Research

1. Metabolic regulation of bacterial growth, division, and morphogenesis

Cell growth and division are fundamental processes for cells to survive and proliferate. Therefore, cells developed various strategies to precisely regulate the processes. The single-cell organism E. coli evolved a mechanism involving the Min proteins to mediate placement of the division septum at the midcell. The MinD and MinE proteins oscillate back and forth between two cell poles to partition the division inhibitor MinC to the poles in order to block aberrant polar division. At the molecular level, sophisticated interactions between the Min proteins, and between the Min proteins and the membrane are critical factors to drive the oscillation cycle.

Since the Min protein-mediated division site placement is not essential for cell survival, a puzzling question has been whether there is unanticipated physiological importance that allows the system to be preserved through evolution. Because the membrane interaction is critical to sustain the Min function, we took a systems approach to tackle the question by comparing the inner membrane proteomes of the ∆min mutant and the wild-type strain. Using the quantitative proteomic method, we identified proteins of interest (POIs) whose abundance in the inner membrane was affected in the absence of the Min system. Interestingly, functional analysis of POIs pointed at a link between metabolism and the Min system. In accordance with this observation, we detected changes in the metabolite profile of the mutant. Therefore, we now focus on investigating the mechanisms that underlie the metabolic regulation of cell growth and division, and the coordination with cell morphology and size.

2. Partition of membrane components by the Min proteins

Alongside studying the biological function of the Min proteins, my lab developed an interest in using the membrane mimetic systems in combination with the fluorescence microscopy to study the protein-membrane interactions. By these methods that allow us to appreciate the ‘membrane’ side of the story, we discovered the intrinsic properties of MinE to self-assemble on the membrane surface using the supported lipid bilayers, and to sculpt the membrane and to induce tubulation from liposomes. The in vitro phenomena may reflect the fact that the cell membrane at the division site is actively remodeled and highly unstable due to assembly of the septal proteins that are responsible for growth and division.

Under the same theme, we discovered that dynamic motion of the self-organizing Min proteins can transport the lipid-anchored components on the bilayer surface. The observation assimilates into the knowledge that the MinD/ParA Walker-type ATPase family of proteins can partition various cellular components in bacteria. To follow up, we will investigate the physiological significance of the phenomenon.

3. Cell wall synthesis in response to environmental stresses

The bacterial cell envelope maintains cell integrity, determines morphology, and protects the cell from environmental assaults. It can be the primary target for treating bacterial infection, but on the other side of a coin, it can become a boundary to interfere with the antibiotic treatment. Therefore, understanding the physiology and synthesis of the bacterial cell envelope, including the cell wall, has fundamental importance in formulating strategies to combat bacterial infection.

The bacterial cell wall is synthesized through multiple steps of enzymatic reactions to form a mesh-like structure, peptidoglycan (PG). Although chemical composition, structure, and function of PG have been studied for many decades, the understanding about the spatiotemporal coordination of the protein complexes that are responsible for synthesis and remodeling is still limited. The goal of our study is to investigate the dynamical changes of PG synthesis under different physiological conditions.

Degrees and Positions Held
Positions Held
  • 2014 – present   Associate Research Fellow, Institute of Biological Chemistry, Academia Sinica
  • 2006 – 2014   Assistant Research Fellow, Institute of Biological Chemistry, Academia Sinica
  • 2004 – 2006   Instructor, Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, USA
  • 1999 – 2003   Postdoctoral Fellow, Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, USA
Degrees
  • 1996 – 1999   Ph.D., Department of Biochemistry, University of Cambridge, UK
  • 1992 – 1994   M.Sc., Department of Plant Pathology and Entomology, National Taiwan University
  • 1988 – 1992   B.Sc., Department of Plant Pathology and Entomology, National Taiwan University
Selected Publications
Shih YL*, Huang LT, Tu YM, Lee BF, Bau YC, Hong CY, Lee HL, Shih YP, Hsu MF, Lu ZX, Chen JS, Chao L*
Biophysical Journal (2019)
Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, KY Wang, Lin SY, Shih YL
MOLECULAR & CELLULAR PROTEOMICS (2016)
Zheng M, Chiang YL, Lee HL, Kong LR, Hsu ST, Hwang IS, Rothfield LI and Shih YL
J Biol Chem (2014)
Shih YL, Huang KF, Lai HM, Liao JH, Lee CS, Chang CM, Mak HM, Hsieh CW & Lin CC
PLoS One (2011)
Hsieh CW, Lai HM, Lin CC, Lin TY, Hsieh TS, Shih YL
Molecular Microbiology (2010)
Shih YL*, Kawagishi I and Rothfield LI*
Mol Microbiol (2005)
Shih YL, Le T, Rothfield LI*
Proc Natl Acad Sci USA (2003)
Shih YL, Fu X, King GF, Le T and Rothfield LI*
EMBO J (2002)
Publications List
  1. Wu CF, Lien YW, Bondage D, Lin JS, Pilhofer M, (Shih YL), Chang JH, Lai EM*  (2020-01)  EMBO Reports  21(1), e47961  "Effector loading onto the VgrG carrier activates type VI secretion system assembly."
  2. (Shih YL)*, Huang LT, Tu YM, Lee BF, Bau YC, Hong CY, Lee HL, Shih YP, Hsu MF, Lu ZX, Chen JS, Chao L*  (2019-04)  BIOPHYSICAL JOURNAL  116(8), 1469-1482  "Active Transport of Membrane Components by Self-Organization of the Min Proteins."
  3. Chen WJ, Kuo TY, Hsieh FC, Chen PY, Wang CS, (Shih YL), Lai YM, Liu JR, Yang YL, and Shih MC*  (2016-09)  Scientific Reports  6, 32950  "Involvement of type VI secretion system in secretion of iron chelator pyoverdine in Pseudomonas taiwanensis"
  4. Liang SY, Lin SY, Chiang IC, (Shih YL*)  (2016-05)  Data in Brief  8, 304-307  "Quantitative inner membrane proteome datasets of the wild-type and the Δmin mutant of Escherichia coli"
  5. Liao JH, Chien CT, Wu, HY, Huang KF, Wang I, Ho MR, Tu IF, Lee IM, Li W, (Shih YL), Wu CY, Lukyanov P, Hsu STD, Wu SH*  (2016-04)  J Am Chem Soc  138(14), 4787-4795  "A multivalent marine lectin from Crenomytilus grayanus possesses anti-cancer activity through recognizing globotriose Gb3"
  6. Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, KY Wang, Lin SY, (Shih YL*)  (2016-02)  MOLECULAR & CELLULAR PROTEOMICS  15, 1572-1583  "Quantitative proteomics analysis reveals the Min system of Escherichia coli modulates reversible protein association with the inner membrane"
  7. Chiang YL, Chang YC, Chiang IC, Mak HM, Hwang IS*, (Shih YL)*  (2015-11)  PloS one  10(11), e0142506  "Atomic Force Microscopy Characterization of Protein Fibrils Formed by the Amyloidogenic Region of the Bacterial Protein MinE on Mica and a Supported Lipid Bilayer."
  8. Rujiviphat J, Wong MK, Won A, (Shih YL), Yip CM and McQuibban AG*  (2015-03)  J Mol Biol  427(16), 2595-2598  "Mitochondrial Genome Maintenance 1 (Mgm1) Protein alters membrane topology and promotes local membrane bending"
  9. Zheng M, Chiang YL, Lee HL, Kong LR, Hsu ST, Hwang IS, Rothfield LI, (Shih YL)*   (2014-08)  J Biol Chem  289(31), 21252-21266  "Self-Assembly of MinE on the Membrane Underlies Formation of the MinE-Ring to Sustain Function of the E. coli Min System"
  10. (Shih YL)*, Zheng M  (2013-12)  Environmental Microbiology  15(12), 3229-3239  "Spatial control of the cell division site by the Min system in E. coli"
  11. (Shih YL)*, Huang KF, Lai HM, Liao JH, Lee CS, Chang CM, Mak HM, Hsieh CW & Lin CC  (2011)  PLoS One  6(6), e21425  "The N-terminal amphipathic helix of the topological specificity factor MinE is associated with shaping membrane curvature"
  12. Hsieh CW, Lai HM, Lin CC, Lin TY, Hsieh TS, (Shih YL)*  (2010)  MOLECULAR MICROBIOLOGY  75(2), 499-512  "Direct MinE-membrane interaction contributes to the proper localization of MinDE in E. coli"
  13. Vats P, Shih YL, Rothfield L  (2009)  Molecular microbiology  72(1), 170-182  "Assembly of the MreB-associated cytoskeletal ring of Escherichia coli."
  14. Pradel N, Santini CL, Bernadac A, Shih YL, Goldberg MB, Wu LF  (2007)  Biochemical and biophysical research communications  353(2), 493-500  "Polar positional information in Escherichia coli spherical cells."
  15. Y-L Shih, LI Rothfield  (2006)  Microbiology and Molecular Biology Reviews  70, 729-754  "The bacterial cytoskeleton"
  16. LI Rothfield, A Taghbalout and Y-L Shih  (2005)  Nat Rev Microbiol  3, 959-968  "Spatial control of bacterial division-site placement"
  17. Y-L Shih, I Kawagishi and LI Rothfield  (2005)  Mol Microbiol  58, 917-928  "The MreB and Min cytoskeletal-like systems play independent roles in prokaryotic polar differentiation"
  18. Shih YL, Le T, Rothfield L  (2003)  Proceedings of the National Academy of Sciences of the United States of America  100(13), 7865-7870  "Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles."
  19. Y-L Shih, X Fu, GF King , T Le and LI Rothfield  (2002)  EMBO J  21, 3347-3357  "Division site placement in E.coli: mutations that prevent formation of the MinE ring lead to loss of the normal midcell arrest of growth of polar MinD membrane domains"
  20. Rothfield LI, Shih YL, King G  (2001)  Cell  106(1), 13-16  "Polar explorers: membrane proteins that determine division site placement."
  21. Fu X, Shih YL, Zhang Y, Rothfield LI  (2001)  Proceedings of the National Academy of Sciences of the United States of America  98(3), 980-985  "The MinE ring required for proper placement of the division site is a mobile structure that changes its cellular location during the Escherichia coli division cycle."
  22. King GF, Shih YL, Maciejewski MW, Bains NP, Pan B, Rowland SL, Mullen GP, Rothfield LI  (2000)  Nature Structural Biology  7(11), 1013-1017  "Structural basis for the topological specificity function of MinE."
  23. Shih YL, Harris SJ, Borner G, Rivet MM, Salmond GP  (1999)  Environmental microbiology  1(6), 535-547  "The hexY genes of Erwinia carotovora ssp. carotovora and ssp. atroseptica encode novel proteins that regulate virulence and motility co-ordinately."
  24. Harris SJ, Shih YL, Bentley SD, Salmond GP  (1998)  Molecular microbiology  28(4), 705-717  "The hexA gene of Erwinia carotovora encodes a LysR homologue and regulates motility and the expression of multiple virulence determinants."
  25. Toth I, Mulholland V, Copper V, Bentley S, Shih Y-L, Perombelon M, and Salmond GPC  (1997)  Microbiology  143, 2433-2438  "Generalized transduction in the potato blackleg pathogen Erwinia carotovora subsp. atroseptica by bacteriophage φM1"

1. Metabolic regulation of bacterial growth, division, and morphogenesis

Cell growth and division are fundamental processes for cells to survive and proliferate. Therefore, cells developed various strategies to precisely regulate the processes. The single-cell organism E. coli evolved a mechanism involving the Min proteins to mediate placement of the division septum at the midcell. The MinD and MinE proteins oscillate back and forth between two cell poles to partition the division inhibitor MinC to the poles in order to block aberrant polar division. At the molecular level, sophisticated interactions between the Min proteins, and between the Min proteins and the membrane are critical factors to drive the oscillation cycle.

Since the Min protein-mediated division site placement is not essential for cell survival, a puzzling question has been whether there is unanticipated physiological importance that allows the system to be preserved through evolution. Because the membrane interaction is critical to sustain the Min function, we took a systems approach to tackle the question by comparing the inner membrane proteomes of the ∆min mutant and the wild-type strain. Using the quantitative proteomic method, we identified proteins of interest (POIs) whose abundance in the inner membrane was affected in the absence of the Min system. Interestingly, functional analysis of POIs pointed at a link between metabolism and the Min system. In accordance with this observation, we detected changes in the metabolite profile of the mutant. Therefore, we now focus on investigating the mechanisms that underlie the metabolic regulation of cell growth and division, and the coordination with cell morphology and size.

2. Partition of membrane components by the Min proteins

Alongside studying the biological function of the Min proteins, my lab developed an interest in using the membrane mimetic systems in combination with the fluorescence microscopy to study the protein-membrane interactions. By these methods that allow us to appreciate the ‘membrane’ side of the story, we discovered the intrinsic properties of MinE to self-assemble on the membrane surface using the supported lipid bilayers, and to sculpt the membrane and to induce tubulation from liposomes. The in vitro phenomena may reflect the fact that the cell membrane at the division site is actively remodeled and highly unstable due to assembly of the septal proteins that are responsible for growth and division.

Under the same theme, we discovered that dynamic motion of the self-organizing Min proteins can transport the lipid-anchored components on the bilayer surface. The observation assimilates into the knowledge that the MinD/ParA Walker-type ATPase family of proteins can partition various cellular components in bacteria. To follow up, we will investigate the physiological significance of the phenomenon.

3. Cell wall synthesis in response to environmental stresses

The bacterial cell envelope maintains cell integrity, determines morphology, and protects the cell from environmental assaults. It can be the primary target for treating bacterial infection, but on the other side of a coin, it can become a boundary to interfere with the antibiotic treatment. Therefore, understanding the physiology and synthesis of the bacterial cell envelope, including the cell wall, has fundamental importance in formulating strategies to combat bacterial infection.

The bacterial cell wall is synthesized through multiple steps of enzymatic reactions to form a mesh-like structure, peptidoglycan (PG). Although chemical composition, structure, and function of PG have been studied for many decades, the understanding about the spatiotemporal coordination of the protein complexes that are responsible for synthesis and remodeling is still limited. The goal of our study is to investigate the dynamical changes of PG synthesis under different physiological conditions.

Positions Held
  • 2014 – present   Associate Research Fellow, Institute of Biological Chemistry, Academia Sinica
  • 2006 – 2014   Assistant Research Fellow, Institute of Biological Chemistry, Academia Sinica
  • 2004 – 2006   Instructor, Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, USA
  • 1999 – 2003   Postdoctoral Fellow, Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, USA
Degrees
  • 1996 – 1999   Ph.D., Department of Biochemistry, University of Cambridge, UK
  • 1992 – 1994   M.Sc., Department of Plant Pathology and Entomology, National Taiwan University
  • 1988 – 1992   B.Sc., Department of Plant Pathology and Entomology, National Taiwan University
Shih YL*, Huang LT, Tu YM, Lee BF, Bau YC, Hong CY, Lee HL, Shih YP, Hsu MF, Lu ZX, Chen JS, Chao L*
Biophysical Journal (2019)
Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, KY Wang, Lin SY, Shih YL
MOLECULAR & CELLULAR PROTEOMICS (2016)
Zheng M, Chiang YL, Lee HL, Kong LR, Hsu ST, Hwang IS, Rothfield LI and Shih YL
J Biol Chem (2014)
Shih YL, Huang KF, Lai HM, Liao JH, Lee CS, Chang CM, Mak HM, Hsieh CW & Lin CC
PLoS One (2011)
Hsieh CW, Lai HM, Lin CC, Lin TY, Hsieh TS, Shih YL
Molecular Microbiology (2010)
Shih YL*, Kawagishi I and Rothfield LI*
Mol Microbiol (2005)
Shih YL, Le T, Rothfield LI*
Proc Natl Acad Sci USA (2003)
Shih YL, Fu X, King GF, Le T and Rothfield LI*
EMBO J (2002)
  1. Wu CF, Lien YW, Bondage D, Lin JS, Pilhofer M, (Shih YL), Chang JH, Lai EM*  (2020-01)  EMBO Reports  21(1), e47961  "Effector loading onto the VgrG carrier activates type VI secretion system assembly."
  2. (Shih YL)*, Huang LT, Tu YM, Lee BF, Bau YC, Hong CY, Lee HL, Shih YP, Hsu MF, Lu ZX, Chen JS, Chao L*  (2019-04)  BIOPHYSICAL JOURNAL  116(8), 1469-1482  "Active Transport of Membrane Components by Self-Organization of the Min Proteins."
  3. Chen WJ, Kuo TY, Hsieh FC, Chen PY, Wang CS, (Shih YL), Lai YM, Liu JR, Yang YL, and Shih MC*  (2016-09)  Scientific Reports  6, 32950  "Involvement of type VI secretion system in secretion of iron chelator pyoverdine in Pseudomonas taiwanensis"
  4. Liang SY, Lin SY, Chiang IC, (Shih YL*)  (2016-05)  Data in Brief  8, 304-307  "Quantitative inner membrane proteome datasets of the wild-type and the Δmin mutant of Escherichia coli"
  5. Liao JH, Chien CT, Wu, HY, Huang KF, Wang I, Ho MR, Tu IF, Lee IM, Li W, (Shih YL), Wu CY, Lukyanov P, Hsu STD, Wu SH*  (2016-04)  J Am Chem Soc  138(14), 4787-4795  "A multivalent marine lectin from Crenomytilus grayanus possesses anti-cancer activity through recognizing globotriose Gb3"
  6. Lee HL, Chiang IC, Liang SY, Lee DY, Chang GD, KY Wang, Lin SY, (Shih YL*)  (2016-02)  MOLECULAR & CELLULAR PROTEOMICS  15, 1572-1583  "Quantitative proteomics analysis reveals the Min system of Escherichia coli modulates reversible protein association with the inner membrane"
  7. Chiang YL, Chang YC, Chiang IC, Mak HM, Hwang IS*, (Shih YL)*  (2015-11)  PloS one  10(11), e0142506  "Atomic Force Microscopy Characterization of Protein Fibrils Formed by the Amyloidogenic Region of the Bacterial Protein MinE on Mica and a Supported Lipid Bilayer."
  8. Rujiviphat J, Wong MK, Won A, (Shih YL), Yip CM and McQuibban AG*  (2015-03)  J Mol Biol  427(16), 2595-2598  "Mitochondrial Genome Maintenance 1 (Mgm1) Protein alters membrane topology and promotes local membrane bending"
  9. Zheng M, Chiang YL, Lee HL, Kong LR, Hsu ST, Hwang IS, Rothfield LI, (Shih YL)*   (2014-08)  J Biol Chem  289(31), 21252-21266  "Self-Assembly of MinE on the Membrane Underlies Formation of the MinE-Ring to Sustain Function of the E. coli Min System"
  10. (Shih YL)*, Zheng M  (2013-12)  Environmental Microbiology  15(12), 3229-3239  "Spatial control of the cell division site by the Min system in E. coli"
  11. (Shih YL)*, Huang KF, Lai HM, Liao JH, Lee CS, Chang CM, Mak HM, Hsieh CW & Lin CC  (2011)  PLoS One  6(6), e21425  "The N-terminal amphipathic helix of the topological specificity factor MinE is associated with shaping membrane curvature"
  12. Hsieh CW, Lai HM, Lin CC, Lin TY, Hsieh TS, (Shih YL)*  (2010)  MOLECULAR MICROBIOLOGY  75(2), 499-512  "Direct MinE-membrane interaction contributes to the proper localization of MinDE in E. coli"
  13. Vats P, Shih YL, Rothfield L  (2009)  Molecular microbiology  72(1), 170-182  "Assembly of the MreB-associated cytoskeletal ring of Escherichia coli."
  14. Pradel N, Santini CL, Bernadac A, Shih YL, Goldberg MB, Wu LF  (2007)  Biochemical and biophysical research communications  353(2), 493-500  "Polar positional information in Escherichia coli spherical cells."
  15. Y-L Shih, LI Rothfield  (2006)  Microbiology and Molecular Biology Reviews  70, 729-754  "The bacterial cytoskeleton"
  16. LI Rothfield, A Taghbalout and Y-L Shih  (2005)  Nat Rev Microbiol  3, 959-968  "Spatial control of bacterial division-site placement"
  17. Y-L Shih, I Kawagishi and LI Rothfield  (2005)  Mol Microbiol  58, 917-928  "The MreB and Min cytoskeletal-like systems play independent roles in prokaryotic polar differentiation"
  18. Shih YL, Le T, Rothfield L  (2003)  Proceedings of the National Academy of Sciences of the United States of America  100(13), 7865-7870  "Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles."
  19. Y-L Shih, X Fu, GF King , T Le and LI Rothfield  (2002)  EMBO J  21, 3347-3357  "Division site placement in E.coli: mutations that prevent formation of the MinE ring lead to loss of the normal midcell arrest of growth of polar MinD membrane domains"
  20. Rothfield LI, Shih YL, King G  (2001)  Cell  106(1), 13-16  "Polar explorers: membrane proteins that determine division site placement."
  21. Fu X, Shih YL, Zhang Y, Rothfield LI  (2001)  Proceedings of the National Academy of Sciences of the United States of America  98(3), 980-985  "The MinE ring required for proper placement of the division site is a mobile structure that changes its cellular location during the Escherichia coli division cycle."
  22. King GF, Shih YL, Maciejewski MW, Bains NP, Pan B, Rowland SL, Mullen GP, Rothfield LI  (2000)  Nature Structural Biology  7(11), 1013-1017  "Structural basis for the topological specificity function of MinE."
  23. Shih YL, Harris SJ, Borner G, Rivet MM, Salmond GP  (1999)  Environmental microbiology  1(6), 535-547  "The hexY genes of Erwinia carotovora ssp. carotovora and ssp. atroseptica encode novel proteins that regulate virulence and motility co-ordinately."
  24. Harris SJ, Shih YL, Bentley SD, Salmond GP  (1998)  Molecular microbiology  28(4), 705-717  "The hexA gene of Erwinia carotovora encodes a LysR homologue and regulates motility and the expression of multiple virulence determinants."
  25. Toth I, Mulholland V, Copper V, Bentley S, Shih Y-L, Perombelon M, and Salmond GPC  (1997)  Microbiology  143, 2433-2438  "Generalized transduction in the potato blackleg pathogen Erwinia carotovora subsp. atroseptica by bacteriophage φM1"