Set Of Ribosomal RNA Genes Research Articles

Gene Expression Dominance in Allopolyploids: Hypotheses and Models.

The classical example of nonadditive contributions of the two parents to allopolyploids is nucleolar dominance, which entails silencing of one parental set of ribosomal RNA genes. This has been observed for many other loci. The prevailing explanation for this genome-wide expression disparity is that the two merged genomes differ in their transposable element (TE) complement and in their level of TE-mediated repression of gene expression. Alternatively, and not exclusively, gene expression dominance may arise from mismatches between trans effectors and their targets. Here, we explore quantitative models of regulatory mismatches leading to gene expression dominance. We also suggest that, when pairs of merged genomes are similar from one allopolyploidization event to another, gene-level and genome dominance patterns should also be similar.

Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae.

BackgroundEntomopathogenic associations between nematodes in the genera Steinernema and Heterorhabdus with their cognate bacteria from the bacterial genera Xenorhabdus and Photorhabdus, respectively, are extensively studied for their potential as biological control agents against invasive insect species. These two highly coevolved associations were results of convergent evolution. Given the natural abundance of bacteria, nematodes and insects, it is surprising that only these two associations with no intermediate forms are widely studied in the entomopathogenic context. Discovering analogous systems involving novel bacterial and nematode species would shed light on the evolutionary processes involved in the transition from free living organisms to obligatory partners in entomopathogenicity.ResultsWe report the complete genome sequence of a new member of the enterobacterial genus Serratia that forms a putative entomopathogenic complex with Caenorhabditis briggsae. Analysis of the 5.04 MB chromosomal genome predicts 4599 protein coding genes, seven sets of ribosomal RNA genes, 84 tRNA genes and a 64.8 KB plasmid encoding 74 genes. Comparative genomic analysis with three of the previously sequenced Serratia species, S. marcescens DB11 and S. proteamaculans 568, and Serratia sp. AS12, revealed that these four representatives of the genus share a core set of ~3100 genes and extensive structural conservation. The newly identified species shares a more recent common ancestor with S. marcescens with 99 % sequence identity in rDNA sequence and orthology across 85.6 % of predicted genes. Of the 39 genes/operons implicated in the virulence, symbiosis, recolonization, immune evasion and bioconversion, 21 (53.8 %) were present in Serratia while 33 (84.6 %) and 35 (89 %) were present in Xenorhabdus and Photorhabdus EPN bacteria respectively.ConclusionThe majority of unique sequences in Serratia sp. SCBI (South African Caenorhabditis briggsae Isolate) are found in ~29 genomic islands of 5 to 65 genes and are enriched in putative functions that are biologically relevant to an entomopathogenic lifestyle, including non-ribosomal peptide synthetases, bacteriocins, fimbrial biogenesis, ushering proteins, toxins, secondary metabolite secretion and multiple drug resistance/efflux systems. By revealing the early stages of adaptation to this lifestyle, the Serratia sp. SCBI genome underscores the fact that in EPN formation the composite end result – killing, bioconversion, cadaver protection and recolonization- can be achieved by dissimilar mechanisms. This genome sequence will enable further study of the evolution of entomopathogenic nematode-bacteria complexes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1697-8) contains supplementary material, which is available to authorized users.

Nucleolar dominance: uniparental gene silencing on a multi-megabase scale in genetic hybrids.

Nucleolar dominance is a phenomenon in hybrids or allopolyploids in which nucleoli form on chromosomes inherited from only one of the two parents. The molecular basis for nucleolar dominance is the transcription by RNA polymerase I of only one parental set of ribosomal RNA genes (rRNA genes). These rRNA genes are clustered by the hundreds, or thousands, of copies, often spanning tens of millions of basepairs of chromosomal DNA at loci known as nucleolus organizer regions (NORs). Enforcement of nucleolar dominance appears to be accomplished by selectively silencing one set of rRNA genes via chemical modifications of chromatin. However, the mechanisms responsible for initially discriminating among the parental sets of rRNA genes and establishing nucleolar dominance remain unclear. Possibilities include mechanisms that act on each rRNA gene or mechanisms that affect whole NORs or even larger chromosomal domains. This review provides a historical perspective of nucleolar dominance research, explores the most popular hypotheses and their shortcomings, and offers some speculations concerning alternative hypotheses to be considered.

RNA polymerase I transcription in a Brassica interspecific hybrid and its progenitors: Tests of transcription factor involvement in nucleolar dominance.

In interspecific hybrids or allopolyploids, often one parental set of ribosomal RNA genes is transcribed and the other is silent, an epigenetic phenomenon known as nucleolar dominance. Silencing is enforced by cytosine methylation and histone deacetylation, but the initial discrimination mechanism is unknown. One hypothesis is that a species-specific transcription factor is inactivated, thereby silencing one set of rRNA genes. Another is that dominant rRNA genes have higher binding affinities for limiting transcription factors. A third suggests that selective methylation of underdominant rRNA genes blocks transcription factor binding. We tested these hypotheses using Brassica napus (canola), an allotetraploid derived from B. rapa and B. oleracea in which only B. rapa rRNA genes are transcribed. B. oleracea and B. rapa rRNA genes were active when transfected into protoplasts of the other species, which argues against the species-specific transcription factor model. B. oleracea and B. rapa rRNA genes also competed equally for the pol I transcription machinery in vitro and in vivo. Cytosine methylation had no effect on rRNA gene transcription in vitro, which suggests that transcription factor binding was unimpaired. These data are inconsistent with the prevailing models and point to discrimination mechanisms that are likely to act at a chromosomal level.

A model for the evolution of the Vicia faba chloroplast genome

The Vicia faba chloroplast genome lacks inverted repeat sequences and contains only one set of ribosomal RNA genes. The genetic organization has been altered by inversions, relative to the typical arrangement of most higher plant chloroplast genomes. The Vicia faba plastid genome thus represents one of the more interesting results of chloroplast genomic evolution. The present study employs small DNA probes and Southern blot hybridizations to investigate the steps involved in the evolution of the Vicia faba chloroplast genome. The data from heterologous hybridizations between chloroplast DNA of Brassica napus (a conserved genome) and of Vicia faba led to three observations: 1) The inverted repeat segment closest to the psbA gene was deleted prior to the rearrangements. 2) A quarter of the ancestral small single copy region was lost during the deletion. 3) The genetic organization observed in Vicia faba resulted from three inversions after the deletion event. Our findings, combined with previous observations, helped devise a stepwise model for the evolution of the Vicia faba chloroplast genome. The area of the small single copy region absent from the Vicia faba chloroplast chromosome lacks in vivo transcription activity in Brassica napus.

Chloroplast DNA evolution among legumes: Loss of a large inverted repeat occurred prior to other sequence rearrangements

We have compared the sequence organization of four previously uncharacterized legume chloroplast DNAs - from alfalfa, lupine, wisteria and subclover — to that of legume chloroplast DNAs that either retain a large, ribosomal RNA-encoding inverted repeat (mung bean) or have deleted one half of this repeat (broad bean). The circular, 126 kilobase pair (kb) alfalfa chloroplast genome, like those of broad bean and pea, lacks any detectable repeated sequences and contains only a single set of ribosomal RNA genes. However, in contrast to broad bean and pea, alfalfa chloroplast DNA is unrearranged (except for the deletion of one segment of the inverted repeat) relative to chloroplast DNA from mung bean. Together with other findings reported here, these results allow us to determine which of the four possible inverted repeat configurations was deleted in the alfalfa-pea-broad bean lineage, and to show how the present-day broad bean genome may have been derived from an alfalfa-like ancestral genome by two major sequence inversions. The 147 kb lupine chloroplast genome contains a 22 kb inverted repeat and has essentially complete colinearity with the mung bean genome. In contrast, the 130 kb wisteria genome has deleted one half of the inverted repeat and appears colinear with the alfalfa genome. The 140 kb subclover genome has been extensively rearranged and contains a family of at least five dispersed repetitive sequence elements, each several hundred by in size; this is the first report of dispersed repeats of this size in a land plant chloroplast genome. We conclude that the inverted repeat has been lost only once among legumes and that this loss occurred prior to all the other rearrangements observed in subclover, broad bean and pea. Of those lineages that lack the inverted repeat, some are stable and unrearranged, other have undergone a moderate amount of rearrangement, while still others have sustained a complex series of rearrangement either with or without major sequence duplications and transpositions.

A stochastic mechanism controls the relative replication of equally competent ribosomal RNA gene sets in individual dipteran polyploid nuclei.

The endoreplication of the two nucleolar organizers (NOs) of the diploid genome has been examined in individual polyploid nuclei of the dipteran Calliphora erythrocephala. Crosses between two strains with diagnostic nontranscribed spacer polymorphisms in their rRNA genes were used to provide progeny with distinguishable NOs, and single nuclei of two highly polyploid cell types--salivary gland and nurse cells--were examined from individual F1 animals. Initially the representation of the two NOs in total polyploid tissue DNA was determined. This revealed that, although the NO regions present in one of the strains (Tom) were very similar in spacer composition, they displayed two types of behavior in the hybrids containing the single NO region typical of the second strain (Karla). In TW phenotype F1 progeny, very little replication of the Tom NO relative to the Karla NO occurred, whereas in TS phenotype progeny replication of the Tom and Karla NOs was approximately equivalent. When individual polyploid nuclei of the TS phenotype animals were examined, however, the relative replication of the Tom and Karla NOs was found not to be a fixed genetic property but to vary dramatically from cell to cell. This was true even for the nurse cell nuclei within a single ovarian follicle, which are the products of only four mitotic divisions of a single germ-line cell. These findings indicate that for NOs of similar replicative competence, a stochastic mechanism governs the relative usage of each NO for endoreplication and that the relative activity of the two NOs is not stably determined through the mitotic divisions preceding polyploidization. Stochastic selection after mitotic DNA replication could be a general phenomenon governing the relative usage (transcription) of different, but equally competent, alleles of any gene in individual cells, if the required factors are in short supply.

Two large clusters with thirty-seven transfer RNA genes adjacent to ribosomal RNA gene sets in Bacillus subtilis. Sequence and organization of trrnD and trrnE gene clusters.

Sequences of two large tRNA gene clusters (trrnD and trrnE) in Bacillus subtilis 168 revealed 16 and 21 tRNA genes, respectively, as identified by anticodon assignments. Each cluster contains upstream flanking 23 and 5 S rRNA sequences. The 23-5 S intergenic space in trrnE corresponds exactly to the analogous space in trrnB, which was previously sequenced (Wawrousek, E.F., and Hansen, J.N. (1983) J.Biol. Chem. 258, 291-298). The 5 S rRNA genes in trrnB and trrnE are B. subtilis major species; but trrnD possesses a minor species (Raue, H.A., and Planta, R. J. (1977) Mol. Gen. Genet. 156, 185-193) gene with a putative promoter that may allow differential expression with respect to the upstream rRNA gene set. Most of the tRNA genes are probably expressed as large transcriptional units, except for a LeuTTG tRNA in the trrnD cluster that appears to constitute its own operon with putative promoter and terminator sequences. Although all the amino acids are represented among the tRNA anticodons, there are few repeats of amino acid types within clusters; trrnD with 16 tRNA genes has anticodons corresponding to 15 amino acids. About two-thirds of the tRNA genes encode a 3'-terminal-CCA, and these are intermingled with those that do not, with no apparent pattern.

Structure and organization of a cluster of sic tRNA genes in the space between tandem ribosomal RNA gene sets in Bacillus subtilis.

Hybridization of Southern blots of EcoRI digests of total Bacillus subtilis DNA with ribosomal RNA and transfer RNA probes provides evidence of highly clustered tRNA and rRNA genes, with several tRNA clusters being located in spaces which span between tandem ribosomal RNA gene sets. Clones containing these tRNA clusters were isolated from a Charon 4A library. One of them, denoted trrnB, was partially sequenced. A cluster of six tRNA genes was found, with anticodon assignments of Asn, Thr, Gly, Arg, Pro, Ala. This cluster is closely flanked on both sides by ribosomal RNA gene sets, which were identified by sequencing upward through the 5 S rRNA gene, across a space, and into the 23 S rRNA gene, and also sequencing downward into the 16 S rRNA gene. The tRNA gene cluster appears to be organized into at least two transcriptional units separated by an attenuator region. These transcriptional units may be components of the flanking ribosomal RNA operons. The putative promoter region of the downstream 16 S rRNA is organized differently from Escherichia coli; it is smaller and seems less complex. This gene organization provides insight into possible mechanisms for coordinate and differential control of transfer and ribosomal RNA gene expression.

TRNA genes are found between 16S and 23S rRNA genes in Bacillus subtilis.

There are at least nine, and probably ten, ribosomal RNA gene sets in the genome of Bacillus subtilis. Each gene set contains sequences complementary to 16S, 23S and 5S rRNAs. We have determined the nucleotide sequences of two DNA fragments which each contain 165 base pairs of the 16S rRNA gene, 191 base pairs of the 23S rRNA gene, and the spacer region between them. The smaller space region is 164 base pairs in length and the larger one includes an additional 180 base pairs. The extra nucleotides could be transcribed in tRNAIIe and tRNA Ala sequences. Evidence is also presented for the existence of a second spacer region which also contains tRNAIIe and tRNA Ala sequences. No other tRNAs appear to be encoded in the spacer regions between the 16S and 23S rRNA genes. Whereas the nucleotide sequences corresponding to the 16S rRNA, 23S rRNA and the spacer tRNAs are very similar to those of E. coli, the sequences between these structural genes are very different.

Physical mapping of the pea chloroplast DNA and localization of the ribosomal RNA genes

The closed circular DNA of pea chloroplast has been digested with restriction endonucleases SalI, SmaI, BamHI, XbaI, XhoI, HindIII, and EcoRI. A physical restriction map of pea ctDNA has been constructed by mapping the SalI and SmaI sites. The pea ctDNA has been found to contain one set of ribosomal RNA genes by Southern hybridization of restriction endonuclease digest, R-loop studies, and DNA-DNA heteroduplex mapping. The 23 S and 16 S RNA genes are confined to a DNA region of 3.0 and 1.5 kbp, respectively. The two rRNA chains are separated by a spacer region of 2.2 kbp.

Vicia faba chloroplast DNA has only one set of ribosomal RNA genes as shown by partial denaturation mapping and R-loop analysis

Broad-bean (Vicia faba) chloroplast DNA (cpDNA) was isolated and characterized. The intact DNA is circular and has a molecular weight of 79.8x 106 dalton. Electron microscopic analysis of self-annealed intact single-strand circles show that it does not have a large double-stranded inverse repeat as seen in spinach chloroplast DNA. Only one ribosomal RNA gene (one set of 16S and 23S rRNA sequences) was found in preparations of R-loops between the Vicia rRNA and cpDNA circles. A restriction enzyme map for SalI and KpnI was derived by comparing the partial denaturation pattern of the fragments with the pattern of the intact circle. The map was confirmed by gel analysis. The ribosomal RNA gene was localized on the SalI fragment 3b by R-loop analysis. SalI fragment 1a although it contains a G-C rich region did not form R-loops with rRNA. Partial denaturation patterns of spinach cpDNA circles and BglI fragments were determined and from this the position of the fragments mapped. This confirmed the reliability of these methods for the arrangement of restriction enzyme fragments along circular molecules. The structures of the two cpDNAs were compared.

Electron microscope heteroduplex studies of sequence relations among plasmids of Escherichia coli: VII. Mapping the ribosomal RNA genes of plasmid F14

Escherichia coli episome F14 contains two 16 S + 23 S ribosomal RNA gene sets. Their positions and structure have been studied by electron microscope heteroduplex methods. The A gene set maps from 81.4 to 86.7 kilobases from the counterclockwise junction of F DNA with bacterial chromosomal DNA of F14; the B gene set maps very close to the clockwise junction, that is, at map position 204.4 to 209.7 kilobases from the counterclockwise junction. The structure of the rRNA-rDNA hybrids indicates that each gene set consists of one 16 S gene (r16) of length 1.28 ± 0.12 kilobases, a spacer (rsp) of length 0.57 ± 0.12 kilobase and a 23 S gene (r23) of length 2.60 ± 0.20 kilobases. We propose the genetic notation rrn for the entire gene set. The structure of the DNA/DNA duplexes between the rrnA set and the rrnB set shows that there is a region of non-homology of length 0.29 ± 0.06 kilobase within the otherwise homologous rrnA and rrnB sequences. This non-homology region is probably part, but not all, of the spacer between the 16 S and 23 S genes.

Chloroplast ribosomal RNA genes in the chloroplast DNA of Euglena gracilis

Euglena chloroplast DNA has a buoyant density in CsCI of 1.686. Shearing this DNA produces a satellite band at density 1.700. The satellite, easily lost during preparative CsCI gradient centrifugation of chloroplast DNA, contains the genes for chloroplast ribosomal RNA. Pure Euglena chloroplast DNA is shown to contain one set of ribosomal RNA genes for each 90 × 10 6 daltons of DNA.