Abraham S. and Gertrude Burg Professor of Microbiology
Mechanisms of DNA repair and mutation avoidance
All organisms must preserve the integrity of their genomes. In humans, genetic instability is associated with cancer and aging. Our laboratory seeks to understand the fundamental mechanisms by which cells preserve genetic information by the study of DNA damage repair and mutation avoidance in the model organism Escherichia coli. In addition, we have recently begun to ask how cell cycle events including DNA replication and chromosome segregation are coupled to cellular physiology and to the status of the chromosome. We employ genetics, molecular biology, cell biology, and biochemistry in the study of these pathways.
Replication fork repair and coordination with cell cycle: Some of our studies in E. coli address the mechanism of replication fork repair and its integration with the bacterial cell cycle. We are particularly interested in how recombination reactions are integrated and regulated in the disassembly and reassembly of the replication fork, how the organization of the chromosome influences fork repair or whether the sensing of fork damage triggers control of cell division, fork stabilization and replication initiation. We have discovered a GTPase protein that may couple cell division or chromosome segregation with events at the replication fork and this protein is the subject of genetic and biochemical analysis. We can provoke the accumulation of replication gaps by treatment with the chain-terminating drug, azidothymidine—we have identified and are studying several new repair factors that promote tolerance of the drug, as well as pathways that regulate them. We also investigate how cellular nutrition impacts the capacity for replication and repair, as well as structure of the bacterial chromosome.
Mutational hotspots, exonucleases and mutation avoidance: A class of mutational hotspots occurs by misalignment of DNA strands during replication. We have studied chromosomal rearrangements that occur as a result of this aberrant replication and have found additional factors that may promote or inhibit such events. We have identified a potent mutational hotspot that promotes frequent switching between alterative replication templates. We are examining cis- and trans-acting factors, including exonucleases that control these “template-switch” hotspot mutations in E. coli.
mRNA translation in cellular differentiation and disease
A fundamental question in cell biology is how cells sharing the same DNA produce drastically distinct phenotypes. In one organism, the same genome allows for the development of different tissues, controlled cell cycle progression, and specialized responses to environmental stimuli. This occurs through a process known as gene regulation, where modulation of RNA transcription and protein synthesis allow the level of expression of a gene or its gene product to be controlled. The importance of gene regulation is further underscored by its disruption being associated with a myriad of human diseases ranging from developmental diseases to carcinogenesis.
We are focused on understanding how gene regulation occurs through novel mechanisms of mRNA translation. Specifically, we study how non-canonical translation pathways shape cell growth and differentiation. Accumulating evidence supports the essentiality of mRNA translation control in these cell fate decisions, including abundant genetic links between dysregulation of translation initiation factors with malignancy, inheritable diseases, and behavioral disorders.
During my postdoctoral research, I studied the translation mechanisms by which dysregulation of the eukaryotic initiation factor 3 (eIF3) leads to overactive cell proliferation. Using a genome-wide sequencing approach, I identified ~500 mRNA targets in human cells that bind directly to eIF3, with the major site of interaction in the 5′ UTR. By using in vitro biochemical and cell-based assays, I discovered that eIF3 binds to distinct stem loop structures, and this leads to either translation activation of cell proliferation mRNAs or repression of cell differentiation mRNAs. Gene ontology analyses of eIF3 targets stratify into functional categories that are implicated in carcinogenesis, including differentiation, cell cycling, and apoptosis. Circumventing eIF3 translational control in lung cancer cells overexpressing eIF3a is sufficient to reduce cell invasiveness, suggesting that targeting eIF3–RNA binding may be a therapeutic target. These results highlight the critical importance of translational control during cell growth regulation.
Our research is at the nexus of combining discovery and mechanism-based studies, and thus we use genome-wide and computational approaches together with molecular genetics, cell biology, biochemistry, and structural biology techniques. We aim to contribute to understanding the significance of translational control during cell growth decisions by addressing the following questions:
- How do we discover non-canonical translation pathways that shape the decisions of the cell to undergo cell growth, proliferation, or differentiation into different cell types?
- How are the functions of RNA-binding proteins and translation factors regulated by intra- and extracellular environmental signals?
- Why does dysregulation of transcript-specific translation lead to carcinogenesis and developmental diseases; and can we therapeutically target RNA-protein interactions for disease intervention?
- Lovett ST. "Template-switching during replication fork repair in bacteria." DNA Repair (Amst). 2017 Aug;56:118-128.
- Laranjo LT, Gross SJ, Zeiger DM, Lovett ST. "SSB recruitment of Exonuclease I aborts template-switching in Escherichia coli." DNA Repair(Amst). 2017 Sep;57:12-16.
- Cooper DL and Lovett ST (2016). "Recombinational branch migration by the RadA/Sms paralog of RecA in Escherichia coli." Elife. 2016 Feb 4;5. pii: e10807..
Cooper DL, Lovett ST (2016). "Genetic analysis of Escherichia coli RadA: functional motifs and genetic interactions." Mol Microbiol 95(5): 769-779.
- Brown LT, Sutera VA Jr, Zhou S, Weitzel CS, Cheng Y, Lovett ST. (2015) Connecting Replication and Repair: YoaA, a Helicase-Related Protein, Promotes Azidothymidine Tolerance through Association with Chi, an Accessory Clamp Loader Protein. PLoS Genet. 2015 Nov 6;11(11):e1005651.
- Anand RP, Lovett ST, Haber JE (2013). "Break-induced DNA replication." Cold Spring Harb Perspect Biol 5(12): a010397.
- Lovett ST (2012). "Biochemistry: A glimpse of molecular competition." Nature 491(7423): 198-200.
- Seier T, Zilberberg G, Zeiger DM, Lovett ST (2012). "Azidothymidine and other chain terminators are mutagenic for template-switch-generated genetic mutations." Proc Natl Acad Sci USA 109(16): 6171-6174.
- Zhao F, Weitzel CS, Gao Y, Browdy HM, Shi J, Lin HC, Lovett ST, Xu B (2011). "beta-Galactosidase-instructed formation of molecular nanofibers and a hydrogel." Nanoscale 3(7): 2859-2861.
- Seier T, Padgett DR, Zilberberg G, Sutera VA Jr, Toha N, Lovett ST (2011). Insights into mutagenesis using Escherichia coli chromosomal lacZ strains that enable detection of a wide spectrum of mutational events. Genetics. 2011 Jun;188(2):247-62.
- Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA (2011). Phenotypic landscape of a bacterial cell. Cell. 2011 Jan 7;144(1):143-56.
- Cooper DL, Lovett ST (2011). Toxicity and tolerance mechanisms for azidothymidine, a replication gap-promoting agent, in Escherichia coli. DNA Repair (Amst). 2011 Mar 7;10(3):260-70.
- Merrikh H, Ferrazzoli AE, Lovett ST (2009). Growth phase and (p)ppGpp control of IraD, a regulator of RpoS stability, in Escherichia coli. J Bacteriol. 2009 Dec;191(24):7436-46.
- Persky NS, Ferullo DJ, Cooper DL, Moore HR, Lovett ST (2009). The ObgE/CgtA GTPase influences the stringent response to amino acid starvation in Escherichia coli. Mol Microbiol. 2009 Jul;73(2):253-66.
- Molt KL, Sutera VA, Moore KK, Lovett ST (2009). A Role for Non-essential Domain II of Initiator Protein DnaA in Replication Control. Genetics. 2009 Sep;183(1):39-49..
- Handa N, Morimatsu K, Lovett ST, Kowalczykowski SC (2009). Reconstitution of initial steps of dsDNA break repair by the RecF pathway of E. coli. Genes Dev.2009 May 15;23(10):1234-45.
- Ferullo DJ, Cooper DL, Moore HR, Lovett ST. (2009) Cell cycle synchronization of Escherichia coli using the stringent response, with fluorescence labeling assays for DNA content and replication. Methods. 2009 May; 48(1):8-13.
- Merrikh H, Ferrazzoli AE, Bougdour A, Olivier-Mason A, Lovett ST. (2009) A DNA damage response in Escherichia coli involving the alternative sigma factor, RpoS. Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):611-6. 2009.
- Persky NS, Lovett ST (2008). Mechanisms of Recombination: Lessons from E. coli. Crit Rev Biochem Mol Biol.2008;43(6):347-70.
- Ferullo DJ, Lovett ST (2008). The stringent response and cell cycle arrest in Escherichia coli. Plos Genet. 2008;4(12):e1000300.
- Lovett ST (2007). Polymerase switching in DNA replication. Mol Cell. 2007;27(4):523-6.
- Foti JJ, Persky NS, Ferullo DJ, Lovett ST (2007). Chromosome segregation control by Escherichia coli ObgE GTPase. Mol Microbiol. 2007;65(2):569-81.
- Dutra BE, Sutera VA, Jr., Lovett ST (2007). RecA-independent recombination is efficient but limited by exonucleases. Proc Natl Acad Sci U S A.2007;104(1):216-21.
- Sutera VA, Jr., Lovett ST (2006). The role of replication initiation control in promoting survival of replication fork damage. Mol Microbiol.2006;60(1):229-39.
- Lovett ST (2006). Microbiology: Resurrecting a broken genome. Nature. 2006.
- Lovett ST (2006). Replication arrest-stimulated recombination: Dependence on the RecA paralog, RadA/Sms and translesion polymerase, DinB. DNA Repair (Amst). 2006.
- Han ES, Cooper DL, Persky NS, Sutera VA, Jr., Whitaker RD, Montello ML, et al (2006). RecJ exonuclease: substrates, products and interaction with SSB. Nucleic Acids Res. 2006;34(4):1084-91.
- Goldfless SJ, Morag AS, Belisle KA, Sutera VA, Jr., Lovett ST (2006). DNA Repeat Rearrangements Mediated by DnaK-Dependent Replication Fork Repair. Mol Cell. 2006;21(5):595-604.
- Dutra BE, Lovett ST (2006). Cis and trans-acting effects on a mutational hotspot involving a replication template switch. J Mol Biol.2006;356(2):300-11.
- Lovett ST (2005). Filling the gaps in replication restart pathways. Mol Cell. 2005;17(6):751-2.
- Foti JJ, Schienda J, Sutera VA, Jr., Lovett ST (2005). A bacterial G protein-mediated response to replication arrest. Mol Cell. 2005;17(4):549-60.
View Complete Publication List on PubMed: Susan Lovett