Conserved gene arrangement in the origin region of the Streptomyces coelicolor chromosome

Abstract

A 23-kb fragment of the Streptomyces coelicolor chromosome spanning the dnaA region has been isolated as a cosmid clone. Nucleotide sequence analysis of a 5-kb portion shows that the genes for the RNase P protein (rnpA), ribosomal protein L34 (rpmH), the replication initiator protein (dnaA4), and the beta subunit of DNA polymerase III (dnaN) are present in the highly conserved gene arrangement found in all eubacterial genomes studied so far. The dnaA-dnaN intergenic region is approximately 1 kb and contains a cluster of at least 12 DnaA boxes with a consensus sequence of TTGTCCACA matching the consensus DnaA box in the phylogenetically related Micrococcus luteus. Two DnaA boxes precede the dnaA sequence. We propose that the chromosomal origin (oriC) of S. coelicolor lies between dnaA and dnaN. In related work, J. ZakrzewskaCzerwinska and H. Schrempf (J. Bacteriol. 174:2688Bacteriol. 174: -2693Bacteriol. 174: , 1992 have identified the homologous sequence from the closely-related Streptomyces lividans as capable of self-replication.The genus Streptomyces represents a group of grampositive soil bacteria containing DNA with a high (approximately 73%) G+C content (1). The remarkable features of this group include the ability to elaborate a vast array of structurally diverse secondary metabolites and to undergo a complex cycle of mycelial growth and sporulation (for reviews, see references 4, 5, and 15). In recent years, considerable progress has been made in identifying genes involved in primary metabolism, antibiotic production, morphological differentiation, and the regulation of these processes. In contrast, some of the fundamental aspects of the flow of genetic information have not been addressed at a molecular level. This is especially true of DNA replication in these organisms. Little is known about the cellular machinery and regulatory events that are required to initiate and complete the synthesis of plasmid molecules, bacteriophage genomes, or the chromosome.It is known that in Streptomyces coelicolor, the most genetically characterized member of the genus, all of the essential genetic information is present on a single circular chromosome of approximately 8 Mb (13). Since, in other bacteria, chromosome replication begins at a unique sequence (the origin, oriC; see reference 28 for a review) and it is this site that may be a target for regulatory proteins (12), we decided to clone the oriC homolog from S. coelicolor. To do this, we took advantage of the striking conservation of gene arrangement that was apparent when the oriC regions of Pseudomonas putida, Bacillus subtilis, and Micrococcus luteus were compared (7,21). Thus, the genes for ribosomal protein L34 (rpmH), the protein subunit of RNase P (mpA), the replication initiator protein (dnaA), and the beta subunit of DNA polymerase III (dnaN) were present in the same order and relative orientation in each genome, and oriC was adjacent to dnaA. Since, in a previous study, we had isolated the rpmH-rnpA gene cluster from a streptomycete (19), this was used ...

A combined genetic and physical map of the Streptomyces coelicolor A3(2) chromosome

“…(iii) Two promoters (PTH4 and PTH270) that appear to depend on the sigma factor encoded by the whiG gene (87) were shown to map to two well-separated positions on the chromosome, rather than being part of a cluster. (iv) A cloned fragment isolated on the basis of its hybridization to dnaA of Pseudomonas putida and therefore likely to lie near a chromosomal origin of replication (30) was mapped to a position (on AseI fragment H) at about 8 o'clock; the conclusion that this DNA includes an origin of replication of the S. coelicolor chromosome is established by the recent work of Calcutt and Schmidt (14) and Zakrzewska-Czerwinska and Schrempf (92). (v) The afsR gene (46) was originally cloned by its ability to stimulate antibiotic production in S. lividans and was then found to complement an afsB mutation, which had been mapped genetically close to cysD (33).…”

Forty years of genetics with Streptomyces: from in vivo through in vitro to in silico

“…The discovery has helped to change our ideas about bacterial chromosomes. It was also linked to elegant experiments on linear plasmids which proposed a model for Streptomyces chromosome replication in which conventional bidirectional replication takes place from a typical, centrally located oriC (Calcutt & Schmidt, 1992 ;Zakrzewska-Czerwinska & Schrempf, 1992), followed by ' patching ' replication primed by proteins attached covalently to the free 5h ends of the chromosome to fill the gap left by removal of the RNA primer for the last Okazaki fragment on each discontinuous strand (Chang & Cohen, 1994).…”

Interactions of DnaA Proteins from Distantly Related Bacteria with the Replication Origin of the Broad Host Range Plasmid RK2

“…The S. lividans dnaA gene has not been sequenced, but the dnaA gene from Streptomyces coelicolor, which is closely related to S. lividans, has been sequenced (29), and was used for the purpose of sequence alignment. The dnaA gene of P. aeruginosa has not been published, but BLASTN searches against the unfinished P. aeruginosa genome project resulted in a match to a DNA stretch (within contig 54) with 85% identity to the P. putida dnaA gene.…”