U.S. Department of Health and Human Services

Laboratory of Molecular Biology

Susan K. Buchanan, Ph.D., Chief

​Publications

A selection of recent and significant publications can be viewed below.

Publications
Gorrepati L, Krause MW, Chen W, Brodigan TM, Correa-Mendez M, Eisenmann DM. Identification of Wnt Pathway Target Genes Regulating the Division and Differentiation of Larval Seam Cells and Vulval Precursor Cells in Caenorhabditis elegans. G3 (Bethesda). 2015 Jun 5; (2015 Jun 5). [Full Text/Abstract]
Liu Z, Shi H, Szymczak LC, Aydin T, Yun S, Constas K, Schaeffer A, Ranjan S, Kubba S, Alam E, McMahon DE, He J, Shwartz N, Tian C, Plavskin Y, Lindy A, Dad NA, Sheth S, Amin NM, Zimmerman S, Liu D, Schwarz EM, Smith H, Krause MW, Liu J. Promotion of bone morphogenetic protein signaling by tetraspanins and glycosphingolipids. PLoS Genet. 2015 May; 11 (2015 May; 5; 11):e1005221. [Full Text/Abstract]
Paix A, Wang Y, Smith HE, Lee CY, Calidas D, Lu T, Smith J, Schmidt H, Krause MW, Seydoux G. Scalable and Versatile Genome Editing Using Linear DNAs with Micro-Homology to Cas9 Sites in Caenorhabditis elegans. Genetics. 2014 Sep 23; 198 (2014 Sep 23; 4; 198):1347-56. [Full Text/Abstract]
Vecchiarelli AG, Li M, Mizuuchi M, Mizuuchi K. Differential affinities of MinD and MinE to anionic phospholipid influence Min Patterning dynamics in vitro. Mol Microbiol. 2014 Aug; 93 (93; 2014 Aug; 3):453-63. [Full Text/Abstract]
Noinaj N, Buchanan SK. Structural insights into the transport of small molecules across membranes. Curr Opin Struct Biol. 2014 Mar 26; 27 (2014 Mar 26; 27):8-15. [Full Text/Abstract]
Zhang T, Ye Y. The final moments of misfolded proteins en route to the proteasome. DNA Cell Biol. 2014 Aug; 33 (8; 33; 2014 Aug):477-83. [Full Text/Abstract]
Hickman AB, Ewis HE, Li X, Knapp JA, Laver T, Doss AL, Tolun G, Steven AC, Grishaev A, Bax A, Atkinson PW, Craig NL, Dyda F. Structural basis of hAT transposon end recognition by Hermes, an octameric DNA transposase from Musca domestica. Cell. 2014 Jul 17; 158 (2014 Jul 17; 2; 158):353-367. [Full Text/Abstract]
Noinaj N, Kuszak AJ, Balusek C, Gumbart JC, Buchanan SK. Lateral opening and exit pore formation are required for BamA function. Structure. 2014 Jul 8; 22 (7; 2014 Jul 8; 22):1055-62. [Full Text/Abstract]
Noinaj N, Buchanan SK. FhaC takes a bow to FHA in the two-partner do-si-do. Mol Microbiol. 2014 Jun; 92 (6; 92; 2014 Jun):1155-8. [Full Text/Abstract]
Jackson BM, Abete-Luzi P, Krause MW, Eisenmann DM. Use of an Activated Beta-Catenin to Identify Wnt Pathway Target Genes in Caenorhabditis elegans, Including a Subset of Collagen Genes Expressed in Late Larval Development. G3 (Bethesda). 2014 Apr 16; 4 (2014 Apr 16; 4):733-47. [Full Text/Abstract]
Christianson JC, Ye Y. Cleaning up in the endoplasmic reticulum: ubiquitin in charge. Nat Struct Mol Biol. 2014 Apr; 21 (4; 21; 2014 Apr):325-35. [Full Text/Abstract]
Yan L, Liu W, Zhang H, Liu C, Shang Y, Ye Y, Zhang X, Li W. Ube2g2-gp78-mediated HERP polyubiquitylation is involved in ER stress recovery. J Cell Sci. 2014 Apr 1; 127 (127; Pt 7; 2014 Apr 1):1417-27. [Full Text/Abstract]
Vecchiarelli AG, Neuman KC, Mizuuchi K. A propagating ATPase gradient drives transport of surface-confined cellular cargo. Proc Natl Acad Sci U S A. 2014 Apr 1; 111 (2014 Apr 1; 111; 13):4880-5. [Full Text/Abstract]
Huang CH, Chu YR, Ye Y, Chen X. Role of HERP and a HERP-related protein in HRD1-dependent protein degradation at the endoplasmic reticulum. J Biol Chem. 2014 Feb 14; 289 (2014 Feb 14; 7; 289):4444-54. [Full Text/Abstract]
Lee JG, Kim W, Gygi S, Ye Y. Characterization of the deubiquitinating activity of USP19 and its role in endoplasmic reticulum-associated degradation. J Biol Chem. 2014 Feb 7; 289 (6; 289; 2014 Feb 7):3510-7. [Full Text/Abstract]
Zhuang X, Semenova E, Maric D, Craigie R. Dephosphorylation of barrier-to-autointegration factor by protein phosphatase 4 and its role in cell mitosis. J Biol Chem. 2014 Jan 10; 289 (2014 Jan 10; 2; 289):1119-27. [Full Text/Abstract]
Liu W, Shang Y, Zeng Y, Liu C, Li Y, Zhai L, Wang P, Lou J, Xu P, Ye Y, Li W. Dimeric Ube2g2 simultaneously engages donor and acceptor ubiquitins to form Lys48-linked ubiquitin chains. EMBO J. 2014 Jan 7; 33 (2014 Jan 7; 33; 1):46-61. [Full Text/Abstract]
Liu Y, Soetandyo N, Lee JG, Liu L, Xu Y, Clemons WM Jr, Ye Y. USP13 antagonizes gp78 to maintain functionality of a chaperone in ER-associated degradation. Elife. 2014; 3 (2014; 3):e01369. [Full Text/Abstract]
Felsenfeld G. A brief history of epigenetics. Cold Spring Harb Perspect Biol. 2014 Jan 1; 6 (6; 2014 Jan 1; 1). [Full Text/Abstract]
Ghosh SK, Bond MR, Love DC, Ashwell GG, Krause MW, Hanover JA. Disruption of O-GlcNAc Cycling in C. elegans Perturbs Nucleotide Sugar Pools and Complex Glycans. Front Endocrinol (Lausanne). 2014; 5 (2014; 5):197. [Full Text/Abstract]
Kallampallil J, Wood SJ, O'Dempsey T, Craigie RJ. Nematode infection mimicking paratesticular malignancy. BMJ Case Rep. 2013 (2013). [Full Text/Abstract]
Huang CH, Hsiao HT, Chu YR, Ye Y, Chen X. Derlin2 facilitates HRD1-mediated retro-translocation of sonic hedgehog at the endoplasmic reticulum. J Biol Chem. 2013 Aug 30; 288 (35; 288; 2013 Aug 30):25330-9. [Full Text/Abstract]
Chandler M, de la Cruz F, Dyda F, Hickman AB, Moncalian G, Ton-Hoang B. Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat Rev Microbiol. 2013 Aug; 11 (8; 2013 Aug; 11):525-38. [Full Text/Abstract]
Xu Y, Liu Y, Lee JG, Ye Y. A Ubiquitin-like Domain Recruits an Oligomeric Chaperone to a Retrotranslocation Complex in Endoplasmic Reticulum-associated Degradation. J Biol Chem. 2013 Jun 21; 288 (25; 2013 Jun 21; 288):18068-76. [Full Text/Abstract]
Reinke V, Krause M, Okkema P. Transcriptional regulation of gene expression in C. elegans. WormBook. 2013 Jun 4; (2013 Jun 4):1-31. [Full Text/Abstract]
Hwang LC, Vecchiarelli AG, Han YW, Mizuuchi M, Harada Y, Funnell BE, Mizuuchi K. ParA-mediated plasmid partition driven by protein pattern self-organization. EMBO J. 2013 May 2; 32 (2013 May 2; 32; 9):1238-49. [Full Text/Abstract]
Vecchiarelli AG, Hwang LC, Mizuuchi K. Cell-free study of F plasmid partition provides evidence for cargo transport by a diffusion-ratchet mechanism. Proc Natl Acad Sci U S A. 2013 Apr 9; 110 (110; 15; 2013 Apr 9):E1390-7. [Full Text/Abstract]
Lee JG, Ye Y. Bag6/Bat3/Scythe: a novel chaperone activity with diverse regulatory functions in protein biogenesis and degradation. Bioessays. 2013 Apr; 35 (35; 4; 2013 Apr):377-85. [Full Text/Abstract]
Lapkouski M, Tian L, Miller JT, Le Grice SF, Yang W. Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation. Nat Struct Mol Biol. 2013 Feb; 20 (20; 2; 2013 Feb):230-6. [Full Text/Abstract]
Lee JG, Baek K, Soetandyo N, Ye Y. Reversible inactivation of deubiquitinases by reactive oxygen species in vitro and in cells. Nat Commun. 2013; 4 (4; 2013):1568. [Full Text/Abstract]
Xu Y, Cai M, Yang Y, Huang L, Ye Y. SGTA recognizes a noncanonical ubiquitin-like domain in the Bag6-Ubl4A-Trc35 complex to promote endoplasmic reticulum-associated degradation. Cell Rep. 2012 Dec 27; 2 (2012 Dec 27; 6; 2):1633-44. [Full Text/Abstract]
Nakamura T, Zhao Y, Yamagata Y, Hua YJ, Yang W. Watching DNA polymerase η make a phosphodiester bond. Nature. 2012 Jul 11; 487 (7406; 2012 Jul 11; 487):196-201. [Full Text/Abstract]
Zhao Y, Biertümpfel C, Gregory MT, Hua YJ, Hanaoka F, Yang W. Structural basis of human DNA polymerase η-mediated chemoresistance to cisplatin. Proc Natl Acad Sci U S A. 2012 May 8; 109 (109; 19; 2012 May 8):7269-74. [Full Text/Abstract]
Gowher H, Brick K, Camerini-Otero RD, Felsenfeld G. Vezf1 protein binding sites genome-wide are associated with pausing of elongating RNA polymerase II. Proc Natl Acad Sci U S A. 2012 Feb 14; 109 (109; 7; 2012 Feb 14):2370-5. [Full Text/Abstract]
Li M, Ivanov V, Mizuuchi M, Mizuuchi K, Craigie R. DNA requirements for assembly and stability of HIV-1 intasomes. Protein Sci. 2012 Feb; 21 (2012 Feb; 2; 21):249-57. [Full Text/Abstract]
Gupta S, Gellert M, Yang W. Mechanism of mismatch recognition revealed by human MutSβ bound to unpaired DNA loops. Nat Struct Mol Biol. 2011 Dec 18; 19 (2011 Dec 18; 19; 1):72-8. [Full Text/Abstract]
He S, Hickman AB, Dyda F, Johnson NP, Chandler M, Ton-Hoang B. Reconstitution of a functional IS608 single-strand transpososome: role of non-canonical base pairing. Nucleic Acids Res. 2011 Oct; 39 (19; 39; 2011 Oct):8503-12. [Full Text/Abstract]
Chappie JS, Mears JA, Fang S, Leonard M, Schmid SL, Milligan RA, Hinshaw JE, Dyda F. A pseudoatomic model of the dynamin polymer identifies a hydrolysis-dependent powerstroke. Cell. 2011 Sep 30; 147 (147; 2011 Sep 30; 1):209-22. [Full Text/Abstract]
Zhong Y, Wang Y, Yang H, Ballar P, Lee JG, Ye Y, Monteiro MJ, Fang S. Importin beta interacts with the endoplasmic reticulum-associated degradation machinery and promotes ubiquitination and degradation of mutant alpha1-antitrypsin. J Biol Chem. 2011 Sep 30; 286 (39; 2011 Sep 30; 286):33921-30. [Full Text/Abstract]
Li X, Wang S, Li Y, Deng C, Steiner LA, Xiao H, Wu C, Bungert J, Gallagher PG, Felsenfeld G, Qiu Y, Huang S. Chromatin boundaries require functional collaboration between the hSET1 and NURF complexes. Blood. 2011 Aug 4; 118 (118; 2011 Aug 4; 5):1386-94. [Full Text/Abstract]
Weniger MA, Rizzatti EG, Pérez-Galán P, Liu D, Wang Q, Munson PJ, Raghavachari N, White T, Tweito MM, Dunleavy K, Ye Y, Wilson WH, Wiestner A. Treatment-induced oxidative stress and cellular antioxidant capacity determine response to bortezomib in mantle cell lymphoma. Clin Cancer Res. 2011 Aug 1; 17 (2011 Aug 1; 17; 15):5101-12. [Full Text/Abstract]
Fairman JW, Noinaj N, Buchanan SK. The structural biology of β-barrel membrane proteins: a summary of recent reports. Curr Opin Struct Biol. 2011 Aug; 21 (4; 21; 2011 Aug):523-31. [Full Text/Abstract]
Nery FC, Armata IA, Farley JE, Cho JA, Yaqub U, Chen P, da Hora CC, Wang Q, Tagaya M, Klein C, Tannous B, Caldwell KA, Caldwell GA, Lencer WI, Ye Y, Breakefield XO. TorsinA participates in endoplasmic reticulum-associated degradation. Nat Commun. 2011 Jul 12; 2 (2011 Jul 12; 2):393. [Full Text/Abstract]
Engel A, Shewmaker F, Edskes HK, Dyda F, Wickner RB. Amyloid of the Candida albicans Ure2p prion domain is infectious and has an in-register parallel β-sheet structure. Biochemistry. 2011 Jul 12; 50 (2011 Jul 12; 50; 27):5971-8. [Full Text/Abstract]
Hübener J, Vauti F, Funke C, Wolburg H, Ye Y, Schmidt T, Wolburg-Buchholz K, Schmitt I, Gardyan A, Driessen S, Arnold HH, Nguyen HP, Riess O. N-terminal ataxin-3 causes neurological symptoms with inclusions, endoplasmic reticulum stress and ribosomal dislocation. Brain. 2011 Jul; 134 (Pt 7; 134; 2011 Jul):1925-42. [Full Text/Abstract]
Wang Q, Liu Y, Soetandyo N, Baek K, Hegde R, Ye Y. A ubiquitin ligase-associated chaperone holdase maintains polypeptides in soluble states for proteasome degradation. Mol Cell. 2011 Jun 24; 42 (2011 Jun 24; 6; 42):758-70. [Full Text/Abstract]
Liu Y, Ye Y. Proteostasis regulation at the endoplasmic reticulum: a new perturbation site for targeted cancer therapy. Cell Res. 2011 Jun; 21 (6; 2011 Jun; 21):867-83. [Full Text/Abstract]
Xiao T, Wallace J, Felsenfeld G. Specific sites in the C terminus of CTCF interact with the SA2 subunit of the cohesin complex and are required for cohesin-dependent insulation activity. Mol Cell Biol. 2011 Jun; 31 (2011 Jun; 11; 31):2174-83. [Full Text/Abstract]
Mondoux MA, Love DC, Ghosh SK, Fukushige T, Bond M, Weerasinghe GR, Hanover JA, Krause MW. O-linked-N-acetylglucosamine cycling and insulin signaling are required for the glucose stress response in Caenorhabditis elegans. Genetics. 2011 Jun; 188 (188; 2; 2011 Jun):369-82. [Full Text/Abstract]
Tong J, Dolezal P, Selkrig J, Crawford S, Simpson AG, Noinaj N, Buchanan SK, Gabriel K, Lithgow T. Ancestral and derived protein import pathways in the mitochondrion of Reclinomonas americana. Mol Biol Evol. 2011 May; 28 (28; 5; 2011 May):1581-91. [Full Text/Abstract]