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Steven Clarke Lab Publications - 2012 - Present

305. Yamamoto, J., Inubushi, S., Han, Q., Tashiro, Y., Sugisawa, N., Hamada, K., Aoki, Y., Miyake, K., Matsuyama, R., Bouvet. M., Clarke, S. G., Endo, I., Hoffman, R. M. (2022) "Linkage of methionine addiction, histone lysine hypermethylation, and malignancy" iScience 25, 104162. DOI: 10.1016/j.isci.2022.104162.  

 

304. Clarke, S. G. ""Guido Guidotti (1933 - 2021) Remembering a biochemist’s biochemist."" ASBMB Today, Mar. 2022, pp.9-12. 

 

303. Yamamoto, J., Aoki, Y., Inubushi, S., Han, Q., Hamada, K., Tashiro, Y., Miyake, K., Matsuyama, R., Bouvet, M., Clarke, S. G., Endo, I., and Hoffman, R. M. (2022) "Extent and Instability of Trimethylation of Histone H3 Lysine Increases with Degree of Malignancy and Methionine Addiction" Cancer Genomics Proteomics 19, 12-18. DOI: 10.21873/cgp.20299.  

 

302. Gladyshev, V. N., Kritchevsky, S. B., Clarke, S. G., Cuervo, A. M., Fiehn, O., de Magalhaes, J. P., Mau, T., Maes, M., Moritz, R., Niedernhofer, L. J., Van Schaftingen, E., Tranah, G. J., Walsh, K., Yura, Y., Zhang, B., and Cummings, S. R. (2021) "Molecular Damage in Aging" Nature Aging 1, 1096-1106. DOI: 10.1038/s43587-021-00150-3.  

 

301. Ayer, A., Fazakerley D. J., Suarna, C., Maghzal, G. J., Sheipouri, D., Lee, K. J., Bradley, M. C., Fernández-del-Rio, L., Tumanov, S., Kong, S. M. Y., van der Veen, J. N., Yang, A., Ho, J. W. K., Clarke, S. G., James, D. E., Dawes. I. W., Vance, D. E., Clarke, C. F., Jacobs, R. L., and Stocker, R. (2021) "Genetic screening reveals phospholipid metabolism as a key regulator of the biosynthesis of the redox-active lipid coenzyme Q" Redox Biol. 46, 102127. DOI: 10.1016/j.redox.2021.102127.  

 

300. Soliman, R., Cordero-Maldonado, M. L., Martins, T. G., Moein, M., Conrotte, J.-F., Warmack, R.A., Skupin, A., Crawford, A. D., Clarke, S.G., and Linster, C.L. (2021) "L-Isoaspartyl methyltransferase deficiency in zebrafish leads to 1 impaired calcium signaling in the brain" Front. Genet. 11, 612343. DOI: 10.3389/fgene.2020.612343.  

 

299. Dennis, T. N., Kang, A. S., Lowenson, J. D., Kenjic, N., Kirkwood, J. S., Clarke, S. G., and Perry J. (2020) "Human ARM1 structure and substrate specificity indicates that it is a DUF89 family damage-control phosphatase" J. Struct. Biol. 212, 107576. DOI: 10.1016/j.jsb.2020.107576.  

 

298. White, J. T., Cato, T., Deramchi, N., Gabunilas, J., Roy, K. R., Wang, C., Chanfreau, G. F., and Clarke, S. G. (2019) "Protein methylation and translation: Role of lysine modification on the function of yeast elongation factor 1A" Biochemistry 58, 4997-5010. PMCID: PMC6913935. 

 

297. Warmack, R. A., Shawa, H., Liu, K., Lopez, K., Loo, J., Horwitz, J., and Clarke, S. G. (2019) "The L-isoaspartate modification within protein fragments in the aging lens can promote protein aggregation" J. Biol. Chem. 294, 12210-12219. PMCID: PMC6690693. 

 

296. Warmack, R. A., Boyer, D. R., Zee, C.-T., Richards, L. S., Sawaya, M. R., Cascio, D., Gonen, T., Eisenberg, D. S., and Clarke, S. G. (2019) "Structure of amyloid-β (20-34) with Alzheimer’s-associated isomerization at Asp23 reveals a distinct protofilament interface" Nature Commun. 10:3357. DOI: 10.1038/s41467-019-11183-z. PMCID: PMC6659688.

 

295. Jain, K., and Clarke, S. G. (2019) "PRMT7 as a unique member of the protein arginine methyltransferase family: A review" Arch. Biochem. Biophys. 665, 36-45. PMCID: PMC6461449.

 

294. Yang, M.-L., Doyle, H. A., Clarke, S. G., Herold, K. C., and Mamula, M. J. (2018) "Oxidative Modifications in Tissue Pathology and Autoimmune Disease" Antioxidants Redox Signaling 29, 1415-1431.  PMCID: PMC6166690.

 

293. Clarke, S. G. (2018) "Retrospective: Paul D. Boyer (1918-2018)" ASBMB Today, August 2018 issue, pages 8-10.

 

292. Clarke, S. G. (2018) "The Ribosome: A Hot Spot for the Identification of New Types of Protein Methyltransferases" J Biol. Chem. 293, 10438-10446.  PMCID: PMC6036201.

291. Roher, A. E., Kokjohn, T. A., Clarke, S. G., Sierks, M. R., Maarouf, C. L., Serrano, G. E., Sabbagh, M. S., and Beach, T. G. (2017) "APP/Aβ Structural Diversity and Alzheimer’s Disease Pathogenesis" Neurochemistry International, 110, 1-13. PMCID: PMC5688956.

290. Jain, K., Jin, C.Y., and Clarke, S.G. (2017) "Epigenetic control via allosteric regulation of mammalian protein arginine methyltransferases." Proc. Natl. Acad. Sci. U. S. A. 114, 10101-10106. PMCID: 5617285.

289. Hadjikyriacou, A. and Clarke, S. G. (2017) "Caenorhabditis elegans PRMT-7 and PRMT-9 Are Evolutionarily Conserved Protein Arginine Methyltransferases with Distinct Substrate Specificities" Biochemistry. 56, 2612-2626. PMCID: 5503151.

288. Kafkova, L., Debler, E.W., Fisk, J.C., Jain, K., Clarke, S.G., and Read, L.K.(2016) "The Major Protein Arginine Methyltransferase in Trypanosoma brucei Functions as an Enzyme-Prozyme Complex" J. Biol. Chem. 292, 2089-2100. PMCID: 5313084.

287. Caslavka Zemple, K. E., Vashisht, A. A., Barshop, W. D., Wohlschlegel, J. A., and Clarke, S. G. (2016) "Determining the Mitochondrial Methylome in Saccharomyces cerevisiae using Heavy Methyl SILAC" J. Proteome Res. 15, 4436-4451. PMCID: 5148652.

286. Lowenson, J. D., Shmanai, V. V., Shklyaruck, D., Clarke, S. G., and Shchepinov, M. S. (2016) "Deuteration can protect an asparagine residues from racemization" Amino Acids 48, 2179-2188. PMCID: PMC4990494.

285. Jain, K., Warmack, R. A., Debler, E. W., Hadjikyriacou, A., Stavropoulos, P., and Clarke, S. G. (2016) "Protein arginine methyltransferase product specificity is mediated by distinct active-site architectures" J. Biol. Chem. 291, 18299-18308. PMCID: PMC5000077.

284. Warmack, R. A., Mansilla, E., Goya, R. G., and Clarke, S. G. (2016) "Racemized and Isomerized Proteins in Aging Rat Teeth and Eye Lens" Rejuvenation Res. 19, 309-317. PMCID: PMC4971426.

283. Sherkhanov, S., Korman, T. P., Clarke, S. G., and Bowie, J. U. (2016) "Production of FAME biodiesel in E. coli by direct methylation with an insect enzyme" Sci. Rep. 6:24239. DOI: 10.1038/srep24239. PMCID: PMC4823748.

282. Al-Hadid, Q., Roy, K., Chanfreau, G., and Clarke, S. G. (2016) "Methylation of Yeast Ribosomal Protein Rpl3 Promotes Translational Elongation Fidelity" RNA 22, 489-499. PMCID: PMC4793205.

281. Debler, E. W., Jain, K., Warmack, R. A., Feng, Y., Clarke, S. G., Blobel, G., and Stavropolousa, P. (2016) "A Glutamate/Aspartate Switch Controls Product Specificity in a Protein Arginine Methyltransferase" Proc. Natl. Acad. Sci. U. S. A. 113, 2068-2073. PMCID: PMC4776506.

280. Al-Hadid, Q., White, J., and Clarke, S. (2016) "Ribosomal Protein Methyltransferases in the Yeast Saccharomyces cerevisiae: Roles in Ribosome Biogenesis and Translation" Biochem. Biophys. Res. Commun. 470, 552-557. PMCID: PMC4750496.

279. Fu, X., Chin, R. M., Vergenes, L., Hwang H., Deng, G., Xing, Y., Pai, M. Y., Li, S., Ta, L., Fazlollahi, F., Chen, C., Prins, R. M., Teitell, M. A., Nathanson, D. A., Lai, A., Faull, K. F., Jiang, M., Clarke, S. G., Cloughesy, T. F., Graeber, T. G., Brass, D., Cristofk, H. R., Jung, M. E., Reue, K., and Huang, J. (2015) "2-Hydroxyglutarate Inhibits ATP Synthase and mTOR Signaling" Cell Metabolism,  22,508-515. PMCID: PMC4663076.

278. Hadjikyriacou, A., Yang, Y., Espejo, A., Bedford, M.T., and Clarke, S.G. (2015) "Unique Features of Human Protein Arginine Methyltransferase 9 (PRMT9) and its Substrate RNA Splicing Factor SF3B2" Journal of Biological Chemistry, E pub.

277. Yang, Y., Hadjikyriacou, A., Xia, Z., Gayatri, S., Kim, D., Zurita-Lopez, C., Kelly, R., Guo, A., Li, W., Clarke, S.G., and Bedford, M.T. (2015) "PRMT9 is a Type II methyltransferase that methylates the splicing factor SAP145" Nature Communications,  6:6428.

276. Patananan, A.N., Budenholzer, L.M., Pedraza, M.E., Torres, E.R., Adler, L.N., and Clarke, S.G. (2015) "The invertebrate Caenorhabditis elegans biosynthesizes ascorbate" Archives of Biochemistry and Biophysics. DOI: 10.1016/j.abb.2015.02.002.

275. Patananan, A.N., Budenholzer, L.M., Eskin, A., Torres, E.R., and Clarke, S.G. (2015) "Ethanol-induced differential gene expression and acetyl-CoA metabolism in a longevity model of the nematode Caenorhabditis elegans" Experimental Gerontology, 61, 20-30.

274. Dzialo, M.C., Travaglini, K.J., Shen, S., Loo, J.A., and Clarke, S.G. (2014) "A new type of protein lysine methyltransferase trimethylates Lys-79 of elongation factor 1A" Biochemical and Biophysical Research Communications, 455, 382-389.

273. Dzialo, M.C., Travaglini, K.J., Shen, S., Roy, K., Chanfreau, G.F., Loo, J.A., and Clarke, S.G. (2014) "Translational Roles of Elongation Factor 2 Protein Lysine Methylation" Journal of Biological Chemistry, 289, 30511-30524.

272. Feng, Y., Hadjikyriacou, A., and Clarke, S.G. (2014) "Substrate specificity of human protein arginine methyltransferase 7 (PRMT7): the importance of acidic residues in the double E loop" Journal of Biological Chemistry, 289, 32604-32616.

271. Al-Hadid, Q., Roy, K., Munroe, W., Dzialo, M.C., Chanfreau, G.F., and Clarke, S.G. (2014) "Histidine Methylation of Yeast Ribosomal Protein Rpl3p is Required for Proper 60S Subunit Assembly" Molecular and Cellular Biology, 34, 2903-2916.

270. Patananan, A.N., Capri, J., Whitelegge, J.P., and Clarke, S.G. (2014) "Non-Repair Pathways for Minimizing Protein Isoaspartyl Damage in the Yeast Saccharomyces cerevisiae" Journal of Biological Chemistry, 289, 16936-16953.

269. Feng, Y., Maity, R., Whitelegge, J.P., Hadjikyriacou, A., Li, Z., Zurita-Lopez, C., Al-Hadid, Q., Clark, A.T., Bedford, M.T., Masson, J.Y., and Clarke, S.G. (2013) "Mammalian protein arginine methyltransferase 7 (PRMT7) specifically targets RXR sites in lysine- and arginine-rich regions" Journal of Biological Chemistry, 288, 37010-25.

268. Lissina, E., Weiss, D., Young, B., Rella, A., Cheung-Ong, K., Del Poeta, M., Clarke, S. G., Giaever, G., and Nislow, C. (2013) "A Novel Small Molecule Methyltransferase is Important for Virulence in Candida albicans" ACS Chem. Biol. 8, 2785-2793. PMCID: PMC3928151.

267. Shen-Miller, J., Linder, P., Xie, Y., Villa, S., Wooding, K., Clarke, S.G., Loo, R.R.O, and Loo, J.A. (2013) "Thermal-Stable Proteins of Fruit of Long-Lived Sacred Lotus Nelumbo nucifera Gaertn var China Antique" Tropical Plant Biology, 6, 69-84.

266. Yang, H., Lowenson, J.D., Clarke, S., and Zubarev, R.A. (2013) "Brain Proteomics Supports the Role of Glutamate Metabolism and Suggests Other Metabolic Alterations in Protein L-Isoaspartyl Methyltransferase (PIMT)-Knockout Mice" J. Proteome Research, 12, 4566-4576.

265. Nayak, N.R., Putnam, A.A., Addepalli, B., Lowenson, J.D., Chen, T., Jankowsky, E., Perry, S.E., Dinkins, R.D., Limbach, P.A., Clarke, S.G., and Downie, A.B. (2013) "An Arabidopsis ATP-Dependent, DEAD-Box RNA Helicase Loses Activity Upon IsoAsp Formation but Is Restored by Protein Isoaspartyl Methyltransferase" Plant Cell, 25, 2573-2586.

264. MacKay, K. B., Tu., Y., Young, S. G., and Clarke, S. G. (2013) "Circumventing Embryonic Lethality with Lcmt1 Deficiency: Generation of Hypomorphic Lcmt1 Mice with Reduced Protein Phosphatase 2A Methyltransferase Expression and Defects in Insulin Signaling" PLos One, 8, 1-11.

263. Patananan, A. N., Palmer, J. M., Garvey, G. S., Keller, N. P., and Clarke, S. G. (2013) "A Novel Automethylation Reaction in the Aspergillus nidulans LaeA Protein Generates S-Methylmethionine" J. Biol. Chem. 288, 20, 14032-14045.

262. Clarke, S. G. (2013) "Protein Methylation at the Surface and Buried Deep: Thinking Outside the Histone Box" Trends in Biochemical Sciences, May 2013, 38, 5, 243-252.

261. Dai, S., Ni, W., Patananan, A. N., Clarke, S. G., Karger, B. L., and Zhou, Z. S. (2013) "Integrated Proteomic Analysis of Major Isoaspartyl-Containing Proteins in the Urine of Wild Type and Protein L-Isoaspartate O-Methyltransferase-Deficient Mice" Analytical Chemistry 2013, 85, 2423-2430.

260. Dhar, S., Vemulapalli, V., Patananan, A. N., Huang, G. L., Di Lorenzo, A., Richard, S., Comb, M. J., Guo, A., Clarke, S. G., and Bedford, M. T. (2013) "Loss of the major Type I arginine methyltransferase PRMT1 causes substrate scavenging by other PRMTs" Scientific Reports, 3:3011, 1-6.

259. Yang, M-L., Gee, A. J. P., Gee, R. J., Zurita-Lopez, C. I., Khare, S., Clarke, S. G., and Mamula, M. J. (2013) "Lupus Autoimmunity Altered by Cellular Methylation Metabolism" Autoimmunity, 46(1), 21-31.

258. Patananan, A. N., and Clarke, S. G. (2013) "Isoaspartyl Dipeptidase (IadA)" In Handbook of Proteolytic Enzymes, Vol. 1, Ed. Rawlings, N. D., and Salvesen, G. S., Oxford: Academic Press, 1654-1663.

257. Urzica, E. I., Casero, D., Yamasaki, H., Hsieh, S., Adler, L. N., Karpowicz, S. J., Blaby-Haas, C. E., Clarke, S. G., Loo, J. A., Pellegrini, M., and Merchant, S. M. (2012) "Systems and Trans-System Level Analysis Identifies Conserved Iron Defciency Responses in the Plant Lineage" The Plant Cell 24, 3921-3948.

256. MacKay, K., Lowenson, J. D., and Clarke, S. G. (2012) "Wortmannin Reduces Insulin Signaling and Death in Seizure-Prone Pcmt1-/- Mice" PLOS One, 7, 1-14.

255. Young, B. D., Weiss, D. I., Zurita-Lopez, C. I., Webb, K. J., Clarke, S., G., and McBride, A. E. (2012) "Identification of Methylated Proteins in the Yeast Small Ribosomal Subunit: A Role for SPOUT Methyltransferases in Protein Arginine Methylation" Biochemistry 51, 5091-5104.

254. Urzica, E. I., Adler, L. N., Page, M. D., Linster, C., Arbing, M. A., Casero, D., Pellegrini, M., Merchant, S. S., and Clarke, S. G. (2012) "Impact of Oxidative Stress on Ascorbate Biosynthesis in Chlamydomonas via Regulation of the VTC2 Gene Encoding a GDP-L-galactose Phosphorylase" J. Biol. Chem. 287, 17, 14234-14245.

253. Zurita-Lopez, C. I., Sandberg, T., Kelly, R., and Clarke, S.G. (2012) "Human Protein Arginine Methyltransferase 7 (PRMT7) Is a Type III Enzyme Forming ω -NG-Monomethylated Arginine Residues" J. Biol. Chem. 287, 11, 7859-7870.

252. Castro, P. V., Khare, S., Young, B. D., and Clarke, S. G. (2012) "Caenorhabditis elegans Battling Starvation Stress: Low Levels of Ethanol Prolong Lifespan in L1 Larvae" PLos One, 7, 1-12.