Bioinformatic analyses of sense and antisense expression from terminal inverted repeat transposons in Drosophila somatic cells

ABSTRACT Cloning and sequencing of the telomere of Streptomyces griseus revealed five palindromic sequences in the terminal 116 nucleotides, all of which can make a hairpin loop structure. However, the end sequence cannot form the foldback secondary structure that is common in Streptomyces telomeres and is suggested to be necessary for terminal replication. Both inside ends of the terminal inverted repeat (TIR) were also cloned and sequenced. The results confirmed the size of the TIR to be 24 kb and identified two almost identical open reading frames that might have been involved in the formation of the TIR.

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A Novel Replicative Enzyme Encoded by the Linear Arthrobacter Plasmid pAL1

Journal of Bacteriology ◽

10.1128/jb.00614-10 ◽

2010 ◽

Vol 192 (19) ◽

pp. 4935-4943 ◽

Cited By ~ 7

Author(s):

Stephan Kolkenbrock ◽

Bianca Naumann ◽

Michael Hippler ◽

Susanne Fetzner

Keyword(s):

Inverted Repeat ◽

Bioinformatic Analysis ◽

Dna Helicase ◽

Terminal Segment ◽

Helicase Domain ◽

Terminal Inverted Repeat ◽

Sequence Motifs ◽

Dna Topoisomerase ◽

Central Regions

ABSTRACT The soil bacterium Arthrobacter nitroguajacolicus Rü61a contains the linear plasmid pAL1, which codes for the degradation of 2-methylquinoline. Like other linear replicons of actinomycetes, pAL1 is characterized by short terminal inverted-repeat sequences and terminal proteins (TPpAL1) covalently attached to its 5′ ends. TPpAL1, encoded by the pAL1.102 gene, interacts in vivo with the protein encoded by pAL1.101. Bioinformatic analysis of the pAL1.101 protein, which comprises 1,707 amino acids, suggested putative zinc finger and topoisomerase-primase domains and part of a superfamily 2 helicase domain in its N-terminal and central regions, respectively. Sequence motifs characteristic of the polymerization domain of family B DNA polymerases are partially conserved in a C-terminal segment. The purified recombinant protein catalyzed the deoxycytidylation of TPpAL1 in the presence of single-stranded DNA templates comprising the 3′-terminal sequence (5′-GCAGG-3′), which in pAL1 forms the terminal inverted repeat, but also at templates with 5′-(G/T)CA(GG/GC/CG)-3′ ends. Enzyme assays suggested that the protein exhibits DNA topoisomerase, DNA helicase, and DNA- and protein-primed DNA polymerase activities. The pAL1.101 protein, therefore, may act as a replicase of pAL1.

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The MuDR transposon terminal inverted repeat contains a complex plant promoter directing distinct somatic and germinal programs

The Plant Journal ◽

10.1111/j.1365-313x.2001.00939.x ◽

2001 ◽

Vol 25 (1) ◽

pp. 79-91 ◽

Cited By ~ 2

Author(s):

Manish N. Raizada ◽

Maria-Ines Benito ◽

Virginia Walbot

Keyword(s):

Inverted Repeat ◽

Terminal Inverted Repeat ◽

Plant Promoter

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DNase I hypersensitivity of the terminal inverted repeat DNA sequences in the macronucleus of the ciliate Stylonychia mytilus

FEBS Letters ◽

10.1016/0014-5793(81)80246-3 ◽

1981 ◽

Vol 126 (2) ◽

pp. 219-222 ◽

Cited By ~ 9

Author(s):

Hans J. Lipps ◽

Petra Erhardt

Keyword(s):

Dna Sequences ◽

Inverted Repeat ◽

Dnase I ◽

Terminal Inverted Repeat ◽

Dnase I Hypersensitivity ◽

Repeat Dna ◽

Stylonychia Mytilus

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Phylogenetic analysis reveals Stowaway-like elements may represent a fourth family of the IS630-Tc1-mariner superfamily

Genome ◽

10.1139/g01-127 ◽

2002 ◽

Vol 45 (1) ◽

pp. 82-90 ◽

Cited By ~ 12

Author(s):

Kime Turcotte ◽

Thomas Bureau

Keyword(s):

Phylogenetic Analysis ◽

Inverted Repeat ◽

Evolutionary Relationship ◽

Open Reading Frames ◽

Published Data ◽

Terminal Inverted Repeat ◽

Predominant Type ◽

Sequence Signature ◽

Eukaryotic Organisms ◽

Reading Frames

The genomes of plants, like virtually all other eukaryotic organisms, harbor a diverse array of mobile elements, or transposons. In terms of numbers, the predominant type of transposons in many plants is the miniature inverted-repeat transposable element (MITE). There are three archetypal MITEs, known as Tourist, Stowaway, and Emigrant, each of which can be defined by a specific terminal inverted-repeat (TIR) sequence signature. Although their presence was known for over a decade, only recently have open reading frames (ORFs) been identified that correspond to putative transposases for each of the archetypes. We have identified two Stowaway elements that encode a putative transposase and are similar to members of the previously characterized IS630Tc1-mariner superfamily. In this report, we provide a high-resolution phylogenetic analysis of the evolutionary relationship between Stowaway, Emigrant, and members of the IS630Tc1-mariner superfamily. We show that although Emigrant is closely related to the pogo-like family of elements, Stowaway may represent a novel family. Integration of our results with previously published data leads to the conclusion that the three main types of MITEs have different evolutionary histories despite similarity in structure.Key words: Stowaway, Emigrant, MITE, mariner, transposon.

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Conserved motifs and dynamic aspects of the terminal inverted repeat organization within Bari-like transposons

Molecular Genetics and Genomics ◽

10.1007/s00438-008-0324-7 ◽

2008 ◽

Vol 279 (5) ◽

pp. 451-461 ◽

Cited By ~ 9

Author(s):

Roberta Moschetti ◽

Sarantis Chlamydas ◽

Renè Massimiliano Marsano ◽

Ruggiero Caizzi

Keyword(s):

Inverted Repeat ◽

Terminal Inverted Repeat ◽

Conserved Motifs

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DNA transposons mediate duplications via transposition-independent and -dependent mechanisms in metazoans

Nature Communications ◽

10.1038/s41467-021-24585-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Shengjun Tan ◽

Huijing Ma ◽

Jinbo Wang ◽

Man Wang ◽

Mengxia Wang ◽

...

Keyword(s):

Inverted Repeat ◽

Replication Fork ◽

Single Copy ◽

Terminal Inverted Repeat ◽

Gap Filling ◽

New Genes ◽

Repeat Dna ◽

New Gene ◽

Gene Structures ◽

Reference Genomes

AbstractDespite long being considered as “junk”, transposable elements (TEs) are now accepted as catalysts of evolution. One example is Mutator-like elements (MULEs, one type of terminal inverted repeat DNA TEs, or TIR TEs) capturing sequences as Pack-MULEs in plants. However, their origination mechanism remains perplexing, and whether TIR TEs mediate duplication in animals is almost unexplored. Here we identify 370 Pack-TIRs in 100 animal reference genomes and one Pack-TIR (Ssk-FB4) family in fly populations. We find that single-copy Pack-TIRs are mostly generated via transposition-independent gap filling, and multicopy Pack-TIRs are likely generated by transposition after replication fork switching. We show that a proportion of Pack-TIRs are transcribed and often form chimeras with hosts. We also find that Ssk-FB4s represent a young protein family, as supported by proteomics and signatures of positive selection. Thus, TIR TEs catalyze new gene structures and new genes in animals via both transposition-independent and -dependent mechanisms.

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A Mutation in the Flanking 5′-TA-3′ Dinucleotide Prevents Excision of an Internal Eliminated Sequence From the Paramecium tetraurelia Genome

Genetics ◽

10.1093/genetics/151.2.597 ◽

1999 ◽

Vol 151 (2) ◽

pp. 597-604 ◽

Cited By ~ 1

Author(s):

Kimberly M Mayer ◽

James D Forney

Keyword(s):

Inverted Repeat ◽

Mutant Cell ◽

Consensus Sequence ◽

Terminal Inverted Repeat ◽

Paramecium Tetraurelia ◽

Wild Type ◽

Coding Region ◽

Discrete Elements ◽

Additional Information ◽

Gene Excision

Abstract The germline chromosomes in Paramecium and other ciliated protozoa contain regions of DNA that are excised and eliminated during the development of a new macronuclear genome. Paramecium tetraurelia internal eliminated sequences (IESs) are invariably flanked by a 5′-TA-3′ dinucleotide sequence that is part of a larger 8-bp terminal inverted-repeat consensus sequence. Both features, the absolutely conserved 5′-TA-3′ and the remaining 6-bp terminal inverted repeat, are shared with the mariner/Tc1 class of transposons. In this article we describe a mutant cell line (AIM-2) defective in excision of a single IES from the coding region of the A51 surface antigen gene. Excision of the 370-bp IES6649 is prevented by a single A to G transition in the invariably conserved 5′-TA-3′ dinucleotide. Failure to excise IES6649 also revealed a 29-bp IES located inside IES6649. Additional experiments with the previously isolated AIM-1 mutant, which also contains an internal IES, shows that alternate excision using the wild-type end of IES2591 with an end from the internal IES is extremely rare or nonexistent. These results indicate that IESs are discrete elements whose excision depends upon nucleotides located within the consensus sequence, but also suggest that additional information is required to match one end of an IES with its excision partner.

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Recent amplification of microsatellite-associated miniature inverted-repeat transposable elements in the pineapple genome

BMC Plant Biology ◽

10.1186/s12870-021-03194-0 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lianyu Lin ◽

Anupma Sharma ◽

Qingyi Yu

Keyword(s):

Transposable Elements ◽

Inverted Repeat ◽

Sequence Similarity ◽

Genome Structure ◽

Terminal Inverted Repeat ◽

Essential Information ◽

Dna Transposon ◽

Genome Wide ◽

Identification And Characterization

Abstract Background Miniature inverted-repeat transposable elements (MITEs) are non-autonomous DNA transposable elements that play important roles in genome organization and evolution. Genome-wide identification and characterization of MITEs provide essential information for understanding genome structure and evolution. Results We performed genome-wide identification and characterization of MITEs in the pineapple genome. The top two MITE families, accounting for 29.39% of the total MITEs and 3.86% of the pineapple genome, have insertion preference in (TA) n dinucleotide microsatellite regions. We therefore named these MITEs A. comosus microsatellite-associated MITEs (Ac-mMITEs). The two Ac-mMITE families, Ac-mMITE-1 and Ac-mMITE-2, shared sequence similarity in the terminal inverted repeat (TIR) regions, suggesting that these two Ac-mMITE families might be derived from a common or closely related autonomous elements. The Ac-mMITEs are frequently clustered via adjacent insertions. Among the 21,994 full-length Ac-mMITEs, 46.1% of them were present in clusters. By analyzing the Ac-mMITEs without (TA) n microsatellite flanking sequences, we found that Ac-mMITEs were likely derived from Mutator-like DNA transposon. Ac-MITEs showed highly polymorphic insertion sites between cultivated pineapples and their wild relatives. To better understand the evolutionary history of Ac-mMITEs, we filtered and performed comparative analysis on the two distinct groups of Ac-mMITEs, microsatellite-targeting MITEs (mt-MITEs) that are flanked by dinucleotide microsatellites on both sides and mutator-like MITEs (ml-MITEs) that contain 9/10 bp TSDs. Epigenetic analysis revealed a lower level of host-induced silencing on the mt-MITEs in comparison to the ml-MITEs, which partially explained the significantly higher abundance of mt-MITEs in pineapple genome. The mt-MITEs and ml-MITEs exhibited differential insertion preference to gene-related regions and RNA-seq analysis revealed their differential influences on expression regulation of nearby genes. Conclusions Ac-mMITEs are the most abundant MITEs in the pineapple genome and they were likely derived from Mutator-like DNA transposon. Preferential insertion in (TA) n microsatellite regions of Ac-mMITEs occurred recently and is likely the result of damage-limiting strategy adapted by Ac-mMITEs during co-evolution with their host. Insertion in (TA) n microsatellite regions might also have promoted the amplification of mt-MITEs. In addition, mt-MITEs showed no or negligible impact on nearby gene expression, which may help them escape genome control and lead to their amplification.

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DNA sequence homology between the terminal inverted repeats of Shope fibroma virus and an endogenous cellular plasmid species

Molecular and Cellular Biology ◽

10.1128/mcb.6.1.265-276.1986 ◽

1986 ◽

Vol 6 (1) ◽

pp. 265-276

Author(s):

C Upton ◽

G McFadden

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Sequence Homology ◽

Inverted Repeat ◽

Specific Activity ◽

High Specific Activity ◽

Cesium Chloride ◽

Open Reading Frame ◽

Terminal Inverted Repeat ◽

Reading Frame

DNA hybridization experiments indicate that the genome of a tumorigenic poxvirus. Shope fibroma virus (SFV), possesses sequence homology with DNA isolated from uninfected rabbit cells. Southern blotting experiments, either with high-complexity rabbit DNA as probe and SFV restriction fragments as targets or with high-specific activity, 32P-labeled, cloned SFV sequences as probes and rabbit DNA as target, indicate that the homologous sequences map at two locations within the viral genome, one in each copy of the terminal inverted repeat sequences. Unexpectedly, Southern blots revealed that the homologous host sequences reside in a rabbit extrachromosomal DNA element. This autonomous low-molecular-weight DNA species could be specifically amplified by cycloheximide treatment and was shown by isopycnic centrifugation in cesium chloride-ethidium bromide to consist predominantly of covalently closed circular DNA molecules. DNA sequencing of pSIC-9, a cloned 1.9-kilobase fragment of the rabbit plasmid species, indicated extensive homology at the nucleotide level over a 1.5-kilobase stretch of the viral terminal inverted repeat. Analysis of open reading frames in both the plasmid and SFV DNA revealed that (i) the N-terminal 157-amino acid sequence of a potential 514-amino acid SFV polypeptide is identical to the N-terminal 157 amino acids of one pSIC-9 open reading frame, and (ii) a second long pSIC-9 open reading frame of 361 amino acids, although significantly diverged from the comparable nucleotide sequence in the virus, possessed considerable homology to a family of cellular protease inhibitors, including alpha 1-antichymotrypsin, alpha 1-antitrypsin, and antithrombin III. The potential role of such cellular plasmid-like DNA species as a mediator in the exchange of genetic information between the host cell and a cytoplasmically replicating poxvirus is discussed.

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