The < em > Bacillus subtilis ywbD < /em > gene encodes RlmQ, the 23S rRNA methyltransferase forming m < sup > 7 < /sup > G2574 in the A-site of the peptidyl transferase center
RNA. 2023 Dec 5:rna.079853.123. doi: 10.1261/rna.079853.123. Online ahead of print.ABSTRACTRibosomal RNA contains many posttranscriptionally modified nucleosides, particularly in the functional parts of the ribosome. The distribution of these modifications varies from one organism to another. In Bacillus subtilis , the model organism for Gram-positive bacteria, mass spectrometry experiments revealed the presence of 7-methylguanosine (m7G) at position 2574 of the 23S rRNA, which lies in the A-site of the peptidyl transferase center of the large ribosomal subunit. Testing several m7G methyltransferase candidates allowed to i...
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Philippe Wolff Geoffray Labar Antony Lechner Dany Van Elder Romuald Soin Cyril Gueydan V éronique Kruys Louis Droogmans Martine Roovers Source Type: research

Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain
RNA. 2023 Nov 28:rna.079866.123. doi: 10.1261/rna.079866.123. Online ahead of print.ABSTRACTIntron branch point (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Sacch...
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Oarteze Hunter Jason Talkish Jen Quick-Cleveland Haller Igel Asako Tan Scott Kuersten Sol Katzman John Paul Donohue Melissa S Jurica Manuel Ares Source Type: research

Balanced cell division is secured by two different regulatory sites in OxyS RNA
In this study, we report that in addition to cell division, OxyS inhibits mepS encoding an essential peptidoglycan endopeptidase, responsible for cell elongation. Our study indicates that cell cycle arrest and balancing between cell division and cell elongation are important and conserved functions of the oxidative stress-induced sRNA OxyS.PMID:38071477 | DOI:10.1261/rna.079836.123 (Source: RNA)
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Maya Elgrably-Weiss Fayyaz Hussain Jens Georg Bushra Shraiteh Shoshy Altuvia Source Type: research

A tRNA-specific function for tRNA methyltransferase Trm10 is associated with a new tRNA quality control mechanism in Saccharomyces cerevisiae
RNA. 2023 Dec 8:rna.079861.123. doi: 10.1261/rna.079861.123. Online ahead of print.ABSTRACTIn Saccharomyces cerevisiae a single homolog of the tRNA methyltransferase Trm10 performs m1G9 modification on 13 different tRNAs. Here we provide evidence that the m1G9 modification catalyzed by S. cerevisiae Trm10 plays a biologically important role for one of these tRNA substrates, tRNATrp. Overexpression of tRNATrp (and not any of 38 other elongator tRNAs) rescues growth hypersensitivity of the trm10Δ strain in the presence of the antitumor drug 5-fluorouracil (5FU). Mature tRNATrp is depleted in trm10Δ cells, and its levels ar...
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Isobel E Bowles Jane E Jackman Source Type: research

3D Feasibility of 2D RNA-RNA Interaction Paths by stepwise Folding Simulations
RNA. 2023 Dec 1:rna.079756.123. doi: 10.1261/rna.079756.123. Online ahead of print.ABSTRACTThe structure of an RNA, and even more so the interactions it forms with other RNAs, provide valuable information about its function. Secondary structure-based tools for RNA-RNA interaction prediction provide a quick way to identify possible interaction targets and structures. However, these tools ignore the effect of steric hindrance on the tertiary (3D) structure level, and do not consider whether a suitable folding pathway exists to form the interaction. As a consequence, these tools often predict interactions that are unrealistic...
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Irene K Beckmann Maria Waldl Sebastian Will Ivo L Hofacker Source Type: research

Tributes to Yoshiro Shimura: Yoshiro Shimura (1932-2023)
RNA. 2023 Dec 7:rna.079913.123. doi: 10.1261/rna.079913.123. Online ahead of print.NO ABSTRACTPMID:38071474 | DOI:10.1261/rna.079913.123 (Source: RNA)
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Naoyuki Kataoka Iain Mattaj Source Type: research

The < em > Bacillus subtilis ywbD < /em > gene encodes RlmQ, the 23S rRNA methyltransferase forming m < sup > 7 < /sup > G2574 in the A-site of the peptidyl transferase center
RNA. 2023 Dec 5:rna.079853.123. doi: 10.1261/rna.079853.123. Online ahead of print.ABSTRACTRibosomal RNA contains many posttranscriptionally modified nucleosides, particularly in the functional parts of the ribosome. The distribution of these modifications varies from one organism to another. In Bacillus subtilis , the model organism for Gram-positive bacteria, mass spectrometry experiments revealed the presence of 7-methylguanosine (m7G) at position 2574 of the 23S rRNA, which lies in the A-site of the peptidyl transferase center of the large ribosomal subunit. Testing several m7G methyltransferase candidates allowed to i...
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Philippe Wolff Geoffray Labar Antony Lechner Dany Van Elder Romuald Soin Cyril Gueydan V éronique Kruys Louis Droogmans Martine Roovers Source Type: research

Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain
RNA. 2023 Nov 28:rna.079866.123. doi: 10.1261/rna.079866.123. Online ahead of print.ABSTRACTIntron branch point (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Sacch...
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Oarteze Hunter Jason Talkish Jen Quick-Cleveland Haller Igel Asako Tan Scott Kuersten Sol Katzman John Paul Donohue Melissa S Jurica Manuel Ares Source Type: research

Balanced cell division is secured by two different regulatory sites in OxyS RNA
In this study, we report that in addition to cell division, OxyS inhibits mepS encoding an essential peptidoglycan endopeptidase, responsible for cell elongation. Our study indicates that cell cycle arrest and balancing between cell division and cell elongation are important and conserved functions of the oxidative stress-induced sRNA OxyS.PMID:38071477 | DOI:10.1261/rna.079836.123 (Source: RNA)
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Maya Elgrably-Weiss Fayyaz Hussain Jens Georg Bushra Shraiteh Shoshy Altuvia Source Type: research

A tRNA-specific function for tRNA methyltransferase Trm10 is associated with a new tRNA quality control mechanism in Saccharomyces cerevisiae
RNA. 2023 Dec 8:rna.079861.123. doi: 10.1261/rna.079861.123. Online ahead of print.ABSTRACTIn Saccharomyces cerevisiae a single homolog of the tRNA methyltransferase Trm10 performs m1G9 modification on 13 different tRNAs. Here we provide evidence that the m1G9 modification catalyzed by S. cerevisiae Trm10 plays a biologically important role for one of these tRNA substrates, tRNATrp. Overexpression of tRNATrp (and not any of 38 other elongator tRNAs) rescues growth hypersensitivity of the trm10Δ strain in the presence of the antitumor drug 5-fluorouracil (5FU). Mature tRNATrp is depleted in trm10Δ cells, and its levels ar...
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Isobel E Bowles Jane E Jackman Source Type: research

3D Feasibility of 2D RNA-RNA Interaction Paths by stepwise Folding Simulations
RNA. 2023 Dec 1:rna.079756.123. doi: 10.1261/rna.079756.123. Online ahead of print.ABSTRACTThe structure of an RNA, and even more so the interactions it forms with other RNAs, provide valuable information about its function. Secondary structure-based tools for RNA-RNA interaction prediction provide a quick way to identify possible interaction targets and structures. However, these tools ignore the effect of steric hindrance on the tertiary (3D) structure level, and do not consider whether a suitable folding pathway exists to form the interaction. As a consequence, these tools often predict interactions that are unrealistic...
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Irene K Beckmann Maria Waldl Sebastian Will Ivo L Hofacker Source Type: research

Tributes to Yoshiro Shimura: Yoshiro Shimura (1932-2023)
RNA. 2023 Dec 7:rna.079913.123. doi: 10.1261/rna.079913.123. Online ahead of print.NO ABSTRACTPMID:38071474 | DOI:10.1261/rna.079913.123 (Source: RNA)
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Naoyuki Kataoka Iain Mattaj Source Type: research

The < em > Bacillus subtilis ywbD < /em > gene encodes RlmQ, the 23S rRNA methyltransferase forming m < sup > 7 < /sup > G2574 in the A-site of the peptidyl transferase center
RNA. 2023 Dec 5:rna.079853.123. doi: 10.1261/rna.079853.123. Online ahead of print.ABSTRACTRibosomal RNA contains many posttranscriptionally modified nucleosides, particularly in the functional parts of the ribosome. The distribution of these modifications varies from one organism to another. In Bacillus subtilis , the model organism for Gram-positive bacteria, mass spectrometry experiments revealed the presence of 7-methylguanosine (m7G) at position 2574 of the 23S rRNA, which lies in the A-site of the peptidyl transferase center of the large ribosomal subunit. Testing several m7G methyltransferase candidates allowed to i...
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Philippe Wolff Geoffray Labar Antony Lechner Dany Van Elder Romuald Soin Cyril Gueydan V éronique Kruys Louis Droogmans Martine Roovers Source Type: research

Broad variation in response of individual introns to splicing inhibitors in a humanized yeast strain
RNA. 2023 Nov 28:rna.079866.123. doi: 10.1261/rna.079866.123. Online ahead of print.ABSTRACTIntron branch point (BP) recognition by the U2 snRNP is a critical step of splicing, vulnerable to recurrent cancer mutations and bacterial natural product inhibitors. The BP binds a conserved pocket in the SF3B1 (human) or Hsh155 (yeast) U2 snRNP protein. Amino acids that line this pocket affect binding of splicing inhibitors like Pladienolide-B (Plad-B), such that organisms differ in their sensitivity. To study the mechanism of splicing inhibitor action in a simplified system, we modified the naturally Plad-B resistant yeast Sacch...
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Oarteze Hunter Jason Talkish Jen Quick-Cleveland Haller Igel Asako Tan Scott Kuersten Sol Katzman John Paul Donohue Melissa S Jurica Manuel Ares Source Type: research

Balanced cell division is secured by two different regulatory sites in OxyS RNA
In this study, we report that in addition to cell division, OxyS inhibits mepS encoding an essential peptidoglycan endopeptidase, responsible for cell elongation. Our study indicates that cell cycle arrest and balancing between cell division and cell elongation are important and conserved functions of the oxidative stress-induced sRNA OxyS.PMID:38071477 | DOI:10.1261/rna.079836.123 (Source: RNA)
Source: RNA - December 10, 2023 Category: Genetics & Stem Cells Authors: Maya Elgrably-Weiss Fayyaz Hussain Jens Georg Bushra Shraiteh Shoshy Altuvia Source Type: research