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J Bacteriol, March 1998, p. 1596-1599, Vol. 180, No. 6
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
Cloning and Sequencing of a Form II
Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase from the Bacterial
Symbiont of the Hydrothermal Vent Tubeworm Riftia
pachyptila
Jonathan J.
Robinson,1
Jeffrey L.
Stein,2 and
Colleen M.
Cavanaugh1,*
Department of Organismic and Evolutionary
Biology, Harvard University, Cambridge, Massachusetts
02138,1 and
Diversa Corp., San Diego,
California 921212
Received 4 August 1997/Accepted 13 January 1998
 |
ABSTRACT |
The bacterial symbiont of the hydrothermal vent tubeworm fixes
carbon via the Calvin-Benson cycle and has been shown previously to
express a form II ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). The gene cbbM, which encodes this enzyme, has
been cloned and sequenced. The gene has the highest identity with the cbbM gene from Rhodospirillum rubrum, and
analysis of the inferred amino acid sequence reveals that all
active-site residues are conserved. This is the first form II RubisCO
cloned and sequenced from a chemoautotrophic symbiont and from a
deep-sea organism.
 |
TEXT |
Hydrothermal vent environments are
dominated by dense assemblages of invertebrates which harbor
chemoautotrophic sulfur-oxidizing bacteria within their tissues. This
nutritional interaction between prokaryotic symbionts and various
animal hosts is dependent upon the biological fixation of inorganic
carbon by the symbionts and the subsequent supply of organic carbon to
the host in a manner analogous to the chloroplasts of green plants and
algae (reviewed in reference 2). Fundamental to the
initial and subsequent characterization of these symbioses has been the
detection of the key Calvin-Benson cycle enzyme,
ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) (1,
8). The hydrothermal vent tubeworm Riftia pachyptila
is of particular interest with regard to its carbon fixation abilities,
as this animal completely lacks a mouth, gut, or anus (13)
but is capable of extreme size and high growth rates due to its
symbiotic association (16).
The primary carbon fixation step in the Calvin-Benson cycle is
catalyzed by RubisCO, which carboxylates ribulose-1,5-bisphosphate with
CO2 to yield two molecules of 3-phosphoglyceric acid. The enzyme is found in two forms, called form I and form II
(30), which are distinct in primary and quaternary structure
(26), reaction mechanism, and kinetic isotope effect (KIE)
(22, 23). The form I RubisCO, found in the vast majority of
eukaryotic and prokaryotic autotrophs, consists of eight large subunits
and eight small subunits, with the holoenzyme having a molecular weight between 500 and 560 kDa (26). The form II enzyme is
structurally less complicated, consisting of a dimer of only two large
(L) subunits found in either an L2 configuration
(26), as in Rhodospirillum rubrum, or an
L2-to-L6 configuration, as reported for other
species (30). The two forms are ~25% identical to each
other at the amino acid level (18). To date, the form II
enzyme has only been characterized at the nucleic acid sequence level
from five prokaryotes (31) and two dinoflagellates (17,
24).
The bacterial symbiont of the vestimentiferan R. pachyptila
has been shown to express a form II RubisCO (21). In this
work we report the cloning and sequencing of the cbbM gene,
which encodes a form II enzyme, from the R. pachyptila
symbiont.
Bacterial strains, plasmids, and polyclonal antisera.
The
Escherichia coli construct pRR2119 (ATCC 37846) was used to
generate probes for hybridization during library screening. This clone
harbors the plasmid pXG9 containing the cloned form II RubisCO from
Rhodospirillum rubrum (28). E. coli
INFaF' (Invitrogen) was used for cloning steps and grown in
Luria broth supplemented with ampicillin (40 mg liter
1).
Plasmid pCRII (Invitrogen) was used for subcloning, DNA sequence analysis, and protein expression studies.
The lambda DNA library (see below) was screened with polyclonal
antiserum directed against the R. rubrum form II RubisCO
(anti-RrFII) (antiserum generously provided by George Lorimer
[DuPont]), which has been shown to be specific to form II RubisCOs
and to cross-react with the R. pachyptila enzyme
(21). In all cases antiserum was used at a 1:3,000 dilution.
R. pachyptila genomic DNA library construction.
Tubeworm specimens used for genomic DNA library construction were
collected from a depth of 2,600 m using the DSV Alvin from hydrothermal vents on the East Pacific Rise at the 13°N site
(12°48'N, 103°56'W; November 1987). The worms were transported to
the surface in a thermally insulated container and the
symbiont-containing trophosome tissue was immediately dissected on
board ship. Tissue was homogenized in a 1:1 (wt/vol) solution of
ice-cold Riftia saline (46 mM imidazole, 0.46 M NaCl, 30 mM
MgSO4, 2.5 mM KCl, 10 mM CaCl2; pH 7.1) at 30 to 40% speed in an Ultraturrax homogenizer for 2 min on ice. Symbionts
in this solution were separated from host cells on 80% Percoll density
gradients according to the method of Distel and Felbeck (6)
with modifications.
DNA was extracted from the symbiont preparation by using a 5 M
guanidinium isothiocyanate solution (
15). DNA (75 µg) was
sheared to an average size of 3 to 6 kbp by vigorous passage through
a
25-gauge needle in a 1-ml syringe. The sheared DNA was blunt
ended with
mung bean nuclease and ligated to
EcoRI linkers, and
3- to
6-kbp fragments were cloned into lambda gt11 (
27). The
library titer was estimated to be 1.5 × 10
10 PFU
(
25).
Library screening.
Phage were plated and screened by standard
methods on a lawn of E. coli Y1090 (25). Plaques
were screened for the expression of the form II RubisCO by incubation
with anti-RrFII antiserum (25). Plaques which were
immunologically positive were rescreened with a
32P-labelled BglII/SmaI fragment of
the R. rubrum form II RubisCO derived from plasmid pXG9
(28).
Two lambda clones were isolated. Inserts were amplified from purified
lambda DNA by PCR with primers specific to the
lacZ cloning
region (Promega) and subcloned into the pCR II vector
for
transformation into
E. coli host strain INF
aF'
and subsequent DNA sequencing. The two clones are different
sizes, with
insert sizes of ~3,300 bp for pRpR-1 and ~2,200 bp
for pRpR-2, and
are oriented in opposite directions.
DNA sequence analysis.
Oligonucleotide primer walking was used
to generate a double-stranded sequence for the region encoding the form
II RubisCO and immediate flanking regions for both clones. Sequencing
was conducted with the Applied Biosystems Inc. (ABI) Dye Terminator Cycle Sequencing kit under standard conditions, an Ericomp thermal cycler, and an ABI model 373 automated sequencer. Sequences of regions
flanking the EcoRI cloning sites were also determined, by
using the M13 universal primers designated reverse and
40 forward.
Sequencing of a 1,678-bp region from both clones revealed open reading
frames with high identity to previously sequenced
cbbM genes
(Fig.
1 and
2).
cbbM is preceded by an in-frame TAG stop
codon at position

9 and then begins with an ATG and proceeds
1,383 bp to a TAA stop
codon, followed by a putative hairpin loop
beginning 27 bp downstream
(Fig.
1). The
cbbM coding region is
composed of 57.5 mol%
G+C, and a 461-amino-acid protein with a
calculated molecular weight of
50,552 Da is predicted. Efforts
to express active recombinant form II
RubisCO failed to yield
enzyme with significant activity, suggesting
that the recombinant
does not fold properly in
E. coli or is
posttranslationally modified
by the bacterial symbiont.
Therefore, biochemical characterization
of this RubisCO is currently
being conducted on native enzyme.

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FIG. 1.
Nucleic acid sequence of the R. pachyptila
cbbM gene. The deduced amino acid sequence of the form II RubisCO
is shown, with the putative Shine-Dalgarno sequence and hairpin loop
underlined. An asterisk marks the TAA stop codon.
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FIG. 2.
Alignment of R. pachyptila RubisCO with other
form II enzymes and a representative form I from S. oleracea
(shown for comparison). Asterisks refer to residues known to be
involved in the active site and activating CO2 binding
site. Dots indicate residues identical to those in the R. pachyptila sequence, and dashes are added to preserve the
alignment. The alignment of form I and II RubisCOs is based on the
three-dimensional structure (26).
|
|
Analysis of sequence flanking the
EcoRI cloning sites
revealed the presence of an open reading frame sharing identity to the
LysR type regulator
cbbR (not shown). This gene is upstream
of
cbbM and in the opposite orientation. The deduced amino
acid sequence
of the cbbR element has 61% identity with the
cbbR of
Chromatium vinosum (
31) over
the region sequenced, which spans 71 residues
at the 5' end.
Translation of the open reading frame and alignment with other form II
enzymes and a representative form I RubisCO (Fig.
2)
revealed strict
conservation of residues known to form the enzyme
active site (
11,
26), e.g., the specific lysine residue which
is carbamylated
during enzyme activation and corresponds to position
191 of the
R. rubrum sequence. N-terminal sequence analysis indicates
that the first-position methionine residue is posttranslationally
cleaved (
3), a situation encountered in plant RubisCO
enzymes
(
12). Amino acid identity with other form II
RubisCOs ranges
from a high of 76.2% with
R. rubrum to a
low of 69.1% with the
dinoflagellate
Gonyaulax polyedra.
With regard to amino acid similarity,
i.e., by comparison of major
amino acid biochemical groupings,
the
R. pachyptila enzyme
is most similar (89.2%) to the
Rhodobacter sphaeroides
form II enzyme and shows 78 to 89% similarity with
all the other form
II enzymes. In contrast, the
R. pachyptila RubisCO shows
only 22 to 32% amino acid identity with the gene
encoding the large
subunit of representative form I RubisCOs,
including that of
Spinacia oleracea.
The discovery of a form II RubisCO in a deep-sea organism indicates
that this enzyme is found in diverse settings and is not
as rare as
once thought. Indeed, six other deep-sea symbionts
and two bacterial
mats have recently been shown to express this
form of RubisCO (
3,
20,
21). While both forms of RubisCO
are expressed in some
free-living bacteria (
30,
31), the
R. pachyptila
symbiont appears to encode and express only a form
II enzyme. In the
R. pachyptila symbiosis, hybridization to a
form I
heterologous gene probe was not detected during library
screening or
Southern analysis of trophosome DNA, in contrast
to earlier reports
(
29,
32), nor was a form I gene product
detected
(
21). Indeed, other researchers have also failed to
detect
the gene encoding the form I enzyme in the
R. pachyptila symbiont, detecting only the
cbbM gene (
14).
Physiologically,
the use of a form II RubisCO in this symbiosis is not
surprising,
given that form II enzymes typically have a low affinity
for CO
2 and that concentrations of CO
2 are
extremely high in the blood
of the tubeworm, where concentrations of
total dissolved inorganic
carbon can be greater than 30 mM
(
5).
The expression of form I and II RubisCO has recently been suggested to
account for the difference observed in stable carbon
isotope ratios
(
13C) of hydrothermal vent invertebrate-chemoautotrophic
bacterial
symbioses (
3,
21). These symbioses fall into two
groups based
upon their
13C values, with
13C =

27 to

35% for mollusc symbioses and
13C =

9 to 16% for tubeworm and shrimp symbioses
(references
21 and references within). Several
hypotheses, such as carbon limitation
(
9,
19), a
C
4-type pathway in the tubeworms (
7), or the
use
of isotopically different source CO
2 utilized by the two
groups
(
4), have been proposed to explain the differences in
13C values but have failed to be corroborated by
experimental data.
The KIEs of the few form I (for
S. oleracea, 29%; for
Anacystis nidulans, 22%
[
10,
22]) and form II (for
R. rubrum, 17.8 to
23% [
10,
23]) RubisCOs examined by high-precision
methods
indicate that the two forms fractionate carbon isotopes to
differing
degrees. Given the high identity between the
R. rubrum and
R. pachyptila cbbM sequences, the expression
of a form II RubisCO
in
R. pachyptila could account for the
heavier isotopic composition
if the extreme values for the KIE of the
form II RubisCO are considered.
Chemoautotrophic symbioses and free-living chemoautotrophs represent a
vast resource for examining different adaptations that
have occurred in
RubisCO biochemistry and evolution. These organisms
promise to yield
important new information regarding enzymological
adaptation,
regulation, and genetic diversity, as they inhabit
many niches which
are too inhospitable for photoautotrophs. The
examination of a greater
diversity of species for the form II
RubisCO is necessary to determine
the distribution of this enzyme
among autotrophs.
Nucleotide sequence accession number.
The R. pachyptila symbiont cbbM gene sequence has been
deposited in GenBank under accession no. AF047688.
 |
ACKNOWLEDGMENTS |
We thank the chief scientists and captains and crew of the RV
Atlantis II and DSV Alvin for their excellent
assistance in sample collection, George Lorimer for the generous gift
of antiserum, and Marjory Snead for the R. pachyptila DNA
library construction.
This work was supported in part by NSF grants OCE-9317734 (J.L.S.) and
OCE-9504257 (C.M.C.). J.J.R. was also supported by a Graduate
Assistance in Areas of National Need fellowship from the Department of
Education.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138. Phone: 617-495-2177. Fax: 617-496-6933. E-mail: cavanaug{at}hump.harvard.edu.
 |
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J Bacteriol, March 1998, p. 1596-1599, Vol. 180, No. 6
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
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