Divergent rRNAs as regulators of gene expression at the ribosome level

Song, Woo-Seok; Joo, Minju; Yeom, Ji-Hyun; Shin, Eunkyoung; Lee, Minho; Choi, Hyung‐Kyoon; Hwang, Jihwan; Kim, Young Dong; Seo, Ramin; Lee, J. Eugene; Moore, Christopher; Kim, Yong‐Hak; Eyun, Seong‐il; Hahn, Yoonsoo; Bae, Jang–Ho; Lee, Kangseok

doi:10.1038/s41564-018-0341-1

Cited by 51 publications

(49 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…There are numerous human diseases associated with rDNA dysfunction (ribosomopathies) caused by structural or functional abnormalities in the ribosomal components—including rDNA, which has a principal role in ribosomal function [ 32 , 53 , 61 ]. It is believed that, being a source of hypervariable genomic diversity, rDNA provides a mechanism for cellular homeostasis and adaptation, and ribosome heterogeneity is considered as ribosome-mediated control of gene regulation [ 61 , 62 , 63 , 64 ]. In addition, tissue-specific effects of ribosome dysfunction have also been demonstrated [ 63 ].…”

Section: Discussionmentioning

confidence: 99%

Age-Dependent and Tissue-Specific Alterations in the rDNA Clusters of the Panax ginseng C. A. Meyer Cultivated Cell Lines

et al. 2020

View full text Add to dashboard Cite

Long-term cultivation of Panax ginseng cell lines leads to a decreasing synthesis of the biologically active substances used in traditional medicine. To gain insight into the cellular mechanisms which may influence this process, we analyzed variations within the rDNA cluster of the Oriental ginseng cell lines. The cell lines were cultivated for 6 and 24 years; the number of nucleoli and chromosomes was analyzed. The complete 18S rDNA sequences were cloned and sequenced. The nucleotide polymorphism and phylogenetic relations of the sequences were analyzed, and the secondary structures for separate 18S rRNA regions were modeled. The 18S rDNA accumulated mutations during cell cultivation that correlate well with an increase in the number of chromosomes and nucleoli. The patterns of nucleotide diversity are culture-specific and the increasing polymorphism associates with cytosine methylation sites. The secondary structures of some 18S rRNA regions and their interaction can alter during cultivation. The phylogenetic tree topologies are particular for each cell line.The observed alterations in rDNA clusters are associated with a somaclonal variation, leading to changes in the pattern of intracellular synthesis during cell cultivation. The identified divergent rRNAs could provide additional gene expression regulation in P. ginseng cells by forming heterogeneous ribosomes.

show abstract

Section: Discussionmentioning

confidence: 99%

Age-Dependent and Tissue-Specific Alterations in the rDNA Clusters of the Panax ginseng C. A. Meyer Cultivated Cell Lines

et al. 2020

View full text Add to dashboard Cite

show abstract

“…Regardless, increased resistance to predation (phage attack) at the cost of reduced maximum potential growth rates is a widely observed ecological trade-off (Bohannan and Lenski, 2000). Finally, recent work has showed that some rRNA loci specialize in the translation of certain types of genes in Vibrio vulnificus (Song et al, 2019). It is thus tempting to speculate that unlinked rRNA genes could facilitate the production of heterogeneous ribosomes with a diverse range of characteristics.…”

Section: Discussionmentioning

confidence: 99%

Unlinked rRNA genes are widespread among bacteria and archaea

et al. 2019

View full text Add to dashboard Cite

Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in Bacteria and Archaea. These ribosomal rRNA genes are typically organized into a single operon, an arrangement that is thought to facilitate gene regulation. In reality, some Bacteria and Archaea do not share this canonical rRNA arrangement-their 16S and 23S rRNA genes are not co-located, but are instead separated across the genome and referred to as "unlinked". This rearrangement has previously been treated as a rare exception or a byproduct of genome degradation in obligate intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are much more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, Planctomycetes, and Euryarchaeota, and occur in differential frequencies across natural environments. We found that up to 41% of the taxa in soil, including dominant taxa, had unlinked rRNA genes, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slowgrowing free-living species and obligatory intracellular species. Unlinked rRNA genes are also associated with changes in RNA metabolism, notably the loss of RNaseIII. We propose that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. .

show abstract

“…Regardless, increased resistance to predation (phage attack) at the cost of reduced maximum potential growth rates is a 492 widely observed ecological trade-off (Bohannan and Lenski, 2000). Finally, recent work has showed that some rRNA loci specialize in the translation of certain types of genes in Vibrio 494 vulnificus (Song et al, 2019). It is thus tempting to speculate that unlinked rRNA genes could facilitate the production of heterogeneous ribosomes with a diverse range of characteristics.…”

Section: Discussion 398mentioning

confidence: 99%

Unlinked rRNA genes are widespread among Bacteria and Archaea

Brewer¹,

Albertsen²,

Edwards

et al. 2019

Preprint

View full text Add to dashboard Cite

16Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in Bacteria and Archaea. These ribosomal rRNA genes 18 are typically organized into a single operon, an arrangement that is thought to facilitate gene regulation. In reality, some Bacteria and Archaea do not share this canonical rRNA arrangement 20 -their 16S and 23S rRNA genes are not co-located, but are instead separated across the genome and referred to as "unlinked". This rearrangement has previously been treated as a rare 22 exception or a byproduct of genome degradation in obligate intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S 24 rRNA genes are much more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, Planctomycetes, and 26 Euryarchaeota, and occur in differential frequencies across natural environments. We found that up to 41% of the taxa in soil, including dominant taxa, had unlinked rRNA genes, in contrast to 28 the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-30 growing free-living species and obligatory intracellular species. Unlinked rRNA genes are also associated with changes in RNA metabolism, notably the loss of RNaseIII. We propose that 32 unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. 34 sequencing reveals intraspecies diversity in the human microbiome. Nat Biotechnol 34: 64-69.

show abstract

Divergent rRNAs as regulators of gene expression at the ribosome level

Cited by 51 publications

References 59 publications

Age-Dependent and Tissue-Specific Alterations in the rDNA Clusters of the Panax ginseng C. A. Meyer Cultivated Cell Lines

Age-Dependent and Tissue-Specific Alterations in the rDNA Clusters of the Panax ginseng C. A. Meyer Cultivated Cell Lines

Unlinked rRNA genes are widespread among bacteria and archaea

Unlinked rRNA genes are widespread among Bacteria and Archaea

Contact Info

Product

Resources

About