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Wali Karzai, PhD

Professor and Chair
Department of Biochemistry and Cell Biology 
Stony Brook University
Phone: (631) 632-1688
Fax: (631) 632-8575

Wali Karzai

Karzai Lab Website

We are accepting new lab members (Graduate Students and Postdocs).

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 Wali Karzai is a 2003 PEW SCHOLAR.

  • Research Interests

    Biochemical, Structural, and Mechanistic Explorations of Protein and RNA Homeostasis.

    Our current focus is on Post-transcriptional Regulation of Gene Expression

    Post-transcriptional regulation plays a crucial role in controlling gene expression. Our research is aimed at elucidating post-transcriptional gene regulatory processes in bacteria. We are particularly interested in investigating: 

    1- Protein Homeostasis and Adaptor Guided Proteolysis
          * Substrate Recognition Principles of AAA+ Proteases
         * Adaptor Mediate Proteolysis 
         *Discovery of Novel Protease Adaptors
    2- Quality Control of Nascent Polypeptide Synthesis
        *Molecular Recognition of Aberrant Translation
        *Ribosome-Associated Protein Quality Control Pathway
        *Function and Regulation of Ribosome-Associated Factors 
    3- Quality Control of mRNA Decoding and Decay 
       *Defective mRNA Recognition During Translation
        *RNase R Recruitment to Rescued Ribosome
        *Functionally Specialized Ribosomes and Selective mRNA Decay

    Our Approach

    We use a combination of protein biochemistry, molecular genetics, functional genomics, bioinformatics, and structural approaches to determine the biological function and mechanism of action of RNA-protein complexes that participate in regulation of gene expression.

    Lab Introduction

  • Research Description

    Current Projects in the Lab

    1. Co-translational regulation of gene expression

    Our research endeavors in this area are aimed at gaining a thorough and detailed mechanistic understanding of the tmRNA mediated trans-translation process. We have identified a protein factor, small protein B (SmpB), that is essential for the initial binding and subsequent accommodation of tmRNA into the ribosomal A-site. We have identified key amino acid residues in SmpB that are essential for tmRNA binding. We are currently exploring the biochemical and mechanistic details of how these and additional SmpB residues participate in binding of tmRNA and the recognition of stalled ribosomes. Using mutational analysis and biochemical experiments, we have discovered a novel SmpB function associated with its C-terminal unstructured domain. This function is required for a step in the tagging process downstream of tmRNA binding and ribosome association but prior to transpeptidation and establishment of the tmRNA reading frame. Our studies have demonstrated that residues in the C-terminal tail of SmpB confer a previously unknown function that is essential for trans-translation. We are currently exploring the mechanistic detail of exactly how the SmpB C-terminal tail facilitates tmRNA accommodation into the ribosomal A-site, and what steps of the accommodation process are defective with the C-terminal tail variants.

    2. Nonstop mRNA decay

    We have discovered that defective mRNAs that promote ribosome stalling are selectively degraded by RNase R, a processive 3’-to-5’ exoribonuclease. This targeted RNase R activity is dependent on the presence of SmpB protein and tmRNA, suggesting a requirement for active trans-translation in facilitating RNase R engagement and nonstop mRNA decay. Interestingly, this RNase R activity targets aberrant (nonstop and multiple-rare-codon containing) mRNAs and does not affect the decay of related messages containing in-frame stop codons. Efforts are underway to elucidate the mechanism of how RNase R is targeted to nonstop mRNAs.

    3. Directed proteolysis and the Lon Protease

    We have recently demonstrated a direct role for the ATP-dependent protease Lon in the degradation of tmRNA-tagged proteins, in vivo and in vitro. We are interested in deciphering how tmRNA tagged proteins are recognized by Lon and what sequence determinants are required for the selective recognition and directed degradation by Lon.

    4. Physiological Significance of the tmRNA System

    We are investigating the role of the SmpB-SsrA system the in survival and virulence of two pathogenic bacterial species, Yersinia and Francisella. Our studies demonstrate that the SmpB-tmRNA tagging and ribosome rescue system is functional in both bacterial species. Furthermore, our investigations have shown that a ΔsmpB-ssrA mutant strain is avirulent and unable to cause mortality in a mouse infection model. Consistent with these observations, we have demonstrated that the expression of a key type three secretion system (TTSS) transcriptional activator, VirF, and a number of other Ysc-Yop system genes is reduced in the ΔsmpB-ssrA mutant. We are currently investigating the regulatory role of the SmpB-tmRNA system in controlling expression of the TTSS.

    5. We are also interested in understanding how sequence and structure in RNA-binding proteins contributes to the formation of specific RNA-protein complexes and how these complexes promote specific biological functions.

  • Publications
    1. J. L. Coleman, J. L. Benach, A. W. Karzai, Endogenous and Borrowed Proteolytic Activity in the Borrelia. Microbiol Mol Biol Rev85, (2021).
    2. M. Shin et al., Structural basis for distinct operational modes and protease activation in AAA+ protease Lon. Sci Adv6, eaba8404 (2020).
    3. N. Puri, A. W. Karzai, HspQ Functions as a Unique Specificity-Enhancing Factor for the AAA+ Lon Protease. Mol Cell66, 672-683 e674 (2017).
    4. L. R. Friedlander, N. Puri, M. A. Schoonen, A. Wali Karzai, The effect of pyrite on Escherichia coli in water: proof-of-concept for the elimination of waterborne bacteria by reactive minerals. J Water Health13, 42-53 (2015).
    5. K. Venkataraman, H. Zafar, A. W. Karzai, Distinct tmRNA sequence elements facilitate RNase R engagement on rescued ribosomes for selective nonstop mRNA decay. Nucleic Acids Res, (2014).
    6. K. Venkataraman, K. E. Guja, M. Garcia-Diaz, A. W. Karzai, Non-stop mRNA decay: a special attribute of trans-translation mediated ribosome rescue. Front Microbiol5, 93 (2014).
    7. N. P. Lonia R. Friedlander, Martin A. A. Schoonen and A. Wali Karzai, The effect of pyrite on Escherichia coli in water: proof-of-concept for the elimination of waterborne bacteria by reactive minerals. Journal of Water and Health, (2014).
    8. K. E. Guja et al., Structural basis for S-adenosylmethionine binding and methyltransferase activity by mitochondrial transcription factor B1. Nucleic Acids Res41, 7947-7959 (2013).
    9. D. Camenares, D. P. Dulebohn, A. Svetlanov, A. W. Karzai, Active and accurate trans-translation requires distinct determinants in the C-terminal tail of SmpB protein and the mRNA-like domain of transfer messenger RNA (tmRNA). J Biol Chem288, 30527-30542 (2013).
    10.  A. Svetlanov, N. Puri, P. Mena, A. Koller, A. W. Karzai, Francisella tularensis tmRNA system mutants are vulnerable to stress, avirulent in mice, and provide effective immune protection. Mol Microbiol85, 122-141 (2012).
    11.  P. Mehta, P. Woo, K. Venkataraman, A. W. Karzai, Ribosome purification approaches for studying interactions of regulatory proteins and RNAs with the ribosome. Methods Mol Biol905, 273-289 (2012).
    12.  M. Srinivasan et al., The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. EMBO J30, 873-881 (2011).
    13.  N. A. Okan, P. Mena, J. L. Benach, J. B. Bliska, A. W. Karzai, The smpB-ssrA mutant of Yersinia pestis functions as a live attenuated vaccine to protect mice against pulmonary plague infection. Infect Immun78, 1284-1293 (2010).
    14.  Z. Ge, P. Mehta, J. Richards, A. W. Karzai, Non-stop mRNA decay initiates at the ribosome. Mol Microbiol78, 1159-1170 (2010).
    15.  H. S. Fukuto, A. Svetlanov, L. E. Palmer, A. W. Karzai, J. B. Bliska, Global gene expression profiling of Yersinia pestis replicating inside macrophages reveals roles of a putative stress-induced operon in regulating type III secretion and intracellular cell division. Infect Immun, (2010).
    16.  Z. Ge, A. W. Karzai, Co-evolution of multipartite interactions between an extended tmRNA tag and a robust Lon protease in Mycoplasma. Mol Microbiol74, 1083-1099 (2009).
    17.  T. Sundermeier, Z. Ge, J. Richards, D. Dulebohn, A. W. Karzai, Studying tmRNA-mediated surveillance and nonstop mRNA decay. Methods Enzymol447, 329-358 (2008).
    18.  J. Richards, T. Sundermeier, A. Svetlanov, A. W. Karzai, Quality control of bacterial mRNA decoding and decay. Biochim Biophys Acta1779, 574-582 (2008).
    19.  T. R. Sundermeier, A. W. Karzai, Functional SmpB-ribosome interactions require tmRNA. J Biol Chem282, 34779-34786 (2007).
    20.  D. Dulebohn, J. Choy, T. Sundermeier, N. Okan, A. W. Karzai, Trans-translation: the tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decay. Biochemistry46, 4681-4693 (2007).
    21.  J. S. Choy, L. L. Aung, A. W. Karzai, Lon protease degrades transfer-messenger RNA-tagged proteins. Journal of Bacteriology189, 6564-6571 (2007).
    22.  J. Richards, P. Mehta, A. W. Karzai, RNase R degrades non-stop mRNAs selectively in an SmpB-tmRNA-dependent manner. Mol Microbiol62, 1700-1712 (2006).
    23.  N. A. Okan, J. B. Bliska, A. W. Karzai, A Role for the SmpB-SsrA system in Yersinia pseudotuberculosis pathogenesis. PLoS Pathog2, e6 (2006).
    24.  P. Mehta, J. Richards, A. W. Karzai, tmRNA determinants required for facilitating nonstop mRNA decay. RNA12, 2187-2198 (2006).
    25.  D. P. Dulebohn, H. J. Cho, A. W. Karzai, Role of conserved surface amino acids in binding of SmpB protein to SsrA RNA. The Journal of biological chemistry281, 28536-28545 (2006).
    26.  T. R. Sundermeier, D. P. Dulebohn, H. J. Cho, A. W. Karzai, A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation. Proc Natl Acad Sci U S A102, 2316-2321 (2005).
    27.  A. W. Karzai, R. T. Sauer, Protein factors associated with the SsrA.SmpB tagging and ribosome rescue complex. Proc Natl Acad Sci U S A98, 3040-3044 (2001).
    28.  S. Barends, A. W. Karzai, R. T. Sauer, J. Wower, B. Kraal, Simultaneous and functional binding of SmpB and EF-Tu-TP to the alanyl acceptor arm of tmRNA. J Mol Biol314, 9-21 (2001).
    29.  A. W. Karzai, E. D. Roche, R. T. Sauer, The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nature Structural Biology7, 449-455 (2000).
    30.  J. F. Schildbach, A. W. Karzai, B. E. Raumann, R. T. Sauer, Origins of DNA-binding specificity: role of protein contacts with the DNA backbone. Proc Natl Acad Sci U S A96, 811-817 (1999).
    31.  R. Russell, A. Wali Karzai, A. F. Mehl, R. McMacken, DnaJ dramatically stimulates ATP hydrolysis by DnaK: insight into targeting of Hsp70 proteins to polypeptide substrates. Biochemistry38, 4165-4176 (1999).
    32.  A. W. Karzai, M. M. Susskind, R. T. Sauer, SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J18, 3793-3799 (1999).
    33.  A. W. Karzai, R. McMacken, A bipartite signaling mechanism involved in DnaJ-mediated activation of the Escherichia coli DnaK protein. The Journal of biological chemistry271, 11236-11246 (1996).
    34.  B. Learn, A. W. Karzai, R. McMacken, Transcription stimulates the establishment of bidirectional lambda DNA replication in vitro. Cold Spring Harbor symposia on quantitative biology58, 389-402 (1993).
    35.  A. W. Karzai, W. W. Wright, Regulation of the synthesis and secretion of transferrin and cyclic protein-2/cathepsin L by mature rat Sertoli cells in culture. Biology of reproduction47, 823-831 (1992).
    36.  S. D. Zabludoff, A. W. Karzai, W. W. Wright, Germ cell-Sertoli cell interactions: the effect of testicular maturation on the synthesis of cyclic protein-2 by rat Sertoli cells. Biol Reprod43, 25-33 (1990).
    37.  W. W. Wright, S. D. Zabludoff, M. Erickson-Lawrence, A. W. Karzai, Germ cell-Sertoli cell interactions. Studies of cyclic protein-2 in the seminiferous tubule. Annals of the New York Academy of Sciences564, 173-185 (1989).


  • Lab Personnel
    Current Lab Members
    • Thiago Rodrigues, PhD
    • Melanie Cragan
    • Javon Lo
    • Nina Cheng
    • Anton Svetlanov, Ph.D.
    • Preeti Mehta, Ph.D.
    • Jamie Richards, Ph.D. 
    • Junjei Feng, Ph.D.
    Graduate students
    • Krithika Venkataraman
    • Devin Camenares
    • Neha Puri
    • Zhiyun Ge
    • Perry Woo
    • Daniel Dulebohn
    • Nihal Okan
    • Tom Sundermeier
    • Jennifer Choy
    • Arnav Choksi
    • Eric Adjei
    • Pei-Ni Tsai
    • Andrew Michaels
    • Hina Zafar
    • Poorna Kannan
    Undergraduate students
    • Adnan Ziahulla                                 
    • Omar saleh               
    • Jassica Shynn                         
    • Andrew Chang (HS)                          
    • Daniel La                           
    • Francesco  Liotino                            
    • Palwasha Kennedy                            
    • Ahmad Zehni                                                                                               
    • Hisham Talukder                                          
    • Maryam Torab Parhiz            
    • Rose Deblanco                                 
    • James Byrnes                                   
    • Aisha Akhtar                                               
    • Stephen Campbell                
    • Muath Bishawi
    • Nauman Khankhel
    • Izzat Kamran
    • Corinne McGuirk                
    • Arthur Korman                                 
    • Robert Furatero                                
    • Allison Chang 
    • Felo Shenouda