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Indiana University Bloomington

Department of Biology

Faculty & Research

Faculty Profile

Malcolm Winkler

Photo of Malcolm Winkler
Research Images
Research photo by Malcolm Winkler

Cell morphology defects caused by underexpression of the essential PcsB division protein (or WalRK TCS; not shown).  

Research photo by Malcolm Winkler

Localization of FtsZ rings (green) and DNA (red) in pneumococcus cells by 3D deconvolution.  

Research photo by Malcolm Winkler

Morphology defects of a ΔdacA mutant (right) lacking an important PG hydrolase compared to its dacA+ parent (left). Cells were stained with DAPI + fluorescent vancomycin.

Professor of Biology; Microbiology Section Associate Chair

IU Affiliations
Indiana Molecular Biology Institute

Contact Information
By telephone: 856-1318/6-1184/6-1781
JH A414 / JH A410 (lab)
Research Areas
  • Genomics and Bioinformatics
  • Microbial Cell Biology and Environmental Responses
  • Microbial Interactions and Pathogenesis

Ph.D., Johns Hopkins University
Helen Hay Whitney Postdoctoral Fellow, Stanford University
Infectious Diseases Research Advisor, Eli Lilly and Company, 1999-2003


Young Investigator Award, American Society of Microbiology
Dissertation Opponent and Lecturer, Umeå University, Sweden
Dissertation Opponent and Lecturer, University of Groningen, Netherlands
Fellow, American Academy of Microbiology (AAM)
Fellow, American Association for the Advancement of Science (AAAS)

Research Description

Streptococcus pneumoniae (pneumococcus) is an extremely serious human opportunistic respiratory pathogen that kills well over two million people annually worldwide. Multidrug resistance is increasing in S. pneumoniae clinical isolates at an alarming rate. The overall goal of my research program is to understand signal transduction, regulatory mechanisms, and supramolecular complexes that mediate the stress responses, metabolism, cell structure, and pathogenesis of this bacterium. At one level, our work is providing fundamental information about the roles played by physiology, protein complexes, and metabolism in the pathogenesis of this bacterial species. At another level, we are gaining insights into the biology of S. pneumoniae, and by inference other Streptococcus species, which are distinctive, fascinating organisms that carry out many processes by mechanisms different from those of model bacteria like Bacillus subtilis. Therefore, besides understanding pathogenesis, there is the expectation of learning new biological principles from studies of S. pneumoniae. In addition, these investigations have very real practical implications in the discovery of new targets for antibiotic and vaccine development. In pursuit of these goals, we use a combination of sophisticated physiology, molecular genetic, biochemical, and cell biology approaches and animal models of infection. Three ongoing projects are outlined below. We also have a fruitful collaboration with the Giedroc laboratory in the IUB Chemistry Department on metal homeostasis in S. pneumoniae.

Project 1. Determine the signal transduction pathways used by the essential WalRKSpn (VicRK) two-component system (TCS) and its associated third component, WalJSpn (VicX), in S. pneumoniae. The WalRKSpn TCS is a major regulator of cell wall and surface homeostasis and plays roles in antibiotic stress responses, biofilm formation, anaerobic growth, and virulence. The goals of this project are to learn the signals that are sensed by the WalRKSpn TCS, the mechanisms by which WalRKJSpn respond to these signals to change gene expression, and the integration of WalRKJSpn signal transduction with other pneumococcal systems that sense and respond to antibiotics and cell-wall stresses. Meeting these goals will provide fundamental insights into the biology and virulence properties of this serious bacterial pathogen.

Project 2. Determine the locations, interactions, regulatory dynamics, and functions of the supramolecular protein complexes that mediate peptidoglycan (PG) biosynthesis on the cell surface of S. pneumoniae. Many clinically relevant antibiotics, including b-lactams and vancomycin, target peptidoglycan (PG) biosynthesis. PG forms the major rigid structure in the cell wall that determines cell shape and size and serves as the scaffolding onto which other pneumococcal virulence factors are covalently attached, including capsule, teichoic acids, and sortase-transferred proteins. Despite its importance to physiology and pathogenesis, little is known about the supramolecular protein complexes that mediate PG biosynthesis on the cell surface of S. pneumoniae and other ellipsoid-shaped ovococcus gram- positive pathogens. The goal of this project is to fill in this major knowledge gap.

Project 3. Determine the roles played by small non-coding RNAs (sRNAs) in regulating pneumococcal stress and virulence responses. Pneumococcus synthesizes numerous sRNAs, including some regulated by a TCS. The goal of this project is to learn the functions of these sRNAs during growth and stress and in virulence. This project will also determine the roles of RNA metabolism and RNA binding proteins in sRNA function. 

Select Publications

Tsui H.-C. T., M. J. Boersma, S. A. Vella, O. Kocaoglu, E. Kuru E, J. K. Peceny, E. E. Carlson, M. S. VanNieuwenhze, Y. V. Brun, S. L. Shaw, and M. E. Winkler. (2014). Pbp2x Localizes Separately from Pbp2b and Other Peptidoglycan Synthesis Proteins During Laters Stages of Cell Division of Streptococcus pneumoniae D39. Molec Microbiol 94:21-40. (PMC4209751).
Cover photo of volume 94, number 1 (October) of Molecular Microbiology. MicroCommentary: Cadby I.T. and A. L. Lovering. 2014. Molecular Surveillance of the Subtle Septum: Discovering a New Mode of Peptidoglycan Synthesis in Streptococcus. Molec Microbiol 94: 1-4.  

Yue F, H.-C. T. Tsui, K. E. Bruce, L.-T. Sham, K. A. Higgins, J. P. Lisher, K. M. Kazmierczak, M. J. Maroney, C. E. Dann III, M. E. Winkler, and D. P. Giedroc. (2013). A New Structural Paradigm in Copper Resistance in Streptococcus pneumoniae. Nature Chem Biol 9: 177-83. (PMC3578076).

Land, A.D., H.-C. T. Tsui, O. Kocaoglu, S. Vella, S. L. Shaw, S. K. Keen, L.-T. Sham, E. E. Carlson, and M. E. Winkler. (2013). Requirement of Essential Pbp2x and GpsB for Septal Ring Closure in Streptococcus pneumoniae D39. Molec Microbiol 90: 939-55.(PMC4120849).
Cover photo of volume 90, number 5 (December) of Molecular Microbiology.

Sham, L. T., K. R.  Jensen, K. E. Bruce, and M. E. Winkler. (2013). Involvement of FtsE ATPase and FtsX Extracellular Loops 1 and 2 in FtsEX:PcsB Complex Function in Cell Division of Streptococcus pneumoniae D39. MBio 4: pii: e00431-13. doi: 10.1128/mBio.00431-13. (PMC3735124).

Kocaoglu, O., R. A. Calvo, L.T. Sham, L. M. Cozy, S. Francis, B. R. Lanning, M. E. Winkler, D. B. Kearns, and E. E. Carlson. (2012). Selective Penicillin-Binding Protein Imaging Probes Reveal Substructure in Bacterial Cell Division. ACS Chem Biol 7: 1746-1753. (PMC3663142). Highlighted by the Faculty of 1000.

Sham, L.-T,, H.-C. T. Tsui, A. D. Land, S. M. Barendt, and M. E. Winkler. (2012). Recent Advances in Pneumococcal Peptidoglycan Biosynthesis Suggest New Vaccine and Antimicrobial Targets. Curr Opin Microbiol. 15:194-203. (PMC3322672).

Wayne, K. J., S. Li, K. M. Kazmierczak, H.-C. T. Tsui, and M. E. Winkler. (2012). Involvement of WalK (VicK) Phosphatase Activity in Setting WalR (VicR) Response Regulator Phosphorylation Level and Limiting Crosstalk in Streptococcus pneumoniae D39 Cells. Molec Microbiol 86:645-60. (PMC3638944).

Biller, S. J., K. J. Wayne, M. E. Winkler, and W. F. Burkholder. (2011). The Putative Hydrolase YycJ (WalJ) Affects the Coordination of Cell Division with DNA Replication in Bacillus subtilis and May Play a Conserved Role in Cell Wall Metabolism. J. Bacteriol. 193:896-908.
Major textbook: Wilson, B. A., A. A. Salyers, D. D. Whitt, and M. E. Winkler. (2011). Bacterial Pathogenesis - A Molecular Approach. Third Edition. ASM Press. Washington, D. C.
Sham, L.-T., S. M. Barendt, K. E. Kopecky, and M. E. Winkler. (2011). Essential PcsB Putative Peptidoglycan Hydrolase Interacts with the Essential FtsXSpn Cell Division Protein in Streptococcus pneumoniae D39. Proc. National Acad. of Sci., U. S. A. 108: 1061-2069.
Nichols, R. J., Y. J. Choo, S. Sen, P. Beltrao, M. Zietek, R. Chaba, S. Lee, K. M. Kazmierczak, K. J. Lee, A. Wong, M. Shales, S. Lovett, M. E. Winkler, N. J. Krogan, A. Typas, and C. A. Gross. (2011). Phenotypic Landscape of a Bacterial Cell. Cell 144:1-14.
Land, A. D., and M. E. Winkler (2011). Requirement for Pneumococcal MreC and MreD Is Relieved by Inactivation of the Gene Encoding PBP1a. J. Bacteriol. 193: 4166-4179.
Hsueh, Y.-H., L. M. Cozy, L.-T. Sham, R. A. Calvo, A. D. Gutu, M. E. Winkler, and D. B. Kearns. (2011). DegU-Phosphate Activates Expression of the Anti-Sigma Factor FlgM in Bacillus subtilis. Molec. Microbiol. 81: 1092-1108.
Barendt, S. M., L.-T. Sham, and M. E. Winkler. (2011). Characterization of Mutants Deficient in the L,D-Carboxypeptidase (DacB) and WalRK-Spn (VicRK) Regulon Involved in Peptidoglycan Maturation of Streptococcus pneumoniae Serotype 2 Strain D39. J. Bacteriol. 193: 2290-2300.
Jacobsen, F. E., K. M. Kazmierczak, J. P. Lisher, M. E. Winkler, and D. P. Giedroc. (2011). Interplay between Manganese and Zinc Homeostasis in the Human Pathogen Streptococcus pneumoniae. Metallomics 3: 38-41. [cover article].
Tsui, H.-C. T., S. K. Keen, L.-T. Sham, K. J. Wayne, and M. E. Winkler. (2011). Dynamic Distribution of the SecA and SecY Translocase Subunits and Septal Localization of the HtrA Surface Chaperon/Protease During Cell Division of Streptococcus pneumoniae D39. mBio 2(5). pii: e00202-11. doi: 10.1128/mBio.00202-11.
Tsui, H.-C. T., D. Mukherjee, V. A. Ray, L.-T. Sham, A. L. Feig, and M. E. Winkler. (2010). Identification and Characterization of Non-Coding Small RNAs in Streptococcus pneumoniae Serotype 2 Strain D39. J. Bacteriol 192:264-279.
Gutu, A. D., K. J. Wayne, L-T. Sham, and M. E. Winkler. (2010). Kinetic Characterization of the WalRKSpn (VicRK) Two-Component System of Streptococcus pneumoniae: Dependence of WalKSpn (VicK) Phosphatase Activity on Its PAS Domain. J. Bacteriol. 192: 2346-2358..
Reyes-Caballero, H, A. J. Guerra, F. E. Jacobsen, K. M. Kazmierczak, D. Cowart, U. M. Kumar-Koppolu, R. A. Scott, M. E. Winkler, and D. P. Giedroc. (2010). The Metalloregulatory Zinc Site in Streptococcus pneumoniae AdcR, A Zinc-Activated MarR Family Repressor. J. Mol. Biol. 403:197-216.
Ramos-Montañez, S., K. M. Kazmierczak, K. L. Hentchel, and M. E. Winkler. (2010). Instability of ackA (Acetate Kinase) Mutations and Their Effects on Acetyl Phosphate (AcP) and ATP Amounts in Streptococcus pneumoniae D39. J. Bacteriol. 192: 6390-6400.
Wayne, K. J., L.-T. Sham, H.-C. T. Tsui, A. D. Gutu, S. M. Barendt, S. K. Keen, and M. E. Winkler. (2010). Localization and Cellular Amounts of the WalRKJSpn (VicRKX) Two-Component Regulatory System Proteins in Serotype 2 Streptococcus pneumoniae. J. Bacteriol. 192: 4388-4394. .
Kazmierczak, K. M., K. J. Wayne, A. Rechtsteiner, and M. E. Winkler. (2009). Roles of relSpn in the Stringent Response, Global Regulation, and Virulence of Serotype 2 Streptococcus pneumoniae. Molec Micro 72: 590-611.
Barendt, S. M., A. D. Land, L.-T. Sham, W.-L. Ng, H.-C. T. Tsui, R. J. Arnold, and M. E. Winkler. (2009). Capsule Influences the Cell Shape and Chain Length of pcsB Mutants in Serotype 2 Streptococcus pneumoniae. J. Bacteriol 191: 3024-3040. [cover article].

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