scholarly journals IS1630 of Mycoplasma fermentans, a Novel IS30-Type Insertion Element That Targets and Duplicates Inverted Repeats of Variable Length and Sequence during Insertion

1999 ◽  
Vol 181 (24) ◽  
pp. 7597-7607 ◽  
Author(s):  
Michael J. Calcutt ◽  
Jennifer L. Lavrrar ◽  
Kim S. Wise
Keyword(s):  
Amino Acid ◽  
Inverted Repeat ◽  
Insertion Sequence ◽  
Target Site ◽  
Inverted Repeats ◽  
Amino Acid Residues ◽  
Mycoplasma Fermentans ◽  
Is Elements ◽  
Repeat Sequences ◽  
Target Sites

ABSTRACT A new insertion sequence (IS) of Mycoplasma fermentansis described. This element, designated IS1630, is 1,377 bp long and has 27-bp inverted repeats at the termini. A single open reading frame (ORF), predicted to encode a basic protein of either 366 or 387 amino acids (depending on the start codon utilized), occupies most of this compact element. The predicted translation product of this ORF has homology to transposases of the IS30 family of IS elements and is most closely related (27% identical amino acid residues) to the product of the prototype of the group, IS30. Multiple copies of IS1630 are present in the genomes of at least two M. fermentans strains. Characterization and comparison of nine copies of the element revealed that IS1630 exhibits unusual target site specificity and, upon insertion, duplicates target sequences in a manner unlike that of any other IS element. IS1630 was shown to have the striking ability to target and duplicate inverted repeats of variable length and sequence during transposition. IS30-type elements typically generate 2- or 3-bp target site duplications, whereas those created by IS1630 vary between 19 and 26 bp. With the exception of two recently reported IS4-type elements which have the ability to generate variable large duplications (B. B. Plikaytis, J. T. Crawford, and T. M. Shinnick, J. Bacteriol. 180:1037–1043, 1998; E. M. Vilei, J. Nicolet, and J. Frey, J. Bacteriol. 181:1319–1323, 1999), such large direct repeats had not been observed for other IS elements. Interestingly, the IS1630-generated duplications are all symmetrical inverted repeat sequences that are apparently derived from rho-independent transcription terminators of neighboring genes. Although the consensus target site for IS30 is almost palindromic, individual target sites possess considerably less inverted symmetry. In contrast, IS1630appears to exhibit an increased stringency for inverted repeat recognition, since the majority of target sites had no mismatches in the inverted repeat sequences. In the course of this study, an additional copy of the previously identified insertion sequence ISMi 1 was cloned. Analysis of the sequence of this element revealed that the transposase encoded by this element is more than 200 amino acid residues longer and is more closely related to the products of other IS3 family members than had previously been recognized. A potential site for programmed translational frameshifting in ISMi 1 was also identified.

scholarly journals The IS1111 Family Members IS4321 and IS5075 Have Subterminal Inverted Repeats and Target the Terminal Inverted Repeats of Tn21 Family Transposons

2003 ◽  
Vol 185 (21) ◽  
pp. 6371-6384 ◽  
Author(s):  
Sally R. Partridge ◽  
Ruth M. Hall
Keyword(s):  
Inverted Repeat ◽  
Insertion Sequence ◽  
Family Members ◽  
Target Site ◽  
Inverted Repeats ◽  
Terminal Inverted Repeats ◽  
Is Elements ◽  
Target Sites ◽  
Specific Position ◽  
The Right

ABSTRACT IS5075 and IS4321 are closely related (93.1% identical) members of the IS1111 family that target a specific position in the 38-bp terminal inverted repeats of Tn21 family transposons and that are inserted in only one orientation. They are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (TAATGAG) or 6 bp (AATGAG) to the left of the left inverted repeats and 3 bp (AGA) or 4 bp (AGAT) to the right of the right inverted repeat. Circular forms of IS5075 and IS4321 in which the inverted repeats are separated by abutting terminal sequences (AGATAATGAG) were detected. A similar circular product was found for the related ISPa11. Transposition of IS4321 into the 38-bp target site was detected, but a flanking duplication was not generated. The precisely reconstituted target site was also identified. Over 50 members of the IS1111 family were identified. They encode related transposases, have related inverted repeats, and include related bases that lie outside these inverted repeats. In some, the flanking bases number 5 or 6 on the left and 4 or 3 on the right. Specific target sites were found for several of these insertion sequence (IS) elements. IS1111 family members therefore differ from the majority of IS elements, which are characterized by terminal inverted repeats and a target site duplication, and from members of the related IS110 family, which do not have obvious inverted repeats near their termini.

scholarly journals H3 Lysine 9 Methylation Is Maintained on a Transcribed Inverted Repeat by Combined Action of SUVH6 and SUVH4 Methyltransferases

2005 ◽  
Vol 25 (23) ◽  
pp. 10507-10515 ◽  
Author(s):  
Michelle L. Ebbs ◽  
Lisa Bartee ◽  
Judith Bender
Keyword(s):  
Dna Methylation ◽  
Chromatin Immunoprecipitation ◽  
Inverted Repeat ◽  
Histone H3 ◽  
Inverted Repeats ◽  
Chromatin Modifications ◽  
Double Stranded Rna ◽  
Repeat Sequences ◽  
Endogenous Genes ◽  
Combined Action

ABSTRACT Transcribed inverted repeats are potent triggers for RNA interference and RNA-directed DNA methylation in plants through the production of double-stranded RNA (dsRNA). For example, a transcribed inverted repeat of endogenous genes in Arabidopsis thaliana, PAI1-PAI4, guides methylation of itself as well as two unlinked duplicated PAI genes, PAI2 and PAI3. In previous work, we found that mutations in the SUVH4/KYP histone H3 lysine 9 (H3 K9) methyltransferase cause a loss of DNA methylation on PAI2 and PAI3, but not on the inverted repeat. Here we use chromatin immunoprecipitation analysis to show that the transcribed inverted repeat carries H3 K9 methylation, which is maintained even in an suvh4 mutant. PAI1-PAI4 H3 K9 methylation and DNA methylation are also maintained in an suvh6 mutant, which is defective for a gene closely related to SUVH4. However, both epigenetic modifications are reduced at this locus in an suvh4 suvh6 double mutant. In contrast, SUVH6 does not play a significant role in maintenance of H3 K9 or DNA methylation on PAI2, transposon sequences, or centromere repeat sequences. Thus, SUVH6 is preferentially active at a dsRNA source locus versus targets for RNA-directed chromatin modifications.

scholarly journals Target-Site Mutations Conferring Herbicide Resistance

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 382 ◽  
Author(s):  
Brent P. Murphy ◽  
Patrick J. Tranel
Keyword(s):  
Amino Acid ◽  
Herbicide Resistance ◽  
Target Site ◽  
Single Amino Acid ◽  
Cross Resistance ◽  
Target Sites ◽  
Resistance Patterns ◽  
Experimental Approaches ◽  
Sites Of Action ◽  
Multiple Amino Acid

Mutations conferring evolved herbicide resistance in weeds are known in nine different herbicide sites of action. This review summarizes recently reported resistance-conferring mutations for each of these nine target sites. One emerging trend is an increase in reports of multiple mutations, including multiple amino acid changes at the glyphosate target site, as well as mutations involving two nucleotide changes at a single amino acid codon. Standard reference sequences are suggested for target sites for which standards do not already exist. We also discuss experimental approaches for investigating cross-resistance patterns and for investigating fitness costs of specific target-site mutations.

scholarly journals Coding palindromes in mitochondrial genes of Nematomorpha

2019 ◽  
Vol 47 (13) ◽  
pp. 6858-6870 ◽  
Author(s):  
Kirill V Mikhailov ◽  
Boris D Efeykin ◽  
Alexander Y Panchin ◽  
Dmitry A Knorre ◽  
Maria D Logacheva ◽  
...  
Keyword(s):  
Amino Acid ◽  
Protein Function ◽  
Inverted Repeat ◽  
Amino Acid Level ◽  
Nucleotide Composition ◽  
Mitochondrial Genomes ◽  
Inverted Repeats ◽  
Protein Coding ◽  
Dna Elements ◽  
And Function

Abstract Inverted repeats are common DNA elements, but they rarely overlap with protein-coding sequences due to the ensuing conflict with the structure and function of the encoded protein. We discovered numerous perfect inverted repeats of considerable length (up to 284 bp) embedded within the protein-coding genes in mitochondrial genomes of four Nematomorpha species. Strikingly, both arms of the inverted repeats encode conserved regions of the amino acid sequence. We confirmed enzymatic activity of the respiratory complex I encoded by inverted repeat-containing genes. The nucleotide composition of inverted repeats suggests strong selection at the amino acid level in these regions. We conclude that the inverted repeat-containing genes are transcribed and translated into functional proteins. The survey of available mitochondrial genomes reveals that several other organisms possess similar albeit shorter embedded repeats. Mitochondrial genomes of Nematomorpha demonstrate an extraordinary evolutionary compromise where protein function and stringent secondary structure elements within the coding regions are preserved simultaneously.

scholarly journals Characterization of IS1515, a Functional Insertion Sequence in Streptococcus pneumoniae

1998 ◽  
Vol 180 (6) ◽  
pp. 1381-1388 ◽  
Author(s):  
Rosario Muñoz ◽  
Rubens López ◽  
Ernesto García
Keyword(s):  
Streptococcus Pneumoniae ◽  
Insertion Sequence ◽  
Frameshift Mutation ◽  
Lactobacillus Helveticus ◽  
Inverted Repeats ◽  
Insertion Sequences ◽  
Amino Acid Residues ◽  
Streptomyces Albus

ABSTRACT We describe the characterization of a new insertion sequence, IS1515, identified in the genome of Streptococcus pneumoniae I41R, an unencapsulated mutant isolated many years ago (R. Austrian, H. P. Bernheimer, E. E. B. Smith, and G. T. Mills, J. Exp. Med. 110:585–602, 1959). A copy of this element located in the cap1E I41R gene was sequenced. The 871-bp-long IS1515 element possesses 12-bp perfect inverted repeats and generates a 3-bp target duplication upon insertion. The IS encodes a protein of 271 amino acid residues similar to the putative transposases of other insertion sequences, namely IS1381 from S. pneumoniae, ISL2from Lactobacillus helveticus, IS702 from the cyanobacterium Calothrix sp. strain PCC 7601, and IS112 from Streptomyces albus G. IS1515 appears to be present in the genome of most type 1 pneumococci in a maximum of 13 copies, although it has also been found in the chromosome of pneumococcal isolates belonging to other serotypes. We have found that the unencapsulated phenotype of strain I41R is the result of both the presence of an IS1515 copy and a frameshift mutation in the cap1E I41Rgene. Precise excision of the IS was observed in the type 1 encapsulated transformants isolated in experiments designed to repair the frameshift. These results reveal that IS1515 behaves quite differently from other previously described pneumococcal insertion sequences. Several copies of IS1515 were also able to excise and move to another locations in the chromosome ofS. pneumoniae. To our knowledge, this is the first report of a functional IS in pneumococcus.

scholarly journals FARE, a New Family of Foldback Transposons in Arabidopsis

Genetics ◽  
2000 ◽  
Vol 156 (4) ◽  
pp. 1983-1995
Author(s):  
Aaron J Windsor ◽  
Candace S Waddell
Keyword(s):  
Inverted Repeat ◽  
Inverted Repeats ◽  
Insertion Polymorphism ◽  
Mobile Dna ◽  
Internal Region ◽  
Repeat Sequences ◽  
New Family ◽  
Distinct Subset ◽  
Dna Elements ◽  
Palindromic Sequences

Abstract A new family of transposons, FARE, has been identified in Arabidopsis. The structure of these elements is typical of foldback transposons, a distinct subset of mobile DNA elements found in both plants and animals. The ends of FARE elements are long, conserved inverted repeat sequences typically 550 bp in length. These inverted repeats are modular in organization and are predicted to confer extensive secondary structure to the elements. FARE elements are present in high copy number, are heterogeneous in size, and can be divided into two subgroups. FARE1’s average 1.1 kb in length and are composed entirely of the long inverted repeats. FARE2’s are larger, up to 16.7 kb in length, and contain a large internal region in addition to the inverted repeat ends. The internal region is predicted to encode three proteins, one of which bears homology to a known transposase. FARE1.1 was isolated as an insertion polymorphism between the ecotypes Columbia and Nossen. This, coupled with the presence of 9-bp target-site duplications, strongly suggests that FARE elements have transposed recently. The termini of FARE elements and other foldback transposons are imperfect palindromic sequences, a unique organization that further distinguishes these elements from other mobile DNAs.

scholarly journals IS481 and IS1002 ofBordetella pertussis Create a 6-Base-Pair Duplication upon Insertion at a Consensus Target Site

1998 ◽  
Vol 180 (18) ◽  
pp. 4963-4966 ◽  
Author(s):  
Scott Stibitz
Keyword(s):  
Dna Sequence ◽  
Bordetella Pertussis ◽  
Base Pair ◽  
Insertion Sequence ◽  
Target Site ◽  
Inverted Repeats ◽  
Recognition Sequence ◽  
Base Pairs ◽  
Terminal Inverted Repeats ◽  
Ofbordetella Pertussis

ABSTRACT The insertion sequence IS481 and its isoform IS1002 have been observed to transpose into thebvgAS locus of Bordetella pertussis, for which the DNA sequence has previously been determined. Upon insertion of IS481 at three different sites and IS1002 at one site, a 6-bp sequence originally present was found at the junction of bvg and insertion sequence DNA. This indicates that, contrary to prior reports, IS481 and IS1002 do create a duplication upon insertion. In this light, examination of these and other examples of IS481 and IS1002reported in the literature leads to the observation that the 6-bp recognition sequence usually fits the consensus NCTAGN. The near-palindromic nature of this sequence, when directly repeated at the ends of IS481 or IS1002, apparently led to the interpretation that 5 of these base pairs were part of the terminal inverted repeats flanking these elements.

scholarly journals New Insertion Sequence Elements in the Upstream Region of cfiA in Imipenem-Resistant Bacteroides fragilis Strains

2003 ◽  
Vol 47 (3) ◽  
pp. 979-985 ◽  
Author(s):  
Naoki Kato ◽  
Kikuo Yamazoe ◽  
Chang-Gyun Han ◽  
Eiichi Ohtsubo
Keyword(s):  
Insertion Sequence ◽  
Bacteroides Fragilis ◽  
Target Site ◽  
Homology Search ◽  
Upstream Region ◽  
Nucleotide Sequencing ◽  
Insertion Mutation ◽  
Terminal Inverted Repeat ◽  
Loop Formation ◽  
Is Elements

ABSTRACT The 747-bp cfiA gene, which encodes a metallo-β-lactamase, and the regions flanking cfiA in six imipenem-resistant and four imipenem-susceptible Bacteroides fragilis strains isolated in Japan were analyzed by PCR and DNA sequencing. The nucleotide sequences of the cfiA genes (designated cfiA1 to cfiA10 ) of all 10 strains tested varied from that of the standard cfiA gene from B. fragilis TAL2480. However, putative proteins encoded by the cfiA variants contained conserved amino acid residues important for zinc binding and hairpin loop formation, suggesting that cfiA variants have the capability of producing metallo-β-lactamases with full catalytic activities. PCR assay indicated that six metallo-β-lactamase-producing, imipenem-resistant strains had an insertion mutation in the region immediately upstream of cfiA. Nucleotide sequencing of the PCR-amplified fragments along with the upstream region of cfiA revealed that there were five new kinds of insertion sequence (IS) elements (designated IS612, IS613, IS614, IS615, and IS616, with a size range of 1,594 to 1,691 bp), of which only IS616 was found to be almost identical to IS1188, one of the IS elements previously identified in the upstream region of cfiA. These elements had target site duplications of 4 or 5 bp in length, terminal inverted repeats (14, 15, or 17 bp in size), and a large open reading frame encoding a putative transposase which is required for the transcription of IS elements. Each element was inserted such that the transcriptional direction of the transposase was opposite to that of cfiA. A computer-aided homology search revealed that, based on the homology of their putative transposases, the sizes of their terminal inverted repeat sequences, and their target site duplications, IS612, IS613, IS614, and IS615 belong to the IS4 family, which includes IS942, previously found in some drug-resistant B. fragilis strains, but that IS616 belongs to the IS1380 family. All the IS elements appear to have putative promoter motif sequences (the −7 region's TAnnTTTG motif and the −33 region's TTG or TG) in their end regions, suggesting that the IS elements provide a promoter for the transcription of cfiA upon insertion. These data provide additional proof that various IS elements may exist to provide a promoter to express the cfiA gene.

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