Recent Student Publications

  • Singh R, Ranaivoarisoa TA, Gupta D, Bai W, Bose A (2020) Genetic redundancy in iron and manganese transport in the metabolically versatile bacterium Rhodopseudomonas palustris TIE-1.  Appl Environ Micro (in press)

  • Ganguly A, Zhu CM, Chen W, Dixit R (2020) FRA1 kinesin modulates the lateral stability of cortical microtubules through cellulose synthase-microtubule uncoupling protein.  Plant Cell (in press)

  • Lee SG, Chung MS, DeMarsilis AJ, Holland CK, Jaswaney RV, Jiang C, Kroboth JHP, Kulshrestha K, Marcelo RZW, Meyyappa VM, Nelson GB, Patel JK, Petronio AJ, Powers SKQin PR, Ramachandran M, Rayapati D, Rincon JA, Rocha A, Rodinho Nunes Ferreira JG, Steinbrecher MK, Yao K, Zhang EJ, Zou AJ, Gang M, Sparks M, Cascella B, Cruz W, Jez JM (2020) Structural and biochemical analysis of phosphoethanolamine methyltransferase from the pine wilt nematode Bursaphelenchus xylophilus.  Mol Biochem Parasitol 238, 111291

  • Djami-Tchatchou AT, Harrison GA, Harper CP, Wang R, Prigge M, Estelle M, Kunkel BN (2020) Dual role of auxin in regulating plant defense and bacterial virulence gene expression during Pseudomonas syringae strain DC3000 pathogenesis.  Mol Plant Microbe Interact (in press)

  • Liu D, Johnson VM, Pakrasi HB (2020) A reversibly induced CRISPRi system targeting photosystem II in the cyanobacterium Synechocystis sp. PCC 6803.  ACS Syn Biol (in press)

  • Basu D, Shoots JM, Haswell ES (2020) Interactions between the N- and C- termini of mechanosensitive ion channel AtMSL10 are consistent with a three-step mechanism for activating its signaling function.  J Exp Bot (in press)

  • Trujillo-Hernandez JA, Bariat L, Enders TA, Strader LC, Reichheld JP, Belin C (2020) A glutathione-dependent control of IBA pathway supports Arabidopsis root system adaptation to phosphate deprivation.  J Exp Bot (in press)

  • Schlegel AM, Haswell ES (2020) Analyzing plant mechanosensitive ion channels expressed in giant E. coli spheroplasts by single channel patch-clamp electrophysiology.  Meth Cell Biol (in press)

  • Campbell TP, Sun XQ, Patel VH, Sanz C, Morgan D, Dantas G (2020) The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography.  ISME J 14, 1584-99

  • Guo K, Mellinger P, Doan V, Allen J, Pringle RN, Jammes F (2020) Identification of novel regulators of plant transpiration by imaging screening in Helianthus annuus.  J Vis Exp 10.3791/60535

  • Schlegel AM, Haswell ES (2020) Plant biomechanics:  no pain, no gain for birch tree stems.  Curr Biol 30, R164-6

  • Emenecker R, Strader LC (2020) Auxin-abscisic acid interactions in plant growth and development.  Biomolecules 10, 281

  • Powers SK, Strader LC (2020) Regulation of auxin transcriptional responses.  Dev Dyn 249, 483-95

  • Verma M, Choi J, Cottrell KA, Lavagnino Z, Thomas EN, Pavlovic-Djuranovic S, Szczesny P, Piston DW, Zaher HS, Puglisi JD, Djuranovic S (2019) A short-translational ramp determines the efficiency of protein synthesis. Nature Commun 10, 5774

  • Yan LL, Simms CL, McLoughlin F, Vierstra RD, Zaher HS (2019) Oxidation and alkylation stresses activate ribosome-quality control.  Nature Commun 10, 5611

  • Gupta D, Sutherland MC, Rengasamy K, Meacham J, Kranz RG, Bose A (2019) Photoferrotrophs produce a PioAB electron conduit for extracellular electron uptake.  mBio 10, e02668-19

  • Holland CK, Westfall CS, Schaffer JE, De Santiago A, Zubieta C, Alvarez S, Jez JM (2019) Brassicaceae-specific Gretchen Hagen 3 acyl acid amido synthetases conjugate amino acids to chorismate, a precursor of aromatic amino acids and salicylic acid.  J Biol Chem 294, 16855-64

  • Balkunde R, Foroughi L, Ewan E, Emenecker R, Cavalli V, Dixit R (2019) Mechanism of microtubule plus-end tracking by the plant-specific SPR1 protein and its development as a versatile plus-end marker.  J Biol Chem 294, 16374-84

  • Weisz DA, Johnson VM, Niedzwiedzki DM, Shinn MK, Liu H, Klitze CF, Gross ML, Blankenship RE, Lohman TM, Pakrasi HB (2019) A novel chlorophyll protein complex in the repair cycle of photosystem II.  Proc Natl Acad Sci USA 116, 21907-13

  • Davenport EJ, Neudeck MJ, Matson PG, Bullerjahn GS, Davis TW, Wilhelm SW, Denney MK, Krausfeldt LE, Stough JMA, Meyer KA, Dick GH, Johengen TH, Lindquist E, Tringe SG, McKay RML (2019) Metatranscriptomic analyses of diel metabolic functions during a microcystis bloom in western Lake Erie (United States).  Front Microbiol 10, 2081

  • Nagarajan A, Zhou M, Nguyen AY, Liberton M, Kedia K, Shi T, Piehowski P, Shukla A, Fillmore TL, Nicora C, Smith RD, Koppenaal DW, Jacobs JM, Pakrasi HB (2019) Proteomic insights into phycobilisome degradation, a selective and tightly controlled process in the fast-growing cyanobacterium Synechococcus elongatus UTEX2973.  Biomolecules 9, 374

  • Yan LL,  Zaher HS (2019) How do cells cope with RNA damage and its consequences? J Biol Chem 294, 15158-71

  • Thomas EN, Simms CL, Keedy HE, Zaher H (2019) Insights into the base pairing preferences of 8-oxoguanosine on the ribosome.  Nucleic Acids Res 47, 9857-79

  • Wolf BM, Blankenship RE (2019) Far-red light acclimation in diverse oxygenic photosynthetic organisms.  Photosynth Res 142, 349-59

  • Powers SK, Holehouse AS, Korasick DA, Schreiber KH, Clark NM, Jing H, Emenecker R, Han S, Tycksen E, Hwang I, Sozzani R, Jez JM, Pappu RV, Strader LC (2019) Nucleo-cytoplasmic partitioning of ARF proteins controls auxin responses in Arabidopsis thaliana.  Mol Cell 76, 177-90

  • Zhu D, Bullock J, He Y, Sun X (2019) Cwp22, a novel peptidoglycan cross-linking enzyme, plays pleiotropic roles in Clostridioles difficile.  Environ Micro 21, 3076-90

  • Michniewicz M, Ho CH, Enders TA, Floro E, Damodoran S, Gunther LK, Powers SKFrick EM, Topp CN, Frommer WB, Strader LC (2019) Transporter of IBA1 links auxin and cytokinin to influence root architecture.  Dev Cell 50, 599-609

  • Anthony WE, Carr RR, DeLorenzo DM, Campbell TP, Shang Z, Foston M, Moon TS, Dantas G (2019) Development of Rhodococcus opacus as a chassis for lignin valorization and bioproduction of high-value compounds.  Biotechnol Biofuels 12, 192

  • Simms CL, Yan LL, Qiu JK, Zaher HS (2019) Ribosome collisions result in +1 frameshifting in the absence of no-go decay.  Cell Rep 28, 1679-89

  • Lou W, Wolf BM, Blankenship RE, Liu H (2019) Cu+ contributes to the orange carotenoid protein-related phycobilisome fluorescence quenching and photoprotection in cyanobacteria.  Biochemistry 58, 3109-15

  • Zhu DX, Garner AL, Galburt EA, Stallings CL (2019) CarD contributes to diverse gene expression outcomes throughout the genome of Mycobacterium tuberculosis.  Proc Natl Acad Sci USA 116, 13573-81

  • Yeh A, Conners EM, Ramos-Jimenez RG, Firek B, Novak EA, Rogers MB, Cheek R, Ozolek J, Mollen KP, Morowitz MJ (2019) Plant-based enteral nutrition modified the gut microbiota and improves outcomes in murine models of colitis.  Cell Mol Gastroenterol Hepatol 7, 872-4

  • Roell GW, Carr RR, Campbell T, Shang Z, Henson WR, Czajka JJ, Martin HG, Zhang F, Foston M, Dantas G, Moon TS, Tang YJ (2019) A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630.  Metab Engr 55, 120-30

  • Allen J, Guo K, Zhang D, Ince M, Jammes F (2019) ABA-glucose ester hydrolyzing enzyme ATBG1 and PHYB antagonistcally regulate stomatal development.  PLoS One 14, e0218605

  • Borodinov N, Bilkey N, Foston M, Ievlev AV, Belianinov A, Jesse S, Vasudevan RK, Kalinin SV, Ovchinnikova OS (2019) Application of pan-sharpening algorithm for correlative multimodal imaging using AFR-IR.  Comp Materials 5, 49

  • Flentie K, Harrison GA, Tukenmez H, Livny J, Good JAD, Sarkar S, Zhu DX, Kinsella RL, Weiss LA, Solomon SD, Schene ME, Hansen MR, Cairns AG, Kulen M, Wixe T, Lindgren AEG, Chorell E, Bengtsson C, Krishnan KS, Hultgren SJ, Larsson C, ALmqvist F, Stallings CL (2019) Chemical disarming of isoniazid restistance in Mycobacterium tuberculosis.  Proc Natl Acad Sci USA 116, 10510-7

  • Taylor I, Baer J, Calcutt R, Walker JC (2019) Regulation of abscission signaling.  Plant Physiol 180, 1219-29

  • Huang H, McLoughlin KE, Sorkin ML, Burgie ES, Bindbeutel RK, Vierstra RD, Nusinow DA (2019) PCH1 regulates light, temperature, and circadian signaling as a structural component of phytochrome B-photobodies in Arabidopsis.  Proc Natl Acad Sci USA 116, 8603-8

  • Hu Y*, Qi Y*, Stumpf S, D'Alessandro JM, Blodgett JAV (2019) Bioinformatic and functional evaluation of actinobacterial piperazate metabolism.  ACS Chem Biol 14, 696-703

  • Niedzwiedzki DM, Wolf BM, Blankenship RE (2019) Excitation energy transfer in the far-red absorbing violaxanthin/vaucheriaxanthin chlorophyll a complex from the eustigmatophyte alga FP5.  Photosynth Res 140, 337-54

  • Yan LL, Zaher HS (2019) Ubiquitin -  a beacon for all during quality control of the ribosome.  EMBO J 38, e101633

  • Kim SC, Nusinow DA, Sorkin ML, Pruneda-Paz J, Wang X (2019) Interaction and regulation between lipid mediator phosphatidic acid and circadian clock regulators in Arabidopsis.  Plant Cell 31, 399-416

  • Gupta D, Guzman MS, Bose A (2019) Draft genome sequence of a marine photoferrotrophic bacterium, Rhodovulum robiginosum DSM 12329 (T).  Microbiol Resour Announc 8, e01684-18

  • Onyshchenko A, Ruck EC, Nakov T, Alverson AJ (2019) A single loss of photosynthesis in the diatom order Bacillariales (Bacillariophyta).  Am J Bot 106, 560-572

  • Tomlinson L, Ying Y, Emenecker R, Smoker M, Taylor J, Perkins S, Smith J, MacLean D, Olszewski NE, Jones JDG (2018) Using CRISPR/Cas9 genome editing in tomato to create a gibberellin-responsive dominant dwarf DELLA allele.  Plant Biotech J 17, 132-40

  • Sherp AM, Lee SG, Schraft E, Jez JM (2018) Modification of auxinic phenoxyalkanoid acid herbicides by the acyl acid amido synthetase GH3.15 from Arabidopsis.  J Biol Chem 293, 17731-8

  • Simms CL, Kim KQ, Yan LL, Qiu J, Zaher HS (2018) Interactions between the mRNA and Rps3/uS3 at the entry tunnel of the ribosome small unit are important for no-go decay.  PLoS Genet 14, e1007818

  • Holland CK, Jez JM (2018) Arabidopsis:  the original plant chassis organism.  Plant Cell Rep 37, 1359-66

  • Roth S, Kilgore MB, Kutchan TM, Mueller M (2018) Exploiting the catalytic diversity of short-chain dehydrogenases/reductases: versatile enzymes from plants with extended imine substrate scope.  ChemBioChem 19, 1849-52

  • Xiao Y, Wang S, Rommelfanger S, Balassy A, Barba-Ostria C, Gu P, Galazka JM, Zhang F (2018) Developing a Cas9-based tool to engineer native plasmids in Synechocystis sp. PCC 6803.  Biotech Bioengr 115, 2305-14

  • Ramadoss N, Gupta D, Vaidya BN, Joshee N, Basu C (2018) Functional characterization of 1-aminocyclopropane-1-carboxylic acid oxidase gene in Arabidopsis thaliana and its potential in providing flood tolerance.  Biochem Biophys Res Comm 503, 365-70

  • Henson WR*, Campbell T*, DeLorenzo DM*, Gao Y, Berla B, Kim SJ, Foston M, Moon TS, Dantas G (2018) Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus.  Metab Eng 49, 69-83

  • Holland CK, Jez JM (2018) Structural biology of jasmonic acid metabolism and responses in plants.  In Plant Structural Biology: Hormonal Regulators (Hejatko J and Takoshima T, eds), pp 67-82, Springer-Verlag, NY

  • Prusa J, Zhu DX, Stallings CL (2018) The stringent response and Mycobacterium tuberculosis pathogenesis.  Pathog Dis 76, fty054

  • Keedy HE*, Thomas EN*, Zaher HS (2018) Decoding on the ribosome depends on the structure of the mRNA phosphodiester backbone.  Proc Natl Acad Sci USA 115, E6731-40 (*equal contribution)

  • Maksaev G, Shoots J, Ohri S, Haswell ES (2018) Nonpolar residues in the presumptive pore-lining helix of mechanosensitive channel MSL10 influence channel behavior and confirm its non-conducting function.  Plant Direct 2, e00059

  • Haynsen MS, Vatanparast M, Mahadwar G, Zhu D, Moger-Reischer RZ, Doyle JJ, Crandall KA, Egan AH (2018) De novo transcriptome assembly of Pueraria montana var. lobata and Neustanthus phaseoloides for the development of eSSR and SNP markers:  narrowing the US origin(s) of the invasive kudzu.  BMC Genomics 19, 439

  • Holland CK, Jez JM (2018) Reaction mechanism of prephenate dehydrogenase from the alternate tyrosine biosynthesis pathway in plants.  ChemBioChem 19, 1132-6

  • Phillips AZ, Wheeler T, Woodward J, Bart RS (2018) Pseudomonas syringae pathogen causes foliar disease of upland cotton in Texas.  Plant Disease 102, 1171

  • Holland CK, Berkovich DA, Kohn ML, Maeda H, Jez JM (2018) Structural basis for substrate recognition and inhibition of prephenate aminotransferase from Arabidopsis.  Plant J 94, 304-14

  • Ganguly A, DeMott L, Zhu C, McClosky DD, Anderson CT, Dixit R (2018) Importin-beta directly regulates the motor activity and turnover of a kinesin-4.  Dev Cell 44, 642-51

  • Sherp AM, Westfall CS, Alvarez S, Jez JM (2018) Arabidopsis thaliana GH3.15 acyl acid amido synthetase has a highly specific substrate prefernce for the auxin precursor indole-3-butryic acid.  J Biol Chem 293, 4277-88

  • Frick EM, Strader LC (2018) They can handle the stress: MPK17 and PMD1 act in a salt-specific pathway.  Plant Signal Behav 13, e1428518

  • Qi Y, Ding E, Blodgett JAV (2018) Native and engineered clifednamide biosynthesis in mulitple Streptomyces spp.  ACS Synth Biol 16, 357-62

  • Krishnan HB, Song B, Oehrle NW, Cameron JC, Jez JM (2018) Impact of overexpression of cytosolic isoform of O-acetylserine sulfhydrylsae on soybean nodulation and nodule metabolome.  Sci Rep 8, 2367

  • Wolf BM, Niedzwiedzki DM, Magdaong NCM, Roth R, Goodenough U, Blankenship RE (2018) Characterization of a newly isolated freshwater Eustigmatophyte alga capable of utilizing far-red light as its sole light source.  Photosynth Res 135, 177-89

  • Liu H, Lu Y, Wolf B, Saer R, King JD, Blankenship RE (2018) Photoactivation and relaxation studies on the cyanobacterial orange carotenoid protein in the presence of copper ion.  Phytosynth Res 135, 143-7

  • McClerklin S*, Lee SG*, Harper CP, Nwumeh R, Jez JM, Kunkel BN (2018) Indole-3-acetaldehyde dehydrogenase-dependent auxin synthesis contributes to virulence of Pseudomonas syringae strain DC3000.  PLoS Pathogens 14, e1006811  (*equal contribution)

  • Kunkel BN, Harper CP (2018) The roles of auxin during interactions between bacterial plant pathogens and their hosts.  J Exp Bot 69, 245-254

  • Frick EM, Strader LC (2018) Roles for IBA-derived auxin in plant development.  J Exp Bot 69, 169-77

  • Frick EM, Strader LC (2018) Kinase MPK17 and peroxisome division factor PMD1 influence salt-induced peroxisome proliferation.  Plant Physiol 176, 340-51

  • Qi Y, D'Alessandro JM, Blodgett JAV (2018) Draft genome sequence of Streptomyces sp. strain JV178, a producer of clifednamide-type polycyclic tetramate macrolactams.  Genome Announc.  6, e01401-17

  • Hwang SG, Lee CY, Tseng CS (2018) Heterologous expression of rice 9-cis-epoxycarotenoid dioxygenase 4 (OsNCED4) in Arabidopsis confers sugar oversensitivity and drought tolerance.  Bot Studies 59: 2

  • Guillory WX, Onyshchenko A, Ruck EC, Parks M, Nakov T, Wickett NJ, Alverson AJ (2018) Recurrent loss, horizontal transfer, and the obscure origins of mitochondrial introns in diatoms (Bacillariophyta).  Genome Biol Evol 10, 1504-1515

  • Cho S*, Yu SI*, Park J, Mao Y, Zhu JK, Yun DJ, Lee BH (2017) Accession-dependent CBF gene deletion by CRISPR/Cas system in Arabidopsis.  Front Plant Sci 8, 1910 (*equal contribution)

  • Hays SG, Yan LL, Silver PA, Ducat DC (2017) Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction.  J Biol Engr 11, 4

  • Kroll K*, Holland CK*, Starks CM, Jez JM (2017) Evolution of allosteric regulation in chorismate mutases from early plants.  Biochem J 474, 3705-17 (*equal contribution)

  • Simms CL, Yan LL, Zaher HS (2017) Ribosome collision is critical for quality control during no-go decay.  Mol Cell 68, 361-73

  • Majumder EL, Wolf BM, Liu H, Berg RH, Timlin JA, Chen M, Blankenship RE (2017) Subcellular pigment distribution is altered under far-red light acclimation in cyanobacteria that contrain chlorophyll f.  Photosynth Res 134, 183-92

  • Murton J, Nagarajan A, Nguyen AY, Liberton M, Hancock HA, Pakrasi HB, Timlin JA (2017) Population-level coordination of pigment response in individual cyanobacterial cells under altered nitrogen conditions. Photosynth Res 134, 165-74

  • Bao Z, Clancy MA, Carvalho RF, Elliott K, Folta KM (2017) Identification of novel growth regulators in plant populations expressing random peptides.  Plant Physiol 175, 619-27

  • Phillips AZ, Berry JC, Wilson MC, Vijayaraghaven A, Burke J, Bunn JI, Allen TW, Wheeler T, Bart R (2017) Genomics-enababled analysis of the emergent disease cotton bacterial blight.  PLoS Genetics 13, e1007003

  • Enders TAFrick EM, Strader LC (2017) An Arabidopsis kinase cascade influences auxin-responsive cell expansion.  Plant J 92, 68-81

  • Schenck CA*, Holland CK*Schneider MR, Men Y, Lee SG, Jez JM, Maeda HA (2017) Molecular basis of the evolution of alternative tyrosine biosynthesis pathways in plants.  Nature Chem Biol 13, 1029-35 (*equal contribution)

  • Vincent TR, Avramova M, Canham J, Higgins P, Bilkey N, Mugford ST, Pitino M, Toyota M, Gilroy S, Miller TJ, Hogenhout S, Sanders D (2017) Interplay of plasma membrane and vacuolar ion channels, together with BAK1, elicits rapid cytosolic calcium elevations in Arabidopsis during aphid feeding.  Plant Cell 29, 1460-79

  • Hamilton ES, Haswell ES (2017) The tension-sensitive ion transport activity of MSL8 is critical for its function in pollen hydration and germination.  Plant Cell Physiol 58, 1222-37

  • Immethun CM, DeLorenzo DM, Focht CM, Gupta D, Johnson CB, Moon TS  (2017) Physical, chemical, and metabolic state sensors expand the synthetic biology toolbox for Synechocystis sp. PCC 6803.  Biotechnol Bioeng 114, 1561-9

  • Diani-Moore S, Shoots J, Singh R, Zuk JB, Rifkind AB (2017) NAD+ loss, a new player in AhR biology: prevention of thymus atrophy and hepatosteatosis by NAD+ repletion.  Sci Rep 7, 2268

  • Willbur JF, Ding S, Marks ME, Lucas H, Grau CR, Groves CL, Kabbage M, Smith DL (2017) Comprehensive Sclerotinia stem rot screening of soybean germplasm requires multiple isolates of Sclerotinia sclerotiorumPlant Disease 101, 344-53

  • Guzman MS, McGinley B, Santiago-Merced N, Gupta D, Bose A (2017) Draft genome sequences of three closely related isolates of the purple nonsulfur bacterium Rhodovulum sulfidophilum.  Genome Announc 5, e00029-17

  • Aanderud ZT, Schoolmaster DR, Rigby D, Bybee J, Campbell TRoundy BA (2017) Soils mediate the impact of fine woody debris on invasive and native grasses as whole trees are mechanically shredded into firebreaks in piñon-juniper woodlands.  J Arid Environ  137, 60-8

  • Chairs M, Gupta D, Joshee N, Cooper KK, Basu C (2017) RNA-seq analysis of the salt stress-induced transcripts in fast-growing bioenergy tree, Paulownia elongataPlant Environ Interact 12, 128-36

  • Souza CA, Li S, Lin AZ, Boutrot F, Grossman G, Zipfel C, Somerville SC (2017) Cellulose-derived oligomers act as damage-associated molecular patterns and trigger defense-like responses.  Plant Physiol 173, 2383-98

  • Augustin MM, Shukla AK, Starks CM, O'Neil-Johnson M, Han L, Holland CK, Kutchan TM (2017) Biosynthesis of Veratrum californicum specialty chemicals in Camelina sativa seed.  Plant Biotech Rep 11, 29-41

  • Nguyen AY, Bricker WP, Zhang H, Weisz DA, Gross ML, Pakrasi HB (2017) The proteolysis adaptor, NblA, binds to the N-terminus of beta-phycocyanin: implications for the mechanism of phycobilisome degradation.  Photosynth Res 132, 95-106

  • Mendez DL, Babbitt SE, King JD, D'Alessandro J, Watson MB, Blankenship RE, Mirica TM, Kranz RG (2017) Engineered holocytochrome c synthases that biosynthesize new cytochromes c.  Proc Natl Acad Sci USA 114, 2235-40

  • Simms CL, Thomas EN, Zaher HS (2017) Ribosome-based quality control of mRNA and nascent peptides.  Wiley Interdiscip Rev RNA 8, e1366

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