James L. Keck

James L. Keck Headshot

Professor; also Associate Dean for Basic Sciences, UW SMPH

6214A Biochemical Sciences Building

440 Henry Mall

Madison WI 53706

Phone: (608) 263-1815

Email: jlkeck@wisc.edu

 

Education

• B.S. 1992, University of Massachusetts
• Ph.D. 1997, University of California-Berkeley (S. Marqusee)
• Postdoctoral, 1997-98, Harvard University (J. Wang);1999-01, University of California-Berkeley (J. Berger)

Honors & Awards

• Jane Coffin Childs Memorial Fund Postdoctoral Fellow, 1997-2000
• Shaw Scientist Award, 2003
• American Cancer Society Research Scholar, 2006
• WARF Romnes Faculty Fellowship, 2009
• School of Medicine and Public Health Dean's Teaching Award, 2010
• UW Health Community Service Award 2013
• UW Madison Kellett Mid-Career Award, 2017

Research Interests

Research in the Keck lab examines the structural mechanisms that drive DNA replication, replication restart, recombination, and repair reactions. Successful execution of these pathways is essential in all cells, and defects in the proteins that facilitate genome maintenance reactions lead to genome instability, cell death, and disease. Our studies combine structural approaches with biochemical and cell biological methods to answer fundamental structure-function questions in genome biology.

Single-stranded DNA-binding proteins. Bacterial single-stranded (ss) DNA-binding proteins (SSBs) play essential protective and organizational roles in genome biology. In their protective functions, SSBs bind and sequester ssDNA intermediates that are formed during genome maintenance reactions. As organizational centers, SSB/ssDNA complexes form dynamic protein-docking "hubs" at which over a dozen different DNA replication, recombination, and repair enzymes gain access to genomic substrates through direct interactions with SSB. This clustering of enzymes is thought to help integrate cellular genome maintenance reactions by facilitating the exchange of ssDNA substrates between DNA replication, recombination, and repair pathways. In all cases examined to date, the last ~6 residues of SSB's flexible C-terminus (SSB-Ct) form its protein docking site. Eukaryotic SSBs also interact with a diverse array of genome maintenance proteins but, since they lack the SSB-Ct element found in bacterial SSBs, they do so through distinct mechanisms.

We have mapped the SSB-Ct binding sites in several genome maintenance proteins. The examples we have focused on include bacterial proteins involved in DNA replication (chi subunit from the replicative DNA polymerase), recombination (RecQ DNA helicase), and repair (Exonuclease I and Uracil DNA glycosylase). The SSB-docking sites on these proteins are remarkably similar in spite their lack of structural similarity. Binding to SSB often stimulates enzyme activity through recruitment of the protein partner to its SSB/DNA substrate. In cells, these interactions are essential for the proper localization and functions of SSB-associated proteins.

Future work aims to establish the full extent of the SSB interaction network though protein interaction studies. We plan to examine how multiple SSB-binding proteins might function cooperatively on SSB/ssDNA substrates and to determine the mechanisms that regulate assembly of SSB-interacting proteins on SSB/ssDNA complexes in cells. The essential nature of bacterial SSB/protein interactions also makes the complexes attractive targets for the development of novel antibacterial therapeutics that block SSB/protein interactions.

Mechanisms of DNA replication restart. Nearly all replication complexes (replisomes) formed at bacterial replication origins are thought to stall during the course of DNA replication. This stalling may occur at sites of DNA damage and can lead to dramatic rearrangement of the replication fork DNA and disassembly of the replisome. Reassembly of the DNA replication machinery on abandoned replication forks is therefore often required for complete DNA replication. "DNA replication restart" is mediated several proteins (PriA, PriB, PriC, and DnaT in E. coli) that function in a coordinated manner to reload the replisome. Currently, little is known about the structural mechanisms that support this essential cellular function.

We have developed a model based on work from our group and others that explains the linkage between abandoned replication fork recognition and replisome reloading. In this model, PriA acts as a first-responder protein, binding directly to the abandoned replication fork DNA. Subsequent stepwise assembly of PriB and DnaT or PriC onto the PriA/DNA complex creates a platform for recruiting the replisome on the replication fork. As a step toward understanding the structure of the primosome, we have determined the structures of PriA and PriB and have initiated structural efforts on the remaining replication restart proteins. Our future work will focus on understanding the critical steps in formation of the fully assembled primosome through crystallographic and other structural approaches, along with biochemical and genetic studies.

Coordination of human DNA repair complexes. Eukaryotic cells have an astonishing number of DNA repair pathways that are regulated and coordinated, at least in part, by dynamic physical interactions. We have recently begun a study of a key protein interaction interface that links the Fanconi Anemia Core Complex and Bloom Dissolvasome, two DNA repair complexes. Our lab has determined the high-resolution crystal structure of the minimal protein interface that links these complexes, which is comprised of a short peptide from the FANCM protein from the Fanconi Anemia Core Complex binding to the RMI heterodimer from the Bloom Dissolvasome. Using our structure as a guide, we have shown that mutations that block interaction between these complexes induces genomic instability in cells-a hallmark of nearly all cancers. We are continuing to investigate this and other repair interfaces as examples of regulation by dynamic protein assembly and as potential chemotherapeutic targets.

Publications of Note

Perform a customized PubMed literature for Dr. Keck.

• Liu K, Myers AR, Pisithkul T, Claas KR, Satyshur KA, Amador-Noguez D, Keck JL,
Wang JD. Molecular Mechanism and Evolution of Guanylate Kinase Regulation by
(p)ppGpp. Mol Cell. 2015 Feb 19;57(4):735-49. doi: 10.1016/j.molcel.2014.12.037.
Epub 2015 Feb 5. PubMed PMID: 25661490; PubMed Central PMCID: PMC4336630.

• Bhattacharyya B, Keck JL. Grip it and rip it: structural mechanisms of DNA
helicase substrate binding and unwinding. Protein Sci. 2014 Nov;23(11):1498-507.
doi: 10.1002/pro.2533. Epub 2014 Aug 22. PubMed PMID: 25131811; PubMed Central
PMCID: PMC4241101.

• Walsh BW, Bolz SA, Wessel SR, Schroeder JW, Keck JL, Simmons LA. RecD2
helicase limits replication fork stress in Bacillus subtilis. J Bacteriol. 2014
Apr;196(7):1359-68. doi: 10.1128/JB.01475-13. Epub 2014 Jan 17. PubMed PMID:
24443534; PubMed Central PMCID: PMC3993351.

• Bhattacharyya B, George NP, Thurmes TM, Zhou R, Jani N, Wessel SR, Sandler SJ,
Ha T, Keck JL. Structural mechanisms of PriA-mediated DNA replication restart.
Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1373-8. doi:
10.1073/pnas.1318001111. Epub 2013 Dec 30. PubMed PMID: 24379377; PubMed Central
PMCID: PMC3910646.

• Wessel SR, Marceau AH, Massoni SC, Zhou R, Ha T, Sandler SJ, Keck JL.
PriC-mediated DNA replication restart requires PriC complex formation with the
single-stranded DNA-binding protein. J Biol Chem. 2013 Jun 14;288(24):17569-78.
doi: 10.1074/jbc.M113.478156. Epub 2013 Apr 29. PubMed PMID: 23629733; PubMed
Central PMCID: PMC3682556.

• Manthei KA, Keck JL. The BLM dissolvasome in DNA replication and repair. Cell
Mol Life Sci
. 2013 Nov;70(21):4067-84. doi: 10.1007/s00018-013-1325-1. Epub 2013
Mar 31. Review. PubMed PMID: 23543275; PubMed Central PMCID: PMC3731382.

• Marceau AH, Bernstein DA, Walsh BW, Shapiro W, Simmons LA, Keck JL. Protein
interactions in genome maintenance as novel antibacterial targets. PLoS One.
2013;8(3):e58765. doi: 10.1371/journal.pone.0058765. Epub 2013 Mar 11. PubMed
PMID: 23536821; PubMed Central PMCID: PMC3594151.

• Cahoon LA, Manthei KA, Rotman E, Keck JL, Seifert HS. Neisseria gonorrhoeae
RecQ helicase HRDC domains are essential for efficient binding and unwinding of
the pilE guanine quartet structure required for pilin antigenic variation. J
Bacteriol
. 2013 May;195(10):2255-61. doi: 10.1128/JB.02217-12. Epub 2013 Mar 8.
PubMed PMID: 23475972; PubMed Central PMCID: PMC3650551.

• Norais C, Servant P, Bouthier-de-la-Tour C, Coureux PD, Ithurbide S, Vannier
F, Guerin PP, Dulberger CL, Satyshur KA, Keck JL, Armengaud J, Cox MM, Sommer S.
The Deinococcus radiodurans DR1245 protein, a DdrB partner homologous to YbjN
proteins and reminiscent of type III secretion system chaperones. PLoS One.
2013;8(2):e56558. doi: 10.1371/journal.pone.0056558. Epub 2013 Feb 18. PubMed
PMID: 23441204; PubMed Central PMCID: PMC3575483.

• Rymer RU, Solorio FA, Tehranchi AK, Chu C, Corn JE, Keck JL, Wang JD, Berger
JM. Binding mechanism of metal⋅NTP substrates and stringent-response alarmones to
bacterial DnaG-type primases. Structure. 2012 Sep 5;20(9):1478-89. doi:
10.1016/j.str.2012.05.017. Epub 2012 Jul 12. PubMed PMID: 22795082; PubMed
Central PMCID: PMC3438381.

• George NP, Ngo KV, Chitteni-Pattu S, Norais CA, Battista JR, Cox MM, Keck JL.
Structure and cellular dynamics of Deinococcus radiodurans single-stranded DNA
(ssDNA)-binding protein (SSB)-DNA complexes. J Biol Chem. 2012 Jun
22;287(26):22123-32. doi: 10.1074/jbc.M112.367573. Epub 2012 May 7. PubMed PMID:
22570477; PubMed Central PMCID: PMC3381170.

• Hoadley KA, Xue Y, Ling C, Takata M, Wang W, Keck JL. Defining the molecular
interface that connects the Fanconi anemia protein FANCM to the Bloom syndrome
dissolvasome. Proc Natl Acad Sci U S A. 2012 Mar 20;109(12):4437-42. doi:
10.1073/pnas.1117279109. Epub 2012 Mar 5. PubMed PMID: 22392978; PubMed Central
PMCID: PMC3311393.

• Yadav T, Carrasco B, Myers AR, George NP, Keck JL, Alonso JC. Genetic
recombination in Bacillus subtilis: a division of labor between two single-strand
DNA-binding proteins. Nucleic Acids Res. 2012 Jul;40(12):5546-59. doi:
10.1093/nar/gks173. Epub 2012 Feb 28. PubMed PMID: 22373918; PubMed Central
PMCID: PMC3384303.

• Smith BC, Anderson MA, Hoadley KA, Keck JL, Cleland WW, Denu JM. Structural
and kinetic isotope effect studies of nicotinamidase (Pnc1) from Saccharomyces
cerevisiae
. Biochemistry. 2012 Jan 10;51(1):243-56. doi: 10.1021/bi2015508. Epub
2011 Dec 29. PubMed PMID: 22229411; PubMed Central PMCID: PMC3257521.

• Marceau AH, Bahng S, Massoni SC, George NP, Sandler SJ, Marians KJ, Keck JL.
Structure of the SSB-DNA polymerase III interface and its role in DNA
replication. EMBO J. 2011 Aug 19;30(20):4236-47. doi: 10.1038/emboj.2011.305.
PubMed PMID: 21857649; PubMed Central PMCID: PMC3199393.