Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome

Meydan, Sezen, Marks, James, Klepacki, Dorota, Sharma, Virag, Baranov, Pavel V., Firth, Andrew E., Margus, Tōnu, Kefi, Amira +2 more·2019·Molecular Cell
DOI 10.1016/j.molcel.2019.02.017

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  26. Determining the off-target activity of antibiotics and novel translation initiation sites in mitochondria
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  31. A bacterial regulatory uORF senses multiple classes of ribosome-targeting antibiotics
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    Scott H. Saunders, Ayesha Ahmed, Manuel Razo‐Mejia · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
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  50. TRAINSPOTTER: profiling nascent protein N-termini indicative of bacterial translation initiation via deformylation-assisted N-terminomics
    Petra Van Damme · 2026 · Nucleic Acids Research
  51. Frame-shifted proteins of a given gene are unlikely to retain the same function
    Alexander S. Mankin · 2020 · RNA
  52. AzuCR RNA modulates carbon metabolism as a dual-function RNA in Escherichia coli
    Medha Raina, Jordan J. Aoyama, Shantanu Bhatt, Brian J. Paul, Gisela Storz · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  53. Shadow Orfs Illuminated: Long Overlapping Genes in Pseudomonas Aeruginosa are Translated and Under Purifying Selection
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  54. Tetracycline-dependent inhibition of mitoribosome protein elongation in mitochondrial disease mutant cells suppresses IRE1α to promote cell survival
    Conor T. Ronayne, Christopher F. Bennett, Elizabeth A. Perry, Noa Kantorovic, Pere Puigserver · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
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  58. Monitoring Bacterial Translation Rates Genome-Wide
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  59. Faculty Opinions recommendation of Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens.
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  61. Genome-Scale Analysis of the Structure and Function of RNA Pathways and Networks in Pseudomonas aeruginosa
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  62. Synthesis of retapamulin from plueromutilin enhancing the purity and yield via altered halogenations process
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  63. Determining the off-target activity of antibiotics and novel translation initiation sites in mitochondria
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  64. A bacterial regulatory uORF senses multiple classes of ribosome-targeting antibiotics
    Gabriele Baniulyte, Joseph T. Wade · 2024 · eLife
  65. A bacterial regulatory uORF senses multiple classes of ribosome-targeting antibiotics
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  66. Transcriptome-wide analysis of protein synthesis: Ribosome profiling and beyond
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  67. A bacterial regulatory uORF senses multiple classes of ribosome-targeting antibiotics
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  68. Additional file 1 of ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events
    Mary O.G. Richardson, Sean R. Eddy · 2023 · Figshare
  69. Additional file 2 of Deciphering the molecular and cellular atlas of immune cells in septic patients with different bacterial infections
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  70. Additional file 1 of Deciphering the molecular and cellular atlas of immune cells in septic patients with different bacterial infections
    Sun, Ping, Mintian Cui, Jing, Jiongjie, Kong, Fanyu, Wang, Shixi, 唐伦先, Leng, Junling, Kun Chen · 2024 · Figshare
  71. Additional file 1 of Improvement of putrescine production through the arginine decarboxylase pathway in Escherichia coli K-12
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  72. Determining the off-target activity of antibiotics and novel translation initiation sites in mitochondria
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  78. Advances in Decoding Bacterial N-Terminal Proteoforms: Technologies, Challenges, and Functional Insights
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  79. Sparsomycin inhibits translation through a conserved mechanism across all domains of life
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  81. Ribosome profiling reveals translational dynamics between an archaeal virus and its host
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