Functional and structural studies
of the Presequence protease, PreP
Licentiate thesis
Hans G Bäckman
Supervisor: Elzbieta Glaser
Department of Biochemistry and Biophysics
Stockholm University
2014
2
Contents
Abstract ................................................................................................................................. 5
Publications ........................................................................................................................... 6
The thesis is based on the following publications............................................................................... 6
Abbreviations ........................................................................................................................ 7
Mitochondria and chloroplasts ............................................................................................... 8
The mitochondrial genome ................................................................................................................. 9
Function and structure of mitochondria ............................................................................................. 9
The chloroplast genome .................................................................................................................... 10
Function and structure of chloroplasts ............................................................................................. 10
Protein targeting and import into the mitochondrial matrix ............................................................ 11
Mitochondrial processing peptidases ............................................................................................... 13
Protein targeting and import into chloroplast stroma ...................................................................... 14
Stromal processing peptidase ........................................................................................................... 16
Dual-targeting to mitochondria and chloroplasts ............................................................................. 16
Proteolysis in mitochondria and chloroplasts ........................................................................17
The ATP dependent proteases .......................................................................................................... 17
Clp proteases ................................................................................................................................. 17
FtsH proteases ............................................................................................................................... 17
Lon proteases ................................................................................................................................ 18
The ATP independent proteases ....................................................................................................... 19
Rhomboid proteases ..................................................................................................................... 19
Deg proteases ................................................................................................................................ 19
OOP................................................................................................................................................ 20
PreP ............................................................................................................................................... 20
Material & Methods ..............................................................................................................21
Paper I................................................................................................................................................ 21
Generation of mutant Arabidopsis plants, single and double knockouts ..................................... 21
Growth conditions of A. thaliana plants ....................................................................................... 21
Purification of mitochondria and chloroplasts .............................................................................. 21
Degradation assays........................................................................................................................ 22
Respiratory measurements ........................................................................................................... 22
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Protein gel and immunoblot analysis of thylakoid membranes ................................................... 22
Protein extractions and analysis of AtPreP1 and AtPreP2 content ............................................... 22
Biomass.......................................................................................................................................... 23
Paper II............................................................................................................................................... 23
Generation of AtPreP1 variants .................................................................................................... 23
Expression and purification of AtPreP1 and its variants ............................................................... 23
Degradation assays........................................................................................................................ 24
Paper III.............................................................................................................................................. 24
Generation of hPreP-SNP variants ................................................................................................ 24
Degradation assays........................................................................................................................ 24
Summary of results ..............................................................................................................25
The Presequence protease, PreP ...................................................................................................... 25
Paper I - Deletion of an organellar peptidasome PreP affects early development in Arabidopsis
thaliana ............................................................................................................................................. 26
Paper II - Binding of divalent cations is essential for the activity of the organellar peptidasome in
Arabidopsis thaliana, AtPreP ............................................................................................................. 28
Paper III - Biochemical studies of SNPs of the mitochondrial Aβ-degrading protease, hPreP .......... 29
Future perspectives ..............................................................................................................31
Structure and catalytic function of AtPreP1...................................................................................... 31
Acknowledgements ..............................................................................................................32
References ...........................................................................................................................33
4
Abstract
AtPreP (Arabidopsis thaliana Presequence Protease) is a zink metallooligopeptidase that is dually
targeted to both mitochondria and chloroplasts. In these organelles it functions as a peptidasome that
degrades the N-terminal targeting peptides that are cleaved off from the mature protein after protein
import, as well as other unstructured peptides. In A. thaliana there are two isoforms of PreP, AtPreP1
and AtPreP2.
We have performed characterization studies of single and double prep knockout plants. Immunoblot
analysis revealed that both PreP isoforms are expressed in all tissues with highest expression levels in
flowers and siliques. Furthermore, AtPreP1 was shown to be the most abundant isoform of the two.
When comparing phenotype, the atprep2 mutant was similar to wild type, whereas the atprep1 mutant
had a slight pale-green phenotype in the early developmental stages. The atprep1 atprep2 double
knockout plants showed a chlorotic phenotype in true leaves, especially prominent during the early
developmental stages. When analysing the first true leaves of double knockout plants, we found a
significant decrease in chlorophyll a and b content. Mitochondrial respiratory rates measurements
showed partially uncoupled mitochondria. Ultrastructure analysis using electron microscopy on double
knockout plants showed aberrant chloroplasts with altered grana stacking and clearly fewer starch
granules. Older plants showed less altered phenotype, although there was a significant decrease in the
accumulated biomass of about 40% compared to wild type. Peptidolytic activity studies showed no
sign of compensatory mechanisms in the absence of AtPreP in mitochondria; in contrast we found a
peptidolytic activity in the chloroplast membranes not related to AtPreP.
In addition to zinc located in the catalytic site, crystallographic data revealed two Mg-binding sites in
the AtPreP structure. To further investigate the role of these Mg-binding sites, we have made AtPreP
variants that are unable to bind metal ions. Our data shows that one of these sites located close to the
catalytic site is important for the activity of AtPreP.
We also measured proteolytic activity of four human PreP-SNP variants and observed that the activity
of all the hPreP-SNPs variants was lower; especially the hPreP-SNP (A525D) variant that displayed
only 20-30 % of wild type activity. Interestingly, the activity was fully restored for all SNP-variants by
addition of Mg2+.
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Publications
The thesis is based on the following publications
I
Nilsson S*, Bäckman HG*, Pesaresi P, Leister D, Glaser E. Deletion of an organellar
peptidasome PreP affects early development in Arabidopsis thaliana. Plant Molecular
Biology (2009) 71:497-508.
II
Bäckman HG, Pessoa J, Eneqvist T, Glaser E. Binding of divalent cations is essential
for the activity of the organellar peptidasome in Arabidopsis thaliana, AtPreP. FEBS
Letters (2009) 583:2727-2733.
III
Moreira Pinho C*, Björk Behnosh F*, Alikhani N, Bäckman HG, Eneqvist T,
Fratiglioni L, Glaser E, Graff C. Genetic and biochemical studies of SNPs of the
mitochondrial Aβ-degrading protease, hPreP. Neuroscience Letters (2010) 469:204208.
* These authors contributed equally
6
Abbreviations
IE
Inner envelope membrane of chloroplast
IES
Interenvelope space
IM
Inner membrane
IMS
Intermembrane space
MA
Mitochondrial matrix
OE
Outer envelope membrane of chloroplast
OM
Outer membrane
PAM
Presequence translocase Associated Motor
PreP
Presequence protease
PSI
Photosystem 1
PSII
Photosystem 2
TIC
Translocase of the inner chloroplast envelope
TIM
Translocase of the inner mitochondrial membrane
TM
Transmembrane
TOC
Translocase of the outer chloroplast envelope
TOM
Translocase of the outer mitochondrial membrane
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Mitochondria and chloroplasts
The mitochondrion is the power generating organelle that resides in the eukaryotic cell. It is generating
adenosine triphosphate (ATP), which in turn can be used by the cell to do chemical work.
Mitochondria are also involved in other tasks such as signaling, cellular differentiation, cell death, cell
cycle control and cell growth [1]. The word mitochondrion is of Greek origin, where “mitos” stands
for a thread and “chondrion” stands for a grain. In the year 1949 mitochondria were identified as the
site of oxidative energy metabolism by Kennedy and Lehninger [2].
Chloroplasts are members of the plant organell class called plastids that all originate from
protoplastids. The protoplastids differentiate during the plant development to form three major groups
of plastids, the green chloroplasts, the coloured chromoplasts and the colourless leucoplasts. The
plastids that are most abundant and most important are the chloroplasts. The word chloroplast is of
Greek origin, where “chloro” stands for green and “plast” stands for form or entity. Chloroplasts
harvest the energy of the sun to do work in form of splitting water and fixing carbon dioxide to
produce sugars.
Origin and evolution
In 1970 Lynn Margulis proposed the endosymbiotic theory [3]. This theory was at first controversial,
but today it is the most accepted theory about the origin of the intralcellular compartments that we
now call mitochondria and chloroplasts. According to the endosymbiotic theory mitochondria arose
from aerobic prokaryotes that were engulfed by and began to live in symbiosis with a primitive,
anaerobic eukaryotic cell. The genomic data point towards α-proteobacteria as being the first cell to be
engulfed. There are several important factors that support this theory. First of all, mitochondria are not
synthesized by the cell, instead they originate from pre-existing organelles and are proliferated by a
fission process. Secondly, mitochondria have its own genome and a transcription and translation
system that is remnant to what is found in bacteria. Thirdly, there is a strong group correlation
between proteins found in mitochondria and those found in α-proteobacteria [4]. Finally, the inner
membrane (IM) of mitochondria contains a certain lipid, such as cardiolipin, that only can be found in
the bacterial plasma membrane and in the IM of mitochondria. The closest now living ancestor to
mitochondria is Rickettsia prowazekii, which is an obligate intracellular parasite [5, 6].
Just like mitochondria, the evolution of the chloroplast is also the result of a single endosymbiotic
event. More than one billion years ago a single eukaryotic cell containing mitochondria, engulfed and
established an endosymbiotic relationship with a cyanobacterium. Around 450 million years ago these
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cells colonized the planet outside the oceans, and by that time the engulfed cyanobacteria already had
turned into what we know as chloroplasts [7].
The mitochondrial genome
Mitochondria harbor their own genome in form of a circular DNA. Mitochondrial genomes (mtDNA)
have changed over time since the ancient endosymbiotic event. During evolution of mitochondria
some genes have been lost or transfered from mitochondria to the cell nucleus resulting in a very small
mtDNA. At the same time the organelle has retained much of its prokaryotic biochemistry, mtDNA
now only encodes a small fraction ranging from 3 to 67 of the organelle’s proteins [8]. A free living αproteobacteria such as Caulobacter contains over 3600 protein encoding genes. There are at least two
distinct modes of how genetic loss has reduced the coding capacities of mitochondrial genomes, going
from approximately 1600 proteins in the free-living ancestor to 67 or less in modern mitochondria.
First, mitochondria have lost nonessential coding sequences, and rather than synthesize compounds
such as amino acids, nucleosides and pyruvate, mitochondria now relay on import of these
compounds. Secondly, mitochondria have lost essential genes due to extensive gene transfer to the
nuclear genome, and therefore relay on import of these proteins. This transfer event has led to that
nearly all of the genes required for the normal function and also propagation of mitochondria normally
reside in the host nucleus [9, 10]. When comparing over 100 different animal mitochondrial genomes,
the majority contains the same 13 genes encoding proteins of the respiratory chain and ATPsynthase,
namely the cytochrome c oxidase subunit I, II and III, the ATP synthase subunits 6 and 8, the
cytochrome b apoenzyme and the NADH dehydrogenase subunits 1-6 and 4L [11, 12].
Function and structure of mitochondria
Mitochondria can be found in almost all eukaryotic cells and are typically 0.5-1.5 µm wide and 1-2
µm long. They can vary in size, shape and number, especially when compared between different
species. Mitochondria are organelles surrounded by two membranes, the outer mitochondrial
membrane (OM) and the inner mitochondrial membrane (IM). The two membranes divide the
organelle into two distinct compartments, the intermembrane space (IMS) and the mitochondrial
matrix (MA). The composition of the OM is relatively simple, consisting of a phospholipid bilayer and
proteins. The most abundant protein in the OM is porin, which makes the OM permeable to molecules
of about 8 kDa or less. The inner membrane is more complex and contains the enzymes of the
respiratory chain and oxidative phosphorylation as well as other proteins. The inner membrane is also
highly convoluted that increases the surface area, forming folds called cristae. Cristae are connected to
the IM by narrow tubular segments, called cristae junctions.
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Mitochondria play an important role in metabolism, apoptosis, disease and aging. Mitochondria are
also the site of oxidative phosphorylation, which is essential for the production of ATP. The energy
required for the ATP production predominantly comes from the oxidation of reduced compounds such
as NADH and FADH2, which are generated in the citric acid cycle and during β-oxidation of fatty
acids. The oxidation of NADH and FADH2 releases electrons that are funneled to oxygen through a
chain of electron carriers in the respiratory chain. This electron transfer releases energy that is used to
transfer protons across the IM from the matrix to the IMS side. This proton translocation is generates
an electrochemical proton motive force (PMF). The PMF consists of a membrane potential (∆ѱ) and a
trans-membrane proton gradient (∆pH) [13]. The potential energy trapped in the PMF can then be used
to synthesize ATP from ADP and Pi by the ATP synthase located in the IM of mitochondria. ATP is
then exported from the mitochondria out to different parts of the cell where it provides the energy
required for a vast type of reactions.
The chloroplast genome
Chloroplasts harbor their own genome in form of the circular DNA and just like the mitochondrial
genome, the chloroplast genome is also of procaryotic origin. During the evolution of the plastids,
many genes have been transferred to the cell nucleus. Compared to cyanobacterial genomes, which
contain between 3168 (Synechocystis sp.) and 7400 (Notoc punctiforme) protein encoding genes, the
chloroplast genome has been substantially reduced in size and vary between 58 (Euglena gracilis) and
200 protein coding genes (Porphyra purpurea). In chloroplasts of green plants there are about 100
protein encoding genes [14, 15].
Function and structure of chloroplasts
The chloroplasts are disc shaped organelles that belong to a broader group of plastids. Chloroplasts are
usually between 5-10 µm in diameter and about 1 µm thick, and are surrounded by two membranes,
the outer envelope (OE) membrane and the inner envelope (IE) membrane. The OE membrane is
permeable to small molecules up to about 10 kDa in size, but it is impermeable to bigger molecules
such as proteins. The inner envelope membrane works as a permeability barrier, and molecules must
be transported across the membrane via specific translocators. The compartment between these two
envelopes is called the interenvelope space (IES). Enclosed by the inner envelope membrane is the
chloroplast stroma. The stroma contains a third membrane system, called the thylakoids. The
thylakoids consist of a network of small disks that is forming stacks or grana. The grana stacks are in
turn connected by a non-stacked membrane system called stroma lamellae. The thylakoid membrane is
one continuous membrane system enclosing the thylakoid lumen [7].
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Chloroplasts have a very important function within plant cells, they constitute the location for
photosynthesis and the fixation of CO2 along with other essential processes such as starch metabolism,
biosynthesis of lipids and secondary metabolites. The main components of the thylakoids are the two
photosystems (PSI and PSII), the cytochrome b6f complex and the ATP synthase. In the photosystems
the light is harvested and the energy is used for creating a charge separation within PSII. This then
leads to the oxidation of water to oxygen in the thylakoid lumen, and four electrons and two protons
are released in this process. The electrons are then transported via the Q cycle and b6f complex and
further to the PSI and causing more protons to be transferred into the lumen. The final electron
acceptor is NADP+ that is reduced to NADPH. The protons that are transferred to the thylakoid lumen
generate a proton gradient that is used to generate ATP by the ATP synthase. The energy stored in
form of ATP can then be used in the fixation of CO2, an important step in the plant metabolism [16].
Protein targeting and import into the mitochondrial matrix
Since the vast majority of the protein coding genes has been transferred to the cell nucleus,
mitochondria have to rely on protein import for its normal function. The genes are transcribed in the
cell nucleus and translated to precursor proteins on cytosolic ribosomes and then posttranslationally
transferred to its final destination in mitochondria. From the cytosol the precursor proteins are
translocated through the outer mitochondrial membrane via the TOM (Translocase of the outer
mitochondrial membrane) complex and then through the inner membrane via the TIM (Translocase of
the inner mitochondrial membrane) complex. Finally, in the mitochondrial matrix the protein is further
processed to reach a final and functional conformation (for recent review see [17]).
Protein targeting to mitochondria relies on two main types of targeting signals. The first and most
common way of targeting mitochondrial proteins is by the use of cleavable amino-terminal extensions
in the mitochondrial precursor proteins, called presequences. About 70% of mitochondrial proteins are
recognized via an N-terminal presequence [18]. Presequences vary in length and range in size between
18 to 136 amino acid residues in plants with an average length of 42 residues; most presequences are
in the range of 20-60 amino acid residues long [19]. The presequences share little sequence similarity
except that they are generally enriched in positively charged, hydroxylated and hydrophobic amino
acid residues, while acidic residues are almost absent [19, 20]. Further, it has been shown that
presequences have the ability to form amphiphilic α-helices in a membrane mimetic environment [2125]. The presequence is cleaved off by the mitochondrial processing peptidase (MPP) [26]. The
second type of signals consists of an internal targeting sequence located internally in the mature
protein. This signal is not cleaved off after import into mitochondria. In the cytosol, precursor proteins
are protected by molecular chaperones, which maintain precursor proteins in an unfolded import
competent conformation [27].
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With the aid of chaperones and other cytosolic factors, precursor proteins are recognized by receptors
on the mitochondrial surface. There are three main receptors for recognition of precursor proteins on
the outer membrane of mitochondria, Tom20, Tom22 (in plants Tom9) and Tom70 (absent in plants).
Tom70 binds proteins with internal non-cleavable targeting signals [28, 29]. The main receptor for Nterminal presequences is Tom20, which binds presequences via hydrophobic interactions in a
hydrophobic grove. Studies have shown that A. thaliana Tom20 is a non-essential protein [30]. Tom20
redirects the bound precursor protein to Tom40 to begin the translocation [27, 31].
Tom40 is a β-barrel protein and acts as the translocation pore for almost all mitochondrial proteins.
Tom40 was the first mitochondrial membrane protein that was shown to be essential for yeast viability
[32]. Tom40 has also been shown to be essential in Arabidopsis [33]. The precursor protein is then
assisted by chaperones (Tim8-10 and 13) in the IMS, where it interacts with translocase of the
mitochondrial IM [17].
Many proteins that are destined for IMS have a cysteine motif (or MISS signal) as a targeting signal
that forms an intramolecular disulfide bond, which in turn traps the protein in the IMS. Mia40 and
Erv1 form a disulfide bond relay system where Mia40 oxidizes substrates and Erv1 is reoxidizing
Mia40 [17, 27, 34-36].
In the mitochondrial IM there are at least three complexes that are responsible for the translocation
across the IM to the MA and insertion of proteins into the IM. The two major complexes are the
TIM23 and TIM22 complexes. The TIM23 complex is responsible for the translocation of all
precursors of matrix proteins and most of the IM proteins and many IMS proteins. The TIM22
complex is responsible for the translocation and IM insertion of carrier type membrane proteins
containing internal targeting signals [37]. The third complex is OXA1 that is a component involved in
the insertion of MA imported or mitochondria encoded proteins into the IM [38]. Compared to the
outer membrane import components, the Arabidopsis inner membrane components are more similar to
the ones found in yeast [39, 40].
The initial translocation through the TIM23 complex is dependent on an electrical membrane potential
(∆ѱ). The TIM23 complex consists of two structurally and functionally distinct forms [34]. The initial
form, termed TIM23-SORT, contains the channel forming proteins Tim23 and Tim17, together with
its associated proteins Tim50 and Tim21. All these components of the TIM23-SORT complex are
fundamental for the translocation of precursor proteins from the Tom40 to the matrix or for insertion
into the inner membrane [41]. In yeast the second form of the TIM23 complex is called the TIM23PAM complex. This complex also contains Tim17, Tim23 and Tim50 along with the Presequence
translocase Associated Motor (PAM) complex, comprising mtHSP70 (mitochondrial heat shock
protein 70), Tim44 and its associated co-chaperones; Pam16, Pam17 and Pam18 [42, 43]. The TIM23PAM complex drives the translocation through the inner membrane via ATPase activity and cyclic
12
binding of the presequence to promote transfer of the precursor protein towards the matrix [41].
Pam16, 17 and 18 are molecular chaperones that are thought to modulate mtHSP70 (mitochondrial
heat shock protein, 70 kDa) activity and association with the TIM23 channel [44, 45]. With the
exception of Pam17, which is absent in plants, there is a high level of similarity between the yeast
inner membrane proteins and the ones found in A. thaliana; therefore it is likely that these pathways
are also functionally conserved in plants.
Mitochondrial processing peptidases
When the mitochondrial precursor proteins have been transported across the inner membrane into the
matrix, there are processing steps that are necessary before the imported protein is fully functional.
There are several proteins involved in these processing steps, the mitochondrial processing peptidase
(MPP), the inner membrane peptidase (IMP), the Octapeptidyl aminopeptidase 1 (Oct1), and the
intermediate cleaving peptidase 55 (Icp55) [46, 47].
MPP is a ~ 100 kDa heterodimeric metalloendopeptidase encoded by two genes, α-MPP and β-MPP,
where both subunits are essential and highly conserved [46]. MPP cleaves off the N-terminal
presequence from the translocated precursor protein. The cleavage sites typically contain an arginine
at position -2 from the scissile peptide bond and an aromatic residue at position +1 [48]. The α-MPP is
responsible for the peptide binding and the β-MPP contains the active site for proteolysis. MPP
belongs to the M16C family in the MEROPS protease database [49]. The β-MPP contains an essential
inverted zinc binding motif (HXXEH), thereby placing it among the metalloproteases [50]. Although
there is similarity (31 and 41% for the α- and β-MPP, respectively) between the Arabidopsis and the
yeast counterparts, there are significant differences in these organisms. In Saccharomyces cerevisiae
the MPP resides in the MA as a soluble protease [51], whereas in plants it is a part of the cytochrome
bc1 complex of the electron transport chain in the IM. This means that the plant MPP is bi-functional,
and is involved in both processing and electron transfer [52-55]. In 2001 the 3D structure of MPP was
solved, both for the active form and an inactive variant. The structures revealed a large central cavity
containing the active site situated between the α- and β-MPP. This cavity is lined with hydrophilic
amino acids, including many glutamate and aspartate residues, from both subunits. This negative
charge could facilitate the recognition and binding of the basic presequences of precursor proteins
[48].
IMP is a serine endopeptidase that catalyzes the maturation of mitochondrial precursor proteins
delivered to the intermembrane space. In S. cerevisiae, the enzyme exists as a heterodimeric complex
composed of two different subunits: Imp1 and Imp2, and the auxiliary protein Som1. Imp1 and Imp2
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are both bound to the outer face of the IM through an N-terminal membrane spanning domain and
have a C-terminal catalytic site facing the IMS [47, 56].
Oct1 is a soluble monomeric metalloprotease in the mitochondrial matrix. The protease has a putative
zink-binding motif H-E-X-X-H that is required for the catalytic activity, and two highly conserved
cysteine residues are important for the stability of the protein. Oct1 only recognizes and cleaves
proteins that have already been processed by MPP. The protease was formerly known as MIP
(mitochondrial intermediate peptidase), and it removes an additional octapeptide from the precursor
after MPP cleavage. The octapeptide is required for an efficient first processing by MPP, and it is
believed that the function of the octapeptide might be to provide a more compatible MPP cleavage site
by separating the first processing site from a positive structure in the mature part of the protein. Finally
it is also believed that the removal of the octapeptide is contributing to a more stable mature protein
[47, 57, 58].
Icp55 is a novel metalloprotease belonging to the aminopeptidase P family and is found in the
mitochondrial matrix. In contrast to other aminopeptidase P proteases it does not require a proline
residue at the cleavage site, which gives the protease a different specificity compared to other
proteases in this family. Instead the cleavage site motif for Icp55 is: R-X-(F/L/Y) | (S/A). Icp55
cleaves off a single phenylalanine, tyrosine or leucine residues appearing at the N-terminus of
precursor import intermediates after initial processing by MPP. These three amino acids are classified
as destabilizing amino acids according to the N-end rule [18, 47, 59].
Protein targeting and import into chloroplast stroma
As mitochondria, chloroplasts are dependent on protein import from the cytosol. The precursor
proteins are translocated through the outer chloroplast envelope via the TOC (Translocase of the outer
chloroplast envelope) complex and then through the inner envelope via the TIC (Translocase of the
inner chloroplast envelope) complex. In the chloroplast stroma the protein is further processed to reach
its final and functional conformation.
The precursor protein carries an amino-terminal extension called a transit peptide. Transit peptides are
remarkably diverse in both length and sequence, as they vary from 20 to >100 residues, and possess no
extended blocks of sequence conservation. They seem to have some conserved properties in form of
abundance of hydroxylated residues (serine in particular), and they are deficient in acidic residues
giving them a net positive charge; so in this regard transit peptides are very similar to mitochondrial
presequences [60].
14
Hsp70 is one of the cytosolic factors that is believed to play a role in the cytosol until the precursor
protein reaches the import machinery of the chloroplast outer surface. Most of the chloroplast transit
peptides have indeed an Hsp70 binding site and direct contact between Hsp70 and transit peptides has
been reported, but it is still unclear how important this interaction is for the import of a specific
precursor protein [61].
Other cytosolic factors are found in the 14-3-3 protein family that includes regulatory molecules and
chaperones that bind specifically to phosphorylated proteins and thereby mediate various signal
transduction processes and also protein translocation. Many chloroplast transit peptides contain a 143-3-binding phosphopeptide motif, and it has been shown that 14-3-3 proteins can form a type of
“guidance complex” together with Hsp70 and the precursor protein, directing precursors to the surface
of chloroplasts [60, 62].
The TOC complex is responsible for the precursor protein recognition at the chloroplast surface and
for outer envelope translocation. The TOC core complex is composed of three different proteins,
Toc159, Toc34 and Toc75, according to their predicted molecular masses. These three proteins
constitute a complex that is between 500 and 1000 kDa in size, as there are reports of different
possible stoichiometric configurations.
The Toc159 and Toc34 proteins can be regarded as receptors as they control precursor protein
recognition. They are both GTPases and are anchored to the membrane via the C-terminal domain.
The third component of the core complex, Toc75 is embedded within the outer membrane, is similar to
the functionally equivalent Tom40 protein of mitochondria and has a β-barrel structure [63, 64]. Toc75
has a topology of 16-18 transmembrane (TM) strands that together form an aqueous pore with a
minimal diameter of approximately 14 Å. This is very similar in size to the Tom40 channel, as well as
other protein translocation pores, and it is sufficient to accept only largely unfolded substrates [65].
After the GTP dependent translocation through the Toc75, the precursor protein is translocated
through the TIC complex in the inner envelope to finally reach the chloroplast stroma. The
configuration and function of the TIC complex is still under debate, but several actual or putative
components have been identified – Tic110, Tic62, Tic55, Tic40, Tic32, Tic22 and Tic20. It is believed
that Toc12, Hsp70 and Tic22 act to facilitate the passage of precursor proteins across the interenvelope
space. Tic110 has been proposed to be a channel forming protein consisting of six transmembrane
domains and a scaffold with two N-terminal transmembrane domains followed by a large soluble
domain for binding of transit peptides and other stromal translocon components [66]. The
translocation through the Tim110 channel occurs in an ATP-dependent manner, where a C-terminal
domain of Tic40 stimulates the ATPase activity of Hsp93, which in turn facilitates the import of the
precursor protein to the chloroplast stroma [60].
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Stromal processing peptidase
When the precursor protein has been translocated into the chloroplast stroma it is processed by the
stromal processing protease (SPP). Studies in A. thaliana using T-DNA insertion lines have shown
that SPP is an essential protease [67].
SPP is a soluble metalloendopeptidase in the chloroplast stroma. It contains an inverted Zn-binding
motif, HXXEH, and belongs to the (MEROPS) metallopeptidase family M16B. It recognizes and
binds to transit peptides of precursor proteins and cleaves off the transit peptide in one endoproteolytic
step, which leads to the formation of a functional mature protein. After cleavage, the transit peptide is
still bound to SPP and can then be trimmed [68]. The free transit peptide may then be degraded by the
Presequence Protease, PreP.
Dual-targeting to mitochondria and chloroplasts
Despite that the import mechanisms of mitochondria and chloroplast have been developed
independently there are proteins that are imported to each organelle using the same targeting sequence,
these proteins are called dual-targeted proteins. More than 100 proteins have been reported to be dualtargeted, usually determined by experimental procedures using fluorescent markers such as GFP,
followed by specific import assays to each organelle to establish that a single protein is a substrate for
both import machineries. It appears that the majority of the dual-targeted proteins are using an
identical targeting peptide, which in turn is recognized by receptors on both organelles [69]. These
targeting peptides are called ‘ambiguous’, as they carry a dual function [70]. Most of the dual-targeted
proteins are soluble matrix/stromal proteins involved in processes such as DNA replication,
transcription and translation, protein processing and other metabolic processes. Only a few are
membrane-bound, and most of them are bound to the outer membrane [71].
16
Proteolysis in mitochondria and chloroplasts
The ATP dependent proteases
The ATP dependent proteases are a group of proteases that are dependent on ATP to complete their
function in the cell. ATP is not needed for the catalytic function of the protesase, instead it is used to
unfold larger proteins to make them accessible for degradation by the protease. Proteases usually have
the catalytic site hidden in a cavity to prevent unspecific proteolysis. The major ATP dependent
proteases in mitochondria and chloroplasts are ClpP, FtsH and Lon [72].
Clp proteases
The Clp endopeptidases are ATP dependent serine proteases belonging to the S14 Merops family of
proteases, which are involved in the degradation of misfolded proteins. There are 26 genes encoding
Clp proteases in A. thaliana. Clp proteases are multi-subunit enzymes, and the ATPase domain and the
catalytic domain are residing in different subunits. In structural terms they are very similar to the
proteasome 26S in eukaryotes. Most of the knowledge about Clp proteases comes from investigations
in E. coli. In E. coli the protease is composed by two ClpP subunits, which form a barrel structure with
narrow (~10 Å) axial openings, with the catalytic sites facing the inner chamber. In addition to this
proteolytic chamber there are ATP dependent chaperones, ClpA or ClpX (members of the HSP100
family of chaperones in E. coli) forming dynamic hexameric rings that interact with the core complex
at the entrances, functioning as unfoldases and recognition elements [73, 74]. Plants have a high
number of Clp proteins and in A. thaliana plastids there are at least 15 different Clp proteases. There
are five serine-type ClpP (ClpP1, ClpP3–ClpP6) proteases; four ClpP-related ClpR (ClpR1–ClpR4)
proteins; three Clp AAA+ chaperones (ClpC1, ClpC2 and ClpD), which are similar to ClpA from E.
coli and three members (ClpS1, ClpS2, ClpT) with unknown functions. The ClpR proteins are
homologous to the ClpP proteins, but are inactive as they lack the three conserved (Ser and His)
catalytic amino-acid residues. The ClpS1 and ClpS2 are only found in land plants and have sequence
homology to the amino-terminus of ClpC [75, 76].
FtsH proteases
FtsH proteases are membrane bound ATP dependent metalloproteases that harbour an AAA (or triple
A) domain (ATPases associated with various cellular activities) [77]. The term FtsH comes from the
E. coli enzyme (Filamentous temperature sensitive H) [78]. FtsH proteases are found in eubacteria as
well as in mitochondria and chloroplasts. The main function of organellar FtsH proteases is selective
degradation of non-assembled, incompletely assembled and damaged membrane-anchored proteins. It
is believed that the thylakoid FtsH protease has a function in the degradation of the high turnover D1
17
protein of the PSII reaction center [79]. The FtsH protease is also involved in processing of precursor
proteins and degradation of regulatory proteins. Substrate proteins are unfolded and translocated
through the central pore of the ATPase domain into the proteolytic chamber, where the polypeptide
chains are cleaved into short peptides.
In mitochondria there are two types of AAA protease complexes, which differ in their topology in the
inner membrane; there are i-AAA proteases that are active in the intermembrane space and m-AAA
proteases with catalytic sites exposed to the mitochondrial matrix. These proteases have homologous
subunits that are assembled into homo- or hetero-oligomeric complexes, forming a hexameric ring.
FtsH protease subunits have two trans-membrane domains in the N-terminal portion, followed by an
ATPase domain, and a zinc-binding motif, which serves as the catalytic site of the protease. Most
eubacteria have only one gene encoding FtsH, whereas three genes have been found in yeast and
humans, while 17 orthologs have been identified in A. thaliana [72, 80]. 5 of these 17 genes are coding
for inactive isoforms (FtsHi 1-5) targeted to chloroplasts, and are all lacking the zinc-binding motif
(HEXXH) [81]. Out of the 12 active isoforms three (AtFtsH3, 4 and 10) are located in mitochondria
and 8 (AtFtsH1, 2, 5-10, 12) in chloroplasts. FtsH11 is dually targeted to both mitochondria and
chloroplasts [82].
Lon proteases
Lon proteases are members of the S16 family in the MEROPS protease database. They are serine
proteases that are responsible for the degradation of abnormal, damaged and unstable proteins. Lon
proteases have no membrane-spanning domain and contain the AAA and protease domains in one
polypeptide. In contrast to the Ser-His-Asp triad at the catalytic site, Lon proteases consist of a SerLys dyad [83, 84]. A crystal structure of Lon in E. coli has been determined and shows that Lon forms
a hexameric ring [85]. Lon proteases have been reported as mitochondrial proteases, while some
studies have also predicted their presence in chloroplasts and peroxisomes [86, 87]. In E. coli Lon is
divided into two subfamilies, LonA and LonB. Both contain an ATPase domain as the proteolytic
domain, but differ in that the LonA enzymes contain a large N-terminal domain, whereas LonB lacks
this domain. Instead LonB harbours an N-terminal transmembrane domain. In A. thaliana there are 11
genes encoding Lon family proteases, named AtLon1-11, however there are data suggesting that only
four Lon proteases are functional in organellar proteolysis in A. thaliana (AtLon1-4) [72, 88].
18
The ATP independent proteases
Rhomboid proteases
The name ‘rhomboid’ comes from a discovery made in the field of Drosophila genetics. When
analysing the phenotype of a mutant larval cuticle, a misshapen rhombus-like head skeleton of the
mutant embryo was discovered, which gave rise to the name rhomboid protease [89]. The rhomboid
gene was identified in Drosophila screens of the late 1970s and early 1980s [90], and it was cloned
and sequenced by Bier and colleagues in 1990. They discovered a protein with no homology to any
known sequence at the time [91]. Sequencing of genomes from diverse organisms has shown that
rhomboids indeed are present in every form of cellular life [92]. There are three different topological
forms of rhomboid proteases. The simplest consist of a 6 TM core, which itself is the smallest
catalytically active unit. This form is common in bacteria, but can also be found rarely in eukaryotes
including animals. The second form has the 6 TM core plus an additional TM segment (6+1 TM
form). This form is represented by five out of the seven Drosophila, human and mouse rhomboid
proteins. The last form is the 7 TM rhomboid proteases that exist in endosymbiotic organelles, which
adds another TM domain to the 6+1 TM form. The Rhomboid-1 protease in Drosophila is localized in
the Golgi apparatus where it cleaves a substrate called Spitz. The released product is secreted to
activate epidermal growth factor (EGF) signaling in neighboring cells.
Rhomboid proteases are serine proteases belonging to the S54 family of the MEROPS peptidase
database, and contain the characteristic Ser-His catalytic dyad. In mitochondria rhomboids are
intramembrane proteases consisting of seven transmembrane helices [89]. The fourth transmembrane
segment is slightly tilted in relation to the others, and enters the center of the protein as an extended
loop, converting to an α-helix at the catalytic serine. There are 15 annotated rhomboid proteases in
A. thaliana. Two of these (AtRbl1 and 2) have been located to the Gogi apparatus [93], the subcellular
localization of most of the others is predicted to be in mitochondria. The AtRbl9 and 10 are predicted
to be localized in chloroplasts using the programs TargetP and Predator. There are no known
substrates for the Arabidopsis rhomboid proteases; hence their function is not well documented in
plants.
Deg proteases
Degradation of periplasmic proteins DegP proteases [94], also referred to as high temperature
requirement A (HtrA) proteases was initially characterized in E. coli in 1989 [95, 96]. Since then
DegP/HtrA proteases have been characterized as ATP independent temperature sensitive serine
endopeptidases and have been found in almost every organism, where the ones in metazoans are
designated as ‘HtrA proteases’ and the ones in plants as ‘DegP proteases’. The Deg proteases belong
19
to the S1B subfamily in the MEROPS protease database, with a catalytic triad comprised of His, Asp
and Ser [97, 98].
Deg proteases form homo-oligomeric complexes and contain a trimer as the basic structural unit,
formed by the interactions of protease domains. These trimers may in turn assemble into higher
oligomeric complexes, such as hexamers that have been reported from studies in E. coli [97], and
Deg1 from A. thaliana [99], or even 12-mers and 24-mers, as described for E. coli DegP [100]. There
are 16 genes coding for Deg proteases in A. thaliana AtDeg1-16. AtDeg1, 2, 5 and 8 have all been
localized to the chloroplast. AtDeg2 is localized on the stromal side of the thylakoid membrane, while
AtDeg1, 5 and 8 are located in the thylakoid lumen. AtDeg3, 4, 6, 10-13 and 15 have all been predicted
to be mitochondrial [72]. AtDeg1 has been shown to be an essential protease; even reduced level of
AtDeg1 gave rise to a relatively strong phenotype in form of reduced growth and early flowering in
combination with a chlorotic phenotype [101]. Reported substrates for the AtDeg proteases are
proteins of the PSII, such as the high turnover protein D1, and other proteins of the PSII as the D2,
CP43 and CP47 [94].
OOP
Organellar oligopeptidase (OOP) is a peptide-degrading metalloprotease belonging to the M3A family
in the MEROPS database. OOP is a soluble protein, dually localized to the mitochondrial matrix and
chloroplast stroma. The recently solved structure of OOP revealed an ellipsoidal shape consisting of
two major domains enclosing the catalytic cavity of 3000 Å3. The protease degrades short peptides
with a size restriction from 8 to 23 amino acid residues. Experiments have shown that OOP is able to
cleave both N- and C-terminal fragments of mitochondrial presequences, as well as short transit
peptides and other short peptides [102].
PreP
Presequence protease called PreP is an ATP independent protease that is located in both mitochondria
and chloroplasts. PreP will be described in more detail below as it is the main subject of this thesis.
20
Material & Methods
Paper I
Generation of mutant Arabidopsis plants, single and double knockouts
Several T-DNA insertion lines for both AtPreP1 and AtPreP2 were ordered from the Nottingham
Arabidopsis Stock Centre and the Arabidopsis Biological Resource Centre. The samples were
genotyped using PCR in combination with Western blot analysis. Homozygous double knockout
plants were generated by crossing of homozygous single mutants. The double mutant plants were
identified using PCR screening.
Growth conditions of A. thaliana plants
Plants were grown on MSO (Murashige and Skoog medium) agar plates for genotyping in a growth
chamber under continuous light. For all other experiments, plants were grown on soil in a growth
chamber with either 8 or 16 hours of light each day, with a night and day temperature of 18 °C and 22
°C, respectively.
Purification of mitochondria and chloroplasts
To obtain a crude mitochondrial fraction, 5 g of leaves were homogenized with sand and grinding
buffer. The grinded leaves were then filtrated and the homogenate was centrifuged and washed [103].
The pellet containing crude mitochondria was resuspended in wash buffer and used for respiratory
measurements.
Highly purified mitochondria were purified using the methods described in [103].
To isolate mitochondrial matrix and membrane fractions, highly purified mitochondria fractions were
incubated in a degradation buffer to obtain osmotic swelling, followed by sonication and
centrifugation. The supernatant was used as mitochondrial matrix fraction and the pellet was further
washed in degradation buffer and sonicated and centrifuged one more time. The resulting pellet was
then resuspended in degradation buffer and was used as membrane fraction.
Chloroplasts were isolated by using 10 g of tissue that was mixed in a blender in homogenization
buffer. The resulting homogenate was filtered and centrifuged, and then loaded onto a Percoll gradient
and centrifuged. Chloroplasts were then harvested from the gradient for further use [104].
21
Stroma and chloroplast membrane isolation was performed by osmotic swelling of chloroplasts in
degradation buffer followed by sonication and centrifugation steps. The supernatant was used as
stroma fraction and the pellet was further washed and resuspended in degradation buffer and used as
membrane fraction.
Thylakoids were isolated using 2 g of leaves, which were homogeniezed in a preparation buffer using
a mixer. The homogenate was then filtered and centrifuged and the pellet was washed and resuspended
in lysis buffer and centrifuged. The resulting pellet was resuspended in incubation buffer and
homogenized. Thylakoid membranes were collected after centrifugation.
Degradation assays
Degradation assays were performed using a HEPES degradation buffer at pH 8.0. For the analysis of
the mitochondrial and chloroplast membrane fractions 0.1 µg of the pF1β(2-54) peptide was degraded
for two hours at 30 °C by 2,5 µg of membrane protein. Samples were separated on 15% SDS-PAGE
and transferred by Western blot to Hybond ECL membranes and treated with primary and secondary
antibodies for detection.
For the mitochondrial matrix and chloroplast stroma fractions 1 µg of pF1β(2-54) peptide was degraded
for two hours at 30 °C. Samples were separated on 15% SDS-PAGE and stained with Coomassie blue.
Respiratory measurements
Respiratory measurements were performed in similar fashion as described in [103].
Protein gel and immunoblot analysis of thylakoid membranes
2 mg chlorophyll per ml sample was separated on 15 % SDS-PAGE followed by Blue Native PAGE.
Quantification of results was done using scanned triplicates, which were analyzed using the PDQuest
software. Immunoblot analysis was done using a semi dry Western blot transfer followed by detection
with antibodies for Lhcb2 and the F1β subunit of the ATPase.
Protein extractions and analysis of AtPreP1 and AtPreP2 content
Plant tissues from mature plants were frozen and grinded. The resulting tissue powder was
resuspended in a Tris-buffer and centrifuged. 10 µg of protein was loaded onto a 12 % SDS-PAGE
22
and PreP content was analyzed using Western blot with an antibody recognizing both AtPreP1 and
AtPreP2.
Biomass
Plants were cut at the base excluding the roots. Harvested plants were kept dry in the dark for more
than 3 days to fully dry before they were weighted.
Paper II
Generation of AtPreP1 variants
To generate the AtPreP variants mutations were introduced at D705N, D859N, D861N for the inner
Mg-binding site and D828N, T947N, D952N for the outer Mg-binding site. All mutations were
introduced to wild type AtPreP1 gene on pGEX-6P-2 plasmid (Amersham Biosciences) using the
Quick-Change Site Directed Mutagenesis Kit (Stratagene). All constructs were verified by DNA
sequencing.
Expression and purification of AtPreP1 and its variants
Wild type AtPreP and the three variants were linked to a Glutathione S-Transferase (GST) tag at the
N-terminus. All constructs were transformed into E. coli BL21 (DE3). Colonies were inoculated in LB
medium and overexpressed with 1mM Isopropyl β-D-1-thiogalactopyranoside (IPTG) and incubated at
30 °C to OD600 of 2. Cells were harvested by centrifugation and stored at -80 °C. The pellet was
resuspended in phosphate-buffered saline buffer and cells were lysed with lysozyme and sonication.
The soluble protein fraction was separated by centrifugation and filtration and incubated with
Glutathione Sepharose® beads (Amersham Biosciences) in phosphate-buffered saline buffer at 4 °C
for 4 hours. Bead solution was washed and bound AtPreP was cleaved over night using PreScission™
Protease. After cleavage the solution was centrifuged and AtPreP was collected from the supernatant.
Protein samples were analyzed on 12 % SDS-PAGE, and final protein concentration was determined
using BioRad Protein Assay (BioRad). The protein was stored at -20 °C.
23
Degradation assays
Degradation assays with hPrPss(1-28), Cecropin A(1-33), Penetratin, Galanin and the F1β presequence
peptides were done using 1 µg of peptide and 1 µg of AtPreP incubated in HEPES buffer at 30 °C for
1 hour. Degradation was analyzed on 15 % SDS-PAGE. Degradation of the 11 amino acids C1 peptide
was done using 1 µg of peptide and 1 µg of AtPreP incubated in HEPES buffer at 30 °C for 1 hour and
analyzed by electrophoresis on 1 % agarose gels and the C1 peptide was detected by UV light.
Substrate V (R&D Systems), a bradykinin derived peptide of 9 amino acids was used to monitor the
kinetics of proteolysis using a fluorometer. For these experiments 1 µg of Substrate V and 1 µg of
AtPreP protein were mixed with a HEPES degradation buffer in a cuvette. Degradation data for
Substrate V was recorded for 90 seconds with excitation and emission wavelength set at 320 nm and
405 nm, respectively.
Paper III
Generation of hPreP-SNP variants
To generate the hPreP-SNP variants substitutions were introduced at L116V, F140S, A525D and
I924M. All mutations were introduced to the wild type AtPreP1 gene in the pGEX-6P-2 plasmid
(Amersham Biosciences) using the Quick-Change Site Directed Mutagenesis Kit (Stratagene). All
constructs were verified by DNA sequencing.
Degradation assays
Degradation assays using hPreP and hPreP-SNP variants were done using 1 µg of hPreP protein and 1
µg of following peptide substrates; Aβ(1-40) or Aβ(1-42), or pF1β(2-54). hPreP and the substrate were mixed
in a HEPES degradation buffer and incubated at 37 °C for 5-30 minutes (for pF1β(2-54) and for 30
minutes for Aβ(1-40) or Aβ(1-42). Degradation was analyzed on 10-20 % Tris-Tricine gels (Bio-Rad).
Substrate V was used to monitor the kinetics of proteolysis using a fluorometer. For these experiments
1,5 µg of Substrate V and 1 µg of hPreP protein were mixed with a HEPES degradation buffer in a
cuvette. Degradation data for Substrate V was recorded for 120 seconds.
24
Summary of results
The Presequence protease, PreP
After import into the respective organelle the targeting peptide is cleaved off. In mitochondria the
presequence is cleaved off by the mitochondrial processing peptidase (MPP) and in chloroplasts the
transit peptide is cleaved off by the stromal processing peptidase (SPP). The mature proteins are then
able to fold into the native form and fulfil various important activities inside the organelles. The free
targeting peptides are subsequently degraded by the Presequence protease (PreP).
PreP is a 110 kDa zinc metallooligopeptidase that belongs to the M16C family of peptidases
(MEROPS database) [49]. The M16 peptidases are commonly referred to as inverzincins, due to an
inverted zinc-binding motif, HXXEH, at the active site [105]. In A. thaliana there are two isoforms of
PreP, referred to as AtPreP1 and AtPreP2, with high sequence conservation (86% identity). AtPreP1
and AtPreP2 are dually targeted to both the mitochondrial matrix and the chloroplast stroma [106]. The
human homolog of AtPreP, hPreP (or MP1 for metalloprotease 1) is located in the mitochondrial
matrix as is the yeast homolog MOP112 (or CYM1p) [107].
The crystal structure of AtPreP1(E80Q) with a bound peptide in the active site was determined at 2.1
Å [108]. The structure showed that the 995-residue polypeptide folds into four topologically similar
domains, which form two bowl-shaped halves connected by a V-shaped hinge that protrudes from the
protease [108]. Although the inverted zinc binding motif of the active site (H77XXEH81) is positioned
in the N-terminal domain, distal residues (Y854, R848) from the C-terminal domain come together to
complete the active site. This leads to the hypothesis that the shift between an open and closed state is
crucial for the activity of the protease [108]. Magnesium ions were added to facilitate the
crystallization of AtPreP1 and the structure revealed two hydrated magnesium ions coordinated by
acidic residues [108]. The structure of AtPreP1 revealed a unique proteolytic chamber of more than
10 000 Å3. Within this chamber lies the active site and it is estimated that the chamber has room for
peptides up to about 65 amino acids in length. Mitochondrial and chloroplastic targeting peptides are
about 30-50 amino acids long but do not show any sequence similarity. On the other hand they share
some overall properties as they are generally enriched in positively charged, hydroxylated and
hydrophobic amino acids [20]. Presequences also have the ability to form a positively charged
amphipathic α-helix in the presence of a membrane-like environment [109]. The α-helix formation has
also been observed for transit peptides [110]. Substrate specificity experiments have shown that PreP
is actually a general peptidase and that it cleaves not just presequences and transit peptides, but also
other unstructured peptides between 9-65 amino acids in length [106].
25
The inside surface of the chamber is negatively charged and it is proposed that the binding of a
positively charged peptide induces the closing of the protease. After the chamber has been closed, the
peptide can be cleaved and the protease is restored to an open conformation. This novel mechanism of
action has led to that PreP and other M16 proteases now are referred to as peptidasomes [108, 111].
In general, proteolysis plays a vital role in the cell. Proteins and peptides have to be continuously
degraded to sustain cell homeostasis. Presequences have membrane binding properties and also the
ability to penetrate membranes, which can lead to loss of membrane potential and uncoupling of
respiration [112]. Accumulation of free presequences could be toxic to the cell, and therefore they are
proteolytically removed by PreP. It has been shown that the human homolog hPreP is able to degrade
amyloid-beta peptide (Aβ) [113], the toxic agent that accumulates in mitochondria in Alzheimers
disease [114].
When a mutation of a single nucleotide occurs within a genome and the frequency of this change is
greater than 1 % it is called a SNP (single nucleotide polymorphism). SNPs can be either silent
(synonymous), which do not lead to a change in the amino-acid composition, or non-synonymous that
will give rise to a change in the amino-acid composition.
Our goal was to further study the AtPreP by constructing PreP knockout plants and make comparison
with wild type plants, and to investigate the role of the magnesium-binding sites found in the AtPreP1
structure. Further, we localized four non-synonymous SNPs in hPreP that were situated in structural
positions that might be important for the catalytic activity. We were interested in the role of these
SNPs found in hPreP, and we compared the activity of the hPreP-SNP variants with wild type hPreP.
Paper I - Deletion of an organellar peptidasome PreP affects early development in
Arabidopsis thaliana
After extensive investigation of the two PreP isoforms AtPreP1 and AtPreP2 in our laboratory we
wanted to study the effect of PreP peptidasome deletion in A. thaliana. The aim of this project was to
study the in vivo effects of PreP knockout and how the plant would cope with the toxic stress caused
by a possible accumulation of peptides. The aim was to create single knockouts, atprep1 and atprep2,
and double knockout atprep1 atprep2 strains.
T-DNA (Salk) insertion lines of A. thaliana (for both isoforms) was ordered and screened for
homozygous single mutants. The homozygous single mutants of AtPreP1 and AtPreP2 were then
crossed in order to generate a double knockout strain. According to the Genevestigator database,
26
which is based on micro array data, PreP1 is the most abundant isoform of the two isoforms and our
Western blot analysis supported this data. Immunoblot analysis of different wild type plant tissues
showed that PreP is most abundant in flowers and siliques, but also present at significant levels in
roots, leaves and shoots, indicating that PreP is required in all plant tissues.
Investigation of the phenotype revealed a difference in growth rate, where the double knockout
atprep1 atprep2 grew significantly slower compared to wild type plants. In contrast, the atprep1 and
atprep2 mutant grew similarly as the wild type. When we analysed the growth rates of plants grown
during 16 hours of light per day we found a statistically significant decrease in the accumulated
biomass with about 38 % (dry weight) for the double knockout plants compared to wild type.
A chlorotic phenotype was present in the double knockout and a weaker, but still noticeable chlorotic
phenotype in the single knockout atprep1. The chlorotic phenotype was most pronounced during early
development in the first true leaves. A pigment comparison study was done and the results showed a
clear reduction of the different pigments in double knockout plants compared to wild type plants. The
single knockouts did not show any significant reduction. To further analyze the chlorotic phenotype
we applied electron microscopy to investigate the ultrastructure of chloroplast and mitochondria in the
first true leaves. We found that atprep1 and double knockout chloroplasts contained less starch and
poorly developed thylakoids and grana. The PreP2 knockout showed similar structural features as the
wild type. The found differences in the chloroplast development could be a result of the observed
slower growth rate, which means that the organelle ultrastructure could be in different developmental
stages.
Respiratory measurements of mitochondria from the first true leaves showed a significant decrease in
respiratory rate for atprep1 atprep2 compared to wild type, measured with malate and glutamate as
substrates in the presence of ADP. In addition, the respiratory control ratio (RCR) decreased by 50%
indicating partial uncoupling of mitochondria in PreP double knockout plants.
We also investigated the proteolytic activity of the PreP double knockout plants using the F1β(2-54)
presequence. Mitochondria and chloroplasts were purified and then sub-fractionated into membrane
and soluble fractions. No proteolytic activity could be detected in the mitochondria fractions or in the
chloroplast stroma, whilst in the chloroplast membrane fractions a metal dependent activity was
detected both in the wild type as well as in the double knockout. This study shows that PreP is
important for normal plant growth, but not essential for plant survival in a laboratory environment.
27
Paper II - Binding of divalent cations is essential for the activity of the organellar
peptidasome in Arabidopsis thaliana, AtPreP
To investigate the role of the two magnesium sites that were found in the structure of AtPreP1 [108],
the six amino acids that coordinate the two magnesium ions were substituted by neutral amino acids.
The aspartates were changed to asparagines and threonine was changed to valine. In this way the
magnesium binding capacity was depleted and made it possible to compare the activity of the protease
with and without bound magnesium at these sites. One of the sites is positioned in the close proximity
of the active site and thereby called the inner site or ∆1. In this site the magnesium is coordinated by
three aspartate residues, where one (D705) is located in domain three and the other two (D859, D861)
in domain four of AtPreP. The other magnesium binding site (composed by D828, T947, and D952) is
positioned on the outside surface of the protease in domain four and hence called the outer site or ∆2.
Sequence similarity searches of AtPreP using 19 different sequences showed that the inner magnesium
binding site was conserved in plant PrePs. The outer magnesium binding site was only fully conserved
in A. thaliana and Physcomitrella patens (moss).
We investigated the metal depleted variants lacking the inner, outer or both metal binding sites, using
a native substrate, the mitochondrial presequence from the F1β subunit of ATP synthase, pF1β2-54 at
increasing concentrations of Mg2+, Ca2+ and Zn2+ ions. Our results showed that without metal ions no
degradation of pF1β(2-54) could be observed for wild type or any of the variants. The addition of Mg2+
and Ca2+ ions clearly stimulated the catalytic activity of both wild type AtPreP1 and the ∆2 variant at
metal concentrations of 1 mM or higher. In contrast, the ∆1 and ∆1,2 variants were only partially
active at increasing concentrations of Mg2+ and did not show any activity even at 10 mM of Ca2+.
These results suggest that the inner magnesium binding site plays a role for the proteolytic function of
the protease. Addition of Zn2+ did not stimulate the degradation of the pF1β(2-54) peptide. In contrast to
Mg2+ and Ca2+, addition of Zn2+ completely inhibited the activity of AtPreP1 already at 1 mM Zn2+.
The proteolytic activity was also tested against 8 other peptides, 9-33 amino acids in length, and an
overall degradation pattern could be observed with a higher proteolytic activity in the presence of
magnesium ions for all AtPreP1 variants (figure 4-6 in paper II).
The reason for the increased activity when adding MgCl2 is not known, but we speculate that since
PreP is very acidic and the enzyme halves are both negatively charged, Mg2+ may assist to stabilize the
protein by neutralizing this charge and enable the two halves to come together to form the active site
and to enable proteolysis.
28
Paper III - Biochemical studies of SNPs of the mitochondrial Aβ-degrading protease,
hPreP
The aim of this project was to study four SNPs located at interesting sites in the hPreP structure, and
compare the proteolytic activity with and without Mg2+. The SNPs that were investigated in this study
were L116V, F140S, A525D and I924M. SNP L116V is located close to the active site inside the
proteolytic chamber and could be in direct contact with the substrate side chains. The substitution to
valine may affect substrate binding. SNPs F140S and A525D are found close to the hinge region of
PreP and substitutions in this region may affect the opening and closing of the enzyme. Finally, the
SNP I924M is located close to the surface of domain 4 about 20 Å from the hinge region and may play
a role for protein stability.
We selected four peptides of different lengths and properties to investigate the proteolytic activity of
the selected SNP variants: Aβ(1-40), Aβ(1-42), the presequence of ATP synthase F1β subunit (pF1β) and a
fluorescent peptide, Substrate V.
Both wild type and hPreP-SNP variants were able to degrade the Aβ peptides. However, we found that
the SNP-variants displayed lower activity compared to wild type hPreP. The SNP-variant A525D
showed the lowest activity with a degradation of 11 % for the Aβ(1-40) peptide and only 4 %
degradation for the Aβ(1-42) peptide compared to wild type hPreP. The activity of the SNP-variants
increased in the presence of MgCl2 and reached the same activity as wild type for Aβ(1-40), and almost
similar to wild type with Aβ(1-42).
Time titration of the pF1β(2-54) peptide without Mg2+ showed lower activity for the SNP F140S and
A525D (about 30% activity compared to wild type hPreP). Interestingly, the activity was fully restored
upon addition of 10 mM of Mg2+.
We also studied the kinetics of degradation for the SNP variants compared to wild type hPreP using
fluorometry. As substrate we used the fluorogenic Substrate V, which is derived from bradykinin.
Substrate V is a nine amino acid long peptide and is positively charged [MCA–Arg-Pro-Pro-Gly-PheSer-Ala-Phe-Lys-(Dnp)–OH, where MCA is (7-methoxycoumarin-4-yl) acetyl and Dnp is 2,4dinitrophenol]. The peptide harbours a fluorescent MCA group that is efficiently quenched by
resonance energy transfer to Dnp. When the peptide is cleaved the two groups can be separated and
the quenching is lost, which leads to an increase in fluorescence. Both wild type and hPreP-SNP
variants were able to degrade Substrate V, both with and without MgCl2. In contrast, the
hPreP(A525D) variant only had 20 % of normal activity in the absence of MgCl2, but interestingly the
activity increased to 60 % after the addition of MgCl2.
In summary, these results show that hPreP-SNP variants show reduced activity compared to wild
type, and that Mg2+ ions stimulate the proteolytic activity of both wild type hPreP and hPreP-SNP
29
variants. The reason for the increased activity when adding MgCl2 is not known. Similar to AtPreP,
hPreP is very acidic and the enzyme halves are both negatively charged. This leads to the hypothesis
that Mg2+ may assist to stabilize the protein by neutralizing this charge and enable the two halves to
come together to form the active site and enable proteolysis.
30
Future perspectives
Structure and catalytic function of AtPreP1
In future, it would be interesting to solve the structure of wild type AtPreP1 and the inactive variant
AtPreP1 (E80Q) with bound substrate, the F1β presequence (pF1β) or other shorter peptide. In addition
to this we would like to solve the structure of the AtPreP1 variant ∆1,2 lacking the two metal binding
sites (described above). These structures together with biochemical catalytic activity assays will help
to get a better understanding for the catalytic mechanism and the role of non-catalytic metal ions. The
initial screening and optimization experiments have led to production of crystals from both wild type
AtPreP1 as for AtPreP1(E80Q)+ F1β presequence, but so far we have not been able to get crystals that
diffract better than about 4 Å.
31
Acknowledgements
I would like to thank my supervisor Elzbieta for giving me the opportunity to try the life as a scientist.
It has for sure been an interesting time and a journey between despair and joy. From day one you made
me feel welcome in the group and the great personal chemistry in the group made me decide to stay.
Thank you for your support during these years and for all interesting discussions about science or
anything in life.
Stefan, working with you was a huge inspiration and a lot of fun! I was learning so much every day
during the DKO project. Shashi, thanks for all the help during my first time in the lab. Nyosha and
Anna-Karin, you always kept the EG-lab spirit on top, when you were around anything could and
would happen. Catarina, it was fun to work in the dark with you, even if we didn’t see that much we
actually got some results. Erika, the Aurora Borealis of the lab, thanks for all the nice moments in the
lab and during our travel adventures. Beata and Pedro, thanks for helping out in the lab and for
interesting discussions.
Amin, thank you for introducing me to the world of crystallography! It was an interesting but
frustrating time. You were my teacher some ten years ago, and to work with you again was a great
opportunity for serious discussions about most things. Thank you for always supporting me and
believing in me!
Stefan Nordlund, thanks for accepting me as a PhD student at the department. Inger, thanks for
teaching me how to teach, and for having answers to my questions.
Thanks to all former EG-lab members that I had the joy to work with, and all other people at the
department that I met during my eight years at DBB.
32
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