Short Interspersed Nuclear Element (SINE) Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293

Abstract

Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4–14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140–493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3’-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50–65% and 60–75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259–343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity.

The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules

“…Notably, of the approximately 1000 still identifiable copies of AmnSINE1 in the human genome, 105 correspond to loci phylogenetically highly conserved among mammalian orthologs.” This high degree of conservation strongly suggests evolutionary selection for functionality. Other examples of SINE3 have been found in fruit bats [48], fungi [49], and zebrafish [50] among other organisms [51]. In zebrafish, Kapitonov and Jurka report that, “SINE3s are transcribed from the type 1 internal pol III promoter.…”

Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome

“…Retrotransposons of the SINE (Short Interspersed Nuclear Element) superfamily, in particular the Alu elements, are a compelling example of this process. The non-autonomous SINEs, which range in size from 100 to 600 base pairs (bps), are widely distributed in the eukaryotes, where they play an important role in the organization of the genome, given their involvement in cell survival during many different types of physiological stress, for example [ 62 ]. The Alu elements, which are primate-specific, are considered to be the most widespread of the transposable elements, representing approximately 11% of the human genome [ 63 , 64 , 65 ].…”

Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew

“…Notably, the rapid and continuous expansion that we observed here resembles the activity of TEs rather than tRNAs and protein-coding genes. SINEs are Class I TEs, propagating by copy-paste mechanism, although they do not encode any proteins and thus are depedend on other TEs for their expansion (Kanhayuwa and Coutts, 2016). Most SINEs are caracterised by the presence of a tRNA-like sequence at the 5’ terminal region, by a central conserved region, and by a relatively short sequence of 200-700 bp (Kanhayuwa and Coutts, 2016).…”