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Luciano Marraffini, Ph.D.

Assistant Professor
Laboratory of Bacteriology

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Faculty Bio

Luciano Marraffini

Dr. Marraffini is interested in understanding how bacteria evolve by incorporating DNA sequences from mobile genetic elements or from the environment into their genomes. His research focuses on the mechanisms that control the traffic of DNA molecules between bacteria.

As many as one quarter of all deaths worldwide are caused by infectious disease, and the rise of antimicrobial-resistant bacterial strains in the hospital setting has become a major health care crisis. To limit the spread of such antibiotic-resistant pathogens, a greater understanding of their means of emergence and survival is required. The major route for the acquisition of antimicrobial resistance is the exchange of genetic material between related or unrelated bacterial species, known as horizontal gene transfer. Dr. Marraffini’s research focuses on the study of mechanisms that prevent horizontal gene transfer and how they impact the evolution of bacterial pathogens.

Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. In many bacteria and most archaea, clustered, regularly interspaced, short palindromic repeats (CRISPRs) specify a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids and therefore prevents two major routes of horizontal gene transfer: bacteriophage infection and plasmid conjugation. CRISPRs are separated by short spacer sequences that match bacteriophage or plasmid sequences and specify the targets of interference. These sequences are transcribed into CRISPR RNAs (crRNAs) — small RNAs that target invasive nucleic acids. Upon infection, CRISPR arrays can acquire new repeat-spacer units that match the challenging phage or plasmid. Therefore the spacer content of CRISPR arrays reflects the many different invaders encountered by the host and can be expanded rapidly in response to new ones. Accordingly, CRISPR loci constitute a “genetic memory” that ensures the rejection of new, returning and ever-present invading DNA molecules.

Dr. Marraffini uses Staphylococcus epidermidis as a model system for studying CRISPR interference. A clinical isolate of this bacterium (S. epidermidis RP62a) harbors a CRISPR spacer that matches the nickase gene (nes) present in nearly all staphylococcal conjugative plasmids, including those that confer antibiotic resistance in pathogenic Staphylococcus aureus. By deleting the CRISPR locus and introducing mutations in the nes target, Dr. Marraffini demonstrated that CRISPR interference prevents conjugation and plasmid transformation in S. epidermidis. Insertion of a self-splicing intron into nes blocks interference despite the reconstitution of the target sequence in the spliced nes messenger RNA, indicating that the interference machinery targets DNA, rather than RNA, directly. By modifying flanking sequences and introducing compensatory mutations, he has demonstrated that CRISPR systems use the base-pairing potential of crRNA precursors not only to specify a target, but also to spare the CRISPR locus from self-destruction. He has found that in S. epidermidis, extended complementarity between crRNA and CRISPR DNA flanking sequences prevents self-targeting and that the absence of this complementarity in bona fide targets licenses interference.

Dr. Marraffini’s current research employs molecular genetic approaches to analyze the genesis and function of CRISPR arrays in different pathogenic bacteria. Recently he determined that CRISPR interference, by preventing natural transformation of the human pathogen Streptococcus pneumoniae, can prevent pneumococcal capsule switching during infection. He is also working on the biochemical characterization of crRNA-containing ribonucleoprotein complexes. He ultimately hopes to answer fundamental questions about how CRISPR function affects the rise and evolution of pathogens, perform detailed analyses of the underlying CRISPR interference molecular mechanisms and facilitate the manipulation of this natural pathway to develop new technologies.

Dr. Marraffini is a faculty member in the Tri-Institutional Ph.D. Program in Chemical Biology.


Dr. Marraffini, a native of Argentina, received his undergraduate degree from the University of Rosario in Argentina in 1998 and his Ph.D. from the University of Chicago in 2007, where he studied bacterial pathogenesis in the laboratory of Olaf Schneewind. He was a postdoc at Northwestern University from 2008 to 2010, when he joined Rockefeller as assistant professor.

He is a 2012 Rita Allen Foundation Scholar and a 2011 Searle Scholar and is the recipient of a 2012 NIH Director’s New Innovator Award, a 2010 RNA Society Award, a 2009 Nestle Award and a 2008 Jane Coffin Childs Memorial Fund for Medical Research fellowship.

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