Genesis of mitochondria, plastids, peroxisomes Flashcards
Model systems
Major model systems studied are S. cerevisiae (bakers yeast), Neurospora crass (a fungus), Mammalia and more and more Viridiplanta. As mitochondria of these organisms differ in their protein content, the details of the models discussed in this section are perhaps only valid for taxa of the Opistokonta (“animals” and “fungi”).
Four main types of signals target proteins to Mitochondria
- simple cleavable N-terminal signals (here signal to matrix)
- complex signals (here cleavable matrix signal + cleavable targeting signal to inter membrane space)
- internal signals (here internal signal to inner membrane (carrier-protein type))
- C-terminal signals (here sigmal to outer membrane (tail-anchored membrane proteins))
Matrix-Targeting Sequence
- positive charged amphipatic helix
Different signals may direct to the same compartment - signals for sorting to the inner membrane
Proteins are coded in nucleus (nu) or mitochondria (mt)
a) Cleavable signal to matrix - nu
b) Complex signal - nu
c) Non-cleavable signal to matrix - nu
d) IMS-targeting signal - mt
e) Internal signals (carrier protein type) - nu / mt (Mt-coded possible without charged regions?)
Targeting and quality control I
MT-membrane anchors require special factors
Ubiquilins support the targeting of MT membrane proteins (in particular tail-anchored protein) and are essential for degradation of non-targeted proteins.
Import of beta-barrel proteins
- TOM
- Porin
- SAM
- Tom40
Function of SAM50 during import
1) Closed gate
2) Open lateral gate: beta-signal exchange -> beta-hairpin insertion
3) Release of folded beta-barrel protein
Import of proteins with alpha-helices
-> tail anchored
-> MIM dependent
- Mim1
-> SAM dependent
-TOM
- SAM
Import of small TIMs
1) Precursor recognition
2) Disulphide transfer
3) Release of oxidized precursor
4) Reoxidation of Mia40 by Erv1
tRNA import into mitochondria
- observed in many species; some, like yeast, import only one type, others, like plants, several and kinetoplastida (Leishmania, Trypanosoma) have to import all needed tRNAs (= 24)
- in many cases specific signals in the tRNA exist implicating a selective import
- import mechanisms are different between different organisms and evolved several times
Modification, Folding, Quality control and degradation
- Processing by MPP (soluble in the matrix) and MIPs (anchored in the inner membrane and exposed to the inter membrane space); MIPs are homologous to let B in bacteria
- second processing of several matrix proteins by Oct
- N-terminal processing of single large destabilizing AA by lcp55
- Most mitochondrial proteases are also involved run degradation of damaged proteins.
Modification, Folding, Quality and degradation - example
- Folding by systems homologue to bacterial ones (e.g. DnaK-like systems and mtHSP60 system)
- Degradation by systems homologue to bacterial ones (e.g. mtClpXP, mtLON or FisH-like membrane-bound proteases)
- HtrA-like protease and ATP23 in inter-membrane space
- Mts1p (AAA ATPase) at the cyt side of OM for relocation in cyt (e.g. TA-proteins)
Role of cytoplasm in degradation of mitochondrial proteins
a) MAD (mitochondria Associated Degradation)
- substrate are ubiquitinylated OM proteins
- components: CDC48-Npl4,Udf1 / Doa1 / proteasom
b) Identification of mistargeted tail-anchored proteins
- degradation by AAA Msp1
c) Identification of blocked protein import
mitoCPR (mitochondrial Compromised Protein import Response)
mitoRQC (release of stalled ribosomes engaged in mitochondrial protein import)
mitoTAD (mitochondrial Translocation Associated >Degradation)
mitoTAD
-> Accumulating precursors
-> Burden on proteasome system
-> Proteostatic imbalance
-> Burden on chaperone system
Mitochondrial Stress Response
a) UPRmt
b) mPOS (precursor over accumulation stress)
c) UPRam (unfolded protein response activated by mistargeted proteins)
UPRmt - signalling via TIM/TOM
Transport to the nucleus:
- OXPHOS recovery
- Mitochondrial proteostasis
- ROS detoxification
- Mitochondrial import
Can be inhibited by:
- OXPHOS defects
- ROS
- Mitonuclear protein imbalance
- Unfolded proteins
Could mitochondria evolve before protoeukaryote development?
- common idea is, that only eukaryotic organisms that a developed phagocytosis could give rise for endosymbionts
- however, new findings suggest, that also prokaryotes can harbor endosymbionts
Endosymbionts in prokaryotes
gamma-protepbacterium as endosymbiont in a beta-proteobacterium, which in turn is an endosymbiont in an insect cell
The different plastid types in viridiplantae
Proplastid:
- Etioplast
- Amyloplast
- Chloroplast -> Chromoplast
Targeting of nucleus-encoded proteins to plastids
- OM pathway
- ER-CP pathway
- Uncleaved TP pathway
- TOC-TIC pathways
Major targeting and sorting signals of plastid proteins
A) TARGETING TO THE OUTER MEMBRANE
usually no transit peptide (24 proteins in A.t.)
- tail-anchored proteins have the signal probably located in their flanking region
- some proteins with alpha-helical membrane anchor use TOC75
- beta-barrel TOC75 has a bipartid transit peptide (transit peptide followed by a glycine-rich sequence); is imported via TOC/TIC and processed by an inner-membrane lepB-like protease
- signals in other beta-barrel proteins unknown
B) IMPORT TO INTER MEMBRANE SPACE
very few proteins, transit-peptide like signal
- some use TOC/TIC and stroll processing peptidase
- some use only TOC
C) TARGETING TO INNER MEMBRANE
- with transit peptide via TOC/TIC using either a stroll intermediate (conservative sorting!) employing a cpSEC2 called systems or a stop-transfer mechanism without such intermediate
- without cleavable signal, nut using TOC159 system, pathway unknown
D) IMPORT INTO STROMA
- with cleavable transit peptide, across TOC/TIC system (90% of all nuclear coded proteins)
* transit peptides have very variable structure; (e.g. length from 25 to 150 amino acids)
* are usually processed in the storm by a specific peptidase
* are enriched basic AS, hydrophobic AS and Ser
* show no defined secondary structure in water but may adopt an amphipathic helix in lipid (especially in the presence of monogalactolipids)
- with uncleared signal, not using TOC159 system, pathway unknown (about 100 polypeptides)
- with signal sequence and unknown features via the ER using an unknown pathway (few N-glycosylated proteins)
E) IMPORT INTO THYLAKOIDS
- thylakoid targeting signal - signal (leader) peptide like hydrophobic sequence using different pathways (e.g. I)
- Tat-like signal
* nuclear coded proteins have a composite signal with a transit peptide in front of the thylakoid targeting signal/Tat-like signal
Main types of signals target proteins to plastids
- simple cleavable N-terminal signals (here transit peptide to stroma)
- Complex signals (here cleavable transit-peptide + cleavable targeting signal to thylakoid)
- Internal signals (no special example; any membrane anchor forms an internal signal)
- C-terminal signals (here signal to outer membrane (tail-anchored membrane proteins))
Targeting to chloroplasts
Transit peptide
-> phosphorylation sites (common); depending on substrate addition of phosphate leads to:
a) formation of guidance complexes consisting of 14-3-3 proteins, HSP70 a.o.
b) higher affinity to import receptors
binding of precursors to import receptors needs ATP and GTP
Import into the storma via TIC/TOC
- TOC159-GTP binds precursor; alteration of conformations during GTP/GDP-cycle as driving force for import across oE?
- TOC34-GTP binds precursor and 14-3-3
- ATP (< 100µM?) via imsHSP70?
- for some outer membrane proteins (e.g. TOC75) the second part of a bipartid transit peptide is cleaved by plastid signal peptidase 1 (Plsp1)
Import via TIC ATP-dependent (>3 mM), due to involvement of cpHSP70, HSP90C, and HSP93
- regulation of import capacity depending on the redox-potential (=photosynthetic activity) via Tic32/Tic55/Tic62/FNR or the Ca-level via calmodulin (CAL)
