Ribosomal DNA insertion elements R1Bm and R2Bm can transpose in a sequence specific manner to locations outside the 28S genes

A fraction of the ribosomal 28S genes in some insects are interrupted at specific sites by insertion elements R1 and R2 (also called Type I and II). These elements contain long open-reading frames with homology to reverse transcriptase. We have identified in the silkmoth, Bombyx mori, copies of these elements which have inserted into sites outside the ribosomal DNA (rDNA) units. The 3' ends of all "non-rDNA" elements are identical to the elements within the 28S genes; however their 5' ends are often truncated. Each non-rDNA copy has inserted into sequences that exhibit similarity to their target sites in the 28S gene. We also demonstrate by genomic blot analysis of different strains of B. mori that insertions of R1 and R2 outside the rDNA units have been infrequent, while considerable turnover of elements has occurred within the rDNA locus. One race of B. mori has lost all copies of R1 from its rDNA units, while retaining normal levels of R2. The level of both R1 and R2 have significantly increased in a tissue culture line. These findings add considerable support to the model that R1 and R2 are retrotransposable elements that utilize sequence specific endonucleases in their integration into the genome.

Similarity of reverse transcriptase-like sequences of viruses, transposable elements, and mitochondrial introns

Sequences similar to reverse transcriptase (RT) of retroviruses have been found in certain DNA viruses, mitochondrial intron sequences, and a wide variety of transposable elements. While total amino acid similarity between these diverse elements is quite low, we have identified seven regions, consisting of 182 amino acids, that are common to all elements. Highly conserved residues identified in each of these regions are diagnostic for the identification and alignment of these and for future RT-like sequences. Using both the neighbor-joining and the unweighted-pair-group methods, we have derived a probable phylogenetic tree for all RT-containing elements. These elements can be divided into two major groups. Retroviruses and DNA viruses whose propagation involves an RNA intermediate are grouped with a series of transposable elements containing long terminal repeats (LTRs). The second group is made up of RT-containing sequences of fungal mitochondrial introns and a series of transposable elements that lack LTRs. The transposable elements, copia and Ty, were found to be the most difficult to position on the phylogenetic tree, as a result of their higher rate of sequence divergence. The data are most consistent with their being distant members of the LTR group (retroviruses/LTR retrotransposons).

The site-specific ribosomal DNA insertion element R1Bm belongs to a class of non-long-terminal-repeat retrotransposons

Two types of insertion elements, R1 and R2 (previously called type I and type II), are known to interrupt the 28S ribosomal genes of several insect species. In the silkmoth, Bombyx mori, each element occupies approximately 10% of the estimated 240 ribosomal DNA units, while at most only a few copies are located outside the ribosomal DNA units. We present here the complete nucleotide sequence of an R1 insertion from B. mori (R1Bm). This 5.1-kilobase element contains two overlapping open reading frames (ORFs) which together occupy 88% of its length. ORF1 is 461 amino acids in length and exhibits characteristics of retroviral gag genes. ORF2 is 1,051 amino acids in length and contains homology to reverse transcriptase-like enzymes. The analysis of 3' and 5' ends of independent isolates from the ribosomal locus supports the suggestion that R1 is still functioning as a transposable element. The precise location of the element within the genome implies that its transposition must occur with remarkable insertion sequence specificity. Comparison of the deduced amino acid sequences from six retrotransposons, R1 and R2 of B. mori, I factor and F element of Drosophila melanogaster, L1 of Mus domesticus, and Ingi of Trypanosoma brucei, reveals a relatively high level of sequence homology in the reverse transcriptase region. Like R1, these elements lack long terminal repeats. We have therefore named this class of related elements the non-long-terminal-repeat (non-LTR) retrotransposons.

Mutational analysis of the Klebsiella pneumoniae nitrogenase promoter: sequences essential for positive control by nifA and ntrC (glnG) products

ntr (nitrogen regulated) and nif (nitrogen fixation) promoters are structurally similar to each other but bear no resemblance to canonic Escherichia coli promoters. ntr promoters are normally activated by the ntrC (glnG) product, but they can also be activated by the ntrC-related Klebsiella pneumoniae nifA product. In contrast, nif promoters of K. pneumoniae such as the nitrogenase (nifH) promoter can only be nifA activated. In this paper, we report the isolation and characterization of 28 mutants of the K. pneumoniae nifH promoter. Class A mutants no longer respond to nifA-mediated transcription, and class B mutants can now respond to ntrC-mediated activation. These two classes of mutants define sequences important to nifA- and ntrC-mediated transcription. Most surprising is that a single base change is sufficient to convert a nifA-activated promoter into an ntrC-activated one.