Diversity of LTR-retrotransposons and Enhancer/Suppressor Mutator-like transposons in cassava (Manihot esculenta Crantz)

Mutator-like transposable element 9A interacts with metacaspase 1 and modulates the incidence of Al-induced programmed cell death in peanut

The toxicity of aluminum (Al) in acidic soil inhibits plant root development and reduces crop yields. In the plant response to Al toxicity, the initiation of programmed cell death (PCD) appears to be an important mechanism for the elimination of Al-damaged cells to ensure plant survival. In a previous study, the type I metacaspase AhMC1 was found to regulate the Al stress response and to be essential for Al-induced PCD. However, the mechanism by which AhMC1 is altered in the peanut response to Al stress remained unclear. Here, we show that a nuclear protein, mutator-like transposable element 9A (AhMULE9A), directly interacts with AhMC1 in vitro and in vivo. This interaction occurs in the nucleus in peanut and is weakened during Al stress. Furthermore, a conserved C2HC zinc finger domain of AhMULE9A (residues 735-751) was shown to be required for its interaction with AhMC1. Overexpression of AhMULE9A in Arabidopsis and peanut strongly inhibited root growth with a loss of root cell viability under Al treatment. Conversely, knock down of AhMULE9A in peanut significantly reduced Al uptake and Al inhibition of root growth, and alleviated the occurrence of typical hallmarks of Al-induced PCD. These findings provide novel insight into the regulation of Al-induced PCD.

Cloning of Maize TED Transposon into Escherichia coli Reveals the Polychromatic Sequence Landscape of Refractorily Propagated Plasmids

MuDR, the founder member of the Mutator superfamily and its MURA transcripts, has been identified as toxic sequences to Escherichia coli (E. coli), which heavily hindered the elucidation of the biochemical features of MURA transposase and confined the broader application of the Mutator system in other organisms. To harness less constrained systems as alternatives, we attempted to clone TED and Jittery, two recently isolated autonomous Mutator-like elements (MULEs) from maize, respectively. Their full-length transcripts and genomic copies are successfully cloned when the incubation time for bacteria to recover from heat shock is extended appropriately prior to plating. However, during their proliferation in E. coli, TED transformed plasmids are unstable, as evidenced by derivatives from which frameshift, deletion mutations, or IS transposon insertions are readily detected. Our results suggest that neither leaky expression of the transposase nor the presence of terminal inverse repeats (TIRs) are responsible for the cloning barriers, which were once ascribed to the presence of the Shine–Dalgarno-like sequence. Instead, the internal sequence of TED (from 1250 to 2845 bp), especially the exons in this region, was the most likely causer. The findings provide novel insights into the property and function of the Mutator superfamily and shed light on the dissection of toxic effects on cloning from MULEs.

Cobalt-induced retrotransposon polymorphism and humic acid protection on maize genome

Retrotransposon activity and genomic template stability (GTS) are one of the most significant rearranging mechanisms in environmental stress. Therefore, in this study, it is aimed to elucidate effecting of Cobalt (Co) on the instability of genomes and Long Terminal Repeat retrotransposon polymorphism in Zea mays and whether humic acid (HA) has any role on these parameters. For this purpose, Retrotransposon-microsatellite amplified polymorphism (REMAP) and Inter-Retrotransposon Amplified Polymorphism (IRAP) markers were applied to evaluate retrotransposon polymorphism and the GTS levels. It was found that IRAP and REMAP primers generate unique polymorphic band structures on maize plants treated with various doses of Co. Retrotransposon polymorphism increased and GTS decreased while increasing Co concentration. On the other hand, there was a reduction in negative effects of Co on retrotransposon GTS and polymorphism after treatment with HA. The results indicate that HA may be used effectively for the protection of maize seedlings from the destructive effects of Co toxicity.

Sequences enhancing cassava mosaic disease symptoms occur in the cassava genome and are associated with South African cassava mosaic virus infection

Cassava is an important food security crop in Sub-Saharan Africa. Two episomal begomovirus-associated sequences, named Sequences Enhancing Geminivirus Symptoms (SEGS1 and SEGS2), were identified in field cassava affected by the devastating cassava mosaic disease (CMD). The sequences reportedly exacerbated CMD symptoms in the tolerant cassava landrace TME3, and the model plants Arabidopsis thaliana and Nicotiana benthamiana, when biolistically co-inoculated with African cassava mosaic virus-Cameroon (ACMV-CM) or East African cassava mosaic virus-UG2 (EACMV-UG2). Following the identification of small SEGS fragments in the cassava EST database, the intention of this study was to confirm their presence in the genome, and investigate a possible role for these sequences in CMD. We report that multiple copies of varying lengths of both SEGS1 and SEGS2 are widely distributed in the sequenced cassava genome and are present in several other cassava accessions screened by PCR. The endogenous SEGS1 and SEGS2 are in close proximity or overlapping with cassava genes, suggesting a possible role in regulation of specific biological processes. We confirm the expression of SEGS in planta using EST data and RT-PCR. The sequence features of endogenous SEGS (iSEGS) are unique but resemble non-autonomous transposable elements (TEs) such as MITEs and helitrons. Furthermore, many SEGS-associated genes, some involved in virus-host interactions, are differentially expressed in susceptible (T200) and tolerant TME3) cassava landraces infected by South African cassava mosaic virus (SACMV) of susceptible (T200) and tolerant (TME3) cassava landraces. Abundant SEGS-derived small RNAs were also present in mock-inoculated and SACMV-infected T200 and TME3 leaves. Given the known role of TEs and associated genes in gene regulation and plant immune responses, our observations are consistent with a role of these DNA elements in the host's regulatory response to geminiviruses.

Transposon variation by order during allopolyploidisation between Brassica oleracea and Brassica rapa

Although many studies have shown that transposable element (TE) activation is induced by hybridisation and polyploidisation in plants, much less is known on how different types of TE respond to hybridisation, and the impact of TE-associated sequences on gene function. We investigated the frequency and regularity of putative transposon activation for different types of TE, and determined the impact of TE-associated sequence variation on the genome during allopolyploidisation. We designed different types of TE primers and adopted the Inter-Retrotransposon Amplified Polymorphism (IRAP) method to detect variation in TE-associated sequences during the process of allopolyploidisation between Brassica rapa (AA) and Brassica oleracea (CC), and in successive generations of self-pollinated progeny. In addition, fragments with TE insertions were used to perform Blast2GO analysis to characterise the putative functions of the fragments with TE insertions. Ninety-two primers amplifying 548 loci were used to detect variation in sequences associated with four different orders of TE sequences. TEs could be classed in ascending frequency into LTR-REs, TIRs, LINEs, SINEs and unknown TEs. The frequency of novel variation (putative activation) detected for the four orders of TEs was highest from the F1 to F2 generations, and lowest from the F2 to F3 generations. Functional annotation of sequences with TE insertions showed that genes with TE insertions were mainly involved in metabolic processes and binding, and preferentially functioned in organelles. TE variation in our study severely disturbed the genetic compositions of the different generations, resulting in inconsistencies in genetic clustering. Different types of TE showed different patterns of variation during the process of allopolyploidisation.

Ty1-copia group retrotransposons and the evolution of retroelements in several angiosperm plants: evidence of horizontal transmission

The phylogenetic relationships among thirty-seven new Ty1-copia group retrotransposons in seven angiosperm plants were examined by reverse transcriptase and ribonuclease H sequence analysis. Distribution pattern of the retrotransposons of closely related plant species generally reflects a close phylogenetic relationship. In contrast, we found that several retrotransposon sequences from the same genome exhibited a high degree of divergence and had a relatively high degree of identity versus retrotransposon sequences from widely divergent species, including an ancestral phytopathogen fungus. This finding supports the hypothesis that the horizontal transmission from phytopatogen organism to the host flowering plants could have played a role in the evolutionary dynamics of Ty1-copia group retrotransposons.

Polymorphism of a new Ty1-copia retrotransposon in durum wheat under salt and light stresses

Long terminal repeat retrotransposons are the most abundant mobile elements in the plant genome and play an important role in the genome reorganization induced by environmental challenges. Their success depends on the ability of their promoters to respond to different signaling pathways that regulate plant adaptation to biotic and abiotic stresses. We have isolated a new Ty1-copia-like retrotransposon, named Ttd1a from the Triticum durum L. genome. To get insight into stress activation pathways in Ttd1a, we investigated the effect of salt and light stresses by RT-PCR and S-SAP profiling. We screened for Ttd1a insertion polymorphisms in plants grown to stress and showed that one new insertion was located near the resistance gene. Our analysis showed that the activation and mobilization of Ttd1a was controlled by salt and light stresses, which strengthened the hypothesis that stress mobilization of this element might play a role in the defense response to environmental stresses.

Proteome characterization of cassava (Manihot esculenta Crantz) somatic embryos, plantlets and tuberous roots

Background

Proteomics is increasingly becoming an important tool for the study of many different aspects of plant functions, such as investigating the molecular processes underlying in plant physiology, development, differentiation and their interaction with the environments. To investigate the cassava (Manihot esculenta Crantz) proteome, we extracted proteins from somatic embryos, plantlets and tuberous roots of cultivar SC8 and separated them by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE).

Results

Analysis by liquid chromatography-electrospray ionisation-tandem mass spectrometry (LC-ESI-MS/MS) yielded a total of 383 proteins including isoforms, classified into 14 functional groups. The majority of these were carbohydrate and energy metabolism associated proteins (27.2%), followed by those involved in protein biosynthesis (14.4%). Subsequent analysis has revealed that 54, 59, 74 and 102 identified proteins are unique to the somatic embryos, shoots, adventitious roots and tuberous roots, respectively. Some of these proteins may serve as signatures for the physiological and developmental stages of somatic embryos, shoots, adventitious roots and tuberous root. Western blotting results have shown high expression levels of Rubisco in shoots and its absence in the somatic embryos. In addition, high-level expression of α-tubulin was found in tuberous roots, and a low-level one in somatic embryos. This extensive study effectively provides a huge data set of dynamic protein-related information to better understand the molecular basis underlying cassava growth, development, and physiological functions.

Conclusion

This work paves the way towards a comprehensive, system-wide analysis of the cassava. Integration with transcriptomics, metabolomics and other large scale "-omics" data with systems biology approaches can open new avenues towards engineering cassava to enhance yields, improve nutritional value and overcome the problem of post-harvest physiological deterioration.