Biochemistry and Molecular Biology
108 N. Greene St., 408
Education and Training
- BS - Biochemistry, The University of Chicago (Honors, Phi Beta Kappa)
- PhD - 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.
genome structure, viral nucleic acid packaging, translocate DNA into an empty procapsid
Recent Publications (2015-2020)
Lindsay W. Black, Bingxue Yan, Krishanu Ray. The T4 TerL Prohead Packaging Motor Does Not Drive DNA Translocation by a Proposed Dehydration Mechanism. Viruses 2020, 12(5), 522; 09 May 2020.
Dixit AB, Ray K, Black LW. A viral small terminase subunit (TerS) twin ring pac synapsis DNA packaging model is supported by fluorescent fusion proteins. Virology. 2019;536:39-48. doi: 10.1016/j.virol.2019.07.021. PubMed PMID: 31400548; PMCID: PMC6760839.
Black LW. Old, new, and widely true: The bacteriophage T4 DNA packaging mechanism. Virology. 2015;479-480:650-6. doi: 10.1016/j.virol.2015.01.015. PubMed PMID: 25728298; PMCID: PMC4424107.
Thomas JA, Benitez Quintana AD, Bosch MA, Coll De Pena A, Aguilera E, Coulibaly A, Wu W, Osier MV, Hudson AO, Weintraub ST, Black LW. Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly. J Virol. 2016;90(22):10284-98. doi: 10.1128/JVI.01492-16. PubMed PMID: 27605673; PMCID: PMC5105663.
Weintraub ST, Mohd Redzuan NH, Barton MK, Md Amin NA, Desmond MI, Adams LE, Ali B, Pardo S, Molleur D, Wu W, Newcomb WW, Osier MV, Black LW, Steven AC, Thomas JA. Global Proteomic Profiling of Salmonella Infection by a Giant Phage. J Virol. 2019;93(5):e01833-18. doi: 10.1128/JVI.01833-18. PubMed PMID: 30541839; PMCID: PMC6384053.
He X, Hull V, Thomas JA, Fu X, Gidwani S, Gupta YK, Black LW, Xu SY. Expression and purification of a single-chain Type IV restriction enzyme Eco94GmrSD and determination of its substrate preference. Sci Rep. 2015;5:9747. doi: 10.1038/srep09747. PubMed PMID: 25988532; PMCID: PMC4437046.
Hardies SC, Thomas JA, Black L, Weintraub ST, Hwang CY, Cho BC. Identification of structural and morphogenesis genes of Pseudoalteromonas phage phiRIO-1 and placement within the evolutionary history of Podoviridae. Virology. 2016;489:116-27. doi: 10.1016/j.virol.2015.12.005. PubMed PMID: 26748333; PMCID: PMC4819975.
Bryson AL, Hwang Y, Sherrill-Mix S, Wu GD, Lewis JD, Black L, Clark TA, Bushman FD. Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9. mBio. 2015;6(3):e00648. doi: 10.1128/mBio.00648-15. PubMed PMID: 26081634; PMCID: PMC4471564.
Black LW, Ray K. Same function from different structures among pac site bacteriophage (TerS) terminase small subunits. CRC Reviews. 2017.
Ali B, Desmond MI, Mallory SA, Benitez AD, Buckley LJ, Weintraub ST, Osier MV, Black LW, Thomas JA. To Be or Not To Be T4: Evidence of a Complex Evolutionary Pathway of Head Structure and Assembly in Giant Salmonella Virus SPN3US. Front Microbiol. 2017;8:2251. doi: 10.3389/fmicb.2017.02251. PubMed PMID: 29187846; PMCID: PMC5694885.
Thomas JA, Orwenyo J, Wang LX, Black LW. The Odd "RB" Phage-Identification of Arabinosylation as a New Epigenetic Modification of DNA in T4-Like Phage RB69. Viruses. 2018;10(6):E313. doi: 10.3390/v10060313. PubMed PMID: 29890699; PMCID: PMC6024577.
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. Virology. 446, 293-302.
Bubblegrams reveal the inner body of bacteriophage fKZ. 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 fKZ. 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]
Bacteriophage T4 capsid packaging and unpackaging of DNA and proteins. Mullaney JM, Black LW. 2014. Methods Mol Biol 1108:69-85. doi: 10.1007/978-1-62703-751-8_5.
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)
My primary interest is in viral nucleic acid packaging which is highly conserved. A powerful packaging motor is required to translocate DNA into an empty procapsid. The ATP powered phage motor consists of a packaging enzyme docked to a unique procapsid vertex containing a dodecameric portal. It packages DNA through the portal channel to ~500 mg/ml. We have shown that a long favored rotary portal motor mechanism does not apply (see reference #1 for recent review). Instead packaging in vitro of short dye labeled model DNA substrates provides evidence for a transient linear torsional B form to A form DNA "crunching" or spring-like motor mechanism to translocate DNA by the large terminase subunit (1, 3, 6, 9, 11, 12, 17) . A four strand "synapsis" of two homologous pac sequences in the DNA concatemer by a twin ring form of the small terminase subunit gauges DNA maturation and regulates cutting of the DNA by the large terminase to initiate packaging in vivo (1).
We have developed a bipartite phage display system to study the complex integration of DNA packaging with other viral development steps in vivo (18) and to use for cell docking. 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 (15, 14, 11, 10).
Packaging DNA and protein together into a phage T4 procapsid in vitro with specific proteins and DNAs has useful applications. Virtually any active protein (100s of copies) can be transferred along with any DNA or multiple DNAs (170 kb total) by such a viral nanocontainer into cells. Capsid decoration proteins allow specific cell targeting and uptake of the nanocargo (2, 5, 8).
We have recently studied the giant PhiKZ bacteriophage. Its capsid contains a remarkable protein rod-like structure within the densely packaged DNA that is displaced from the portal apex axis (4). This >10 MD structure is assembled from more than six structural proteins processed (~50 % protein removal) by a morphogenetic protease to make the structure found in the virion (5, 7). The function of this structure is unknown but this bacteriophage and its relatives inject these structural proteins and large enzymatically active proteins such as multi-subunit RNA polymerases into the infected host together with the DNA.
The Tquatrovirinae can contain highly modified hmC (hydroxymethylcytosine) DNA that prevents DNA breakdown by host restriction modification enzymes. A glucose modified restriction gmrS/gmrD enzyme that targets diverse glycosyl-hmC modified phage DNAs has been isolated from pathogenic E. coli CT596 (16). 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 and DNA modifications (13).
Efficient packaging of short heteroduplex DNA:RNA molecules with (20 bps) and without a short DNA:DNA helper (25, 30, & 35 bps) shows 1) that DNA packaging is not driven by a widely disseminated hypothetical dehydration motor mechanism; and 2) that the motor drives packaging by ATP driven TerL motion toward the prohead portal.
Phage T4 prohead portal gp20 binding to TerL from the C-terminal TerL nuclease containing domain. Two duplex nucleic acid segments are depicted as being translocated by the TerL ATP-driven motor; where top segment is pushing the bottom segment through the portal tunnel into the prohead. TerL intercalating ac and q dye resistance mutations at residues 96, 249 are circled; mutations at residue 267 are closely coordinated with mutations at the ac and q sites; the circled residue 473 ts DNA translocation mutation is suppressed by portal cs mutation clip domain residue 308 (blue arrow). A FRET determined distance of ca.7.5 nm between portal clip domain Alexa488 maleimide dye labeled residue 316 and the terminase C-terminal ReAsH dye is found in this study (blue arrow). Structures are not to scale, nor are the numbers of terminase or portal monomers represented in the multimeric structure constituting the two-component packaging motor complex.
Active Grant Support
Role: Black (PI)
Title: Mechanism of bacteriophage DNA packaging initiation and DNA translocation.
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.
- Julie Thomas, Research Associate
- Aparna Dixit, Postdoctoral Fellow
- Qin Dan, Research Assistant
Former Black Lab Postdocs and Research Associates
- Mitsuhiro Yanagida
- Dalin Rifat
- Julienne Mullaney
- Venigalla Rao
- Arthur H. Zachary
- Naglis Malys
- Dau Y. Chang
- Mark Oram
- Julie A.Thomas
- Aparna Banerjee Dixit
Former Black Lab Graduate Students
- Chu-lai Hsiao
- Kenneth Abremski
- Du-Gong Wu
- Herbert Wu
- Jinny Lin Liu
- Richard G. Baumann
- Joanne Andreadis
- Gregory Michaud