Timothy C. Meredith

About Me

Tim Meredith attended Villanova University for his undergraduate degree in chemistry and biochemistry, before joining the University of Michigan graduate program to work with Professor Ronald Woodard on studying lipopolysaccharide biosynthesis in Gram-negative bacteria. He then did post doctoral study at Harvard Medical School with Professor Suzanne Walker in the Microbiology and Immunobiology department studying wall teichoic acid biosynthesis in Staphylococcus aureus, before joining Merck Research Laboratories as a research scientist in the infectious diseases department. After a second position as an antimicrobial laboratory head at Novartis Institutes of Research, Dr. Meredith returned to Harvard as an instructor before starting his own laboratory at Pennsylvania State University in the department of Biochemistry and Molecular Biology in 2014. The lab studies lipopolysaccharide, lipoteichoic acids, and lipoprotein biosynthesis in bacteria, and how these complex lipids interact with receptors of innate immunity.

Program or Departmental Affiliations

Centers

Research Interest

Bacterial cell envelope biosynthesis

Research Summary

Lipoprotein Biosynthesis in Firmicutes

Lipoproteins are abundant, globular proteins (1-5% of all open reading frames in a typical bacterium) located on the surface of bacterial cell membranes. Lipoproteins are anchored to the membrane through an acylated N-terminal cysteine residue, where they serve numerous cellular roles including as cell envelope structural components, in adhesion, in cell-cell interactions, and in the capture and transport of nutrients. The ubiquitous distribution of lipoproteins among bacteria, as well as their unique structure, makes lipoproteins important ligands for bacterial detection by innate immunity. Lipoproteins are recognized by binding to Toll-like receptor 2 (TLR2) on macrophages and other host cells, triggering a pro-inflammatory signaling cascade intended to clear the bacterial infection. 

While the structure of lipoproteins is otherwise highly conserved across both gram positive and negative bacteria, the acylation pattern can vary even at the species levels within a given genera among Firmicutes. We are interested in identifying the enzymes responsible for specific lipoprotein acylation patterns, understanding why bacteria have evolved specific lipoprotein chemotypes, and in turn how these structural changes influence detection by TLR2. 

To this end, we recently identified the intramolecular transacylase (Lit) protein in Enterococcus faecalis that makes lyso-form lipoproteins. Lyso-form lipoproteins are poor TLR2 ligands, suggesting a role in immune evasion. Lit orthologs (Lit2) residing in mobile genetic elements have now been identified, including in Listeria monocytogenes where Lit2 is part of a plasmid-borne copper resistance operon. Current efforts are focused on understanding how lyso-form lipoproteins are connected to copper resistance. 

Functional genomics in Staphylococcus aureus

Methicillin resistant Staphylococcus aureus (MRSA) is a leading cause of hospital acquired infections, and ever increasingly outside of the clinic with the rise of hyper virulent community acquired S. aureus lineages.  With nearly 30% of the ~3 Mb genome subject to genetic exchange (via plasmids, transposons, bacteriophage, etc.), S. aureus demonstrates remarkable genomic plasticity that confers a high level of adaptability.  Certain members within clonal complexes account for a disproportionate number of infections.  We are interested in understanding the molecular determinants that impart increased fitness, focusing on contemporary clinical isolates. 

We have developed a comprehensive phage based delivery transposon system in S. aureus to generate high coverage libraries in diverse strains belonging to widely circulating clonal complexes.  Each cassette contains a distinct promoter or transcriptional terminator element of varying intrinsic strength, so a gradient of gene expression levels can be achieved proximal to the insertion site.

By installing a unique 3-bp DNA barcode on each cassette, the different cassettes can be pulled in a single transposon library, probed for phenotype, and then de-multiplexed using the DNA bar code tag in a massively parallel fashion using next generation sequencing.  In collaboration with Suzanne Walker’s laboratory (Department of Microbiology and Immunobiology, Harvard Medical School), we have identified a number of uncharacterized cell envelop related genes involved in resistance to clinically relevant cell envelope targeting antibiotics, and are currently determining their function.

Using this approach, we recently identified the genetic determinants responsible for glycosylation of lipoteichoic acid (LTA), a key membrane bound lipid. LTA is a poly glycerol-phosphate chain attached to a diglucosyl-diacyl glycerol anchor that is specifically modified with N-acetyl glucosamine residues under cell envelope stress inducing conditions. We are interested in understanding how LTA glycosylation impacts cell envelope physiology.

Honors and Awards

Selected Publications

• Substrate structure-activity relationship reveals a limited lipopolysaccharide chemotype range for intestinal alkaline phosphatase
  
  Komazin, G., Maybin, M., Woodard, R.W., Scior, T., Schwudke, D., Schombel, U., Gisch, 
  
  N., Mamat, U., and Meredith T.C. Journal of Biological Chemistry 2019 294(X) doi:  10.1074/jbc.RA119.010836
  
   
• Lipoteichoic acid (LTA) is important to surface protein biogenesis in the gram-positive human oral commensal Streptococcus gordonii
  
  Bruno, L.P., Kho, K., Nairn, B.L., Davies, J., Svensater, G., Chen, R., Steffes, A., Vreeman, 
  
  G.W., Meredith, T.C., and Herzberg, M.C. mSphere 2019 4(6) e00814-19 doi:  10.1128/mSphere.00814-19 
  
   
• Multi-strain Tn-Seq reveals common daptomycin resistance determinants in Staphylococcus aureus 
  
  Coe, K.A., Lee, W., Komazin, G., Meredith, T.C.*, Grad, Y.H.*, and Walker, S.* 
  
  PLOS Pathogens 2019 15(11) e1007862 doi: 10.1371/journal.ppat.1007862
  
   
• Copper-induced expression of transmissible lipoprotein intramolecular transacylase alters lipoprotein acylation and the Toll-like receptor 2 response to Listeria monocytogenes
  
  Armbruster, K.M., Komazin, G., and Meredith, T.C.
  
  Journal of Bacteriology 2019 201(13) pii: JB.00195-19 doi: 10.1128/JB.00195-19
  
   
• Extraction and analysis of bacterial teichoic acids
  
  Kho, K., and Meredith, T.C. Bio-protocols 2018 8(21) doi: 10.21769/BioProtoc.3078
  
   
• Cell-based screen for discovering lipopolysaccharide biogenesis inhibitors
  
  Zhang, G., Baidin, V., Pahil, K. S., Moison, E., Tomasek, D., Ramadoss, N.S., Chatterjee, A.K., McNamara, C.W., Young, T.S., Schultz, P.G.*, Meredith, T.C.*, and Kahne, D.*
  
  Proceedings of the National Academy of Sciences 2018 115(26), 6834-6839 doi: 10.1073/pnas.1804670115
  
   
• Antibiotic combinations that enable one-step, targeted mutagenesis of chromosomal genes 
  
  Lee, W., Do, T., Zhang, G., Kahne, D., Meredith, T.C., and Walker, S. ACS Infectious    
  
  Diseases 2018 4(6), 1007-1018 doi: 10.1021/acsinfecdis.8b00017
  
   
• Genome-wide mutant profiling predicts the mechanism of a lipid II binding antibiotic
  
  Santiago, M., Lee, W., Fayad, A. A., Coe, K.A., Rajagopal, M., Do, T., Hennessen, F., Srisuknimit, V., Müller, R.*, Meredith, T.C.*, and Walker, S.* Nature Chemical Biology 2018  14(6) 601-608 doi: 10.1038/s41589-018-0041-4
  
       
• Salt-induced stress stimulates a lipoteichoic acid-specific three component glycosylation system in Staphylococcus aureus
  
  Kho, K., and Meredith, T.C.
  
  Journal of Bacteriology 2018 200(12) pii: e00017-18 doi: 10.1128/JB.00017-18
  
   
• Enrichment of Bacterial Lipoproteins and Preparation of N-terminal Lipopeptides for Structural Determination by Mass Spectrometry
  
  Armbruster K.M., and Meredith T.C.
  
  Journal of Visual Experiments 2018 (135) doi: 10.3791/56842 
  
    
• Antibiotic That Inhibits the ATPase Activity of an ATP-Binding Cassette Transporter by Binding to a Remote Extracellular Site
  
  Matano L.M., Morris, H.G., Hesser, A.R., Martin, S.E.S., Lee ,W, Owens, T.W., Laney, E., Nakaminami, H., Hooper, D., Meredith T.C.*, and Walker S.*
  
  Journal of the American Chemical Society 2017 139(31):10597-10600 doi: 10.1021/jacs.7b04726    
  
   
• Identification of the Lyso-Form N-Acyl Intramolecular Transferase in Low-GC Firmicutes
  
  Armbruster, K.M., and Meredith, T.C.
  
  Journal of Bacteriology 2017 199(11). pii: e00099-17  doi: 10.1128/JB.00099-17
  
   
• Fluorescent Probe Distinguishes between Inhibition of Early and Late Steps of Lipopolysaccharide Biogenesis in Whole Cells
  
  Moison, E., Xie, R., Zhang, G., Lebar, M.D., Meredith, T.C.*, and Kahne, D.*
  
  ACS Chemical Biology 2017 12(4):928-932 doi: 10.1021/acschembio.7b00159
  
   
• Accelerating the discovery of antibacterial compounds using pathway-directed whole cell screening 
  
  Matano L.M., Morris H.G., Wood B.M., Meredith T.C., and Walker S.
  
  Bioorganic Medicinal Chemistry 2016 24(24):6307-6314 doi: 10.1016/j.bmc.2016.08.003
  
   
• Multidrug Intrinsic Resistance Factors in Staphylococcus aureus Identified by Profiling Fitness within High-Diversity Transposon Libraries
  
  Rajagopal M, Martin M.J., Santiago M, Lee W, Kos V.N., Meredith T.C., Gilmore, M.S, and Walker S.
  
  mBio 2016 7(4). pii: e00950-16 doi: 10.1128/mBio.00950-16
  
   
• A synthetic lethal approach for compound and target identification in Staphylococcus aureus  
  
  Pasquina, L., Santa Maria, J.P. Jr., McKay, Wood B., Moussa, S.H., Matano, L.M., Santiago, M., Martin, S.E., Lee, W., Meredith, T.C., and Walker, S.
  
  Nature Chemical Biology 2016 12(1) 40-5 doi: 10.1038/nchembio.1967
  
   
• Detoxifying Escherichia coli for endotoxin-free production of recombinant proteins
  
  Mamat, U., Wilke, K., Bramhill, D., Schrommc, A.B., Lindner, B., Kohle, T.A., Corcherof, J.L., Villaverde, A., Schafferi, L., Head, S.R., Souvignier, C., Meredith, T.C., and   Woodard, R.W.
  
  Microbial Cell Factories 2015 14(1):57. doi: 10.1186/s12934-015-0241-5
  
   
• A new platform for ultra-high density Staphylococcus aureus transposon libraries  
  
  Santiago, M., Matano, L.M., Moussa, S.H., Gilmore, M.S., Walker, S.* and Meredith, T.C.*        
  
  BMC Genomics 2015 16:252. doi: 10.1186/s12864-015-1361-3
  
   
• Deletion of the β-acetoacetyl synthase FabY in Pseudomonas aeruginosa induces hypoacylation of lipopolysaccharide and increases antimicrobial susceptibility
  
  Six, D.A., Yuan, Y., Leeds, J.A., and Meredith, T.C.
  
  Antimicrobial Agents & Chemotherapy 2014 58(1): 153-61 doi: 10.1128/AAC.01804-13
  
   
• On the essentiality of lipopolysaccharide to gram-negative bacteria
  
  Zhang, G., Meredith, T.C., and Kahne, D.
  
  Current Opinion in Microbiology 2013 16(6):779-85 doi: 10.1016/j.mib.2013.09.007
  
   
• Pleiotropic regulatory genes bldA, adpA and absB are implicated in production of phosphoglycolipid antibiotic moenomycin
  
  Makitrynskyy, R., Ostash, B., Tsypik, O., Rebets, Y., Doud, E., Meredith, T.C., Luzhetskyy, A., Bechthold, A., Walker, S., and Fedorenko V.
  
  Open Biology 2013 3(10): 130121 doi: 10.1098/rsob.130121
  
   
• Discovery of wall teichoic acid inhibitors as potential anti-MRSA β-lactam combination agents  
  
  Wang, H., Gill, C.J., Lee, S.H., Mann, P., Zuck, P., Meredith, T.C., Murgolo, N., She, S., Kales, S., Liang, L., Liu, J., Wu, J., Santa Maria, J., Su, J., Pan, J., Hailey, J., Mcguinness, D., Tan, C.T., Flattery, A., Walker, S., Black, T., and Roemer, T.
  
  Chem. & Biol. 2013 20(2): 272–84 doi: 10.1016/j.chembiol.2012.11.013
  
   
• Methicillin resistance in Staphylococcus aureus requires glycosylated wall teichoic acids 
  
  Brown, S., Xia, G., Luhachack, L.G., Campbell, J., Meredith, T.C., Chen, C., Winstel, V., Gekeler,  C., Irazoqui, J.E., Peschel, A., and Walker, S.
  
  Proceedings of the National Academy of the Sciences 2012 109(46): 18909-14 doi: 10.1073/pnas.1209126109
  
   
• Harnessing the power of transposon mutagenesis for antibacterial target identification and evaluation
  
  Meredith, T.C.*, Wang, H., Beaulieu, P., Gründling, A., and Roemer, T.*
  
  Mobile Genetic Elements 2012 2(4): 171-8 doi: 10.4161/mge.21647
  
   
• Pseudomonas aeruginosa directly shunts β-oxidation degradation intermediates into de novo fatty acid biosynthesis
  
  Yuan, Y., Leeds, J.A., and Meredith, T.C.
  
  Journal of Bacteriology 2012 194(19): 5185-96  doi: 10.1128/JB.00860-12
  
   
• Fatty acid biosynthesis in Pseudomonas aeruginosa is initiated by FabY: A new class of β- ketoacyl acyl carrier protein synthases
  
  Yuan, Y., Sachdeeva, M., Leeds, J.A., and Meredith, T.C.
  
  Journal of Bacteriology 2012 194(19): 5171-84 doi: 10.1128/JB.00792-12
  
   
• Restoring methicillin-resistant Staphylococcus aureus susceptibility to β-lactam antibiotics
  
  Tan, C.M., et. al. (28 co-authors on Merck project team)
  
  Science Translational Medicine 2012 4(126):126ra35 doi: 10.1126/scitranslmed.3003592
  
   
• Antagonism of chemical genetic interaction networks re-sensitize MRSA to β-lactam antibiotics 
  
  Lee, S.H., Jarantow, L.W., Wang, H., Sillaots, S., Cheng, H., Meredith, T.C., Thompson, J., and Roemer, T.
  
  Chemistry & Biology 2011 18(11): 1379-89 doi: 10.1016/j.chembiol.2011.08.015
  
   
• High-frequency transposition for determining antibacterial mode of action
  
  Wang, H., Claveau, D., Vaillancourt, J., Roemer, T., and Meredith, T.C.
  
  Nature Chemical Biology 2011 7(10): 720-9 doi: 10.1038/nchembio.643
  
   
• A unique arabinose 5-phosphate isomerase found within a genomic island associated with the uropathogenicity of Escherichia coli CFT073
  
  Mosberg, J.A., Yep, A., Meredith, T.C., Smith,S., Wang, P.F., Holler,T., Mobley, H., and Woodard, R.W.
  
  Journal of Bacteriology 2011 193(12): 2981-8 doi: 10.1128/JB.00033-11
  
   
• Staphylococcus aureus and Bacillus subtilis W23 make polyribitol wall teichoic acids using different enzymatic pathways
  
  Brown, S., Meredith, T.C., Swoboda, J.G., and Walker, S.
  
  Chemistry & Biology 2010 17(10):1101-10 doi: 10.1016/j.chembiol.2010.07.017
  
   
• Wall teichoic acid function, biosynthesis, and inhibition
  
  Swoboda, J.G., Campbell, J., Meredith, T.C., and Walker, S.
  
  Chembiochem 2010 11(1): 35-45 doi: 10.1002/cbic.200900557
  
   
• Discovery of a small molecule that blocks wall teichoic acid biosynthesis in Staphylococcus aureus
  
  Swoboda, J.G.*, Meredith, T.C.*, Campbell, J., Brown, S., Suzuki,  T., Bollenbach, T., 
  
  Malhowski, A.J., Kishony, R., Gilmore, M.S., and Walker, S.
  
  ACS Chemical Biology 2009 4(10):875-83 doi: 10.1021/cb900151k
  
   
• WaaA of the hyperthermophilic bacterium Aquifex aeolicus is a monofunctional 3-deoxy-D-manno-oct-2-ulosonic acid transferase involved in lipopolysaccharide biosynthesis
  
  Mamat, U., Schmidt, H., Munoz, E., Lindner ,B., Fukase, K., Hanuszkiewicz, A., Meredith, T.C., Woodard, R.W., Hilgenfeld, R., Mesters, J.R., and Holst, O.
  
  Journal of Biological Chemistry 2009 284(33):22248-62 doi: 10.1074/jbc.M109.033308
  
   
• Late-stage polyribitol phosphate wall teichoic acid biosynthesis in Staphylococcus aureus
  
  Meredith, T.C., Swoboda, J.G., and Walker, S.
  
  Journal of Bacteriology 2008 190(8): 3046-56 doi: 10.1128/JB.01880-07
  
   
• Single amino acid substitutions in either YhjD or MsbA confer viability to 3-deoxy-D-manno-oct- 2-ulosonic acid-depleted Escherichia coli
  
  Mamat, U., Meredith, T.C., Aggarwal, P., Kühl, A., Kirchhoff, P., Lindner, B., Hanuszkiewicz, A., Sun, J., Holst, O., and Woodard R.W.
  
  Molecular Microbiology 2008 67(3): 633-48 doi: 10.1111/j.1365-2958.2007.06074.x
  
   
• Modification of lipopolysaccharide with colanic acid (M-antigen) repeats in Escherichia coli
  
  Meredith, T.C., Mamat, U., Kaczynski, Z, Lindner, B, Holst, O, and Woodard, R.W.
  
  Journal of Biological Chemistry 2007 282(11): 7790-8 doi: 10.1074/jbc.M611034200
  
   
• Characterization of Escherichia coli D-arabinose 5-phosphate isomerase encoded by KpsF: Implications for group 2 capsule biosynthesis
  
  Meredith, T.C. and Woodard, R.W.
  
  Biochemical Journal 2006 395(2): 427-32 doi: 10.1042/BJ20051828
  
   
• Redefining the requisite lipopolysaccharide structure in Escherichia coli
  
  Meredith, T.C., Aggarwal, P., Mamat, U., Lindner, B. and Woodard, R.W.
  
  ACS Chemical Biology 2006 1(1): 33-42 doi: 10.1021/cb0500015
  
   
• Identification of GutQ from Escherichia coli as a D-arabinose 5-phosphate isomerase
  
  Meredith, T.C. and Woodard, R.W.
  
  Journal of Bacteriology 2005 187(20): 6936-42 doi: 10.1128/JB.187.20.6936-6942.2005
  
   
• Escherichia coli YrbH is a D-arabinose 5-phosphate isomerase
  
  Meredith, T.C. and Woodard, R.W.
  
  Journal of Biological Chemistry 2003 278(35): 32771-7 doi:10.1074/jbc.M303661