Localization of Insertion Sequences in Plasmids for L-Cysteine Production in E. coli.

Insertion sequence elements (ISE) are often found to be responsible for the collapse of production in synthetically engineered Escherichia coli. By the transposition of ISE into the open reading frame of the synthetic pathway, E. coli cells gain selection advantage over cells expressing the metabolic burdensome production genes. Here, we present the exact entry sites of insertion sequence (IS) families 3 and 5 within plasmids for l-cysteine production in evolved E. coli populations. Furthermore, we identified an uncommon occurrence of an 8-bp direct repeat of IS5 which is atypical for this particular family, potentially indicating a new IS5 target site.

IS481EU Shows a New Connection between Eukaryotic and Prokaryotic DNA Transposons.

DDD/E transposase gene is the most abundant gene in nature and many DNA transposons in all three domains of life use it for their transposition. A substantial number of eukaryotic DNA transposons show similarity to prokaryotic insertion sequences (ISs). The presence of IS481-like DNA transposons was indicated in the genome of Trichomonas vaginalis. Here, we surveyed IS481-like eukaryotic sequences using a bioinformatics approach and report a group of eukaryotic IS481-like DNA transposons, designated IS481EU, from parabasalids including T. vaginalis. The lengths of target site duplications (TSDs) of IS481EU are around 4 bps, around 15 bps, or around 25 bps, and strikingly, these discrete lengths of TSDs can be observed even in a single IS481EU family. Phylogenetic analysis indicated the close relationships of IS481EU with some of the prokaryotic IS481 family members. IS481EU was not well separated from IS3EU/GingerRoot in the phylogenetic analysis, but was distinct from other eukaryotic DNA transposons including Ginger1 and Ginger2. The unique characteristics of IS481EU in protein sequences and the distribution of TSD lengths support its placement as a new superfamily of eukaryotic DNA transposons.

Growth by Insertion: The Family of Bacterial DDxP Proteins.

We have identified a variety of proteins in species of the Legionella, Aeromonas, Pseudomonas, Vibrio, Nitrosomonas, Nitrosospira, Variovorax, Halomonas, and Rhizobia genera, which feature repetitive modules of different length and composition, invariably ending at the COOH side with Asp-Asp-x-Pro (DDxP) motifs. DDxP proteins range in size from 900 to 6200 aa (amino acids), and contain 1 to 5 different module types, present in one or multiple copies. We hypothesize that DDxP proteins were modeled by the action of specific endonucleases inserting DNA segments into genes encoding DDxP motifs. Target site duplications (TSDs) formed upon repair of staggered ends generated by endonuclease cleavage would explain the DDxP motifs at repeat ends. TSDs acted eventually as targets for the insertion of more modules of the same or different types. Repeat clusters plausibly resulted from amplification of both repeat and flanking TSDs. The proposed growth shown by the insertion model is supported by the identification of homologous proteins lacking repeats in Pseudomonas and Rhizobium. The 85 DDxP repeats identified in this work vary in length, and can be sorted into short (136-215 aa) and long (243-304 aa) types. Conserved Asp-Gly-Asp-Gly-Asp motifs are located 11-19 aa from the terminal DDxP motifs in all repeats, and far upstream in most long repeats.

Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding.

Plant molecular breeding is expected to give significant gains in cultivar development through development and utilization of suitable molecular marker systems for genetic diversity analysis, rapid DNA fingerprinting, identification of true hybrids, trait mapping and marker-assisted selection. Transposable elements (TEs) are the most abundant component in a genome and being used as genetic markers in the plant molecular breeding. Here, we review on the high copious transposable element belonging to class-II DNA TEs called "miniature inverted-repeat transposable elements" (MITEs). MITEs are ubiquitous, short and non-autonomous DNA transposable elements which have a tendency to insert into genes and genic regions have paved a way for the development of functional DNA marker systems in plant genomes. This review summarises the characteristics of MITEs, principles and methodologies for development of MITEs based DNA markers, bioinformatics tools and resources for plant MITE discovery and their utilization in crop improvement.

[Active miniature inverted-repeat transposable elements transposon in plants: a review].

Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family. Moreover, we summarize the structure (terminal inverse repeats and target site duplications), copy number, evolution pattern and transposition characteristics of these active MITEs, to provide the foundation for the identification of other active MITEs and subsequent research on MITE transposition and amplification mechanism.

Active miniature inverted-repeat transposable elements transposon in plants: a review / 生物工程学报

Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family. Moreover, we summarize the structure (terminal inverse repeats and target site duplications), copy number, evolution pattern and transposition characteristics of these active MITEs, to provide the foundation for the identification of other active MITEs and subsequent research on MITE transposition and amplification mechanism.

New insights into helitron transposable elements in the mesopolyploid species Brassica rapa.

Helitrons are DNA transposable elements that are widely present in the genomes of diverse eukaryotic taxa. Helitrons are distinct from other transposons in their ability to capture gene fragments and their rolling-replication mechanism. Brassica rapa is a mesopolyploid species and one of the most important vegetable and oil crops globally. A total of 787 helitrons were identified in the B. rapa genome and were assigned to 662 families and 700 subfamilies. More than 21,806 repetitive sequences were found within the helitrons, whose G+C content correlated negatively to that of the host helitron. Each helitron contained an average of 2.9 gene fragments and 1.9 intact genes, of which the majority were annotated with binding functions in metabolic processes. In addition, a set of 114 nonredundant microRNAs were detected within 174 helitrons and predicted to regulate a set of 787 nonredundant target genes. These results suggest that helitrons contribute to genomic structural and transcriptional variation by capturing gene fragments and generating microRNAs.

Conserved domains and SINE diversity during animal evolution.

Eukaryotic genomes harbour a number of mobile genetic elements (MGEs); moving from one genomic location to another, they are known to impact on the host genome. Short interspersed elements (SINEs) are well-represented, non-autonomous retroelements and they are likely the most diversified MGEs. In some instances, sequence domains conserved across unrelated SINEs have been identified; remarkably, one of these, called Nin, has been conserved since the Radiata-Bilateria splitting. Here we report on two new domains: Inv, derived from Nin, identified in insects and in deuterostomes, and Pln, restricted to polyneopteran insects. The identification of Inv and Pln sequences allowed us to retrieve new SINEs, two in insects and one in a hemichordate. The diverse structural combination of the different domains in different SINE families, during metazoan evolution, offers a clearer view of SINE diversity and their frequent de novo emergence through module exchange, possibly underlying the high evolutionary success of SINEs.