Past Recombination Research Articles

Mosaic plasmids and mosaic replicons: evolutionary lessons from the analysis of genetic diversity in IncFII-related replicons.

The alpha replicons of the multi-replicon plasmids pGSH500 and pLV1402 have been characterized by DNA sequence analysis. Analysis of the DNA sequence of a 3672 bp HIN:dIII fragment from pFDT100, which contains the pGSH500 alpha replicon, revealed similarity to a number of replicons belonging to, or related to, those of the IncFII family. The replicon region contains copA, tapA, repA and oriR, and replication initiation and termination sites are related to those from the IncFII replicon of R1. A copB gene was found to lie upstream of the HIN:dIII site in the parental plasmid pGSH500. Downstream of oriR, a 707 bp region shows 72.6% identity to a region of the Escherichia coli chromosome at 43.3', suggesting this region of pGSH500 may have been incorporated into the plasmid during a past chromosomal recombination event. Oligonucleotide primers homologous to consensus regions in the copB and repA genes, and the oriR regions from a number of IncFII-related replicons were used to amplify replication regions from pLV1402. Analysis of the amplified regions has shown the presence of copB, copA, tapA and repA genes. Phylogenetic analysis of Rep protein sequences from the RepFIIA family of antisense-control-regulated replicons revealed the presence of three distinct subgroups of Rep proteins. Comparative analysis of DNA and protein sequences from members of the RepFIIA family provides evidence supporting the roles of both non-selective divergence in co-integrate (multi-replicon) plasmids and Chi-mediated-recombination in replicon evolution, and in particular, that such processes may have been widespread in the evolution of the RepFIIA family.

Clonal Spread of Sclerotium cepivorum in Onion Production with Evidence of Past Recombination Events

Three field populations of Sclerotium cepivorum from Ontario and Que-bec in Canada, one field sample from the North Island of New Zealand, as well as isolates from other onion- and garlic-growing areas were classified in mycelial compatibility groups (MCGs) and further characterized by DNA fingerprints and DNA sequence polymorphisms at six genomic regions. MCGs in the population samples were genetically distinct clones. Members of a clone belonged to a unique MCG with an associated multi-locus genotype and DNA fingerprint. The structure in each field population was predominantly clonal based on the repeated sampling of genotypes over a wide geographic area. Only three clones were identified within each of the population samples. The hypothesis that these clones were introduced to the three agricultural production areas is supported by their recovery from additional locations. Some evidence for past recombination was detected when genotypes from the three population samples and from other locations were pooled.

A Bayesian model for detecting past recombination events in DNA multiple alignments.

Most phylogenetic tree estimation methods assume that there is a single set of hierarchical relationships among sequences in a data set for all sites along an alignment. Mosaic sequences produced by past recombination events will violate this assumption and may lead to misleading results from a phylogenetic analysis due to the imposition of a single tree along the entire alignment. Therefore, the detection of past recombination is an important first step in an analysis. A Bayesian model for the changes in topology caused by recombination events is described here. This model relaxes the assumption of one topology for all sites in an alignment and uses the theory of Hidden Markov models to facilitate calculations, the hidden states being the underlying topologies at each site in the data set. Changes in topology along the multiple sequence alignment are estimated by means of the maximum a posteriori (MAP) estimate. The performance of the MAP estimate is assessed by application of the model to data sets of four sequences, both simulated and real.

Haplotype Structure and Population Genetic Inferences from Nucleotide-Sequence Variation in Human Lipoprotein Lipase

Allelic variation in 9.7 kb of genomic DNA sequence from the human lipoprotein lipase gene (LPL) was scored in 71 healthy individuals (142 chromosomes) from three populations: African Americans (24) from Jackson, MS; Finns (24) from North Karelia, Finland; and non-Hispanic Whites (23) from Rochester, MN. The sequences had a total of 88 variable sites, with a nucleotide diversity (site-specific heterozygosity) of .002+/-.001 across this 9.7-kb region. The frequency spectrum of nucleotide variation exhibited a slight excess of heterozygosity, but, in general, the data fit expectations of the infinite-sites model of mutation and genetic drift. Allele-specific PCR helped resolve linkage phases, and a total of 88 distinct haplotypes were identified. For 1,410 (64%) of the 2,211 site pairs, all four possible gametes were present in these haplotypes, reflecting a rich history of past recombination. Despite the strong evidence for recombination, extensive linkage disequilibrium was observed. The number of haplotypes generally is much greater than the number expected under the infinite-sites model, but there was sufficient multisite linkage disequilibrium to reveal two major clades, which appear to be very old. Variation in this region of LPL may depart from the variation expected under a simple, neutral model, owing to complex historical patterns of population founding, drift, selection, and recombination. These data suggest that the design and interpretation of disease-association studies may not be as straightforward as often is assumed.

Evidence of past recombination events among the genes encoding the Erp antigens of Borrelia burgdorferi.

A single Borrelia burgdorferi bacterium may contain six or more different 32 kb circular plasmids (cp32s). Although these plasmids are homologous throughout much of their sequences, two loci have been identified at which they can vary significantly. The cp32 plasmids and their relatives each contain two adjacent genes, orfC and orf3, that vary in sequence between plasmids found within clones of individual bacteria. The orfC gene product is homologous to proteins involved in partitioning of bacterial plasmids, and the differences at this locus between plasmids may account for their compatibility. The orfC-orf3 loci are located approximately 5 kb from another variable locus called erp. The orfC-orf3 loci were used as physically linked markers to assess genetic rearrangements in the erp loci; this revealed examples of recombination involving both individual genes and entire erp loci. Recombination of the genes encoding the Erp antigens might contribute to the evasion of the mammalian immune response and could play roles in the establishment and persistence of B. burgdorferi infections in mammalian hosts.

PspA and PspC: their potential for use as pneumococcal vaccines.

PspA and PspC: their potential for use as pneumococcal vaccines.

Peptide binding function and the paradox of HLA disease associations.

Many studies have found associations between HLA loci and susceptibility or resistance to both infectious and autoimmune diseases, but often subsequent studies fail to find the same association. Such inconsistencies are not surprising if we consider what is known of the population biology and evolution of HLA genes, especially the consequences of natural selection favouring heterozygosity in the peptide binding regions (PBR) of HLA molecules. Because of past recombination event and/or convergent evolution, alleles that are not closely related in overall sequence may come to resemble each other in the PBR. Because peptide binding is likely to be important for the role of HLA molecules in both infectious and autoimmune disease, a strategy of searching for HLA disease associations that groups alleles in functional categories based on PBR motifs may prove more successful than conventional strategies. Likewise, in developing approaches for molecular typing, it may be advisable to develop methods that group alleles on the basis of shared PBR motifs rather than simply on the basis of shared primer sites in less functionally important regions.

RNA-RNA RECOMBINATION AND EVOLUTION IN VIRUS-INFECTED PLANTS

Viruses that depend on RNA-dependent RNA polymerases (RdRp) for repli­ cation of their genomic and subgenomic RNAs are subject to high inherent misincorporation of nucleotides that can lead to heterogeneous mixtures of related species (46, 93). It has been proposed that RNA viruses evolved the means for correcting high error rates through an ability to recombine mutant genomes with wild-type genomes, thereby maintaining functional integrity (72). Although originally found only in a select number of animal viruses, RNA recombination is now thought to have been a major factor in the evolution of all viruses (lOS). This view is based on sequence comparisons that suggest past recombination events,as well as the detection of de novo recombinant molecules. The role of RNA recombination in virus evolution is also supported by studies indicating that recombinant viruses have a selective advantage over parental viruses in certain instances ( l0, 72, 86). All types of crossover events can occur intergenically or intragenically. Intergenic recombination occurs between the genetic material derived from two different viruses, whereas intragenic events are possible for viruses with

Homology among Escherichia coli K1 and K92 polysialytransferases.

The neuS-encoded polysialytransferase (polyST) in Escherichia coli K1 catalyzes synthesis of polysialic acid homopolymers composed of unbranched sialyl alpha 2,8 linkages. Subcloning and complementation experiments showed that the K1 neuS was functionally interchangeable with the neuS from E. coli K92 (S. M. Steenbergen, T. J. Wrona, and E. R. Vimr, J. Bacteriol. 174:1099-1108, 1992), which synthesizes polysialic acid capsules with alternating sialyl alpha 2,8-2,9 linkages. To better understand the relationship between these polySTs, the complete K92 neuS sequence was determined. The results demonstrated that K1 and K92 neuS genes are homologous and indicated that the K92 copy may have evolved from its K1 homolog. Both K1 and K92 structural genes comprised 1,227 bp. There were 156 (12.7%) differences between the two sequences; among these mutations, 55 did not affect the derived primary structure of K92 polyST and hence were synonymous with the K1 sequence. Assuming maximum parsimony, another estimated 17 synonymous mutations plus 84 nonsynonymous mutations could account for the 70 amino acid replacements in K92 polyST; 36 of these replacements were judged to be conservative when compared with those of K1 polyST. There were no changes detected in the first 146 5' or last 129 3' bp of either gene, suggesting, in addition to the observed mutational differences, the possibility of a past recombination event between neuS loci of two different kps clusters. The results indicate that relatively few amino acid changes can account for the evolution of a glycosyltransferase with novel linkage specificity.

Positive selection and interallelic recombination at the merozoite surface antigen-1 (MSA-1) locus of Plasmodium falciparum.

DNA sequences of alleles at the merozoite surface antigen-1 (MSA-1) gene locus of the malaria parasite Plasmodium falciparum show evidence of repeated past recombination events between alleles. These include both (1) nonreciprocal recombination events that have homogenized certain gene regions among alleles and (2) reciprocal recombination events that have combined allelic segments with divergent evolutionary histories, thereby enhancing allelic diversity. In three different gene regions, the rate of nonsynonymous nucleotide substitution significantly exceeds that of synonymous nucleotide substitution, implying that positive Darwinian selection has acted to diversify alleles at the amino acid level. The MSA-1 polymorphism seems to be quite ancient; the two major allelic types have been maintained for approximately 35 Myr.

Polymorphism, recombination, and linkage disequilibrium within the HLA class II region.

Thirty-nine CEPH (Centre d'Etude du Polymorphisme Humain) families, comprised of 502 individuals, have been typed for the HLA class II genes DRB1, DQA1, DQB1, and DPB1 using nonradioactive sequence-specific oligonucleotide probes to analyze polymerase chain reaction amplified DNA. This population, which consists of 266 independent chromosomes, contains 27 DRB1, 7 DQA1, 12 DQB1, and 17 DPB1 alleles. Analysis of the distribution of allele frequencies using the homozygosity statistic, which gives an indication of past selection pressures, suggests that balancing selection has acted on the DRB1, DQA1, and DQB1 loci. The distribution of DPB1 alleles, however, suggests a different evolutionary past. Family data permits the estimation of recombination rates and the unambiguous assignment of haplotypes. No recombinants were found between DRB1, DQA1, and DQB1; however, recombinants were detected between DQB1 and DPB1, resulting in an estimated recombination fraction of greater than or equal to 0.008 +/- 0.004. Only 33 distinct DRB1-DQA1-DQB1 haplotypes were found in this population which illustrates the extreme nonrandom haplotypic association of alleles at these loci. A few of these haplotypes are unusual (previously unreported) for a Caucasian population and most likely result from past recombination events between the DR and DQ subregions. Examination of disequilibrium across the HLA region using these data and the available serologic HLA-A and HLA-B types of these samples shows that global disequilibrium between these loci declines with the recombination fraction, approaching statistic nonsignificance at the most distant interval, HLA-A to HLA-DP.DR-DQ haplotypes in linkage disequilibrium with DPB1 and B are noted and, finally, the evolutionary origin of certain class II haplotypes is addressed.

Gene conversion in the evolution of both the H-2 and Qa class I genes of the murine major histocompatibility complex.

In order to better understand the role of gene conversion in the evolution of the class I gene family of the major histocompatibility complex (MHC), we have used a computer algorithm to detect clustered sequence similarities among 24 class I DNA sequences from the H-2, Qa, and Tla regions of the murine MHC. Thirty-four statistically significant clusters were detected; individual analysis of the clusters suggested at least 25 past gene conversion or recombination events. These clusters are comparable in size to the conversions observed in the spontaneously occurring H-2Kbm and H-2Kkm2 mutations, and are distributed throughout all exons of the class I gene. Thus, gene conversion does not appear to be restricted to the regions of the class I gene encoding their antigen-presentation function. Moreover, both the highly polymorphic H-2 loci and the relatively monomorphic Qa and Tla loci appear to have participated as donors and recipients in conversion events. If gene conversion is not limited to the highly polymorphic loci of the MHC, then another factor, presumably natural selection, must be responsible for maintaining the observed differences in level of variation.

The location and possible evolutionary significance of small dispersed repeats in wheat ctDNA

Low-stringency hybridisation between recombinant plasmids representing the complete T. aestivum chloroplast genome has revealed small repeated DNA segments dispersed through the molecule. Thirty-two repeated DNA segments were detected, and they could be divided into 12 unrelated sets; no repeat was detected as multiple copies. The longest of the small repeats mapped just within the large inverted repeat in spinach and mung-bean ctDNAs. It was found to have been duplicated after the divergence of a cereal progenitor to generate a third, dispensible copy, 0.2 kbp downstream of rbcL. In maize at least, this copy has also become integrated, with rbcL, in the mitochondrial genome. Another of the repeats is thought to have mediated a chloroplast DNA inversion (Howe 1985). Thus the diverse collection of small repeats probably represents some consequences and causes of past recombination events as well as a mechanism for further intramolecular ctDNA recombination. Their possible significance in the restructuring and evolution of chloroplast genomes is discussed.

Correlation between Physical Stability Map and Genetic Map of DNA Double Strand

Several facts showing that stability heterogeneity along DNA double-strand has a remarkable positional correlation with the distribution of genes are presented. The distribution of physical stability of the double-helix seems to play some role in the genetic function of DNA, and/or may be a relic of the past recombination. In any case, the authors would like to suggest that the full understanding of the genetic function of DNA may not be achieved without a detailed study of `physical property map' along its long molecular thread.

Allelic immunoglobulin VH genes in two mouse strains: possible germline gene recombination.

The nucleotide sequence of two germline immunoglobulin heavy chain variable region (VH) genes of mouse BALB/c origin was determined. These two genes are highly homologous to each other. They both have the unusual codon CCT for proline at position 7, which so far has been found only in a specific set of VH genes, called the NPb family. We show that the two VH genes belong to this set. One of our BALB/c genes, VH124, is more homologous to a C57BL/6 NPb VH gene than to any BALB/c VH gene, and we propose that these two genes are alleles. A comparison of the substitutions between these two genes with published sequences of all other BALB/c and C57BL/6 NPb VH genes reveals evidence for past homologous recombination events between related germline VH genes Homologous recombination may play an important role in the diversification of germline immunoglobulin VH genes.