Faculty of Technology and Science
Chemistry
Anna Smedja Bäcklund
c Cytochromes as
Electron Carrier in
Microbial Chlorate
Respiration
DISSERTATION
Karlstad University Studies
2011:40
Anna Smedja Bäcklund
c Cytochromes as
Electron Carrier in
Microbial Chlorate
Respiration
Karlstad University Studies
2011:40
Anna Smedja Bäcklund. c Cytochromes as Electron Carrier in Microbial Chlorate
Respiration
DISSERTATION
Karlstad University Studies 2011:40
ISSN 1403-8099
ISBN 978-91-7063-375-1
© The author
Distribution:
Karlstad University
Faculty of Technology and Science
Chemistry
S-651 88 Karlstad
Sweden
+46 54 700 10 00
www.kau.se
Print: Universitetstryckeriet, Karlstad 2011
Abstract
Microbial respiration of oxochlorates is important for the biotreatment of
effluents from industries where oxochlorates are produced or handled. Several
bacterial species are capable to use perchlorate and/or chlorate as an alternative
electron acceptor in absence of oxygen. The present study deals with the
electron transport from the membrane-bound components to the periplasmic
chlorate reductase, in the gram-negative bacterium Ideonella dechloratans. Both
chlorate reductase and the terminal oxidase of I. dechloratans were found to
utilize soluble c cytochromes as electron donors. For further investigation, two
major heme-containing components were purified and characterized. The most
abundant was a 9 kDa c-type cytochrome (class I), denoted cytochrome c-Id1.
This protein was shown to serve as electron donor for both chlorate reductase,
and for a terminal oxidase. The other major component was a 55 kDa
homotetrameric cytochrome c', (class II). A function for this cytochrome could
not be demonstrated but it does not appear to serve as electron donor to
chlorate reductase. A gene predicted to encode a soluble c cytochrome was
found in close proximity to the gene cluster for chlorate reduction. The
predicted sequence did not match any of the cytochromes discussed above. The
gene was cloned and expressed heterologously, and the resulting protein was
investigated as a candidate electron donor for chlorate reductase. Electron
transfer from this protein could not be demonstrated, suggesting that the gene
product does not serve as immediate electron donor for chlorate reductase.
Table of contents
Abstract................................................................................................................... 2
Table of contents .................................................................................................. 3
List of papers ......................................................................................................... 4
List of abbreviations ............................................................................................. 5
1. Introduction....................................................................................................... 6
1.2 Oxyanions of chlorine ................................................................................................. 6
1.3 Perchlorate and chlorate in the environment ........................................................... 7
1.3.1 Sources .................................................................................................................... 7
1.3.2 Environmental effects .......................................................................................... 7
1.3.3 Treatment of perchlorate- and chlorate containing effluents ......................... 8
1.4 Bacterial perchlorate- and chlorate respiration ......................................................... 9
1.4.1 Mechanism and enzymes ..................................................................................... 9
1.4.2 Perchlorate- and chlorate respiring bacteria .................................................... 10
1.4.3 Electron transfer pathway in chlorate respiration .......................................... 12
1.5 c-type cytochromes ..................................................................................................... 14
2. Methods used in present study..................................................................... 18
2.1 Analysis of periplasmic c cytochromes .................................................................... 18
2.1.1 Separation ............................................................................................................. 18
2.1.2 Detection .............................................................................................................. 19
2.2 Mass spectrometry ...................................................................................................... 19
2.2 Protein purification .................................................................................................... 21
3. Results and discussion ................................................................................... 23
3.1 Native periplasmic c cytochromes in Ideonella dechloratans ..................................... 23
3.2 Characterization of a candidate cytochrome c gene associated with the
gene cluster for chlorate respiration ....................................................................... 26
3.3 Purification and characterization of soluble cytochrome c capable of
delivering electrons to chlorate reductase in Ideonella dechloratans ....................... 29
3.4 Purification and characterization of a cytochrome c' in the chlorate
respiring bacterium Ideonella dechloratans ................................................................. 32
5. Conclusion ....................................................................................................... 37
6. Tack................................................................................................................... 39
7. References ........................................................................................................ 41
3
List of papers
I
Bäcklund A. S., Bohlin J., Gustavsson N. & Nilsson T. (2009)
Periplasmic c cytochromes and chlorate reduction in Ideonella dechloratans.
Appl Environ Microbiol 75 (8) 2439-2445
II
Bohlin J., Bäcklund A. S., Gustavsson N., Wahlberg S. & Nilsson T.
(2010) Characterization of a cytochrome c gene located at the gene
cluster for chlorate respiration in Ideonella dechloratans. Microbiol Res 165 (6)
450-457
III
Bäcklund A. S. & Nilsson T. (2011), Purification and characterization of
a soluble cytochrome c capable of delivering electrons to chlorate
reductase in Ideonella dechloratans. FEMS Microbiol Lett 321 (2)115-120
IV
Bäcklund A. S. & Nilsson T., Purification and characterization of a
cytochrome c' from the chlorate respiring bacterium Ideonella dechloratans,
Manuscript
4
List of abbreviations
BOD
COD
Cld
Clr
Ddh
DMS
DMSO
DTT
Edh
GF
HIC
IEF
IEX
IMAC
IPG
LC
LTQ
MALDI
MES
MS
MS/MS
Nap
Nir
ORF
PAGE
PCR
Pcr
Q/QH2
SDS
Ser
TFA
TMAO
TMBZ
TOF
Biological oxygen demand
Chemical oxygen demand
Chlorite dismutase
Chlorate reductase
Dimethyl sulfide dehydrogenase
Dimethyl sulfide
Dimethyl sulfoxide
Dithiothreitol
Ethylbenzene dehydrogenase
Gel filtration
Hydrophobic interaction chromatography
Isoelectric focusing
Ion exchange chromatography
Immobilized metal ion affinity chromatography
Immobilized pH gradient
Liquid chromatography
Linear trap quadrupole
Matrix assisted laser desorption ionization
2-(N-morpholino)ethanesulfonic acid
Mass spectrometry
Tandem mass spectrometry
Periplasmic respiratory nitrate reductase
Nitrate reductase
Open reading frame
Polyacrylamide gel electrophoresis
Polymerase chain reaction
Perchlorate reductase
Quinone pool
Sodium dodecyl sulfate
Selenate reductase
Trifluoroacetic acid
Trimethylamine-N-oxide
3, 3’, 5, 5’- tetramethylbenzidine
Time of flight
5
1. Introduction
Sustainable development of industrial processes include the minimization of the
release of waste products in the environment. In many industrial operations,
biological treatment of effluents is used to reduce their content of harmful
substances. Knowledge about the organisms involved, and their physiological
and biochemical properties, is important for the design, operation and
optimization of waste-treatment plants. Chlorate and perchlorate are examples
of toxic industrial by-products, which need to be removed from waste streams.
The present work deals with the chemistry of microbial respiration of chlorate
and perchlorate. Here, chlorate and/or perchlorate are used as alternative
respiratory electron acceptors in absence of oxygen with chloride as the end
product. The specific aim of this work was to elucidate the electron transport
pathways in chlorate respiration.
1.2 Oxyanions of chlorine
Chlorine can combine with oxygen to produce four different oxyanions, shown
in table I. The most oxidized form is perchlorate. Most salts of chlorate and
perchlorate are highly soluble in water and chemically inert under ambient
conditions (Kang et al., 2006; Urbansky & Schock, 1999). In contrast, chlorite
and hypochlorite are highly reactive in different reactions.
Table I Oxyanions of chlorine
Name
Formula
Hypochlorite
Chlorite
Chlorate
Perchlorate
ClOClO2ClO3ClO4-
Oxidation state of chlorine
I
III
V
VI
6
1.3 Perchlorate and chlorate in the environment
1.3.1 Sources
For long, the only known occurrence of perchlorate in the environment was
deposits in Chile (Urbansky et al., 2001). Recently it has been shown that
perchlorate is readily formed by atmospheric processes when chloride is
exposed to high concentrations of ozone. This suggests that some natural
perchlorate background from the atmosphere should exist (Dasgupta et al.,
2005). Also, Kang et al. (2006) demonstrated that perchlorate can be generated
by photochemical transformations of aqueous chlorine anions such as
hypochlorite, chlorite, and chlorate, upon exposure to UV-radiation. In the
latter case there is a combination of anthropogenic and natural sources since
the chlorine oxyanions are introduced to the environment by human activities.
A major anthropogenic source is the manufacture of perchlorate compounds.
Perchlorate salts are used as oxidants in rockets and missiles (Urbansky &
Schock, 1999), and most of the perchlorate contamination in the ground and
surface water is a result of discharge from rocket fuel manufacturing plants,
decades ago (Urbansky, 1998).
At the present, there is no evidence for any natural sources of chlorate in the
environment, but there are several anthropogenic sources. In agriculture,
chlorate is applied as herbicide or as defoliant (Logan, 1998). When
hypochlorite is used as disinfectant in drinking water, chlorate is formed as a
by-product (van Ginkel et al., 1995). Another considerable source of chlorate is
the pulp- and paper industry. Pulp is bleached with chlorine dioxide and
chlorate is formed both by decomposition of chlorine dioxide and in the
bleaching process (Germgård et al., 1981; Rosemarin et al., 1994). Furthermore,
chlorate can be formed during the manufacture and storage of hypochlorite
solutions (Siddiqui, 1996).
1.3.2 Environmental effects
In Kalmar Strait, in the Baltic Sea, it was recorded in 1992 that the brown algae
bladder wrack had disappeared from an area of 12 km2 caused by the effluent
from Mönsterås pulp mill (Lehtinen et al., 1988; Rosemarine et al., 1994). Studies
of the marine environment have shown that groups of marine algae are
7
sensitive to high concentration of the chlorate anions, especially the benthic
brown macro algae (van Wijk and Hutchinson, 1995). The mechanism of
toxicity is not clear and appears to differ among species. It has been suggested
that chlorate can be reduced by nitrate reductase and that the resulting chlorite
ion inhibits nitrate reduction, with nitrogen starvation as the result (Åberg,
1947; Stauber, 1998). Further support for this hypothesis is the finding that the
cyanobacterium Nostoc muscorum, which is lacking the nitrate reduction system, is
chlorate resistant (Singh et al., 1977). In conflict with this hypothesis, chlorate
toxicity in plants and bacteria lacking nitrate reduction systems have also been
reported (Siddiqi et al., 1992; Prieto & Fernadez, 1993). This suggests that other
metabolic pathways are affected by chlorate. For example, in the microalga
Nitzschia closterium chlorate has no effect on the nitrate reductase activity, but
the alga is still chlorate sensitive. Stauber (1998) suggests that the toxicity can be
a result of decreasing flow of electrons in the electron transport chain, caused
by chlorate-dependent altering of membrane-bound components, or
inactivation of cytochromes.
1.3.3 Treatment of perchlorate- and chlorate containing effluents
Traditionally, waste water treatment in the pulp and paper industry has been
focused on removal of biological and chemical oxygen demand (BOD and
COD, respectively) by biological active sludge processes in aerated lagoons.
However, the introduction of chlorine-containing chemicals in the pulpbleaching process made the removal of the resulting chlorate necessary (Yu &
Welander, 1994). The toxicity of chlorate is suggested to be coupled to
reduction of chlorate to the highly reactive chlorite by the nitrate reduction
systems, as was described in the above section. However, non-toxic
decomposition of chlorate by microbial respiration has been known since the
beginning of the 20th century (Åslander, 1928). The difference between toxic
and non-toxic decomposition of perchlorate and chlorate depends on the
bacterial enzyme systems, as will be discussed in the next section. Several
bacterial species, able to grow with perchlorate and/or chlorate as an alternative
electron acceptor under anaerobic conditions, have been isolated (Korenkov et
al., 1976; Malmqvist et al., 1994; Rikken et al., 1996; Wallace et al., 1996; Bruce et
al., 1999; Achenbach et al., 2001; Wolterink et al., 2002). These strains can be
utilized for anaerobic biotreatment of water and waste water.
8
One method, developed by Ødegaard et al. 1994, is a process where biomass is
grown on small carrier elements that move along with waste water in reactor
tanks. The carriers are made by polyethylene and are shaped like small cylinders
(Johnson et al., 2000). This technique was introduced into Swedish paper mill
industries in the 1990th (Kindh & Johansson, 1999). Another method,
described by Kroon and van Ginkel (2004), is chlorate reduction in a gas-lift
reactor, where microorganisms are attached to pumice particles in the reactor.
1.4 Bacterial perchlorate- and chlorate respiration
1.4.1 Mechanism and enzymes
Bacterial perchlorate or chlorate reduction is coupled to cell growth (Malmqvist
et al., 1994), and therefore a part of a respiratory chain that generates an
electrochemical gradient, which can serve as driving force for ATP synthesis.
Many bacteria use several types of acceptors like nitrate, sulfate, manganese
(IV), iron (III), selenate, iodate, bromate and DMSO. Respiration of chlorate
and perchlorate is unique because it involves formation of molecular oxygen.
The complete reaction takes place in three steps: ClO4- → ClO3- → ClO2- →
O2 + Cl- (Kengen et al., 1999) and is catalyzed by two soluble enzymes,
(per)chlorate reductase and chlorite dismutase (Bender et al., 2002; Stenklo et al.,
2001; van Ginkel et al., 1996). In bacteria able to reduce perchlorate, the first
and second step is catalyzed by the same enzyme, perchlorate reductase
(Kengen et al., 1999). However, some bacteria are not able to reduce perchlorate
and in that case the first step will be the reduction of chlorate into chlorite,
catalyzed by chlorate reductase (Kengen et al., 1999; Wolterink et al., 2003). The
last step, where chlorite is decomposed to chloride ion and oxygen, is catalyzed
by chlorite dismutase.
9
1.4.2 Perchlorate- and chlorate respiring bacteria
During the last two decades many different species and strains of bacteria,
capable of growth with chlorate or perchlorate as the sole electron acceptor,
have been isolated and further investigated. A selection of these is listed in
Table II.
The subject of the present study is chlorate respiration in the Gram-negative
bacterium Ideonella dechloratans. It belongs to the beta subgroup of proteobacteria
and was isolated at the environmental biotechnical company ANOX AB
(presently AnoxKaldnes) in 1994 (Malmqvist et al.). This bacterium can grow by
reduction of chlorate, but is not capable to reduce perchlorate. The enzyme
chlorite dismutase was isolated and purified by Stenklo et al. 2001. Also, the
gene encoding chlorite dismutase was cloned, characterized and expressed by
Danielsson Thorell et al. 2002. This enzyme, located in the periplasm, is a
homotetrameric heme b- containing protein with the molecular weight of 100
kDa.
10
Table II Examples of isolated perchlorate and/or chlorate respiring bacteria.
Bacteria strain
Electron acceptor
Reference
Ideonella dechloratans
ClO3-, NO3- *, IO3-, BrO3-, O2
Malmqvist et al. 1994
Azospira oryzae
(Strain Gr-1)
ClO4-, ClO3-, NO3-, Mn(IV)
Rikken et al. 1996
Dechloromonas agitata
(Strain CKB)
ClO4-, ClO3-, O2,
Bruce et al. 1999;
Achenbach 2001
Wolinella succinogenes
ClO4-, ClO3-, NO3-, O2
Wallace et al. 2001
Dechloromonas aromatica
(Strain RCB)
ClO4-, ClO3-, NO3-, O2
Coates et al. 2001;
Bender et al. 2005
Pseudomonas
chloritidismutans (Strain
AW-1)
ClO3-, O2
Wolterink et al. 2004
Pseudomonas
chloritidismutans (Strain
ASK-1)
ClO3-, O2
Wolterink et al. 2005
Dechloromonas hortensis
(Strain MA-1)
ClO4-, ClO3-, NO3-, O2
Wolterink et al. 2005
Alicycliphilus denitrificans
(Strain BC)
ClO3-, O2, NO3-, NO2-
Weelink et al. 2008
* After several subcultivations on chlorate, Ideonella dechloratans loses the ability to use nitrate as
electron acceptor (Malmqvist et al, 1994).
11
Chlorate reductase was isolated and the gene cluster for the chlorate
metabolism in I. dechloratans was investigated by Danielsson Thorell and
coworkers, 2003. Also this enzyme was found to be located in the periplasm.
The protein is heterotrimeric and contains molybdopterin, iron-sulfur cluster
and heme b bound to subunits A, B and C, respectively. The molecular weight
of the native protein was estimated by gel filtration to 160 kDa. The enzyme
belongs to the type II subgroup of the dimethyl sulfoxide (DMSO) reductase
family. For several years, the most similar known member in the DMSO
reductase family was Thauera selenatis selenate reductase (Ser) (Schröder, 1997).
The similarity between Ser and Clr is 84 %. However, selenate is a poor
substrate for chlorate reductase. More recently, the benzene-degrading
bacterium A. denitrificans strain BC was isolated and characterized by Weelink
and co-workers (2008). The similarity of the amino acid sequence of Clr from
this bacterium compared with Clr from I. dechloratans show 100 % identity for
the B- subunits, and 99 % for the A- and C-subunits. Other related enzymes,
based on sequence similarities and cofactor contents, are found in the marine
photosynthetic bacterium Rhodovulum sulfidophilum (dimethyl sulfide (DMS)
dehydrogenase, Ddh) and in Azoarcus sp. Strain EbN1 (ethylbenzene
dehydrogenase, Edh) (Danielsson Thorell et al., 2002). The A-subunit,
containing molybdopterin, is similar to subunits in several other
oxidoreductases, e.g. in DMSO reductase, TMAO reductase, and in periplasmic
nitrate reductase (NapAB) (Karlsson & Nilsson, 2005). The C-subunit of
chlorate reductase was expressed, purified, refolded, and heme reconstituted.
The results confirmed the C subunit as the cytochrome b moiety of chlorate
reductase in I. dechloratans (Karlsson & Nilsson, 2005).
1.4.3 Electron transfer pathway in chlorate respiration
Although many perchlorate- and chlorate respiring species have been isolated
and investigated, electron transport between the inner membrane components
and the periplasmic oxidoreductases is not well understood. In the case of
nitrate respiration relying on the periplasmic Nap system, electrons are
mediated from the quinone pool to the soluble periplasmic NapAB by a
membrane-anchored multi-heam c-type cytochrome, belonging to the
NapC/NirT family (Berks et al., 1995; Roldan et al., 1998) or by the NapGH
complex (Wolinella succinogenes), (Simon et al., 2003; Simon & Kern, 2008).
12
In other cases the electron transfer agent is soluble and located in the
periplasm. The oxidation of quinol is performed by the membrane-bound
cytochrome bc1 complex, followed by electron transfer to a soluble c-type
cytochrome, which further acts as electron donor to the periplasmic reductase.
In T. selenatis, electron transfer to Ser has been shown to be organized in this
way. Electrons are mediated between membrane-bound quinol:cytochrome c
oxidoreductase (bc1-complex) and periplasmic selenate reductase (Ser) by the 24
kDa di-heme cytochrome cytc-Ts4 (Lowe, et al., 2010). In the photosynthetic
bacterium R. sulfidophilum a soluble c cytochrome is utilized for transfer of
electrons, but in the reverse direction. The B subunit in Ddh donates electrons
to the membrane-bound photochemical center, mediated by the soluble
cytochrome c2 (McDevitt et al., 2002; Creevey et al., 2008). Figure 1 illustrates
different electron transfer pathways in anaerobic respiration.
Figure 1 Electron transport in anaerobic respiration, proposed for D. agitata, D. aromatica, P.
denitrificans and T. selenatis. The gray arrows show the direction of electron transfer suggested for
D. agitata, D. aromatica, P. denitrificans (napC/NirT) and W. succinogenes (Nap GH). In T. selenatis
electrons are transferred through the bc1 complex to selenate reductase via a soluble cytochrome c,
as illustrates by black arrows.
13
In the perchlorate-reducing bacteria D. agitata and D. aromatica a NapC/NirTtype cytochrome gene was found, suggesting that a membrane-bound
cytochrome acts as the link between the quinone pool and the periplasmic
perchlorate reductase (Bender et al., 2005). In an earlier investigation we tried to
identify a gene for a NapC/NirT-like protein in I. dechloratans by touchdown
PCR, using degenerate primers based on conserved features of the NapC/NirT
proteins. Such a gene, however, was not found (unpublished, 2004). Using the
same primers we searched for a candidate in A. oryzae strain Gr-1 and obtained
a gene product which showed nucleotide sequence similarity (69 %) to a
NapC/NirT-type cytochrome gene in D. aromatica (unpublished, 2007/2008.)
I. dechloratans is classified as a facultative anaerobe, but does in fact never grow
on chlorate in strictly absence of oxygen. Decomposition of chlorite results in
formation of molecular oxygen, which further can be utilized as electron
acceptor by terminal cytochrome c oxidase. Malmqvist et al. have shown that I.
dechloratans is cytochrome c oxidase positive (1994), suggesting an electron
transport chain containing a bc1-type complex transferring electrons from the
quinone pool to terminal cytochrome c oxidase mediated by a soluble
cytochrome c. Several varieties of the latter occur in bacterial respiration. One
classic heme-copper oxidase is the aa3-type. Another oxidase is the cbb3-type,
which has an exceptional high affinity for oxygen (Preisig et al., 1996) and is
therefore more often expressed in bacteria growing in microaerophilic
environments. The cbb3 oxidase can be identified by characteristic spectral
changes, induced by CO-binding (Pitcher et al., 2002). This has been done with
I. dechloratans membrane, and the result strongly indicated presence of cbb3
oxidase (unpublished, 2004).
1.5 c-type cytochromes
Many different types of c cytochromes occur in bacteria as electron carriers.
They are characterized by covalently bound heme as a prosthetic group. Heme
consists of a Fe-atom coordinated to four nitrogen atoms of a porhyrin ring.
The Fe atom is the redox component, either in the reduced ferrous [Fe (II)] or
in the oxidized ferric [Fe (III)] state. The heme-group is attached to the protein
by two thioether linkages. These are formed by reaction of the vinyl groups of
heme with two cysteine residues within a CXXCH sequence motif (Kranz et al.,
14
1998) of the polypeptide chain, as shown in figure 2a. The fifth ligand of the
heme iron is always a histidine residue. Several types of c cytochromes are
classified according to their binding of the sixth ligand. Class I (e.g. low-spin
soluble cytochrome c of mitochondria and bacteria) have a methionine residue
occupied as the sixth ligand. The class II subgroup, divided into class IIa and
IIb, includes the high-spin cytochrome c' (IIa), but also a number of low-spin
cytochromes (IIb) (e.g. cytc556). Class IIa (cytochrome c') is either penta- or
hexacoordinated and only small ligands (e.g. CO, NO or CN-) can be attached
to the free position of the iron ion in the former case (Kintner & Dawson
1991).
(a)
(b)
Class I
Class IIa
Figure 2 (a) The prosthetic group of heme c consists of a central Fe ion, coordinated to four nitrogen
atoms of a porphyrin ring. (b) Hexacoordinated cytochrome c (class I) with the fifth and sixth binding
site attached to His and Met respectively. Pentacoordinated cytochrome c' (Class IIa).
15
In bacteria, cytochromes of c-type are often found in the periplasmic space
where they are connected to the respiratory components of the cytoplasmic
membrane, acting as electron carriers. They can either be parts of multisubunit
enzyme complexes or occur as mobile electron shuttles (Thöny-Meyer, 1997).
Cytochromes exhibit three characteristic absorption bands, designated alpha(α), beta- (β) and Soret-band. In oxidized form the alpha- and beta-bands are
broad whereas the reduced form shows three distinct peaks, as shown in figure
3. Different types of cytochromes can be identified on the basis of the position
of their alpha band in the region 550 – 610 nm (Nicholls & Ferguson, 2002).
For c-type cytochromes the maximum of the alpha band is usually found
between 550 – 557 nm, whereas the maximum for b-type is between 555 – 565
nm (Thöny-Meyer, 1997).
Figure 3 The characteristic spectra of cytochrome c, class I, (here from horse heart), in oxidized
(dashed) and reduced (solid) state. In the reduced spectrum there is a shift in the Soret-band and the
α- and β-bands appear as distinct peaks at 551 and 521 nm respectively.
16
The aim of the present work is to investigate the scenario that electron transfer
in I. dechloratans is mediated by one or several soluble c-type cytochromes. In this
case, electrons are expected to be passed from the quinone pool to a soluble c
cytochrome by a membrane-bound bc1 complex. This hypothesis was based on
the apparent absence of a NapC/NirT-gene in I. dechloratans and the similarity
between chlorate reductase and Ddh in R. sulfidophilum and Ser in T. selenatis.
Soluble c-type cytochromes were extracted from the periplasm of I. dechloratans
(paper I) and two different monoheme proteins have been purified and
investigated (papers III and VI). One of the cytochromes is a 9 kDa member of
the subgroup class I (paper III). The other cytochrome is a homotetramer
consisting of four 13 kDa subunits and is characterized as a class II or
cytochrome c' (paper IV). Further, a gene encoding a candidate c cytochrome
has been expressed heterologously (paper II). This gene is associated with the
gene cluster for chlorate reduction.
We can demonstrate that the 9 kDa soluble c-type cytochrome is able to
mediate the electron transfer between the membrane-bound components and
the soluble chlorate reductase (paper III). This ability could not be
demonstrated for neither the recombinant c cytochrome (paper II) nor the
cytochrome c' (paper IV) and the role of their participation in the chlorate
metabolism remains to be clarified. The gene product of the cytochrome c gene
associated with the gene cluster for chlorate reduction (paper II) was not found
in the periplasmic extract.
17
2. Methods used in present study
2.1 Analysis of periplasmic c cytochromes
2.1.1 Separation
A common technique for analytical separation of proteins is sodium dodecyl
sulphate polyacrylamide gel electrophoresis, SDS-PAGE using discontinuous
buffer systems. Proteins denatured by SDS are separated in a polyacrylamide gel
and the migration of the protein is a function of its size. In a discontinuous
system, introduced by Ornstein, L. and Davis, B.J. (1964) and adapted by
Laemmli (1970), the gel and running buffer consists of different ions and, most
commonly, a discontinuous pH. In the Laemmli buffer system the stacking-gel
buffer (pH 6.8) contains chloride ions and the running buffer in the upper
reservoir consists of glycine, which has a low net charge and low effective
mobility at pH 6.8. NuPAGE® Bis-Tris Discontinuous Buffer System
(Invitrogen) is a modified system where the gel buffer (pH 6.4) contains
chloride and the running buffer (pH 7.3-7.7) contains MES (2-(N-morpholino)
ethanesulfonic acid). Bis-tris is the common counter-ion present in both geland running buffer. The combination of pH results in an operating pH of 7
during electrophoresis which improves the protein stability, resulting in sharper
bands and better resolution. MES buffer is optimal for resolving small
molecular weight proteins, due to its fast ion migration. When using 4-12 %
bis-tris gels and MES SDS running buffer, the separation range for proteins is
between 2.5-200 kDa compared to the Laemmli tris-glycine system which needs
18 % gels to resolve low molecular weight proteins (NuPAGE® Technical
Guide, Invitrogen). In a variation of the method, proteins can be separated
under non-denaturing conditions. Blue native gel electrophoresis is a technique
in which the proteins obtain a negative charge by using Coomassie G-250 as a
charge-shift molecule, instead of SDS (Schägger & von Jagow, 2004).
Proteins in the same molecular weight range can be distinguished by their
different isoelectric point (pI), using isoelectric focusing (IEF). The pI is the pH
at which a protein has a neutral net charge and thus, no migration in an electric
field. The combination of IEF and SDS-PAGE, referred as two-dimensional
gel electrophoresis, is widely used for analysis of complex protein mixtures. In
the first dimension IEF is performed using an immobilized pH gradient (IPG).
When proteins are loaded on to a gel strip, a voltage is applied to the system
and the proteins will migrate in the pH gradient until its net charge is zero.
18
After the complete focusing, the gel strip is sealed on to a conventional
polyacrylamide gel and SDS-PAGE is performed as described above. The
proteins will migrate into the second dimension gel from different horizontal
positions, according to their migration in the first dimension. Thereby, proteins
with same molecular weight but different pI can be separated using this method
(Bjellqvist et al., 1982).
2.1.2 Detection
Proteins containing heme can be detected after SDS-PAGE by using a staining
procedure relying on the peroxidase activity of the heme group (Thomas et al.,
1976). The heme-catalyzed reaction between 3, 3’, 5, 5’-tetramethylbenzidine
(TMBZ) and hydrogen peroxide results in the formation of a deep blue color.
Cytochrome c, in which the heme group is bound covalently by thioether
bonds, is readily detected on SDS-PAGE gels using this method.
Agents used for reduction of disulphides (such 2-mercaptoethanol or DTT)
may affect the coordination state of the heme and either stimulate or inhibit
peroxidase activity (Dorward et al., 1992). Therefore, reducing agents are
specifically omitted from the samples in the electrophoresis. In most cases,
non-covalently bound heme is released from proteins by the denaturation with
SDS, but incomplete denaturation can occur. Consequently, one complication is
that other cytochromes than the c-types may be visualized by heme staining.
Another problem is the possibility of non-specific binding of released heme to
other proteins, resulting in a false signal (Thomas et al., 1976).
2.2 Mass spectrometry
For analysis of larger proteins, peptides can be generated by the enzyme trypsin,
which catalyzes the hydrolysis of peptide bounds. Trypsin cleaves peptide
bonds in which the carbonyl group is contributed by either an arginine or lysine
residue. In-gel digestion is a method for enzymatic cleavage of proteins in
polyacrylamide gels, after SDS-PAGE (Rosenfeld et al., 1992). After protein
identification by staining, the protein band is excised from the gel and destained
19
by ethanol/NH4HCO3. Small gel pieces are incubated with trypsin and peptides
are extracted from the gel pieces by trifluoroacetic acid. The resulting peptides
can be further analyzed by using various mass spectrometry (MS) techniques.
To accomplish mass analysis, the molecules need to be ionized and in gas-phase
state and there are several methods to achieve ionization. One of the methods
in the present work is Matrix Assisted Laser Desorption/Ionization (MALDI)
where the sample is mixed with a matrix compound, capable of absorbing UVlight (Karas & Hillenkamp, 1987). The matrix will absorb energy from a laser
beam and the embedded peptides are transferred to the gas phase and ionized
by protonation. Another method is Electro Spray Injection (ESI) where an
acidic aqueous solution containing peptides or small proteins is sprayed trough
a needle and a high positive voltage is applied. This high voltage produces a
cone-shaped drop (Taylor cone) at the end of the needle, from which small
drops (< 10 nm) are released as a spray. The solvent will be evaporated from
the small droplets by heat, leaving protonated and multiply charged ions in the
gas phase (Sihlbom, 2006; de Hoffman & Stroobant, 2001).
For further analysis the ions need to be separated according to their masses.
The ions are separated by a mass analyzer according to their mass-to-charge
ratio (m/z). There are several types of mass analyzers based on different
principles. TOF is an analysis method, often in combination to MALDI, where
strong electric field is applied and the ions accelerate, followed by travel in a
field-free flight tube. The flight time to reach the MS detector is proportional to
the square root of the m/z ratio (Guilhaus et al., 2000). Another method, used
in the present work, is a combination of linear trap quadrupole (LTQ) mass
spectrometer and an Orbitrap mass analyzer (LTQ-Orbitrap). Ions from the
ionization source are trapped into a quadrupole made up by four parallel
hyperbolic rods and when the ions collide with an inert gas, they slow down
and will be accumulated at the end of the quadrupole. Pulses of ions are then
injected into the Orbitrap for mass analysis (Hu et al., 2005). The masses
obtained by mass spectrometry can be compared to predicted masses of
peptides or whole proteins, by data base search. Combination of liquid
chromatography (LC) and MS produces efficient separation and sensitive
identification of peptides and proteins, especially when the sample is a complex
mixture of several proteins (Mann & Pandey, 2001).
20
To obtain more specific information of a single peptide, tandem mass
spectrometry (MS/MS) can be used. This is an instrument consisting of two MS
analyzers where a single peptide ion can be selected out of the spectrum
obtained from the first mass spectrometer. This peptide ion is further
fragmented by collision with inert gas and the fragments are separated by the
second mass spectrometer. Cleavage at the peptide bond is the most common
mode of fragmentation and the resulting ions, in this case called b- and y- ions,
retain their charge on the N or C terminus, respectively. Fragmentation is
random and the process generates a series of fragments, differing by a single
amino acid residue (Mann et al., 2001). In case of unknown proteins, with no
corresponding sequences in data bases, fragmentation is the only possibility to
obtain information about the protein. It is possible to reconstruct the sequence
of a single peptide by studying its fragmentation pattern. This method, called de
novo peptide sequencing, is based on knowledge about peptide decomposition
mechanisms (Cañas et al., 2006).
2.2 Protein purification
The isolation and capture of one particular protein from a complex mixture of
several proteins, (e.g. periplasmic extract of bacteria) practically always includes
more than on step. The choice of purification methods is depending on several
factors, for example the condition of the starting material and the characteristic
of the target protein. It is also important to consider the goal of the
purification. Sometime the purity is the most important aspect, but the yield can
also be the more central priority. To achieve both aspects, it is important to
design and optimize the purification steps by a well-chosen approach (Protein
Purification Handbook). The protein purification described in present thesis
involves chromatographic techniques combined in different order, depending
on the target protein.
One method is Ion Exchange Chromatography (IEX), based on different net
surface charge of proteins at a given pH. A column is packed with charged
stationary phase (matrix) and the proteins with opposite net surface charge will
bind to the surface of the IEX matrix. The pH and the ionic strength of the
buffer is selected to provide a protein-matrix interaction to ensure binding of
the target protein when the sample is loaded on to the column. The proteins
21
bound to the column can be eluted by changing the buffer condition by alter
ionic strength or pH of the buffer. Usually proteins are eluted by adding salt
ions (often Na+ or Cl-) which compete with the bound proteins for the charge
of the matrix. It is important to reduce ion strength in the sample before the
application on to the column. Otherwise the ions in the sample will prevent
binding of the proteins.
Another method is Hydrophobic Interaction Chromatography (HIC) which
separates proteins according to difference in surface hydrophobicity. The
column is packed with a porous material composed of ligands containing alkyl
or aryl groups. In high concentration of salt (usually 1-2 M ammonium sulphate
or 3 M sodium chloride) hydrophobic proteins interact with the packing bed
and the elution is achieved by decreasing the salt concentration. This method is
a suitable step if the sample is at high salt concentration, e.g. after a salt
precipitation.
Separation can also be based on the size of the proteins by Gel Filtration (GF).
The column is packed with a porous matrix of spherical gel particles. When a
protein mixture is applied, small proteins can diffuse in and out of the gel
particles whereas large molecules move down in the column as the buffer is
pumped through the system. Thus, smaller proteins will have longer distance to
move and are retained longer in the column. This separation method is often
used as a final polishing step.
The methods described above are applicable to all proteins. In addition, there
are several methods based on specific protein features. One example is
immobilized metal ion affinity chromatography (IMAC), often used for
proteins expressed with an N- or C- terminal poly-His extension (paper II).
Histidine has high affinity for metal ions (e.g. Ni2+) immobilized on the column
matrix. The protein is eluted by increasing concentration of imidazole, which
competes with proteins for binding.
22
3. Results and discussion
The aim of the present study was to elucidate the route of electron transfer
between the inner membrane and the periplasmic chlorate reductase. Soluble c
cytochromes have been isolated from I. dechloratans by extraction of periplasm
from the cells (paper I) and purified and characterized (paper III and VI). Also,
a gene encoding a candidate soluble c-type cytochrome, located in association
with the gene cluster for chlorate reduction, was cloned and expressed
heterologously (paper II).
3.1 Native periplasmic c cytochromes in Ideonella dechloratans [Paper I]
Periplasmic proteins were extracted from chlorate-grown I. dechloratans by
osmotic lysis. The periplasmic extract was first reduced by dithionite and then
exposed to chlorate in the presence of chlorate reductase. Spectrophotometric
analysis showed a sharp peak at 551 nm, indicating reduction of c-type
cytochromes. After addition of chlorate partial reoxidation of the cytochromes
was observed, demonstrated the presence of at least one soluble c cytochrome
capable of supplying electrons for chlorate reduction.
In order to identify c cytochromes the extracted proteins were separated by
SDS-PAGE and stained by the heme-detecting procedure, described in section
2.1.2. Several bands were observable and the result is shown in figure 4. Since
the soluble forms of c-type cytochromes usually occurs in the range 8-14 kDa
(Thöny-Meyer, 1997) further attention was focused on proteins with molecular
weights in that range. Five candidate c cytochromes, with apparent molecular
weights of 20-, 10-, 9-, 8-, and 6 kDa, were observed. The ones most abundant,
according to the heme staining, were the 10- and 6 kDa cytochromes. Among
the minor components, the bands at 8 and 9 kDa were not always observed. As
discussed below, it appears that the 8 kDa protein derives from the 9 kDa
cytochrome. Several high-molecular weight proteins with low stain intensity
were visible, but this could be an artifact caused by unspecific binding of heme
or by incomplete denaturation, as discussed in section 2.1.2.
23
kDa
188
98
62
49
38
28
17
20
14
10
9/8
6
6
3
Figure 4. Periplasmic cytochromes separated by SDS-PAGE (NuPAGE™). Lane 2 shows hemestained proteins in the range 20-6 kDa. SeeBlue® Plus2 Pre-Stained Standard is used as marker in
lane 1.
For further investigation, an attempt was made to fractionate the c
cytochromes. Using ion-exchange chromatography, we were able to obtain one
fraction containing the 6 kDa cytochrome, one fraction containing the 10 kDa
cytochrome, and a flow-through fraction containing all cytochromes except the
10 kDa.
The redox activities of the partially fractionated cytochromes were investigated
with periplasmic extract or cell homogenate as sources of catalyst. The latter
serves as a source for both chlorate reductase and membrane-bound
components of the respiratory chain, including the terminal oxidase. Reduction
of chlorate is expected to result in production of oxygen due to decomposition
of chlorite by chlorite dismutase. Therefore, chlorate-dependent oxidation of
cytochromes observed when membrane-bound components are present can be
due to electron transfer to both chlorate and oxygen. Periplasmic extract,
lacking membrane-bound oxidase, was used for investigation of the chloratedependent oxidation in the flow-through fraction which contained a mixture of
several cytochromes.
The cytochromes in the different fractions were first reduced by a slight excess
of dithionite. Then, oxidant (chlorate or oxygen) was added and the UV/VISspectra were recorded in the region 450-650 nm. Table III summarizes the
24
results obtained. The 6 kDa cytochrome was completely reoxidized by both
chlorate and oxygen in the presence of cell homogenate. This result suggests
that the cytochrome is able to donate electrons both to chlorate reductase and
to terminal oxidase. The spectrum obtained from the fraction containing the
10-kDa cytochrome showed two peaks at 552 and 558 nm respectively. When
oxygen was added, spectral changes dominated by a decreased absorbance at
558 nm occurred. This suggests reoxidation of a heme b-containing component.
As the spectral change appears dominated by the 558-nm component, it is
difficult to interpret the reoxidation of the 552-cytochrome c component. No
spectral changes were observed after addition of chlorate.
In the periplasmic extract, partial reoxidation was observed after the addition of
chlorate as judged by the decrease at 551 nm. Also, in the flow-through
fraction, a complete reoxidation was observed when a catalytic amount of
periplasmic extract was used as source of chlorate reductase. No terminal
oxidase was present. The extent of reoxidation in both cases were about 40%,
which most likely can be accounted for by the major 6 kDa cytochrome since
this component was shown to donate electrons to chlorate reductase. In
presence of cell homogenate, the flow-through fraction was completely
reoxidized both by addition of chlorate and oxygen. This suggests that
components which were not oxidized by chlorate can be oxidized by oxygen,
produced as the result of chlorite dismutase activity, in presence of terminal
oxidase. Taken together, these results suggest the minor components (that give
rise to the band at 8-, 9-, and 20 kDa) as candidates as electron donors to the
terminal oxidase but most likely not to chlorate reductase. However, the
individual roles of these cytochromes cannot be assigned.
Table III Reoxidation of dithionite-reduced fractions with different oxidants, as judged by decrease of
absorbance at 551 nm.
Substrate
Clr-source
Oxidant
Chlorate
Oxygen
Flow-through fraction
Periplasmic extract
Cell homogenate
6 kDa
Cell homogenate
partial (40 %)
complete
complete
complete
complete
complete
25
For further investigation of the c cytochromes peptides were generated by
trypsin in-gel digestion of bands excised from SDS-PAGE gels. Mass
spectrometric analyzes of peptides were performed by MALDI-TOF MS and
MS/MS. One of the peptides from the 6 kDa cytochrome was identical in
mass-to-charge ratio (m/z = 1094.56) to that predicted for the sequence
YAGQKDAVDK from a cytochrome c (class I) in Acidovorax avenae subsp.
citrulli AAC00-1, [YP_969867]. A majority of the theoretical b- and y-ions,
expected from this fragment, could be matched to signals in the MS/MSspectrum. Further, the sequence KLVGPSQDVAAR was generated by de novo
from of a peptide with m/z = 1403.76. Also this sequence can be matched to
Acidovorax avenae subsp. citrulli, [YP_969867] located next to YAGQKDAVDK
(1094.56). Furthermore, the sequences show similarity to sequences in three
different cytochrome c (class I), of the chlorate reducer Dechloromonas aromatica.
For the 8- and 9 kDa proteins, no matches were obtained from database
searches. However, the presence of same peptide masses in digest obtained
from these proteins supports the suggestion that the 8 kDa is a degradation
product of the 9 kDa cytochrome. Several of the peptides obtained from the 10
kDa band were, unexpectedly, identified as originating from chlorite dismutase,
suggesting contamination by degradation products of this protein.
3.2 Characterization of a candidate cytochrome c gene associated with
the gene cluster for chlorate respiration [Paper II]
In close proximity to the gene cluster for the chlorate reduction, downstream
from the C subunit of chlorate reductase, two open reading frames were found
by further sequencing of a clone from the GenomeWalker™ library (Karlsson
& Nilsson, 2005). In the ORF closest to the C subunit, the highly conserved
heme-binding motif CXXCH was found in the corresponding translated amino
acid sequence. This finding suggests a gene encoding c-type cytochrome. The
sequence showed similarity to soluble c cytochromes, class I, in Pfam database
and by BLASTP search. The hydrophobic N-terminal sequence is suggested by
SignalP to be a 19-residue signal peptide, and the molecular weight of the whole
apoprotein is predicted to 10,9 kDa after processing. The second ORF further
downstream was identified as a mobB gene encoding a protein functional for the
maturation of molybdopterin as a co-factor for chlorate reductase A subunit.
26
Figure 5 shows comparison of the gene cluster for chlorate metabolism in I.
dechloratans with the corresponding genes in other chlorate reducers. In addition
to those discussed in paper II, this includes the gene arrangement in A.
denitrificans which was described recently (Weelink et al., 2008). This bacterium is
able to degrade benzene under anaerobic conditions in conjunction with
chlorate reduction. The oxygen produced in the degradation of chlorate is
rapidly reduced by the oxidation of benzene. The organization of the gene
cluster for chlorate reduction in A. denitrificans is very similar to that of I.
dechloratans. This cluster includes genes encoding both mobB (YP_004124055)
and a c-type cytochrome, class I (YP_004124056.1) with 100 % identity of the
nucleotide sequences compared to I. dechloratans. Also, the genes encoding, clrB,
and clrD show 100 % identities, but for clrA, clrC, and cld the identity are 99%.
Comparison of the 16S rRNA from both organisms shows 92 % identities,
which excludes the possibility that I. dechloratans and A. denitrificans is the same
organism. Most likely, this similarity of the gene cluster for chlorate metabolism
is caused by lateral gene transfer. However, there are small differences between
the clusters. There is a larger distance between cytC and clrC in A. denitrificans
compared to I. dechloratans. Furthermore, the region between cld and clrA lacks
the insertion element ISIde1, which is located in this region in I. dechloratans.
Figure 5 Comparison of the gene cluster for chlorate metabolism in I. dechloratans, A. denitrificans,
D. aromatica and D. agitata. The sequence downstream pcrD in D. agitata is not known.
27
The results presented in paper I suggest an electron transfer route where
soluble c-type cytochromes serve as mediators. A 6 kDa c cytochrome was
shown to serve as electron donor to chlorate reductase, whereas a 10 kDa
protein did not. However, none of the peptide masses or sequences obtained
from the soluble periplasmic c cytochromes in paper I matched the predicted
sequence of the gene above. In order to assess the role of this gene in chlorate
reduction, the gene was expressed heterologously and the resulting protein was
investigated. The gene, excluding the part encoding the 19-residue signal
peptide, was amplified by PCR and the product was ligated into the expression
vector pET-26b. This vector contributes a pelB leader for export to the
periplasm and a C-terminal six-residue His-tag for subsequent purification by
IMAC. The construct was co-transformed with plasmid pEC86, which includes
the cytochrome c maturation system (ccm), into the E. coli expression host
BL21(DE3). The use of the ccm genes was based on the finding that E. coli
expression hosts usually not express c cytochromes under aerobic conditions
(Thöny-Meyer et al., 1996). For the purpose of synthesizing active holo-c-typecytochromes the heme needs to be attached to the apo-protein after export to
the periplasm, which is done by the ccm system.
In transformant BL21(DE3), the target protein was produced at high level but
it was not exported as apo-protein into the periplasm. Instead, insoluble
inclusion bodies were found in the cytosol, lacking the heme-group. In E. coli
NovaBlue(DE3) the construct generated a very low yield of the recombinant c
cytochrome. From these results we decided to produce inclusion bodies for
purification, refolding, and heme reconstitution. The inclusion bodies were
solubilized with urea and the protein was purified in the denatured state by
IMAC. After refolding, reduced heme was added to the protein in the ratio 1:1.
The incorporation of heme was followed spectrophotometrically. At first it was
detected by the appearance of a distinct peak in the α-band at 556.5 nm,
indicating a b-type cytochrome, but within seven days the α-peak was shifted to
553 nm. The formation of covalently bound heme, with two thioether bonds
produced, was confirmed by pyridine hemochrome analysis (Berry &
Trumpower, 1987). The pyridine hemochrome showed a peak in the α-band at
551 nm, which is characteristic for c-type cytochromes.
28
The recombinant cytochrome was investigated by peptide mass fingerprinting
using MALDI-TOF MS, as in the previous paper I. Peptides from the
recombinant c cytochrome could be identified and verified (by MS/MS) with a
coverage of 56 % of the amino acid sequence.
Spectrophotometric studies of the redox activity were performed using the
same approach as for the native proteins, described in paper I. The reduced
form of the recombinant cytochrome c did not reoxidize after addition of
chlorate in presence of chlorate reductase. This result suggests that the gene
product does not serve as an immediate electron donor for chlorate reductase.
However, we cannot exclude that the inability of donating electrons for
chlorate reduction is a result of incorrect refolding or incorporation of heme.
Since the protein was very sensitive to air oxidation, we were not able to test
enzyme-dependent reoxidation by oxygen.
3.3 Purification and characterization of soluble cytochrome c capable of
delivering electrons to chlorate reductase in Ideonella dechloratans
[Paper III]
In the periplasmic extract of I. dechloratans, there is at least one soluble
cytochrome c capable of serving as electron donor to chlorate reductase in the
chlorate reduction reaction (paper I). This paper deals with the purification of
cytochrome c-Id1, denoted as the 6 kDa cyt c in paper I.
If the knowledge of the target protein is limited, the standard protocol for a
Tree Phase Strategy of chromatography techniques is the use of IEX as a
starting step, followed by HIC and GF (Protein Purification Handbook). The
use of IEX is suitable when the sample has low ionic strength, as the case of
periplasmic extract. c-type cytochromes usually have a high pI (~10), which
consequently leads to the choice of a cation exchange column. However, in the
attempt to separate the cytochromes into single fractions in paper I, this
cytochrome did not bind sufficient to the column matrix, but was eluted as a
delayed flow-through fraction.
In the purification of chlorite dismutase (Stenklo et al., 2001) we have earlier
observed the elution of a c-type cytochrome slightly before chlorite dismutase
29
during HIC. Due to the unsuccessful attempt to purify the cytochrome by IEX,
we tried to start with HIC as was preceded by ammonium sulfate precipitation,
as described previously (Stenklo et al., 2001). The collected fractions containing
the desired cytochrome, together with a majority of chlorite dismutase, were
pooled and further applied on to a gel filtration column and pure cytochrome c
was eluted using sodium phosphate at a very low flow rate. The overall yield
was poor, about 0.18 mg from an 8-L culture, but the purity was satisfactory, as
shown in figure 6. The heme content was estimated to 0.9 mol mol-1 protein by
pyridine hemochrome analysis and the absorption maximum of the reducedminus-oxidized difference spectrum of 549.7 nm, confirms the notion of a ctype cytochrome.
(a)
(b)
Figure 6 SDS-PAGE of the fractions collected from gel filtration, stained with TMBZ (a) and
Coomassie Brilliant Blue (b). The arrows indicate the fractions of the purified cytochrome c-Id1.
To determine the accurate molecular weight of the protein with the apparent
molecular weight of 6 kDa (according to SDS-PAGE) a sample of the protein
was analyzed by MS (Proteomics Core Facilities, Göteborg) with 9.4 kDa as the
result. To confirm the identity of the protein, tryptic peptides from in-gel
30
digestion were analyzed by MS/MS. The peptides KLVGPSYQDVAAR (m/z
=1403.76) and YAGQKDAVDK (m/z = 1094.56) described in paper I, were
also detected from this digest. Furthermore, peptides with the suggested
sequences AVDQYSPGV (m/z =1276.76) and APNAQALATSK (m/z =
1071.57) was identified by de novo sequencing. These masses have been obtained
earlier and are listed in table 1 (paper I) with the exception of the difference of
one mass unit, for the peptide 1276.76. The difference can be a result of
protonation/de-protonation of the peptide. None of these sequences resulted
in any identity or similarity of other c-type cytochromes from data base search.
The redox midpoint potential of the cytochrome c-Id1 was estimated to 0.261
V. The value for midpoint potential at pH 7 of the chlorate/chlorite couple was
calculated to 0.708 V, which is considerably higher and thereby makes chlorate
as a thermodynamically favorable acceptor in the electron transfer between
cytochrome c-Id1 and chlorate, catalyzed by chlorate reductase.
For kinetic study of the reaction, chlorate reductase was purified as previously
described (Danielsson Thorell et al., 2003; Karlsson & Nilsson, 2005).
Dithionite-reduced cytochrome c was mixed with a catalytic amount of purified
chlorate reductase. When chlorate was added, the chlorate-dependent oxidation
was studied by recording spectra at 1 min intervals. The amount of cytochrome
c was varied in the range 0.6 - 4 µM. First-order reactions were observed for all
concentrations of cytochrome c, and initial rates increased linearly with the
substrate concentration. We were not able to calculate a KM value since this
seemed to be substantially higher than the highest substrate concentration of 4
µM. The poor yield of the cytochrome lead to very limited supply of substrate.
From the results we could calculate a kcat/KM value of 7×102 M-1s-1, but this
value is probably underestimated since chlorate reductase loses activity during
purification (Danielsson Thorell et al., 2003).
In a study by Creevy and coworkers (2008), the interaction between
cytochrome c2 and DMS dehydrogenase of R. sulfidophilum was investigated, and
a KM value of 21 µM was obtained. DMS dehydrogenase and chlorate reductase
of I. dechloratans is close relatives, and it is of interest to compare the kinetic
behavior in the case of R. sulfidophilum with that observed in present study. The
observation with chlorate reductase is consistent with a KM value in the same
range, observed for DMS dehydrogenase. An explanation of a high KM value
could be a low affinity as a result of fast off-rate for the substrate, or a fast
31
electron transfer subsequent to substrate binding. To get a more clear
understanding of the reaction mechanism between the cytochrome c-Id1 and
chlorate reductase, a more detailed kinetic characterization is required.
However, the present study confirms the observation of a soluble cytochrome c
as electron donor to the periplasmic chlorate reductase in the reduction of
chlorate. This is similar to the electron transfer routes reported for DMS
dehydrogenase in R. sulfidophilum and selenate reductase in T. selenatis (Creevey et
al., 2008; Lowe et al., 2010), but different from that suggested in the
(per)chlorate respiring bacteria Dechloromonas species and A. oryzae strain GR-1
(Bender et al., 2005).
3.4 Purification and characterization of a cytochrome c' in the chlorate
respiring bacterium Ideonella dechloratans [Paper IV]
In paper I and III, we concluded that the soluble cytochrome c- Id1 serves as an
electron carrier, capable to deliver electrons in reduction of both chlorate and
oxygen. According to heme-stained SDS-PAGE there is one additional major c
cytochrome present in the periplasmic extract, with an apparent molecular
weight of 10 kDa. The role of this cytochrome was not clarified in paper I.
However, a fraction enriched in this component did not appear to serve as
electron donor for chlorate reduction. On the addition of oxygen, spectral
changes were observed but could have been due to the oxidation of other
heme-containing components, also present in the fraction. The present paper
deals with the purification and characterization of the presumed 10 kDa c-type
cytochrome, in order to clarify its function and to investigate the possibility that
this protein is a product of the cytochrome c gene characterized in paper II.
In paper I we observed that the 10 kDa cytochrome was retained on a cation
exchange column at acidic pH. To get further information of the pI and the
occurrence of other heme containing proteins in this region, the periplasmic
extract was analyzed by 2-dimensional IEF-SDS-PAGE, followed by heme
staining. The isoelectric point of c-type cytochromes is generally high (~10) and
thus an IPG-strip with pH in the range 9-12 was used. The result is shown in
figure 7. Heme staining components with apparent molecular weights at 6- and
10 kDa are clearly visible, confirming that these are the major components. In
32
this case, the sample loading is too low to detect the minor components
discussed in paper I.
Figure 7 Analysis of the periplasmic extract with 2D IEF-SDS-PAGE, followed by heme staining.
For further purification of the 10 kDa cytochrome c, a cation exchange column
was chosen as the initial step. Periplasmic extract was dialyzed against starting
buffer, applied to a HiTrap SP FF column and heme-containing proteins were
eluted by increasing concentration of NaCl. The second purification step was
performed by hydrophobic interaction chromatography resulting in improved,
but not sufficient purity. A substantial amount of chlorite dismutase and several
non-heme proteins in the range 35-60 kDa were still present. In most cases, a
polishing step by gel filtration would be preferred as a following purification
step. However, we have observed that the target protein was eluted together
with other proteins with molecular weights of 30-50 kDa. Instead, we used a
strong cation exchange column (Mono S HR). With very shallow gradient of
increasing NaCl the purity of the target protein was sufficient. The purification
is summarized in figure 8, with the final result shown in lane 6.
33
Figure 8 The Coomassie-stained SDS-PAGE as a summary of the purification. Lanes: (1)
Novex®Sharp Pre-Stained Protein Standard, Invitrogen, (2) periplasmic extract, (3) periplasmic
extract after dialysis, (4) pooled fractions from the first ion exchange chromatography step, (5)
pooled fractions from the hydrophobic interaction chromatography step, (6) pooled fractions from the
second ion exchange chromatography step (MonoS)
Figure 9 shows optical spectra of the purified protein. These are characteristic
for c-type cytochromes class II, also referred to cytochrome c'. They contain
pentacoordinated heme in the high-spin state (Weiss et al., 2006; Barbieri et al.,
2008). In the oxidized state at neutral pH a distinct peak at about 640 nm is
observed, indicating a high-spin heme, and the Soret band at 401 nm exhibits a
shoulder at about 377 nm, as shown in figure 9 A. In the reduced state the
Soret band exhibits a maximum at 428 nm with a shoulder at 435 nm. At pH 9
the maximum shifts to 407 nm with the shoulder at 371 nm in the oxidized
state, figure 9B.
Cytochromes c' are found in a variety of bacteria with different kinds of
metabolism but its function is, with a few exceptions, not well understood. In
Methylococcus capsulatus Bath, it has been demonstrated that a low-spin
cytochrome c' acts as an electron carrier (Weiss et al., 2006) and in Rhodobacter
capsulatus PSA100, it is shown that cytochrome c' protects the bacterium against
NO by binding NO as a sixth ligand (Cross et al., 2000).
34
Figure 9 (A) Optical spectra of the purified cytochrome c in the oxidized (solid line) and reduced
(dashed line) state at neutral pH. (B) Optical spectra in the oxidized state at pH 9.
35
In order to clarify whether this cytochrome participates in electron transport
during chlorate respiration, a slight excess dithionite was added to a nitrogenflushed mixture containing the purified protein and cell homogenate. Addition
of chlorate did not produce any spectral changes. Addition of oxygen led to
oxidation, as judged from the spectrum. However, this spectral change was
observed even in absence of cell homogenate, indicating an uncatalyzed
reaction with oxygen. Accordingly, we cannot evaluate a possible function as
electron donor for terminal oxidase. However, we conclude that this
cytochrome c' does not serve as electron donor for chlorate reductase.
For further characterization, a more accurate molecular weight analysis of the
SDS-PAGE was performed, resulting in 13 kDa for a monomer. Using Blue
native PAGE followed by heme staining, a molecular weight of 55 kDa was
found for the native form of the protein. These results suggest that the native
form of the protein is a homotetramer. Most class II c cytochromes described in
the literature appear as mono- or dimers. A tetrameric protein in this family has
not been reported earlier. The heme content was found to be 1.0 mol/mol
protein, by pyridine hemochrome analysis.
De novo sequencing of tryptic peptides by mass spectrometry gave peptide
sequences AGNXDQXK or GAXNDQXK or QNXDQXK (X denoting I or
L in this case). None of these sequences does match the predicted sequence of
the cytochrome c gene located downstream from the chlorate reductase genes
(Paper II), excluding this gene as the source of the protein.
36
5. Conclusion
The aim of this study was to clarify the electron transport pathway in the
chlorate reduction in I. dechloratans, in particular the route between the
membrane-bound components and the periplasmic chlorate reductase. We have
demonstrated that electron transport is mediated by soluble electron carriers. A
c-type cytochrome with a molecular weight of 9.3 kDa denoted cytochrome cId1 is the major donor to chlorate reductase when cells are grown anaerobically
in presence of chlorate. This protein can also serve as donor for the reduction
of oxygen. The periplasmic extract contains several other minor hemecontaining proteins. According to their low concentration, it is difficult to
purify and investigate their function as electron donors. However, the result
described in paper I suggest that these proteins can serve as electron donors in
the reduction of oxygen by the membrane-bund terminal oxidase, but do not
deliver electrons to chlorate reductase.
Another major c cytochrome found in the periplasm was shown to belong to
the class II subgroup of c cytochromes, (cytochrome c'), containing high-spin
pentacoordinated heme. The function of this protein is not clear, but it does
not appear to serve as electron donor, at least not in the chlorate reduction. A
function as NO-protector, as have been suggested in denitrifying bacteria, does
not appear likely in I. dechloratans.
Furthermore, a gene found downstream from the gene encoding the C subunit
of chlorate reductase has been characterized. The gene was identified as a
soluble cytochrome c (class I) which is defined as a soluble electron transfer
protein. The gene was expressed heterologously for the purpose of investigating
its role as electron carrier in the chlorate reduction mechanism. However, the
reconstituted protein was not able to serve as electron donor to chlorate
reductase. We could not identify any product of this gene in the periplasmic
extract and thus, it appears likely that expression of this gene does not occur
under the present conditions. The significance of the location of this gene still
remains to be elucidated.
Since the anaerobic respiration involves production of molecular oxygen, the
reduction of both chlorate and the produced oxygen (with the overall reaction
ClO3- → Cl- + H2O as the result), requires transfer of six electrons. The
37
reduction of chlorate to chlorite is a two-electron reaction whereas reduction of
oxygen, produced by the subsequent decomposition of chlorite, requires four
electrons. This requires a branched electron pathway, with about one third of
the electrons serving as reductant for chlorate, and two thirds as reductant for
oxygen. Based on the results presented in this thesis, I suggest in figure 10 an
arrangement containing two branches. One is at cytochrome c-Id1 which can
serve as electron donor for both chlorate reductase and for terminal oxidase.
The presence of additional cytochromes, which can denote electrons to oxygen
but not to chlorate reductase, suggests a second branch point earlier in the
electron transport chain. In figure 10, this is depicted at the level of complex
III. With this arrangement, all six electrons required for the complete reduction
of chlorate pass through complex III and contribute to the formation of a
proton gradient across the cell membrane.
chlorate reductase
chlorite dismutase
ClO32e-
periplasm
A
B
ClO2ClCl
O2- 2
Cl-
4e-
O2
H2
O
Q
dehydrogenases
III
IV
V
e-
cbb3 oxidase
cytoplasm
Figure 10 The proposed electron-transfer pathways in Ideonella dechloratans.
(A) cytochrome c-Id1, (B) minor soluble heme-containing components.
38
6. Tack
Jag vill rikta stort och hjärtligt tack till min handledare Prof. Thomas Nilsson,
som har varit ett oersättligt stöd under min tid som doktorand. Din entusiasm,
men även ditt lugn har inspirerat och gjort att jag velat gå vidare i arbetet även
när motgångarna varit som störst. Tack!
Jag vill även rikta ett stort tack till mina biträdande handledare Birgitta
Sundström och Maria Rova. Birgitta, du har inte haft möjlighet att följa mitt
arbete så ingående men du har alltid tagit tig tid och engagerat dig när jag
behövt tips och råd. Dessutom har du varit ett stöd i din roll som avdelningens
prefekt. Maria, du är själv aktiv i projektet och har varit ett mycket bra stöd. Du
har i alla lägen ställt upp med både tid och råd på ett mycket lugnt och
pedagogiskt sätt. Tack till er båda!
Jan Bohlin, du var min doktorandkollega när jag började i projektet. Jag vill
tacka dig för att du tog emot mig som ny kollega på allra bästa sätt och för allt
samarbete i både med- och motgång. Med ett ständigt glatt humör tog du de
flesta problem med en axelryckning. Positivt tänkande ger energi. Tack Jan!
Det finns många på min avdelning som jag vill tacka, helt enkelt för att ni finns
där. Men det finns speciellt två personer som är värda ett särskilt stort tack,
nämligen Elisabeth Björk och Mikael Andersén. Ni är två klippor
(laboratorieingenjörer) som ställer upp med det mesta i alla lägen. Många
guldstjärnor till er!
Tyvärr är det några som inte längre är kvar eftersom ni har disputerat och (eller)
fått andra jobb. Jag tänker särskilt på Sandra, Rozbeh (Robban), Cecilia, Sofia,
Tina, Björn, Jeanette och Stina. Vi hade mycket roligt tillsammans och jag
saknar er verkligen. Robban, jag väntar fortfarande på en J.D. & S.A.
Alla ni andra som fortfarande ”plaskar omkring i Möckeln” om dagarna, tack
för att ni bidrar till att vi är ett trivsamt gäng. Särskilt vill jag nämna mina
närmsta doktorandkollegor Miriam, Hanna, Maria, Christina, Sara, Ola och
Alexander, samt doktorerna Gunilla, Patrik och Marcus. Jag vill tacka för allt
roligt vi haft ihop, men jag hoppas att vi ska få ha kul ihop ett tag till. För övrigt
ska ingen känna sig glömd. Tack alla på avdelningen!
39
Jag vill även tacka Prof. Jan van Stam. Tack var dig har jag under den senare
delen av min doktorandtid fått uppdraget att jobba halvtid som
Kemilektorslänk. Jag vill även tacka Kungliga vetenskapsakademien och
Ljungbergsfonden som gett mig uppdraget.
Till hela min familj; tack för att ni finns! Livet består ju tack och lov av mer än
bara bakterier och även om jag periodvis har varit väldigt upptagen av dessa
små ”baggar” är det ändå ni som gör livet värt att leva. Bosse, du har ställt upp
oerhört mycket för mig och skött marktjänsten hemma under de tuffaste tider.
Älskling, vad ska jag nu skylla på för att slippa städa?
40
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48
c Cytochromes as Electron Carrier in
Microbial Chlorate Respiration
Microbial respiration of oxochlorates is important for the biotreatment of effluents from
industries where oxochlorates are produced or handled. Several bacterial species are
capable to use perchlorate and/or chlorate as an alternative electron acceptor in absence
of oxygen. The present study deals with the electron transport from the membrane-bound
components to the periplasmic chlorate reductase, in the gram-negative bacterium Ideonella
dechloratans. Both chlorate reductase and the terminal oxidase of I. dechloratans were found
to utilize soluble c cytochromes as electron donors. For further investigation, two major
heme-containing components were purified and characterized. The most abundant was a
9 kDa c-type cytochrome (class I), denoted cytochrome c-Id1. This protein was shown to
serve as electron donor for both chlorate reductase, and for a terminal oxidase. The other
major component was a 55 kDa homotetrameric cytochrome c’, (class II). A function for
this cytochrome could not be demonstrated but it does not appear to serve as electron
donor to chlorate reductase. A gene predicted to encode a soluble c cytochrome was found
in close proximity to the gene cluster for chlorate reduction. The predicted sequence did
not match any of the cytochromes discussed above. The gene was cloned and expressed
heterologously, and the resulting protein was investigated as a candidate electron donor
for chlorate reductase. Electron transfer from this protein could not be demonstrated,
suggesting that the gene product does not serve as immediate electron donor for chlorate
reductase.
Karlstad University Studies
ISSN 1403-8099
ISBN 978-91-7063-375-1