Institute of Genetics, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan1
Author for correspondence: Carton W. Chen. Tel: +886 2 2826 7040. Fax: +886 2 2826 4930. e-mail: cwchen{at}ym.edu.tw
![]() |
ABSTRACT |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Keywords: Streptomyces, conjugation, recombination, genetic map, plasmid
Abbreviations: TP, terminal protein
a Present address: Department of Family Medicine, Taipei Veterans General Hospital, Shih-Pai, Taipei, Taiwan.
b Present address: Food Industrial Research Institute, Hsin-Chu, Taiwan.
![]() |
INTRODUCTION |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
The circularity of the genetic maps was first established in Streptomyces coelicolor A3(2) through extensive conjugation analysis (Hopwood, 1965 , 1966
). Subsequently, it was extended to other species (e.g. Friend & Hopwood 1971
) and to protoplast fusion analysis. All the linkage analyses in different Streptomyces species have been consistent with the circularity of genetic maps, without exceptions.
In his papers, Hopwood made these discerning remarks: ...while the linkage map of S. coelicolor is circular, it appears at present to be impossible to decide by this kind of formal analysis whether the chromosome is circular or linear (Hopwood, 1965 ), and ...whether, like that of E. coli, the genome of S. coelicolor can actually be a closed loop, remains to be determined (Hopwood, 1966
). These statements were based on the careful conclusion that there was a lack of constant genome ends in S. coelicolor, which did not rule out the possibility that the S. coelicolor chromosome is a linear DNA molecule with circularly permuted sequences and variable ends, as in the closely related T2 and T4 phages (Streisinger et al., 1964
).
The T2/T4 model has been the only other known case where a linear replicon exhibits a circular genetic map. The sequences of these linear genomes are circularly permuted and contain terminal direct repeats generated by formation of linear concatemers during replication followed by headful packaging of more than one genome equivalent of DNA. The circular permutation of the T2 and T4 DNA sequences means that the linkage of any pair of proximal markers on the circular genetic map is interrupted only in rare molecules, where they occupy opposite ends of the DNA. This lack of constant genomic ends (Hopwood, 1966 ) leads to a circular genetic map.
The T2/T4 prototype is, however, not applicable to the Streptomyces chromosomes, which, although also linear, have very different basic structures. The chromosomal DNA of Streptomyces (mostly about 8 Mb) contains proteins covalently bound at the 5' ends (Lin et al., 1993 ). The overall sequences are not circularly permuted as in T2/T4 (Leblond et al., 1993
; Lin et al., 1993
). The chromosomal ends are fixed and contain long (24500 kb) inverted repeats (Leblond et al, 1993
; Lezhava et al., 1995
; Lin et al., 1993
; Pandza et al., 1997
; Redenbach et al., 1993
).
A completely different model was proposed more than 30 years ago by Stahl & Steinberg (1964 ), and was also taken into account by Hopwood (1965
, 1966
) and Stahl (1967
) in linkage analyses of S. coelicolor. In a hypothetical scenario, the linear replicons recombine with a bias toward even numbers of crossovers, such that markers at opposite ends of each mating molecule tend to finish in the same recombinant molecule (instead of segregating independently to different ones). The result of this would be that the terminal markers exhibit genetic linkage, which would then close the genetic map into a circle.
There have been no hints whether this scenario may apply to Streptomyces (Hopwood, 1965 , 1966
; Stahl, 1967
). Little is known about the biochemical mechanisms of conjugal transfers and recombination of these linear chromosomes. Conjugation in Streptomyces occurs in surface culture when two mating strains are mixed and grown together. Conjugation is mediated by naturally occurring linear or circular plasmids, both of which are abundant in Streptomyces. Some naturally integrated plasmids also appear to be conjugative, such as the integrated plasmid SLP1 in S. coelicolor (Bibb et al., 1981
), which on transfer to Streptomyces lividans can be circularized or integrated into the chromosome via a site-specific recombination system.
Conjugative plasmids are transferred from the donor mycelium to recipient mycelia (intermycelial transfer; Kieser et al., 1982 ), and presumably spread along the recipient mycelia. The transfer of chromosomes during Streptomyces conjugation cannot be studied biochemically, and can be detected only by the appearance of recombinants. The transfer has been assumed (without proof) to be essentially the same as that of the conjugative plasmid from donor to recipient, although there are circumstances in which back transfers of the chromosome from the recipient to the donor are also indicated (Hopwood, 1984
).
Recombination has been postulated to occur mostly in the merozygote (partial diploid) state during conjugation in most bacteria studied, including Streptomyces (Hopwood, 1967 ), but probably not in protoplast fusion in which complete genomes are expected to be involved in recombination (Hopwood & Wright, 1978
). Studies of recombination during protoplast fusion in Streptomyces have also been consistent with circular genetic maps.
In this study, taking advantage of the possibility of distinguishing between the termini of the chromosomes of S. coelicolor and S. lividans by hybridization (Huang et al., 1998 ), we examined the terminal sequences of the recombinant chromosomes resulting from interspecies mating. From the results, we inferred the numbers of crossovers that had taken place between the parental chromosomes. An odd number of crossovers would have given a recombinant chromosome with one telomere from each parental chromosome, whereas an even number of crossovers would have led to a recombinant chromosome with both telomeres from the same parent. Here we present the physical evidence that supports the Stahl & Steinberg (1964
) model, i.e. the circular genetic maps of the Streptomyces are generated by a strong bias for even numbers of crossovers.
![]() |
METHODS |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
|
Physical and chemical analyses of Streptomyces chromosomes.
For BamHI restriction analysis, chromosomal DNA was isolated, digested and probed by Southern hybridization according to Hopwood et al. (1985 ). The hybridization probes were the terminal 1·4 kb BamHI fragment of the S. coelicolor chromosome (Huang et al., 1998
) and the terminal 0·65 kb BamHI fragment of the S. lividans chromosome. For AseI restriction analysis, preparation, PFGE and Southern hybridization of the genomic DNA were as described previously (Lin et al., 1993
).
![]() |
RESULTS |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Because Streptomyces cultures occasionally undergo spontaneous deletions, leading to circularization of the chromosomes (Lin et al., 1993 ), there exists a possibility that the mutant strains used in the heteroclone experiments had circular chromosomes, and that these accounted for the final circular linkage map. To examine this possibility, the chromosomal DNA of two parental strains studied by Hopwood (1966
), 773 and 928 (D. A. Hopwood, personal communication), was isolated and subjected to restriction and PFGE analysis. The AseI restriction patterns (not shown) of these strains were identical to that of S. coelicolor M145 except for a fragment that contained the integrated SCP1 (Kieser et al., 1992
). The terminal sequences of these two chromosomes were shown to be intact by hybridization analysis using the telomere DNA of S. coelicolor chromosome as the probe (not shown). These results indicated that the 773 and 928 chromosomes were linear, and thus circularity of the parental chromosomes in the heteroclone experiment is not a possible explanation for the lack of constant genomic ends (Hopwood, 1966
).
The basic strategy of crossover analysis
To test the Stahl & Steinberg (1964 ) model for the generation of circular genetic maps of Streptomyces, one would need to differentiate between odd and even numbers of crossovers that have occurred between the linear chromosomes. A simple strategy is to isolate recombinant chromosomes and examine their ends. The presence of both ends from the same parent would indicate an even number of crossovers, whereas the presence of ends from different parents (mixed ends) would indicate an odd number of crossovers.
There are two practical prerequisites for the application of this strategy. Firstly, in order to reach a definite conclusion, ideally one must examine the very ends of chromosomes, not merely certain genetic markers located near the termini. Secondly, it is necessary to have a tool to inspect and distinguish the parental chromosomal ends experimentally. For recombination between two homologous chromosomes, such as in intraspecies conjugation of Streptomyces, it is generally impossible to distinguish the ends of the two mating chromosomes, which are usually identical.
We have recently cloned terminal DNA from the chromosomes of several species of Streptomyces (Huang et al., 1998 ). These terminal sequences, being highly conserved for only the first 166168 bp, could be distinguished by restriction and hybridization analysis. This makes it plausible after interspecies conjugation to examine directly the inheritance of the different parental telomeres in the recombinants.
For interspecies conjugation analysis we chose two model species, S. lividans 66 and S. coelicolor A3(2), of which many strains with defined genetic markers and plasmid status (circular or linear plasmids) are available. The other important consideration was the relative global arrangements of essential and housekeeping genes in the mating pairs. Gross deviations in the gene orders would demand complex or even illegitimate recombination schemes to achieve viable recombinant chromosomes with the selected phenotypes. The general orders of the genes that have been characterized in S. coelicolor and S. lividans are in relatively good correspondence (Hopwood et al., 1983 , 1985
; Leblond et al., 1993
). The overall similarity in chromosomal sequences in the two species was further demonstrated by the similarity in their macro-restriction maps, in which most of the restriction sites (AseI and DraI) not only are similarly located (Fig. 3c
), but also contain homologous neighbouring sequences as revealed by cross-hybridization (Leblond et al., 1993
).
|
Hybridization probes for the respective telomeres were the 1·4 kb BamH1 terminal fragment of the S. coelicolor chromosome and the 0·65 kb BamH1 terminal fragment of the S. lividans chromosome (Huang et al., 1998 ). Each probe hybridized to its own chromosomal DNA, but not to the other under our conditions (Figs 1
and 2
). The S. lividans probe also hybridized to the right end of SLP2 plasmid.
|
|
The integrated plasmids contribute little, if at all, to interspecies recombination
No recombination was detectable in conjugation between SLP2- SLP3- strains of S. lividans (Hopwood et al., 1983 ). On the other hand, in matings between the SCP1- SCP2- strains of S. coelicolor the chromosomes recombine at a low but real frequency of about 10-8, presumably mediated by the integrated SLP1 plasmid present in all S. coelicolor A3(2) strains (Bibb & Hopwood, 1981
). We set out to determine the extent to which integrated SLP1 (and any other plasmid) might contribute to chromosome recombination in our interspecies situation. Two strains devoid of free plasmids, S. lividans ZX7 (pro-2 str-6 rec-46
dndA SLP2- SLP3-) and S. coelicolor M145 (SCP1- SCP2-; Hopwood et al., 1985
) were crossed. The
dndA mutation in ZX7 removed a DNA modification system that causes DNA degradation during PFGE (Zhou et al., 1988
), and the rec-46 mutation decreased plasmid recombination (Tsai & Chen, 1987
), but not chromosome recombination during conjugation (Kieser et al., 1989
). M145 is a prototroph cured of two intrinsic plasmids, SCP1 and SCP2, but still possessing the integrated plasmid SLP1 (Bibb et al., 1981
).
Proline prototrophic (Pro+) and streptomycin-resistant (Strr) cultures were isolated at a frequency of about 8·0x10-8 by screening the spores recovered after mixed growth of the two parents (Hopwood et al., 1985 ). This was not significantly different from the spontaneous occurrence of the same phenotype in M145 alone (4·3x10-7; presumably through a mutation to streptomycin resistance) or in ZX7 alone (5·4x10-8; presumably through a reversion to proline prototrophy). Therefore, the contribution of SLP1 to chromosomal recombination in our interspecies mating system was negligible and could be safely ignored in the following analyses.
Chromosomes recombine with a bias toward even numbers of crossovers in linear-plasmid-mediated conjugation
We next analysed conjugation mediated by the linear plasmid SCP1. From matings between S. coelicolor M146 (hisA1 uraA1 strA1 SCP1+ SCP2-; Hopwood et al., 1985 ), and plasmidless S. lividans ZX7, His+ Pro+ recombinants were isolated at a frequency (1·5 x 10-6) comparable to SCP1-mediated intraspecies recombination in S. lividans (3·56·8x10-6; Hopwood et al., 1983
) or S. coelicolor (about 10-6; Bibb & Hopwood, 1981
). In contrast, spontaneous mutations giving rise to the selected His+ Pro+ phenotype appeared at much lower frequencies in M146 (5·3x10-8) or ZX7 (9·2x10-8). Analysis of the chromosomal DNA from 10 recombinants by hybridization revealed that all had inherited both telomeres from M146 (Fig. 1a
). No recombinant chromosomes with mixed ends were observed. This result indicated that an even number of crossovers had occurred in these recombinants. Since only one crossover was necessary to generate His+ Pro+ recombinants, an additional crossover must have occurred between the hisA1 marker and the left telomere. Whilst the extra crossover might have occurred between pro-2 and the right telomere, giving rise to recombinant chromosomes with both ends from ZX7, these alternative recombinant products were not found.
Further inspection of the non-selected phenotypes among His+ Pro+ recombinants revealed that all of them (15/15) were uracil-auxotrophic and agarase-positive, both of which were present only in S. coelicolor M146 (S. lividans does not possess the agarase gene).
A similar result was obtained using another linear plasmid, SLP2. Conjugation between S. lividans ZX7(SLP2) and S. coelicolor M145 yielded Pro+ Strr recombinants at a frequency of 2·7x10-5, comparable to SLP2-mediated intraspecies recombination in S. lividans (1·73·2x10-4; Hopwood et al., 1983 ) or S. coelicolor (5x10-5; Bibb & Hopwood, 1981
), and much higher than the frequencies of 1·0x10-7 and 4·3x10-7, respectively, for spontaneous appearance of Pro+ Strr in ZX7(SLP2) and M145. DNA was isolated from 11 of these recombinants and hybridized with the terminal probes (Fig. 1b
). No hybridization was observed with the terminal probe of S. coelicolor, whereas the terminal probe of S. lividans hybridized to all recombinant chromosomes. In 10 out of the 11 samples, it hybridized to presumably both the terminal DNA of the recombinant chromosomes and the right end of SLP2. In the remaining sample (no. 4), there was a weaker hybridization to a 10 kb BamHI fragment. This indicated that the chromosomal termini in this strain had undergone deletions. The chromosomal deletions might have caused the loss of SLP2 (Denapaite & Cullum, 1998
; Lin, 1998
; Wu, 1994
).
In another cross between S. lividans ZX7(SLP2) and plasmidless S. coelicolor M130 (hisA1 uraA1 strA1 SCP1- SCP2-), Pro+ Ura+ recombinants were isolated at a frequency of 1·0x10-6 against background mutation frequencies of about 10-8 in the parents. Chromosomal DNA from 10 recombinants analysed contained only the telomeres of the donor S. lividans (data not shown). Thus, the observed non-reciprocity in recombination did not appear to be limited to a particular selection scheme.
Of the unselected markers in these two crosses [ZX7(SLP2)xM145 and ZX7(SLP2)xM130], most (9/12) were of the donor type, and the remainder (3/12) were of a mixed type (agarase-positive and His-).
Chromosomes recombine with a bias toward even numbers of crossovers in circular-plasmid-mediated conjugation
The preference for even numbers of crossovers was also observed in conjugation promoted by a circular plasmid. In crosses between S. coelicolor 1190 (hisA1 uraA1 strA1 SCP1- SCP2+) and plasmidless S. lividans ZX7, His+ Pro+ recombinants were isolated at a frequency of 1·1x10-6 against spontaneous mutation frequencies of 39x10-8 in the parent strains. SCP2-mediated intraspecies recombination occurred at about the same frequencies (10-6) in S. coelicolor (Bibb & Hopwood, 1981 ). Chromosomal DNA from 12 recombinants was isolated and examined: 10 of them contained only the telomeres of ZX7, while the other two (nos 5 and 9) contained one telomere from each parent (Fig. 2a
). The two recombinant cultures with mixed ends grew normally, and the observed mixed telomeres persisted on extended subculturing and in each reisolated culture (Fig. 2b
). This indicated that (i) the mixed ends observed were on the same chromosome and did not reflect a mixed population of two chromosomes with the same telomeres from different parents, and (ii) the recombinant chromosomes with the mixed telomeres did not suffer from an obvious growth disadvantage.
All the non-selected genetic markers in these recombinants were those of the recipient ZX7 (Ura+ and agarase-negative). While a single crossover (between hisA1 and pro-2) was sufficient to give rise to the selected His+ Pro+ phenotype, for the 10 recombinants with both recipient telomeres an additional crossover must have occurred between pro-2 and dag. For the two recombinants with mixed ends, at least one (or a larger odd number of) crossover(s) must have occurred either to the left of hisA1 or to the right of uraA1. The AseI restriction analysis (see later) indicated the former event.
In the repeat of the same cross, Pro+ Ura+ recombinants were isolated at a frequency of 2·1x10-6. Eighteen recombinants were picked and their chromosomes examined. In all of them, only the termini of the S. lividans chromosome were present (data not shown). All the non-selected genetic markers were those of the recipient ZX7 (His+ and agarase-negative). No recombinants with mixed ends were found.
From these results we conclude that (i) there was a strong bias for even numbers of crossovers between the recombining chromosomes during conjugation, and (ii) there was a surprising correlation between the topology of the conjugative plasmids and the parental telomeres inherited by the recombinants the telomeres and genetic markers from the plasmid donor were predominantly inherited in linear-plasmid-driven conjugation; whereas the telomeres and genetic markers from the recipients were preferentially maintained in circular-plasmid-driven transfer.
PFGE analysis of the recombinant chromosomes
The recombinant chromosomes of two crosses were examined by AseI digestion and PFGE (Fig. 3). The restriction patterns of these chromosomal DNA molecules confirmed the foregoing conclusions regarding the inheritance patterns of the recombination chromosomes. The origins of many fragments in the recombinants could be readily assigned to one or the other parent. No obviously new fragments resulting from recombination were present, indicating that relatively few crossovers had taken place.
Most of the AseI fragments in the four His+ Pro+ recombinants in the M146(SCP1)xZX7 cross appeared to originate from the donor M146 (Fig. 3a). While several fragments from the two parents could not be readily distinguished, all those that could corresponded to the fragments of S. coelicolor, such as fragments C, D, E, I, J, L and K (Kieser et al., 1992
). In contrast, fragments B, C, E1, E2 and G of S. lividans (Leblond et al., 1993
) were absent. Tracing the organization of the recombinant chromosomes from the arrangement of genetic markers and restriction fragments revealed that achieving this organization required a minimum of two crossovers one between hisA1 and pro-2. and the other close to the left side of his-2 (Fig. 3c
). Although the two events presumably occurred on fragment C (and probably I) of S. coelicolor, the sizes of these two fragments appeared not to have changed, probably because the corresponding restriction sites in the S. lividans chromosome were similarly located. Overall, the prevalence of the donor sequences in these recombinants was apparent.
In the 1190(SCP2)xZX7 cross, both the His+ Pro+ and Ura+ Pro+ recombinants were analysed (Fig. 3b, d, e, f). The three His+ Pro+ recombinant chromosomes (nos 3, 4, 7) with both recipient ends were almost in perfect contrast to their counterparts in the M146(SCP1)xZX7 cross (panels a, c): the S. coelicolor fragments D, E, I, J and L were absent and the S. lividans fragments C, E1, E2, E3, F, H1, and H2 were present (Fig. 3b
). This pattern suggested that, in addition to the crossover between hisA1 and pro-2 (on fragment C of S. coelicolor and fragment B of S. lividans), another one had occurred between pro-2 and dag (Fig. 3d
). This placed the dag0 and uraA1+ markers and the S. lividans telomeres on the recombinant chromosomes. The terminal probe of S. lividans hybridized to the terminal H1 fragment of S. lividans and one of the largest fragments (presumably the A fragment of S. lividans; data not shown), supporting the deduction and the results of the BamHI analysis (Fig. 2
). The presence of the H fragment of S. coelicolor and the absence of the G fragment of S. lividans (both of which contained the uraA1 locus) suggested the possible occurrence of an additional double crossover in this region (Fig. 3d
).
In the two His+ Pro+ recombinant chromosomes with mixed ends (nos 5, 9), both parents appeared to contribute multiple fragments, such as fragments H, I, J and L from S. coelicolor, and fragments C and F from S. lividans (Fig. 3b, e). Most significant was the presence of the J fragment at the left end of the S. coelicolor chromosome. This fragment hybridized to the terminal probe of S. coelicolor. The presence of the S. lividans end on the A fragment (right end of chromosome) was also demonstrated by hybridization to the S. lividans terminal probe (not shown). The H1 fragment containing the left end of the S. lividans chromosome was absent, based on the lack of hybridization of the S. lividans terminal probe to the DNA corresponding to the co-migrating H1 and H2 fragments (not shown) and the diminished fluorescent intensity of this population (Fig. 3b
). These results, consistent with the mixed ends observed among the BamHI fragments (Fig. 1
), indicated one (or an odd number of) additional crossover(s) to the left of the hisA1 marker in these two recombinants (Fig. 2a
). Like the recombinant chromosomes with the same ends, these recombinant chromosomes appeared to contain the H fragment of S. coelicolor but not the G fragment of S. lividans, suggesting a possible double crossover in this region.
The Ura+ Pro+ recombinants of the 1190(SCP2)xZX7 cross exhibited a very similar pattern to those of the His+ Pro+ recombinants. Compared to the His+ Pro+ recombinants in the same cross, the most notable difference was the preservation of the G fragment of S. lividans and absence of the H fragment of S. coelicolor. The reason for the difference is not clear. It may presumably reflect the difference in selection schemes. The terminal probe of S. lividans hybridized to fragments A and H1, whereas no hybridization was observed with the terminal probe of S. coelicolor (not shown). This is consistent with the previous conclusion based on BamHI analysis (Fig. 2a).
![]() |
DISCUSSION |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
The even-numbered crossovers, however, produced only one of the two types of products expected from reciprocal recombination, and the type of recombination products recovered appeared to depend on the topology of the conjugative plasmids. In circular-plasmid-mediated conjugation (with only one plasmid tested), most of the recombinant chromosomes possessed the recipient-type termini. The reciprocal products, i.e. recombinant chromosomes with the donor-type ends, were not recovered. The preponderance of unselected markers as well as the AseI restriction fragments of the recipient type in these recombinants suggested that the recipient chromosomes had picked up only a relatively small internal segment(s) of the donor chromosome that was presumably mobilized from the donor cell. This merozygous state of recombination resembles that in Escherichia coli conjugation (also mediated by circular plasmids), in which the donor chromosome rarely enters the recipient cell in its entirety. Bibb & Hopwood (1981 ) did not observe this strongly preferred inheritance of recipient markers in intraspecies mating between SCP2+ and SCP2- S. coelicolor. It has been proposed that the inheritance of donor chromosomal markers depends on recombination in the immediate recipient cells as well as subsequent recombination in adjacent cells on further (intramycelial) transfer of the recombinant chromosomes (Lydiate et al., 1985
). The partial donor chromosome in the recipient is not or is rarely transferred intramycelially unless incorporated into an intact chromosome through homologous recombination. Thus, the shortage of donor markers in the recombinant chromosomes in the interspecies SCP2+xSCP2- crosses may simply reflect the lower efficiency of recombination between the chromosomal sequences of S. coelicolor and S. lividans due to lower sequence homology.
In contrast, in the linear-plasmid-mediated conjugation of Streptomyces (with two plasmids tested), double crossovers gave rise to recombinant chromosomes consisting mainly of donor chromosome plus an internal stretch(es) of the recipient chromosome. Again, the reciprocal products, i.e. recombinant chromosomes with both ends of the recipient type, were not found. This predominant presence of donor markers in the recombinants has also been observed in the classical SCP1+xSCP1- crosses in S. coelicolor by Hopwood et al. (1973 ). Although the SCP2 status in this earlier study was not yet established, the absence of the tendency for progeny to inherit donor markers in SCP1- SCP2+xSCP1- SCP2- crosses of S. coelicolor (Hopwood, 1984
) indicated that the linear plasmid SCP1 was involved in the skewed inheritance pattern. These authors proposed that some high-frequency donors (like Hfr strains of E. coli) present in the SCP1+ culture contributed markers preferentially to the progeny. An alternative conjecture is presented below.
The selectivity in recombinant types recovered was probably not due to inhibition exerted by one particular parental species on the other during conjugation. Although SCP1 encodes genes for biosynthesis of the antibiotic methylenomycin A (Wright & Hopwood, 1976 ), which may inhibit SCP1- strains, there appears to be no or little effect of the methylenomycin A on the patterns of chromosome recombination during conjugation or protoplast fusion (Hopwood, 1984
; Kirby & Hopwood, 1977
). Furthermore, the other linear plasmid, SLP2, which does not encode any detectable antibiotic activities, displays the same skewed inheritance. Thus, the plasmid status (donor/recipient), rather than the species, appeared to determine the inheritance of non-selected sequences (including the telomeres) on the recombinant chromosomes selected.
While the contrasting effect exerted by plasmid topology on chromosome inheritance is intriguing, the very limited number of plasmids tested (one circular and two linear) may not justify formulating a general rule. Further studies employing more plasmids of both categories are necessary. Nevertheless, whether the hypothesis is confirmed or not does not affect the support our results lend to the scenario postulated by Stahl & Steinberg (1964 ) a circular genetic map generated by preferred even numbers of crossovers between linear genomes.
If the preference for an even number of crossovers is real, what is the biochemical basis for this constraint? An even number of crossovers is necessary for linear chromosomes if recombination occurs in merozygotes consisting of an intact chromosome and an internal chromosomal sequence (Fig. 4b). An odd number of crossovers would result in two partial chromosomes each lacking a telomere. This scenario probably represents the recombination events in circular-plasmid-mediated conjugation of Streptomyces. The partial exogenote is likely mobilized from the donor by the circular plasmid from an internal origin on the chromosome. Occasionally, the transfer may reach one end of the donor chromosome, which would make odd-numbered crossovers possible (Fig. 4a
), resulting in a recombinant chromosome with mixed ends.
|
Although protoplast fusion was not used directly to address the topology of the genetic maps of Streptomyces, a constraint for even numbers of crossovers has always been imposed successfully in the formal analysis of genetic linkage (e.g. Hopwood & Wright, 1978 ). The rationale is based on the assumption that intact circular chromosomes are involved in recombination, and an odd number of crossovers would result in dimeric chromosomes. Interestingly, the circular genetic maps based on this imposed condition have been essentially consistent for S. coelicolor and other species. Now that the assumption of circular chromosomes is known to have been incorrect, a different reason is needed for the demand for even-numbered crossovers. Whether the mating linear chromosomes are intact or not in protoplast fusion, there is no a priori topological constraint that demands even numbers of crossovers (Fig. 4c
). Odd-numbered crossovers give rise to a recombinant chromosome with mixed ends, whereas even-numbered crossovers give the same ends. An even number of crossovers would be necessary if the ends of the chromosomes were not free (Fig. 4d
). This is true even if the chromosomes are fragmented as long as complete genomes are to be restored. A likely constraint is a strong interaction between the telomeres, mediated by the covalently bound terminal proteins (TPs), as has been observed in adenoviruses (Robinson et al., 1973
) and
29 (Ortin et al., 1971
), the other linear replicons with TPs. Circular configurations of these linear viral DNA molecules were observed when they were released from the virion particles without proteolytic or detergent treatment.
During electrophoresis, the TP-capped DNA of these linear replicons appears to form a proteinase- and detergent-sensitive complex that cannot enter the gel. The linear chromosomes and plasmids of Streptomyces also exhibit the same behaviour, suggesting strong interactions between the TPs (Lin et al., 1993 ), which may be implicated in important biological functions, such as replication, conjugal transfer and structural stability (Chen, 1996
).
The strength of the constraint imposed by terminal interactions on chromosome recombination should depend on the strength of the terminal interactions. The existence of rare recombinants with mixed ends indicates that the terminal interactions are not irreversible during recombination and exchange of telomeres is still possible.
The scheme portrayed in Fig. 4(c) implies that both products of reciprocal recombination, i.e. recombinant chromosomes with both ends from either parent, may be recovered from protoplast fusion. This hypothesis remains to be tested experimentally. Since plasmids are not necessary for recombination in protoplast fusion, it would be interesting to investigate their effect on the outcome of the recombination, if any.
An alternative to the imposed even-numbered crossovers scenario is that there is no constraint on the numbers of crossovers allowed, but that the products of even-numbered crossovers are selectively recovered. This would imply that the products of odd-numbered crossovers, i.e. chromosomes with mixed ends, are biologically disadvantaged. The rarity of recombinant chromosomes with mixed ends suggests that the selection against them would be severe in this hypothesis. Thus the stable maintenance of the S. coelicolor/S. lividans mixed ends in the recombinant cultures (nos 5 and 9) and their normal growth characteristics do not support this view.
A third theoretical possibility exists that is independent of the number of crossovers: it is possible that identical telomeres are preserved on the recombinant chromosomes through conversion of one terminal sequence into the other. Again, the stable maintenance of mixed ends in the recombinant chromosomes on prolonged subculturing without signs of conversion reduces the likelihood of conversions. Moreover, if conversion is involved, it must exert a specific directionality in a very selective way, i.e. donor to recipient conversion of telomere sequences in circular-plasmid-mediated conjugation, and conversion in the opposite direction in linear-plasmid-mediated conjugation. The range spanned by this homogenotization would also have to be relatively long at least 1·4 kb (to reach the restriction sites used in the analysis). Qin & Cohen (1998 ) in their study of the replication of the linear plasmid pSLA2 of Streptomyces rochei failed to observe any homogenotization between the two termini.
Of the three possible hypotheses (i) even-numbered crossovers constrained by the demand for merozygosity and by terminal interactions, (ii) selective recovery of even-numbered crossovers and (iii) homogenotization the first, with its in vitro evidence and interesting biological implications, is currently the working model of our choice.
While our systematic analysis was performed using only one free conjugative plasmid in each cross, the classical conjugation studies of Streptomyces often involve more than one free plasmid (circular and linear) and sometimes in both parental strains. The directionality of transfer (of the plasmids and of the chromosomes) would be more difficult to predict or establish, and the molecular genetic analysis would be more complex. However, there are no obvious reasons why the constraints for even-numbered crossovers would be absent in multi-plasmid schemes.
Considering the broader scope, the validation of the Stahl & Steinberg (1964 ) hypothesis indicates that the danger of equating the topology of genetic maps to that of genomes is not limited to the special case of T2/T4 phages. The well-founded prudence displayed by Hopwood (1965
, 1966
) more than three decades ago should still be observed vigorously in the physical and sequence analyses of microbial genomes. For the latter, the popular shotgun sequencing approach in assembling whole genome sequences, if applied to T2/T4 genomes, would certainly give a circular physical map. Therefore, not only is the topology of circular genetic maps not a reliable guideline, the topology derived from assembled sequence contigs is also not free from similarly hidden pitfalls and traps.
![]() |
ACKNOWLEDGEMENTS |
---|
![]() |
REFERENCES |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Bibb, M. J., Ward, J. M., Kieser, T., Cohen, S. N. & Hopwood, D. A. (1981). Excision of chromosomal DNA sequences from Streptomyces coelicolor forms a novel family of plasmids detectable in Streptomyces lividans. Mol Gen Genet 184, 230-240.[Medline]
Chen, C. W. (1996). Complications and implications of linear bacterial chromosomes. Trends Genet 12, 192-196.[Medline]
Chen, C. W., Yu, T.-W., Lin, Y. S., Kieser, H. M. & Hopwood, D. A. (1993). The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule. Mol Microbiol 7, 925-932.[Medline]
Denapaite, D. & Cullum, J. (1998). Chromosome end of Streptomyces lividans 66 is necessary for the maintenance of the linear plasmid SLP2. In Abstracts of the 141st Ordinary Meeting of the Society for General Microbiology, University of East Anglia, UK, p. 47.
Friend, E. J. & Hopwood, D. A. (1971). The linkage map of Streptomyces rimosus. J Gen Microbiol 68, 187-197.[Medline]
Hopwood, D. A. (1965). A circular linkage map in the actinomycete Streptomyces coelicolor. J Mol Biol 12, 514-516.[Medline]
Hopwood, D. A. (1966). Lack of constant genome ends in Streptomyces coelicolor. Genetics 54, 1177-1184.
Hopwood, D. A. (1967). Genetic analysis and genome structure in Streptomyces coelicolor. Bacteriol Rev 31, 373-403.[Medline]
Hopwood, D. A. (1984). Conjugative sex plasmids of Streptomyces. In Plasmids in Bacteria, pp. 615-634. Edited by D. Helinski, S. Cohen & D. Clewell. New York: Plenum.
Hopwood, D. A. & Wright, H. M. (1978). Bacterial protoplast fusion: recombination in fused protoplasts of Streptomyces coelicolor. Mol Gen Genet 162, 307-317.[Medline]
Hopwood, D. A., Chater, K. F., Dowding, J. E. & Vivian, A. (1973). Advances in Streptomyces coelicolor genetics. Bacteriol Rev 37, 371-405.[Medline]
Hopwood, D. A., Kieser, T., Wright, H. M. & Bibb, M. J. (1983). Plasmids, recombination and chromosomal mapping in Streptomyces lividans 66. J Gen Microbiol 129, 2257-2269.[Medline]
Hopwood, D. A., Bibb, M. J., Chater, K. F. & 7 other authors (1985). Genetic Manipulation of Streptomyces: a Laboratory Manual. Norwich: John Innes Foundation.
Huang, C.-H., Lin, Y.-S., Yang, Y.-L., Huang, S.-w. & Chen, C. W. (1998). The telomeres of Streptomyces chromosomes contain conserved palindromic sequences with potential to form complex secondary structures. Mol Microbiol 28, 905-926.[Medline]
Kieser, T., Hopwood, D. A., Wright, H. M. & Thompson, C. J. (1982). pIJ101, a multi-copy broad host-range Streptomyces plasmid: functional analysis and development of DNA cloning vectors. Mol Gen Genet 185, 223-238.[Medline]
Kieser, H. M., Henderson, D. J., Chen, C. W. & Hopwood, D. A. (1989). A mutation of Streptomyces lividans which prevents intraplasmid recombination has no effect on chromosomal recombination. Mol Gen Genet 220, 60-64.[Medline]
Kieser, H. M., Kieser, T. & Hopwood, D. A. (1992). A combined genetic and physical map of the Streptomyces coelicolor A3(2) chromosome. J Bacteriol 174, 5496-5507.[Abstract]
Kinashi, H. & Shimaji-Murayama, M. (1991). Physical characterization of SCP1, a giant linear plasmid from Streptomyces coelicolor. J Bacteriol 173, 1523-1529.[Medline]
Kirby, R. & Hopwood, D. A. (1977). Genetic determination of methylenomycin synthesis by the SCP1 plasmid of Streptomyces coelicolor A3(2). J Gen Microbiol 98, 239-252.[Medline]
Leblond, P., Redenbach, M. & Cullum, J. (1993). Physical map of the Streptomyces lividans 66 genome and comparison with that of the related strain Streptomyces coelicolor A3(2). J Bacteriol 175, 3422-3429.[Abstract]
Lezhava, A. L., Mizukami, T., Kajitani, T., Kameoka, D., Redenbach, M., Shinkawa, H., Nimi, O. & Kinashi, H. (1995). Physical map of the linear chromosome of Streptomyces griseus. J Bacteriol 177, 6492-6498.[Abstract]
Lin, Y.-L. (1998). Involvement of terminal sequence of the Streptomyces chromosome in the maintenance of linear plasmids. MSc thesis, National Yang-Ming University, Taipei.
Lin, Y.-S., Kieser, H. M., Hopwood, D. A. & Chen, C. W. (1993). The chromosomal DNA of Streptomyces lividans 66 is linear. Mol Microbiol 10, 923-933.[Medline]
Lydiate, D. J., Malpartida, F. & Hopwood, D. A. (1985). The Streptomyces plasmid SCP2*: its functional analysis and development into useful cloning vectors. Gene 35, 223-235.[Medline]
Ortin, J., Vinuela, E., Salas, M. & Vasquez, C. (1971). DNAprotein complex in circular DNA from phage 29. Nature New Biol 234, 275-277.[Medline]
Pandza, K., Pfalzer, G., Cullum, J. & Hranueli, D. (1997). Physical mapping shows that the unstable oxytetracycline gene cluster of Streptomyces rimosus lies close to one end of the linear chromosome. Microbiology 143, 1493-1501.[Abstract]
Qin, Z. & Cohen, S. N. (1998). Replication at the telomeres of the Streptomyces linear plasmid pSLA2. Mol Microbiol 28, 893-904.[Medline]
Redenbach, M., Flett, F., Piendl, W., Glocker, I., Rauland, U., Wafzig, O., Leblond, P. & Cullum, J. (1993). The Streptomyces lividans 66 chromosome contains a 1 Mb deletogenic region flanked by two amplifiable regions. Mol Gen Genet 241, 255-262.[Medline]
Robinson, A. J., Younghusband, H. B. & Bellett, A. J. (1973). A circular DNAprotein complex from adenoviruses. Virology 56, 54-69.[Medline]
Stahl, F. W. (1967). Circular genetic maps. J Cell Physiol 70, 1-12.
Stahl, F. W. & Steinberg, C. M. (1964). The theory of formal phage genetics for circular maps. Genetics 50, 531-538.
Streisinger, G., Edgar, R. S. & Denhardt, G. H. (1964). Chromosome structure in phage T4. I. Circularity of the linkage map. Proc Natl Acad Sci USA 51, 775-779.[Medline]
Tsai, J. F.-Y. & Chen, C. W. (1987). Isolation and characterization of Streptomyces lividans mutants deficient in intraplasmid recombination. Mol Gen Genet 208, 211-218.[Medline]
Wright, L. F. & Hopwood, D. A. (1976). Identification of the antibiotic determined by the SCP1 plasmid of S. coelicolor A3(2). J Gen Microbiol 95, 96-106.[Medline]
Wu, M.-Y. (1994). Analyses of the linear plasmid SLP2 of Streptomyces lividans 66. MSc thesis, National Yang-Ming University, Taipei.
Zhou, X., Deng, Z., Firmin, J. L., Hopwood, D. A. & Kieser, T. (1988). Site-specific degradation of Streptomyces lividans DNA during electrophoresis in buffers contaminated with ferrous iron. Nucleic Acids Res 16, 4341-4354.[Abstract]
Received 23 February 1999;
revised 1 June 1999;
accepted 2 June 1999.