycle, a single flagellar filament and multiple receptor sites for the swarmer-specific phage phi Cbk are assembled at one pole of the predivisional cell. One cluster of genes required for this morphogenesis, the flaYG region, includes the flgJKL genes, which encode structural proteins of the flagellar filament. These flagellin genes are flanked by genes required for filament assembly, the flaYE genes at one end and the flaF-flbT-flbA-flaG genes at the other. In this study, we characterized mutants carrying large chromosomal deletions within this region. Several of these strains are phi CbK resistant and produce a novel 22-kDa flagellin that is not assembled into flagella. Merodiploid strains containing either the entire flaFG region or individual fla transcription units from this region were constructed. These strains were used to correlate the presence or absence of specific gene products to changes in flagellin synthesis, filament assembly, or phage sensitivity. As a result of these studies, we were able to conclude that (i) the production of the 22-kDa flagellin results from the absence of the flbA and flaG gene products, which appear to be components of a flagellin-processing pathway common to the 25-, 27-, and 29-kDa flagellins; (ii) flbT negatively modulates the synthesis of the 27- and 25-kDa flagellins from two genetically unlinked gene clusters; (iii) flgL is the only flagellin gene able to encode the 27-kDa flagellin, and this flagellin appears to be required for the efficient assembly of the 25-kDa flagellins; (iv) flaF is required for filament assembly; and (v) phi CbK resistance results from the deletion of at least two genes in the flaFG region.

Molecular genetics of the flgI region and its role in flagellum biosynthesis in Caulobacter crescentus

The differentiating bacterium Caulobacter crescentus has been studied extensively to understand how a relatively simple life form can govern the timing of expression of genes needed for the production of stage-specific structures. In this study, a clone containing the 5.3-kb flaP region was shown to contain the flgI, cheL, and flbY genes arranged in an operon with transcription proceeding from flgI to flbY. The predicted flgI polypeptide shows remarkable identity (44%) to the flagellar basal body P-ring protein encoded by the flgI gene of Salmonella typhimurium. flgI mutations case a reduction in the levels of flagellin production and the overproduction of the hook proteins. Therefore, the flgI-encoded P-ring protein is required for normal flagellin and hook protein synthesis, suggesting that basal body assembly may play a role in the regulation of flagellar gene expression. The flbY gene probably is a basal body component as well, since flbY mutants have flagellin and hook protein synthesis patterns similar to those exhibited by other basal body mutants. The smaller cheL gene complements a mutant that is unable to respond to chemotactic signals despite possessing a functional flagellum. This is the first example of an operon containing both flagellar and chemotaxis genes in C. crescentus.

DNA sequence of the 3' end of the Caulobacter crescentus 16S rRNA gene

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Introduction of intersubunit disulfide bonds in the membrane-distal region of the influenza hemagglutinin abolishes membrane fusion activity

Influenza virus hemagglutinin (HA) mediates viral entry into cells by a low pH-induced membrane fusion event in endosomes. A number of structural changes occur throughout the length of HA at the pH of fusion. To probe their significance and their necessity for fusion activity, we have prepared a site-directed mutant HA containing novel intersubunit disulfide bonds designed to cross-link covalently the membrane-distal domains of the trimer. These mutations inhibited the low pH-induced conformational changes and prevented HA-mediated membrane fusion; conditions that reduced the novel disulfide bonds restored membrane fusion activity. We conclude that structural rearrangements in the membrane distal region of the HA are required for membrane fusion activity.

Mutated interleukin-5 monomers are biologically inactive

Interleukin-5 contains only two cysteine residues both of which appear to be involved in the dimerisation of the molecule to form a disulphide-linked homodimer (Minamitake et al., J. Biochem. 107, 292-297, 1990). However, it remains unclear whether this linkage is necessary for the bioactivity of this cytokine. Site-directed mutagenesis was used to produce amino acid substitutions of either or both of the cysteines. The mutant proteins were all biologically inactive monomers, however when the two single mutant constructs were co-transfected, biologically active IL5 was produced. This is consistent with the dimer forming in a head-to-tail configuration.

Nucleotide sequence of the Caulobacter crescentus flaF and flbT genes and an analysis of codon usage in organisms with G + C-rich genomes

The Caulobacter crescentus flaFG region encodes trans-acting, regulatory factors that modulate flagellin synthesis during flagellum biogenesis. In this study, sequence analysis and experiments utilizing a promoterless cat gene demonstrated that the flaF and flbT genes have overlapping transcripts with the same orientation. In addition, the 5' ends of the flgL and flbA genes were located. A sequence resembling an Rho-factor-independent terminator was found in the 3' region of the flaF gene. This region was uniquely A + T-rich and the encoded mRNA contained an inverted repeat sequence which could form a stable stem-loop structure followed by nine U-residues. The codon usage of C. crescentus genes was examined and indicated a preference for specific codons from each of the synonymous codon groups. Furthermore, comparison to the codon usage of other organisms with G + C-rich genomes indicated a strong preference for the same codons preferred by C. crescentus.

Copper-zinc superoxide dismutase of Caulobacter crescentus: cloning, sequencing, and mapping of the gene and periplasmic location of the enzyme

Although widely found in the cytoplasm of eucaryotes, the copper-zinc form of superoxide dismutase (CuZnSOD) has been identified in only a small number of bacterial species. One species is the freshwater bacterium Caulobacter crescentus, which also contains an SOD with iron as the metal cofactor (FeSOD). To investigate the function of this CuZnSOD and its structural relationship to the eucaryotic CuZnSODs, the gene encoding CuZnSOD (sodC) of C. crescentus CB15 was cloned and sequenced. By hybridization to pulsed-field electrophoresis gels, sodC was mapped near cysE in the C. crescentus chromosome. Through analysis of spheroplasts, the two SODs of C. crescentus were shown to be differently localized, CuZnSOD in the periplasm and FeSOD in the cytoplasm. In its natural habitat, C. crescentus is frequently associated with blue-green algae (cyanobacteria). The oxygen evolved by these photosynthetic algae may create an extracellular oxidative stress against which the periplasmic CuZnSOD may defend more effectively than the cytoplasmic FeSOD. Amino acid sequence alignments of C. crescentus CuZnSOD with eucaryotic CuZnSODs and with CuZnSOD of Photobacterium leiognathi (the only other bacterium from which CuZnSOD has been isolated and sequenced) suggest similar supersecondary structures for bacterial and eucaryotic CuZnSODs but reveal four novel substitutions in C. crescentus CuZnSOD: a phenylalanine critical to intrasubunit hydrophobic bonding replaced by alanine, a histidine ligand of zinc replaced by aspartate, and substitutions of two other previously invariant residues that stabilize zinc or both copper and zinc. These amino acid substitutions in C. crescentus CuZnSOD may have implications for its catalysis and stability.

A Caulobacter gene involved in polar morphogenesis

At specific times in the cell cycle, the bacterium Caulobacter crescentus assembles two major polar organelles, the flagellum and the stalk. Previous studies have shown that flbT mutants overproduce flagellins and are unable to form chemotaxis swarm rings. In this paper, we report alterations in both the stalk and the flagellar structure that result from a mutation in the flagellar gene flbT. Mutant strains produce some stalks that have a flagellum, produce some stalks that have an extra lobe protruding from their sides, have filaments lacking the 29-kilodalton flagellin, and produce several unusual cell types, including filamentous cells as well as predivisional cells with two stalks and predivisional cells with no stalk at all. We propose that flagellated stalks arise as a consequence of a failure to eject the flagellum at the correct time in the cell cycle and that the extra stalk lobe is due to a second site for the initiation of stalk biogenesis. Thus, a step in the pathway that establishes the characteristic asymmetry of the C. crescentus cell appears to be disrupted in flbT mutants. We have also identified a new structural feature at the flagellated pole and the tip of the stalk: the 10-nm polar particle. The polar particles appear as a cluster of approximately 1 to 10 stain-excluding rings, visible in electron micrographs of negatively stained wild-type cells. This structure is absent at the flagellar pole but not in the stalks of flbT mutant predivisional cells.

Circularity of the Caulobacter crescentus chromosome determined by pulsed-field gel electrophoresis

Previous genetic analyses of the Caulobacter crescentus chromosome have resulted in the construction of a linear genetic map. To establish the circularity of the C. crescentus chromosome, restriction fragments generated by digestion with AseI and SpeI were analyzed by pulsed-field gel electrophoresis and Southern hybridization. The size of each fragment was calculated and used to demonstrate that C. crescentus has a genome size of approximately 4,000 kilobases. In addition, both enzymes gave rise to large DNA fragments which contained genes from both ends of the genetic map. Thus, there is physical linkage between the genes at the ends of the genetic map and the chromosome is circular. Since this region of the chromosome appears to contain the replication terminus, we propose that recombination occurs at a high frequency in the vicinity of the terminus. This high frequency of recombination would prevent genetic linkage from being observed between genes on opposite sides of the terminus. Additional experiments using insertions which introduced new AseI and DraI restriction sites into the genome allowed us to calculate the physical distance between genes located in the vicinity of the replication terminus.

Identification, distribution, and sequence analysis of new insertion elements in Caulobacter crescentus

We describe two insertion elements isolated from Caulobacter crescentus that are designated IS298 and IS511. These insertion elements were cloned from spontaneous flagellar (fla) gene mutants SC298 and SC511 derived from the wild-type strain CB15 (ATCC 19089), in which they were originally identified as insertions in the flbG operon of the hook gene cluster (N. Ohta, E. Swanson, B. Ely, and A. Newton, J. Bacteriol. 158:897-904, 1984). IS298 and IS511 were each present in C. crescentus CB2 and CB15 in at least four different positions, but neither was present in strain CB13 or in several Caulobacter species examined, including C. vibrioides, C. leidyia, and C. henricii. Nucleotide sequence analysis across the chromosome-insertion element junctions showed that IS298 is located 152 base pairs (bp) upstream from the ATG translation start of the hook protein gene flaK, where it is bounded by a 4-bp direct repeat derived from the site of insertion, and that IS511 is inserted at codon 186 of the flaK coding sequence, where it is also bounded by a 4-bp direct repeat duplicated from the site of insertion. The ilvB102 mutation in strain SC125 was also shown to result from insertion sequence IS511, but no duplication of the genomic sequence was present at the insertion element junctions. IS298 contains an imperfect terminal inverted repeat 16 bp long, and IS511 contains a 32-bp inverted repeat at the termini. IS298 and IS511 are the first insertion elements described in C. crescentus.

Use of pulsed field gel electrophoresis and transposon mutagenesis to estimate the minimal number of genes required for motility in Caulobacter crescentus

To facilitate the mapping of transposon insertion mutations in Caulobacter crescentus, we have used pulsed field gel electrophoresis to construct a detailed physical and genetic map of the C. crescentus genome. Restriction fragments were generated by DraI, AseI, or SpeI which cleave the C. crescentus 40, 13, and 26 times, respectively, and Tn5 insertions were used to align the restriction fragments generated by each of the enzymes. The utility of the resulting map was demonstrated by determining the chromosomal locations of a collection of flagellar mutations. As a result of this study, we were able to identify ten new flagellar genes at various locations on the chromosome. Thus, at least 48 genes are required for the assembly of a functional flagellum in C. crescentus.

Medical and dental staffing prospects in the NHS in England and Wales in 1988

The Medical Manpower and Education Division of the Department of Health publishes information in this journal each year on the current state of medical and dental manpower in England and Wales, to assist medical and dental students and newly-qualified doctors and dentists in their career choices. Additional information can be obtained from the national and regional census tables which are usually published by the Department of Health each spring. These are circulated widely to all health authorities, postgraduate deans and clinical tutors.

Organization of the flaFG gene cluster and identification of two additional genes involved in flagellum biogenesis in Caulobacter crescentus

In Caulobacter crescentus, mutations have been isolated in more than 30 flagellar genes (fla, flb, and flg) which are required in the cell cycle event of flagellum biogenesis. The flaF and flaG mutations and two newly identified mutations, flbT and flbA (P.V. Schoenlein and B. Ely, J. Bacteriol. 171:000-000, 1989), have been localized to the flaFG region. In this study, the genetic and physical organization of this region was analyzed, using the cloned 4.0-kilobase flaFG region in the recombinant plasmid pPLG727. Plasmid pPLG727 complemented flaF, flaG, flbA, and flbT mutations. Further complementation studies with pPLG727 derivatives indicated that flaF and flbT are unique but overlapping transcription units, whereas flbA and flaG constitute a single transcription unit. To determine the direction of transcription of the putative flbA-flaG operon, the promoterless chloramphenicol transacetylase gene was inserted into various positions in the flbA-flaG region, and merodiploid strains containing these transcriptional fusions were assayed for gene function and expression of chloramphenicol resistance. These studies showed that transcription proceeds from flbA to flaG. To confirm the complementation analysis, Southern analyses were performed on chromosomal DNAs isolated from strains containing insertion and deletion mutations. Taken together, these studies defined the relative gene order at one end of the flaYG flagellar gene cluser as flgL-flaF-flbT-flbA-flaG.