scholarly journals Spontaneous Chloroplast Mutants Mostly Occur by Replication Slippage and Show a Biased Pattern in the Plastome of Oenothera

2016 ◽  
Vol 28 (4) ◽  
pp. 911-929 ◽  
Author(s):  
Amid Massouh ◽  
Julia Schubert ◽  
Liliya Yaneva-Roder ◽  
Elena S. Ulbricht-Jones ◽  
Arkadiusz Zupok ◽  
...  
Keyword(s):  
Replication Slippage ◽  
Chloroplast Mutants

scholarly journals Deletion Formation Between the Two Salmonella typhimurium Flagellin Genes Encoded on the Mini F Plasmid: Escherichia coli ssb Alleles Enhance Deletion Rates and Change Hot-Spot Preference for Deletion Endpoints

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 563-572 ◽  
Author(s):  
Takafumi Mukaihara ◽  
Masatoshi Enomoto
Keyword(s):  
Escherichia Coli ◽  
Salmonella Typhimurium ◽  
Hot Spots ◽  
Hot Spot ◽  
Direct Repeats ◽  
Replication Slippage ◽  
Detection Systems ◽  
Deletion Formation ◽  
Homologous Sequences ◽  
Deletion Detection

Deletion formation between the 5′-mostly homologous sequences and between the 3′-homeologous sequences of the two Salmonella typhimurium flagellin genes was examined using plasmid-based deletion-detection systems in various Escherichia coli genetic backgrounds. Deletions in plasmid pLC103 occur between the 5′ sequences, but not between the 3′ sequences, in both RecA-independent and RecA-dependent ways. Because the former is predominant, deletion formation in a recA background depends on the length of homologous sequences between the two genes. Deletion rates were enhanced 30- to 50-fold by the mismatch repair defects, mutS, mutL and uvrD, and 250-fold by the ssb-3 allele, but the effect of the mismatch defects was canceled by the ΔrecA allele. Rates of the deletion between the 3′ sequences in plasmid pLC107 were enhanced 17- to 130-fold by ssb alleles, but not by other alleles. For deletions in pLC107, 96% of the endpoints in the recA+ background and 88% in ΔrecA were in the two hot spots of the 60- and 33-nucleotide (nt) homologous sequences, whereas in the ssb-3 background >50% of the endpoints were in four- to 14-nt direct repeats dispersed in the entire 3′ sequences. The deletion formation between the homeologous sequences is RecA-independent but depends on the length of consecutive homologies. The mutant ssb allele lowers this dependency and results in the increase in deletion rates. Roles of mutant SSB are discussed with relation to misalignment in replication slippage.

scholarly journals Creation of a Chloroplast Microsatellite Reporter for Detection of Replication Slippage in Chlamydomonas reinhardtii

2008 ◽  
Vol 7 (4) ◽  
pp. 639-646 ◽  
Author(s):  
Monica GuhaMajumdar ◽  
Ethan Dawson-Baglien ◽  
Barbara B. Sears
Keyword(s):  
Chlamydomonas Reinhardtii ◽  
Forensic Analysis ◽  
Direct Repeats ◽  
Reporter Construct ◽  
Chloroplast Microsatellite ◽  
Replication Slippage ◽  
Reading Frame ◽  
Viable Cells ◽  
Short Tandem

ABSTRACT Microsatellites are composed of short tandem direct repeats; deletions or duplications of those repeats through the process of replication slippage result in microsatellite instability relative to other genomic loci. Variation in repeat number occurs so frequently that microsatellites can be used for genotyping and forensic analysis. However, an accurate assessment of the rates of change can be difficult because the presence of many repeats makes it difficult to determine whether changes have occurred through single or multiple events. The current study was undertaken to experimentally assess the rates of replication slippage that occur in vivo in the chloroplast DNA of Chlamydomonas reinhardtii. A reporter construct was created in which a stretch of AAAG repeats was inserted into a functional gene to allow changes to be observed when they occurred at the synthetic microsatellite. Restoration of the reading frame occurred through replication slippage in 15 of every million viable cells. Since only one-third of the potential insertion/deletion events would restore the reading frame, the frequency of change could be deduced to be 4.5 × 10−5. Analysis of the slippage events showed that template slippage was the primary event, resulting in deletions rather than duplications. These findings contrasted with events observed in Escherichia coli during maintenance of the plasmid, where duplications were the rule.

scholarly journals Postreplication Repair Inhibits CAG · CTG Repeat Expansions in Saccharomyces cerevisiae

2006 ◽  
Vol 27 (1) ◽  
pp. 102-110 ◽  
Author(s):  
Danielle L. Daee ◽  
Tony Mertz ◽  
Robert S. Lahue
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Trinucleotide Repeats ◽  
Dna Microsatellites ◽  
Dinucleotide Repeats ◽  
Replication Slippage ◽  
Postreplication Repair ◽  
Epistasis Analysis ◽  
Repeat Expansions ◽  
The Relationship ◽  
Ctg Repeat

ABSTRACTTrinucleotide repeats (TNRs) are unique DNA microsatellites that can expand to cause human disease. Recently, Srs2 was identified as a protein that inhibits TNR expansions inSaccharomyces cerevisiae. Here, we demonstrate that Srs2 inhibits CAG · CTG expansions in conjunction with the error-free branch of postreplication repair (PRR). Likesrs2mutants, expansions are elevated inrad18andrad5mutants, as well as the PRR-specific PCNA allelespol30-K164Randpol30-K127/164R. Epistasis analysis indicates that Srs2 acts upstream of these PRR proteins. Also, likesrs2mutants, thepol30-K127/164Rphenotype is specific for expansions, as this allele does not alter mutation rates at dinucleotide repeats, at nonrepeating sequences, or for CAG · CTG repeat contractions. Our results suggest that Srs2 action and PRR processing inhibit TNR expansions. We also investigated the relationship between PRR and Rad27 (Fen1), a well-established inhibitor of TNR expansions that acts at 5′ flaps. Our results indicate that PRR protects against expansions arising from the 3′ terminus, presumably replication slippage events. This work provides the first evidence that CAG · CTG expansions can occur by 3′ slippage, and our results help define PRR as a key cellular mechanism that protects against expansions.

scholarly journals Replication slippage between distant short repeats in Saccharomyces cerevisiae depends on the direction of replication and the RAD50 and RAD52 genes.

1995 ◽  
Vol 15 (10) ◽  
pp. 5607-5617 ◽  
Author(s):  
H T Tran ◽  
N P Degtyareva ◽  
N N Koloteva ◽  
A Sugino ◽  
H Masumoto ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Stability ◽  
Genome Instability ◽  
Temperature Sensitive ◽  
Direct Repeats ◽  
Dna Polymerase Delta ◽  
Dna Double Strand Breaks ◽  
Yeast Saccharomyces Cerevisiae ◽  
Replication Slippage ◽  
Random Sequences

Small direct repeats, which are frequent in all genomes, are a potential source of genome instability. To study the occurrence and genetic control of repeat-associated deletions, we developed a system in the yeast Saccharomyces cerevisiae that was based on small direct repeats separated by either random sequences or inverted repeats. Deletions were examined in the LYS2 gene, using a set of 31- to 156-bp inserts that included inserts with no apparent potential for secondary structure as well as two quasipalindromes. All inserts were flanked by 6- to 9-bp direct repeats of LYS2 sequence, providing an opportunity for Lys+ reversion via precise excision. Reversions could arise by extended deletions involving either direct repeats or random sequences and by -1-or +2-bp frameshift mutations. The deletion breakpoints were always associated with short (3- to 9-bp) perfect or imperfect direct repeats. Compared with the POL+ strain, deletions between small direct repeats were increased as much as 100-fold, and the spectrum was changed in a temperature-sensitive DNA polymerase delta pol3-t mutant, suggesting a role for replication. The type of deletion depended on orientation relative to the origin of replication. On the basis of these results, we propose (i) that extended deletions between small repeats arise by replication slippage and (ii) that the deletions occur primarily in either the leading or lagging strand. The RAD50 and RAD52 genes, which are required for the recombinational repair of many kinds of DNA double-strand breaks, appeared to be required also for the production of up to 90% of the deletions arising between separated repeats in the pol3-t mutant, suggesting a newly identified role for these genes in genome stability and possibly replication.

Nucleotide Insertions and Deletions in Chronic Lymphocytic Leukemia. A CLL Specific Deletion among IGHV3-21 Expressing Cases with Stereotyped Receptors.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2100-2100
Author(s):  
Chrysoula Belessi ◽  
Frédéric Davi ◽  
Kostas Stamatopoulos ◽  
Massimo Degano ◽  
Thanassis Andreou ◽  
...  
Keyword(s):  
Somatic Hypermutation ◽  
Close Association ◽  
Variable Region ◽  
Lymphocytic Leukemia ◽  
Sequencing Analysis ◽  
Sequence Motifs ◽  
Replication Slippage ◽  
Reading Frame ◽  
Nucleotide Insertions ◽  
Dynamics Simulations

Abstract Insertions/duplications and deletions (I/D/Ds) in IG variable region genes are infrequent sequelae of the somatic hypermutation process. In the present study, we document the occurrence of nucleotide I/D/Ds in rearranged IGHV genes in CLL patients. Among 809 IGHV-D-J sequences amplified in 760 CLL cases, 9 (1.11%) and 15 (1.85%) sequences exhibited IGHV sequence changes consistent with nucleotide insertions/duplications or deletions, respectively. I/D/Ds were found in genes of the IGHV1, IGHV3 and IGHV4 subgroups, always within mutated IGHV-D-J rearrangements. In 21/24 cases, the inserted/duplicated or lost nucleotides occurred in multiples of 3; therefore, the original reading frame was maintained and a potentially intact receptor was coded. I/D/Ds were located completely or in part within CDRs in 21/24 cases; sequence motifs (AGY, AGA, AAC trinucleotides) that resemble intrinsic hotspots for somatic hypermutation were identified in 21/24 sequences. Short stretches with high homology (misalignment feet) that would offer the DNA polymerase an alternative template for re-annealing in cases of replication slippage were identified in all CLL sequences carrying I/D/Ds. I/D/Ds were generated somatically since (i) they always occurred in cases with somatic mutations, (ii) they could not be found on sequencing analysis of the corresponding germline IGHV genes amplified on DNA isolated from selected patients’ neutrophils, thus excluding a possible genetic polymorphism. The incidence of I/D/Ds in CLL is consistent with previous reports in normal, autoreactive and neoplastic human B cells, thus seemingly indicating that these modifications generally arise without any particular disease-specific associations. A striking exception to this rule was identified in the case of CLL IGHV3-21 expressing cases: one aminoacid was deleted from the CDR2 region in 16/74 (21.6%) IGHV3-21 CLL sequences (database-derived IGHV3-21 CLL cases + present series) vs. only 2/340 (0.59%) non-CLL IGHV3-21 sequences; 15/16 CLL IGHV3-21 sequences carrying this deletion belonged to a subset with unique, shared HCDR3s and light chain CDR3 motifs. The effect of the CDR2 deletion on the structure of the IG molecules in this subset of CLL patients was studied with molecular modelling and dynamics simulations. The models suggested that the deletion could be accommodated without significantly affecting the local structure. The close association of deletions in CDR2 with the homologous subset of IGHV3-21 expressing CLL cases provides further evidence for the importance of an antigenic drive in malignant transformation and/or maintenance of the neoplastic clone in at least some CLL cases.

Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae)

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 634-641 ◽  
Author(s):  
T HM Mes ◽  
P Kuperus ◽  
J Kirschner ◽  
J Stepanek ◽  
P Oosterveld ◽  
...  
Keyword(s):  
Chloroplast Dna ◽  
Chloroplast Genome ◽  
Hot Spot ◽  
Phylogenetic Signal ◽  
Direct Repeats ◽  
Nucleotide Substitutions ◽  
Replication Slippage ◽  
Coding Regions ◽  
Chloroplast Genomes ◽  
Structural Mutations

Sequence variation in 2.2 kb of non-coding regions of the chloroplast genome of eight dandelions (Taraxacum: Lactuceae) from Asia and Europe is interpreted in the light of the phylogenetic signal of base substitutions vs. indels (insertions-deletions). The four non-coding regions displayed a total of approximately 30 structural mutations of which 9 are potentially phylogenetically informative. Insertions, deletions, and an inversion were found that involved consecutive stretches of up to 172 bases. When compared to phylogenetic relationships of the chloroplast genomes based on nucleotide substitutions only, many homoplasious indels (33%) were detected that differed considerably in length and did not comprise simple sequence repeats typically associated with replication slippage. Though many indels in the intergenic spacers were associated with direct repeats, frequently, the variable stretches participated in inverted repeat stabilized hairpins. In each intergenic spacer or intron examined, nucleotide stretches ranging from 30 to 60 bp were able to fold into stabilized secondary structures. When these indels were homoplasious, they always ranked among the most stabilized hairpins in the non-coding regions. The association of higher order structures that involve both classes of repeats and parallel structural mutations in hot spot regions of the chloroplast genome can be used to differentiate among mutations that differ in phylogenetic reliability.Key words: Taraxacum, indel, non-coding chloroplast DNA, hairpin, evolution.

A comparative study of convicilin storage protein gene sequences in species of the tribe Vicieae

Genome ◽  
2008 ◽  
Vol 51 (7) ◽  
pp. 511-523 ◽  
Author(s):  
L. E. Sáenz de Miera ◽  
J. Ramos ◽  
M. Pérez de la Vega
Keyword(s):  
Amino Acids ◽  
Storage Proteins ◽  
Seed Storage ◽  
Seed Storage Proteins ◽  
Gene Sequences ◽  
Replication Slippage ◽  
Charged Amino Acids ◽  
Arginine Residues ◽  
Related Group ◽  
Additional Sequence

Convicilins, a set of seed storage proteins, differ from vicilins, a related group of seed storage proteins, mainly because of the presence of the N-terminal extension, an additional sequence of amino acids in the sequence corresponding to the first exon. Convicilins have been described only in species of the legume tribe Vicieae. One or two genes for convicilins have been identified in most species of this tribe. The genus Pisum is the main exception, since two genes have been identified in most of its species. Thirty-four new convicilin gene sequences from 29 different species ( Lathyrus , Lens , Pisum, and Vicia spp.) have been analyzed here. Convicilin gene sequences are generally organized in 6 exons, but in some instances one of the internal introns (2nd or 4th) is lost. In these 29 species, the N-terminal extension is formed by a stretch of 99 to 196 amino acids particularly rich in polar and charged amino acids (on average, it contains 29.43% glutamic acid and 15.38% arginine residues). This N-terminal extension has the characteristics of an intrinsically unstructured region (IUR), one of the categories of protein “degenerate sequences”. A comparative analysis indicates that the N-terminal extension sequence has evolved faster than the surrounding sequence, which is common to all vicilins, and it evolved mainly through a series of duplications of short internal sequences and triplet expansions, the predominant one being GAA. This agrees with the evolution of IURs, which is faster than the evolution of surrounding sequences and is mainly due to replication slippage and unequal crossover recombination. Alternative maximum-likelihood trees of phylogenetic relationships among the 29 Vicieae species based on the convicilin exon sequences are presented and discussed.

scholarly journals Signature of backward replication slippage at the copy number variation junction

2014 ◽  
Vol 59 (5) ◽  
pp. 247-250 ◽  
Author(s):  
Tamae Ohye ◽  
Hidehito Inagaki ◽  
Mamoru Ozaki ◽  
Toshiro Ikeda ◽  
Hiroki Kurahashi
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Replication Slippage ◽  
Number Variation
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