scholarly journals Structures and stability of simple DNA repeats from bacteria

2020 ◽  
Vol 477 (2) ◽  
pp. 325-339 ◽  
Author(s):  
Vaclav Brazda ◽  
Miroslav Fojta ◽  
Richard P. Bowater
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Genetic Instability ◽  
Repetitive Sequences ◽  
Biological Significance ◽  
Human Diseases ◽  
Repetitive Dna Sequences ◽  
Dna Repeats ◽  
Diverse Range ◽  
Dna Structures

DNA is a fundamentally important molecule for all cellular organisms due to its biological role as the store of hereditary, genetic information. On the one hand, genomic DNA is very stable, both in chemical and biological contexts, and this assists its genetic functions. On the other hand, it is also a dynamic molecule, and constant changes in its structure and sequence drive many biological processes, including adaptation and evolution of organisms. DNA genomes contain significant amounts of repetitive sequences, which have divergent functions in the complex processes that involve DNA, including replication, recombination, repair, and transcription. Through their involvement in these processes, repetitive DNA sequences influence the genetic instability and evolution of DNA molecules and they are located non-randomly in all genomes. Mechanisms that influence such genetic instability have been studied in many organisms, including within human genomes where they are linked to various human diseases. Here, we review our understanding of short, simple DNA repeats across a diverse range of bacteria, comparing the prevalence of repetitive DNA sequences in different genomes. We describe the range of DNA structures that have been observed in such repeats, focusing on their propensity to form local, non-B-DNA structures. Finally, we discuss the biological significance of such unusual DNA structures and relate this to studies where the impacts of DNA metabolism on genetic stability are linked to human diseases. Overall, we show that simple DNA repeats in bacteria serve as excellent and tractable experimental models for biochemical studies of their cellular functions and influences.

Cloning and characterization of repetitive DNA sequences from genomes of Oryza minuta and Oryza australiensis

Genome ◽  
1991 ◽  
Vol 34 (5) ◽  
pp. 790-798 ◽  
Author(s):  
H. Aswidinnoor ◽  
R. J. Nelson ◽  
J. F. Dallas ◽  
C. L. McIntyre ◽  
H. Leung ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Repetitive Sequences ◽  
Rice Genome ◽  
Repetitive Dna Sequences ◽  
Cross Hybridization ◽  
Oryza Minuta ◽  
Wild Rice Species ◽  
Oryza Australiensis

The value of genome-specific repetitive DNA sequences for use as molecular markers in studying genome differentiation was investigated. Five repetitive DNA sequences from wild species of rice were cloned. Four of the clones, pOm1, pOm4, pOmA536, and pOmPB10, were isolated from Oryza minuta accession 101141 (BBCC genomes), and one clone, pOa237, was isolated from Oryza australiensis accession 100882 (EE genome). Southern blot hybridization to different rice genomes showed strong hybridization of all five clones to O. minuta genomic DNA and no cross hybridization to genomic DNA from Oryza sativa (AA genome). The pOm1 and pOmA536 sequences showed cross hybridization only to all of the wild rice species containing the C genome. However, the pOm4, pOmPB10, and pOa237 sequences showed cross hybridization to O. australiensis genomic DNA in addition to showing hybridization to the O. minuta genomic DNA.Key words: rice, genome-specific repetitive sequences, Oryza.

scholarly journals Comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Octavio M. Palacios-Gimenez ◽  
Julia Koelman ◽  
Marc Palmada-Flores ◽  
Tessa M. Bradford ◽  
Karl K. Jones ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Species Complex ◽  
Repetitive Dna Sequences ◽  
Dna Repeats ◽  
Large Genome ◽  
Chromosomal Races

Abstract Background Repetitive DNA sequences, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), collectively called the “repeatome”, are found in high proportion in organisms across the Tree of Life. Grasshoppers have large genomes, averaging 9 Gb, that contain a high proportion of repetitive DNA, which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of repetitive DNA sequences in four chromosomal races of the morabine grasshopper Vandiemenella viatica species complex and determine their contribution to genome evolution. Results We obtained linked-read genome assemblies of 2.73–3.27 Gb from estimated genome sizes of 4.26–5.07 Gb DNA per haploid genome of the four chromosomal races of V. viatica. These constitute the third largest insect genomes assembled so far. Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs, constituting 66 to 75% per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314–463 Mb per assembly), indicating that their large genome sizes are likely due to similar rates of TE accumulation. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a diversity of satDNA families in the ancestor of the V. viatica chromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of the V. viatica species complex. Conclusion This in-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entire Drosophila genomes, which likely explains the large genome sizes in grasshoppers. Despite an overall high similarity of the TE and satDNA diversity between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.

scholarly journals Genome-wide analysis of DNA repeats in Burkholderia cenocepacia J2315 identifies a novel adhesin-like gene unique to epidemic-associated strains of the ET-12 lineage

Microbiology ◽  
2010 ◽  
Vol 156 (4) ◽  
pp. 1084-1096 ◽  
Author(s):  
Dalila Mil-Homens ◽  
Eduardo P. C. Rocha ◽  
Arsenio M. Fialho
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Matrix Protein ◽  
Cellular Adhesion ◽  
The Other ◽  
Burkholderia Cenocepacia ◽  
Extracellular Matrix Protein ◽  
Repetitive Dna Sequences ◽  
Type I ◽  
Dna Repeats

Members of the Burkholderia cepacia complex (Bcc) are respiratory pathogens in patients with cystic fibrosis (CF). Close repetitive DNA sequences often associate with surface antigens to promote genetic variability in pathogenic bacteria. The genome of Burkholderia cenocepacia J2315, a CF isolate belonging to the epidemic lineage Edinburgh–Toronto (ET-12), was analysed for the presence of close repetitive DNA sequences. Among the 422 DNA close repeats, 45 genes potentially involved in virulence were identified and grouped into 12 classes; of these, 13 genes were included in the antigens class. Two trimeric autotransporter adhesins (TAA) among the 13 putative antigens are absent from the other Burkholderia genomes and are clustered downstream of the cci island that is a marker for transmissible B. cenocepacia strains. This cluster contains four adhesins, one outer-membrane protein, one sensor histidine kinase and two transcriptional regulators. By using PCR, we analysed three genes among 47 Bcc isolates to determine whether the cluster was conserved. These three genes were present in the isolates of the ET-12 lineage but absent in all the other members. Furthermore, the BCAM0224 gene was exclusively detected in this epidemic lineage and may serve as a valuable new addition to the field of Bcc diagnostics. The BCAM0224 gene encodes a putative TAA that demonstrates adhesive properties to the extracellular matrix protein collagen type I. Quantitative real-time PCR analysis indicated that BCAM0224 gene expression occurred preferentially for cells grown under high osmolarity, oxygen-limited conditions and oxidative stress. Inactivation of BCAM0224 in B. cenocepacia attenuates the ability of the mutant to promote cell adherence in vitro and impairs the overall bacterial virulence against Galleria mellonella as a model of infection. Together, our data show that BCAM0224 from B. cenocepacia J2315 represents a new collagen-binding TAA with no bacterial orthologues which has an important role in cellular adhesion and virulence.

Variations of two repetitive DNA sequences in several Triticeae genomes revealed by polymerase chain reaction and sequencing

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1221-1229 ◽  
Author(s):  
Richard R.-C. Wang ◽  
Jun-Zhi Wei
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Sequence ◽  
Repetitive Sequences ◽  
Evolutionary Significance ◽  
Repetitive Dna Sequences ◽  
Chain Reaction ◽  
Pcr Product ◽  
Polymerase Chain ◽  
Thinopyrum Elongatum

Genomes of Triticeae were analyzed using PCR with synthesized primers that were based on two published repetitive DNA sequences, pLeUCD2 (pLe2) and l-E6hcII-l (L02368), which were originally isolated from Thinopyrum elongatum. The various genomes produced a 240 bp PCR product having high homology with the repetitive DNA pLe2. The PCR fragments produced from different genomes differed mainly in amplification quantity and in base composition at 89 variable sites. On the other hand, amplification products from the primer set for L02368 were of different sizes and nucleotide sequences. These results show that the two repetitive DNA sequences have different evolutionary significance. pLe2 is present in all genomes tested, although differences in copy number and nucleotide sequence are notable. L02368 is more genome specific, i.e., fewer genomes possess this family of repetitive sequences. It was concluded that the repetitive sequence pLe2 family is an ancient one that existed in the progenitor genome prior to divergence of annual and perennial genomes. In contrast, sequences similar to L02368 have only evolved following genome divergence.Key words: repetitive sequence, PCR, genome, evolution, Thinopyrum, Triticeae.

scholarly journals Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome

2020 ◽  
Author(s):  
Mariela Sader ◽  
Magdalena Vaio ◽  
Luiz Augusto Cauz-Santos ◽  
Marcelo Carnier Dornelas ◽  
Maria Lucia Carneiro Vieira ◽  
...  
Keyword(s):  
Genome Size ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Large Scale ◽  
Repetitive Sequences ◽  
Size Variation ◽  
Repetitive Dna Sequences ◽  
Ltr Retrotransposons ◽  
Genome Size Variation ◽  
Satellite Dnas

ABSTRACTRepetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a ten-fold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of these genera representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified Long Terminal Repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicate that while large genome evolve by an accumulation of retrotransponsons, small genomes most evolved by diversification of different repeat types, particularly satDNAs.MAIN CONCLUSIONSWhile two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome.

Quantitative and qualitative genomic characterization of cultivated Ilex L. species

2014 ◽  
Vol 13 (2) ◽  
pp. 142-152 ◽  
Author(s):  
Alexandra Marina Gottlieb ◽  
Lidia Poggio
Keyword(s):  
Genome Size ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Repetitive Sequences ◽  
Representational Difference Analysis ◽  
Ilex Paraguariensis ◽  
Repetitive Dna Sequences ◽  
A Genome

The development of modern approaches to the genetic improvement of the tree crops Ilex paraguariensis (‘yerba mate’) and Ilex dumosa (‘yerba señorita’) is halted by the scarcity of basic genetic information. In this study, we characterized the implementation of low-cost methodologies such as representational difference analysis (RDA), single-strand conformation polymorphisms (SSCP), and reverse and direct dot-blot filter hybridization assays coupled with thorough bioinformatic characterization of sequence data for both species. Also, we estimated the genome size of each species using flow cytometry. This study contributes to the better understanding of the genetic differences between two cultivated species, by generating new quantitative and qualitative genome-level data. Using the RDA technique, we isolated a group of non-coding repetitive sequences, tentatively considered as Ilex-specific, which were 1.21- to 39.62-fold more abundant in the genome of I. paraguariensis. Another group of repetitive DNA sequences involved retrotransposons, which appeared 1.41- to 35.77-fold more abundantly in the genome of I. dumosa. The genomic DNA of each species showed different performances in filter hybridizations: while I. paraguariensis showed a high intraspecific affinity, I. dumosa exhibited a higher affinity for the genome of the former species (i.e. interspecific). These differences could be attributed to the occurrence of homologous but slightly divergent repetitive DNA sequences, highly amplified in the genome of I. paraguariensis but not in the genome of I. dumosa. Additionally, our hybridization outcomes suggest that the genomes of both species have less than 80% similarity. Moreover, for the first time, we report herein a genome size estimate of 1670 Mbp for I. paraguariensis and that of 1848 Mbp for I. dumosa.

scholarly journals CAG Expansions Are Genetically Stable and Form Nontoxic Aggregates in Cells Lacking Endogenous Polyglutamine Proteins

mBio ◽  
2016 ◽  
Vol 7 (5) ◽  
Author(s):  
Ashley A. Zurawel ◽  
Ruth Kabeche ◽  
Sonja E. DiGregorio ◽  
Lin Deng ◽  
Kartikeya M. Menon ◽  
...  
Keyword(s):  
Schizosaccharomyces Pombe ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Genetic Instability ◽  
Growth Defect ◽  
Pcr Analysis ◽  
Repetitive Dna Sequences ◽  
Stark Contrast ◽  
Almost All ◽  
Evolutionary Emergence

ABSTRACT Proteins containing polyglutamine (polyQ) regions are found in almost all eukaryotes, albeit with various frequencies. In humans, proteins such as huntingtin (Htt) with abnormally expanded polyQ regions cause neurodegenerative diseases such as Huntington’s disease (HD). To study how the presence of endogenous polyQ aggregation modulates polyQ aggregation and toxicity, we expressed polyQ expanded Htt fragments (polyQ Htt) in Schizosaccharomyces pombe . In stark contrast to other unicellular fungi, such as Saccharomyces cerevisiae , S. pombe is uniquely devoid of proteins with more than 10 Q repeats. We found that polyQ Htt forms aggregates within S. pombe cells only with exceedingly long polyQ expansions. Surprisingly, despite the presence of polyQ Htt aggregates in both the cytoplasm and nucleus, no significant growth defect was observed in S. pombe cells. Further, PCR analysis showed that the repetitive polyQ-encoding DNA region remained constant following transformation and after multiple divisions in S. pombe , in contrast to the genetic instability of polyQ DNA sequences in other organisms. These results demonstrate that cells with a low content of polyQ or other aggregation-prone proteins can show a striking resilience with respect to polyQ toxicity and that genetic instability of repetitive DNA sequences may have played an important role in the evolutionary emergence and exclusion of polyQ expansion proteins in different organisms. IMPORTANCE Polyglutamine (polyQ) proteins encoded by repetitive CAG DNA sequences serve a variety of normal biological functions. Yet some proteins with abnormally expanded polyQ regions cause neurodegeneration through unknown mechanisms. To study how distinct cellular environments modulate polyQ aggregation and toxicity, we expressed CAG-expanded huntingtin fragments in Schizosaccharomyces pombe . In stark contrast to many other eukaryotes, S. pombe is uniquely devoid of proteins containing long polyQ tracts. Our results show that S. pombe cells, despite their low content of endogenous polyQ proteins, exhibit striking and unexpected resilience with respect to polyQ toxicity and that genetic instability of repetitive DNA sequences may have played an important role in the emergence and expansion of polyQ domains in eukaryotic evolution.

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