Miniature inverted-repeat transposable elements (MITEs) are ubiquitous in high eukaryotic genomes. More than 178,000 MITE sequences of 338 families are present in the genome of rice (Oryza sativa) cultivar Nipponbare. Interestingly, only two of the 338 MITE families have homologous sequences in the genome of Brachypodium distachyon, a relative in the grass family. Therefore, the vast majority of MITEs in the rice genome were originated and amplified after the divergence of Oryza and Brachypodium. Comparison between rice cultivar Nipponbare and another rice cultivar 93–11 showed 14.8% of MITEs exhibit presence/absence (P/A) polymorphism. The P/A polymorphism was mainly attributed to recent MITE transpositions, while less than 10% of the P/A polymorphism was caused by MITE excisions. Therefore, the high P/A polymorphisms of MITEs may generate considerable gene expression and phenotypic diversity for O. sativa.
Mobile genetic elements (MGEs) are fragments of DNA that can move around within the genome through retrotransposition. These are responsible for various important events such as gene inactivation, transduction, regulation of gene expression and genome expansion. The present work involves the identification and study of the distribution of Alu and L1 retrotransposons in the genome of Macaca mulatta, an extensively used organism in biomedical studies. We also make comparisons with MGE distributions in other primate genomes and study the physicochemical properties of the local DNA structure around the transposon insertion site using ELAN. The present work also includes computational testing of the pre-insertion loci in order to detect unique features based on DNA structure, thermodynamic considerations and protein interaction measures. Although there is significant sequence divergence between the elements of M. mulatta and H. sapiens, their genome wide distribution is very similar; comparing the distribution of L1’s in all available X chromosome sequences suggests a common mechanism behind the spread of MGE’s in primate genomes.
Arabidopsis thaliana is a model plant species and its molecular dissection has greatly contributed to our understanding of the systems preventing genome invasion by transposable elements (TE). Recent advances suggest that A. thaliana may be more efficient than its congener A. lyrata at controlling TE expression and proliferation. The comparative analysis of TE transcription in A. thaliana and A. lyrata, which differ by 40% in genome size, may help understand how silencing mechanisms contribute to the evolution of transposition rate, an important factor controlling genome size variation in plants and animals.
Propionibacterium acnes is a Gram-positive bacterium that is intimately associated with humans. The nature and consequences of this symbiosis are poorly understood; it might comprise both mutualistic and parasitic properties. Recent advances in distinguishing phylotypes of P. acnes have revealed that certain type I lineages are predominantly associated with acne vulgaris. Genome analyses revealed a highly conserved core genome and the existence of island-like genomic regions and possible mobile genetic elements as part of the flexible gene pool. The analysis of clustered regularly interspaced short palindromic repeats (CRISPR), found exclusively in type II P. acnes, recently revealed the presence of CRISPR spacers that derived from mobile genetic elements. These elements are present in a subset of P. acnes type I lineages. Their significance for type-specific host-interacting properties and their contribution to pathogenicity is currently under investigation.
The resident microbiota of the human gastrointestinal (GI) tract is comprised of ~2000 bacterial species, the majority of which are anaerobes. Colonization of the GI tract is important for normal development of the immune system and provides a reservoir of catabolic enzymes that degrade ingested plant polysaccharides. Bacteroides fragilis is an important member of the microbiota because it contributes to T helper cell development, but is also the most frequently isolated Gram-negative anaerobe from clinical infections. During the annotation of the B. fragilis genome sequence, we identified a gene predicted to encode a homolog of the eukaryotic protein modifier, ubiquitin. Previously, ubiquitin had only been found in eukaryotes, indicating the bacterial acquisition as a potential inter-kingdom horizontal gene transfer event. Here we discuss the possible roles of B. fragilis ubiquitin and the implications for health and disease.
Plasmids are episomally replicating genetic elements which carry backbone genes that are important for their replication and maintenance within their host, and accessory genes that might confer an advantage to their host in its ecological niche. As such, they are often perceived as a powerful evolutionary force, which horizontally introduces new traits into bacterial cells and genomes. In our recent publication “Insight into the rumen plasmidome” we characterized the metagenomic plasmid population of the bovine rumen microbial ecological niche. The rumen is the first compartment of the digestive tract of ruminants; it functions as a pre-gastric anaerobic fermentation chamber, where plant fibers are degraded and converted into chemical compounds which are subsequently absorbed and digested by the animal.
Two well-known retroelements, L1 and Alu, comprise about one third of the human genome and are nearly equally distributed between the intergenic and intragenic regions. They carry different regulatory elements and contribute structurally and functionally to the expression of our genes. Recent data also suggest that hundreds of intronic L1s and Alus interfere with the transcription of human genes by inducing intron retention, forcing exonization and cryptic polyadenylation. These novel features can be explained with the RNA polymerase kinetic model and suggest that intronic L1s and Alus are not just “speed bumps” in regulation of RNA polymerase traffic. Here we discuss the complexity of the regulation of gene transcription imposed by intronic retroelements and predict that in addition to transcriptional activity, transcription factor binding and nucleosomal occupancy play a significant role in the transcriptional interference effects of the host genes.
Retroposon presence/absence patterns in orthologous genomic loci are known to be strong and almost homoplasy-free phylogenetic markers of common ancestry. This is evidenced by the comprehensive reconstruction of various species trees of vertebrate lineages in recent years, as well as the inference of the evolution of genes via retroposon-based gene trees of paralogous genes. Recently, it has been shown that retroposon markers are also suitable for the inference of differentiation events of gametologous genes, i.e., homologous genes on opposite sex chromosomes. This is because sex chromosomes evolved via stepwise cessation of recombination, making the presence or absence of a particular retroposon insertion among the two different gametologs in more or less closely related species a clear-cut indicator of the timing of differentiation events. Here, I examine the advantages and current limitations of this novel perspective for understanding avian sex chromosome evolution, compare the retroposon-based and sequence-based insights into gametolog differentiation and show that retroposons promise to be equally applicable to other sex chromosomal systems, such as the human X and Y chromosomes.
The widespread exchange of genes between bacteria must have consequences on the global architecture of their genomes, which are being found in the abundant genomic data available today. Most of the expansion of bacterial protein families can be attributed to transfer events, which are positively biased for smaller evolutionary distances between genomes, and more frequent for classes that are larger, when summed over all known bacteria. Moreover, “innovation” events where horizontal transfers carry exogenous evolutionary families appear to be less frequent for larger genomes. This dynamic expansion of evolutionary families is interconnected with the acquisition of new biological functions and thus with the size and distribution of the genes’ functional categories found on a genome. This commentary presents our recent contributions to this line of work and possible future directions.