• 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 multi

drug 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 cardiovascular 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:

1. Role of Translational Fidelity in Pathogen-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 affects 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. Translational Fidelity in Single Cells

Previous studies of translational fidelity have mostly focused on the population level, and little is known about the distribution and regulation of translational fidelity among genetically identical single cells. It has been shown that gene expression is stochastic and noisy, which can lead to phenotypic heterogeneity among individual cells that may benefit the population during environmental changes and stress conditions. Our current understanding of gene expression noise is mostly limited to the transcription level. We have recently developed a dual-fluorescence reporter system to visualize translation errors in single bacterial cells, and applied these reporters to determine heterogeneity of stop codon readthrough. We are currently interested in understanding the level and sources of translation noise and how such heterogeneity in single cells affects population fitness.

UGA readthrough is heterogeneous among single cells. YFP and mCherry fluorescence in single bacterial cells carrying either the m-y or m-TGA-y reporter. The YFP/mCherry ratio of the m-TGA-y reporter indicates the UGA readthrough level, which varies from cell to cell within a genetically-identical population.

3. Protein Synthesis Defects and Human Diseases

Recent advances in genome sequencing and genetics have allowed a rapid growth of identified mutations in aaRSs that cause human diseases. In collaboration with Dr. Christopher Walsh and Ganesh Mochida’s laboratories, we have identified novel disease-causing mutations in QARS (encoding glutaminyl-tRNA synthetase) and AARS (alanyl-tRNA synthetase). Patients carrying such mutations develop microcephaly and seizure during early childhood. We are currently exploring the molecular mechanism by which QARS and AARS defects impair cellular function.

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

Evans CR, Fan Y, Weiss K, and Ling J†. (2018) Errors during Gene Expression: Single-Cell heterogeneity, stress resistance, and microbe-host interactions. mBio. 9:e01018-18. (†Corresponding author).  PMCID: PMC6030554

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. 67:1-11. (†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. (†Corresponding author). 43:1740-1748. PMID: 25578967

Ling J*, O’Donoghue P*, and 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. (†Corresponding author). 42:6523-6531. 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 mito­chondrial 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