Spontaneous chromosome inversions of guatemalan teosintes (Zea mexicana)

Two paracentric inversions,In3 andIn9, were found in the F1 hybrids of maize and Florida teosinte and these inversions were contributed by the teosinte parent. The length ofIn3 was equivalent to about 35 percent of the length of the long arm of chromosome 3, while that ofIn9, about 60 percent of the length of the short arm of chromosome 9.There were also two paracentric inversions,In1 andIn9, in the F1 hybrids of maize and Jutiapa teosinte and these inversions were inherited from the teosinte parent. The length of theIn1 occupied 22 percent of the total length of the long arm of chromosome 1, while that ofIn9, 60 percent of the total length of the short arm of chromosome 9.Only one paracentric inversion,In9, was identified in the F1 hybrids of maize and Lake Retana teosinte, and this inversion was also from the teosinte parent. As length and location are considered, thisIn9 is the same as theIn9's of Florida teosinte and Jutiapa teosinte.At anaphases I and II of the microsporocyte divisions of the F1 hybrids, evidences of crossovers within the inverted segments, such as bridges and fragments, were obtained for all of these inversions. The interchromosome effect ofIn3 of Florida teosinte, and that ofIn1 of Jutiapa teosinte on the frequency of crossovers within the inverted segment ofIn9's are discussed.Chromosome inversions have probably accompanied the divergence of geographical races of teosinte. This might also be true for the race diversities of maize. The absence ofIn9 in certain teosinte races of southern Mexico and northern Guatemala is accounted for by the substitution of maize chromosome for this inversion.     

Pervasive gene conversion in chromosomal inversion heterozygotes

Chromosomal inversions shape recombination landscapes, and species differing by inversions may exhibit reduced gene flow in these regions of the genome. Though single crossovers within inversions are not usually recovered from inversion heterozygotes, the recombination barrier imposed by inversions is nuanced by noncrossover gene conversion. Here, we provide a genomewide empirical analysis of gene conversion rates both within species and in species hybrids. We estimate that gene conversion occurs at a rate of 1 × 10^–5 to 2.5 × 10^–5 converted sites per bp per generation in experimental crosses within Drosophila pseudoobscura and between D. pseudoobscura and its naturally hybridizing sister species D. persimilis. This analysis is the first direct empirical assessment of gene conversion rates within inversions of a species hybrid. Our data show that gene conversion rates in interspecies hybrids are at least as high as within‐species estimates of gene conversion rates, and gene conversion occurs regularly within and around inverted regions of species hybrids, even near inversion breakpoints. We also found that several gene conversion events appeared to be mitotic rather than meiotic in origin. Finally, we observed that gene conversion rates are higher in regions of lower local sequence divergence, yet our observed gene conversion rates in more divergent inverted regions were at least as high as in less divergent collinear regions. Given our observed high rates of gene conversion despite the sequence differentiation between species, especially in inverted regions, gene conversion has the potential to reduce the efficacy of inversions as barriers to recombination over evolutionary time.     

Abundance and chromosomal distribution of six Drosophila buzzatii transposons: BuT1, BuT2, BuT3, BuT4, BuT5, and BuT6

The abundance and chromosomal distribution of six class-II transposable elements (TEs) of Drosophila buzzatii have been analyzed by Southern blotting and in situ hybridization. These six transposons had been previously found at the breakpoints of inversions 2j and 2q ⁷ of D. buzzatii. These two polymorphic inversions were generated by an ectopic recombination event between two copies of Galileo, a Foldback element. The four breakpoints became hotspots for TE insertions after the generation of the inversion and the transposons analyzed in this work are considered to be secondary invaders of these regions. Insertions of the six transposons are present in the euchromatin but show an increased density in the pericentromeric euchromatin–heterochromatin transition region and the dot chromosome. They are also more abundant in the inverted segments of chromosome 2 rearrangements. We further observed that the accumulation of TE insertions varies between elements and is correlated between dot, proximal regions, and inverted segments. These observations fully agree with previous data in Drosophila melanogaster and support recombination rate as the chief force explaining the chromosomal distribution of TEs.Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users.Sequence data from this article have been deposited in the EMBL/GenBank Data Libraries under accession number DQ402469.     

Molecular analysis of recombination in a family with Duchenne muscular dystrophy and a large pericentric X chromosome inversion.

It has been demonstrated in animal studies that, in animals heterozygous for pericentric chromosomal inversions, loop formation is greatly reduced during meiosis. This results in absence of recombination within the inverted segment, with recombination seen only outside the inversion. A recent study in yeast has shown that telomeres, rather than centromeres, lead in chromosome movement just prior to meiosis and may be involved in promoting recombination. We studied by cytogenetic analysis and DNA polymorphisms the nature of meiotic recombination in a three-generation family with a large pericentric X chromosome inversion, inv(X)(p21.1q26), in which Duchenne muscular dystrophy (DMD) was cosegregating with the inversion. On DNA analysis there was no evidence of meiotic recombination between the inverted and normal X chromosomes in the inverted segment. Recombination was seen at the telomeric regions, Xp22 and Xq27-28. No deletion or point mutation was found on analysis of the DMD gene. On the basis of the FISH results, we believe that the X inversion is the mutation responsible for DMD in this family. Our results indicate that (1) pericentric X chromosome inversions result in reduction of recombination between the normal and inverted X chromosomes; (2) meiotic X chromosome pairing in these individuals is likely initiated at the telomeres; and (3) in this family DMD is caused by the pericentric inversion.     

Establishment of Escherichia coli cells with an integrated high copy number plasmid

Summary The dnaA46 cells can grow at high temperature when a high copy number plasmid pKY31, a derivative of pBR322 carrying a segment of the E. coli chromosome, integrates into the bacterial chromosome. In contrast, the dnaA46 polA ^- cells with the integrated plasmid can not grow at high temperature. Therefore, integration of the plasmid can suppress the dnaA mutation and this suppression requires DNA polymerase I which has been known to be required for plasmid replication. Full reversion of polA or lysogenization of polA ⁺ is lethal for the dnaA46polA ^- bacteria that carry the plasmid only in integrated state. Partial reversion of polA allows these cells to grow at both low and high temperatures. Introduction of the plasmid pBR322 into cytoplasm of these bacteria suppresses the lethal effect caused by full reversion of polA or lysogenization of polA ⁺. This lethal effect expresses independent of the presence or absence of the dnaA mutation. In partial revertants of polA which have only integrated plasmid, the number of copies of a region near the replication origin of integrated plasmid increases. The number is reduced by the presence of extrachromosomal pBR322. It is suggested that the lethal effect of normal levels of DNA polymerase I in strains that carry only the integrated plasmid is due to excessive initiation of replication of the bacterial chromosome from the plasmid origin and high potential of initiation can be absorbed in many copies of cytoplasmic plasmid, probably, in their replication origins.Abbreviations Amp^r ampicillin resistant (resistance) - Tet^s tetracycline sensitive - Tet^r tetracycline resistant - MMS^r methyl methane sulfonate resistant (resistance) - ts temperature sensitive - Kb kilobase pairs     

The influence of heterochromatin, inversion-heterozygosity and somatic pairing on x-ray induced mitotic recombination in Drosophila melanogaster

Summary Mitotic recombination has been induced with X-rays in Drosophila melanogaster larvae and assayed later as twin mosaic spots in the adult eyes. When the X-chromosomes are marked with zeste and white and the third chromosomes with roughoid and sepia, the frequency of twin spots was about 20 times higher for the X-chromosome than for the third chromosome. The greater amount of heterochromatin in the X-chromosome was considered responsible for the difference.Experiments with different inversion heterozygotes support this interpretation. Euchromatic inversions of different lengths have, when heterozygous, little or no influence on the twin spot frequency. The shorter the heterochromatic segment between the kinetochore and the proxomal break point of the inversion the stronger is the reduction of the twin spot frequency.The heterozygotes for the long sc ⁸ and sc ^S1 inversions gave exceptionally low twin spot frequencies. It seems possible that potential twin spot daughter cells die after recombination because of genetic imbalance and/or lack of proper cell separation resulting from the persistence of the dikinetic chromosome elements.To test whether inaccurate somatic pairing in inversion heterozygotes could help explain the low twin spot frequencies in those of sc ⁸ and sc ^S1, neuroblast chromosomes were investigated. They show that chromosomal arrangement during metaphase is determined exclusively by the location of the kinetochore, which always points, irrespective of earlier somatic pairing, toward the center of the metaphase plate. It is possible that there is a lack of proper chromosome alignment at the X-ray sensitive stage for mitotic recombination.     

Recombination and selection in the maintenance of the adaptive value of inversions

A huge amount of data seem to confirm the adaptive value of inversions in Drosophila. The inhibition of recombination in heterokaryotypes mediated by inversions seems fundamental in maintaining their adaptive role. This study shows that recombination is highly suppressed in Drosophila subobscura because of chromosomal inversions, not only inside the inversions but also outside them. It seems that the region outside the inversion where recombination is inhibited is asymmetrical and independent of the inversion length. Despite the difficulty of crossovers taking place near inversion breakpoints, the only two recombination events detected inside inversions were located close to the breakpoint. Thus, selection could be largely responsible for the recombination reduction maintaining sets of adaptive alleles inside the inverted region. Heterokaryotype descendants were always in higher frequency than inbred or outbred homokaryotypes, regardless of the geographical origin of the chromosome, suggesting that chromosomes carrying the same arrangement, although with a different set of alleles for neutral markers, could be submitted to the same selection processes.     

Functional substitution of the recE gene of Bacillus subtilis by the recA gene of Proteus mirabilis

Summary Rec mutants of Bacillus subtilis have been tested for complementation by the recA gene of Proteus mirabilis (recApm) which was introduced into B. subtilis via the plasmid pHP334. In the recE4 mutant of B. subtilis the plasmid pHP334 restored significantly the defects in RecE functions tested: UV-sensitivity, homologous recombination (transduction and transformation) and prophage induction.Although serological methods to detect the presence of RecApm protein in B. subtilis have been unsuccessful, our results strongly indicate that the recE function of B. subtilis is analogous to the recA function of P. mirabilis.Abbreviations Cm^r resistance to chloramphenicol - Em^r resistance to erythromycin - Tc^r resistance to tetracycline - SDS sodium dodecyl sulfate - UV ultraviolet - AS ammonium sulfate     

Genetic Methods for Analysis and Manipulation of Inversion Mutations in Bacteria

A number of genetic methods for the isolation, characterization and manipulation of large chromosomal inversions in Salmonella typhimurium are described. One inversion-carrying mutant is characterized in detail and used to demonstrate a number of unique genetic properties of bacterial inversions.—Contrary to expectation, it was found that large inversion mutations can be repaired by generalized transduction. The repair results from the simultaneous introduction of two wild-type transduced fragments into a single recipient cell. Homologous recombination between the two transduced fragments and the two inversion breakpoints causes the inverted segment to be reinverted. This results in regeneration of the wild-type orientation of this chromosome segment. Similar recombination events allow a large inversion mutation to be introduced into a wild-type strain; two transduced fragments from an inversion strain cause recombination events resulting in inversion of a large chromosome segment.—Genetic methods for mapping the extent of a large inversion mutation by generalized transduction are described and tested. The methods are operationally simple and allow good resolution of the two inversion breakpoints.     

The recQ gene of Escherichia coli K12: molecular cloning and isolation of insertion mutants

Summary The recQ gene of Escherichia coli K12 was subcloned from plasmid pKO1 (Oeda et al. 1981) by monitoring the capacity of the resulting recombinant plasmids partially to reverse the increased ultraviolet (UV) sensitivity of a recF143 recQ1 double mutant. We were able to trace this complementation activity to a 3.4 kilobase (kb) SalI-PvuII fragment. Furthermore, analysis of the Tn3 insertion mutations that abolished the complementation revealed the exclusive localisation of such insertions in the same 3.4 kb segment. This segment was situated about 4 kb clockwise from corA on the chromosome, a result consistent with the transductional data previously reported. In addition, a comparison of our restriction endonuclease cleavage map with the published data has placed recQ between pldA and pldB. When relocated to the recQ site on the chromosome, the recQ::Tn3 mutations conferred partial resistance to thymineless death (TLD) or, in the case of a recBC sbcB background, recombination deficiency and increased UV sensitivity. This has provided the firm evidence that both the TLD resistance and the deficiency in the RecF recombination pathway result from loss of the functional recQ gene. We also identified the recQ gene product as a 74 kilodalton polypeptide by using the maxicell technique.Abbreviations TLD thymineless death - UV ultraviolet light - Ap ampicillin - Km kanamycin - Sm streptomycin - Tc tetracycline - ^r resistant - ^s sensitive - kb kilobase - kdal kilodalton     

R plasmid R6-5 retains an active tet protein repressor gene

The Tc determinants responsible for R plasmid-mediated resistance to tetracycline carry a resistance gene and a repressor gene, here designated tetA and tetI. With derepressed (tetI⁻) mutants of the Tc determinant in the plasmid R57, it is shown that R6-5, which has lost expression of Tc resistance through insertion of IS3 into or near tetA, retains an active tetI gene and is therefore a source of tet repressor product without the resistance protein. Tc^r revertants of R6-5, presumed to have regained resistance by excision of IS3, are also found to retain an active tetI gene.     

The interchromosomal effect of inversions in maize

Summary The interchromosomal effect of inversions in maize along the short arm of chromosome 9 yields results which are distinctly different from those which are reported with Drosophila melanogaster. Recombination was increased in the c ₁-sh₁ region of chromosome 9 while the sh ₁-wx region was unaffected. This increased frequency of recombination appears to be due to an increase in single exchange events as multiple events were unchanged. Increases in recombination were accompanied by either an increase in chromosome interference or normal interference levels. The magnitude of increase in recombination was much smaller than that seen in interchromosomal effects in Drosophila and is consistent with other observations made in maize. When two inversions were present in the same nucleus simultaneously, the effect on recombination was of the same magnitude as the effect of a single inversion. All inversions tested, regardless of size or position with respect to the centromere showed the same magnitude of increase.     

Insertion sequence inversions mediated by ectopic recombination between terminal inverted repeats

Transposable elements are widely distributed and diverse in both eukaryotes and prokaryotes, as exemplified by DNA transposons. As a result, they represent a considerable source of genomic variation, for example through ectopic (i.e. non-allelic homologous) recombination events between transposable element copies, resulting in genomic rearrangements. Ectopic recombination may also take place between homologous sequences located within transposable element sequences. DNA transposons are typically bounded by terminal inverted repeats (TIRs). Ectopic recombination between TIRs is expected to result in DNA transposon inversions. However, such inversions have barely been documented. In this study, we report natural inversions of the most common prokaryotic DNA transposons: insertion sequences (IS). We identified natural TIR-TIR recombination-mediated inversions in 9% of IS insertion loci investigated in Wolbachia bacteria, which suggests that recombination between IS TIRs may be a quite common, albeit largely overlooked, source of genomic diversity in bacteria. We suggest that inversions may impede IS survival and proliferation in the host genome by altering transpositional activity. They may also alter genomic instability by modulating the outcome of ectopic recombination events between IS copies in various orientations. This study represents the first report of TIR-TIR recombination within bacterial IS elements and it thereby uncovers a novel mechanism of structural variation for this class of prokaryotic transposable elements.     

Genetic mapping of the Escherichia coli gene for the stringent starvation protein and its dispensability for normal cell growth

Summary To determine its map position, the sSP gene was cloned into plasmid pBR322 and the recombinant plasmid was integrated into the chromosome of a polA mutant at the site of the sSP gene by homologous recombination. The chromosomal location of Amp^r was then determined by P1 phage-mediated transduction. Thus, the sSP gene was mapped between gltB and glnF at min 69.5 on the Escherichia coli chromosome. Strains were constructed in which the sSP gene was brought under the control of the lac regulatory system. This indicated that the stringent starvation protein (SSP) is dispensable for growth, at least under normal culture conditions.Abbreviations SSP stringent starvation protein - Amp^r ampicillin resistant - IPTG isopropyl -d-thiogalactopyranoside     

A cointegrate of the bacteriophage P1 genome and the conjugative R plasmid R100

Restriction cleavage analysis identified a P1CmSmSuTc plasmid isolated by Mise and Arber (1976) (Virology 69, 191–205) as a cointegrate between bacteriophage P1 and the R plasmid R100. Cointegration occurred by reciprocal recombination between the IS1 element of P1 and IS1b of R100. It involved neither gain nor loss of genetic material, so that the cointegrate carries three IS1 elements in the same orientation. The cointegrate propagates with relatively high stability as plasmid in Escherichia coli host bacteria. It displays the Tra⁺ functions of R100, incompatibility FII of R100, and incompatibility Y of P1, Res⁺ (P1), Mod⁺ (P1) functions of P1 and P1 immunity. Production of P1 phage particles is inducible as for wild type P1. However, because of the large genome size of 180 kb, progeny phage particles contain only a fraction (about 100 kb) of the cointegrate genome. Because of cyclic permutation all genome regions are equally represented in a population of the phage particles of an induced lysate. Occasionally, reciprocal recombination between IS1 elements allows the restoration of the P1 genome. These segregants are found as plaque formers at a rate of about 1 per 300 phage particles in induced lysates.     

A derivative of Tn5 with direct terminal repeats can transpose

The 5.7 kb⁴ transposable kanamycin resistance determinant Tn5 contains 1.5 kb terminal inverted repeats which we here call arms. Tn5's arms contain the genes and sites necessary for Tn5 transposition, and are not homologous to previously described transposable elements. To determine whether one or both arms is a transposable (IS) element, we transposed Tn5 to pBR322 and used restriction endonuclease digestion and ligation in vitro to generate plasmid derivatives designated pTn5-DR1 and pTn5-DR2 in which Tn5's arms were present in direct rather than in inverted orientation. Analysis of transposition products from dimeric forms of the pTn5-DR1 plasmid to phage λ showed that the outside and inside termini of right and of left arms could function in transposition. We conclude that both of Tn5's arms are transposable elements and name them IS50L (left) and IS50R (right). IS50R, which encodes transposase, was used several-fold more frequently than IS50L, which contain an ochre mutant allele of transposase: this implies that Tn5's transposase acts preferentially on the DNA segment which encodes it. Analysis of transpositions of the amp^rkan^r element Tn5-DR2 to the lac operon showed that Tn5-DR2, like Tn5 wild-type, exhibits regional preference without strict site specificity in the choice of insertion sites.     

STRUCTURE AND POPULATION GENETICS OF THE BREAKPOINTS OF A POLYMORPHIC INVERSION IN DROSOPHILA SUBOBSCURA

Drosophila subobscura is a paleartic species of the obscura group with a rich chromosomal polymorphism. To further our understanding on the origin of inversions and on how they regain variation, we have identified and sequenced the two breakpoints of a polymorphic inversion of D. subobscura—inversion 3 of the O chromosome—in a population sample. The breakpoints could be identified as two rather short fragments (～300 bp and 60 bp long) with no similarity to any known transposable element family or repetitive sequence. The presence of the ～300‐bp fragment at the two breakpoints of inverted chromosomes implies its duplication, an indication of the inversion origin via staggered double‐strand breaks. Present results and previous findings support that the mode of origin of inversions is neither related to the inversion age nor species‐group specific. The breakpoint regions do not consistently exhibit the lower level of variation within and stronger genetic differentiation between arrangements than more internal regions that would be expected, even in moderately small inversions, if gene conversion were greatly restricted at inversion breakpoints. Comparison of the proximal breakpoint region in species of the obscura group shows that this breakpoint lies in a small high‐turnover fragment within a long collinear region (～300 kb).     

Are dicentric anaphase bridges formed by somatic recombination in X chromosome inversion heterozygotes of Drosophila melanogaster?

Summary Mitotic recombination has been induced with X-rays in Drosophila melanogaster larvae and assayed later as twin mosaic spots on the adult tergites. With the use of the In(1)sc ^4L sc ^8R chromosome which lacks the nucleolar organizer and is marked with yellow (y) indirect evidence was obtained that mitotic recombination between ring and rod chromosomes results, in a majority of cases, in XO spots, bearing the rod-X only. This was concluded from the relative scarcity and small sizes of y NO^- spots (uncovering the sc ⁴ sc ⁸ chromosome), compared to control sisters bearing an extra Y chromosome with its NO locus. Thus, dicentric chromatid bridges formed by mitotic recombination between the ring and rod chromosomes are probably eliminated at the next division.In In(1)sc ⁴ sc ⁸/f^36a (rod/rod) females, no effect of the Y chromosome on the frequency and sizes of cross-over spots was observed. Either any dicentric chromatid bridges formed by recombination between inverted rod chromosomes fragment at division, with a centromeric piece going to each pole, or such bridges are not usually formed by recombination. The latter case would indicate that somatic pairing of homologues is not accurate in X chromosome inversion heterozygotes and consequently, that recombination yields aneuploid cells.Additional studies are cited which indicate that X chromosome heterozygotes for entire arm inversions may not pair in the typical loop at the time of mitotic recombination.Supported in part by U.S.P.H.S. Grant GM 17096 to J.R.M., and the Kredit zur Förderung des akademischen Nachwuchses an der Universität Zürich to R.N.     

In vivo transfer of genes from Escherichia coli to Bacillus subtilis

Summary Escherichia coli cells, carrying plasmid pRD1 with (a) drug resistance markers from Pseudomonas (km^r, carb^r, tc^r) and (b) the nif-gene group from Klebsiella, were incubated together with Bacillus subtilis cells (str^r), whose cell wall had been disintegrated with lysozyme. Upon plating the cell mixtures onto appropriately supplemented selective medium, multiple drug resistant Bacillus subtilis cells were obtained. Their nature was verified by suitable biochemical tests and checking for the presence of additional genetic markers. The majority of the isolates was unstable. Some however retained multiple drug resistance for longer periods of time, and several produced nitrogenase activity. The data are interpreted as evidence not only for the transfer of the respective genes but also for their expression in the gram-positive recipient cells.Abbreviations pRD1 a hybrid plasmid, renamed by Ray Dixon - pRP4 plasmid from Pseudomonas, originally described by Datta et al., J. Bacteriol 108, 1244 (1971) - km ^r, carb ^r, tc ^r, str ^r resistance against kanamycin, carbenicillin, tetracyclin and streptomycin, respectively - r restriction negative. For other bacterial markers refer to Bachmann, B.J. et al., Bacteriological Reviews 40, 116 (1976)