The HydA2 gene encodes a protein of 505 amino acids that is 74% similar and 68% identical to the known HydA1 hydrogenase from C.. We demonstrate that both the HydA1 and the HydA2 transcr
Trang 1Expression of two [Fe]-hydrogenases in Chlamydomonas reinhardtii
under anaerobic conditions
Marc Forestier1,*, Paul King1, Liping Zhang1, Matthew Posewitz1, Sarah Schwarzer2, Thomas Happe2, Maria L Ghirardi1and Michael Seibert1
1
National Renewable Energy Laboratory, Golden, CO USA;2Ruhr-Universitaet-Bochum, Lehrstuhl Biochemie der Pflanzen AG Photobiotechnologie, Bochum, Germany
We have isolated and characterized a second
[Fe]-hydro-genase gene from the green alga, Chlamydomonas reinhardtii
The HydA2 gene encodes a protein of 505 amino acids that
is 74% similar and 68% identical to the known HydA1
hydrogenase from C reinhardtii HydA2 contains all the
conserved residues and motifs found in the catalytic core of
the family of [Fe]-hydrogenases We demonstrate that both
the HydA1 and the HydA2 transcripts are expressed upon
anaerobic induction, achieved either by neutral gas purging
or by sulfur deprivation of the cultures Furthermore, the
expression levels of both transcripts are regulated (in some
cases differently) by incubation conditions, such as the length
of anaerobiosis, the readdition of O2, the presence of acetate,
and/or the absence of nutrients such as sulfate during
growth Antibodies specific for HydA2 recognized a protein
of about 49 kDa in extracts from anaerobically induced
C reinhardtiicells, strongly suggesting that HydA2 encodes for an expressed protein Homology-based 3D modeling of the HydA2 hydrogenase shows that its catalytic site models well to the known structure of Clostridium pasteurianum CpI, including the H2-gas channel The major differences between HydA1, HydA2 and CpI are the absence of the N-terminal Fe-S centers and the existence of extra sequences
in the algal enzymes To our knowledge, this work represents the first systematic study of expression of two algal [Fe]-hydrogenases in the same organism
Keywords: green algae; anaerobic induction; hydrogenase; sulfur deprivation; gene expression
Hydrogen metabolism, catalyzed by hydrogenases in green
algae, was first observed over 60 years ago in Scenedesmus
obliquus[1,2] Since then, hydrogenase enzymes that either
uptake or evolve H2have been found in many other green
algae [3,4], including Chlamydomonas reinhardtii This
particular alga is capable of evolving H2 gas in the dark
[5,6] or in the light, using H2O [7] or starch [8,9] as the source
of reductant The reaction is catalyzed by a monomeric,
49 kDa reversible [Fe]-hydrogenase enzyme, which has been
isolated to purity by Happe and Naber [10]
Other [Fe]-hydrogenases, identified in a small group of nonphotosynthetic anaerobic microbes (bacteria and pro-tists) also catalyze either H2production or H2uptake in vivo [11,12] They play an important role in the anaerobic energy metabolism of these organisms, mainly by reoxidizing accumulated reducing equivalents All [Fe]-hydrogenases whose X-ray structures have been analyzed to date incor-porate a [2Fe-2S] center bridged by a cysteine residue to a [4Fe-4S] center at the catalytic site (the H-cluster) It is also known that most [Fe]-hydrogenases contain additional iron-sulfur centers that act as electron relays between carrier molecules and the H-cluster [13,14] However, the addi-tional centers are absent in the green algal enzymes [15,16]
In addition, [Fe]-hydrogenases usually exhibit high specific activity but are easily inactivated by either O2or CO Green algal [Fe]-hydrogenases have been cloned and sequenced from S obliquus [15], C reinhardtii [16,17] and Chlorella fusca [18] Besides the physiologically and bio-chemically characterized HydA1 [Fe]-hydrogenase [15],
S obliquuspossesses a gene sequence that encodes a second polypeptide with all the essential attributes of an [Fe]-hydrogenase protein [19] The expression of the second putative S obliquus hydrogenase gene was shown to be constitutive (in contrast to the inducible expression of its HydA1), suggesting different physiological roles for the two enzymes However, the expression and activities of the two hydrogenases have not been studied concomitantly in the same organism, under the same physiological conditions Hydrogenase activity in C reinhardtii is induced by anaerobiosis Anaerobic states can be achieved either
Correspondence to M L Ghirardi, National Renewable Energy
Laboratory, 1617Cole Blvd., Golden CO 80401, USA.
Fax: + 1 303 384 6150; Tel.: + 1 303 384 6312;
E-mail: maria_ghirardi@nrel.gov
Abbreviations: CpI, one of the cloned [Fe]-hydrogenases from
Clostridium pasteurianum; PSII, photosystem II; BS, basal salts;
EST, expressed sequence tag; ORF, open-reading frame; PAR,
photosynthetically active radiation; TAP, tris-acetate-phosphate.
Accession numbers: AY055756 (C reinhardtii HydA2 cDNA
sequence); AY090770 (C reinhardtii HydA2 promoter region and
genomic DNA sequence).
Note: Operated for the US Department of Energy by the Midwest
Research Institute, Batelle and Bechtel under contract number
DE-AC36–99G010337.
*Present address: Limnological Station, Plant Biology Department,
University of Zurich, Seestrasse 187, 8802 Kilchberg, Switzerland.
(Received 1 April 2003, revised 29 April 2003,
accepted 30 April 2003)
Trang 2physically, by purging algal cultures with a neutral gas, or
physiologically, by incubating algal cultures in sulfur-free
medium [20,21] The latter condition prevents the turnover
of the D1 protein of photosystem II (PSII), causes the
partial inhibition of PSII, and leads to a reduction of
photosynthetic O2evolution The partial inhibition of PSII
is sufficient to create anaerobic culture conditions and
induce H2-production activity, which lasts for 3–4 days
under continuous illumination
In this paper, we characterize a second hydrogenase gene,
HydA2, in C reinhardtii, and use the terminology
estab-lished by the international hydrogenase community [12] to
name both prokaryotic and eukaryotic hydrogenase genes
The primary amino-acid sequence of HydA2 (a) contains all
the strictly preserved motifs present in the core, catalytic-site
sequences found in algal [Fe]-hydrogenases; (b) shows high
similarity to the [Fe]-hydrogenases from Clostridium
pasteu-rianum[22], Trichomonas vaginalis [23], and Desulfovibrio
vulgaris [24]; and (c) is 68% identical to C reinhardtii
HydA1 [16] Additional evidence shows that HydA1 and
HydA2 are encoded by different genes, HydA2 is expressed
both at the transcript and protein levels, and its expression is
regulated by anaerobiosis and growth conditions We also
demonstrate that both HydA1 and HydA2 transcripts are
expressed under anaerobic conditions induced by sulfur
deprivation However, the expression of the two transcripts
differs during the sulfur-deprivation period This suggests
differences in the regulation of expression of the two genes,
also suggested by differences in their promoter regions Our
current work provides information on the expression of
the two C reinhardtii hydrogenases under three different
physiological conditions
Materials and methods
Cell growth and anaerobic induction
Chlamydomonas reinhardtii strain 400 (cell wall-less) was
grown photoheterotrophically in tris/acetate/phosphate
(TAP) medium [25] supplemented with 5% (v/v) CO2 in
air or photoautotrophically on basal salts (BS) [26] The
cultures were illuminated with cool white fluorescent light
(150 lEÆm)2Æs)1, PAR) Cells were harvested at D750 1,
corresponding to a concentration of about 15 lg
chloro-phyll per mL, and the harvested cells were anaerobically
induced as described previously [27] for 4–5 h For
sulfur-deprivation experiments, cells grown as above were washed
with sulfur-free TAP medium and resuspended in the same
medium at a final chlorophyll concentration of 20 lgÆmL)1
[20] The cultures were then incubated in sealed glass bottles
under continuous fluorescent light for up to 4 days
cDNA library screening
Two specific primers, BE5P1 (5¢-AACATCTTCAAGGA
GCGTGGCATC-3¢) and BE3P1 (5¢-AGACAGCAGGA
GACTCACAATCAC-3¢), were used to amplify a C
rein-hardtii expressed sequence tag (EST), BE337478, from a
strain 21gr cDNA library kindly provided by J Davies,
Exelixis Inc., South San Francisco, CA, USA [17] Clone
EST_26, was then used to generate an approximately
1200 bp NotI/EcoRI restriction fragment that was
dig-oxigenin-labeled and used as a probe for cDNA library screening The HydA2 clone was retrieved in pBluescript SK(–), purified and submitted to the Iowa State University Sequencing and DNA Synthesis Facility for sequencing Sequences were evaluated based on the chromatograms, and they were assembled using the WISCONSIN PACKAGE V.10 software by Genetics Computer Group, Inc (San Diego, CA, USA) Both strands of DNA were sequenced independently, and the sequence data for HydA2 cDNA has been deposited in GenBank under Accession No AY055756
Isolation and sequencing of genomicHydA2 The HydA2 gene was isolated from an E coli BAC library of C reinhardtii chromosomal DNA (Invitrogen, San Diego, CA, USA) Probing of the filter was performed as described by the manufacturer using a HydA2-specific probe that encompassed the 5¢-UTR and approximately 150 bp of the coding region of HydA2 The probe was radiolabeled using the Rediprime random primer labeling kit (Amersham, Piscataway, NJ, USA) Four positive clones were identified and obtained as pure strains from P Lefebvre (University of Minnesota, USA) The HydA2 portion of each BAC clone was amplified by PCR in 50 lL reactions that contained 1 lL of KOD HOTSTART polymerase (Novagen, Madison, WI, USA),
25 lL of BAC clone cell-free lysate as template, 125 ng each of forward (5¢-CTGGACGTGACAAACAAGA CCC-3¢, located at the start of the 5¢-UTR) and reverse (5¢-TGACACTGTCTGTGCG-3¢, near the stop codon) primers complementary to HydA2, 1 mMMgSO4, 0.2 mM each dNTPs, and 2% (v/v) dimethylsulfoxide in 1· reaction buffer (Novagen, Madison, WI, USA) All four clones produced a similar sized PCR product of 3.3 kb The PCR product from clone 27d1 was gel purified and sequenced Sequencing of the purified product was performed at Davis Sequencing, LLC (Davis, CA, USA) on an Applied Biosystems 3730 automated sequencer The HydA2 gene sequence has been deposited
in GenBank under Accession no AY090770
Northern blot analysis
To obtain transcript hybridization signals that truly reflect the aerobic state of the algae at t¼ 0, it proved essential to lyse noninduced algal cells as quickly as possible to avoid the establishment of anaerobiosis in the dark by respiratory
O2consumption Total RNA was isolated at different time points from anaerobically induced samples using the SNAP RNA Isolation Kit (Invitrogen, San Diego, CA, USA) DNA was removed by treatment with RNase-free DNaseI (0.013 units per lL) Ten micrograms of RNA were separated by electrophoresis on denaturing 1.1% (w/v) agarose, 0.22Mformaldehyde gels and then blotted onto a Nytran N+nylon membrane with 10· NaCl/Cit [28] as the transfer buffer Radiolabeled probes specific for either HydA1or HydA2 were generated using Rediprime random primer labeling kits (Amersham, Piscataway, NJ, USA) Denatured probes were hybridized to the membranes in prehybridization buffer [6· NaCl/Cit buffer, 5 · Den-hardt’s solution, 0.1% (w/v) SDS] overnight at 65C
Trang 3Following hybridization, the membranes were washed and
exposed to X-ray film at)80 C for 1–4 days
Southern blot analysis ofC reinhardtii genomic DNA
forHydA1 and HydA2
Total genomic DNA was prepared from C reinhardtii
using the Qiagen DNeasy Genomic Kit (Qiagen, Valencia,
CA, USA) and digested with PstI Digested DNA
(0.5 lg) was separated by agarose gel electrophoresis
Southern hybridizations were performed under identical
conditions as described above for Northern hybridizations
using the radiolabeled probes specific for either HydA1 or
HydA2
Heterologous overexpression of HydA1 and HydA2
The HydA1 and HydA2 ORF was amplified by PCR
using primer pairs containing flanking NdeI/BamHI sites
(HydA1 forward 5¢-GCCGCACCCGCTGCGGAG-3¢,
reverse 5¢-TCACTTCTTCTCGTCCTT-3¢; HydA2
for-ward 5¢-GCGACCGCAACTGATGCT-3¢, reverse
5¢-CTAAGCATCGGCCTCGGC-3¢) After restriction
digestion, the HydA1 and HydA2 genes were cloned into
the corresponding site of the pET-16b expression vector
(Novagen, Madison, WI, USA) producing pET-HydA1
and HydA2 The inserts of HydA1 and
pET-HydA2 were sequenced, confirming that the fragments
contained the exact full coding region of each
hydro-genase without the corresponding transit peptide sequences
The E coli strain BL21(DE3)pLysS was transformed with
both constructs pET-HydA1 and pET-HydA2 Expression
was induced with 1 mM isopropyl thio-b-D-galactoside
(IPTG) at an A600¼ 0.3
Antibody generation and immunoblot analysis
A region of low amino acid sequence homology between
HydA1 and HydA2 (the insert between motifs 2 and 3) was
screened for high antigenicity using two methods, Alpha
Diagnostic (San Antonio, Texas) and the JaMBW online
program (http://members.aol.com/_ht_a/lucatoldo/myhome
page/JaMBW) Both methods identified a 14-residue long
oligopeptide (VAE RLAHKVEEAAA) in HydA2 as a
possible candidate The oligopeptide was synthesized by
Sigma Genosys (The Woodlands, TX, USA), coupled to the
keyhole limpet hemacyanin (KLH) protein carrier and
injected into rabbits to induce antibody generation The
resulting serum was immunoaffinity purified and tested for
reaction against HydA1 and HydA2 overexpressed in
E coliand against HydA2 in anaerobically induced algal
extracts
Algal cells were harvested during the mid-logarithmic
phase by centrifugation at 2000 g for 2 min Pellets were
resuspended in 50 mMTris/HCl pH 8.5 with 20 mMsodium
dithionite at 200 lg chlorophyll per mL and induced
anaerobically After induction, all steps were performed
under strictly anaerobic condition The
hydrogenase-con-taining fraction was partially purified as described
previ-ously [29] and run on SDS/PAGE under denaturing
conditions with a 10% acrylamide gel in Tris/glycine buffer
The separated proteins were then blotted onto a
poly(viny-lidene difluoride) membrane and probed with the HydA2-specific antibody The cross-reaction was detected with a chromogenic reaction using anti-IgG secondary Igs conju-gated with alkaline phosphatase (Bio-Rad, Hercules, CA, USA)
H2-Production assays The rates of H2-production were measured with a modified Clark electrode, as described previously [27] Hydrogen production by sulfur-deprived cultures was measured by gas chromatography, using a Hewlett Packard 5890A Series II instrument equipped with a thermal conductivity detector [16]
Homology structure modeling Homology structure models of the putative C reinhardtii HydA2 hydrogenase relative to the known structure of the C pasteurianum CpI enzyme [30] were generated using the programSWISS-MODEL[31].CLUSTAL Walignments of the predicted processed HydA2 sequence to CpI were used to manually optimize backbone threading Final versions of the models were submitted toSWISS-MODELfor validation The resulting homology structures were further refined by energy minimization withGROMOS Calculated rmsd values between the resulting HydA2 model and CpI include all shared backbone atoms
Results and discussion
Genetic analysis ofHydA2 The first [Fe]-hydrogenase from C reinhardtii, HydA1, was recently cloned (GenBank, accession numbers CRE012098, AY055755, AF289201), and was shown to encode a functional enzyme [16] The deduced amino acid sequence
of the HydA1 catalytic site was further utilized in aBLAST search and revealed a close match to an expressed sequence tag (EST) from C reinhardtii, BE33478 The EST was amplified from a cDNA library (Materials and methods) The resulting clone was identical in nucleotide sequence to BE33478 However, it was distinct from the original HydA1 amplification probe, as it contained a unique NotI restric-tion site This partial clone was then used as a probe to screen a cDNA library, which led to the retrieval of a full-length clone The sequence of the retrieved clone shows
an ORF for a polypeptide of 505 amino acid residues According to the classification of hydrogenase genes reported in the review from Vignais et al [12], the ORF was termed HydA2
The HydA2 cDNA has a 139 nucleotide 5¢-UTR and an
873 nucleotide 3¢-UTR (excluding the polyadenylated tail)
A polyadenylation signal (TGTAA) characteristic of nuc-lear-encoded genes in C reinhardtii [32] is located 854 bp downstream from the stop codon, 19 bp upstream from the end of the 3¢-UTR Figure 1 shows an amino acid sequence alignment of the translated C reinhardtii HydA1 and HydA2 ORFs compared to S obliquus HydA1 [15], a partial amino acid sequence for the second, highly homologous protein (which we call HydA2) found in
S obliquus[19], and Clostridium pasteurianum CpI
Trang 4All the distinctive structural features of algal
[Fe]-hydrogenases are also present in the C reinhardtii HydA2
amino-acid sequence [33–35], including the well-conserved
C-terminal part (C-domain) that binds the catalytic
H-cluster As seen in other algal [Fe]-hydrogenases, the
N-terminal part (F-domain) of HydA2 also lacks the
additional [4Fe-4S] or [2Fe-2S] centers (F-cluster) found in
nonalgal [Fe] hydrogenases The three complete motifs
found in the catalytic H-cluster of [Fe]-hydrogenases, motif
1 (PMFTSCCPxW), motif 2 (MPCxxKxxExxR) and motif
3 (FxExMACxGxCV), have also been found in the algal
sequences and are marked in Fig 1 Each contains cysteine
residues (*) that ligate the catalytic [4Fe-4S] center The
cysteine residue in motif 3 (#) bridges the [4Fe-4S] to the
[2Fe-2S] center of the active H-cluster Comparisons of
C reinhardtii HydA2 with the [Fe]-hydrogenases from
C reinhardtiiand S obliquus HydA1 show 68% and 61%
identity, respectively
Algal [Fe]-hydrogenases also share the following
charac-teristic features (Fig 1): (a) an amino acid residue insertion
(eight residues in both S obliquus and C reinhardtii HydA1
and HydA2) upstream of the H-cluster motif 1 and (b) a
second amino acid insertion (16 residues in C fusca,
16 residues in S obliquus HydA1 and HydA2, 45 residues
in C reinhardtii HydA1, and 54 residues in C reinhardtii
HydA2) between H-cluster motifs 2 and 3 The biological
implications of these unique features are not known at
present, but, given their ubiquity in all cloned algal
hydrogenases, they might be critical to specific functional
or structural peculiarities of the algal enzymes
In order to determine that HydA1 and HydA2 are encoded by distinct nuclear genes, C reinhardtii genomic DNA was purified, digested with PstI and probed sepa-rately with HydA1- and HydA2-specific probes (Southern not shown) A single PstI site is present within the HydA1 genomic sequence where the probe hybridizes The same PstI restriction site, however, is absent from the HydA2 sequence (data not shown) As expected, the HydA1 probe detected two PstI fragments at 2.8 kb and 1.0 kb, while the HydA2 probe detected only a single fragment at 6.5 kb, clearly demonstrating that HydA1 and HydA2 are encoded
by distinct DNA sequences It was also observed that the two hydrogenase genes map on different linkage groups (L Mets, University of Chicago, personal communication) The HydA1 gene maps on linkage group III, and HydA2 maps on linkage group IX Finally, the two hydrogenase gene sequences are found to be present in different contigs (10 and 12, respectively) of the recently released C rein-hardtii genome The latter also confirmed the target-specificity of the HydA1 and HydA2 DNA probes Algal hydrogenases are nuclear-encoded and thus must
be transported into the chloroplast to function in H2 metabolism In eukaryotic organisms, transit signal peptide sequences direct nuclear-encoded proteins to specific organ-elles, and these sequences are then cleaved from the mature peptide Chloroplast transit peptides are usually rich in serine, threonine, alanine and valine, but are deficient in acidic residues [36] Moreover, chloroplast transit peptides have three characteristic domains [37] that are present in the first 63 amino acid residues of the HydA2 protein The exact
Fig 1 Sequence alignment of the [Fe]-hydrogenases The protein alignment was performed using the PILEUP / GENEDOC program (http://search launcher.bcm.tmc.edu/multi-align/multi-align.html) Amino acid residues highlighted in black represent identities between at least four of the hydrogenases, and those highlighted in grey show similarity between at least four of the sequences Cr, C reinhardtii HydA1 [16] and HydA2 (this work); So, S obliquus HydA1 [15] and HydA2 [19]; and Cp, C pasteurianum HydI [22].
Trang 5cleavage site recognized by chloroplast stromal processing
peptidases is not known [38], but the motif VXA has been
identified near the transit peptide cleavage site in a number
of Chlamydomonas chloroplast-targeted proteins [39] In
HydA1, the transit peptide is cleaved one amino acid
downstream from the sequence VACAA at position 56 of
the nascent peptide [16] By analogy, a VXA motif cleavage
site is located at amino acid 61 of the HydA2 ORF (VAA),
suggesting a cleavage site after residue 63 This cleavage site
was also identified using the CHLOROP program [40]
Additional studies will be required to determine whether
HydA2 is indeed processed proteolytically, and if so, where
cleavage actually occurs in vivo
The isolation and sequencing of the complete HydA2
gene was done using a HydA2-specific probe (Materials and
methods) to screen a BAC library of cloned C reinhardtii
genomic DNA Following identification of four positive
clones, the HydA2 region of a single BAC clone was
amplified by PCR and directly sequenced (GenBank
Accession number AY090770) The length of the complete
HydA2gene (from the 5¢-UTR to the 3¢-UTR minus the
poly A tail) is 4.62 kb and consists of eight exons and nine
introns (average intron size, 150 bp) The structural
arrangement of HydA2 is thus more complex than HydA1,
which contains only seven introns [16] Interestingly, the
promoter regions of HydA1 and HydA2 are unique and lack
significant regions of sequence homology Whereas the
HydA2 promoter region has a characteristic TATA box located 24 bp upstream from the 5¢-UTR, the HydA1 promoter region [16] has no TATA-like sequence until 187bp upstream from the 5¢-UTR These differences suggest potential differences in the regulation of expression
of the two genes
Gene expression during anaerobic induction The coexpression of the HydA1 and HydA2 transcripts was studied by Northern blot analysis In Fig 2, we used specific probes for the HydA1 (d) or HydA2 (s) transcripts, whose transcription was induced by a shift to anaerobic conditions The transcript levels of both genes increased rapidly during the anaerobic treatment Whereas low but detectable levels
of the HydA2 transcript were observed in the BS-grown cells
at t¼ 0 (Fig 2B, s), none were detected at the same time point in TAP-grown cells (Fig 2A, s) In cells grown on TAP medium (Fig 2A), the accumulation of HydA1 and HydA2transcripts reached a maximum after about 90 min
of treatment, the same time that H2-photoproduction activity levels reached steady-state (Fig 2A, bars) Activity measurements were performed on the same samples at the same time that cells were harvested for mRNA extraction
In cells grown on BS medium (Fig 2B), transcript accu-mulation and induction of H2-photoproduction activity occurred more slowly, reaching steady-state after
Fig 2 Effects of anaerobiosis on hydrogenase transcription, enzyme function, and transcript stability (A) and (B) HydA1 (d) and HydA2 (s) transcript accumulation following incubation under dark, anaerobic conditions Transcript levels were measured in C reinhardtii cells grown on either TAP (A) or BS (B) medium and normalized to the amount of 23S rRNA of the respective sample Simultaneous measurements of H 2
photoproduction activity were performed with the same cultures (C) Northern blots of cultures grown on either TAP or BS medium after incubation under anaerobic conditions at 4 C overnight (O/N), followed by exposure to O 2 for 15 min (+O 2 ) The respective rates of H 2
photoproduction (lmoles H 2 per mg chlorphyll per h) are shown above each blot.
Trang 6240–300 min of anaerobic treatment There were no
observed differences in the rate of accumulation of the
two transcripts under these conditions Induction for longer
periods of time did not further change the levels of the two
transcripts (not shown) The induced rates of H2
photopro-duction vary in different experiments and reach steady-state
at slightly different time points, possibly due to the different
levels of anaerobic induction achieved with different
cultures However, the onset of H2-photoproduction
acti-vity in BS-grown cells was consistently later than for
TAP-grown cells The activity data and the Northern blot
analyses shown in Fig 2 include samples from three
representative experiments
Figure 2C shows that the levels of HydA1 and HydA2
transcripts in TAP-grown cultures remained high during
overnight (O/N) anaerobic incubation at 4C and that the
cultures maintained approximately 75% of their maximum
H2-production activity However, the same 4C O/N
incubation of BS-grown cultures resulted in a significant
decrease in the HydA2 transcript level, but no major effects
on the HydA1 transcript levels or on H2-production activity
Exposure of the induced cultures to O2is known to cause
a loss of H2-photoproduction activity and a reduction in
hydrogenase levels [29] Samples of the O/N anaerobically
induced cultures were tested for H2-photoproduction
activity and transcript levels following a 15 min exposure
to O2 Figure 2C, lane +O2 shows that H2
-photoproduc-tion activity in both cultures was completely lost However,
the transcripts in the photoautotrophic (BS) culture were
virtually undetectable after the cells were exposed to O2,
whereas the transcripts in the photoheterotrophic (TAP)
culture were still present Together, these data demonstrate
the lower stability of the HydA2 transcript on exposure to
O2under photoautotrophic conditions (Fig 2C) and
indi-cate that the levels of the two transcripts may be modulated
by other factors in addition to O2
Gene expression during sulfur deprivation
The expression of HydA1 and HydA2 transcripts was also
studied under sulfur-deprivation conditions In the absence
of sulfur, the rates of photosynthetic O2 evolution drop
below those of O2consumption by respiration after about
24 h of incubation As a consequence, sealed cultures of
green algae become anaerobic in the light [41,42] The
HydA1transcript was detected after 24 h (Fig 3, bottom)
of incubation in sulfur-depleted medium, about the time
that the medium becomes anaerobic and H2 production
starts [20] After that, the levels of HydA1 increased up to
about 48 h, corresponding to the time when H2-production
rates are high (Fig 3, top) In contrast to HydA1, the levels
of the HydA2 transcript increased up to 24 h and then
gradually decrease over a total period of two days The rates
of HydA1 and HydA2 transcript accumulation under
sulfur-deprivation-induced anaerobiosis clearly differ from each
other (Fig 3) Furthermore, the HydA2 transcript appears
to be less stable under these conditions than HydA1 (Fig 3),
as observed in Fig 2C This may be the result of differences
in transcriptional regulation (see above) and may signal
different physiological roles for the two hydrogenases in
algal metabolism This hypothesis will be investigated in the
future
The HydA2 protein is expressed during anaerobic induction
In order to determine whether HydA2 is an expressed protein, HydA2-specific oligo-peptide antibody was syn-thesized and used for Western blotting of C reinhardtii extracts To confirm the specificity of the HydA2 antibody,
it was first tested on recombinant, partially purified
C reinhardtiihydrogenases SDS/PAGE of E coli extracts that overexpressed either HydA1 or HydA2 exhibited a
Fig 3 Induction of hydrogenase activity and gene transcription under sulfur-deprived conditions (Top) Hydrogen-production activity of
C reinhardtii cultures incubated in sulfur-deprived TAP medium for 1–3 days in a sealed photobioreactor The hydrogenase activity at
t ¼ 0 was 0 (Bottom) RNA was isolated from cells subjected to sulfur-deprivation conditions as above, and hybridized as described in the Material and methods The data, showing photographs of typical blots, are from one representative experiment.
Fig 4 Heterologous and homologous expression of the HydA2 protein Western blots of IPTG-induced E coli total protein extracts over-expressing, HydA1 or HydA2 (lanes 1 and 2, respectively) and partially purified C reinhardtii cell extracts, either noninduced (lane 3) or anaerobically induced (lane 4) All blots were probed with the HydA2-specific antibody The presence of a band in lane 1 above 49 kDa represents a nonspecific response seen only in the overexposed blot It
is not HydA1, as the band is also present in E coli that had not been induced by IPTG (data not shown).
Trang 7major band that migrated at the predicted mass of 49 kDa
(data not shown) Whereas recombinant HydA2 was
detec-ted by HydA2 antibody on the Western blot (Fig 4, lane 2),
the same antibody did not detect recombinant HydA1
(Fig 4, lane 1) Thus, the antibody detects the HydA2
protein specifically As expected, extracts of aerobically
grown C reinhardtii cells showed no HydA2 reactive protein
(Fig 4, lane 3) However, the antibody did recognize a
protein in extracts of anaerobically induced cells, which
comigrated with the recombinant HydA2 protein (Fig 4,
lane 4) These results confirm that HydA2 is expressed in
C reinhardtii andaccumulates after anaerobic induction
There is precedence for multiple [Fe]-hydrogenases in
different organisms, and the presence of multiple
hydro-genases (both [Fe] and [NiFe]) involved in different
metabolic pathways in the same organism is not unusual
For example E coli has at least four different hydrogenases
[12,43], Trichomonas vaginalis has two [23,44], and
Desulf-ovibrio vulgarishas three [12] These different hydrogenases
are expressed under different conditions and catalyze either
H2 uptake or H2 evolution However, despite work
suggesting the expression of two different hydrogenases in
the green alga S obliquus [15,19], until now no systematic
studies have been done on the expression and physiological
role of multiple hydrogenases in algae The current work
has addressed some of the expression issues; however, at this
point, we still cannot assign a specific function for the two
C reinhardtii hydrogenases Additional research will be
carried out to specifically knock out each of the hydrogenase
genes independently, so that that specific function of each
gene can be investigated
Structural models of the HydA2 [Fe]-hydrogenase
The alignment of the C reinhardtii HydA2 and CpI peptide
sequences (Fig 1) reveals a high degree of primary sequence
conservation (43% identity and 54% similarity) Peptide
motifs that represent the active site [13,30] and the putative
H2channel [24] located within the hydrogenase core exhibit
a much higher degree of conservation (75% identity, 90%
similarity) In comparison, the mature forms of the HydA1
and HydA2 peptide sequences share 81% identity and 74%
similarity with each other, and in addition, 91% identity is
evident for the active site and H2-channel motifs
In order to visualize the significance of the primary
sequence homology, a theoretical model of HydA2 was
generated from the solved X-ray structure of CpI As shown
in Fig 5, HydA2 (as does HydA1, data not shown) exhibits
a high degree of structural similarity to CpI (rmsd of
1.55 A˚, 1480 backbone atoms) The predicted locations of
HydA2 (and HydA1, data not shown) peptide sequence
motifs that represent the active site and H2-channel match
closely to the positions of the corresponding residues in CpI
The rmsd between the HydA2 and CpI core regions is
0.74 A˚ over 1336 shared atoms (334 Ca atoms) This
information corroborates our assignment of a hydrogenase
function to HydA2, provides us with a model to compare
the catalytic functions of isolated HydA1 and HydA2 in the
future, and serves as a guide to future site-directed
mutagenesis studies of the two algal hydrogenase proteins
In conclusion, we have cloned and sequenced a second
[Fe]-hydrogenase gene from the green alga, C reinhardtii
The promoter regions of the two algal hydrogenase genes exhibit significant differences that may reflect differences in the regulation and/or roles of the two hydrogenases in algal physiology, as has been observed in other multiple hydro-genase systems The transcription of HydA1 and HydA2 in response to the removal of O2depends on the composition
of the growth medium (photoheterotrophic vs photoauto-trophic; sulfur-replete vs sulfur-deprived) These observa-tions underpin the importance of hydrogenases for algal metabolism, and will spur further research on the specific physiological and biochemical pathways related to each hydrogenase in C reinhardtii
Acknowledgements
We thank Dr John Davis, Exelixis Inc for the cDNA library, Prof Lauren Mets, University of Chicago, for providing us with his mapping results, and Scott Plummer, a graduate student from the Colorado School of Mines for his help in screening the cDNA library
Fig 5 Homology structure models of the C reinhardtii HydA2 hydrogenase A model of the predicted structure of HydA2 is shown compared to the X-ray structure of CpI [30] The H-clusters are identified in CPK colors as space-filled atoms The backbone colors correspond to secondary structure type (red, a-helix; cyan, b-sheet; grey, random coil) The nonconserved N-terminal domain of CpI is also colored grey, and the Fe-S centers are represented as ball and stick diagrams Domains unique to HydA2 and not found in CpI are rep-resented in green Images of the structures were made with VIEWERLITE
software (Accelrys).
Trang 8for the HydA2 clone MF would like to acknowledge a grant to
prospective researchers from the Swiss National Science Foundation.
MS and MLG were supported by the U.S DOE Hydrogen program.
TH thanks the Japanese New Energy and Industrial Technology
Development Organization (NEDO-project no 01GB1) for financial
support.
References
1 Gaffron, H (1939) Reduction of carbon dioxide with molecular
hydrogen in green algae Nature 143, 204–205.
2 Gaffron, H & Rubin, J (1942) Fermentative and photochemical
production of hydrogen in algae J General Physiol 26, 219–240.
3 Weaver, P.F., Lien, S & Seibert, M (1980) Photobiological
pro-duction of hydrogen Solar Energy 24, 3–45.
4 Brand, J.J., Wright, J.N & Lien, S (1989) Hydrogen production
by eukaryotic algae Biotechnol Bioeng 33, 1482–1488.
5 Miura, Y., Yagi, K., Nakano, Y & Miyamoto, K (1981)
Requirement of oxygen for dark hydrogen evolution by a green
alga, Chlamydomonas reinhardtii J Ferment Technol 59, 441–
446.
6 Miura, Y., Yagi, K., Shoga, M & Miyamoto, K (1982) Hydrogen
production by a green alga, Chlamydomonas reinhardtii, in an
alternating light/dark cycle Biotechnol Bioeng 24, 1555–1563.
7 Greenbaum, E., Guillard, R.R.L & Sunda, W.G (1983)
Hydro-gen and oxyHydro-gen photoproduction by marine algae Photochem.
Photobiol 37, 649–655.
8 Gfeller, R.P & Gibbs, M (1984) Fermentative metabolism of
Chlamydomonas reinhardtii 1 Analysis of fermentative products
from starch in dark and light Plant Physiol 75, 212–218.
9 Gibbs, M., Gfeller, R.P & Chen, C (1986) Fermentative
meta-bolism of Chlamydomonas reinhardtii 3 Photoassimilation of
acetate Plant Physiol 82, 160–166.
10 Happe, T & Naber, J.D (1993) Isolation, characterization and
N-terminal amino acid sequence of hydrogenase from the green
alga Chlamydomonas reinhardtii Eur J Biochem 214, 475–481.
11 Adams, M.W.W (1990) The structure and mechanism of
iron-hydrogenases Biochim Biophys Acta 1020, 115–145.
12 Vignais, P.M., Billoud, B & Meyer, J (2001) Classification and
phylogeny of hydrogenases FEMS Microbiol Rev 25, 455–501.
13 Peters, J.W (1999) Structure and mechanism of iron-only
hydrogenases Curr Opin Struc Biol 9, 670–676.
14 Nicolet, Y., Lemon, B.J., Fontecilla-Camps, J & Peters, J.W.
(2000) A novel FeS cluster in Fe-only hydrogenases Trends
Bio-chem Sci 25, 138–143.
15 Florin, L., Tsokoglou, A & Happe, T (2001) A novel type of iron
hydrogenase in the green alga Scenedesmus obliquus is linked to the
photosynthetic electron transport chain J Biol Chem 276,
6125–6132.
16 Happe, T & Kaminski, A (2002) Differential regulation of the
Fe-hydrogenase during anaerobic adaptation in the green alga
Chlamydomonas reinhardtii Eur J Biochem 269, 1–11.
17 Forestier, M., Zhang, L., King, P., Plummer, S., Ahmann, D.,
Seibert, M & Ghirardi, M (2001) The cloning of two hydrogenase
genes from the green alga Chlamydomonas reinhardtii In
Pro-ceedings of the 12th International Congress on Photosynthesis,
18–23 August 2001, Brisbane, Australia, http://www.publish.
csiro.au/ps2001 CSIRO Publishing, Melbourne, Australia, S37–
003.
18 Winkler, M., Heil, B., Heil, B & Happe, T (2002) Isolation and
molecular characterization of the [Fe]-hydrogenase from the
uni-cellular green alga Chlorella fusca Biochim Biophys Acta 1576,
330–334.
19 Wu¨nschiers, R., Stangier, K., Senger, H & Schulz, R (2001)
Molecular evidence for a Fe-hydrogenase in the green alga
Sce-nedesmus obliquus Current Microbiol 42, 353–360.
20 Melis, A., Zhang, L., Forestier, M., Ghirardi, M.L & Seibert, M (2000) Sustained photobiological hydrogen gas production upon reversible inactivation of oxygen evolution in the green alga Chlamydomonas reinhardtii Plant Physiol 122, 127–135.
21 Ghirardi, M.L., Zhang, L., Lee, J.W., Flynn, T., Seibert, M., Greenbaum, E & Melis, A (2000) Microalgae: a green source of renewable H 2 Trends Biotechnol 18, 506–511.
22 Meyer, J & Gagnon, J (1991) Primary structure of hydrogenase I from Clostridium pasteurianum Biochemistry 30, 9697–9704.
23 Bui, E.T.N & Johnson, P.J (1996) Identification and character-ization of [Fe]-hydrogenases in the hydrogenosome of Tricho-monas vaginalis Mol Biochem Parasitol 76, 305–310.
24 Nicolet, Y., Piras, C., Legrand, P., Hatchikian, C.E & Fontecilla-Camps, J.C (1999) Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center Structure 7, 13–23.
25 Harris, E.H (1989) The Chlamydomonas Sourcebook Academic Press, Inc, San Diego, CA, USA.
26 Flynn, T., Ghirardi, M.L & Seibert, M (2002) Accumulation of
O 2 -tolerant phenotypes in H 2 -producing strains of Chlamydomo-nas reinhardtii by sequential applications of chemical mutagenesis and selection Int J Hydrogen Res 27, 1421–1430.
27 Ghirardi, M.L., Togasaki, R.K & Seibert, M (1997) Oxygen sensitivity of algal H 2 -production Appl Biochem Biotechnol 63–65, 141–151.
28 Ausubel, F.M., Brent, R., Kingston, R.E., Moore, D.D., Seid-man, J.G., Smith, J.A & Struhl, K (1999) Short Protocols in Molecular Biology John Wiley and Sons, NY, USA.
29 Happe, T., Mosler, B & Naber, J.D (1994) Induction, localiza-tion and metal content of hydrogenase in the green alga Chla-mydomonas reinhardtii Eur J Biochem 222, 769–774.
30 Peters, J.W., Lanzilotta, W.N., Lemon, B.J & Seefeldt, L.C (1998) X-ray crystal structure of the Fe-only hydrogenase (CPI) from Clostridium pasteurianum to 1.8 Angstrom resolution Science 282, 11853–11858.
31 Guex, N & Peitsch, M.C (1997) Model and the Swiss-PdbViewer: An environment for comparative protein modeling Electrophoresis 18, 2714–2723.
32 Silflow, C.D., Chisholm, R.L., Conner, T.W & Ranum, L.P (1985) The two alpha-tubulin genes of Chlamydomonas reinhardtii code for slightly different proteins Mol Cell Biol 5, 2389–2398.
33 Happe, T., Hemschemeier, A., Winkler, M & Kaminski, A (2002) Hydrogenases in green algae: do they save the algae’s life and solve our energy problems? Trends Plant Sci 7, 246–250.
34 Winkler, M., Hemschemeier, A., Gotor, C., Melis, A & Happe, T (2002) [Fe]-hydrogenases in green algae: photofermentation and hydrogen evolution under sulfur deprivation Int J Hydrogen Energy 27, 1431–1439.
35 Melis, A & Happe, T (2001) Hydrogen production Green algae
as a source of energy Plant Physiol 127, 740–748.
36 Keegstra, K., Olsen, J.J & Theg, S.M (1989) Chloroplastic pre-cursors and their transport across the envelope membranes Ann Rev Plant Physiol Plant Mol Biol 40, 415–439.
37 Bruce, B.D (2001) The paradox of plastid transit peptides: con-servation of function despite divergence in primary structure Biochim Biophys Acta 1541, 2–21.
38 Richter, S & Lamppa, G.K (1998) A chloroplast processing _enzyme functions as the general stromal processing peptidase Proc Natl Ac ad Sc i USA 95, 7463–7468.
39 Franzen, L.G., Rochaix, J.D & von Heijne, G (1990) Chloroplast transit peptides from the green alga Chlamydomonas reinhardtii share features with both mitochondrial and higher plant chloro-plast presequences FEBS Lett 260, 165–168.
40 Emanuelsson, O., Nielsen, H & von Heijne, G (1999) ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites Protein Sci 8, 978–984.
Trang 941 Kosourov, S., Tsygankov, A., Seibert, M & Ghirardi, M.L (2002)
Sustained hydrogen photoproduction by Chlamydomonas
reinhardtii: Effects of culture parameters Biotechnol Bioeng 78,
731–740.
42 Zhang, L., Happe, T & Melis, A (2002) Biochemical and
morphological characterization of sulfur-deprived and H 2
-pro-ducing Chlamydomonas reinhardtii (green alga) Planta 214, 552–
561.
43 Skibinski, D.A.G., Golby, P., Chang, Y.-S., Sargent, F., Hoffman, R., Harper, R., Guest, J.R., Attwood, M.M., Berkes, B.C & Andrews, S.C (2002) Regulation of the hydrogenase-4 operon of Escherichia coli by the r 54 -dependent transcriptional activators FhlA and HyfR J Bacteriol 184, 6642–6653.
44 Horner, D.S., Foster, P.G & Embley, T.M (2000) Iron hydro-genases and the evolution of anaerobic eukaryotes Mol Biol Evol 17, 1695–1709.