Lindsay W. Black
Biochemistry and Molecular Biology
108 N. Greene St.,
- B.S. - Biochemistry, The University of Chicago (Honors, Phi Beta Kappa)
- Ph.D. - Biochemistry, Department of Biochemistry, Stanford University School of Medicine
- Post Doctoral Fellow - Jane Coffin Childs Foundation- Institute of Molecular Biology, University of Geneva, Switzerland
I was trained as a biochemist-molecular biologist as a graduate student in the laboratory of David Hogness, then working on lambda phage, in the biochemistry department of Arthur Kornberg in the Stanford Medical School; and then as a Jane Coffin Childs Fund Postdoctoral Fellow in the Institute of Molecular Biology, University of Geneva, Geneva, Switzerland in the laboratory of Eduard Kellenberger, a pioneering electron microscopist and structural biologist. I have maintained my interest in the prokaryotic problems I was introduced to in both of these eminent training centers. My research program has been supported for over 30 years by NIH. During this period I have received an NIH Merit Award.
Viral nucleic acid packaging is highly conserved. A powerful packaging motor translocates DNA into an empty procapsid. The phage ATP powered motor consists of a packaging enzyme docked to a unique procapsid vertex containing a dodecameric portal and packages DNA through this channel to 500 mg/ml (1). We have shown that a long favored rotary portal motor mechanism does not apply (2). Instead we provide evidence by packaging in vitro of short dye labeled model DNA substrates for a linear torsional compression motor mechanism (3,4,5).
Comparable analysis also provides procapsid and packaged DNA structural information (6,7). We have developed a bipartite phage display system to study the complex integration of DNA packaging with other viral development steps in vivo, especially transcription (8,9).
A second current interest is in phage exclusion and anti-exclusion mechanisms. A novel glucose modified restriction gmrS/gmrD enzyme that targets glycosyl-hydroxymethylcytosine modified phage DNAs has been isolated from pathogenic E. coli CT596 (10). In response T-even phages have evolved capsid-targeted internal protein enzyme inhibitors injected into the host with the DNA to shield it. Analysis of the structures of these inhibitors reveals an evolutionary pathway that has elaborated a surprisingly diverse and specifically fitted set of coevolving attack and defense proteins (11).
Lab Techniques and Equipment:
We employ standard molecular and biochemical techniques together with electron microscopy for structure-function studies of phage packaging and assembly. We have developed bipartite phage display as well as a phage internal protein packaging system to study structure and assembly as well as to develop new phage derived technology. Most recently we have pioneered use of fluorescence correlation spectroscopy and smFRET to study viral DNA packaging in real time and to understand packaging structure and dynamics in collaboration with colleagues at the Center for Fluorescence Spectroscopy at UMB.
- Julie Thomas, Research Associate
- Aparna Dixit, Postdoctoral Fellow
- Qin Dan, Research Assistant
- Black, L.W. (2015). Old, New, and Widely True: the Bacteriophage T4 DNA Packaging Mechanism. Review article for the 6oth Anniversary Special Issue of Virology, in press.
- Liu JL, Dixit AB, Robertson KL, Qiao E, Black LW. 2014. Viral nanoparticle-encapsidated enzyme and restructured DNA for cell delivery and gene expression. Proc Natl Acad Sci U S A. 111:13319-24.
- Aparna Banerjee Dixit, Krishanu Ray, Julie A.Thomas, Lindsay W. Black. 2013. The C-terminal domain of the bacteriophage T4 terminase docks on the prohead portal clip region during DNA packaging. 446, 293-302.
- Bubblegrams reveal the inner body of bacteriophage φKZ. Wu W, Thomas JA, Cheng N, Black LW, Steven AC. Science. 2012 Jan 13;335(6065):182.
- Condensed genome structure. Black LW, Thomas JA. Adv Exp Med Biol. 2012;726:469-87.
- Compression of the DNA substrate by a viral packaging motor is supported by removal of intercalating dye during translocation. Dixit AB, Ray K, Black LW. Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20419-24. doi: 10.1073/pnas.1214318109. Epub 2012 Nov 26. PMID: 23185020 [PubMed - in process]
- Extensive proteolysis of head and inner body proteins by a morphogenetic protease in the giant Pseudomonas aeruginosa phage φKZ. Thomas JA, Weintraub ST, Wu W, Winkler DC, Cheng N, Steven AC, Black LW. Mol Microbiol. 2012 Apr;84(2):324-39. doi: 10.1111/j.1365-2958.2012.08025.x. Epub 2012 Mar 20. PMID: 22429790 [PubMed - indexed for MEDLINE]
- Black, LW, Oram, M. Mechanisms of Genome Packaging.
- Dynamics of the T4 bacteriophage DNA packasome motor: endonuclease VII resolvase release of arrested Y-DNA substrates. Dixit A, Ray K, Lakowicz JR, Black LW. J Biol Chem. 2011 May 27;286(21):18878-89. doi: 10.1074/jbc.M111.222828. Epub 2011 Mar 29. PMID: 21454482 [PubMed - indexed for MEDLINE] Free PMC Article
- Ray K, Ma J, Oram M, Lakowicz JR, Black LW. (2010) Single-molecule and FRET fluorescence correlation spectroscopy analyses of phage DNA packaging: colocalization of packaged phage T4 DNA ends within the capsid. J Mol Biol. 395(5):1102-13. (PMID: 19962991)
- Ray K, Sabanayagam CR, Lakowicz JR, Black LW. (2010) DNA crunching by a viral packaging motor: Compression of a procapsid-portal stalled Y-DNA substrate. Virology. 15:224-232. (PMID: 20060554)
- Ray K, Oram M, Ma J, Black LW. (2009) Portal control of viral prohead expansion and DNA packaging. Virology. 15: 391(1):44-50. (PMID: 19541336)
- Rifat D, Wright NT, Varney KM, Weber DJ, Black LW. (2008) Restriction endonuclease inhibitor IPI* of bacteriophage T4: a novel structure for a dedicated target. J Mol Biol. 375(3):720-34. (PMID: 18037438)
- Oram M, Sabanayagam C, Black LW. (2008) Modulation of the packaging reaction of bacteriophage T4 terminase by DNA structure. J Mol Biol. 381(1):61-72. (PMID: 18586272)
- Sabanayagam C, Oram M, Lakowicz JR, Black LW (2007) Viral DNA packaging studied by fluorescence correlation spectroscopy, Biophysical Journal, 93(4), 17-19. (PMID: 175557791)
- Bair CL, Black LW (2007) A Type IV modification dependent restriction nuclease that targets glucosylated hydroxymethyl cytosine modified DNAs. J Mol Biol. 366: 768. (PMID: 17188297)
- Baumann RG, Mullaney J, Black LW. (2006) Portal fusion protein constraints on function in DNA packaging of bacteriophage T4. Mol Microbiol. 61:16-32. (PMID: 16824092)
- Black LW, Peng G (2006) Mechanistic coupling of bacteriophage T4 DNA packaging to components of the replication-dependent late transcription machinery. J Biol Chem. 281(35):25635-43. (PMID: 16807240)