Kazuaki Amikura
@amikura.bsky.social
Pinned
Kazuaki Amikura
@amikura.bsky.social
· Nov 24
Our paper is out! Analysis of 30K+ genomes revealed that CPR bacteria assemble their ribosomes in unconventional ways, and that these assembly processes appear to have co-evolved with ribosome structure. doi.org/10.1093/molb... #Ribosome #Evolution #Patescibacteria #MBE
Reposted by Kazuaki Amikura
Alteromonas macleodii ribosome enables consecutive incorporation of bulky D-amino acids into peptides academic.oup.com/nar/article/...
The Alteromonas macleodii ribosome enables consecutive incorporation of bulky D-amino acids into peptides
Abstract. Genetic code reprogramming allows for ribosomal incorporation of exotic amino acids, such as d-α- and d-β-amino acids, into peptides. However, th
academic.oup.com
April 22, 2026 at 5:57 AM
Alteromonas macleodii ribosome enables consecutive incorporation of bulky D-amino acids into peptides academic.oup.com/nar/article/...
Bacterial GTPases act as successive placeholders to mediate ribosome assembly and its coupling to translation initiation
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
www.biorxiv.org
February 20, 2026 at 11:51 AM
Bacterial GTPases act as successive placeholders to mediate ribosome assembly and its coupling to translation initiation
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Pleased to share our new paper. Group I introns uniquely accumulate in Patescibacteria (formerly CPR bacteria), are inserted at an unusual tRNA position (35/36), and belong to a distinct intron class. Congratulations, Yuna! mSystems journals.asm.org/doi/10.1128/...
Group I introns in tRNA genes of Patescibacteria | mSystems
Introns were traditionally thought to be rare in bacteria, yet their occurrence and
diversity may have been underestimated. Here, we present the first comprehensive overview
of group I and group II in...
journals.asm.org
February 2, 2026 at 3:02 PM
Pleased to share our new paper. Group I introns uniquely accumulate in Patescibacteria (formerly CPR bacteria), are inserted at an unusual tRNA position (35/36), and belong to a distinct intron class. Congratulations, Yuna! mSystems journals.asm.org/doi/10.1128/...
Reposted by Kazuaki Amikura
"Use it or lose it." This is great advice for exercise, but when cells need to slow down or go dormant, they need to store ribosomes to recover growth in the future. They use hibernation factors to do this. Here is our latest story on how archaea hibernate ribosomes (1/7):
doi.org/10.64898/202...
doi.org/10.64898/202...
doi.org
January 20, 2026 at 3:53 PM
"Use it or lose it." This is great advice for exercise, but when cells need to slow down or go dormant, they need to store ribosomes to recover growth in the future. They use hibernation factors to do this. Here is our latest story on how archaea hibernate ribosomes (1/7):
doi.org/10.64898/202...
doi.org/10.64898/202...
Reposted by Kazuaki Amikura
Enhanced tRNA array method version 2 for simultaneous in vitro synthesis of 21 tRNAs https://www.biorxiv.org/content/10.64898/2026.01.06.697847v1
January 6, 2026 at 7:02 PM
Enhanced tRNA array method version 2 for simultaneous in vitro synthesis of 21 tRNAs https://www.biorxiv.org/content/10.64898/2026.01.06.697847v1
Impact of acetate on CO2 fixation pathways in thermophilic and hydrogenotrophic bacteria url: academic.oup.com/ismecommun/a...
Impact of acetate on CO2 fixation pathways in thermophilic and hydrogenotrophic bacteria
Abstract. The bacterial-type Wood-Ljungdahl (WL) pathway and reductive tricarboxylic acid (rTCA) cycle are the dominant chemolithotrophic CO2 fixation path
academic.oup.com
December 8, 2025 at 2:41 PM
Impact of acetate on CO2 fixation pathways in thermophilic and hydrogenotrophic bacteria url: academic.oup.com/ismecommun/a...
Reposted by Kazuaki Amikura
Structure of the Hibernating Francisella tularensis Ribosome and Mechanistic Insights into Its Inhibition by Antibiotics https://www.biorxiv.org/content/10.1101/2025.11.25.690415v1
November 26, 2025 at 2:33 AM
Our paper is out! Analysis of 30K+ genomes revealed that CPR bacteria assemble their ribosomes in unconventional ways, and that these assembly processes appear to have co-evolved with ribosome structure. doi.org/10.1093/molb... #Ribosome #Evolution #Patescibacteria #MBE
November 24, 2025 at 1:15 PM
Our paper is out! Analysis of 30K+ genomes revealed that CPR bacteria assemble their ribosomes in unconventional ways, and that these assembly processes appear to have co-evolved with ribosome structure. doi.org/10.1093/molb... #Ribosome #Evolution #Patescibacteria #MBE
Reposted by Kazuaki Amikura
The evolution lifecycle of ribosome hibernation factors https://www.biorxiv.org/content/10.1101/2025.11.04.686544v1
November 5, 2025 at 1:18 AM
The evolution lifecycle of ribosome hibernation factors https://www.biorxiv.org/content/10.1101/2025.11.04.686544v1
Our new preprint is now available! We found a new Group I intron insertion site in tRNA genes of Patescibacteria. These tRNAs were missed by standard tRNA annotation tools. #microbiology #tRNA #Patescibacteria
A Novel Insertion Site for Group I Introns in tRNA Genes of Patescibacteria https://www.biorxiv.org/content/10.1101/2025.07.03.662931v1
July 4, 2025 at 6:43 AM
Our new preprint is now available! We found a new Group I intron insertion site in tRNA genes of Patescibacteria. These tRNAs were missed by standard tRNA annotation tools. #microbiology #tRNA #Patescibacteria
Reposted by Kazuaki Amikura
🎉 Now out “Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free‑living euryarchaeal‑like ancestors” www.nature.com/articles/s41...
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors - Nature Microbiology
Phylogenetic reconstructions with conserved protein markers from the 11 known DPANN phyla reveal their monophyletic placement within the Euryarchaeota.
www.nature.com
June 17, 2025 at 2:25 PM
🎉 Now out “Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free‑living euryarchaeal‑like ancestors” www.nature.com/articles/s41...
Reposted by Kazuaki Amikura
Here, we show that bacterial ribosomes—often viewed as conserved drug targets—actually vary across species due to extensive sequence variation in their drug-binding residues. In some cases, this divergence may lead to intrinsic drug resistance in certain bacterial clades: doi.org/10.1016/j.ce...
June 19, 2025 at 7:32 AM
Here, we show that bacterial ribosomes—often viewed as conserved drug targets—actually vary across species due to extensive sequence variation in their drug-binding residues. In some cases, this divergence may lead to intrinsic drug resistance in certain bacterial clades: doi.org/10.1016/j.ce...
Reposted by Kazuaki Amikura
"With an apparent inability to live outside its host, and with a genome less than half the size of the previously smallest archaeon genome, Sukunaarchaeum is unlike any other archaeon known." ➡️ www.science.org/content/arti... #MicroSky #Archaea
Microbe with bizarrely tiny genome may be evolving into a virus
With DNA focused almost entirely on replication, newly discovered organism blurs the line between cells and viruses
www.science.org
June 18, 2025 at 6:13 PM
"With an apparent inability to live outside its host, and with a genome less than half the size of the previously smallest archaeon genome, Sukunaarchaeum is unlike any other archaeon known." ➡️ www.science.org/content/arti... #MicroSky #Archaea
Reposted by Kazuaki Amikura
Here we unexpectedly find that the ribosomal protein S20/L26—identified at the dawn of ribosome research but later deemed a biochemical artifact—is indeed a genuine component of the large ribosomal subunit. More on this ribosome content variation is here: www.nature.com/articles/s41...
Structurally heterogeneous ribosomes cooperate in protein synthesis in bacterial cells - Nature Communications
Cells can simultaneously produce structurally dissimilar ribosomes, suggesting functional specialization of distinct ribosome populations. Here, the authors show that distinct ribosomes cooperate rath...
www.nature.com
March 20, 2025 at 10:05 PM
Here we unexpectedly find that the ribosomal protein S20/L26—identified at the dawn of ribosome research but later deemed a biochemical artifact—is indeed a genuine component of the large ribosomal subunit. More on this ribosome content variation is here: www.nature.com/articles/s41...
The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly
Abstract. The intricate process of 50S ribosomal subunit assembly in Bacillus subtilis involves multiple parallel pathways converging into a crucial interm
academic.oup.com
December 11, 2024 at 12:11 AM
The binding of RbgA to a critical 50S assembly intermediate facilitates YphC function in bacterial ribosomal assembly
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Kazuaki Amikura
Evolutionary flexibility of ribosome biogenesis in bacteria www.biorxiv.org/content/10.1... #jcampubs
December 2, 2024 at 3:36 PM
Evolutionary flexibility of ribosome biogenesis in bacteria www.biorxiv.org/content/10.1... #jcampubs
Our preprint is now available!🎊🚀
Ribosome biogenesis in CPR bacteria was unexpectedly flexible, challenging traditional view of this essential process in evolution.
#Ribosome #CPR #Evolution
Ribosome biogenesis in CPR bacteria was unexpectedly flexible, challenging traditional view of this essential process in evolution.
#Ribosome #CPR #Evolution
Evolutionary flexibility of ribosome biogenesis in bacteria https://www.biorxiv.org/content/10.1101/2024.11.29.625318v1
Evolutionary flexibility of ribosome biogenesis in bacteria https://www.biorxiv.org/content/10.1101/2024.11.29.625318v1
Ribosomes are essential for protein synthesis and require ribosome biogenesis factors (RBFs) for ass
www.biorxiv.org
December 8, 2024 at 12:19 PM
Our preprint is now available!🎊🚀
Ribosome biogenesis in CPR bacteria was unexpectedly flexible, challenging traditional view of this essential process in evolution.
#Ribosome #CPR #Evolution
Ribosome biogenesis in CPR bacteria was unexpectedly flexible, challenging traditional view of this essential process in evolution.
#Ribosome #CPR #Evolution