Conditional Proteolysis of the Membrane Protein YfgM by the FtsH Protease Depends on a Novel N-terminal Degron

Bittner, Lisa-Marie; Westphal, Kai; Narberhaus, Franz

doi:10.1074/jbc.m115.648550

Cited by 30 publications

(39 citation statements)

References 80 publications

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“…For example, the FtsH and Lon substrate SoxS was shown to be stabilized tenfold by an N‐terminal His‐tag in comparison to the C‐terminally or untagged variant . In contrast, however, degradation of YfgM, which contains an N‐terminal degron, and several other FtsH substrates was not influenced by tags at the C‐ or N‐terminus . Due to the plasmid‐based expression system, the putative substrates are present at un‐physiological levels.…”

Section: Discussionmentioning

confidence: 99%

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In vivo trapping of FtsH substrates by label‐free quantitative proteomics

et al. 2016

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FtsH is the only membrane-bound and essential protease in Escherichia coli. It is responsible for the degradation of regulatory proteins and enzymes such as the heat-shock sigma factor RpoH or LpxC, the key enzyme of lipopolysaccharide biosynthesis. To find new FtsH targets, we trapped substrates in E. coli cells from exponential and stationary growth phase by using a proteolytically inactive FtsH variant. Subsequent analysis of the isolated FtsH-substrate complexes by label-free nanoLC-MS/MS revealed more than 50 putative FtsH substrates, among them five already known substrates. Four out of thirty-seven tested candidates were found to be novel FtsH substrates as shown by in vivo degradation experiments. Six other candidates were degraded by one or more other protease(s). The FtsH substrates SecD and ExbD are involved in transport processes across the membrane, whereas the physiological roles of YlaC and YhbT are yet unknown. The presence of the previously identified YfgM degron in two of the novel substrates suggests general rules for substrate recognition of this unique protease.

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Section: Discussionmentioning

confidence: 99%

“…Degrons of FtsH substrates have been reported to lie in the C‐terminus (LpxC), N‐terminus (YfgM) or internally (RpoH) pointing out that different substrates are processed via different pathways [. Heterogeneous degrons are also known for other proteases.…”

Section: Discussionmentioning

confidence: 99%

In vivo trapping of FtsH substrates by label‐free quantitative proteomics

et al. 2016

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“…ClpS), but such degron sequences are poorly understood in plastids (see Outstanding Questions). A recent study has identified a novel N-terminal degron for FtsH-driven proteolysis in bacteria (Bittner et al, 2015), raising the question of whether such a target recognition mechanism is conserved in chloroplasts. Meanwhile there have been several well-known examples of proteolytic regulation of specific chloroplast proteins.…”

Section: Proteolytic Remodeling Of the Photosynthetic Machineries In mentioning

confidence: 99%

“…Comprehensive substrate identification is necessary for determination of a common sequence signature or regulatory motif. Using substrate-trapping approaches, multiple substrates for Clp and FtsH proteases have been isolated in bacteria and in mammalian mitochondria Neher et al, 2003;Westphal et al, 2012;Bhat et al, 2013;Feng et al, 2013;Graham et al, 2013;Bittner et al, 2015). Trapping strategies use mutated, inactive forms of the protease or chaperone domains.…”

Section: Proteolytic Remodeling Of the Photosynthetic Machineries In mentioning

confidence: 99%

Chloroplast Proteases: Updates on Proteolysis within and across Suborganellar Compartments

2016

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ORCID IDs: 0000-0003-1718-9121 (Y.K.); 0000-0001-9747-5042 (W.S.).Chloroplasts originated from the endosymbiosis of ancestral cyanobacteria and maintain transcription and translation machineries for around 100 proteins. Most endosymbiont genes, however, have been transferred to the host nucleus, and the majority of the chloroplast proteome is composed of nucleus-encoded proteins that are biosynthesized in the cytosol and then imported into chloroplasts. How chloroplasts and the nucleus communicate to control the plastid proteome remains an important question. Protein-degrading machineries play key roles in chloroplast proteome biogenesis, remodeling, and maintenance. Research in the past few decades has revealed more than 20 chloroplast proteases, which are localized to specific suborganellar locations. In particular, two energy-dependent processive proteases of bacterial origin, Clp and FtsH, are central to protein homeostasis. Processing endopeptidases such as stromal processing peptidase and thylakoidal processing peptidase are involved in the maturation of precursor proteins imported into chloroplasts by cleaving off the amino-terminal transit peptides. Presequence peptidases and organellar oligopeptidase subsequently degrade the cleaved targeting peptides. Recent findings have indicated that not only intraplastidic but also extraplastidic processive protein-degrading systems participate in the regulation and quality control of protein translocation across the envelopes. In this review, we summarize current knowledge of the major chloroplast proteases in terms of type, suborganellar localization, and diversification. We present details of these degradation processes as case studies according to suborganellar compartment (envelope, stroma, and thylakoids). Key questions and future directions in this field are discussed.Over 1 billion years of plastid evolution since the endosymbiosis of ancestral cyanobacteria (Douzery et al., 2004), chloroplast biogenesis has gained complexity, with large sets of the endosymbiont genes being transferred to host nuclear genomes. While only 100 endosymbiont genes remain in the plastid genome, with the corresponding proteins biosynthesized there, the nuclear genes have often gained complexity by duplication and diversification of the original endosymbiotic genes. This complexity raises numerous questions regarding (1) at what level gene expression is coordinately controlled, (2) what molecules coordinate the cross talk between chloroplasts and the nucleus, (3) how proteins get across membranes and become imported into chloroplasts, and (4) how the stoichiometries of nucleus-and chloroplast-encoded subunits within individual chloroplast protein complexes such as photosystems and Rubisco are strictly maintained.Given these questions, chloroplast biogenesis has remained a central subject in plant physiology for the last few decades (Jarvis and López-Juez, 2013). In our view, the aforementioned questions point to the importance of protein homeostasis and posttranslational modificat...

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“…Accordingly, several membrane‐anchored substrates like FdoH, DadA, and YfgM were trapped with FtsH. A detailed analysis of YfgM revealed a novel N‐terminal degron and a function in the stress management in stationary growth phase …”

Section: Substrate Identification Of Aaa+ Proteases By Trapping Appromentioning

confidence: 99%

Mini review: ATP‐dependent proteases in bacteria

2016

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AAA(+) proteases are universal barrel-like and ATP-fueled machines preventing the accumulation of aberrant proteins and regulating the proteome according to the cellular demand. They are characterized by two separate operating units, the ATPase and peptidase domains. ATP-dependent unfolding and translocation of a substrate into the proteolytic chamber is followed by ATP-independent degradation. This review addresses the structure and function of bacterial AAA(+) proteases with a focus on the ATP-driven mechanisms and the coordinated movements in the complex mainly based on the knowledge of ClpXP. We conclude by discussing strategies how novel protease substrates can be trapped by mutated AAA(+) protease variants. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 505-517, 2016.

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Conditional Proteolysis of the Membrane Protein YfgM by the FtsH Protease Depends on a Novel N-terminal Degron

Cited by 30 publications

References 80 publications

In vivo trapping of FtsH substrates by label‐free quantitative proteomics

In vivo trapping of FtsH substrates by label‐free quantitative proteomics

Chloroplast Proteases: Updates on Proteolysis within and across Suborganellar Compartments

Mini review: ATP‐dependent proteases in bacteria

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