Influence of disruption of the recA gene on genetic instability and genome rearrangement in Streptomyces lividans

Role of an FtsK-like protein in genetic stability in Streptomyces coelicolor A3(2)

Streptomyces coelicolor A3(2) does not have a canonical cell division cycle during most of its complex life cycle, yet it contains a gene (ftsK(SC)) encoding a protein similar to FtsK, which couples the completion of cell division and chromosome segregation in unicellular bacteria such as Escherichia coli. Here, we show that various constructed ftsK(SC) mutants all grew apparently normally and sporulated but upon restreaking gave rise to many aberrant colonies and to high frequencies of chloramphenicol-sensitive mutants, a phenotype previously associated with large terminal deletions from the linear chromosome. Indeed, most of the aberrant colonies had lost large fragments near one or both chromosomal termini, as if chromosome ends had failed to reach their prespore destination before the closure of sporulation septa. A constructed FtsK(SC)-enhanced green fluorescent protein fusion protein was particularly abundant in aerial hyphae, forming distinctive complexes before localizing to each sporulation septum, suggesting a role for FtsK(SC) in chromosome segregation during sporulation. Use of a fluorescent reporter showed that when ftsK(SC) was deleted, several spore compartments in most spore chains failed to express the late-sporulation-specific sigma factor gene sigF, even though they contained chromosomal DNA. This suggested that sigF expression is autonomously activated in each spore compartment in response to completion of chromosome transfer, which would be a previously unknown checkpoint for late-sporulation-specific gene expression. These results provide new insight into the genetic instability prevalent among streptomycetes, including those used in the industrial production of antibiotics.

Chromosomal arm replacement in Streptomyces griseus

UV irradiation of Streptomyces griseus 2247 yielded a new chromosomal deletion mutant, MM9. Restriction and sequencing analysis revealed that homologous recombination between two similar lipoprotein-like open reading frames, which are located 450 and 250 kb from the left and right ends, respectively, caused chromosomal arm replacement. As a result, new 450-kb terminal inverted repeats (TIRs) were formed in place of the original 24-kb TIRs. Frequent homologous recombinations in Streptomyces strains suggest that telomere deletions can usually be repaired by recombinational DNA repair functioning between the intact and deleted TIR sequences on the same chromosome.

Once the circle has been broken: dynamics and evolution of Streptomyces chromosomes

Chromosomal instability has been a hallmark of Streptomyces genetics. Deletions and circularization often occur in the less-conserved terminal sequences of the linear chromosomes, which contain swarms of transposable elements and other horizontally transferred elements. Intermolecular recombination involving these regions also generates gross exchanges, resulting in terminal inverted repeats of heterogeneous size and context. The structural instability is evidently related to evolution of the Streptomyces chromosomes, which is postulated to involve linearization of hypothetical circular progenitors via integration of a linear plasmid. This scenario is supported by several bioinformatic analyses.

Transcriptional analysis of the recA gene in Streptomyces rimosus: identification of the new type of promoter

Using primer-extension analysis we identified two transcription start sites for the recA gene in Streptomyces rimosus. A longer, weak transcript is initiated from the distal SEP promoter that contains a Cheo box like sequence: GAAC-N4-ATTC. However, the major start site of transcription is a G at position -36 and this shorter transcript significantly increases in response to DNA damage by UV-light. The -35 box (TTGTCA) and -10 box (TAGCGT) of the strong recA promoter are only 11 bp apart and this proximal promoter is almost identical to the strong, DNA damage-inducible promoter of Mycobacterium tuberculosis recA gene. We inspected the Streptomyces coelicolor database and found this type of promoter in the upstream regions of many (potentially) UV-inducible genes as well as some other genes/ORFs. Moreover, the DNA sequence between the predicted -35 and -10 boxes is also partially conserved. The consensus sequence for this new type of promoter in Streptomyces is: TTGTCAGTGGC-N6-TAGggT.

Evidence that an additional mutation is required to tolerate insertional inactivation of the Streptomyces lividans recA gene

In contrast to recA of other bacteria, the recA gene of Streptomyces lividans has been described as indispensable for viability (G. Muth, D. Frese, A. Kleber, and W. Wohlleben, Mol. Gen. Genet. 255:420-428, 1997.). Therefore, a closer analysis of this gene was performed to detect possible unique features distinguishing the Streptomyces RecA protein from the well-characterized Escherichia coli RecA protein. The S. lividans recA gene restored UV resistance and recombination activity of an E. coli recA mutant. Also, transcriptional regulation was similar to that of E. coli recA. Gel retardation experiments showed that S. lividans recA is also under control of the Streptomyces SOS repressor LexA. The S. lividans recA gene could be replaced only by simultaneously expressing a plasmid encoded recA copy. Surprisingly, the recA expression plasmid could subsequently be eliminated using an incompatible plasmid without the loss of viability. Besides being UV sensitive and recombination deficient, all the mutants were blocked in sporulation. Genetic complementation restored UV resistance and recombination activity but did not affect the sporulation defect. This indicated that all the recA mutants had suffered from an additional mutation, which might allow toleration of a recA deficiency.

Transcriptional and mutational analyses of the Streptomyces lividans recX gene and its interference with RecA activity

The role of the 20,922-Da RecX protein and its interference with RecA activity were analyzed in Streptomyces lividans. The recX gene is located 220 bp downstream of recA. Transcriptional analysis by reverse transcriptase PCR demonstrated that recX and recA constitute an operon. While recA was transcribed at a basal level even under noninducing conditions, a recA-recX cotranscript was only detectable after induction of recA following DNA damage. The recA-recX cotranscript was less abundant than the recA transcript alone. The recX gene was inactivated by gene replacement. The resulting mutant had a clearly diminished colony size, but was not impaired in recombination activity, genetic instability, and resistance against UV irradiation. Expression of an extra copy of the S. lividans recA gene under control of the thiostrepton-inducible tipA promoter was lethal to the recX mutant, demonstrating that RecX is required to overcome the toxic effects of recA overexpression. Since inactivation of the recX gene did not influence transcription of recA, the putative function of the RecX protein might be the downregulation of RecA activity by interaction with the RecA protein or filament.

A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution

Bacterial circular chromosomes have sporadically become linearised during prokaryote evolution. Unrelated bacteria, including the spirochete Borrelia burgdorferi and the actinomycete Streptomyces, have linear chromosomes. Linear chromosomes may have been formed through integration of linear plasmids. Linear chromosomes use linear plasmid strategies to resolve the 'end-of-replication problem', but they have generally retained from their circular ancestors a central origin of replication. Streptomyces linear chromosomes are very unstable and at high frequency undergo amplifications and large deletions, often removing the telomeres. At least in Streptomyces, chromosome linearity is reversible: circular chromosomes arise spontaneously as products of genetic instability or can be generated artificially by targeted recombination. Streptomyces circularised chromosomes are very unstable as well, indicating that genetic instability is not confined to the linearised chromosomes. Bacterial linear chromosomes may contain telomere-linked regions of enhanced genomic plasticity, which undergo more frequent genetic exchanges and rearrangements and allow differential evolution of genes, depending on their chromosomal location.

DNA rearrangements at the extremities of the Streptomyces ambofaciens linear chromosome: evidence for developmental control

In Streptomyces, a genomic instability results from frequent recombination events which occur at the ends of the linear chromosomal DNA. These events are believed to be responsible for the variability observed in these regions among Streptomyces species and strains. In order to identify functions able to control this type of genome plasticity, mutators as well as mutants produced at different stages of development have been characterized in S. ambofaciens. Their characterization suggests the existence of a relationship between genomic instability and colony development.

Evolution of the linear chromosomal DNA in Streptomyces: is genomic variability developmentally modulated?

Genome rearrangements are responsible for the variability observed at the ends of the chromosome among Streptomyces species. The characterization of mutators, which are stimulated for genome plasticity, and of mutants produced at different stages of development support the idea that genome instability is developmentally modulated.

Genetic instability of the Streptomyces chromosome

The Streptomyces wild-type chromosome is linear in all examples studied. The ends of the chromosome or telomeres consist of terminal inverted repeats of various sizes with proteins covalently bound to their 5' ends. The chromosome is very unstable and undergoes very large deletions spontaneously at rates higher than 0.1% of spores. Frequently, the telomeres are included in the deletions. Loss of both telomeres leads to circularization of the chromosome. The wild-type chromosome can also be circularized artificially by targeted recombination. Spontaneously or artificially circularized chromosomes are even more unstable than the linear ones. High-copy-number tandem amplifications of specific chromosomal regions are frequently associated with the deletions. RecA seems to be involved in the amplification mechanism and control of genetic instability.

High-frequency transposition of IS1373, the insertion sequence delimiting the amplifiable element AUD2 of Streptomyces lividans

IS1373 is the putative insertion sequence delimiting the amplifiable unit AUD2 of Streptomyces lividans. Two IS1373-derived thiostrepton-resistant transposons, Tn5492 and Tn5494, transposed into multiple sites of the S. lividans chromosome at frequencies as high as 0.4 and 1%, respectively. Hence, IS1373 is a functional insertion sequence and its unique open reading frame, insA, encodes the transposase.