scholarly journals Personal Perspectives on Plant Ribosomal RNA Genes Research: From Precursor-rRNA to Molecular Evolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Vera Hemleben ◽  
Donald Grierson ◽  
Nikolai Borisjuk ◽  
Roman A. Volkov ◽  
Ales Kovarik
Keyword(s):  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Light And Electron Microscopy ◽  
Scientific Progress ◽  
5S Rdna ◽  
Molecular Organization ◽  
Rrna Genes ◽  
Detailed Knowledge ◽  
And Function ◽  
The Impact

The history of rDNA research started almost 90 years ago when the geneticist, Barbara McClintock observed that in interphase nuclei of maize the nucleolus was formed in association with a specific region normally located near the end of a chromosome, which she called the nucleolar organizer region (NOR). Cytologists in the twentieth century recognized the nucleolus as a common structure in all eukaryotic cells, using both light and electron microscopy and biochemical and genetic studies identified ribosomes as the subcellular sites of protein synthesis. In the mid- to late 1960s, the synthesis of nuclear-encoded rRNA was the only system in multicellular organisms where transcripts of known function could be isolated, and their synthesis and processing could be studied. Cytogenetic observations of NOR regions with altered structure in plant interspecific hybrids and detailed knowledge of structure and function of rDNA were prerequisites for studies of nucleolar dominance, epistatic interactions of rDNA loci, and epigenetic silencing. In this article, we focus on the early rDNA research in plants, performed mainly at the dawn of molecular biology in the 60 to 80-ties of the last century which presented a prequel to the modern genomic era. We discuss – from a personal view – the topics such as synthesis of rRNA precursor (35S pre-rRNA in plants), processing, and the organization of 35S and 5S rDNA. Cloning and sequencing led to the observation that the transcribed and processed regions of the rRNA genes vary enormously, even between populations and species, in comparison with the more conserved regions coding for the mature rRNAs. Epigenetic phenomena and the impact of hybridization and allopolyploidy on rDNA expression and homogenization are discussed. This historical view of scientific progress and achievements sets the scene for the other articles highlighting the immense progress in rDNA research published in this special issue of Frontiers in Plant Science on “Molecular organization, evolution, and function of ribosomal DNA.”

Molecular analysis of a NOR site polymorphism in brown trout (Salmo trutta): organization of rDNA intergenic spacers

Genome ◽  
1997 ◽  
Vol 40 (6) ◽  
pp. 916-922 ◽  
Author(s):  
Jaime Castro ◽  
Laura Sánchez ◽  
Paulino Martínez ◽  
Stefania De Lucchini ◽  
Irma Nardi
Keyword(s):  
Salmo Trutta ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Initial Step ◽  
Molecular Organization ◽  
Rrna Genes ◽  
28S Rrna ◽  
Intergenic Spacers ◽  
Brown Trout Salmo Trutta

Using restriction endonuclease mapping, we have analyzed the organization of rDNA (DNA coding for ribosomal RNA (rRNA)) units in the salmonid fish Salmo trutta, as an initial step toward understand the molecular basis of a nucleolar organizer region (NOR) site polymorphism detected in this species. The size of the rDNA units ranged between 15 and 23 kb, with remarkable variation both within individuals and between populations. Three regions of internal tandem repetitiveness responsible for this length polymorphism were located to the intergenic spacers. NOR site polymorphic individuals showed a higher number of length classes, in some cases forming a complete 1 kb fragment ladder. The amount of rRNA genes was as much as 8-fold higher in polymorphic individuals compared with standard individuals. All individuals from the most polymorphic population showed a 14-kb insertion of unknown nature in a small proportion (below 25%) of the 28S rRNA genes.Key words: rRNA genes, repetitive elements, molecular organization, rDNA amount.

Nucleologenesis in Trypanosoma cruzi

2016 ◽  
Vol 22 (3) ◽  
pp. 621-629 ◽  
Author(s):  
Tomás Nepomuceno-Mejía ◽  
Reyna Lara-Martínez ◽  
Roberto Hernández ◽  
María de Lourdes Segura-Valdez ◽  
Luis F. Jiménez-García
Keyword(s):  
Cell Division ◽  
Trypanosoma Cruzi ◽  
Ethylenediaminetetraacetic Acid ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Light And Electron Microscopy ◽  
Nucleolar Organizer ◽  
Nuclear Bodies ◽  
Nucleolar Organizer Regions ◽  
Nucleolar Material

AbstractNucleolar assembly is a cellular event that requires the synthesis and processing of ribosomal RNA, in addition to the participation of pre-nucleolar bodies (PNBs) at the end of mitosis. In mammals and plants, nucleolar biogenesis has been described in detail, but in unicellular eukaryotes it is a poorly understood process. In this study, we used light and electron microscopy cytochemical techniques to investigate the distribution of nucleolar components in the pathway of nucleolus rebuilding during closed cell division in epimastigotes of Trypanosoma cruzi, the etiologic agent of American trypanosomiasis. Silver impregnation specific for nucleolar organizer regions and an ethylenediaminetetraacetic acid regressive procedure to preferentially stain ribonucleoprotein revealed the conservation and dispersion of nucleolar material throughout the nucleoplasm during cell division. Furthermore, at the end of mitosis, the argyrophilic proteins were concentrated in the nucleolar organizer region. Unexpectedly, accumulation of nucleolar material in the form of PNBs was not visualized. We suggest that formation of the nucleolus in epimastigotes of T. cruzi occurs by a process that does not require the concentration of nucleolar material within intermediate nuclear bodies such as mammalian and plant PNBs.

Evolution of Bird Sex Chromosomes Narrated by Repetitive Sequences: Unusual W Chromosome Enlargement in Gallinula melanops (Aves: Gruiformes: Rallidae)

2019 ◽  
Vol 158 (3) ◽  
pp. 152-159 ◽  
Author(s):  
Ricardo J. Gunski ◽  
Rafael Kretschmer ◽  
Marcelo Santos de Souza ◽  
Ivanete de Oliveira Furo ◽  
Suziane A. Barcellos ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
18S Rdna ◽  
Organizer Region ◽  
Repetitive Sequences ◽  
Nucleolar Organizer Region ◽  
Molecular Cytogenetics ◽  
5S Rdna ◽  
Nucleolar Organizer ◽  
W Chromosome ◽  
Rdna Sites

Among birds, species with the ZZ/ZW sex determination system generally show significant differences in morphology and size between the Z and W chromosomes (with the W usually being smaller than the Z). In the present study, we report for the first time the karyotype of the spot-flanked gallinule (Gallinula melanops) by means of classical and molecular cytogenetics. The spot-flanked gallinule has 2n = 80 (11 pairs of macrochromosomes and 29 pairs of microchromosomes) with an unusual W chromosome that is larger than the Z. Besides being totally heterochromatic, it has a secondary constriction in its long arm corresponding to the nucleolar organizer region, as confirmed by both silver staining and mapping of 18S rDNA probes. This is an unprecedented fact among birds. Additionally, 18S rDNA sites were also observed in 6 microchromosomes, while 5S rDNA was found in just 1 microchromosomal pair. Seven out of the 11 used microsatellite sequences were found to be accumulated in microchromosomes, and 6 microsatellite sequences were found in the W chromosome. In addition to the involvement of heterochromatin and repetitive DNAs in the differentiation of the large W chromosome, the results also show an alternative scenario that highlights the plasticity that shapes the evolutionary history of bird sex chromosomes.

scholarly journals Drug-induced dispersal of transcribed rRNA genes and transcriptional products: immunolocalization and silver staining of different nucleolar components in rat cells treated with 5,6-dichloro-beta-D-ribofuranosylbenzimidazole.

1984 ◽  
Vol 99 (2) ◽  
pp. 672-679 ◽  
Author(s):  
U Scheer ◽  
B Hügle ◽  
R Hazan ◽  
K M Rose
Keyword(s):  
Rna Polymerase ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Ribosomal Subunit ◽  
Rna Polymerase I ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Linear Distribution ◽  
Nucleolar Material ◽  
Polymerase I

Upon incubation of cultured rat cells with the adenosine analogue 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB), nucleoli reversibly dissociate into their substructures, disperse throughout the nuclear interior, and form nucleolar "necklaces". We have used this experimental system, which does not inhibit transcription of the rRNA genes, to study by immunocytochemistry the distribution of active rRNA genes and their transcriptional products during nucleolar dispersal and recovery to normal morphology. Antibodies to RNA polymerase I allow detection of template-engaged polymerase, and monoclonal antibodies to a ribosomal protein (S1) of the small ribosomal subunit permit localization of nucleolar preribosomal particles. The results show that, under the action of DRB transcribed rRNA, genes spread throughout the nucleoplasm and finally appear in the form of several rows, each containing several (up to 30) granules positive for RNA polymerase I and argyrophilic proteins. Nucleolar material containing preribosomal particles also appears in granular structures spread over the nucleoplasm but its distribution is distinct from that of rRNA gene-containing granules. We conclude that, although transcriptional units and preribosomal particles are both redistributed in response to DRB, these entities retain their individuality as functionally defined subunits. We further propose that each RNA polymerase-positive granular unit represents a single transcription unit and that each continuous array of granules ("string of nucleolar beads") reflects the linear distribution of rRNA genes along a nucleolar organizer region. Based on the total number of polymerase I-positive granules we estimate that a minimum of 60 rRNA genes are active during interphase of DRB-treated rat cells.

RIBOSOMAL GENE LOCALIZATION AND DISTRIBUTION (ARRANGEMENT) WITHIN THE NUCLEOLAR ORGANIZER REGION OF ZEA MAYS

Genetics ◽  
1975 ◽  
Vol 80 (3) ◽  
pp. 505-518
Author(s):  
Samuel A Ramirez ◽  
John H Sinclair
Keyword(s):  
Zea Mays ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
B Chromosome ◽  
Ribosomal Gene ◽  
Ribosomal Genes ◽  
Rrna Genes ◽  
Gene Localization ◽  
Chromosome 6

ABSTRACT Cytogenetic and molecular hybridization techniques were used to examine the arrangement of rRNA genes at the nucleolar organizer region (NOR) of maize. TB-6a stocks involving a reciprocal translocation between a B chromosome and the NOR of chromosome 6 were used. The amount of rDNA in the different stocks used varied from 1.5 to 4 NOR equivalents depending on the number of B6 choromosomes present. Cytological measurements show that the medial break through the NOR results in an equal partitioning of the heterochromatic knob (the NOR) between chromosome 6 and the B chromosome to which it was translocated. DNA-rRNA hybridization experiments show a linear relationship between the amount of rRNA capable of hybridizing with DNA and the number of NOR equivalents present. The data confirm McClintock's conclusion that the heterochromatic knob, rather than the constricted portion, is the true NOR region. Further, they show that the number of ribosomal genes is correlated with the amount of cytologically visible NOR, suggesting a uniform distribution of genes throughout the locus.

An ALS-associated mutation in human FUS reduces neurotransmission from C. elegans motor neurons to muscles

2019 ◽  
Author(s):  
Sebastian M. Markert ◽  
Michael Skoruppa ◽  
Bin Yu ◽  
Ben Mulcahy ◽  
Mei Zhen ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Neuromuscular Junctions ◽  
Neurodegenerative Disorder ◽  
Electron Tomography ◽  
Light And Electron Microscopy ◽  
Electrophysiological Recording ◽  
C Elegans ◽  
Fused In Sarcoma ◽  
And Function ◽  
The Impact

AbstractAmytrophic lateral sclerosis (ALS) is a neurodegenerative disorder that has been associated with multiple genetic lesions, including mutations in the gene FUS (Fused in Sarcoma), an RNA/DNA-binding protein. Expression of the ALS-associated human FUS in C. elegans results in mislocalization and aggregation of FUS outside the nucleus, and leads to impaired neuromuscular behaviors. However, the mechanisms by which mutant FUS disrupts neuronal health and function remain partially understood. Here we investigated the impact of ALS-associated FUS on motor neuron health using correlative light and electron microscopy, electron tomography, and electrophysiology. Expression of ALS-associated FUS impairs synaptic vesicle docking at neuromuscular junctions, and leads to the emergence of a population of large and electron-dense filament-filled endosomes. Electrophysiological recording of neuromuscular transmission revealed reduced transmission from motor neurons to muscles. Together, these results suggest a potential direct or indirect role of human FUS in the organization of synaptic vesicles, and reduced transmission from motor neurons to muscles.Summary statementAn ALS-associated mutation in a trafficking protein disrupts the organization of the C. elegans neuromuscular junction.

scholarly journals Overexpression of an ALS-associated FUS mutation in C. elegans disrupts NMJ morphology and leads to defective neuromuscular transmission

Biology Open ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. bio055129 ◽  
Author(s):  
Sebastian M. Markert ◽  
Michael Skoruppa ◽  
Bin Yu ◽  
Ben Mulcahy ◽  
Mei Zhen ◽  
...  
Keyword(s):  
Motor Neurons ◽  
Neuromuscular Junctions ◽  
Neurodegenerative Disorder ◽  
Electron Tomography ◽  
Light And Electron Microscopy ◽  
Ectopic Expression ◽  
Electrophysiological Recording ◽  
Pathological Effect ◽  
And Function ◽  
The Impact

ABSTRACTThe amyotrophic lateral sclerosis (ALS) neurodegenerative disorder has been associated with multiple genetic lesions, including mutations in the gene for fused in sarcoma (FUS), a nuclear-localized RNA/DNA-binding protein. Neuronal expression of the pathological form of FUS proteins in Caenorhabditis elegans results in mislocalization and aggregation of FUS in the cytoplasm, and leads to impairment of motility. However, the mechanisms by which the mutant FUS disrupts neuronal health and function remain unclear. Here we investigated the impact of ALS-associated FUS on motor neuron health using correlative light and electron microscopy, electron tomography, and electrophysiology. We show that ectopic expression of wild-type or ALS-associated human FUS impairs synaptic vesicle docking at neuromuscular junctions. ALS-associated FUS led to the emergence of a population of large, electron-dense, and filament-filled endosomes. Electrophysiological recording revealed reduced transmission from motor neurons to muscles. Together, these results suggest a pathological effect of ALS-causing FUS at synaptic structure and function organization.This article has an associated First Person interview with the first author of the paper.

scholarly journals Molecular organization of 5S rDNA intergenic spacer in Gentiana pneumonanthe L. and G. punctata L.

2021 ◽  
Vol 18 (1-2) ◽  
pp. 9-15
Author(s):  
V. M. Mel’nyk ◽  
I. O. Andreev ◽  
G. Yu. Myryuta ◽  
A. Y. Shelyfist ◽  
R. A. Volkov ◽  
...  
Keyword(s):  
Intergenic Spacer ◽  
5S Rdna ◽  
5S Rrna ◽  
Molecular Organization ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Coding Region ◽  
5S Rrna Genes ◽  
Rdna Igs ◽  
Rdna Intergenic Spacer

Aim. The study was aimed at cloning and analysis of molecular organization of 5S rDNA intergenic spacer (IGS) in two Gentiana species of Ukrainian flora, G. pneumonanthe L. and G. punctata L. Methods. 5S rDNA IGS sequence was amplified using polymerase chain reaction (PCR) with a pair of primers specific for the gene coding region. The produced PCR products were fractionated by gel-electrophoresis, isolated, ligated into plasmid pUC18, cloned into E. coli, and then sequenced. Nucleotide sequences were aligned using the Muscle algorithm and analyzed in the Unipro UGENE software. Results. The intergenic spacer region of the 5S rRNA genes was cloned and sequenced for two Gentiana species of Ukrainian flora, G. pneumonanthe and G. punctata. Based on the analysis of the alignment of the IGS sequences of five Gentiana species from three sections, some features of molecular organization of IGS of 5S rRNA genes in the studied species were established. In particular, motifs typical for other angiosperm families were identified, such as conservative oligo-dT motif at the IGS 3'-end that served as a transcription termination site and AT-rich region preceding the coding region of 5S rRNA gene. However, in the region of transcription initiation, conservative GC-element in position -13 is changed to AC. Conclusions. The interspecific variation of molecular organization of 5S rDNA IGS was identified among Gentiana species that can be used to clarify the phylogenetic relationships between members of this genus.Keywords: Gentiana species, 5S rDNA intergenic spacer, molecular organization, phylogeny.

5S rDNA genome regions of Lens species

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 937-942 ◽  
Author(s):  
M Fernández ◽  
M L Ruiz ◽  
C Linares ◽  
A Fominaya ◽  
M Pérez de la Vega
Keyword(s):  
Lens Culinaris ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
5S Rdna ◽  
Nucleolar Organizer ◽  
Repeated Sequence ◽  
Nontranscribed Spacer ◽  
Selective Hybridization

The length variability of the nontranscribed spacer (NTS) of the 5S rDNA repeats was analyzed in species of the genus Lens by means of PCR amplification. The NTS ranged from ~227 to ~952 bp. The polymorphism detected was higher than previous NTS polymorphisms described in this genus. Three NTS length variants from Lens culinaris subsp. culinaris and 2 from Lens culinaris subsp. orientalis were sequenced. The culinaris NTS fragment lengths were 239, 371, and 838 bp, whereas the orientalis ones were 472 bp and 506 bp, respectively. As a result of sequence similarities, 2 families of sequences were distinguished, 1 including the sequences of 838 and 506 bp, and others with the sequences of 239, 371, and 472 bp. The 1st family was characterized by the presence of a repeated sequence designated A, whereas the 2nd family showed a single A sequence and other repeated sequences designated B, C, and D. The presence of an (AT)n microsatellite was also observed in the 2nd family of sequences. The fragments, which included the 239-bp and 838-bp NTS sequences, as well as the intergenic spacer (IGS) of the 18S–5.8S–26S ribosomal DNA also from L. culinaris subsp. culinaris, were used to localize the nucleolar organizer region (NOR) and the 5S rDNA loci in the chromosomes of several species of the genus Lens by means of fluorescence in situ hybridization (FISH). The selective hybridization of the 2 NTS probes allowed us to distinguish between different 5S rDNA chromosomal loci.Key words: Lens, lentil, ribosomal loci, 5S, FISH, NTS polymorphism, NOR.

scholarly journals Lamin B2 Modulates Nucleolar Morphology, Dynamics, and Function

2017 ◽  
Vol 37 (24) ◽  
Author(s):  
Ayantika Sen Gupta ◽  
Kundan Sengupta
Keyword(s):  
Nuclear Envelope ◽  
Ribosome Biogenesis ◽  
Organizer Region ◽  
Nucleolar Organizer Region ◽  
Nucleolar Organizer ◽  
Intergenic Sequence ◽  
Deletion Mutants ◽  
Nucleolar Proteins ◽  
Dynamics And Function ◽  
And Function

ABSTRACT The nucleolus is required for ribosome biogenesis. Human cells have 2 or 3 nucleoli associated with nucleolar organizer region (NOR)-bearing chromosomes. An increase in number and altered nucleolar morphology define cancer cells. However, the mechanisms that modulate nucleolar morphology and function are unclear. Here we show that in addition to localizing at the nuclear envelope, lamin B2 localizes proximal to nucleolin at the granular component (GC) of the nucleolus and associates with the nucleolar proteins nucleolin and nucleophosmin. Lamin B2 knockdown severely disrupted the nucleolar morphology, which was rescued to intact and discrete nucleoli upon lamin B2 overexpression. Furthermore, two mutually exclusive lamin B2 deletion mutants, ΔHead and ΔSLS, rescued nuclear and nucleolar morphology defects, respectively, induced upon lamin B2 depletion, suggesting independent roles for lamin B2 at the nucleolus and nuclear envelope. Lamin B2 depletion increased nucleolin aggregation in the nucleoplasm, implicating lamin B2 in stabilizing nucleolin within the nucleolus. Lamin B2 knockdown upregulated nucleolus-specific 45S rRNA and upstream intergenic sequence (IGS) transcripts. The IGS transcripts colocalized with aggregates of nucleolin speckles, which were sustained in the nucleoplasm upon lamin B2 depletion. Taken together, these studies uncover a novel role for lamin B2 in modulating the morphology, dynamics, and function of the nucleolus.

Sign in / Sign up

Export Citation Format

Share Document