Anca Mara Segall, Ph. D.
The Segall lab (http://segall-lab.sdsu.edu/) has recently focused on 3 general research topics: the mechanism of site-specific recombination, the identification and characterization of DNA repair inhibitors, and the diversity and lifestyle of bacteriophages. Towards these goals, we employ a variety of tools including biochemistry, genetics, genomics, bioinformatics, various imaging methods, and structural biology.
Site-specific recombination reactions are wide-spread in nature, and perform many functions in cells including control of gene expression, the separation of dimeric bacterial chromosomes to allow their proper segregation to daughter cells, and control of copy number in plasmids and phages. Many temperate bacteriophages use site-specific recombination to integrate their genomes into host cell chromosomes and to excise them prior to resuming the lytic life cycle. In addition, several of these enzymes have been developed as very useful tools for both prokaryotic and eukaryotic genetics.
We have used the phage lambda site-specific recombinase Integrase (Int) as a model system to understand the mechanism of protein machines that rearrange DNA. Four Int molecules, helped by accessory proteins, synapse 2 DNA recombination target sites and perform two rounds of DNA cleavage, exchange and ligation to generate and then to resolve a special DNA intermediate known as a Holliday junction. Int cleaves DNA by a type I topoisomerase mechanism, and like DNA topoisomerases, requires no high energy cofactors. The reaction is very efficient and at the same time highly reversible, which has made the trapping of reaction intermediates very difficult. Our goal is to find the determinants of directionality and efficiency in the Int-mediated recombination reactions. This understanding, in addition to its fundamental insights into how molecular machines work, should allow us to develop even better tools for gene targeting and for generating programmed mutations in any biological system. We have used combinatorial chemistry to find inhibitors that block recombination at different steps. We are currently using these inhibitors to probe the geometry and regulatory features of recombination.
While characterizing the inhibitors of site-specific recombination described above, we discovered that they are structure-selective ligands that bind to central and conserved intermediates of DNA repair, preferentially Holliday junctions and to a lesser replication fork-like structures. The inhibitors block the resolution or branch migration of Holliday junctions by several structurally and mechanistically distinct enzymes, including RecG and RuvABC. We are using X-ray crystallography studies to understand the interactions of the inhibitors with the Holliday junction substrate. Since these inhibitors differ in structure from all other known ligands of Holliday junctions, their structure will provide new insights applicable to the design of more specific and higher affinity ligands. Genetic analysis is confirming that these inhibitors interfere with DNA repair, and that DNA repair is a viable novel target of antibiotics. During our studies of these inhibitors we discovered another major source of DNA damage, envelope stress. We are pursuing new studies on how damaging the bacterial membrane leads to DNA damage, what type of damage is generated, and what genes and regulatory pathways are called into play to fix this damage. A number of antibiotics appear to have this effect, and our studies are exploring the mechanism of these “side activities” that may augment the killing action of this class of drugs.
Bacteriophages are the most abundant biological entity, and profoundly affect the dynamics of microbial populations. They influence carbon cycling in the oceans, shuttle genetic information between bacteria and contribute to the evolution of new bacterial pathogens, and act as a selection force in microbial evolution. Together with Forest Rohwer’s lab, we have explored the diversity of bacterial viruses and their life styles in marine environments. Our current interests in this area are to use computational and bioinformatics tools to develop ways of identifying the potential function and evolutionary relationships of the large fraction of genetic information, much of it encoded by bacteriophages, for which there is no current known function.
Bibliography (reverse chronological order):
Rohwer, F., Seguritan, V., Choi, D.H., Segall, A.M. and Azam, F. (2001)
Production of randomly amplified shotgun libraries for sequencing. BioTechniques
Troy Bankhead and Anca Segall, 2000. Characterization of a mutation
of bacteriophage lambda integrase: putative role for a conserved residue
in the tyrosine recombinase family. J. Biol. Chem. 275: 36949-36956.
Martha Klemm, Chonghui Cheng, Geoffrey Cassell, Stewart Shuman and Anca
Segall, 2000. Peptide inhibitors of DNA cleavage by tyrosine recombinases
and topoisomerases. J. Mol. Biol. 299: 1203-1216.
Geoffrey Cassell, Martha Klemm, Clemencia Pinilla and Anca Segall, 2000.
Dissection of bacteriophage l site-specific recombination with synthetic
peptide combinatorial libraries. J. Mol. Biol. 299: 1193-1202.
Forest Rohwer, Anca Segall, Grieg Steward, Victor Seguritan, Felise
Wolven, Mya Breitbart and Farooq Azam, 2000. The complete genome sequence
of the marine Roseophage SIO1 shares homology with nonmarine phages. Limnol.
Oceanogr. 45: 408-418.
Lea Jessop, David Wong, Troy Bankhead and Anca Segall, 2000. The amino
terminus of bacteriophage l integrase is involved in protein-protein interactions
during recombination. J. Bacteriol. 182: 1024-1034.
Steven Goodman, Nerissa Velten, Qian Gao, Scott Robinson and Anca Segall,
1999. In vitro selection of IHF binding sites. J. Bacteriol.
Cassell,G., Moision, R., Rabani, E. and A. Segall, 1999 The geometry
of a synaptic intermediate in a pathway of bacteriphage lambda site-specific
recombination. Nucl. Acids Res. 27: 1145-1151. Download
Reproduced with permission from NAR Online http://www.oup.co.uk/nar
Segall, AM 1998 Analysis of higher order intermediates and synapsis
in the bent-L pathway of bacteriophage lambda site-specific recombination.
Biol. Chem. 273, 24258-24265.
Anca Segall and Howard Nash, 1996. Architectural flexibility in lambda
site-specific recombination: Three alternate conformations channel the
attL site into three alternate pathways. Genes to Cells, 1: 453-463.
Anca Segall, Steve Goodman and Howard Nash, 1994. Architectural elements
in nucleoprotein complexes: Interchangeability of specific and nonspecific
DNA binding proteins. EMBO J. 13: 4536-4548.
Lynn Miesel, Anca Segall and John Roth, 1994. Construction of chromosomal
rearrangements in Salmonella by P22 transduction: Inversions of nonpermissive
intervals are not lethal. Genetics 137: 919-932.
Anca Segall and John Roth, 1994. Approaches to half-tetrad analysis
in bacteria: Recombination between repeated, inverse-order chromosomal
sequences. Genetics 136: 27-39.
Anca Segall and Howard Nash, 1993. Synaptic intermediates in bacteriophage
lambda site-specific recombination: Integrase can align pairs of attachment
sites. EMBO J. 12: 4567-4576.
Anca Segall and John Roth, 1989. Recombination between homologies in
direct and inverse orientation in the chromosome of Salmonella. Genetics
Anca Segall, Michael J. Mahan, and John Roth, 1988. Rearrangement of
the bacterial chromosome: Forbidden inversions. Science 241: 1314-1318.
Ph.D. students: Troy
Bankhead, Carl Gunderson, Kevin Kepple, Amy Raymond, Leo Su
Master's MBI students: Nelusha Amaladas, Jeff Boldt, I-Wei Feng,
Mark Swift, Felise Wolven
Victor Seguritan (Computational Sciences Master's Program)
Undergraduate students: Maricel Gozo, Ed Manuel, Jordan Thornes
Postdoctoral Fellows: David Fujimoto, Nathalie Garcia-Russell
Research Assistants: Jeff Boldt, Cheryl Elkins-Tripp, Timothy
Anca Segall, Ph.D.
San Diego State University
Dept. of Biology
5500 Campanile Dr.
San Diego, CA 92182-4614
office (619) 594-4490
lab (619) 594-4638
fax (619) 594-5676
page last updated 10/16/09