Publications

Comparative genome analysis of Mycobacteria focusing on tRNA and non-coding RNA

Behra, Phani Rama Krishna; Pettersson, B. M. Fredrik; Ramesh, Malavika; Das, Sarbashis et al.

Part of BMC Genomics, 2022.

DOI for Comparative genome analysis of Mycobacteria focusing on tRNA and non-coding RNA Download full text (pdf) of Comparative genome analysis of Mycobacteria focusing on tRNA and non-coding RNA

Plasticity and conditional essentiality of modification enzymes for domain V of Escherichia coli 23S ribosomal RNA

Liljeruhm, Josefine; Leppik, Margus; Bao, Letian; Truu, Triin et al.

Part of RNA, p. 796-807, 2022.

DOI for Plasticity and conditional essentiality of modification enzymes for domain V of Escherichia coli 23S ribosomal RNA

Rate-limiting hydrolysis in ribosomal release reactions revealed by ester activation

Bao, Letian; Karpenko, Victoriia V.; Forster, Anthony C.

Part of Journal of Biological Chemistry, 2022.

DOI for Rate-limiting hydrolysis in ribosomal release reactions revealed by ester activation Download full text (pdf) of Rate-limiting hydrolysis in ribosomal release reactions revealed by ester activation

Revisiting the Extinction of the RNA World

Forster, Anthony C.

Part of Biochemistry, p. 749-751, 2022.

DOI for Revisiting the Extinction of the RNA World Download full text (pdf) of Revisiting the Extinction of the RNA World

Uncovering translation roadblocks during the development of a synthetic tRNA

Prabhakar, Arjun; Krahn, Natalie; Zhang, Jingji; Vargas-Rodriguez, Oscar et al.

Part of Nucleic Acids Research, p. 10201-10211, 2022.

DOI for Uncovering translation roadblocks during the development of a synthetic tRNA Download full text (pdf) of Uncovering translation roadblocks during the development of a synthetic tRNA

GGQ methylation enhances both speed and accuracy of stop codon recognition by bacterial class-I release factors

Pundir, Shreya; Ge, Xueliang; Sanyal, Suparna

Part of Journal of Biological Chemistry, 2021.

DOI for GGQ methylation enhances both speed and accuracy of stop codon recognition by bacterial class-I release factors Download full text (pdf) of GGQ methylation enhances both speed and accuracy of stop codon recognition by bacterial class-I release factors

In vitro synthesis of 32 translation-factor proteins from a single template reveals impaired ribosomal processivity

Doerr, Anne; Foschepoth, David; Forster, Anthony C.; Danelon, Christophe

Part of Scientific Reports, 2021.

DOI for In vitro synthesis of 32 translation-factor proteins from a single template reveals impaired ribosomal processivity Download full text (pdf) of In vitro synthesis of 32 translation-factor proteins from a single template reveals impaired ribosomal processivity

Intracellular localization of the mycobacterial stressosome complex

Ramesh, Malavika; Nitharwal, Ram Gopal; Behra, Phani Rama Krishna; Pettersson, Fredrik

Part of Scientific Reports, 2021.

DOI for Intracellular localization of the mycobacterial stressosome complex Download full text (pdf) of Intracellular localization of the mycobacterial stressosome complex

Kinetic Analysis Su :rests Evolution of Ribosome Snecificity in Modern Elongation Factor-Tus from "Generalist" Ancestors

De Tarafder, Arindam; Parajuli, Narayan Prasad; Majumdar, Soneya; Kacar, Betul et al.

Part of Molecular biology and evolution, p. 3436-3444, 2021.

DOI for Kinetic Analysis Su :rests Evolution of Ribosome Snecificity in Modern Elongation Factor-Tus from "Generalist" Ancestors

Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin

Parajuli, Narayan Prasad; Mandava, Chandra Sekhar; Pavlov, Michael; Sanyal, Suparna

Part of Nucleic Acids Research, p. 6880-6892, 2021.

DOI for Mechanistic insights into translation inhibition by aminoglycoside antibiotic arbekacin

N-6-Methyladenosines in mRNAs reduce the accuracy of codon reading by transfer RNAs and peptide release factors

Ieong, Ka-Weng; Indrisiunaite, Gabriele; Prabhakar, Arjun; Puglisi, Joseph D. et al.

Part of Nucleic Acids Research, p. 2684-2699, 2021.

DOI for N-6-Methyladenosines in mRNAs reduce the accuracy of codon reading by transfer RNAs and peptide release factors Download full text (pdf) of N-6-Methyladenosines in mRNAs reduce the accuracy of codon reading by transfer RNAs and peptide release factors

Optimization of a fluorescent-mRNA based real-time assay for precise kinetic measurements of ribosomal translocation

Kim, Changil; Holm, Mikael; Mandava, Chandra Sekhar; Sanyal, Suparna

Part of RNA Biology, p. 2363-2375, 2021.

DOI for Optimization of a fluorescent-mRNA based real-time assay for precise kinetic measurements of ribosomal translocation Download full text (pdf) of Optimization of a fluorescent-mRNA based real-time assay for precise kinetic measurements of ribosomal translocation

Real-time measurements of aminoglycoside effects on protein synthesis in live cells

Aguirre Rivera, Javier; Larsson, Jimmy; Volkov, Ivan; Seefeldt, A. Carolin et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, 2021.

DOI for Real-time measurements of aminoglycoside effects on protein synthesis in live cells Download full text (pdf) of Real-time measurements of aminoglycoside effects on protein synthesis in live cells

Repurposing tRNAs for nonsense suppression

Albers, Suki; Beckert, Bertrand; Matthies, Marco C.; Mandava, Chandra Sekhar et al.

Part of Nature Communications, 2021.

DOI for Repurposing tRNAs for nonsense suppression Download full text (pdf) of Repurposing tRNAs for nonsense suppression

Collateral toxicity limits the evolution of bacterial Release Factor 2 towards total omnipotence

Abdalaal, Hind; Pundir, Shreya; Ge, Xueliang; Sanyal, Suparna et al.

Part of Molecular biology and evolution, p. 2918-2930, 2020.

DOI for Collateral toxicity limits the evolution of bacterial Release Factor 2 towards total omnipotence Download full text (pdf) of Collateral toxicity limits the evolution of bacterial Release Factor 2 towards total omnipotence

DNA surface exploration and operator bypassing during target search

Marklund, Emil; van Oosten, Brad; Mao, Guanzhong; Amselem, Elias et al.

Part of Nature, p. 858-+, 2020.

DOI for DNA surface exploration and operator bypassing during target search Download full text (pdf) of DNA surface exploration and operator bypassing during target search

Loss of a single methylation in 23S rRNA delays 50S assembly at multiple late stages and impairs translation initiation and elongation

Wang, Li; Wanqiu, Li; Ge, Xueliang; Kaige, Yan et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 15609-15619, 2020.

DOI for Loss of a single methylation in 23S rRNA delays 50S assembly at multiple late stages and impairs translation initiation and elongation

Overcoming chromoprotein limitations by engineering a red fluorescent protein

Bao, Letian; Menon, P. Navaneeth K.; Liljeruhm, Josefine; Forster, Anthony C.

Part of Analytical Biochemistry, 2020.

DOI for Overcoming chromoprotein limitations by engineering a red fluorescent protein Download full text (pdf) of Overcoming chromoprotein limitations by engineering a red fluorescent protein

Rationally designed Spot 42 RNAs with an inhibition/toxicity profile advantageous for engineering E. coli

Vogel, Carolin; Gynnå, Arvid H.; Yuan, Jinwen; Bao, Letian et al.

Part of ENGINEERING REPORTS, 2020.

DOI for Rationally designed Spot 42 RNAs with an inhibition/toxicity profile advantageous for engineering E. coli Download full text (pdf) of Rationally designed Spot 42 RNAs with an inhibition/toxicity profile advantageous for engineering E. coli

Ribosomal RNA Modulates Aggregation of thePodosporaPrion Protein HET-s

Pang, Yanhong; Kovachev, Petar Stefanov; Sanyal, Suparna

Part of International Journal of Molecular Sciences, 2020.

DOI for Ribosomal RNA Modulates Aggregation of thePodosporaPrion Protein HET-s Download full text (pdf) of Ribosomal RNA Modulates Aggregation of thePodosporaPrion Protein HET-s

Screening cells for crystals: a synergistic approach

Bergfors, Terese; Majumdar, Soneya

Part of Journal of applied crystallography, p. 1414-1415, 2020.

DOI for Screening cells for crystals: a synergistic approach Download full text (pdf) of Screening cells for crystals: a synergistic approach

Selective translation by alternative bacterial ribosomes

Chen, Yu-Xiang; Xu, Zhi-Yu; Ge, Xueliang; Hong, Jia-Yao et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 19487-19496, 2020.

DOI for Selective translation by alternative bacterial ribosomes Download full text (pdf) of Selective translation by alternative bacterial ribosomes

Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

Behra, Phani Rama Krishna; Pettersson, Fredrik; Das, Sarbashis; Dasgupta, Santanu et al.

Part of BMC Evolutionary Biology, 2019.

DOI for Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA Download full text (pdf) of Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

CRISPR-Cas9-mediated knockout of SPRY2 in human hepatocytes leads to increased glucose uptake and lipid droplet accumulation

Cook, Naomi L.; Pjanic, Milos; Emmerich, Andrew G.; Rao, Abhiram S. et al.

Part of BMC Endocrine Disorders, 2019.

DOI for CRISPR-Cas9-mediated knockout of SPRY2 in human hepatocytes leads to increased glucose uptake and lipid droplet accumulation Download full text (pdf) of CRISPR-Cas9-mediated knockout of SPRY2 in human hepatocytes leads to increased glucose uptake and lipid droplet accumulation

Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains

Behra, Phani Rama Krishna; Das, Sarbashis; Pettersson, B. M. Fredrik; Shirreff, Lisa et al.

Part of Scientific Reports, 2019.

DOI for Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains Download full text (pdf) of Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains

Gene miaA for post-transcriptional modification of tRNA_XXA is important for morphological and metabolic differentiation in Streptomyces

Koshla, Oksana; Yushchuk, Oleksandr; Stash, Iryna; Dacyuk, Yuriy et al.

Part of Molecular Microbiology, p. 249-265, 2019.

DOI for Gene miaA for post-transcriptional modification of tRNA_XXA is important for morphological and metabolic differentiation in Streptomyces

Inhibition of translation termination by small molecules targeting ribosomal release factors

Ge, Xueliang; Oliveira, Ana; Hjort, Karin; Bergfors, Terese et al.

Part of Scientific Reports, 2019.

DOI for Inhibition of translation termination by small molecules targeting ribosomal release factors Download full text (pdf) of Inhibition of translation termination by small molecules targeting ribosomal release factors

Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum Glade members

Behra, Phani Rama Krishna; Pettersson, Fredrik; Ramesh, Malavika; Dasgupta, Santanu et al.

Part of Scientific Reports, 2019.

DOI for Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum Glade members Download full text (pdf) of Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum Glade members

Kinetics of D-amino acid incorporation in translation

Liljeruhm, Josefine; Wang, Jinfan; Kwiatkowski, Marek; Sabari, Samudra et al.

Part of ACS Chemical Biology, p. 204-213, 2019.

DOI for Kinetics of D-amino acid incorporation in translation

Reiterative Synthesis by the Ribosome and Recognition of the N-Terminal Formyl Group by Biosynthetic Machinery Contribute to Evolutionary Conservation of the Length of Antibiotic Microcin C Peptide Precursor

Zukher, Inna; Pavlov, Michael; Tsibulskaya, Darya; Kulikovsky, Alexey et al.

Part of mBio, 2019.

DOI for Reiterative Synthesis by the Ribosome and Recognition of the N-Terminal Formyl Group by Biosynthetic Machinery Contribute to Evolutionary Conservation of the Length of Antibiotic Microcin C Peptide Precursor Download full text (pdf) of Reiterative Synthesis by the Ribosome and Recognition of the N-Terminal Formyl Group by Biosynthetic Machinery Contribute to Evolutionary Conservation of the Length of Antibiotic Microcin C Peptide Precursor

RNA modulates aggregation of the recombinant mammalian prion protein by direct interaction

Kovachev, Petar Stefanov; Gomes, Mariana P. B.; Cordeiro, Yraima; Ferreira, Natalia C. et al.

Part of Scientific Reports, 2019.

DOI for RNA modulates aggregation of the recombinant mammalian prion protein by direct interaction Download full text (pdf) of RNA modulates aggregation of the recombinant mammalian prion protein by direct interaction

The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation

Holm, Mikael; Mandava, Chandra Sekhar; Ehrenberg, Måns; Sanyal, Suparna

Part of eLIFE, 2019.

DOI for The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation Download full text (pdf) of The mechanism of error induction by the antibiotic viomycin provides insight into the fidelity mechanism of translation

The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy

Fu, Ziao; Indrisiunaite, Gabriele; Kaledhonkar, Sandip; Shah, Binita et al.

Part of Nature Communications, 2019.

DOI for The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy Download full text (pdf) of The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy

Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction

Das, Sarbashis; Frisk, Christoffer; Eriksson, Maria J.; Walentinsson, Anna et al.

Part of Scientific Reports, 2019.

DOI for Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction Download full text (pdf) of Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction

2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation

Choi, Junhong; Indrisiunaite, Gabriele; DeMirci, Hasan; Leong, Ka-Weng et al.

Part of Nature Structural & Molecular Biology, p. 208-216, 2018.

DOI for 2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation

Accuracy of genetic code translation and its orthogonal corruption by aminoglycosides and Mg2+ ions

Zhang, Jingji; Pavlov, Michael; Ehrenberg, Måns

Part of Nucleic Acids Research, p. 1362-1374, 2018.

DOI for Accuracy of genetic code translation and its orthogonal corruption by aminoglycosides and Mg2+ ions Download full text (pdf) of Accuracy of genetic code translation and its orthogonal corruption by aminoglycosides and Mg2+ ions

C2 '-F Stereoconfiguration As a Puckering Switch for Base Stacking at the Dinucleotide Level

Moriou, Céline; Da Silva, Adilson D.; Vianelli Prado, Marcos Joel; Denhez, Clément et al.

Part of Journal of Organic Chemistry, p. 2473-2478, 2018.

DOI for C2 '-F Stereoconfiguration As a Puckering Switch for Base Stacking at the Dinucleotide Level

Catalytic O- to N-Alkyl Migratory Rearrangement: Transition Metal-Free Direct and Tandem Routes to N-Alkylated Pyridones and Benzothiazolones

Mishra, Abhishek Kumar; Morgon, Nelson Henrique; Sanyal, Suparna; de Souza, Aguinaldo Robinson et al.

Part of Advanced Synthesis and Catalysis, p. 3930-3939, 2018.

DOI for Catalytic O- to N-Alkyl Migratory Rearrangement: Transition Metal-Free Direct and Tandem Routes to N-Alkylated Pyridones and Benzothiazolones

Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering

Goronzy, I. N.; Rawle, R. J.; Boxer, S. G.; Kasson, Peter M.

Part of Chemical Science, p. 2340-2347, 2018.

DOI for Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering Download full text (pdf) of Cholesterol enhances influenza binding avidity by controlling nanoscale receptor clustering

Complementary charge-based interaction between the ribosomal-stalk protein L7/12 and IF2 is the key to rapid subunit association

Ge, Xueliang; Mandava, Chandra Sekhar; Lind, Christoffer; Åqvist, Johan et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 4649-4654, 2018.

DOI for Complementary charge-based interaction between the ribosomal-stalk protein L7/12 and IF2 is the key to rapid subunit association

Critical domain interactions for type A RNase P RNA catalysis with and without the specificity domain

Mao, Guanzhong; Srivastava, Abhishek S.; Wu, Shiying; Kosek, David et al.

Part of PLOS ONE, 2018.

DOI for Critical domain interactions for type A RNase P RNA catalysis with and without the specificity domain Download full text (pdf) of Critical domain interactions for type A RNase P RNA catalysis with and without the specificity domain

Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-Tu(H84A)

Fislage, Marcus; Zhang, Jingji; Brown, Zuben Patrick; Mandava, Chandra Sekhar et al.

Part of Nucleic Acids Research, p. 5861-5874, 2018.

DOI for Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-Tu(H84A) Download full text (pdf) of Cryo-EM shows stages of initial codon selection on the ribosome by aa-tRNA in ternary complex with GTP and the GTPase-deficient EF-Tu(H84A)

Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology

Liljeruhm, Josefine; Funk, Saskia K.; Tietscher, Sandra; Edlund, Anders D. et al.

Part of Journal of Biological Engineering, 2018.

DOI for Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology Download full text (pdf) of Engineering a palette of eukaryotic chromoproteins for bacterial synthetic biology

Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

Das, Sarbashis; Pettersson, B. M. Fredrik; Behra, Phani Rama Krishna; Mallick, Amrita et al.

Part of Scientific Reports, 2018.

DOI for Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing Download full text (pdf) of Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

How 2 '-O-Methylation in mRNA Disrupts tRNA Decoding during Translation Elongation

Choi, Junhong; Indrisiunaite, Gabriele; DeMirci, Hasan; Ieong, Ka-Weng et al.

Part of Biophysical Journal, p. 592A-592A, 2018.

Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI

Kipper, Kalle; Eremina, Nadja; Marklund, Emil; Tubasum, Sumera et al.

Part of PLOS ONE, 2018.

DOI for Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI Download full text (pdf) of Structure-guided approach to site-specific fluorophore labeling of the lac repressor LacI

Synthetic siRNA targeting human papillomavirus 16 E6: a perspective on in vitro nanotherapeutic approaches

Togtema, Melissa; Jackson, Robert; Grochowski, Jessica; Villa, Peter L. et al.

Part of Nanomedicine, p. 455-474, 2018.

DOI for Synthetic siRNA targeting human papillomavirus 16 E6: a perspective on in vitro nanotherapeutic approaches

The Structural Basis for Initiation Factor 2 Activation during Translation Initiation

Caban, Kelvin; Pavlov, Michael; Kaledhonkar, Sandip; Fu, Ziao et al.

Part of Biophysical Journal, p. 593A-593A, 2018.

tRNA tracking for direct measurements of protein synthesis kinetics in live cells

Volkov, Ivan; Lindén, Martin; Aguirre, Javier; Ieong, Ka-Weng et al.

Part of Nature Chemical Biology, p. 618-626, 2018.

DOI for tRNA tracking for direct measurements of protein synthesis kinetics in live cells

What is an archaeon and are the Archaea really unique?

Harish, Ajith

Part of PeerJ, 2018.

DOI for What is an archaeon and are the Archaea really unique? Download full text (pdf) of What is an archaeon and are the Archaea really unique?

Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase

Mellenius, Harriet; Ehrenberg, Måns

Part of Nucleic Acids Research, p. 11582-11593, 2017.

DOI for Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase Download full text (pdf) of Transcriptional accuracy modeling suggests two-step proofreading by RNA polymerase