Shun Lee - Academia.edu (original) (raw)

Papers by Shun Lee

Molecular Cell, 2004

neutral and remain for the duration of the stress (Record P.O. Box 951569 et al., 1998a). Los Ang... more neutral and remain for the duration of the stress (Record P.O. Box 951569 et al., 1998a). Los Angeles, California 90095 Control of this osmotic stress response occurs largely at the level of gene expression (Weber and Jung, 2002) and has been well studied in bacteria (Dinnbier et al., Summary 1988; Larsen et al., 1987). When E. coli encounter environments with high osmolarity, the initial response is Adaptation to high-salt environments is critical for the to rapidly transport free cations (largely K ϩ) into the survival of a wide range of cells, especially for pathocytoplasm. To counterbalance the K ϩ charge, glutamate genic bacteria that colonize the animal gut and urinary levels increase substantially (up to 400 mM) through tract. The adaptation strategy involves production of de novo synthesis and remain high (Dinnbier et al., 1988). the salt potassium glutamate, which induces a specific If glucose is present in the cytoplasm, molecules such gene expression program that produces electro-neutral as trehalose are synthesized with levels approaching osmolytes while inhibiting general 70 transcription. 400 mM in the cytoplasm. Glycine betaine and L-proline These data show that in Escherichia coli potassium often accumulate (over 700 and 400 mM, respectively) glutamate stimulates transcription by disengaging in the cytoplasm and can replace trehalose (Larsen et inhibitory polymerase interactions at a 38 promoter. al., 1987). E. coli stop dividing during the early stages These occur in an upstream region that is marked of an osmotic shock and only begin growth, albeit at a by an osmotic shock promoter DNA consensus seslower rate, when these molecules finally accumulate quence. The disruption activates a poised RNA polyin the cytoplasm (reviewed in Wood, 1999). merase to transcribe. This transcription program leads The early stages of the response are accompanied to the production of osmolytes that are shown to have by a major change in the global gene expression pattern. only minor effects on transcription and therefore help The stress-related sigma factor, 38 , regulates a number to restore normal cell function. An osmotic shock gene of genes involved in the osmotic stress response and expression cycle is discussed. plays a key role in the switch in global gene expression (Hengge-Aronis, 1996; Weber and Jung, 2002). However,

The EMBO Journal, 2000

to be recognition of duplex and single-stranded DNA (Roberts and Roberts, 1996), and of the disti... more to be recognition of duplex and single-stranded DNA (Roberts and Roberts, 1996), and of the distinctive fork The opening of specific segments of DNA is required junction at the upstream boundary between these two for most types of genetic readout, including σ70-(Guo and Gralla, 1998; Guo et al., 1999). It is not clear dependent transcription. To learn how this occurs, a how each nucleotide within the-10 element is recognized series of single point mutations were introduced into and in which state this recognition occurs. σ70 region 2. These were assayed for duplex DNA Various studies have shown that the C-terminal part of binding, DNA opening and DNA double strand-single conserved region 2 (regions 2.3, 2.4 and 2.5) of σ70 is strand fork junction binding. Band shift assays for involved in the use of the-10 region and adjacent DNA closed complex formation implicated a series of arginsequences. Suppression analysis has implicated amino ine and aromatic residues within a minimal 26 amino acids 441, 440 and 437 (in region 2.4) in the recognition acid region. Permanganate assays implicated two addiof nucleotides-13 and-12 (Kenney et al., 1989; Siegele tional aromatic residues in DNA opening, known to et al., 1989; Zuber et al., 1989; Daniels et al., 1990; form a parallel stack of the type that can accept Waldburger et al., 1990; Marr and Roberts, 1997) and a flipped-out base. Substitution for either of these amino acids C-terminal to position 454 (in region 2.5) in aromatics had no effect on duplex probe recognition. the recognition of nucleotides from-14 to-20 (Barne However, when a single unpaired-11 nucleotide is et al., 1997; Bown et al., 1999). These amino acids are added to the probe, the mutants fail to bind approbelieved to be involved in double strand recognition, priately to give heparin resistance. A model for DNA although direct evidence is lacking in the case of 437 and opening is presented in which duplex recognition by 440. Permanganate probing and single strand binding regions 2.3, 2.4 and 2.5 of sigma positions the pair of studies have implicated a series of aromatic residues (all aromatic amino acids, which then create the fork or a subset of 425, 430, 433 and 434 in region 2.3) as junction required for stable opening. potentially involved in the opening of the DNA, most Keywords: Escherichia coli/fork junction/promoter/σ70 probably via recognition of the non-template strand (Juang and Helmann, 1994; Huang et al., 1997; Marr and Roberts, 1997). Some of these studies used components from Bacillus subtilis, which creates uncertainty as its poly-1130

Molecular Cell, 2004

neutral and remain for the duration of the stress (Record P.O. Box 951569 et al., 1998a). Los Ang... more neutral and remain for the duration of the stress (Record P.O. Box 951569 et al., 1998a). Los Angeles, California 90095 Control of this osmotic stress response occurs largely at the level of gene expression (Weber and Jung, 2002) and has been well studied in bacteria (Dinnbier et al., Summary 1988; Larsen et al., 1987). When E. coli encounter environments with high osmolarity, the initial response is Adaptation to high-salt environments is critical for the to rapidly transport free cations (largely K ϩ) into the survival of a wide range of cells, especially for pathocytoplasm. To counterbalance the K ϩ charge, glutamate genic bacteria that colonize the animal gut and urinary levels increase substantially (up to 400 mM) through tract. The adaptation strategy involves production of de novo synthesis and remain high (Dinnbier et al., 1988). the salt potassium glutamate, which induces a specific If glucose is present in the cytoplasm, molecules such gene expression program that produces electro-neutral as trehalose are synthesized with levels approaching osmolytes while inhibiting general 70 transcription. 400 mM in the cytoplasm. Glycine betaine and L-proline These data show that in Escherichia coli potassium often accumulate (over 700 and 400 mM, respectively) glutamate stimulates transcription by disengaging in the cytoplasm and can replace trehalose (Larsen et inhibitory polymerase interactions at a 38 promoter. al., 1987). E. coli stop dividing during the early stages These occur in an upstream region that is marked of an osmotic shock and only begin growth, albeit at a by an osmotic shock promoter DNA consensus seslower rate, when these molecules finally accumulate quence. The disruption activates a poised RNA polyin the cytoplasm (reviewed in Wood, 1999). merase to transcribe. This transcription program leads The early stages of the response are accompanied to the production of osmolytes that are shown to have by a major change in the global gene expression pattern. only minor effects on transcription and therefore help The stress-related sigma factor, 38 , regulates a number to restore normal cell function. An osmotic shock gene of genes involved in the osmotic stress response and expression cycle is discussed. plays a key role in the switch in global gene expression (Hengge-Aronis, 1996; Weber and Jung, 2002). However,

The EMBO Journal, 2000

to be recognition of duplex and single-stranded DNA (Roberts and Roberts, 1996), and of the disti... more to be recognition of duplex and single-stranded DNA (Roberts and Roberts, 1996), and of the distinctive fork The opening of specific segments of DNA is required junction at the upstream boundary between these two for most types of genetic readout, including σ70-(Guo and Gralla, 1998; Guo et al., 1999). It is not clear dependent transcription. To learn how this occurs, a how each nucleotide within the-10 element is recognized series of single point mutations were introduced into and in which state this recognition occurs. σ70 region 2. These were assayed for duplex DNA Various studies have shown that the C-terminal part of binding, DNA opening and DNA double strand-single conserved region 2 (regions 2.3, 2.4 and 2.5) of σ70 is strand fork junction binding. Band shift assays for involved in the use of the-10 region and adjacent DNA closed complex formation implicated a series of arginsequences. Suppression analysis has implicated amino ine and aromatic residues within a minimal 26 amino acids 441, 440 and 437 (in region 2.4) in the recognition acid region. Permanganate assays implicated two addiof nucleotides-13 and-12 (Kenney et al., 1989; Siegele tional aromatic residues in DNA opening, known to et al., 1989; Zuber et al., 1989; Daniels et al., 1990; form a parallel stack of the type that can accept Waldburger et al., 1990; Marr and Roberts, 1997) and a flipped-out base. Substitution for either of these amino acids C-terminal to position 454 (in region 2.5) in aromatics had no effect on duplex probe recognition. the recognition of nucleotides from-14 to-20 (Barne However, when a single unpaired-11 nucleotide is et al., 1997; Bown et al., 1999). These amino acids are added to the probe, the mutants fail to bind approbelieved to be involved in double strand recognition, priately to give heparin resistance. A model for DNA although direct evidence is lacking in the case of 437 and opening is presented in which duplex recognition by 440. Permanganate probing and single strand binding regions 2.3, 2.4 and 2.5 of sigma positions the pair of studies have implicated a series of aromatic residues (all aromatic amino acids, which then create the fork or a subset of 425, 430, 433 and 434 in region 2.3) as junction required for stable opening. potentially involved in the opening of the DNA, most Keywords: Escherichia coli/fork junction/promoter/σ70 probably via recognition of the non-template strand (Juang and Helmann, 1994; Huang et al., 1997; Marr and Roberts, 1997). Some of these studies used components from Bacillus subtilis, which creates uncertainty as its poly-1130