Publications

2022

  • Fung DK, Wang JD. (2022) The τ of alarmone hydrolysis. Nat Chem Biol.  doi: 10.1038/s41589-022-01200-6. PMID: 36470997.
  • Fung DK, Bai K, Yang J, Xu X, Stevenson DM, Amador-Noguez D, Luo L, Wang JD. (2022) Metabolic Promiscuity of an Orphan Small Alarmone Hydrolase Facilitates Bacterial Environmental Adaptation. mBio.  doi: 10.1128/mbio.02422-22. PMID: 36472432
  • Giammarinaro PI, Young MKM, Steinchen W, Mais C-N, Hochberg G, Yang J, Stevenson DM, Amador-Noguez D, Paulus A, Wang JD, Bange G (2022) Diadenosine tetraphosphate regulates biosynthesis of GTP in Bacillus subtilisNat. Microbiol. 7(9):1442-1452 · Pubmed · DOI
  • Yang J, Barra JT, Fung DK, Wang JD (2022) Bacillus subtilis produces (p)ppGpp in response to bacteriostatic antibiotic chloramphenicol to prevent its potential bactericidal effect. mLife 1(2):101-113 · DOI
  • Anderson BW, Schumacher MA, Yang J, Turdiev A, Turdiev H, Schroeder JW, He Q, Lee VT, Brennan RG, Wang JD (2022) The nucleotide messenger (p)ppGpp is an anti-inducer of the purine synthesis transcription regulator PurR in Bacillus. Nucleic Acids Res. 50(2):847-866 PMC8789054 · Pubmed · DOI

2021

  • LM Onder, JD Wang, J Jagodnik, W Ross, RL Gourse (2021) Global Regulation of Transcription by Nucleotides and (p) ppGpp.
    RNA Polymerases as Molecular Motors, 132-152 · DOI
  • Anderson BW, Fung DK, Wang JD (2021) Regulatory Themes and Variations by the Stress-Signaling Nucleotide Alarmones (p)ppGpp in Bacteria. Annu. Rev. Genet. 55:115-133 · Pubmed · DOI
  • Giramma CN, DeFoer MB, Wang JD (2021) The Alarmone (p)ppGpp Regulates Primer Extension by Bacterial Primase. J. Mol. Biol. 433(19):167189 PMC8453095 · Pubmed · DOI
  • Yang J, Anderson BW, Turdiev A, Turdiev H, Stevenson DM, Amador-Noguez D, Lee VT, Wang JD (2021) Author Correction: The nucleotide pGpp acts as a third alarmone in Bacillus, with functions distinct from those of (p)ppGpp. Nat. Commun. 12(1):3857 PMC8208980 · Pubmed · DOI
  • Updegrove TB, Harke J, Anantharaman V, Yang J, Gopalan N, Wu D, Piszczek G, Stevenson DM, Amador-Noguez D, Wang JD, Aravind L, Ramamurthi KS (2021) Reformulation of an extant ATPase active site to mimic ancestral GTPase activity reveals a nucleotide base requirement for function. eLife 10:e65845 PMC7952092 · Pubmed · DOI

2020

  • Yang J, Anderson BW, Turdiev A, Turdiev H, Stevenson DM, Amador-Noguez D, Lee VT, Wang JD (2020) The nucleotide pGpp acts as a third alarmone in Bacillus, with functions distinct from those of (p) ppGpp. Nat. Commun. 11(1):5388 PMC7584652 · Pubmed · DOI
  • Fung DK, Yang J, Stevenson DM, Amador-Noguez D, Wang JD (2020) Small Alarmone Synthetase SasA Expression Leads to Concomitant Accumulation of pGpp, ppApp, and AppppA in Bacillus subtilis. Front. Microbiol. 11:2083 PMC7492591 · Pubmed · DOI
  • Schroeder JW, Sankar TS, Wang JD, Simmons LA (2020) The roles of replication-transcription conflict in mutagenesis and evolution of genome organization. PLoS Genet. 16(8):e1008987 PMC7451550 · Pubmed · DOI
  • Peterson BN, Young MKM, Luo S, Wang J, Whiteley AT, Woodward JJ, Tong L, Wang JD, Portnoy DA (2020) (p)ppGpp and c-di-AMP Homeostasis Is Controlled by CbpB in Listeria monocytogenes. mBio 11((4)):e01625-20 PMC8549634 · Pubmed · DOI
  • Anderson BW, Hao A, Satyshur KA, Keck JL, Wang JD (2020) Molecular Mechanism of Regulation of the Purine Salvage Enzyme XPRT by the Alarmones pppGpp, ppGpp, and pGpp. J. Mol. Biol. 432(14):4108-4126 PMC7323586 · Pubmed · DOI

2019

  • Anderson BW, Wang JD (2019) Toxin discovery reveals fresh ammunition for bacterial warfare. Nature 575(7784):599-600 · Pubmed · DOI
  • Sauls JT, Schroeder JW, Brown SD, Le Treut G, Si F, Li D, Wang JD, Jun S (2019) Mother machine image analysis with MM3. bioRxiv · DOI
  • Anderson BW, Liu K, Wolak C, Dubiel K, She F, Satyshur KA, Keck JL, Wang JD (2019) Evolution of (p)ppGpp-HPRT regulation through diversification of an allosteric oligomeric interaction. eLife 8:e47534 PMC6783271 · Pubmed · DOI
  • Pisithkul T, Schroeder JW, Trujillo EA, Yeesin P, Stevenson DM, Chaiamarit T, Coon JJ, Wang JD, Amador-Noguez D (2019) Metabolic Remodeling during Biofilm Development of Bacillus subtilis. mBio 10(3): PMC6529636 · Pubmed · DOI

Before 2018

  • Schroeder JW, Yeesin P, Simmons LA, Wang JD (2017) Sources of spontaneous mutagenesis in bacteria. Crit. Rev. Biochem. Mol. Biol. 53(1):29-48 PMC5975382 · Pubmed · DOI
  • Vadia S, Tse JL, Lucena R, Yang Z, Kellogg DR, Wang JD, Levin PA (2017) Fatty Acid Availability Sets Cell Envelope Capacity and Dictates Microbial Cell Size. Curr. Biol. 27(12):1757-1767.e5 PMC5551417 · Pubmed · DOI
  • Sankar TS, Wastuwidyaningtyas BD, Dong Y, Lewis SA, Wang JD (2016) The nature of mutations induced by replication–transcription collisions. Nature 535(7610):178-81 PMC4945378 · Pubmed · DOI
  • Li W, Bouveret E, Zhang Y, Liu K, Wang JD, Weisshaar JC (2015) Effects of amino acid starvation on RelA diffusive behavior in live Escherichia coli. Mol. Microbiol. 99(3):571-85 PMC4962531 · Pubmed · DOI
  • Gaca AO, Kudrin P, Colomer-Winter C, Beljantseva J, Liu K, Anderson B, Wang JD, Rejman D, Potrykus K, Cashel M, Hauryliuk V, Lemos JA (2015) From (p)ppGpp to (pp)pGpp: Characterization of Regulatory Effects of pGpp Synthesized by the Small Alarmone Synthetase of Enterococcus faecalis. J. Bacteriol. 197(18):2908-19 PMC4542164 · Pubmed · DOI
  • Liu K, Bittner AN, Wang JD (2015) Diversity in (p)ppGpp metabolism and effectors. Curr. Opin. Microbiol. 24:72-9 PMC4380541 · Pubmed · DOI
  • Liu K, Myers AR, Pisithkul T, Claas KR, Satyshur KA, Amador-Noguez D, Keck JL, Wang JD (2015) Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp. Mol. Cell 57(4):735-49 PMC4336630 · Pubmed · DOI
  • Arjes HA, Kriel A, Sorto NA, Shaw JT, Wang JD, Levin PA (2014) Failsafe mechanisms couple division and DNA replication in bacteria. Curr. Biol. 24(18):2149-55 PMC4175050 · Pubmed · DOI
  • Bittner AN, Kriel A, Wang JD (2014) Lowering GTP level increases survival of amino acid starvation but slows growth rate for Bacillus subtilis cells lacking (p)ppGpp. J. Bacteriol. 196(11):2067-76 PMC4010990 · Pubmed · DOI
  • Zhang Y, Mooney RA, Grass JA, Sivaramakrishnan P, Herman C, Landick R, Wang JD (2014) DksA guards elongating RNA polymerase against ribosome-stalling-induced arrest. Mol. Cell 53(5):766-78 PMC4023959 · Pubmed · DOI
  • Maduike NZ, Tehranchi AK, Wang JD, Kreuzer KN (2014) Replication of the Escherichia coli chromosome in RNase HI-deficient cells: multiple initiation regions and fork dynamics. Mol. Microbiol. 91(1):39-56 PMC3926323 · Pubmed · DOI
  • Kriel A, Brinsmade SR, Tse JL, Tehranchi AK, Bittner AN, Sonenshein AL, Wang JD (2014) GTP dysregulation in Bacillus subtilis cells lacking (p)ppGpp results in phenotypic amino acid auxotrophy and failure to adapt to nutrient downshift and regulate biosynthesis genes. J. Bacteriol. 196(1):189-201 PMC3911124 · Pubmed · DOI
  • Gaca AO, Kajfasz JK, Miller JH, Liu K, Wang JD, Abranches J, Lemos JA (2013) Basal levels of (p)ppGpp in Enterococcus faecalis: the magic beyond the stringent response. mBio 4(5):e00646-13 PMC3781836 · Pubmed · DOI
  • Denapoli J, Tehranchi AK, Wang JD (2013) Dose-dependent reduction of replication elongation rate by (p)ppGpp in Escherichia coli and Bacillus subtilis. Mol. Microbiol. 88(1):93-104 PMC3640871 · Pubmed · DOI
  • Kriel A, Bittner AN, Kim SH, Liu K, Tehranchi AK, Zou WY, Rendon S, Chen R, Tu BP, Wang JD (2012) Direct regulation of GTP homeostasis by (p)ppGpp: a critical component of viability and stress resistance. Mol. Cell 48(2):231-41 PMC3483369 · Pubmed · DOI
  • Rymer RU, Solorio FA, Tehranchi AK, Chu C, Corn JE, Keck JL, Wang JD, Berger JM (2012) Binding mechanism of metal⋅NTP substrates and stringent-response alarmones to bacterial DnaG-type primases. Structure 20(9):1478-89 PMC3438381 · Pubmed · DOI
  • Merrikh H, Zhang Y, Grossman AD, Wang JD (2012) Replication-transcription conflicts in bacteria. Nat. Rev. Microbiol. 10(7):449-58 PMC3467967 · Pubmed · DOI
  • Tehranchi AK, Blankschien MD, Zhang Y, Halliday JA, Srivatsan A, Peng J, Herman C, Wang JD (2010) The transcription factor DksA prevents conflicts between DNA replication and transcription machinery. Cell 141(4):595-605 PMC2919171 · Pubmed · DOI
  • Srivatsan A, Tehranchi A, MacAlpine DM, Wang JD (2010) Co-orientation of replication and transcription preserves genome integrity. PLoS Genet. 6(1):e1000810 PMC2797598 · Pubmed · DOI
  • Wang JD, Levin PA (2009) Metabolism, cell growth and the bacterial cell cycle. Nat. Rev. Microbiol. 7(11):822-7 PMC2887316 · Pubmed · DOI
  • Srivatsan A, Han Y, Peng J, Tehranchi AK, Gibbs R, Wang JD, Chen R (2008) High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genet. 4(8):e1000139 PMC2474695 · Pubmed · DOI
  • Srivatsan A, Wang JD (2008) Control of bacterial transcription, translation and replication by (p)ppGpp. Curr. Opin. Microbiol. 11(2):100-5 · Pubmed · DOI
  • Wang JD, Sanders GM, Grossman AD (2007) Nutritional control of elongation of DNA replication by (p)ppGpp. Cell 128(5):865-75 PMC1850998 · Pubmed · DOI
  • Wang JD, Berkmen MB, Grossman AD (2007) Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis. Proc. Natl. Acad. Sci. U.S.A. 104(13):5608-13 PMC1838449 · Pubmed · DOI
  • Goranov AI, Kuester-Schoeck E, Wang JD, Grossman AD (2006) Characterization of the global transcriptional responses to different types of DNA damage and disruption of replication in Bacillus subtilis. J. Bacteriol. 188(15):5595-605 PMC1540033 · Pubmed · DOI
  • Wang JD, Rokop ME, Barker MM, Hanson NR, Grossman AD (2004) Multicopy plasmids affect replisome positioning in Bacillus subtilis. J. Bacteriol. 186(21):7084-90 PMC523195 · Pubmed · DOI
  • Wang JD, Herman C, Tipton KA, Gross CA, Weissman JS (2002) Directed evolution of substrate-optimized GroEL/S chaperonins. Cell 111(7):1027-39 · Pubmed · DOI
  • Wang JD, Weissman JS (1999) Thinking outside the box: new insights into the mechanism of GroEL-mediated protein folding. Nat. Struct. Biol. 6(7):597-600 · Pubmed · DOI
  • Wang JD, Michelitsch MD, Weissman JS (1998) GroEL-GroES-mediated protein folding requires an intact central cavity. Proc. Natl. Acad. Sci. U.S.A. 95(21):12163-8 PMC22802 · Pubmed · DOI
  • Johnson BL, Sachrajda AS, Kirczenow G, Feng Y, Taylor RP, Henning L, Wang J, Zawadzki P, Coleridge PT (1995) Quantum Hall effect and inter-edge-state tunneling within a barrier. Phys. Rev. B Condens. Matter 51(12):7650-7654 · Pubmed · DOI
  • Sachrajda AS, Feng Y, Taylor RP, Kirczenow G, Henning L, Wang J, Zawadzki P, Coleridge PT (1994) Magnetoconductance of a nanoscale antidot. Phys. Rev. B Condens. Matter 50(15):10856-10863 · Pubmed · DOI
  • Kirczenow G, Sachrajda AS, Feng Y, Taylor RP, Henning L, Wang J, Zawadzki P, Coleridge PT (1994) Artificial impurities in quantum wires: From classical to quantum behavior. Phys. Rev. Lett. 72(13):2069-2072 · Pubmed · DOI