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Taylor AF, Amundsen SK, Smith GR. Unexpected DNA context-dependence identifies a new determinant of Chi recombination hotspots. Nucleic Acids Res 2016; 44:8216-28. [PMID: 27330137 PMCID: PMC5041463 DOI: 10.1093/nar/gkw541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/03/2016] [Indexed: 11/23/2022] Open
Abstract
Homologous recombination occurs especially frequently near special chromosomal sites called hotspots. In Escherichia coli, Chi hotspots control RecBCD enzyme, a protein machine essential for the major pathway of DNA break-repair and recombination. RecBCD generates recombinogenic single-stranded DNA ends by unwinding DNA and cutting it a few nucleotides to the 3′ side of 5′ GCTGGTGG 3′, the sequence historically equated with Chi. To test if sequence context affects Chi activity, we deep-sequenced the products of a DNA library containing 10 random base-pairs on each side of the Chi sequence and cut by purified RecBCD. We found strongly enhanced cutting at Chi with certain preferred sequences, such as A or G at nucleotides 4–7, on the 3′ flank of the Chi octamer. These sequences also strongly increased Chi hotspot activity in E. coli cells. Our combined enzymatic and genetic results redefine the Chi hotspot sequence, implicate the nuclease domain in Chi recognition, indicate that nicking of one strand at Chi is RecBCD's biologically important reaction in living cells, and enable more precise analysis of Chi's role in recombination and genome evolution.
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Affiliation(s)
- Andrew F Taylor
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Susan K Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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2
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Motamedi MR, Szigety SK, Rosenberg SM. Double-strand-break repair recombination in Escherichia coli: physical evidence for a DNA replication mechanism in vivo. Genes Dev 1999; 13:2889-903. [PMID: 10557215 PMCID: PMC317119 DOI: 10.1101/gad.13.21.2889] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
DNA double-strand-break repair (DSBR) is, in many organisms, accomplished by homologous recombination. In Escherichia coli DSBR was thought to result from breakage and reunion of parental DNA molecules, assisted by known endonucleases, the Holliday junction resolvases. Under special circumstances, for example, SOS induction, recombination forks were proposed to initiate replication. We provide physical evidence that this is a major alternative mechanism in which replication copies information from one chromosome to another generating recombinant chromosomes in normal cells in vivo. This alternative mechanism can occur independently of known Holliday junction cleaving proteins, requires DNA polymerase III, and produces recombined DNA molecules that carry newly replicated DNA. The replicational mechanism underlies about half the recombination of linear DNA in E. coli; the other half occurs by breakage and reunion, which we show requires resolvases, and is replication-independent. The data also indicate that accumulation of recombination intermediates promotes replication dramatically.
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Affiliation(s)
- M R Motamedi
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2H7 Canada
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3
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Stahl FW, Shurvinton CE, Thomason LC, Hill S, Stahl MM. On the clustered exchanges of the RecBCD pathway operating on phage lambda. Genetics 1995; 139:1107-21. [PMID: 7768427 PMCID: PMC1206444 DOI: 10.1093/genetics/139.3.1107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Lytic cycle crosses of Red- Gam- phage lambda were conducted in rec+ Escherichia coli carrying one or another plasmid with homology to lambda. Lambda x lambda recombinants and lambda x plasmid recombinants were formed by RecBCD-mediated recombination. We showed previously that the act of recombining with a plasmid alters the disposition of selected lambda x lambda exchanges. This work reports that the relationships between the lambda x plasmid and the lambda x lambda exchanges is unaltered by the removal from one lambda parent of the homology shared with the plasmid. This result supports our view that a reciprocal exchange, allowing for cointegrate formation, is associated with but mechanistically separable from a (presumably) nonreciprocal lambda x lambda exchange. The nature of this relationship is independent of lambda's Rap function, which is shown to alter the ratio of cointegrate formation (splices) to marker pick-up (patches) in lambda x plasmid recombination mediated by the RecBCD pathway.
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Affiliation(s)
- F W Stahl
- Institute of Molecular Biology, University of Oregon, Eugene 97403-1229, USA
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4
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Xu SY, Feiss M. Structure of the bacteriophage lambda cohesive end site. Genetic analysis of the site (cosN) at which nicks are introduced by terminase. J Mol Biol 1991; 220:281-92. [PMID: 1830343 DOI: 10.1016/0022-2836(91)90013-v] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A collection of mutations affecting the site (cosN) at which the bacteriophage lambda DNA packaging enzyme, terminase, introduces nicks to generate mature lambda chromosomes has been studied. A good correlation was found for mutational effects on burst size, accumulation of unused proheads, packaging of DNA into heads and cos cutting by terminase in vitro, indicating that defective cosN cleavage by terminase is the molecular explanation for the phenotypic effects of the mutations. Although the base-pairs of cosN display partial twofold rotational symmetry, cosN was found to be asymmetric functionally. Certain mutations to the left side of the center of rotational symmetry have more pronounced phenotypic effects than rotationally symmetric mutations to the right. The cosN11G mutation has no phenotypic effects when present as a single mutation, but does affect DNA packaging and cosN cutting in the presence of the symmetrically disposed cosN2C mutation. Mutations that decrease cosN cleavage result in the accumulation of unexpanded proheads, indicating that prohead expansion depends on cosN cutting.
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Affiliation(s)
- S Y Xu
- Department of Microbiology, University of Iowa, Iowa City 52242
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5
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Stahl FW, Thomason LC, Siddiqi I, Stahl MM. Further tests of a recombination model in which chi removes the RecD subunit from the RecBCD enzyme of Escherichia coli. Genetics 1990; 126:519-33. [PMID: 2249753 PMCID: PMC1204209 DOI: 10.1093/genetics/126.3.519] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
When one of two infecting lambda phage types in a replication-blocked cross is chi + and DNA packaging is divorced from the RecBCD-chi interaction, complementary chi-stimulated recombinants are recovered equally in mass lysates only if the chi + parent is in excess in the infecting parental mixture. Otherwise, the chi 0 recombinant is recovered in excess. This observation implies that, along with the chi 0 chromosome, two chi + parent chromosomes are involved in the formation of each chi + recombinant. The trimolecular nature of chi +-stimulated recombination is manifest in recombination between lambda and a plasmid. When lambda recombines with a plasmid via the RecBCD pathway, the resulting chromosome has an enhanced probability of undergoing lambda x lambda recombination in the interval into which the plasmid was incorporated. These two observations support a model in which DNA is degraded by Exo V from cos, the sequence that determines the end of packaged lambda DNA and acts as point of entry for RecBCD enzyme, to chi, the DNA sequence that stimulates the RecBCD enzyme to effect recombination. The model supposes that chi acts by ejecting the RecD subunit from the RecBCD enzyme with two consequences. (1) ExoV activity is blocked leaving a highly recombinagenic, frayed duplex end near chi, and (2) as the enzyme stripped of the RecD subunit travels beyond chi it is competent to catalyze reciprocal recombination.
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Affiliation(s)
- F W Stahl
- Institute of Molecular Biology, University of Oregon, Eugene 97403-1229
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6
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Mahan MJ, Roth JR. Role of recBC function in formation of chromosomal rearrangements: a two-step model for recombination. Genetics 1989; 121:433-43. [PMID: 2714635 PMCID: PMC1203631 DOI: 10.1093/genetics/121.3.433] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The role of recBC functions has been tested for three types of chromosomal recombination events: (1) recombination between direct repeats to generate a deletion, (2) recombination between a small circular fragment and the chromosome, and (3) recombination between inversely oriented repeats to form an inversion. Deletion formation by recombination between direct repeats, which does not require a fully reciprocal exchange, is independent of recBC function. Circle integration and inversion formation are both stimulated by the recBC function; these events require full reciprocality. The results suggest that half-reciprocal exchanges can occur without recBC, but recBC functions greatly stimulate completion of a fully reciprocal exchange. We propose that chromosomal recombination is a two-step process, and recBC functions are primarily required for the second step.
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Affiliation(s)
- M J Mahan
- Department of Biology, University of Utah, Salt Lake City 84112
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7
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Kobayashi I, Takahashi N. Double-stranded gap repair of DNA by gene conversion in Escherichia coli. Genetics 1988; 119:751-7. [PMID: 3044922 PMCID: PMC1203461 DOI: 10.1093/genetics/119.4.751] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We demonstrated repair of a double-stranded DNA gap through gene conversion by a homologous DNA sequence in Escherichia coli. We made a double-stranded gap in one of the two regions of homology in an inverted orientation on a plasmid DNA molecule and introduced it into an E. coli strain which has the RecE system of recombination (genotype; sbcA23 recB21 recC22). We detected repair products by genetic selection. The repair products were those expected by the double-strand-gap repair model. Gene conversion was frequently accompanied by crossing over of the flanking sequences as in eukaryotes. This double-strand gap repair mechanism can explain plasmid recombination in the absence of an artificial double-stranded break reported in a companion study by Yamamoto et al.
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Affiliation(s)
- I Kobayashi
- Department of Bacteriology, Faculty of Medicine, University of Tokyo, Japan
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Thaler DS, Stahl MM, Stahl FW. Double-chain-cut sites are recombination hotspots in the Red pathway of phage lambda. J Mol Biol 1987; 195:75-87. [PMID: 2958632 DOI: 10.1016/0022-2836(87)90328-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The Red recombination pathway of phage lambda is shown to target recombination to double-chain ends of DNA. A double-chain cut, delivered in vivo to only one of two parents participating in a lambda lytic cross by a type II restriction endonuclease, increases the proportion of crossing over in the interval containing the cut compared with other intervals. The stimulating effect of a cut is evident whether replication is inhibited or permitted. Cut stimulation can move away from the initial cut-site, presumably by double-chain degradation. Movement of the stimulating effect of a cut is dependent on the Escherichia coli gene recA when the cross is carried out under conditions that inhibit phage replication. When replication is permitted, all aspects of cut-stimulated recombination are independent of recA. Evidence is presented to show that the reaction that is stimulated by cutting is often non-reciprocal at the molecular level.
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Affiliation(s)
- D S Thaler
- Institute of Molecular Biology, University of Oregon, Eugene 97403
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Lafuse WP, Berg N, Savarirayan S, David CS. Mapping of a second recombination hot spot within the I-E region of the mouse H-2 gene complex. J Exp Med 1986; 163:1518-28. [PMID: 3011948 PMCID: PMC2188118 DOI: 10.1084/jem.163.6.1518] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The crossover points of nine intra-I region recombinant mouse strains were determined by restriction fragment analysis. The recombinants were examined for the presence of k and p haplotype specific DNA restriction endonuclease sites. These restriction sites were a Sac I site between the E beta and E beta 2 genes, a Hpa I site within the E beta 2 gene, and a Rsa I site approximately 1 kb to the right of the E alpha gene. Seven of the recombinants were found to have crossovers between the Hpa I and the Rsa I site. This analysis suggests that a recombination hot spot exists within this segment. This segment is approximately 12-14 kb, and contains the E alpha gene and the intervening sequence between the E beta 2 and E alpha genes.
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Stahl FW, Kobayashi I, Thaler D, Stahl MM. Direction of travel of RecBC recombinase through bacteriophage lambda DNA. Genetics 1986; 113:215-27. [PMID: 3013720 PMCID: PMC1202835 DOI: 10.1093/genetics/113.2.215] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We examined linkage relationships for RecBC-mediated recombination in lytic cycle crosses of lambda phages bearing two cohesive end sites (cos) oriented in the same direction. The relationships obtained imply that a given recombinant tends to be packaged from the cos site that is the nearer one to the right of the exchange. In view of the previously established coupling of entry of a recombinase at a cos cut and initiation of DNA packaging by that cos cut, these results imply that the recombinase (presumably the RecBC gene product) enters lambda's chromosome at the right end.
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Stahl FW. Roles of double-strand breaks in generalized genetic recombination. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1986; 33:169-94. [PMID: 2948217 DOI: 10.1016/s0079-6603(08)60023-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Smith GR, Stahl FW. Homologous recombination promoted by Chi sites and RecBC enzyme ofEscherichia coli. Bioessays 1985. [DOI: 10.1002/bies.950020603] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Taylor AF, Schultz DW, Ponticelli AS, Smith GR. RecBC enzyme nicking at Chi sites during DNA unwinding: location and orientation-dependence of the cutting. Cell 1985; 41:153-63. [PMID: 3888405 DOI: 10.1016/0092-8674(85)90070-4] [Citation(s) in RCA: 146] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Homologous recombination by the E. coli RecBC pathway occurs at elevated frequency near Chi sites. We reported previously that Chi induces RecBC enzyme to cleave one DNA strand--that containing the Chi sequence 5'G-C-T-G-G-T-G-G3'. We report here that the Chi-dependent cleavage occurs four, five, or six nucleotides to the 3' side of the Chi octamer and produces nicks with 3'-OH and 5'-PO4 groups. Chi-dependent cleavage occurs if RecBC enzyme approaches the Chi sequence from the right, but not if it approaches only from the left, during unwinding of the duplex DNA substrate. A single RecBC enzyme molecule appears to cleave the DNA and to release part of it as a single-stranded fragment. These and previous results indicate that Chi-dependent cleavage is concomitant with DNA unwinding by RecBC enzyme and provide an enzymatic basis for the orientation-dependence of Chi recombinational hotspot activity. These observations demonstrate a key step of a proposed model of recombination in which RecBC enzyme produces a potentially invasive single-stranded DNA tail extending from Chi to its left. We discuss the relation between the action of Chi sites and that of special sites enhancing eukaryotic recombination.
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15
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Erickson JM, Schmickel RD. A molecular basis for discrete size variation in human ribosomal DNA. Am J Hum Genet 1985; 37:311-25. [PMID: 2984926 PMCID: PMC1684566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The tandemly repeated human ribosomal RNA (rRNA) genes contain a region of size heterogeneity that is present in the nontranscribed spacer of every individual examined. This heterogeneity has been previously examined by Southern analysis of BamHI-digested human DNA. Using a ribosomal DNA (rDNA) probe specific for the 3' end of the 28S rRNA gene, at least four discrete sizes of BamHI fragments were seen in human populations. Molecular analysis of the cloned DNA from this region reveals tandem duplication of a segment of spacer rDNA located 388 base pairs (bp) 3' to the end of the 28S ribosomal RNA gene. Five hundred fifty bp of DNA, flanked on either side by a 150-bp repeated element, is either duplicated or deleted to produce a series of spacers that differ in size by 850 bp. These duplications/deletions appear to be the product of unequal homologous exchange, mediated by the small repeated element. Thus, human rDNA fragments cloned in lambda vectors and propagated in E. coli generate the same apparent size variation seen in genomic DNA. This study suggests that unequal homologous exchange is the molecular basis for the observed length heterogeneity in the spacer rDNA and may be a common mechanism for the generation of human genetic diversity.
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Yagil E, Shtromas I. Rec-mediated recombinational activity of two adjacent Chi elements in bacteriophage lambda. Genet Res (Camb) 1985; 45:1-8. [PMID: 3158572 DOI: 10.1017/s0016672300021911] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
SummaryChi is a sequence of eight nucleotide pairs which stimulaterecBC-mediated recombination (Smith, 1983a, b). The effect of two linked Chis onrecBC-mediated recombination was tested in bacteriophage lambda. It was noticed that the Chi element located on the right side of the phage chromosome is epistatic on the other Chi. These findings support a model proposed by Stahlet al.(1983) which suggests that the recombination machinery moves unidirectionaly in the phage chromosome from right to left. The results also suggest that in the presence of more than one Chi only the rightmost one stimulates recombination.
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Abstract
Among lambda particles carrying chromosomes that have failed to replicate during a lytic cycle cross there is a high frequency of Red-mediated recombination near the right-hand end. Earlier work has shown that this recombination is dependent on cos (cohesive end site), the packaging origin of lambda. In contrast to the prediction of the break-copy model proposed earlier, we find a high recombination rate near cos even when only one of the two participating parents has a functional cos at that locus. The exchange is accompanied by loss of the stimulating cos in the recombination product, irrespective of the marker configurations: a+b+cos- rather than a+b+cos+ is produced in the cross a+b-cos- x a-b+cos+ as well as in the cross a+b-cos+ x a-b+cos-. Further analyses of these and earlier data allow the formulation of a detailed model for cos-stimulated, Red-mediated genetic exchange. In this model, cos stimulates exchange by virtue of being a double-strand cut site. The model has several features like that proposed for yeast. This role of cos in the Red pathway contrasts with the role of cos in the RecBC pathway, in which cos serves as an entry site for a recombinase that stimulates exchanges far from cos.
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Rosenberg SM, Stahl MM, Kobayashi I, Stahl FW. Improved in vitro packaging of coliphage lambda DNA: a one-strain system free from endogenous phage. Gene 1985; 38:165-75. [PMID: 2933300 DOI: 10.1016/0378-1119(85)90215-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In previous systems for in vitro packaging of lambda DNA, phages are produced from the packaging components as well as from added DNA. We have developed a new genetic strategy for in vitro packaging that bypasses this endogenous phage problem. Our system employs a single bacterial strain whose lambda prophage codes for all of the packaging proteins but is deleted for cos, the packaging origin. Crude extracts of the single lysogen: (i) are virtually free from endogenous phages, (ii) package added lambda DNA efficiently and (iii) are easy to prepare. Using the cos- in vitro packaging system we show that packaging of lambda linear monomers is a second-order reaction, but that packaging from concatemers prepared by annealing or ligation is first order. We conclude that in our cos- system, linear monomers are a poor substrate for in vitro packaging but that packaging from concatemers works well.
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Chakravarti A, Buetow KH, Antonarakis SE, Waber PG, Boehm CD, Kazazian HH. Nonuniform recombination within the human beta-globin gene cluster. Am J Hum Genet 1984; 36:1239-58. [PMID: 6097112 PMCID: PMC1684633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Population genetic analysis of 15 restriction site polymorphisms demonstrates nonuniform recombination within the human beta-globin gene cluster. These DNA polymorphisms show two clusters of high nonrandom associations, one 5' and another 3' to the beta-globin structural gene, with no significant linkage disequilibrium between the two clusters. The 5'- and 3'-association clusters are 34.6 kilobases (kb) and 19.4 kb long, respectively, and are separated by 9.1 kb of DNA immediately 5' to the beta-globin gene. For each of these three DNA regions, we have observed a relationship between nonrandom associations and physical distance between the polymorphisms. However, this relationship differed for each of these regions. On the assumption that the effective population size (Ne) is 5,000-50,000, we estimate the total recombination rate to be 0.0017%-0.0002% in the 5' cluster, 0.0931%-0.0093% in the 3' cluster, and 0.2912%-0.0219% in the 9.1-kb region between them. The beta cluster thus shows nonuniformity in recombination. Moreover, the recombination rate in the 9.1-kb DNA segment is 3-30 times greater than expected and is thus a hot spot for meiotic recombination.
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Abstract
In vivo, lambda DNA cannot be cleaved at cos (matured) if proheads are not present; in vitro, however, cos cleavage readily takes place in the absence of proheads. In order to investigate this paradox, we have constructed plasmids that synthesize lambda terminase in vivo upon induction. The plasmids also contain cos at the normal position, about 190 bp upstream of lambda gene Nul. One of the plasmids, pFM3, produces levels of terminase comparable to those found after phage induction. If cells carrying pFM3 are thermoinduced, almost 100% of the intracellular plasmid DNA has a double-strand interruption at or near cos. Since the only lambda genes that pFM3 carries are Nul, A, W and B, this in vivo cleavage is occurring in the absence of proheads. Previous failure to observe lambda maturation with phages carrying prohead mutations may be due to exonucleolytic degradation of the unprotected DNA ends, a different DNA topology or compartmentalization, or terminase inhibition in the absence of prohead by the product of another lambda gene that maps to the right of gene B.
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