• BISI - Molecular and Cellular Biology (MOCB)

Research Interests

Protein synthesis is a central process in all cells, and the protein synthesis machinery has been a major target for antibiotics. The rise of multidrug-resistant bacteria and a shortage of new antibiotics demand further studies of the protein synthesis machinery and the mechanisms of antibiotic resistance. Defects during protein synthesis in humans also lead to developmental and neurological diseases, yet the disease-causing mechanisms remain largely unclear. The overall goal of our laboratory is to understand the molecular basis of protein synthesis and its disease connection.  We are combining biochemical, single-cell, genetic, genomic, and proteomic approaches to study the following research areas:

Defects in protein synthesis. (A) Normal aaRSs active in aminoacylation and editing provide the ribosome with correct aa-tRNAs to allow robust and accurate translation. In addition to the correct amino acids (e.g., Ala for AlaRS), many aaRSs misacylate similar amino acids and require editing to remove the mistakes. The ribosome maintains fidelity through substrate selection and kinetic proofreading. (B) Defects in aminoacylation, aaRS editing, ribosome biogenesis, or ribosomal fidelity may decrease the efficiency and accuracy of translation, affecting various cell functions, bacteria-host interactions, stress responses, etc. Created with BioRender. 

1. The impact of translational defects in bacteria-host Interactions

Protein mistranslation (reduced translational fidelity) has been shown to cause growth defects in bacteria, mitochondrial dysfunction in yeast, and neurodegeneration in mammals. However, the role of translational fidelity during pathogen-host interaction is poorly understood. We have recently shown that optimal translational fidelity is critical for Salmonella to invade host cells. We are currently exploring the mechanisms by which translational fidelity and ribosome assembly affect host interactions, motility, stress responses, and antibiotic tolerance using systems biology and single-cell approaches. 

Model for role of translational fidelity in bacteria-host interaction. Translational fidelity is heterogeneous among single cells. Bacterial cells with optimal translational fidelity are selected to enter host cells. Translational fidelity is further altered by the host environment to promote adaptation.

2. Translation and phenotypic heterogeneity among single cells

Phenotypic heterogeneity among genetically identical bacterial cells is critical for adaptation to the changing environment and leads to tolerance to antibiotics and stresses. We have shown that translational fidelity and ribosomal RNA expression are heterogeneous and sensitive to the fluctuation of the cellular cyclic AMP level. We are interested in understanding how fluctuations in translation arise and affect phenotypic heterogeneity.  

Regulation of translation by cAMP. cAMP promotes amino acid (AA) catabolism and ATP synthesis, increasing transcription of rRNAs and tRNAs. A high aa-tRNA level increases stop-codon readthrough by outcompeting release factors. 

3. Protein Synthesis Defects in Eukaryotes and Human Diseases

Recent advances in genome sequencing and genetics have led to rapid growth of identified mutations in aaRSs and ribosomal proteins that cause human diseases. We are currently using yeast and worm models to understand how translational defects affect stress responses, fitness, and aging. 

Lyu Z, Villanueva P, O’Malley L, Murphy P, Augenstreich J, Briken V, Singh A, Ling J†. (2023) Genome-wide screening reveals metabolic regulation of stop-codon readthrough by cyclic AMP. Nucleic Acids Res. 51:10606-10618. (†Corresponding author). PMID: 37670559

Zhang H, Murphy P, Yu J, Lee S, Tsai FTF, van Hoof A, Ling J†. (2023) Coordination between aminoacylation and editing to protect against proteotoxicity. Nucleic Acids Res. 51:10606-10618. (†Corresponding author). PMCID: PMC10602869

Lyu Z, Yang A, Villanueva P, Singh A, Ling J†. (2021) Heterogeneous flagellar expression in single Salmonella cells promotes diversity in antibiotic tolerance. mBio. 12:e0237421. (†Corresponding author). PMCID: PMC8546535

Zhang H, Wu J, Lyu Z, Ling J†. (2021) Impact of alanyl-tRNA synthetase editing deficiency in yeast. Nucleic Acids Res. 49:9953-9964. (†Corresponding author). PMCID: PMC8464055

Zhang H, Lyu Z, Fan Y, Evans CR, Barber KW, Banerjee K, Igoshin OA, Rinehart J, Ling J†. (2020) Metabolic stress promotes stop-codon readthrough and phenotypic heterogeneity. Proc. Natl. Acad. Sci. USA. 117: 22167-22172. (†Corresponding author). PMCID: PMC8546535.

Fan Y†, Thompson L, Lyu Z, Cameron TA, De Lay, NR, Krachler, AM†, Ling J†. (2019) Optimal translational fidelity is critical for Salmonella virulence and host interactions. Nucleic Acids Res. 47:5356-5367. (†Corresponding author). PMCID: PMC6547416

Fan Y, Evans CR, Barber KW, Banerjee K, Weiss KJ, Margolin W, Igoshin OA, Rinehart J, Ling J†. (2017) Heterogeneity of stop codon readthrough in single bacterial cells and implications for population fitness. Mol. Cell 67:826-836. (†Corresponding author). Featured article. PMCID: PMC5591071

Nakayama T, Wu J, Galvin-Parton P, Weiss J, Andriola MR, Hill RS, Vaughan D, El-Quessny M, Barry BJ, Partlow JN, Barkovich AJ, Ling J†, Mochida GH†. (2017) Deficient activity of alanyl-tRNA synthetase underlies an autosomal recessive syndrome of progressive microcephaly, hypomyelination, and epileptic encephalopathy. Hum. Mutat. 38:1348-1354. (†Corresponding author) PMCID: PMC5599341

Tarailo-Graovac et al. (2016) Exome sequencing and the management of neurometabolic disorders. N. Engl. J. Med. 374:2246-2255. PMCID: PMC4983272

Ognjenović J, Wu J, Matthies D, Baxa U, Subramaniam S, Ling J†, Simonović M†. (2016) The crystal structure of human GlnRS provides basis for the development of neurological disorders. Nucleic Acids Res. 44:3420-3431. (†Corresponding author). PMCID: PMC4838373

Fan Y, Wu J, Ung MH, DeLay N, Cheng C, Ling J†. (2015) Protein mistranslation protects bacteria against oxidative stress. Nucleic Acids Res. 43:1740-1748. (†Corresponding author). PMCID: PMC4330365

Ling J*, O’Donoghue P*, Söll D. (2015) Genetic code flexibility in microorganisms: novel mechanisms and impact on microbial physiology. Nat. Rev. Microbiol. 13:707-721. (*Equal contributions). PMCID: PMC4712924

Wu J, Fang Y, Ling J†. (2014) Mechanism of oxidant-induced mistranslation by threonyl-tRNA synthetase. Nucleic Acids Res. 42:6523-6531. (†Corresponding author). PMCID: PMC4041444

Zhang X*, Ling J*, Barcia G* et al. (2014) Mutations in QARS, encoding glutaminyl-tRNA synthetase, cause progressive microcephaly, cerebral-cerebellar atrophy, and intractable seizures. Am. J. Hum. Genet. 94:547-558 (*Equal contributions). PMCID: PMC3980424

Ling J*, Daoud R*, Lajoie MJ, Church GM, Söll D, Lang BF. (2014) Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria.  Nucleic Acids Res. 42:499-508. (*Equal contributions). PMCID: PMC3874161

O’Donoghue P*, Ling J*, Wang YS, Söll D. (2013) Upgrading protein synthesis for synthetic biology. Nat. Chem. Biol. 9:594-598. (*Equal contributions). PMCID: PMC3975081 

Ling J, Cho C, Guo L, Aerni H, Rinehart J, Söll D. (2012) Protein aggregation caused by aminoglycoside action is prevented by a hydrogen peroxide scavenger. Mol. Cell 48:713-722. Previewed by Drummond in Mol. Cell. PMCID: PMC3525788

Ling J, Peterson KM, Simonović I, Söll D, Simonović M. (2012) The mechanism of pre-transfer editing in yeast mitochondrial threonyl-tRNA synthetase. J. Biol. Chem. 287:28518-28525. PMCID: PMC3436575

Ling J*, Peterson KM*, Simonović I, Cho C, Söll D, Simonović M. (2012) Yeast mito¬chondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment. Proc. Natl. Acad. Sci. USA 109:3281-3286. (*Equal contributions). PMCID: PMC3295322

Guo LT, Helgadóttir S, Söll D†, Ling J†. (2012) Rational design and directed evolution of a bacterial-type glutaminyl-tRNA synthetase precursor. Nucleic Acids Res. 40:7967-7974. (†Corresponding authors). PMCID: PMC3439900

Su D, Lieberman A, Lang BF, Simonović M, Söll D†, Ling J†. (2011) An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. Nucleic Acids Res. 39:4866-4874. (†Corresponding authors). Featured article. PMCID: PMC3113583

Ling J, Söll D. (2010) Oxidative stress induces protein mistranslation through inactivation of an aminoacyl-tRNA synthetase editing site. Proc. Natl. Acad. Sci. USA 107:4028-4033. PMCID: PMC2840151

Ling J, So BR, Yadavalli SS, Roy H, Shoji S, Fredrick K, Musier-Forsyth K, Ibba M. (2009) Resampling and editing of mischarged tRNA prior to translation elongation. Mol. Cell 33:654-660. Featured article. PMCID: PMC2944653

Ling J, Reynolds N, Ibba M. (2009) Aminoacyl-tRNA synthesis and translational quality control. Annu. Rev. Microbiol. 63:61-78. PMID: 19379069

Ling J, Roy H, Qin D, Rubio MA, Alfonzo J, Fredrick K, Ibba M. (2007) Pathogenic mechanism of a human mitochondrial tRNAPhe mutation associated with myoclonic epilepsy with ragged red fibers syndrome. Proc. Natl. Acad. Sci. USA 104:15299-15304. PMCID: PMC2000536

Ling J, Roy H, Ibba M. (2007) Mechanism of tRNA-dependent editing in translational quality control. Proc. Natl. Acad. Sci. USA 104:72-77. PMCID: PMC1765480

Ling J, Yadavalli SS, Ibba M. (2007) Phenylalanyl-tRNA synthetase editing defects result in efficient mistranslation of phenylalanine codons as tyrosine. RNA 13:1881-1886. PMCID: PMC2040089

Complete List of Published Work

https://www.ncbi.nlm.nih.gov/myncbi/1vq-oqz8jgukE/bibliography/public/

Postdoctoral and student positions are available in Dr. Ling’s lab. Interested candidates should send their CV and research interest to Dr. Ling: jling12@umd.edu