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

Artifacts and unassigned masses encountered in peptide mass mapping

In peptide mass mapping of isolated proteins, a significant number of the observed mass spectral peaks are often uninterpreted. These peaks derive from a number of sources: errors in the genome that give rise to incorrect peptide mass predictions, undocumented post-translational modifications, sample handling-induced modifications, contaminants in the sample, non-standard protein cleavage sites, and non-protein components of the sample. In a study of the stalk organelle of Caulobacter crescentus, roughly one-third (782/2215) of all observed masses could not be assigned to the proteins identified in the gel spots (Karty et al., J. Proteome Res., 1 (2002) 325). By interpreting these masses, this work illuminates a number of phenomena that may arise in the course of peptide mass mapping of electrophoretically separated proteins and presents results from a number of related studies.

A family of six flagellin genes contributes to the Caulobacter crescentus flagellar filament

The Caulobacter crescentus flagellar filament is assembled from multiple flagellin proteins that are encoded by six genes. The amino acid sequences of the FljJ and FljL flagellins are divergent from those of the other four flagellins. Since these flagellins are the first to be assembled in the flagellar filament, one or both might have specialized to facilitate the initiation of filament assembly.

FlbT couples flagellum assembly to gene expression in Caulobacter crescentus

The biogenesis of the polar flagellum of Caulobacter crescentus is regulated by the cell cycle as well as by a trans-acting regulatory hierarchy that functions to couple flagellum assembly to gene expression. The assembly of early flagellar structures (MS ring, switch, and flagellum-specific secretory system) is required for the transcription of class III genes, which encode the remainder of the basal body and the external hook structure. Similarly, the assembly of class III gene-encoded structures is required for the expression of the class IV flagellins, which are incorporated into the flagellar filament. Here, we demonstrate that mutations in flbT, a flagellar gene of unknown function, can restore flagellin protein synthesis and the expression of fljK::lacZ (25-kDa flagellin) protein fusions in class III flagellar mutants. These results suggest that FlbT functions to negatively regulate flagellin expression in the absence of flagellum assembly. Deletion analysis shows that sequences within the 5' untranslated region of the fljK transcript are sufficient for FlbT regulation. To determine the mechanism of FlbT-mediated regulation, we assayed the stability of fljK mRNA. The half-life (t(1/2)) of fljK mRNA in wild-type cells was approximately 11 min and was reduced to less than 1.5 min in a flgE (hook) mutant. A flgE flbT double mutant exhibited an mRNA t(1/2) of greater than 30 min. This suggests that the primary effect of FlbT regulation is an increased turnover of flagellin mRNA. The increased t(1/2) of fljK mRNA in a flbT mutant has consequences for the temporal expression of fljK. In contrast to the case for wild-type cells, fljK::lacZ protein fusions in the mutant are expressed almost continuously throughout the C. crescentus cell cycle, suggesting that coupling of flagellin gene expression to assembly has a critical influence on regulating cell cycle expression.

A new class of Caulobacter crescentus flagellar genes

Eight Caulobacter crescentus flagellar genes, flmA, flmB, flmC, flmD, flmE, flmF, flmG, and flmH, have been cloned and characterized. These eight genes are clustered in pairs (flmAB, flmCD, flmEF, and flmGH) that appear to be structurally organized as operons. Homology comparisons suggest that the proteins encoded by the flm genes may be involved in posttranslational modification of flagellins or proteins that interact with flagellin monomers prior to their assembly into a flagellar filament. Expression of the flmAB, flmEF, and flmGH operons was shown to occur primarily in predivisional cells. In contrast, the flmCD operon was expressed throughout the cell cycle, with only a twofold increase in predivisional cells. The expression of the three temporally regulated operons was subject to positive regulation by the CtrA response regulator protein. Mutations in class II and III flagellar genes had no significant effect on the expression of the flm genes. Furthermore, the flm genes did not affect the expression of class II or class III flagellar genes. However, mutations in the flm genes did result in reduced synthesis of the class IV flagellin proteins. Taken together, these data indicate that the flm operons belong to a new class of flagellar genes.

Ordered expression of ftsQA and ftsZ during the Caulobacter crescentus cell cycle

The mechanisms by which bacterial cell division and DNA replication are co-ordinated are still unknown. We have used the easily synchronizable bacterium Caulobacter crescentus to determine when the cell division genes ftsQ and ftsA are transcribed during the DNA replication cycle and to compare their transcription with that of ftsZ. Unlike the situation in Escherichia coli, transcription of ftsQ and ftsA does not extend into ftsZ in Caulobacter. ftsQ and ftsA are co-transcribed by a strong promoter, P(QA), present within the end of the ddl gene upstream of ftsQ. Transcription of P(QA) is turned on at the end of the DNA replication period, coincident with the end of the ftsZ transcription period. ftsA is also transcribed by another promoter, P(A), present between ftsQ and ftsA. P(A) transcription is approximately 10 times weaker than P(QA) and occurs during the DNA replication period. Transcription of ftsA by P(A) is sufficient for cell viability, but is not sufficient for normal cell division. When the transcription of ftsA is increased constitutively, cell division is inhibited and stalks are synthesized at aberrant positions. Thus, transcription of ftsA and ftsZ mimics their order of action in Caulobacter and proper transcription of ftsA has to be maintained for normal cell division and differentiation.

Approaches to DNA mutagenesis: an overview

In the last several years, the use of double-stranded DNA templates together with thermostable-polymerase PCR has essentially replaced the use single-stranded DNA templates using the thermolabile polymerase for in vitro mutagenesis. Numerous PCR methods are now available, such as overlap-extension PCR, megaprimer PCR, and inverse PCR. All these PCR methods are reliable, effective, and convenient, although they are more prone to high rates of spontaneous error in mutant DNAs than are methods using thermolabile polymerases. Some improvements, such as the introduction of methylated templates, have been employed to minimize PCR errors. On the other hand, because of the introduction of many selection measures (e.g., restoration of antibiotic resistance, restoration of replication origin and unique site elimination), both double-stranded and single-stranded DNAs can now be used as templates for mutagenesis using thermolabile polymerase methods. For PCR methods, selection measures such as nested PCR has developed. All these selection measures have greatly improved the efficiency of mutagenesis by removing wild-type templates prior to transformation. Many efficient methods are available for both SDM and REM. Mutations can be introduce in vitro or in vivo, either by mutagenic primers or by erroneous DNA synthesis. Thus, choices largely depend on the experimental needs and resources of the investigator.

A gene coding for a putative sigma 54 activator is developmentally regulated in Caulobacter crescentus

In Caulobacter crescentus, the alternative sigma factor sigma54 plays an important role in the expression of late flagellar genes. Sigma54-dependent genes are temporally and spatially controlled, being expressed only in the swarmer pole of the predivisional cell. The only sigma54 activator described so far is the FlbD protein, which is involved in activation of the class III and IV flagellar genes and repression of the fliF promoter. To identify new roles for sigma54 in the metabolism and differentiation of C. crescentus, we cloned and characterized a gene encoding a putative sigma54 activator, named tacA. The deduced amino acid sequence from tacA has high similarity to the proteins from the NtrC family of transcriptional activators, including the aspartate residues that are phosphorylated by histidine kinases in other activators. The promoter region of the tacA gene contains a conserved sequence element present in the promoters of class II flagellar genes, and tacA shows a temporal pattern of expression similar to the patterns of these genes. We constructed an insertional mutant that is disrupted in tacA (strain SP2016), and an analysis of this strain showed that it has all polar structures, such as pili, stalk, and flagellum, and displays a motile phenotype, indicating that tacA is not involved in the flagellar biogenesis pathway. However, this strain has a high percentage of filamentous cells and shows a clear-plaque phenotype when infected with phage phiCb5. These results suggest that the TacA protein could mediate the effect of sigma54 on a different pathway in C. crescentus.

Transcriptional and mutational analyses of the rpoN operon in Caulobacter crescentus

The alternative sigma factor sigma54 is required for the biogenesis of both the flagellum and the stalk in Caulobacter crescentus. The DNA sequence downstream of the sigma54 gene (rpoN) has been determined, revealing three open reading frames (ORFs) encoding peptides of 203, 208, and 159 amino acids. ORF208 and ORF159 are homologous to ORFs found downstream of rpoN in other microorganisms. The organization of this region in C. crescentus is similar to that in other bacteria, with the exception of an additional ORF, ORF203, immediately downstream from rpoN. There is a single temporally regulated promoter that drives the expression of both rpoN and ORF203. Promoter probe analysis indicates the presence of another promoter downstream from ORF203 which exhibits a temporal control that is different from that of the rpoN promoter. Mutational analysis was used to address the function of the proteins encoded by these three downstream ORFs. The mutations have no effect on the transcription of previously known sigma54-dependent flagellar promoters except for a slight effect of an ORF159 mutation on transcription of fljK.

Identification, characterization, and chromosomal organization of cell division cycle genes in Caulobacter crescentus

We report a detailed characterization of cell division cycle (cdc) genes in the differentiating gram-negative bacterium Caulobacter crescentus. A large set of temperature-sensitive cdc mutations was isolated after treatment with the chemical mutagen N-methyl-N'-nitro-N-nitrosoguanidine. Analysis of independently isolated mutants at the nonpermissive temperature identified a variety of well-defined terminal phenotypes, including long filamentous cells blocked at various stages of the cell division cycle and two unusual classes of mutants with defects in both cell growth and division. The latter strains are uniformly arrested as either short bagel-shaped coils or large predivisional cells. The polar morphology of these cdc mutants supports the hypothesis that normal cell cycle progression is directly responsible for developmental regulation in C. crescentus. Genetic and physical mapping of the conditional cdc mutations and the previously characterized dna and div mutations identified at least 21 genes that are required for normal cell cycle progression. Although most of these genes are widely scattered, the genetically linked divA, divB, and divE genes were shown by genetic complementation and physical mapping to be organized in one gene cluster at 3200 units on the chromosome. DNA sequence analysis and marker rescue experiments demonstrated that divE is the C. crescentus ftsA homolog and that the ftsZ gene maps immediately adjacent to ftsA. On the basis of these results, we suggest that the C. crescentus divA-divB-divE(ftsA)-ftsZ gene cluster corresponds to the 2-min fts gene cluster of Escherichia coli.

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.

Multiple structural proteins are required for both transcriptional activation and negative autoregulation of Caulobacter crescentus flagellar genes

The periodic and sequential expression of flagellar (fla) genes in the Caulobacter crescentus cell cycle depends on their organization into levels I to IV of a regulatory hierarchy in which genes at the top of the hierarchy are expressed early in the cell cycle and are required for the later expression of genes below them. In these studies, we have examined the regulatory role of level II fliF operon, which is located near the top of the hierarchy. The last gene in the fliF operon, flbD, encodes a transcriptional factor required for activation of sigma 54-dependent promoters at levels III and IV and negative autoregulation of the level II fliF promoter. We have physically mapped the fliF operon, identified four new genes in the transcription unit, and determined that the organization of these genes is 5'-fliF-fliG-flbE-fliN-flbD-3'. Three of the genes encode homologs of the MS ring protein (FliF) and two switch proteins (FliG and FliN) of enteric bacteria, and the fourth encodes a predicted protein (FlbE) without obvious similarities to known bacterial proteins. We have introduced nonpolar mutations in each of the open reading frames and shown that all of the newly identified genes (fliF, fliG, flbE, and fliN) are required in addition to flbD for activation of the sigma 54-dependent flgK and flbG promoters at level III. In contrast, fliF, fliG, and flbE, but not fliN, are required in addition to flbD for negative autoregulation of the level II fliF promoter. The simplest interpretation of these results is that the requirements of FlbD in transcriptional activation and repression are not identical, and we speculate that FlbD function is subject to dual or overlapping controls. We also discuss the requirement of multiple structural genes for regulation of levels II and III genes and suggest that fla gene expression in C. crescentus may be coupled to two checkpoints in flagellum assembly.

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.

The Caulobacter crescentus holdfast: identification of holdfast attachment complex genes

Caulobacters are biofilm bacteria that attach to surfaces via a holdfast, an adhesive expressed at discrete cell surface sites. We have described a cluster of at least three genes involved in the adhesive attachment of the holdfast of Caulobacter crescentus CB2A to the cell, analyzing the sequence of two genes, hfaAB. Here we report hfaC and a fourth open reading frame, hfaD. hfaC predicts a protein of 41 kDa homologous to ATP-binding transport-related proteins, with ChvD of Agrobacterium tumefaciens as best match. HfaD is predicted to be 28 kDa with three membrane spanning regions. hfaA, hfaC, and hfaD were expressed in Escherichia coli; Western analysis with antisera against a holdfast-enriched preparation indicated HfaA was likely holdfast-associated. Cumulative findings predict HfaA and HfaB are developmentally regulated and one or both enhance hfaC transcription, HfaA is a mediator of adhesion, possibly between holdfast and a membrane-bound HfaD, and HfaC mediates export of an unidentified component required for holdfast attachment.

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.

Cell-cycle control of a cloned chromosomal origin of replication from Caulobacter crescentus

Caulobacter crescentus cell division is asymmetric and yields distinct swarmer cell and stalked cell progeny. Only the stalked cell initiates chromosomal replication, and the swarmer cell must differentiate into a stalked cell before chromosomal DNA replication can occur. In an effort to understand this developmental control of replication, we employed pulsed-field gel electrophoresis to localize and to isolate the chromosomal origin of replication. The C. crescentus homologues of several Escherichia coli genes are adjacent to the origin in the physical order hemE, origin, dnaA and dnaK,J. Deletion analysis reveals that the minimal sequence requirement for autonomous replication is greater than 430 base-pairs, but less than 720 base-pairs. A plasmid, whose replication relies only on DNA from the C. crescentus origin of replication, has a distinct temporal pattern of DNA synthesis that resembles that of the bona fide C. crescentus chromosome. This implies that cis-acting replication control elements are closely linked to this origin of replication. This DNA contains sequence motifs that are common to other bacterial origins, such as five DnaA boxes, an E. coli-like 13-mer, and an exceptional A + T-rich region. Point mutations in one of the DnaA boxes abolish replication in C. crescentus. This origin also possesses three additional motifs that are unique to the C. crescentus origin of replication: seven 8-mer (GGCCTTCC) motifs, nine 8-mer (AAGCCCGG) motifs, and five 9-mer (GTTAA-n7-TTAA) motifs are present. The latter two motifs are implicated in essential C. crescentus replication functions, because they are contained within specific deletions that abolish replication.

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.

Early Caulobacter crescentus genes fliL and fliM are required for flagellar gene expression and normal cell division

The biogenesis of the Caulobacter crescentus polar flagellum requires the expression of more than 48 genes, which are organized in a regulatory hierarchy. The flbO locus is near the top of the hierarchy, and consequently strains with mutations in this locus are nonmotile and lack the flagellar basal body complex. In addition to the motility phenotype, mutations in this locus also cause abnormal cell division. Complementing clones restore both motility and normal cell division. Sequence analysis of a complementing subclone revealed that this locus encodes at least two proteins that are homologs of the Salmonella typhimurium and Escherichia coli flagellar proteins FliL and FliM. FliM is thought to be a switch protein and to interface with the flagellum motor. The C. crescentus fliL and fliM genes form an operon that is expressed early in the cell cycle. Tn5 insertions in the fliM gene prevent the transcription of class II and class III flagellar genes, which are lower in the regulatory hierarchy. The start site of the fliLM operon lies 166 bp from the divergently transcribed flaCBD operon that encodes several basal body genes. Sequence comparison of the fliL transcription start site with those of other class I genes, flaS and flaO, revealed a highly conserved 29-bp sequence in a potential promoter region that differs from sigma 70, sigma 54, sigma 32, and sigma 28 promoter sequences, suggesting that at least three class I genes share a unique 5' regulatory region.

The lemA gene required for pathogenicity of Pseudomonas syringae pv. syringae on bean is a member of a family of two-component regulators

The lemA gene of the plant pathogen Pseudomonas syringae pv. syringae is required for disease lesion formation on bean plants. Cosmid clones that complemented a lemA mutant in trans were isolated previously. The lemA gene was localized by subcloning and transposon mutagenesis. The lemA region and flanking DNA were sequenced, and an open reading frame of 2.7 kb was identified. The nucleotide and predicted amino acid sequences of the lemA gene showed sequence similarity to a family of prokaryotic two-component regulatory proteins. Unlike most of the previously described two-component systems, the lemA gene product contained homology to both components in one protein. Mutations introduced upstream and downstream of the lemA gene failed to locate a gene for a second protein component but identified the putative cysM gene of P. syringae pv. syringae. The cysM gene was located upstream of the lemA gene and was divergently transcribed. The lemA gene product was expressed at low levels in P. syringae pv. syringae and appeared to be positively auto-regulated.

Characterization of the Caulobacter crescentus flbF promoter and identification of the inferred FlbF product as a homolog of the LcrD protein from a Yersinia enterocolitica virulence plasmid

We have investigated the organization and expression of the Caulobacter crescentus flbF gene because it occupies a high level in the flagellar gene regulatory hierarchy. The nucleotide sequence comprising the 3' end of the flaO operon and the adjacent flbF promoter and structural gene was determined, and the organization of transcription units within this sequence was investigated. We located the 3' ends of the flaO operon transcript by using a nuclease S1 protection assay, and the 5' end of the flbF transcript was precisely mapped by primer extension analysis. The nucleotide sequence upstream from the 5' end of the flbF transcript contains -10 and -35 elements similar to those found in promoters transcribed by sigma 28 RNA polymerase in other organisms. Mutations that changed nucleotides in the -10 or -35 elements or altered their relative spacing resulted in undetectable levels of flbF transcript, demonstrating that these sequences contain nucleotides essential for promoter function. We identified a 700-codon open reading frame, downstream from the flbF promoter region, that was predicted to be the flbF structural gene. The amino-terminal half of the FlbF amino acid sequence contains eight hydrophobic regions predicted to be membrane-spanning segments, suggesting that the FlbF protein may be an integral membrane protein. The FlbF amino acid sequence is very similar to that of a transcriptional regulatory protein called LcrD that is encoded in the highly conserved low-calcium-response region of virulence plasmid pYVO3 in Yersinia enterocolitica (A.-M. Viitanen, P. Toivanen, and M. Skurnik, J. Bacteriol. 172:3152-3162, 1990).

Analysis of a Caulobacter crescentus gene cluster involved in attachment of the holdfast to the cell

Caulobacter crescentus firmly adheres to surfaces with a structure known as the holdfast, which is located at the flagellar pole of swarmer cells and at the stalk tip in stalked cells. A three-gene cluster (hfaAB and hfaC) is involved in attachment of the holdfast to the cell. Deletion and complementation analysis of the hfaAB locus revealed two genes in a single operon; both were required for holdfast attachment to the cell. Sequence analysis of the hfaAB locus showed two open reading frames with the potential to encode proteins of 15,000 and 26,000 Da, respectively. A protein migrating with an apparent size of 21 kDa in gel electrophoresis was encoded by the hfaA region when expressed in Escherichia coli under the control of the lac promoter, but no protein synthesis could be detected from the hfaB region. S1 nuclease analysis indicated that transcription of the hfaAB locus was initiated from a region containing a sequence nearly identical to the consensus for C. crescentus sigma 54-dependent promoters. In addition, a sequence with some similarity to ftr sequences (a consensus sequence associated with other Caulobacter sigma 54-dependent genes) was identified upstream of the hypothesized sigma 54 promoter. At least one of the hfaAB gene products was required for maximal transcription of hfaC. The sequence of hfaB showed some similarity to that of transcriptional activators of other bacteria. The C-terminal region of the putative gene product HfaA was found to be homologous to PapG and SmfG, which are adhesin molecules of enteropathogenic E. coli and Serratia marcescens, respectively. This information suggests that the protein encoded by the hfaA locus may have a direct role in the attachment of the holdfast to the cell, whereas hfaB may be involved in the positive regulation of hfaC.

The use of a rare codon specifically during development?

A range of circumstantial evidence suggests that in Streptomyces spp., genes required for vegetative growth do not contain the leucine codon TTA. Instead, the codon seems to be confined to a few genes necessary during differentiation, when the colonies begin to produce aerial hyphae and antibiotics. Thus, mutations in bldA, the structural gene for tRNATTALeu, do not retard vegetative growth, but they prevent normal aerial mycelium and antibiotic production. Most of the known TTA-containing genes specify regulatory or resistance proteins associated with antibiotic-production clusters. Possibly the ability to translate the UUA codons in mRNA from such genes is confined to late stages of colony development. Factors that might have contributed to the evolution of this unusual situation are discussed.