Virus-induced mutations in maize: on the nature of stress-induction of unstable loci

SUMMARYUnstable alleles, broken chromosomes and stable mutants have arisen in maize out of infected plants of Barley Striped Mosaic Virus and other viruses. Surprisingly, these same events have appeared out of progenies of these infected plants that themselves do not show any infection. These mutants showing instability have resulted from insertions that are not necessarily related. Two of these insertions (BS1 and TZ86) that have been analysed molecularly have the general characteristics of maize insertions with terminal inverted repeats and host duplication at the terminus of the transposon. In other experiments three of the unstable alleles at the a locus in maize (A locus, chromosome 3, short arm; one of genes for anthocyanin control) that arose in derivative lines of the initially treated plants are responsive to a transposable element, the Uq element. It was determined that the Uq element was not present in this initially treated plant but was present in the untreated female plant. It is proposed that the initial treatment induced events that in turn led to the mobilization of elements and that these events continue to occur in later generations. It seems that genomic events once initiated such as mobility of elements cannot be terminated despite a discontinuation of the treatment (virus) and, like a Frankenstein monster, is not responsive to its maker.

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Rearrangements of the DNA in Carbon Ion-Induced Mutants of Arabidopsis thaliana

Genetics ◽

10.1093/genetics/157.1.379 ◽

2001 ◽

Vol 157 (1) ◽

pp. 379-387 ◽

Cited By ~ 1

Author(s):

Naoya Shikazono ◽

Atsushi Tanaka ◽

Hiroshi Watanabe ◽

Shigemitsu Tano

Keyword(s):

Arabidopsis Thaliana ◽

Nonhomologous End Joining ◽

Chromosome 3 ◽

Chromosome 2 ◽

Carbon Ions ◽

Induced Mutations ◽

End Joining ◽

Carbon Ion ◽

Induced Mutants ◽

Dna Strand

Abstract To elucidate the nature of structural alterations in plants, three carbon ion-induced mutations in Arabidopsis thaliana, gl1-3, tt4(C1), and ttg1-21, were analyzed. The gl1-3 mutation was found to be generated by an inversion of a fragment that contained GL1 and Atpk7 loci on chromosome 3. The size of the inverted fragment was a few hundred kilobase pairs. The inversion was found to accompany an insertion of a 107-bp fragment derived from chromosome 2. The tt4(C1) mutation was also found to be due to an inversion. The size of the intervening region between the breakpoints was also estimated to be a few hundred kilobase pairs. In the case of ttg1-21, it was found that a break occurred at the TTG1 locus on chromosome 5, and reciprocal translocation took place between it and chromosome 3. From the sequences flanking the breakpoints, the DNA strand breaks induced by carbon ions were found to be rejoined using, if present, only short homologous sequences. Small deletions were also observed around the breakpoints. These results suggest that the nonhomologous end-joining (NHEJ) pathway operates after plant cells are exposed to ion particles.

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Linear Plasmids with Terminal Inverted Repeats Obtained from Streptomyces Rochei and Kluyveromyces Lactis

Plasmids in Bacteria ◽

10.1007/978-1-4613-2447-8_32 ◽

1985 ◽

pp. 433-451 ◽

Cited By ~ 4

Author(s):

Kenji Sakaguchi ◽

Hirohiko Hirochika ◽

Norio Gunge

Keyword(s):

Kluyveromyces Lactis ◽

Inverted Repeats ◽

Linear Plasmids ◽

Terminal Inverted Repeats

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Functional requirement of terminal inverted repeats for efficient ProtoRAG activity reveals the early evolution of V(D)J recombination

National Science Review ◽

10.1093/nsr/nwz179 ◽

2019 ◽

Vol 7 (2) ◽

pp. 403-417 ◽

Cited By ~ 1

Author(s):

Xin Tao ◽

Shaochun Yuan ◽

Fan Chen ◽

Xiaoman Gao ◽

Xinli Wang ◽

...

Keyword(s):

Consensus Sequence ◽

Protein Stabilization ◽

Inverted Repeats ◽

Functional Requirement ◽

Signal Sequences ◽

Terminal Inverted Repeats ◽

Homologous Sequences ◽

Recombination Signal Sequences ◽

Chordate Evolution ◽

The Common

Abstract The discovery of ProtoRAG in amphioxus indicated that vertebrate RAG recombinases originated from an ancient transposon. However, the sequences of ProtoRAG terminal inverted repeats (TIRs) were obviously dissimilar to the consensus sequence of mouse 12/23RSS and recombination mediated by ProtoRAG or RAG made them incompatible with each other. Thus, it is difficult to determine whether or how 12/23RSS persisted in the vertebrate RAG system that evolved from the TIRs of ancient RAG transposons. Here, we found that the activity of ProtoRAG is highly dependent on its asymmetric 5′TIR and 3′TIR, which are composed of conserved TR1 and TR5 elements and a partially conserved TRsp element of 27/31 bp to separate them. Similar to the requirements for the recombination signal sequences (RSSs) of RAG recombinase, the first CAC in TR1, the three dinucleotides in TR5 and the specific length of the partially conserved TRsp are important for the efficient recombination activity of ProtoRAG. In addition, the homologous sequences flanking the signal sequences facilitate ProtoRAG- but not RAG-mediated recombination. In addition to the diverged TIRs, two differentiated functional domains in BbRAG1L were defined to coordinate with the divergence between TIRs and RSSs. One of these is the CTT* domain, which facilitates the specific TIR recognition of the BbRAGL complex, and the other is NBD*, which is responsible for DNA binding and the protein stabilization of the BbRAGL complex. Thus, our findings reveal that the functional requirement for ProtoRAG TIRs is similar to that for RSS in RAG-mediated recombination, which not only supports the common origin of ProtoRAG TIRs and RSSs from the asymmetric TIRs of ancient RAG transposons, but also reveals the development of RAG and RAG-like machineries during chordate evolution.

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Two Chimeric Chromosomes of Streptomyces coelicolor A3(2) Generated by Single Crossover of the Wild-Type Chromosome and Linear Plasmid SCP1

Journal of Bacteriology ◽

10.1128/jb.186.19.6553-6559.2004 ◽

2004 ◽

Vol 186 (19) ◽

pp. 6553-6559 ◽

Cited By ~ 23

Author(s):

Masayuki Yamasaki ◽

Haruyasu Kinashi

Keyword(s):

Genome Evolution ◽

Streptomyces Coelicolor ◽

Linear Plasmid ◽

Nucleotide Sequencing ◽

Inverted Repeats ◽

Wild Type ◽

Linear Chromosome ◽

Terminal Inverted Repeats ◽

Type Chromosome ◽

Chromosomal Duplication

ABSTRACT Streptomyces coelicolor A3(2) strain 2106 carries a 1.85-Mb linear plasmid, SCP1′-cysD, in addition to a 7.2-Mb linear chromosome. Macrorestriction analysis indicated that both linear DNAs are hybrids of the wild-type chromosome and the linear plasmid SCP1 on each side. Nucleotide sequencing of the fusion junctions revealed no homology between the recombination regions. SCP1′-cysD contains an SCP1 telomere and a chromosomal telomere at each end and therefore does not have terminal inverted repeats. In addition, SCP1′-cysD could not be eliminated from strain 2106 by various mutagenic treatments. Thus, we concluded that both the 7.2-Mb chromosome and SCP1′-cysD are chimeric chromosomes generated by a single crossover of the wild-type chromosome and SCP1. This may be regarded as a model of chromosomal duplication in genome evolution.

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Tumorigenic poxviruses: Transcriptional mapping of the terminal inverted repeats of shope fibroma virus

Virology ◽

10.1016/0042-6822(87)90210-8 ◽

1987 ◽

Vol 158 (2) ◽

pp. 381-393 ◽

Cited By ~ 18

Author(s):

C. Macaulay ◽

C. Upton ◽

G. McFadden

Keyword(s):

Inverted Repeats ◽

Terminal Inverted Repeats ◽

Transcriptional Mapping

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Involvement of two domains with helix-turn-helix and zinc finger motifs in the binding of IS1 transposase to terminal inverted repeats

Molecular Microbiology ◽

10.1111/j.1365-2958.2004.04103.x ◽

2004 ◽

Vol 53 (1) ◽

pp. 193-202 ◽

Cited By ~ 7

Author(s):

Shinya Ohta ◽

Etsuro Yoshimura ◽

Eiichi Ohtsubo

Keyword(s):

Zinc Finger ◽

Inverted Repeats ◽

Terminal Inverted Repeats ◽

Zinc Finger Motifs

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Silencing of Mutator Elements in Maize Involves Distinct Populations of Small RNAs and Distinct Patterns of DNA Methylation

Genetics ◽

10.1534/genetics.120.303033 ◽

2020 ◽

Vol 215 (2) ◽

pp. 379-391 ◽

Cited By ~ 3

Author(s):

Diane Burgess ◽

Hong Li ◽

Meixia Zhao ◽

Sang Yeol Kim ◽

Damon Lisch

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Small Rnas ◽

Cytosine Methylation ◽

De Novo ◽

Epigenetic Silencing ◽

Inverted Repeats ◽

Causal Relationships ◽

Terminal Inverted Repeats ◽

Silencing Pathways

Transposable elements (TEs) are a ubiquitous feature of plant genomes. Because of the threat they post to genome integrity, most TEs are epigenetically silenced. However, even closely related plant species often have dramatically different populations of TEs, suggesting periodic rounds of activity and silencing. Here, we show that the process of de novo methylation of an active element in maize involves two distinct pathways, one of which is directly implicated in causing epigenetic silencing and one of which is the result of that silencing. Epigenetic changes involve changes in gene expression that can be heritably transmitted to daughter cells in the absence of changes in DNA sequence. Epigenetics has been implicated in phenomena as diverse as development, stress response, and carcinogenesis. A significant challenge facing those interested in investigating epigenetic phenomena is determining causal relationships between DNA methylation, specific classes of small RNAs, and associated changes in gene expression. Because they are the primary targets of epigenetic silencing in plants and, when active, are often targeted for de novo silencing, TEs represent a valuable source of information about these relationships. We use a naturally occurring system in which a single TE can be heritably silenced by a single derivative of that TE. By using this system it is possible to unravel causal relationships between different size classes of small RNAs, patterns of DNA methylation, and heritable silencing. Here, we show that the long terminal inverted repeats within Zea mays MuDR transposons are targeted by distinct classes of small RNAs during epigenetic silencing that are dependent on distinct silencing pathways, only one of which is associated with transcriptional silencing of the transposon. Further, these small RNAs target distinct regions of the terminal inverted repeats, resulting in different patterns of cytosine methylation with different functional consequences with respect to epigenetic silencing and the heritability of that silencing.

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Characterization of IS18, an Element Capable of Activating the Silent aac(6′)-Ij Gene ofAcinetobacter sp. 13 Strain BM2716 by Transposition

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.42.10.2759 ◽

1998 ◽

Vol 42 (10) ◽

pp. 2759-2761 ◽

Cited By ~ 13

Author(s):

Eric Rudant ◽

Patrice Courvalin ◽

Thierry Lambert

Keyword(s):

Resistance Gene ◽

Insertion Sequence ◽

Resistant Mutant ◽

Open Reading Frame ◽

Inverted Repeats ◽

Aminoglycoside Resistance ◽

Reading Frame ◽

Terminal Inverted Repeats ◽

Hybrid Promoter

ABSTRACT Insertion sequence IS18 was detected by analysis of the spontaneous aminoglycoside resistant mutant Acinetobactersp. 13 strain BM2716-1. Insertion of the element upstream from the silent acetyltransferase gene aac(6′)-Ij created a hybrid promoter that putatively accounts for the expression of the aminoglycoside resistance gene. The 1,074-bp IS18 element contained partially matched (20 out of 26 bases) terminal inverted repeats, one of which overlapped the 3′ end of a 935-bp open reading frame potentially encoding a protein related to the transposases of the IS30 family. IS18 was found in 6 out of 29 strains of Acinetobacter sp. 13 but not in 10 strains each of A. baumannii and A. haemolyticus.

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Characterization of a Class II Defective Transposon Carrying Two Haloacetate Dehalogenase Genes from Delftia acidovorans Plasmid pUO1

Applied and Environmental Microbiology ◽

10.1128/aem.68.5.2307-2315.2002 ◽

2002 ◽

Vol 68 (5) ◽

pp. 2307-2315 ◽

Cited By ~ 24

Author(s):

Masahiro Sota ◽

Masahiro Endo ◽

Keiji Nitta ◽

Haruhiko Kawasaki ◽

Masataka Tsuda

Keyword(s):

Transposable Elements ◽

Class Ii ◽

Class I ◽

Inverted Repeats ◽

High Homology ◽

Terminal Inverted Repeats ◽

Delftia Acidovorans

ABSTRACT The two haloacetate dehalogenase genes, dehH1 and dehH2, on the 65-kb plasmid pUO1 from Delftia acidovorans strain B were found to be located on transposable elements. The dehH2 gene was carried on an 8.9-kb class I composite transposon (TnHad1) that was flanked by two directly repeated copies of IS1071, IS1071L and IS1071R. The dehH1 gene was also flanked by IS1071L and a truncated version of IS1071 (IS1071N). TnHad1, dehH1, and IS1071N were located on a 15.6-kb class II transposon (TnHad2) whose terminal inverted repeats and res site showed high homology with those of the Tn21-related transposons. TnHad2 was defective in transposition because of its lacking the transposase and resolvase genes. TnHad2 could transpose when the Tn21-encoded transposase and resolvase were supplied in trans. These results demonstrated that Tn Had2 is a defective Tn21-related transposon carrying another class I catabolic transposon.

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