Publications

2020

CueR activates transcription through a DNA distortion mechanism
Fang C
.*, Philips S.J.*, Wu X, Chen K, Shi J, Shen L, Xu J, Feng Y.** , Thomas V. O’Halloran .** , Zhang Y.**

(2020) Nature Chemical Biology

Bio-Art report: link

CEMPS report: link

CAS report: link

Structural basis for transcription inhibition by E. coli SspA

Wang F.*, Shi J.*, He D.*, Tong B, Zhang C, Wen A, Zhang Y.** , Feng Y.** , Lin W.** .

(2020) Nucleic Acids Research, 48(17):9931-9942

Accumulation of the RNA polymerase subunit RpoB depends on RNA editing by OsPPR16 and affects chloroplast development during early leaf development in rice
Huang W, Zhang Y, Shen L, Fang Q, Liu Q, Gong C, Zhang C, Zhou Y, Mao C, Zhu Y, Zhang J, Chen H, Zhang Y, Lin Y, Ralph Bock, Zhou F.**
(2020) New Phytologist

 

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription

Li L.*, Molodstov V.*, Lin W, Ebright R.H.**,  Zhang Y.**

(2020) PNAS.

Bioart plant: link

Media report: CAS; SIPPE

2019

Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a “bond rotation” catalytic mechanism."

Zhuang N.*, Zhang H.*, Li L, Wu X, Yang C .** ,  Zhang Y .**

(2019) Journal of Biological Chemistry , 295, 7: 2113-2124.

Crl activates transcription by stabilizing active conformation of the master stress transcription initiation factor

Xu J .*, Cui K .*, Shen L, Shi J, Li L, You L, Fang C, Zhao G.** , Feng Y .** , Yang B.** ,  Zhang Y.**

 (2019) eLife , 8, e50928.

Media report: CAS; SIPPE

 

Tropane alkaloids biosynthesis involves an unusual type III polyketide synthase and non-enzymatic condensation

Huang J.*, Fang C.*, Ma X.*, Wang L, Yang J, Luo J, Yan Y,  Zhang Y .** ,Huang S.**

(2019) Nature communications, 10(1): 4036.

Media report: CAS; SIPPE

Structural basis of σ appropriation 
Shi J.*, Wen A., Zhao M.,You L.,Zhang Y.,Feng Y.**

(2019) Nucleic Acids Research, 47(17):9423-9432

 

Structural basis of Q-dependent transcription antitermination
Shi J.*,Gao X.*,Tian T.,Yu Z.,Gao B.,Wen A.,You L.,Chang S., Zhang X.,Zhang Y.,& Feng Y.**

(2019) Nature Communications 10(1):2925

 

Structural basis for transcription antitermination at bacterial intrinsic terminator

You L.*, Shi J., Shen L., Li L., Fang C., Yu C., Cheng W., Feng Y.**, Zhang Y.**

(2019) Nature Communications 10(1): 3048.

Bioart Report: link

F1000Prime: link

Structures and mechanism of transcription initiation by bacterial ECF factors

Fang C.*, Li L.*, Shen L.,Shi J.,Wang S **,Feng Y.**, Zhang Y.**

(2019)Nucleic Acids Research

 

Structural basis for transcription initiation by bacterial ECF σ factors

Li L.*, Fang C.*, Zhuang N., Wang T., Zhang Y.**

(2019) Nature Communications 10(1) :1153

Bioart Report: link

2018

Structural insights into the unique mechanism of transcription activation by Caulobacter crescentus GcrA.

Wu X.*, Haakonsen D.L.*, Sanderlin A.G., Liu Y.J., Shen L., Zhuang N., Laub M.T.**, Zhang Y.**

(2018) Nucleic Acids Research, 46 (6), 3245–3256, 

 

CapZyme-Seq Comprehensively Defines Promoter-Sequence Determinants for RNA 5′ Capping with NAD+.

Vvedenskaya I.O.*, Bird J.G.*, Zhang Y.*, Zhang Y., Jiao X., Barvík I., Krásný L., Kiledjian M., Taylor D.M., Ebright R.H.**, Nickels B.E.**

(2018)  Molecular Cell. 70(3): 553-564

2017

2017

Cyclic AMP inhibits the activity and promotes the acetylation of acetyl-CoA synthetase through competitive binding to the ATP/AMP pocket.

Han X.*, Shen L.*, Wang Q., Cen X., Wang J., Wu M., Li P., Zhao W.**, Zhang Y.**, Zhao G.**

(2017) Journal of Biological Chemistry, 292(4), 1374-1384.

Antibacterial nucleoside-analog inhibitor of bacterial RNA polymerase. 

Maffioli, S.I.*, Zhang, Y.*, Degen, D., Carzaniga, T., Del Gatto, G., Serina, S., Monciardini, P., Mazzetti, C., Guglierame, P., Candiani, G., Chiriac, A.I.,  Facchetti G., Kaltofen P., Sahl H., Dehò G., Donadio S.**, Ebright R.H.**

(2017) Cell, 169(7), pp.1240-1248.

 

Structural basis of Mycobacterium tuberculosis transcription and transcription inhibition

Lin W.*, Mandal S.*, Degen D., Liu Y, Ebright Y.W., Li S., Feng Y., Zhang Y., Mandal S., Jiang Y., Liu S., Gigliotti M., Talaue M., Connell N., Das K., Arnold E., Ebright R.H.**

(2017) Molecular Cell, 66(2), 169-179.​

2016

The mechanism of RNA 5' capping with NAD+, NADH, and desphospho-CoA. 

Bird J.G.*, Zhang Y.*, Tian Y., Panova N., Barvík I., Greene L., Liu M., Buckley B., Krásný L., Lee J.K., Kaplan C.D., Ebright R.H.**,  Nickels B.E.**

(2016) Nature, 535(7612): 444-447.

 

Multiplexed protein-DNA cross-linking: Scrunching in transcription start site selection.

Winkelman J.T.*, Vvedenskaya I.O.*, Zhang Y.*, Zhang Y*, Bird J.G., Taylor D.M., Gourse R.L., Ebright R.H.**, Nickels B.E.** 

(2016) Science, 351(6277):1090-1093

Structural basis of transcription activation

Feng Y., Zhang Y., Ebright R.H.**

(2016) Science, 252 (6291):1330-1333

 

2014

Interactions between RNA polymerase and the “core recognition element” counteract pausing

Vvedenskaya I.O.*, Vahedian-Movahed H.*, Bird J.G.*, Knoblauch J.G., Goldman S.R., Zhang Y., Ebright R.H.**, Nickels B.E.**

(2014) Science, 344 (6189), 1285-1289

 

Transcription inhibition by the depsipeptide antibiotic salinamide A

Degen D.*, Feng Y.*, Zhang Y., Ebright K.Y., Ebright Y.W., Gigliotti M., Vahedian-Movahed H., Mandal S., Talaue M., Connell N., Arnold E., Fenical W., Ebright R.H.**

(2014) eLife, 3, e02451

 

GE23077 binds to the RNA polymerase ‘i’and ‘i+ 1’sites and prevents the binding of initiating nucleotides

Zhang Y.*, Degen D.*, Ho M.H.*, Sineva E., Ebright K.Y., Ebright Y.W., Mekler V., Vahedian-Movahed H., Feng Y., Yin R., Tuske S., Irschik H., Jansen R., Maffioli S., Donadio S., Arnold E.**, Ebright R.H.**

(2014) eLife, 3, e02450

2015

Structural basis of transcription inhibition by CBR hydroxamidines and CBR pyrazoles

Feng Y., Degen D., Wang X., Gigliotti M., Liu S., Zhang Y., Das D., Michalchuk T., Ebright Y.W., Talaue M., Connell N., Ebright R.H.**

(2015) Structure, 23 (8), 1470-1481

2012

Structural basis of transcription initiation

Zhang Y., Feng F., Chatterjee S., Tuske S., Ho M.X., Arnold E., Ebright R.H.**

(2012) Science, 338 (6110), 1076-1080

 

(+)-Rutamarin as a dual inducer of both GLUT4 translocation and expression efficiently ameliorates glucose homeostasis in insulin-resistant mice

Zhang Y.*, Zhang H.*, Yao X.*, Shen H., Chen J., Li C.,  Chen L., Zheng M., Ye J., Hu L.**, Shen X.**, Jiang H.**

(2012) Plos One, 7 (2), e31811

before 2012

Danshen extract 15, 16-dihydrotanshinone I functions as a potential modulator against metabolic syndrome through multi-target pathways

Liu Q.*, Zhang Y.*, Lin Z., Shen H., Chen L., Hu L.**, Jiang H.**, Shen X.**

(2010) The Journal of steroid biochemistry and molecular biology, 120 (4), 155-163

 

Novel thiophene derivatives as PTP1B inhibitors with selectivity and cellular activity

Ye D.*, Zhang Y.*, Wang F., Zheng M., Zhang X., Luo X., Shen X.**, Jiang H.**, Liu H.**

(2010) Bioorganic & medicinal chemistry. 18 (5), 1773-1782

 

A sesquiterpene quinone, dysidine, from the sponge Dysidea villosa, activates the insulin pathway through inhibition of PTPases

Zhang Y., Li Y., Guo Y., Jiang H., Shen X**.

(2009)  Acta Pharmacologica Sinica, 30 (3), 333-345

The Zhang Lab

| CAS Key Laboratory of Synthetic Biology | CAS Center for Excellence in Molecular Plant Sciences |

 

300 Fenglin Rd. Shanghai, China​​