Abstract
Cellular proteomes are dynamic and adjusted to permanently changing conditions by ATP-fueled proteolytic machineries. Among the five AAA+ proteases in Escherichia coli FtsH is the only essential and membrane-anchored metalloprotease. FtsH is a homohexamer that uses its ATPase domain to unfold and translocate substrates that are subsequently degraded without the need of ATP in the proteolytic chamber of the protease domain. FtsH eliminates misfolded proteins in the context of general quality control and properly folded proteins for regulatory reasons. Recent trapping approaches have revealed a number of novel FtsH substrates. This review summarizes the substrate diversity of FtsH and presents details on the surprisingly diverse recognition principles of three well-characterized substrates: LpxC, the key enzyme of lipopolysaccharide biosynthesis; RpoH, the alternative heat-shock sigma factor and YfgM, a bifunctional membrane protein implicated in periplasmic chaperone functions and cytoplasmic stress adaptation.
Introduction
All living cells rapidly adapt their proteome in response to changing environmental conditions by a number of transcriptional and translational control mechanisms. Proteolysis acts at the post-translational level and is typically catalyzed by ATP-dependent proteases. The Gram-negative model organism Escherichia coli harbors five different AAA+ (ATPases associated with a variety of cellular activities) proteases, namely ClpXP, ClpAP, HslUV, Lon and FtsH (Baker and Sauer, 2006; Sauer and Baker, 2011; Nyquist and Martin, 2014). All AAA+ proteases have in common that they form oligomeric structures with a central pore through which a substrate is threaded in order to reach the proteolytic chamber. AAA+ proteases can be divided into two functional domains, the ATPase and the protease domain. While the ATPase domain catalyzes ATP-dependent unfolding and translocation of the substrate into the proteolytic chamber, the protease domain degrades the unfolded substrate into small peptide fragments of five to 25 amino acids in length (Sauer et al., 2004; Baker and Sauer, 2006; Sauer and Baker, 2011; Bittner et al., 2016).
FtsH is the only membrane-anchored and essential protease in E. coli. It assembles with the membrane-anchored HflK/HflC complex, which influences the stability of some substrates like SecY or the bacteriophage lambda protein CII (Kihara et al., 1996, 2001; Saikawa et al., 2004), whereas turnover of other FtsH substrates like RpoH is not altered by HflK/C (Kihara et al., 1998). The most important function of FtsH is the regulation of the optimal ratio between phospholipids (PL) and lipopolysaccharides (LPS) in the outer membrane by degrading LpxC, the key enzyme of LPS biosynthesis (for details see the following section) (Tomoyasu et al., 1993, 1995; Ogura et al., 1999). As proteolysis is energy-demanding and irreversible, degradation of natively folded and active proteins is strictly regulated. Access of substrates to the protease requires recognition motifs, so-called degrons that can be localized at either terminus or at internal sites of a protein. A sequestered degron gets exposed when the protein is subjected to degradation. For many protease substrates, the aid of dedicated adaptor proteins is required for conditional degradation (Sauer et al., 2004; Sauer and Baker, 2011; Gur et al., 2013).
This review focusses on FtsH, a universal protease. Proteobacteria code for one copy of FtsH, whereas cyanobacteria like Synechocystis possess four and Arabidopsis chloroplasts even nine orthologs with crucial functions in photosynthesis (Nishimura et al., 2016). Several proteases of the FtsH type are also present in mitochondria of yeast, mammals and plants (Tatsuta and Langer, 2009; Janska et al., 2010, 2013). The ATPase and protease domains of each subunit of the homohexamer are encoded on a single gene, which led to its classification as single-chain charonin (Schumann, 1999). The ATPase domain of FtsH contains typical elements of ATPase function like the Walker A and Walker B motifs, an arginine finger and a sensor 1 residue (Karata et al., 2001; Ito and Akiyama, 2005; Langklotz et al., 2012; Bittner et al., 2016). FtsH is unique among the AAA+ proteases in E. coli as it contains a second region of homology (SRH), which categorizes FtsH into the AAA subfamily (Karata et al., 1999). Moreover, FtsH is the only metalloprotease among the AAA+ proteases. A conserved HEXXH-motif (X=any amino acid) in the protease domain is essential for coordinating the catalytic Zn2+ ion (Bieniossek et al., 2006).
FtsH degrades proteins for two reasons: (i) quality control of aberrant proteins and (ii) regulated proteolysis of intact proteins under specific conditions. Because the number of known FtsH substrates was relatively low, trapping approaches with an ATPase-proficient but proteolytically inactive FtsH variant (FtsHtrap) have been established. FtsHtrap is still capable of unfolding and translocating substrates into the inactivated proteolytic chamber, which contains an amino acid exchange of the first histidine of the HEXXH-motif against tyrosine. Proteins captured with FtsHtrap can then be purified and analyzed via mass-spectrometry (Westphal et al., 2012; Arends et al., 2016; Bittner et al., 2016). Putative substrates are validated by in vivo degradation experiments determining the half-lives of mildly overexpressed recombinant His-tagged proteins after inhibition of protein biosynthesis followed by Western blot analysis. Two independent trapping approaches revealed nine novel FtsH substrates, extending the number of known FtsH substrates in E. coli to 21 (Table 1). The substrate repertoire demonstrates that FtsH is involved in a remarkable variety of cellular processes like the quality control of membrane-anchored (SecY, YccA, Foa and PspC) (Kihara et al., 1995, 1996, 1999; Akiyama et al., 1996a,b; Chiba et al., 2000, 2002; Singh and Darwin, 2011) and cytosolic proteins (SsrA-tagged proteins) (Herman et al., 1998), the lysis/lysogeny decision of phage λ (Herman et al., 1997; Kihara et al., 1997, 2001; Shotland et al., 1997; Leffers and Gottesman, 1998; Kobiler et al., 2002) and various stress responses.
FtsH substrates in E. coli and their mechanism of recognition.
Localization of degrons, involved adaptor proteins and recognition mechanism are listed. Selected references are given for details. ND, Not determined; (?), possible mechanism.
For most of these FtsH substrates, the mechanistic details of recognition and degradation are not yet understood. In this review, we will summarize findings on the three best-studied substrates (LpxC, RpoH and YfgM) and describe when, how and why they are degraded.
Conditional proteolysis of selected FtsH substrates
LpxC, the gate keeper of LPS biosynthesis
Physiologically the most important FtsH substrate in E. coli and other enterobacteria is LpxC, the key enzyme in lipopolysaccharide (LPS) biosynthesis. The outer membrane of Gram-negative bacteria is composed of LPS and phospholipids (PL) and serves as permeability barrier against environmental stresses (Nikaido and Vaara, 1985; Delcour, 2009). The amount of LPS is directly correlated to the level of LpxC, the UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase catalyzing the first committed step in LPS biosynthesis (Anderson et al., 1993; Ogura et al., 1999). LPS and PL biosynthesis are synchronized because they share the same precursor molecule R-3-hydroxymyristoyl-acyl carrier protein (ACP). Both depletion and overproduction of LPS is toxic, which renders LpxC, the enzyme that represents the bottleneck in LPS biosynthesis, and FtsH, the protease that controls its intracellular concentration, essential in E. coli and many other Gram-negative bacteria (Ogura et al., 1999; Langklotz et al., 2011). An E. coliftsH deletion strain is only viable due to a suppressor mutation within the fabZ gene, whose gene product recruits R-3-hydroxymyristoyl-ACP into the PL biosynthesis pathway (Figure 1B).
Degradation pathways of three conditional substrates of the membrane-anchored FtsH protease.
(A) Growth phase-dependent degradation of YfgM. YfgM, a single transmembrane protein with a short cytoplasmic N terminus, acts as negative regulator of RcsB, the response regulator of the Rcs phosphorelay system. This system further consists of the sensor protein RcsF, the sensor kinase RcsC and the phosphotransferase RcsD and is responsible for adaptation to various stress conditions. YfgM stability is adjusted to the growth phase. YfgM is stabilized in exponential growth phase and rapidly degraded in the stationary phase. Original data obtained from (Bittner et al., 2015). (B) Growth rate-dependent degradation of LpxC. LpxC is the key enzyme in lipopolysaccharide (LPS) biosynthesis. It competes with FabZ of the phospholipid biosynthesis pathway for the common precursor R-3-hydroxymyristoyl-ACP. The amount of LpxC is adjusted to the cellular needs by FtsH-dependent degradation. When cells grow slowly, LpxC is rapidly degraded as less LPS is needed. When cells grow fast, LpxC is stable. Original data obtained from (Schäkermann et al., 2013). (C) Temperature-dependent degradation of RpoH. During normal temperature conditions the chaperones DnaK/DnaJ direct RpoH to FtsH-mediated degradation. Upon heat shock, the chaperones are titrated away from RpoH by denaturized/misfolded proteins resulting in RpoH stabilization. Free RpoH forms a complex with the RNA polymerase leading to expression of the heat-shock regulon. Original data obtained from (Obrist and Narberhaus, 2005). The Western blots in the insets show the respective protein stability over time after blocking translation by the addition of spectinomycin. OM: outer membrane; IM: inner membrane; ACP: acyl carrier protein; RNAP: RNA polymerase; HS: heat shock. Protein models are based on the following structures: FtsH (PDB: 3KDS; 4V0B), LpxC (4MDT), RpoH was modeled on the basis of RpoS (5IPL) using swiss-model (Arnold et al., 2006; Bordoli et al., 2009; Biasini et al., 2014), periplasmic domain of YfgM was modeled using I-Tasser (Zhang, 2008; Roy et al., 2010).
The critical importance of LpxC in controlling the flux towards LPS production raised the question whether proteolysis of the enzyme is constitutive or adjusted to the ambient conditions. Consistent with the cellular demand, degradation of LpxC negatively correlates with the growth rate, i.e. the enzyme is stable during fast growth and rapidly degraded when cells grow slowly (Figure 1B) (Schäkermann et al., 2013). A factor that is involved in growth-rate dependent turn-over of LpxC is the alarmone (p)ppGpp (Schäkermann et al., 2013). (p)ppGpp, best known for its role in the stringent response, is involved in regulating many processes in response to various stress and starvation signals (Potrykus and Cashel, 2008; Gaca et al., 2015). In the absence of the signaling molecule, proteolysis of LpxC is mis-regulated. In stark contrast to the situation in wild-type cells, degradation is fast when the (p)ppGpp-negative mutant grows rapidly and is slow when it grows poorly (Schäkermann et al., 2013). The mechanism of alarmone-controlled LpxC degradation is under investigation. Controlled turnover of LpxC seems to be a complex multi-factorial process. Experimental and biocomputational analysis suggests that lipid A disaccharide, an intermediate of the LPS biosynthesis pathway downstream of LpxC, is the feedback source that stimulates FtsH-dependent degradation of LpxC (Emiola et al., 2014, 2016). KdtA (WaaA), an enzyme in LPS biosynthesis acting downstream of LpxC, was reported to be another FtsH substrate suggesting a backup security system in the same pathway (Katz and Ron, 2008).
Degradation of LpxC requires its C terminus in a sequence- and length-dependent manner. The degron at the very C terminus contains the sequence LAXXXXXAVLA (X: any amino acid), and the unstructured C-terminal tail must at least be 20 amino acids long (Figure 2B) (Führer et al., 2006, 2007). Interestingly, this motif is necessary but not sufficient to mediate FtsH-specific degradation. Fusion of the C-terminus to the stable glutathione-S-transferase (GST) from Schistosoma japonicum resulted in FtsH-independent degradation (Führer et al., 2007). This is presumably due to the similarity of the LpxC degron to the SsrA-tag (AANDENYALAA), which acts as a general recognition motif for AAA+ proteases (Figure 3A) (Keiler et al., 1996; Gottesman et al., 1998; Herman et al., 1998; Choy et al., 2007; Moore and Sauer, 2007; Lies and Maurizi, 2008). The SsrA-tag is directly bound by the pore residues of the ATPase domain of ClpX (Levchenko et al., 2003; Martin et al., 2008a,b). Therefore, it is likely that the aromatic FtsH pore directly binds the unstructured C-terminal LpxC motif (Führer et al., 2007). However, routing of the GST protein carrying the LpxC terminus to various proteases suggests that an internal region in LpxC or an additional factor is required for FtsH-specific targeting. A potential candidate as adapter protein is LapB (formerly known as YciM). It is an essential inner membrane protein believed to couple LPS biosynthesis and transport across the membrane (Klein et al., 2014; Mahalakshmi et al., 2014). Interestingly, LapB acts on LPS biosynthesis by altering the LpxC level in dependence of FtsH. Absence or overexpression of LapB lead to increased or decreased LpxC amounts, respectively (Mahalakshmi et al., 2014). Recently, it was proposed that another not yet defined protease contributes to LpxC degradation (Emiola et al., 2016).
Degron diversity of selected FtsH substrates.
Amino acids important for degradation of YfgM (A), LpxC (B) and RpoH (C) are highlighted. Residues marked in red are critical for degradation and substitutions against other amino acids lead to stabilization. Y4 and E5 in YfgM (marked in green) are critical for stabilization during early growth phases. Amino acids marked in gray seem are not involved in recognition. The amino acids of RpoH correspond to positions L47, A50, I54 (region 2.1) and A131, K134 (region C). For more detailed information, see main text.
Comparison of N- and C-terminal FtsH degrons.
(A) The conserved degron of the SsrA-tag and LpxC mainly consists of non-polar amino acids (highlighted in gray). (B) Sequence alignment of the N-terminal degron of YfgM and the N-termini of the membrane-anchored FtsH substrates ExbD and YlaC. Adopted from Arends et al. (2016). Conserved amino acid properties of important residues for degradation are colored from light gray to dark gray (polar, non-polar and acidic).
The essential function of LpxC in Gram-negative bacteria makes it an attractive drug target (Onishi et al., 1996; Vaara, 1996; Mdluli et al., 2006) and various LpxC inhibitors have been reported (Kalinin and Holl, 2016). Since FtsH is essential in balancing LPS and PL biosynthesis in E. coli, it might be another interesting target for antimicrobial agents. It is important to note, however, that not all Gram-negative bacteria seem to control LPS production via FtsH-mediated LpxC degradation. Alpha-proteobacteria are likely to use the Lon protease for this purpose and LpxC of Pseudomonas aeruginosa does not seem to be a protease substrate at all (Langklotz et al., 2011).
RpoH, the master regulator of the heat-shock response
Exposure of all living cells to heat-stress conditions induces a rapid emergency reaction called the heat-shock response. In E. coli, the sigma factor RpoH (σ32) is responsible for transcription of the heat-shock regulon, which encodes most of the heat-shock genes like chaperones and proteases (Yura and Nakahigashi, 1999). Expression of the rpoH gene is primarily regulated at translational and post-translational level. Translation efficiency is controlled via a secondary structure, a so-called RNA thermometer (RNAT) reaching from the 5′-untranslated into the coding region of the rpoH mRNA. At physiological temperatures, the RNAT is closed and ribosome binding is prevented. Melting of the RNAT structure with rising temperatures permits ribosome access and translation initiation (Nagai et al., 1991; Yuzawa et al., 1993; Morita et al., 1999a,b).
A major role in the heat-shock response plays the post-translational regulation through proteolysis of RpoH by FtsH and to a minor extent by other AAA+ proteases (Herman et al., 1995; Tomoyasu et al., 1995; Kanemori et al., 1997; Xu et al., 2015). Here, not the temperature itself is perceived. Instead, the consequences of a temperature upshift are monitored. In concert with the cellular demand, degradation of RpoH is temperature-dependent. The amount of the sigma factor is low (~50 molecules per cell) at physiological temperatures and increases during heat shock (42°C) about 20-fold to ~ 1000 molecules per cell (Straus et al., 1987). RpoH degradation is assisted by the chaperone systems DnaK/DnaJ/GrpE and GroEL/GroES (Straus et al., 1990; Tomoyasu et al., 1998; Guisbert et al., 2004). At physiological temperatures, these chaperones bind to RpoH and direct it to FtsH-mediated degradation resulting in RpoH half-lives of about 1 to 2 min (Figure 1C). The high burden of misfolded proteins after heat shock occupies the chaperone systems titrating them away from RpoH and leaving it free and ready to associate with the core RNA polymerase (RNAP) (Gamer et al., 1992, 1996; Horikoshi et al., 2004). The products of the induced heat-shock genes, among them chaperones and proteases, help to overcome the heat-inflicted damage. As a consequence, the heat-shock response is shut-off when the level of available DnaK/DnaJ is sufficient to sequester RpoH again (Straus et al., 1987, 1990; Blaszczak et al., 1995; Gamer et al., 1996).
The recognition of RpoH follows its own rules and has nothing in common with recognition of other substrates. Because the N- or C-terminal ends of RpoH are not required for degradation, two genetic screens were employed. A bacterial one-hybrid-system aimed at the identification of FtsH-resistant RpoH variants. The system is based on the two functional domains (T18 and T25) of the adenylate cyclase (AC) from Bordetella pertussis, which produces the second messenger cyclic adenosine monophosphate (cAMP). A fusion protein comprised of a stable linker between T18 and T25 is able to complement an AC-deficient (cya) E. coli strain. cAMP production can then be measured in the cya strain, e.g. by β-galactosidase (lacZ) assays (Ladant and Ullmann, 1999; Dautin et al., 2000). A fusion of RpoH between T18 and T25 resulted in low β-galactosidase activity suggesting that the fusion protein is a substrate of FtsH. Generation of random mutations in the RpoH-linker by error prone PCR and screening for elevated β-galactosidase activity identified amino acids crucial for degradation. Exchanges in amino acids L47, A50, and I54 resulted in RpoH stabilization. Interestingly, these residues line up on the face of an exposed α-helix in region 2.1 (Obrist and Narberhaus, 2005) (Figure 2C). Sigma factors are divided into distinct regions based on sequence alignments and numbered from the N to the C terminus (Lonetto et al., 1992; Wösten, 1998). The identified residues in region 2.1 of the N-terminal part of RpoH are known for core-RNAP binding. The same region was identified in a mutant screen for RpoH variants with increased activity based on the assumption that stabilized variants might exhibit higher transcriptional activity (Horikoshi et al., 2004). This internal and structured degron does not seem to be sufficient for FtsH-dependent degradation of RpoH as point mutations in this region did not stabilize RpoH completely. Moreover, introduction of RpoH-region 2.1 into the sigma factor RpoS, a ClpXP substrate, did not convert RpoS into an FtsH substrate (Obrist et al., 2007). A second turnover element for FtsH-dependent RpoH degradation lies in region C, a region located in the center of the sigma factor (Obrist et al., 2009), which is needed for binding of the RNAP (Nakahigashi et al., 1995; Joo et al., 1998; Arsène et al., 1999). Here, amino acids A131 and K134 contribute to RpoH degradation (Obrist et al., 2009) (Figure 2C). Combination of amino acid exchanges in region 2.1 and region C drastically stabilized RpoH. Most importantly, an RpoH fragment (residues 37–147) comprised of region 2.1 and region C is degraded by FtsH suggesting that these two regions are sufficient for specific recognition (Obrist and Narberhaus, 2005; Obrist et al., 2007, 2009). DnaJ interacts directly with region 2.1 (Rodriguez et al., 2008; Suzuki et al., 2012; Noguchi et al., 2014; Miyazaki et al., 2016) and it is assumed that DnaJ-induced conformational changes promote DnaK-binding to region 3.2 of RpoH (Rodriguez et al., 2008). The mechanism of how exactly the concerted binding of the DnaKJ system to two different segments in the native sigma factor targets it to FtsH-mediated proteolysis is not yet fully understood.
Recently, the model of RpoH degradation was further extended by the finding that the signal recognition particle (SRP) composed of the Ffh protein in complex with the 4.5S RNA, and its membrane-anchored receptor FtsY are involved in regulation of RpoH degradation (Lim et al., 2013; Miyazaki et al., 2016). Like dnaK/dnaJ/grpE, groEL/groES and ftsH, the ffh gene is part of the σ32 regulon (Nonaka et al., 2006). Ffh binds via its signal peptide-binding site to the homeostatic control region 2.1 of RpoH in vivo and in vitro (Lim et al., 2013; Miyazaki et al., 2016). This interaction does not require the involvement of DnaK/DnaJ (Miyazaki et al., 2016). Intriguingly, RpoH does not contain a typical signal peptide or transmembrane segment which is usually recognized by Ffh. Region 2.1 seems to form an amphipathic helix of which the hydrophobic part could be bound by Ffh (Miyazaki et al., 2016). Based on these novel findings it is believed that Ffh and the chaperones bind to RpoH in a sequential manner. RpoH is first recruited to the inner membrane via the SRP/FtsY-dependent pathway followed by the transfer to the chaperone-dependent system to induce degradation by FtsH (Lim et al., 2013; Miyazaki et al., 2016).
YfgM, a mediator of the cytoplasmic and extracytoplasmic stress responses
YfgM was identified as FtsH substrate by a trapping approach with an inactive FtsH variant (Westphal et al., 2012). It is a transmembrane protein with a total of 206 amino acids. A short unstructured N-terminus of 19 amino acids faces the cytoplasm. The majority of the protein is alpha helical and the C-terminus is located in the periplasm (Maddalo et al., 2011). YfgM has interaction partners in various compartments. It interacts with the membrane-anchored periplasmic chaperone PpiD and is an ancillary subunit of the Sec translocon (Maddalo et al., 2011; Götzke et al., 2014). YfgM also interacts with the cytoplasmic response regulator RcsB of the Rcs signal transduction system (Lasserre et al., 2006; Bittner et al., 2015). The Rcs system is a multi-component phosphorelay that coordinates the adaptation to various stresses. Briefly, a stress signal is sensed by the sensor lipoprotein RcsF in the outer membrane. The signal is then passed on to the sensor kinase RcsC in the inner membrane. RcsC autophosphorylates and transfers the phosphate group to the phosphotransferase RcsD in the inner membrane, which then phosphorylates the response regulator RcsB (Figure 1A). RcsB forms homodimers or heterodimers with auxiliary proteins. These dimers activate the expression of adaptation genes involved in acid or osmotic tolerance, in cell division and in adaptation to stationary phase (Carballès et al., 1999; Davalos-Garcia et al., 2001; Majdalani et al., 2002; Majdalani and Gottesman, 2005; Peterson et al., 2006; Clarke, 2010; Johnson et al., 2011). YfgM is bifunctional as it serves, on the one hand, as periplasmic chaperone for proteins, which are translocated via the Sec pathway (Götzke et al., 2014, 2015) and, on the other hand, as negative regulator of RcsB (Bittner et al., 2015). To relief the inhibitory effect, YfgM is degraded by FtsH under conditions requiring RcsB-dependent gene expression. This is for instance the case under osmotic shock conditions or during stress conditions related to stationary growth phase (Figure 1A) (Westphal et al., 2012; Bittner et al., 2015).
Degradation of YfgM by FtsH requires its cytosolic N terminus. N-terminally truncated YfgM variants were stable in every growth phase and a detailed point-mutational survey revealed that the degron of YfgM comprises the first 14 N-terminal residues (MEIYENENDQVEAV-) (Figure 2A). The importance of individual amino acids for degradation varies. For instance, E2 and I3 are essential for degradation, Y4 and E5 are important for stabilization of YfgM during early growth phases and the region from the sixth to the 14th amino acid contributes to the characteristic degradation profile of YfgM (Bittner et al., 2015). This sequence-dependent degron is contrasted by the recognition principle used for mis-folded membrane-anchored proteins subjected to FtsH-mediated quality control. They are recognized via a minimal length of about 20 amino acids of their exposed N or C termini and the exact amino acid composition is irrelevant for recognition (Kihara et al., 1999; Chiba et al., 2000, 2002). The YfgM degron contains acidic amino acids that are not expected to directly interact with the aromatic/hydrophobic FtsH pore motif and that do not occur in other degrons like the LpxC recognition motif or the SsrA-tag. Interestingly, the C-terminal degron of the phage λ CII protein contains acidic glutamates like the N-terminal YfgM degron (Kobiler et al., 2002; Datta et al., 2005). Unexpectedly, degradation of YfgM was not altered when its interaction partners PpiD or RcsB are missing (Bittner et al., 2015). This finding further distinguishes YfgM degradation from degradation of other membrane-anchored proteins as they are predominantly degraded when unassembled from their interaction partners (Kihara et al., 1995; Akiyama et al., 1996a,b; Singh and Darwin, 2011).
Provided that a fusion protein has the same topology as YfgM, its degron is able to confer the typical YfgM degradation profile (Figure 1A). This was shown for PpiD. When its N-terminus was exchanged against the N terminus of YfgM, PpiD was stable in exponential phase but degraded in stationary phase. The YfgM degron did not convert the soluble protein GST into an FtsH substrate indicating that both the exact amino acid sequence and membrane anchoring are critical for degradation (Bittner et al., 2015).
Factors responsible for the conditional proteolysis of YfgM are not yet known. The absence of the alarmone (p)ppGpp slightly accelerated YfgM degradation (Bittner et al., 2015) but did by far not have the massive effect that was observed for LpxC (Schäkermann et al., 2013). Most likely, YfgM proteolysis is regulated via an adaptor protein that is expressed in response to the growth phase and during acidic or osmotic stress conditions when YfgM is degraded.
Three FtsH substrates – three degradation pathways
The E. coli FtsH protease modulates a diverse array of cellular processes ranging from the essential LPS biosynthesis to various stress responses (Table 1). In contrast to misfolded substrates prone to protein quality control, the recognition of fully functional substrates under conditions when they are not required poses a substantial challenge and serious threat to the cell. Complex regulatory networks have been established to strictly control the turnover of the LpxC enzyme and the stress response factors RpoH and YfgM. One emerging theme is that factors involved in the FtsH-controlled pathway (chaperones in the heat-shock response or precursors of LPS biosynthesis) play a role in monitoring the cellular status and signaling it to the proteolytic machinery. An inspection of the currently known FtsH degrons suggests at least some commonalities. It has already been reported that the C terminus of LpxC resembles the SsrA tag (Figure 3A) (Führer et al., 2006, 2007). The peculiar YfgM degron might have analogs in the FtsH substrates YlaC and ExbD that are topologically similar to YfgM. Like YfgM, the biopolymer transport protein ExbD has a single transmembrane domain and a short cytosolic N terminus of 22 amino acids (Kampfenkel and Braun, 1992). YlaC, a protein of unknown function, is predicted to have two transmembrane domains and both termini are suggested to face the cytoplasm (Daley et al., 2005). Comparison of the N-terminal YfgM degron with the N termini of ExbD and YlaC indicates some conservation of residues critical for YfgM degradation (Figure 3B) (Arends et al., 2016). Further experimental studies are needed to clarify if these conserved residues are crucial for FtsH-dependent degradation. Time will tell whether all the newly identified FtsH substrates follow their individual degradation schemes or whether some common principles do exist for this unique protease.
Acknowledgments
This work was supported by a grant from the German Research Foundation (DFG) in the Collaborative Research Center SFB642 ‘GTP- and ATP-dependent membrane processes’.
References
Akiyama, Y., Kihara, A., and Ito, K. (1996a). Subunit a of proton ATPase Fo sector is a substrate of the FtsH protease in Escherichia coli. FEBS Lett. 399, 26–28.10.1016/S0014-5793(96)01283-5Search in Google Scholar
Akiyama, Y., Kihara, A., Tokuda, H., and Ito, K. (1996b). FtsH (HflB) is an ATP-dependent protease selectively acting on SecY and some other membrane proteins. J. Biol. Chem. 271, 31196–31201.10.1074/jbc.271.49.31196Search in Google Scholar
Anderson, M.S., Bull, H.G., Galloway, S.M., Kelly, T.M., Mohan, S., Radika, K., and Raetz, C.R.H. (1993). UDP-N-acetylglucosamine acyltransferase of Escherichia coli – the first step of endotoxin biosynthesis is thermodynamically unfavorable. J. Biol. Chem. 268, 19858–19865.10.1016/S0021-9258(19)36592-5Search in Google Scholar
Arends, J., Thomanek, N., Kuhlmann, K., Marcus, K., and Narberhaus, F. (2016). In vivo trapping of FtsH substrates by label-free quantitative proteomics. Proteomics 16, 3161–3172.10.1002/pmic.201600316Search in Google Scholar PubMed
Arnold, K., Bordoli, L., Kopp, J., and Schwede, T. (2006). The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22, 195–201.10.1093/bioinformatics/bti770Search in Google Scholar PubMed
Arsène, F., Tomoyasu, T., Mogk, A., Schirra, C., Schulze-Specking, A., and Bukau, B. (1999). Role of region C in regulation of the heat shock gene-specific sigma factor of Escherichia coli, σ32. J. Bacteriol. 181, 3552–3561.10.1128/JB.181.11.3552-3561.1999Search in Google Scholar PubMed PubMed Central
Baker, T.A. and Sauer, R.T. (2006). ATP-dependent proteases of bacteria: recognition logic and operating principles. Trends Biochem. Sci. 31, 647–653.10.1016/j.tibs.2006.10.006Search in Google Scholar PubMed PubMed Central
Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T.G., Bertoni, M., Bordoli, L., et al. (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 42, W252–W258.10.1093/nar/gku340Search in Google Scholar PubMed PubMed Central
Bieniossek, C., Schalch, T., Bumann, M., Meister, M., Meier, R., and Baumann, U. (2006). The molecular architecture of the metalloprotease FtsH. Proc. Natl. Acad. Sci. USA 103, 3066–3071.10.1073/pnas.0600031103Search in Google Scholar PubMed PubMed Central
Bittner, L.M., Westphal, K., and Narberhaus, F. (2015). Conditional proteolysis of the membrane protein YfgM by the FtsH protease depends on a novel N-terminal degron. J. Biol. Chem. 290, 19367–19378.10.1074/jbc.M115.648550Search in Google Scholar PubMed PubMed Central
Bittner, L.M., Arends, J., and Narberhaus, F. (2016). ATP-dependent proteases in bacteria. Biopolymers 105, 505–517.10.1002/bip.22831Search in Google Scholar PubMed
Blaszczak, A., Zylicz, M., Georgopoulos, C., and Liberek, K. (1995). Both ambient-temperature and the Dnak chaperone machine modulate the heat-shock response in Escherichia coli by regulating the switch between σ70 and σ32 factors assembled with RNA-polymerase. EMBO J. 14, 5085–5093.10.1002/j.1460-2075.1995.tb00190.xSearch in Google Scholar PubMed PubMed Central
Bordoli, L., Kiefer, F., Arnold, K., Benkert, P., Battey, J., and Schwede, T. (2009). Protein structure homology modeling using SWISS-MODEL workspace. Nat. Protocols 4, 1–13.10.1038/nprot.2008.197Search in Google Scholar PubMed
Carballès, F., Bertrand, C., Bouché, J.P., and Cam, K. (1999). Regulation of Escherichia coli cell division genes ftsA and ftsZ by the two-component system rcsC-rcsB. Mol. Microbiol. 34, 442–450.10.1046/j.1365-2958.1999.01605.xSearch in Google Scholar PubMed
Chiba, S., Akiyama, Y., Mori, H., Matsuo, E., and Ito, K. (2000). Length recognition at the N-terminal tail for the initiation of FtsH-mediated proteolysis. EMBO Rep. 1, 47–52.10.1093/embo-reports/kvd005Search in Google Scholar PubMed PubMed Central
Chiba, S., Akiyama, Y., and Ito, K. (2002). Membrane protein degradation by FtsH can be initiated from either end. J. Bacteriol. 184, 4775–4782.10.1128/JB.184.17.4775-4782.2002Search in Google Scholar PubMed PubMed Central
Choy, J.S., Aung, L.L., and Karzai, A.W. (2007). Lon protease degrades transfer-messenger RNA-tagged proteins. J. Bacteriol. 189, 6564–6571.10.1128/JB.00860-07Search in Google Scholar PubMed PubMed Central
Clarke, D.J. (2010). The Rcs phosphorelay: more than just a two-component pathway. Future Microbiol. 5, 1173–1184.10.2217/fmb.10.83Search in Google Scholar PubMed
Daley, D.O., Rapp, M., Granseth, E., Melen, K., Drew, D., and von Heijne, G. (2005). Global topology analysis of the Escherichia coli inner membrane proteome. Science 308, 1321–1323.10.1126/science.1109730Search in Google Scholar PubMed
Datta, A.B., Roy, S., and Parrack, P. (2005). Role of C-terminal residues in oligomerization and stability of lambda CII: implications for lysis-lysogeny decision of the phage. J. Mol. Biol. 345, 315–324.10.1016/j.jmb.2004.09.098Search in Google Scholar PubMed
Dautin, N., Karimova, G., Ullmann, A., and Ladant, D. (2000). Sensitive genetic screen for protease activity based on a cyclic AMP signaling cascade in Escherichia coli. J. Bacteriol. 182, 7060–7066.10.1128/JB.182.24.7060-7066.2000Search in Google Scholar
Davalos-Garcia, M., Conter, A., Toesca, I., Gutierrez, C., and Cam, K. (2001). Regulation of osmC gene expression by the two-component system rcsB-rcsC in Escherichia coli. J. Bacteriol. 183, 5870–5876.10.1128/JB.183.20.5870-5876.2001Search in Google Scholar
Delcour, A.H. (2009). Outer membrane permeability and antibiotic resistance. Biochim. Biophys. Acta Proteins Proteomics 1794, 808–816.10.1016/j.bbapap.2008.11.005Search in Google Scholar
Emiola, A., George, J., and Andrews, S.S. (2014). A complete pathway model for lipid A biosynthesis in Escherichia coli. PLoS One 10, e0121216.10.1371/journal.pone.0121216Search in Google Scholar
Emiola, A., Andrews, S.S., Heller, C., and George, J. (2016). Crosstalk between the lipopolysaccharide and phospholipid pathways during outer membrane biogenesis in Escherichia coli. Proc. Natl. Acad. Sci. USA 113, 3108–3113.10.1073/pnas.1521168113Search in Google Scholar
Führer, F., Langklotz, S., and Narberhaus, F. (2006). The C-terminal end of LpxC is required for degradation by the FtsH protease. Mol. Microbiol. 59, 1025–1036.10.1111/j.1365-2958.2005.04994.xSearch in Google Scholar
Führer, F., Müller, A., Baumann, H., Langklotz, S., Kutscher, B., and Narberhaus, F. (2007). Sequence and length recognition of the C-terminal turnover element of LpxC, a soluble substrate of the membrane-bound FtsH protease. J. Mol. Biol. 372, 485–496.10.1016/j.jmb.2007.06.083Search in Google Scholar
Gaca, A.O., Colomer-Winter, C., and Lemos, J.A. (2015). Many means to a common end: the intricacies of (p)ppGpp metabolism and its control of bacterial homeostasis. J. Bacteriol. 197, 1146–1156.10.1128/JB.02577-14Search in Google Scholar
Gamer, J., Bujard, H., and Bukau, B. (1992). Physical interaction between heat-shock proteins DnaK, DnaJ, and GrpE and the bacterial heat-shock transcription factor σ32. Cell 69, 833–842.10.1016/0092-8674(92)90294-MSearch in Google Scholar
Gamer, J., Multhaup, G., Tomoyasu, T., McCarty, J.S., Rudiger, S., Schonfeld, H.J., Schirra, C., Bujard, H., and Bukau, B. (1996). A cycle of binding and release of the DnaK, DnaJ and GrpE chaperones regulates activity of the Escherichia coli heat shock transcription factor σ32. EMBO J. 15, 607–617.10.1002/j.1460-2075.1996.tb00393.xSearch in Google Scholar
Gottesman, S., Roche, E., Zhou, Y., and Sauer, R.T. (1998). The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev. 12, 1338–1347.10.1101/gad.12.9.1338Search in Google Scholar PubMed PubMed Central
Götzke, H., Palombo, I., Muheim, C., Perrody, E., Genevaux, P., Kudva, R., Müller, M., and Daley, D.O. (2014). YfgM is an ancillary subunit of the SecYEG translocon in Escherichia coli. J. Biol. Chem. 289, 19089–19097.10.1074/jbc.M113.541672Search in Google Scholar PubMed PubMed Central
Götzke, H., Muheim, C., Altelaar, A.F., Heck, A.J., Maddalo, G., and Daley, D.O. (2015). Identification of putative substrates for the periplasmic chaperone YfgM in Escherichia coli using quantitative proteomics. Mol. Cell. Proteomics 14, 216–226.10.1074/mcp.M114.043216Search in Google Scholar PubMed PubMed Central
Griffith, K.L., Shah, I.M., and Wolf, R.E., Jr. (2004). Proteolytic degradation of Escherichia coli transcription activators SoxS and MarA as the mechanism for reversing the induction of the superoxide (SoxRS) and multiple antibiotic resistance (Mar) regulons. Mol. Microbiol. 51, 1801–1816.10.1046/j.1365-2958.2003.03952.xSearch in Google Scholar PubMed
Guisbert, E., Herman, C., Lu, C.Z., and Gross, C.A. (2004). A chaperone network controls the heat shock response in E. coli. Genes Dev. 18, 2812–2821.10.1101/gad.1219204Search in Google Scholar PubMed PubMed Central
Gur, E., Ottofueling, R., and Dougan, D.A. (2013). Machines of destruction – AAA+ proteases and the adaptors that control them. Subcell. Biochem. 66, 3–33.10.1007/978-94-007-5940-4_1Search in Google Scholar PubMed
Herman, C., Thévenet, D., D’Ari, R., and Bouloc, P. (1995). Degradation of σ32, the heat-shock regulator in Escherichia coli is governed by HflB. Proc. Natl. Acad. Sci. USA 92, 3516–3520.10.1073/pnas.92.8.3516Search in Google Scholar PubMed PubMed Central
Herman, C., Thévenet, D., D’Ari, R., and Bouloc, P. (1997). The HflB protease of Escherichia coli degrades its inhibitor lλcIII. J. Bacteriol. 179, 358–363.10.1128/jb.179.2.358-363.1997Search in Google Scholar PubMed PubMed Central
Herman, C., Thévenet, D., Bouloc, P., Walker, G.C., and D’Ari, R. (1998). Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH). Genes Dev. 12, 1348–1355.10.1101/gad.12.9.1348Search in Google Scholar PubMed PubMed Central
Horikoshi, M., Yura, T., Tsuchimoto, S., Fukumori, Y., and Kanemori, M. (2004). Conserved region 2.1 of Escherichia coli heat shock transcription factor σ32 is required for modulating both metabolic stability and transcriptional activity. J. Bacteriol. 186, 7474–7480.10.1128/JB.186.22.7474-7480.2004Search in Google Scholar PubMed PubMed Central
Ito, K. and Akiyama, Y. (2005). Cellular functions, mechanism of action, and regulation of FtsH protease. Annu. Rev. Microbiol. 59, 211–231.10.1146/annurev.micro.59.030804.121316Search in Google Scholar PubMed
Janska, H., Piechota, J., and Kwasniak, M. (2010). ATP-dependent proteases in biogenesis and maintenance of plant mitochondria. Biochim Biophys Acta 1797, 1071–1075.10.1016/j.bbabio.2010.02.027Search in Google Scholar PubMed
Janska, H., Kwasniak, M., and Szczepanowska, J. (2013). Protein quality control in organelles – AAA/FtsH story. Biochim Biophys Acta 1833, 381–387.10.1016/j.bbamcr.2012.03.016Search in Google Scholar PubMed
Johnson, M.D., Burton, N.A., Gutiérrez, B., Painter, K., and Lund, P.A. (2011). RcsB is required for inducible acid resistance in Escherichia coli and acts at gadE-dependent and -independent promoters. J. Bacteriol. 193, 3653–3656.10.1128/JB.05040-11Search in Google Scholar PubMed PubMed Central
Joo, D.M., Nolte, A., Calendar, R., Zhou, Y.N., and Jin, D.J. (1998). Multiple regions on the Escherichia coli heat shock transcription factor σ32 determine core RNA polymerase binding specificity. J. Bacteriol. 180, 1095–1102.10.1128/JB.180.5.1095-1102.1998Search in Google Scholar PubMed PubMed Central
Kalinin, D.V. and Holl, R. (2016). Insights into the zinc-dependent deacetylase LpxC: biochemical properties and inhibitor design. Curr. Top. Med. Chem. 16, 2379–2430.10.2174/1568026616666160413135835Search in Google Scholar PubMed
Kampfenkel, K. and Braun, V. (1992). Membrane topology of the Escherichia coli ExbD protein. J. Bacteriol. 174, 5485–5487.10.1128/jb.174.16.5485-5487.1992Search in Google Scholar PubMed PubMed Central
Kanemori, M., Nishihara, K., Yanagi, H., and Yura, T. (1997). Synergistic roles of HslVU and other ATP-dependent proteases in controlling in vivo turnover of σ32 and abnormal proteins in Escherichia coli. J. Bacteriol. 179, 7219–7225.10.1128/jb.179.23.7219-7225.1997Search in Google Scholar PubMed PubMed Central
Karata, K., Inagawa, T., Wilkinson, A.J., Tatsuta, T., and Ogura, T. (1999). Dissecting the role of a conserved motif (the second region of homology) in the AAA family of ATPases. Site-directed mutagenesis of the ATP-dependent protease FtsH. J. Biol. Chem. 274, 26225–26232.10.1074/jbc.274.37.26225Search in Google Scholar PubMed
Karata, K., Verma, C.S., Wilkinson, A.J., and Ogura, T. (2001). Probing the mechanism of ATP hydrolysis and substrate translocation in the AAA protease FtsH by modelling and mutagenesis. Mol. Microbiol. 39, 890–903.10.1046/j.1365-2958.2001.02301.xSearch in Google Scholar PubMed
Katz, C. and Ron, E.Z. (2008). Dual role of FtsH in regulating lipopolysaccharide biosynthesis in Escherichia coli. J. Bacteriol. 190, 7117–7122.10.1128/JB.00871-08Search in Google Scholar PubMed PubMed Central
Keiler, K.C., Waller, P.R., and Sauer, R.T. (1996). Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990–993.10.1126/science.271.5251.990Search in Google Scholar PubMed
Kihara, A., Akiyama, Y., and Ito, K. (1995). FtsH is required for proteolytic elimination of uncomplexed forms of SecY, an essential protein translocase subunit. Proc. Natl. Acad. Sci. USA 92, 4532–4536.10.1073/pnas.92.10.4532Search in Google Scholar PubMed PubMed Central
Kihara, A., Akiyama, Y., and Ito, K. (1996). A protease complex in the Escherichia coli plasma membrane: HflKC (HflA) forms a complex with FtsH (HflB), regulating its proteolytic activity against SecY. EMBO J. 15, 6122–6131.10.1002/j.1460-2075.1996.tb01000.xSearch in Google Scholar
Kihara, A., Akiyama, Y., and Ito, K. (1997). Host regulation of lysogenic decision in bacteriophage λ: transmembrane modulation of FtsH (HflB), the cII degrading protease, by HflKC (HflA). Proc. Natl. Acad. Sci. USA 94, 5544–5549.10.1073/pnas.94.11.5544Search in Google Scholar PubMed PubMed Central
Kihara, A., Akiyama, Y., and Ito, K. (1998). Different pathways for protein degradation by the FtsH/HflKC membrane-embedded protease complex: an implication from the interference by a mutant form of a new substrate protein, YccA. J. Mol. Biol. 279, 175–188.10.1006/jmbi.1998.1781Search in Google Scholar PubMed
Kihara, A., Akiyama, Y., and Ito, K. (1999). Dislocation of membrane proteins in FtsH-mediated proteolysis. EMBO J. 18, 2970–2981.10.1093/emboj/18.11.2970Search in Google Scholar PubMed PubMed Central
Kihara, A., Akiyama, Y., and Ito, K. (2001). Revisiting the lysogenization control of bacteriophage λ. Identification and characterization of a new host component, HflD. J. Biol. Chem. 276, 13695–13700.10.1074/jbc.M011699200Search in Google Scholar PubMed
Klein, G., Kobylak, N., Lindner, B., Stupak, A., and Raina, S. (2014). Assembly of lipopolysaccharide in Escherichia coli requires the essential LapB heat shock protein. J. Biol. Chem. 289, 14829–14853.10.1074/jbc.M113.539494Search in Google Scholar PubMed PubMed Central
Kobiler, O., Koby, S., Teff, D., Court, D., and Oppenheim, A.B. (2002). The phage lambda CII transcriptional activator carries a C-terminal domain signaling for rapid proteolysis. Proc. Natl. Acad. Sci. USA 99, 14964–14969.10.1073/pnas.222172499Search in Google Scholar PubMed PubMed Central
Ladant, D. and Ullmann, A. (1999). Bordetella pertussis adenylate cyclase: a toxin with multiple talents. Trends Microbiol. 7, 172–176.10.1016/S0966-842X(99)01468-7Search in Google Scholar
Langklotz, S., Schäkermann, M., and Narberhaus, F. (2011). Control of lipopolysaccharide biosynthesis by FtsH-mediated proteolysis of LpxC is conserved in enterobacteria but not in all Gram-negative bacteria. J. Bacteriol. 193, 1090–1097.10.1128/JB.01043-10Search in Google Scholar PubMed PubMed Central
Langklotz, S., Baumann, U., and Narberhaus, F. (2012). Structure and function of the bacterial AAA protease FtsH. Biochim. Biophys. Acta 1823, 40–48.10.1016/j.bbamcr.2011.08.015Search in Google Scholar PubMed
Lasserre, J.P., Beyne, E., Pyndiah, S., Lapaillerie, D., Claverol, S., and Bonneu, M. (2006). A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27, 3306–3321.10.1002/elps.200500912Search in Google Scholar PubMed
Leffers, G.G., Jr. and Gottesman, S. (1998). Lambda Xis degradation in vivo by Lon and FtsH. J. Bacteriol. 180, 1573–1577.10.1128/JB.180.6.1573-1577.1998Search in Google Scholar PubMed PubMed Central
Levchenko, I., Grant, R.A., Wah, D.A., Sauer, R.T., and Baker, T.A. (2003). Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag. Mol. Cell 12, 365–372.10.1016/j.molcel.2003.08.014Search in Google Scholar PubMed
Lies, M. and Maurizi, M.R. (2008). Turnover of endogenous SsrA-tagged proteins mediated by ATP-dependent proteases in Escherichia coli. J. Biol. Chem. 283, 22918–22929.10.1074/jbc.M801692200Search in Google Scholar PubMed PubMed Central
Lim, B., Miyazaki, R., Neher, S., Siegele, D.A., Ito, K., Walter, P., Akiyama, Y., Yura, T., and Gross, C.A. (2013). Heat shock transcription factor σ32 co-opts the signal recognition particle to regulate protein homeostasis in E. coli. PLoS Biol. 11, e1001735.10.1371/journal.pbio.1001735Search in Google Scholar PubMed PubMed Central
Lonetto, M., Gribskov, M., and Gross, C.A. (1992). The σ70 family: sequence conservation and evolutionary relationships. J. Bacteriol. 174, 3843–3849.10.1128/jb.174.12.3843-3849.1992Search in Google Scholar PubMed PubMed Central
Maddalo, G., Stenberg-Bruzell, F., Götzke, H., Toddo, S., Bjorkholm, P., Eriksson, H., Chovanec, P., Genevaux, P., Lehtio, J., Ilag, L.L., et al. (2011). Systematic analysis of native membrane protein complexes in Escherichia coli. J. Proteome Res. 10, 1848–1859.10.1021/pr101105cSearch in Google Scholar PubMed
Mahalakshmi, S., Sunayana, M.R., SaiSree, L., and Reddy, M. (2014). yciM is an essential gene required for regulation of lipopolysaccharide synthesis in Escherichia coli. Mol. Microbiol. 91, 145–157.10.1111/mmi.12452Search in Google Scholar PubMed
Majdalani, N. and Gottesman, S. (2005). The Rcs phosphorelay: a complex signal transduction system. Annu. Rev. Microbiol. 59, 379–405.10.1146/annurev.micro.59.050405.101230Search in Google Scholar PubMed
Majdalani, N., Hernandez, D., and Gottesman, S. (2002). Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol. Microbiol. 46, 813–826.10.1046/j.1365-2958.2002.03203.xSearch in Google Scholar PubMed
Martin, A., Baker, T.A., and Sauer, R.T. (2008a). Diverse pore loops of the AAA+ ClpX machine mediate unassisted and adaptor-dependent recognition of ssrA-tagged substrates. Mol. Cell 29, 441–450.10.1016/j.molcel.2008.02.002Search in Google Scholar PubMed PubMed Central
Martin, A., Baker, T.A., and Sauer, R.T. (2008b). Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding. Nat. Struct. Mol. Biol. 15, 1147–1151.10.1038/nsmb.1503Search in Google Scholar PubMed PubMed Central
Mdluli, K.E., Witte, P.R., Kline, T., Barb, A.W., Erwin, A.L., Mansfield, B.E., McClerren, A.L., Pirrung, M.C., Tumey, L.N., Warrener, P., et al. (2006). Molecular validation of LpxC as an antibacterial drug target in Pseudomonas aeruginosa. Antimicrob. Agents Chemother. 50, 2178–2184.10.1128/AAC.00140-06Search in Google Scholar PubMed PubMed Central
Miyazaki, R., Yura, T., Suzuki, T., Dohmae, N., Mori, H., and Akiyama, Y. (2016). A novel SRP recognition sequence in the homeostatic control region of heat shock transcription factor σ32. Sci. Rep. 6, 24147.10.1038/srep24147Search in Google Scholar PubMed PubMed Central
Moore, S.D. and Sauer, R.T. (2007). The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 76, 101–124.10.1146/annurev.biochem.75.103004.142733Search in Google Scholar PubMed
Morita, M., Kanemori, M., Yanagi, H., and Yura, T. (1999a). Heat-induced synthesis of σ32 in Escherichia coli: structural and functional dissection of rpoH mRNA secondary structure. J. Bacteriol. 181, 401–410.10.1128/JB.181.2.401-410.1999Search in Google Scholar PubMed PubMed Central
Morita, M.T., Tanaka, Y., Kodama, T.S., Kyogoku, Y., Yanagi, H., and Yura, T. (1999b). Translational induction of heat shock transcription factor σ32: evidence for a built-in RNA thermosensor. Genes Dev. 13, 655–665.10.1101/gad.13.6.655Search in Google Scholar PubMed PubMed Central
Nagai, H., Yuzawa, H., and Yura, T. (1991). Interplay of two cis-acting mRNA regions in translational control of σ32 synthesis during the heat shock response of Escherichia coli. Proc. Natl. Acad. Sci. USA 88, 10515–10519.10.1073/pnas.88.23.10515Search in Google Scholar PubMed PubMed Central
Nakahigashi, K., Yanagi, H., and Yura, T. (1995). Isolation and sequence analysis of rpoH genes encoding σ32 homologs from gram negative bacteria: conserved mRNA and protein segments for heat shock regulation. Nucleic Acids Res. 23, 4383–4390.Search in Google Scholar
Nikaido, H. and Vaara, M. (1985). Molecular basis of bacterial outer membrane permeability. Microbiol. Rev. 49, 1–32.10.1128/mr.49.1.1-32.1985Search in Google Scholar PubMed PubMed Central
Nishimura, K., Kato, Y., and Sakamoto, W. (2016). Chloroplast proteases: updates on proteolysis within and across suborganellar compartments. Plant Physiol. 171, 2280–2293.10.1104/pp.16.00330Search in Google Scholar PubMed PubMed Central
Noguchi, A., Ikeda, A., Mezaki, M., Fukumori, Y., and Kanemori, M. (2014). DnaJ-promoted binding of DnaK to multiple sites on σ32 in the presence of ATP. J. Bacteriol. 196, 1694–1703.10.1128/JB.01197-13Search in Google Scholar PubMed PubMed Central
Nonaka, G., Blankschien, M., Herman, C., Gross, C.A., and Rhodius, V.A. (2006). Regulon and promoter analysis of the E. coli heat-shock factor, σ32, reveals a multifaceted cellular response to heat stress. Genes Dev. 20, 1776–1789.10.1101/gad.1428206Search in Google Scholar PubMed PubMed Central
Nyquist, K. and Martin, A. (2014). Marching to the beat of the ring: polypeptide translocation by AAA+ proteases. Trends Biochem. Sci. 39, 53–60.10.1016/j.tibs.2013.11.003Search in Google Scholar PubMed PubMed Central
Obrist, M. and Narberhaus, F. (2005). Identification of a turnover element in region 2.1 of Escherichia coli σ32 by a bacterial one-hybrid approach. J. Bacteriol. 187, 3807–3813.10.1128/JB.187.11.3807-3813.2005Search in Google Scholar PubMed PubMed Central
Obrist, M., Langklotz, S., Milek, S., Führer, F., and Narberhaus, F. (2009). Region C of the Escherichia coli heat shock sigma factor RpoH (σ32) contains a turnover element for proteolysis by the FtsH protease. FEMS Microbiol. Lett. 290, 199–208.10.1111/j.1574-6968.2008.01423.xSearch in Google Scholar PubMed
Obrist, M., Milek, S., Klauck, E., Hengge, R., and Narberhaus, F. (2007). Region 2.1 of the Escherichia coli heat-shock sigma factor RpoH (σ32) is necessary but not sufficient for degradation by the FtsH protease. Microbiology 153, 2560–2571.10.1099/mic.0.2007/007047-0Search in Google Scholar PubMed
Ogura, T., Inoue, K., Tatsuta, T., Suzaki, T., Karata, K., Young, K., Su, L.H., Fierke, C.A., Jackman, J.E., Raetz, C.R., et al. (1999). Balanced biosynthesis of major membrane components through regulated degradation of the committed enzyme of lipid A biosynthesis by the AAA protease FtsH (HflB) in Escherichia coli. Mol. Microbiol. 31, 833–844.10.1046/j.1365-2958.1999.01221.xSearch in Google Scholar PubMed
Onishi, H.R., Pelak, B.A., Gerckens, L.S., Silver, L.L., Kahan, F.M., Chen, M.H., Patchett, A.A., Galloway, S.M., Hyland, S.A., Anderson, M.S., et al. (1996). Antibacterial agents that inhibit lipid A biosynthesis. Science 274, 980–982.10.1126/science.274.5289.980Search in Google Scholar
Peterson, C.N., Carabetta, V.J., Chowdhuryj, T., and Silhavy, T.J. (2006). LrhA regulates rpoS translation in response to the Rcs phosphorelay system in Escherichia coli. J. Bacteriol. 188, 3175–3181.10.1128/JB.188.9.3175-3181.2006Search in Google Scholar
Potrykus, K. and Cashel, M. (2008). (p)ppGpp: still magical? Annu. Rev. Microbiol. 62, 35–51.10.1146/annurev.micro.62.081307.162903Search in Google Scholar
Rodriguez, F., Arsène-Ploetze, F., Rist, W., Rudiger, S., Schneider-Mergener, J., Mayer, M.P., and Bukau, B. (2008). Molecular basis for regulation of the heat shock transcription factor σ32 by the DnaK and DnaJ chaperones. Mol. Cell 32, 347–358.10.1016/j.molcel.2008.09.016Search in Google Scholar
Roy, A., Kucukural, A., and Zhang, Y. (2010). I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protocols 5, 725–738.10.1038/nprot.2010.5Search in Google Scholar
Saikawa, N., Akiyama, Y., and Ito, K. (2004). FtsH exists as an exceptionally large complex containing HflKC in the plasma membrane of Escherichia coli. J. Struct. Biol. 146, 123–129.10.1016/j.jsb.2003.09.020Search in Google Scholar
Sauer, R.T. and Baker, T.A. (2011). AAA+ proteases: ATP-fueled machines of protein destruction. Annu. Rev. Biochem. 80, 587–612.10.1146/annurev-biochem-060408-172623Search in Google Scholar
Sauer, R.T., Bolon, D.N., Burton, B.M., Burton, R.E., Flynn, J.M., Grant, R.A., Hersch, G.L., Joshi, S.A., Kenniston, J.A., Levchenko, I., et al. (2004). Sculpting the proteome with AAA+ proteases and disassembly machines. Cell 119, 9–18.10.1016/j.cell.2004.09.020Search in Google Scholar
Schäkermann, M., Langklotz, S., and Narberhaus, F. (2013). FtsH-mediated coordination of lipopolysaccharide biosynthesis in Escherichia coli correlates with the growth rate and the alarmone (p)ppGpp. J. Bacteriol. 195, 1912–1919.10.1128/JB.02134-12Search in Google Scholar
Schumann, W. (1999). FtsH-a single-chain charonin? FEMS Microbiol. Rev. 23, 1–11.10.1016/S0168-6445(98)00024-2Search in Google Scholar
Shotland, Y., Koby, S., Teff, D., Mansur, N., Oren, D.A., Tatematsu, K., Tomoyasu, T., Kessel, M., Bukau, B., Ogura, T., et al. (1997). Proteolysis of the phage lambda CII regulatory protein by FtsH (HflB) of Escherichia coli. Mol. Microbiol. 24, 1303–1310.10.1046/j.1365-2958.1997.4231796.xSearch in Google Scholar PubMed
Singh, S. and Darwin, A.J. (2011). FtsH-dependent degradation of phage shock protein C in Yersinia enterocolitica and Escherichia coli. J. Bacteriol. 193, 6436–6442.10.1128/JB.05942-11Search in Google Scholar PubMed PubMed Central
Straus, D.B., Walter, W.A., and Gross, C.A. (1987). The heat-shock response of Escherichia coli is regulated by changes in the concentration of σ32. Nature 329, 348–351.10.1038/329348a0Search in Google Scholar PubMed
Straus, D., Walter, W., and Gross, C.A. (1990). DnaK, DnaJ, and GrpE heat-shock proteins negatively regulate heat-shock gene expression by controlling the synthesis and stability of σ32. Genes Dev. 4, 2202–2209.10.1101/gad.4.12a.2202Search in Google Scholar PubMed
Suzuki, H., Ikeda, A., Tsuchimoto, S., Adachi, K., Noguchi, A., Fukumori, Y., and Kanemori, M. (2012). Synergistic binding of DnaJ and DnaK chaperones to heat shock transcription factor σ32 ensures its characteristic high metabolic instability: implications for heat shock protein 70 (Hsp70)-Hsp40 mode of function. J. Biol. Chem. 287, 19275–19283.10.1074/jbc.M111.331470Search in Google Scholar PubMed PubMed Central
Tatsuta, T. and Langer, T. (2009). AAA proteases in mitochondria: diverse functions of membrane-bound proteolytic machines. Res Microbiol. 160, 711–717.10.1016/j.resmic.2009.09.005Search in Google Scholar PubMed
Tomoyasu, T., Yamanaka, K., Murata, K., Suzaki, T., Bouloc, P., Kato, A., Niki, H., Hiraga, S., and Ogura, T. (1993). Topology and subcellular localization of FtsH protein in Escherichia coli. J. Bacteriol. 175, 1352–1357.10.1128/jb.175.5.1352-1357.1993Search in Google Scholar PubMed PubMed Central
Tomoyasu, T., Gamer, J., Bukau, B., Kanemori, M., Mori, H., Rutman, A.J., Oppenheim, A.B., Yura, T., Yamanaka, K., Niki, H., et al. (1995). Escherichia coli FtsH is a membrane-bound, ATP-dependent protease which degrades the heat-shock transcription factor σ32. EMBO J. 14, 2551–2560.10.1002/j.1460-2075.1995.tb07253.xSearch in Google Scholar PubMed PubMed Central
Tomoyasu, T., Ogura, T., Tatsuta, T., and Bukau, B. (1998). Levels of DnaK and DnaJ provide tight control of heat shock gene expression and protein repair in Escherichia coli. Mol. Microbiol. 30, 567–581.10.1046/j.1365-2958.1998.01090.xSearch in Google Scholar PubMed
Vaara, M. (1996). Lipid A: target for antibacterial drugs. Science 274, 939–940.10.1126/science.274.5289.939Search in Google Scholar PubMed
Westphal, K., Langklotz, S., Thomanek, N., and Narberhaus, F. (2012). A trapping approach reveals novel substrates and physiological functions of the essential protease FtsH in Escherichia coli. J. Biol. Chem. 287, 42962–42971.10.1074/jbc.M112.388470Search in Google Scholar
Wösten, M.M. (1998). Eubacterial sigma-factors. FEMS Microbiol Rev. 22, 127–150.10.1016/S0168-6445(98)00011-4Search in Google Scholar
Xu, X.B., Niu, Y.L., Liang, K., Wang, J.M., Li, X.F., and Yang, Y. (2015). Heat shock transcription factor σ32 is targeted for degradation via an ubiquitin-like protein ThiS in Escherichia coli. Biochem. Biophys. Res. Commun. 459, 240–245.10.1016/j.bbrc.2015.02.087Search in Google Scholar
Yura, T. and Nakahigashi, K. (1999). Regulation of the heat-shock response. Curr. Opin. Microbiol. 2, 153–158.10.1016/S1369-5274(99)80027-7Search in Google Scholar
Yuzawa, H., Nagai, H., Mori, H., and Yura, T. (1993). Heat induction of σ32 synthesis mediated by mRNA secondary structure: a primary step of the heat shock response in Escherichia coli. Nucleic Acids Res. 21, 5449–5455.10.1093/nar/21.23.5449Search in Google Scholar PubMed PubMed Central
Zhang, Y. (2008). I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9, 40.10.1186/1471-2105-9-40Search in Google Scholar PubMed PubMed Central
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