N‐degron specificity of chloroplast ClpS1 in plants

Montandon, Cyrille; Dougan, David A.; Wijk, Klaas J. van

doi:10.1002/1873-3468.13378

Cited by 18 publications

(16 citation statements)

References 44 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To understand the substrate specificity of AtClpS1, 60,61 a high‐resolution structure of AtClpS in the presence of bound peptide was needed. Initially, we tried to determine AtClpS1 in complex with an N‐degron using the LC3B fusion technique by attaching the Leu residue at the N‐terminal region of AtClpS1 for easier crystallization 62 .…”

Section: Resultsmentioning

confidence: 99%

“…Furthermore, ClpS1 in Arabidopsis thaliana (AtClpS1) showed a distinct N‐degron specificity that is linked to the translational capacity of plants 59 . It has been reported that AtClpS1 prefers the bulky aromatic residues Phe and Trp at the N‐terminus and shows weak binding to Leu and very weak or no binding to Ile and Tyr N‐termini 60 . This is not easy to explain because of the high‐sequence homology between bacterial and plant ClpS 47,60 .…”

Section: Introductionmentioning

confidence: 99%

“…It has been reported that AtClpS1 prefers the bulky aromatic residues Phe and Trp at the N‐terminus and shows weak binding to Leu and very weak or no binding to Ile and Tyr N‐termini 60 . This is not easy to explain because of the high‐sequence homology between bacterial and plant ClpS 47,60 . Therefore, we determined the structure of AtClpS1 in complex with N‐degron and provided a framework for understanding the substrate specificity of the N‐degron pathway in higher eukaryote plant chloroplasts.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Structural basis for the N‐degron specificity of ClpS1 from Arabidopsis thaliana

et al. 2020

View full text Add to dashboard Cite

The N‐degron pathway determines the half‐life of proteins in both prokaryotes and eukaryotes by precisely recognizing the N‐terminal residue (N‐degron) of substrates. ClpS proteins from bacteria bind to substrates containing hydrophobic N‐degrons (Leu, Phe, Tyr, and Trp) and deliver them to the caseinolytic protease system ClpAP. This mechanism is preserved in organelles such as mitochondria and chloroplasts. Bacterial ClpS adaptors bind preferentially to Leu and Phe N‐degrons; however, ClpS1 from Arabidopsis thaliana (AtClpS1) shows a difference in that it binds strongly to Phe and Trp N‐degrons and only weakly to Leu. This difference in behavior cannot be explained without structural information due to the high sequence homology between bacterial and plant ClpS proteins. Here, we report the structure of AtClpS1 at 2.0 Å resolution in the presence of a bound N‐degron. The key determinants for α‐amino group recognition are conserved among all ClpS proteins, but the α3‐helix of eukaryotic AtClpS1 is significantly shortened, and consequently, a loop forming a pocket for the N‐degron is moved slightly outward to enlarge the pocket. In addition, amino acid replacement from Val to Ala causes a reduction in hydrophobic interactions with Leu N‐degron. A combination of the fine‐tuned hydrophobic residues in the pocket and the basic gatekeeper at the entrance of the pocket controls the N‐degron selectivity of the plant ClpS protein.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Structural basis for the N‐degron specificity of ClpS1 from Arabidopsis thaliana

et al. 2020

View full text Add to dashboard Cite

show abstract

“…This results in the accumulation of Ac-HspQ in the cell, which binds to ClpS and inhibits the turnover of N-degron substrates by ClpAP 70 . Remarkably, in Arabidopsis thaliana another YccV-like protein, termed ClpF is also believed to modulate the activity of ClpS 72 , a putative plastid-localised N-recognin, for delivery of N-degron bearing substrates to the AAA+ protease, ClpCP 73 , 74 . Hence, it appears that YccV-like proteins not only regulate proteolytic pathways and/or machines in bacteria and the plastids of plants but also in human mitochondria as revealed by our data.…”

Section: Discussionmentioning

confidence: 99%

Polymerase delta-interacting protein 38 (PDIP38) modulates the stability and activity of the mitochondrial AAA+ protease CLPXP

et al. 2020

Self Cite

View full text Add to dashboard Cite

Over a decade ago Polymerase δ interacting protein of 38 kDa (PDIP38) was proposed to play a role in DNA repair. Since this time, both the physiological function and subcellular location of PDIP38 has remained ambiguous and our present understanding of PDIP38 function has been hampered by a lack of detailed biochemical and structural studies. Here we show, that human PDIP38 is directed to the mitochondrion in a membrane potential dependent manner, where it resides in the matrix compartment, together with its partner protein CLPX. Our structural analysis revealed that PDIP38 is composed of two conserved domains separated by an α/β linker region. The N-terminal (YccV-like) domain of PDIP38 forms an SH3-like β-barrel, which interacts specifically with CLPX, via the adaptor docking loop within the N-terminal Zinc binding domain of CLPX. In contrast, the C-terminal (DUF525) domain forms an immunoglobin-like β-sandwich fold, which contains a highly conserved putative substrate binding pocket. Importantly, PDIP38 modulates the substrate specificity of CLPX and protects CLPX from LONM-mediated degradation, which stabilises the cellular levels of CLPX. Collectively, our findings shed new light on the mechanism and function of mitochondrial PDIP38, demonstrating that PDIP38 is a bona fide adaptor protein for the mitochondrial protease, CLPXP.

show abstract

“…Amino‐terminal proteomic analysis of the chloroplast stroma indicated that peptides with specific residues at the N‐terminus were underrepresented (Rowland et al ), and reporter proteins in transplastomic plants showed differential stabilities dependent on their Nt‐residues (Apel et al ), suggesting that N‐degron pathway(s) operate in the chloroplast. Recently ClpS1 specificity was investigated in vitro and recognition assays for GFP‐fusion proteins bearing defined Nt‐residues indicated a low specificity for bacterial N‐degrons, but high specificity recognition for Nt‐Phe or Nt‐Trp (Colombo et al ; Montandon et al ). These studies suggest a chloroplast N‐degron pathway with high specificity, though no substrates or transferase activities have yet been identified.…”

Section: Enzymatic Components Of Plant N‐degron Pathwaysmentioning

confidence: 99%

The plant N‐degron pathways of ubiquitin‐mediated proteolysis

Holdsworth

Vicente

Sharma

et al. 2019

JIPB

View full text Add to dashboard Cite

The amino-terminal residue of a protein (or amino-terminus of a peptide following protease cleavage) can be an important determinant of its stability, through the Ubiquitin Proteasome System associated N-degron pathways. Plants contain a unique combination of N-degron pathways (previously called the N-end rule pathways) E3 ligases, PROTEOLYSIS (PRT)6 and PRT1, recognizing non-overlapping sets of amino-terminal residues, and others remain to be identified. Although only very few substrates of PRT1 or PRT6 have been identified, substrates of the oxygen and nitric oxide sensing branch of the PRT6 N-degron pathway include key nuclear-located transcription factors (ETHYLENE RESPONSE FACTOR VIIs and LITTLE ZIPPER 2) and the histone-modifying Polycomb Repressive Complex 2 component VERNALIZATION 2. In response to reduced oxygen or nitric oxide levels (and other mechanisms that reduce pathway activity) these stabilized substrates regulate diverse aspects of growth and development, including response to flooding, salinity, vernalization (cold-induced flowering) and shoot apical meristem function. The N-degron pathways show great promise for use in the improvement of crop performance and for biotechnological applications. Upstream proteases, components of the different pathways and associated substrates still remain to be identified and characterized to fully appreciate how regulation of protein stability through the amino-terminal residue impacts plant biology.

show abstract

N‐degron specificity of chloroplast ClpS1 in plants

Cited by 18 publications

References 44 publications

Structural basis for the N‐degron specificity of ClpS1 from Arabidopsis thaliana

Structural basis for the N‐degron specificity of ClpS1 from Arabidopsis thaliana

Polymerase delta-interacting protein 38 (PDIP38) modulates the stability and activity of the mitochondrial AAA+ protease CLPXP

The plant N‐degron pathways of ubiquitin‐mediated proteolysis

Contact Info

Product

Resources

About