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Journal of Bacteriology, January 1999, p. 68-77, Vol. 181, No. 1
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Cloning and Expression of Three New
Azotobacter vinelandii Genes Closely Related to a Previously
Described Gene Family Encoding Mannuronan C-5-Epimerases
Britt Iren Glærum
Svanem,1
Gudmund
Skjåk-Bræk,2
Helga
Ertesvåg,1 and
Svein
Valla1,*
UNIGEN Center for Molecular
Biology1 and
Department of
Biotechnology,2 Norwegian University of Science
and Technology, N-7005 Trondheim, Norway
Received 17 August 1998/Accepted 26 October 1998
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ABSTRACT |
The cloning and expression of a family of five modular-type
mannuronan C-5-epimerase genes from Azotobacter vinelandii
(algE1 to -5) has previously been reported. The
corresponding proteins catalyze the Ca2+-dependent
polymer-level epimerization of
-D-mannuronic acid to
-L-guluronic acid (G) in the commercially important
polysaccharide alginate. Here we report the identification of three
additional structurally similar genes, designated algE6,
algE7, and algY. All three genes were sequenced
and expressed in Escherichia coli. AlgE6 introduced
contiguous stretches of G residues into its substrate (G blocks), while
AlgE7 acted as both an epimerase and a lyase. The epimerase activity of
AlgE7 leads to formation of alginates with both single G residues and G
blocks. AlgY did not display epimerase activity, but a hybrid gene in
which the 5'-terminal part was exchanged with the corresponding region
in algE4 expressed an active epimerase. Southern blot
analysis of genomic A. vinelandii DNA, using the 5' part of
algE2 as a probe, indicated that all hybridization signals
originated from algE1 to -5 or the three new
genes reported here.
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INTRODUCTION |
Alginate is a linear copolymer
composed of
-D-mannuronic acid (M) and its C-5 epimer,
-L-guluronic acid (G). The M and G residues are
organized in blocks of consecutive M residues (M blocks), consecutive G
residues (G blocks), or alternating M and G (MG blocks), and the
lengths and distributions of the different block types vary among
alginates isolated from brown algae or from different bacteria
belonging to the genera Azotobacter and Pseudomonas (36, 37). Alginates are the most
abundant polysaccharides in brown algae (comprising up to 40% of the
dry matter), and their functions are to supply strength and flexibility
to the algal tissues (38). The bacterium Azotobacter
vinelandii produces alginate both as a vegetative state capsule
and as an integrated part of a particular resting stage form (cyst) of
this organism (31). The opportunistic pathogen
Pseudomonas aeruginosa produces alginate as a capsule-like
exopolysaccharide during infection of the lungs of cystic fibrosis
patients (12, 23). Alginates from brown algae and A. vinelandii have M, G, and MG blocks (29, 36, 37), while
alginates from P. aeruginosa and other
Pseudomonas species do not contain G blocks (34,
36). In contrast to the alginates produced by brown algae,
bacterial alginates are partially O-acetylated at O-2 and/or O-3 on
mannuronic acid residues (36).
The relative amount and distribution of G residues determine most of
the physicochemical properties of the polymer. Alginates with G blocks
can form gels by reversible cross-linking with divalent cations such as
Ca2+, Ba2+, and Sr2+
(41), and the gelling and viscosifying properties of
alginate are utilized in pharmaceutical, food, textile, and paper
industries (26). In addition, alginate has a very
interesting potential in a variety of biotechnological applications and
in biomedicine. Alginate rich in M blocks stimulates cytokine
production (27) and has a much higher antitumor activity
than alginates with a high fraction of G blocks (14). G-rich
alginates can be used for encapsulation of cells and enzymes
(35), and Langerhans islets immobilized in alginates rich in
G have been evaluated as a potential treatment for type 1 diabetes
(39, 40).
Both in brown algae and in alginate-producing bacteria, the polymer is
first synthesized as mannuronan, and the enzyme mannuronan C-5-epimerase catalyzes the epimerization of M to G at the polymer level (7, 12, 21, 22). Ertesvåg et al. (7) have
previously reported the cloning and expression of five genes encoding a
family of Ca2+-dependent epimerases in A. vinelandii (algE1 to -5). The deduced AlgE
protein sequences consist of two types of structural modules, designated A (385 amino acids each; one or two copies) and R (155 amino
acids each; one to seven copies), and each R module contains four to
six nine-amino-acid-long repeated sequences corresponding to putative
Ca2+-binding motifs. The molecular masses of AlgE1 to -5 vary from 57.7 (AlgE4) to 191 kDa (AlgE3), depending on the number of A and R modules in the proteins. Four of the epimerase genes are clustered in the chromosome (algE1 to -4), while
algE5 is located in another part of the A. vinelandii genome. Nuclear magnetic resonance (NMR) spectroscopy
analyses demonstrate that the reaction products at least of AlgE2 and
AlgE4 differ with respect to sequence distributions of M and G
residues. AlgE2 leads to formation of mainly G blocks, while AlgE4
forms predominantly alginates with MG blocks.
The A. vinelandii chromosome also encodes a
Ca2+-independent mannuronan C-5-epimerase, designated AlgG
(30). Sequence alignments demonstrate that algG
does not belong to the algE gene family but shares 66%
sequence identity to a mannuronan C-5-epimerase gene (also designated
algG) from P. aeruginosa (12). The
algG gene in P. aeruginosa is localized in a
cluster of alg genes encoding enzymes involved in alginate
biosynthesis, and sequence analysis of genomic DNA flanking
algG in A. vinelandii suggests that this gene
also is part of an alg gene cluster organized as in P. aeruginosa (30).
Southern blot analysis of genomic A. vinelandii DNA using
the 5'-terminal 800 bp in the A sequence of algE2 as the
probe (A probe) demonstrated that the chromosome probably encodes more A-like sequences than are present in algE1 to -5
(7). In this report, we show that the A. vinelandii genome encodes two additional mannuronan C-5-epimerase
genes, designated algE6 and algE7, and also a
third highly related gene apparently not encoding an active epimerase.
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MATERIALS AND METHODS |
Bacterial strains, phages, and plasmids.
Strains, phages,
and plasmids are listed in Table 1.
Growth of bacteria and phages.
A. vinelandii was grown
at 30°C with shaking in nitrogen-free medium (9.8 mM
K2HPO4-KH2PO4, 0.8 mM
MgSO4 · 7H2O, 3.4 mM NaCl, 8.7 µM
Na2MoO4 · 2H2O, 54 µM
FeSO4 · 7H2O, 1% sucrose).
Escherichia coli cells were for most purposes grown in L
broth or on L agar at 37°C (32). For all activity
measurements, the cells were grown in threefold-concentrated L broth.
When relevant, the E. coli media were supplemented with 0.2 mg of ampicillin per ml (unless otherwise stated). When the cells were
to be used for growth of phages, the L broth was supplemented with 10 mM MgSO4 and 0.2% maltose.
Standard recombinant DNA technology.
Restriction
endonuclease digestions, ligations, and agarose gel electrophoresis
were performed in accordance with standard protocols (32).
Transformations were performed as described by Chung et al.
(2). Genomic DNA from A. vinelandii was isolated by using a genomic DNA kit from Qiagen. Plasmid isolations were performed by the use of a plasmid midi kit from Qiagen (for sequencing) or a Wizard miniprep kit from Promega. DNA sequencing was performed by
using cycle sequencing with an Amply Taq kit on an Applied Biosystems
model 373 automatic sequencer. The genes were sequenced on both strands
by the Biotechnology Centre, University of Oslo, and at Medigene,
Martinsried, Germany.
Screening of an A. vinelandii gene library and
Southern blot analyses.
An EMBL3 gene library prepared from
A. vinelandii DNA (5) was plated on E. coli NM538 on L agar (32). The overlaying agar
contained 0.7% agarose, 0.2% maltose, and 10 mM MgSO4. A total of 6,000 phages were examined in the screening procedure. The Dig
system (Biochemica, Boehringer Mannheim) was used to label the A probe
(random-primed DNA labeling), and gene library screening and Southern
blot analyses were performed as specified by the manufacturer.
Protein sequence comparisons and relationships.
Protein
alignments were done with the MACAW program (33), and
phylogenetic analyses were done with the PHYLIP program package, version 3.5c (9). Protein distance matrices were calculated with the Protdist program, using a Dayhoff PAM matrix (4). The Fitch program rooted with AlgE7A was used to create the unrooted tree for the A modules, while the Neighbour program rooted with AlgE7R2
was used to create the unrooted tree for the R modules (11).
The Drawgram program was used to plot the phenograms.
Cloning of algE6, algE7,
algY, and the hybrid genes algE4-algY and
algY-algE4 into expression vectors.
The open reading
frame encoding AlgE6 was cloned into pTrc99A by a two-step protocol. In
step 1, the 1.0-kb 5' end of algE6 was PCR amplified from
pBG18 (Fig. 1A). PCR primer 1 (5'
GAAGCGGAGCCATGGATTACAACG 3') was constructed to
change two of the bases proximal and upstream of the ATG start codon
from AT to CC (underlined), introducing a new NcoI site.
Primer 2 was a vector primer for pLITMUS28 (5' CGCCAGGGTTTTCCCAGTCACGAC 3' (New England Biolabs). The PCR
fragment was then ligated into pTrc99A, generating pBG24. In step 2, a 1.8-kb DNA fragment from pBG28 containing the 3' part of
algE6 was ligated into pBG24, generating pBG29.

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FIG. 1.
Physical map of genomic A. vinelandii DNA
showing the chromosomal locations of algE1 to -4,
algE6 and algE7 (A), algY (B), and
algE5 (C). The genes and their direction of transcription
are indicated by filled arrows. The modular structure of the deduced
AlgE6, AlgE7, and AlgY proteins are illustrated below the arrows. The
inserts in the different plasmids and phages are presented as lines.
Restriction sites: BglII (B), BsaWI (Bsa),
BstEII (Bst), EcoRI (E), HindIII
(H), KpnI (K), NcoI (N), SalI (S), and
XmaI (X). For BsaWI, EcoRI,
KpnI, XmaI (A), SalI (B), and
BstEII (A and B), only the restriction sites used in the
different cloning steps are shown (see Materials and Methods and Table
1). Note that only part of the insert in EP1 is shown.
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The open reading frame encoding AlgE7 was cloned into pTrc99A by a
two-step PCR protocol. In step 1, primers 3 and 4 were used on pBG23
(Fig. 1A) to PCR amplify the 5' 1.9-kb part of algE7. Primer
3 served to change two of the bases proximal and upstream of the ATG
start codon from AG to CC (underlined) in order to generate a new
NcoI site (5' AGCGAAGCCCATGGAATACAACG 3').
Primer 4 (5' CACACTACCATCGGCGCT ACG 3') is a vector
primer for pTrc99A. The resulting PCR product was ligated into pTrc99A,
generating pBG25. In step 2, PCR was used on pBG18 (Fig. 1A) to amplify
the 3' 0.9 kb of algE7 by using the vector primer 5'
AGCGGATAACAATTTCACACAGGA 3' (New England Biolabs) for pLITMUS28
and primer 5 (5' TCCGAAGCTTGCCCGAATGAAACGATCC 3';
the HindIII site is underlined), which generates a
HindIII site downstream of the 3' end in
algE7. This PCR product was ligated into pBG25, generating pBG27.
The open reading frame encoding AlgY was cloned into pTrc99A as a
2.1-kb DNA fragment from pBG32 (generating pBG33) by using site-specific mutagenesis on pBG31 to change two of the bases proximal
and upstream of the ATG start codon from AA to CC (introducing a new
NcoI site). The site-directed in vitro Altered Sites
mutagenesis system was obtained from Promega and used according to the
manufacturer's instructions. The oligonucleotide used to introduce an
NcoI site overlapping the start codon was 5'
AAGCGGATCCATGGATTTCAACGT 3' (the new bases after
mutagenesis are underlined).
Two new plasmids, designated pBG36 and pBG41, were constructed by using
a common restriction site (BstEII) in algY and
algE4 (bp 598 to 604 in algY and bp 599 to 605 in
algE4). algE4 was previously cloned into pTrc99A,
generating pHH4 (7).
Expression of AlgE6, AlgE7, AlgY, AlgE4-AlgY (encoded by pBG36)
and AlgY-AlgE4 (encoded by pBG41) and preparation of crude
extracts.
One hundred milliliters of culture medium was inoculated
to 1% from an overnight culture of strains SURE(pBG27), SURE(pBG29), SURE(pBG33), JM109(pBG36), and JM109(pBG41) in the same medium. The
JM109(pBG36) medium was supplemented with 0.5 mg of ampicillin per ml
due to some plasmid loss problems. After 3 h of incubation with
shaking, the production of the corresponding enzymes was induced by
adding isopropyl-
-D-thiogalactopyranoside (IPTG) at a
concentration of 0.5 mM. The cells were harvested 3 to 4 h after induction, and the optical density at 600 nm was measured. The harvested cells were resuspended in 10 ml of MC buffer [20 mM 3-(N-morpholino)propanesulfonic acid (pH 6.9), 2.2 mM
CaCl2] and then disrupted by ultrasonication. The broken
cells were centrifuged at 27,000 × g for 30 min, and
the supernatants were filtered through a 0.2-µm-pore-size Millipore
filter prior to activity measurements and partial purification by fast
protein liquid chromatography (FPLC).
Measurements of epimerase activity by radioisotope assays.
5-3H-labeled alginate (specific activity, 144,330 dpm/mg of
alginate, 95% mannuronic acid) was prepared by growing P. aeruginosa in a medium containing 5-3H-labeled glucose
and used as substrate for the crude cell extracts in the radioisotope
assays (30). Epimerase activities were measured in reaction
mixtures (total volume of 0.6 ml) containing 0.1 mg of tritiated
M-enriched alginate, 10 µl of cell extract, and MC buffer.
Incubations were performed at 37°C for 1 h, and the reactions were terminated by adding 15 µl of 5 M NaCl and 0.8 ml of
isopropanol. The alginate was precipitated at
80°C for 30 min and
then centrifuged at 27,000 × g for 30 min. One
milliliter of supernatant was used for determination of released
3H in a scintillation counter. All assays were performed in duplicate.
Partial purification of AlgE6, AlgE7, and AlgE4-AlgY by FPLC and
measurements of epimerase activity by NMR spectroscopy.
The
filtered crude cell extracts were loaded onto a HiTrap Q Sepharose HP
column (Pharmacia) equilibrated with MC buffer. The three enzymes were
eluted with a 0 to 1 M NaCl gradient (in MC buffer). AlgE6 was eluted
between 0.3 and 0.35 M NaCl, AlgE7 was eluted between 0.35 and 0.45 M
NaCl, and AlgE4-AlgY was eluted between 0.37 and 0.42 M NaCl. The
purification factors for AlgE6, AlgE7, and AlgE4-AlgY were 4.2, 9.2, and 14.5, respectively. The fractions with epimerase activity were used
directly as a source of enzyme for incubation with alginate.
The partially purified proteins were incubated with 1 ml M-enriched
unlabeled alginate from P. aeruginosa (7.5-mg/ml stock solution, 95% mannuronic acid; prepared as described for the labeled alginate) in MC buffer, and the reaction mixtures (total volume of 6 ml) were incubated at 37°C for 5, 8, and 18 h (AlgE6), 10 h
(AlgE7), and 8 h (AlgE4-AlgY hybrid). The reactions were
terminated by chelation of Ca2+ with addition of
Na2EDTA (0.5 M, pH 8.0) to 10 mM, and the solutions were
dialyzed extensively against distilled water before preparation for NMR
spectroscopy (17).
Nucleotide sequence accession numbers.
The algE6,
algE7, and algY nucleotide sequence data were
deposited in the GenBank database under accession no. AF099799, AF099800, and AF099801, respectively.
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RESULTS |
Screening of an A. vinelandii gene library and Southern
blot analyses of phage DNA.
The A probe was used to screen a phage
EMBL3 gene library prepared from A. vinelandii DNA. Forty
reproducibly hybridizing plaques were identified, and DNA was prepared
from each of the corresponding clones. The DNA preparations were
digested with a series of restriction endonucleases selected on the
basis of the known sequences of the regions containing algE1
to -5). Southern blot analyses of these digests (using the
same probe as described above) indicated that 10 of the 40 clones
contained A-hybridizing sequences not belonging to algE1 to
-5. Further analyses of the 10 new clones showed that they
originated from two separate regions of the A. vinelandii
chromosome. One of these regions, represented by six phage clones, were
found to be closely linked to the region from algE1 to
-4. Further analyses of the DNA in these phages showed that
one of them (EP35) covered all of the A-hybridizing signals represented
by the group, and the insert in this phage was in addition found to
cover algE4. The remaining four phages all overlapped and
were found to contain only one A-homologous sequence. Phage EP1 was
chosen for further studies of this group.
DNA sequencing and identification of three new putative epimerase
genes.
DNA fragments from the insert of phage EP35 were subcloned
into the plasmid vector pLITMUS28, and the resulting recombinant plasmids were designated pBG5, pBG6, and pBG18 (Fig. 1A). DNA sequencing of parts of the inserts in these plasmids led to the identification of two new putative epimerase genes, designated algE6 and algE7. The 3' end of algE6
was found to lie only 276 bp upstream of algE4, while the 3'
end of algE7 was found to lie about 5 kb upstream of the
start of algE6.
In phage EP1, only one region hybridized to the A probe, and this
region was also subcloned into pLITMUS28, generating plasmid pBG2 (Fig.
1B). Sequencing of the relevant part of the subcloned region led to the
identification of yet another putative epimerase gene. For reasons
described below, this putative gene was assigned another type of
designation, algY.
Amino acid sequence analyses of the deduced proteins encoded by
algE6, algE7, and algY.
Inspection
of the deduced amino acid sequences of AlgE6 and AlgE7 showed that the
A module represented the amino-terminal part of the putative proteins
and that the sequences also contained three repeats each of the
sequences homologous to the R modules found in AlgE1 to -5 (Fig. 1A).
This structure is thus new, since none of the proteins AlgE1 to -5 contain three R modules. A similar analysis of AlgY revealed that the
modular structure of this putative protein is AR, as in AlgE4 (Fig.
1B). Alignment of the sequences of the A modules of the three putative
proteins (Fig. 2) showed that the percentages of homology were 64 (AlgE6-AlgE7), 65 (AlgE6-AlgY), and 63 (AlgE7-AlgY). Based on this
alignment, we constructed a consensus sequence, ConA*, and aligned it
against the previously reported consensus sequence (ConA) of the A
modules in AlgE1 to -5. The percentage of homology between the two
sequences is 72, suggesting that all A sequences have a common
evolutionary origin. However, closer inspection of the alignments
showed that some local regions were not very similar to those
previously reported. This point is most clearly seen for the 11 amino
acids double underlined in Fig. 2 (amino
acids 117 to 127 in the ConA sequence). All of these residues are 100%
conserved in the A modules of AlgE1 to -5 (7). The AlgE6
sequence deviates by only one residue (isoleucine to alanine) from this
sequence, but in AlgE7 and AlgY five and seven, respectively, of the
residues are different. Three of these nonconserved amino acids are
identical in AlgE7 and AlgY (residues 121 to 123 in the ConA sequence).
Similarly, amino acids 92 to 102 in ConA are all identical in AlgE1 to
-5, and two of these residues are different in AlgE6 (single
underlining in Fig. 2). In AlgE7 and AlgY, on the other hand, 6 of the
11 residues are different. Two of these nonconserved amino acids
(residues 98 and 99) are identical in AlgE7A and AlgYA, where a serine
and an asparagine are replaced with a histidine and an aspartic acid, respectively.

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FIG. 2.
Alignment of the A modules in AlgE6, AlgE7, and AlgY.
The ConA* sequence represents the consensus sequence (more than 50%
identity) derived from AlgE6A, AlgE7A, and AlgYA; the ConA sequence
represents the consensus sequence (more than 50% identity) derived
from the A modules in AlgE1 to -5. Open spaces indicate no identity,
and dashes indicate gaps. Single dots indicate that the corresponding
amino acid is the same as in ConA*, while double dots represent amino
acid identity between ConA* and ConA. Each number to the right
indicates the position (relative to the N-terminal end of the deduced
protein) of the terminal residue in that line.
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The R modules of AlgE6, AlgE7, and AlgY were also aligned (Fig.
3); as previously reported for AlgE1 to
-5, these sequences deviate much more from each other than do the A
modules. However, the degree of similarity is clearly sufficient to
conclude that the R sequences of the three new genes are closely
related to those in AlgE1 to -5. The putative Ca2+-binding
motifs found to be repeated four to six times N terminally in the R
modules of AlgE1 to -5 are also found in the modules reported here.
Interestingly, such a motif is repeated seven times in the middle R
module of AlgE7. The deduced consensus sequence (ConR*) of the R
modules of the three new genes shows, as expected, very significant
homology to that previously reported for AlgE1 to -5 (ConR). The
terminal amino acids of all deduced enzymes were given the specific
designation S in AlgE1 to -5 because they seemed to represent extra
residues relative to all the other R modules (7), and the
same appears to be true for the new sequences reported here. Moreover,
the deduced R modules of AlgE6 are separated by short (10 residues)
amino acid sequences, six of which are the same (Fig. 3). Note also
that three of these six residues are prolines.

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FIG. 3.
Alignment of the R modules in AlgE6, AlgE7, and AlgY.
Notation is as in Fig. 2 except that open spaces indicate 50% identity
or less. The vertical lines at the top indicate the start of each
nonameric putative Ca2+-binding motif, while the broken
vertical lines near the termini represent the end of the R modules
(left) and the start of the S motifs (right). The S motif refers to the
extra terminal amino acids in AlgE6, AlgE7, and AlgY, which are not a
formal part of the R modules in the proteins (7). The ConS*
sequence represents the consensus sequence (50% identity or more)
derived from the S motifs in AlgE6A, AlgE7A and AlgYA; the ConS
sequence represents the consensus sequence (more than 50% identity)
derived from AlgE1S to -E5S.
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Based on all available sequence data, we constructed an evolutionary
tree of both the A (Fig. 4A) and R (Fig.
4B) modules. According to this analysis, the A modules in AlgE7 and
AlgY are the two sequences that are most diverse relative to all the
other A sequences. The AlgE6 A module, on the other hand, groups
together with several others and appears to be most closely related to the A module of AlgE4. This analysis therefore correlates well with the
observations of sequence deviations in local regions.

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FIG. 4.
Phenograms constructed on the basis of alignments of the
A modules in AlgE1 to -7 and AlgY (A) and the R modules in AlgE1 to -7 and AlgY (B). The A and R modules in AlgE6, AlgE7, and AlgY are
underlined.
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The relationships among the R modules are more complex than for the A
modules, but in general, strongly related R modules tend to be in the
same position relative to the A modules, as previously reported
(7). However, the three R modules in AlgE6 form a separate
subgroup, and two of the R modules in AlgE7 (R1 and R2) are much less
related to all other modules according to this analysis.
The sequences upstream of algE1 to -5 (M1 to M5)
show significant sequence similarity but do not contain any obvious
promoter sites of the E. coli
70 type
(7). Some of the conserved regions in M1 to M5 are also present upstream of algE6 and algE7 (M6 and M7),
while the upstream region of algY (MY) was very different
from all of the other corresponding regions. No sequences putatively
involved in binding of prokaryotic sigma factors could be identified in
M6, M7, and MY.
Expression analyses and measurements of epimerase activities.
Some of the bases 5' to the putative start ATG of algE6,
algE7, and algY were substituted in order to
generate NcoI restriction endonuclease sites facilitating
insertion of the genes at the ATG start site of the expression vector
pTrc99A. The corresponding plasmids, designated pBG29
(algE6), pBG27 (algE7), and pBG33
(algY), were then transformed into E. coli SURE,
and cultures of the corresponding transformants were used for analyses
of epimerase expression from the trc promoter. The results
of these experiments showed that IPTG-induced cells containing pBG29
and pBG27 expressed activities consistent with the expression of
mannuronan C-5-epimerases. However, no activity was detected in
extracts prepared from cells containing pBG33 (Table
2). This latter result was quite
surprising since it is the only example among eight of a gene
containing A and R modules that do not express epimerase activity in
E. coli.
As described above (Fig. 2), local stretches of amino acid sequences in
the N-terminal half of AlgY (and AlgE7) are quite different from the
corresponding sequences in AlgE1 to -6. One possible interpretation of
this is that AlgY throughout evolution has developed some function
other than epimerization, explaining the observed lack of epimerase
activity after expression in E. coli. To analyze this
hypothesis further, we substituted the 5' part (encoding the first 200 amino acids) of algY with the corresponding part of
algE4, generating plasmid pBG36 (encoding the hybrid protein AlgE4-AlgY). This experiment was facilitated by the presence of a
common BstEII site in the same position (according to the
alignments) in the two genes. We also constructed the reciprocal
plasmid, pBG41 (encoding the hybrid protein AlgY-AlgE4), in which the
corresponding 3'-terminal part of algY (encoding the
terminal 337 amino acids) was substituted with that of
algE4. Plasmids pBG36 and pBG41 were transformed into
E. coli JM109, and the corresponding cell extracts were
analyzed with respect to epimerase activity after IPTG induction (Table
2). These experiments showed that pBG36 expressed strong epimerase
activity, while no activity was detected from pBG41. We therefore
conclude that one or more amino acid residues encoded by the sequence
upstream of the BstEII restriction site in algY is responsible for the lack of epimerase activity.
Analysis of reaction products by NMR spectroscopy.
The
recombinant proteins expressed by plasmids pBG29 (AlgE6), pBG27
(AlgE7), and pBG36 (active AlgE4-AlgY hybrid) were partially purified
by FPLC and incubated with M-rich alginate, and the reaction products
were finally analyzed by NMR spectroscopy. The data confirmed that
AlgE6 is an epimerase and that it introduces G blocks into its
substrate (Fig. 5 and Table
3). This enzyme is therefore functionally
related to AlgE2 (7). The NMR data show that within 18 h the M-rich substrate, initially devoid of G blocks, is
converted to a polymer with an average number of G residues in the G
blocks, NG > 1
15. This finding
signifies a polymer with high cooperative binding capacity for calcium
ions, and with a predicted strong gel-forming capacity.

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FIG. 5.
1H NMR spectroscopy monitoring the action of
AlgE6 on an alginate with molar fractions of 0.95 and 0 for M and GG,
respectively. The samples were incubated for 5, 10, and 18 h, and
the spectra were recorded at 90°C on a Bruker Avance DPX 300 MHz
instrument. The samples contained 10 mg of alginate per ml in
D2O at pH 6.8.
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The NMR spectrum of alginate incubated with AlgE7 also confirmed that
this protein is an epimerase (Fig. 6).
Furthermore, the spectrum shows that the epimerization pattern is
different from that of AlgE6, in that AlgE7 introduces both single G
residues and G blocks. Even more interesting, however, are the high
intensities of the resonance signals from the reducing ends as well as
two additional peaks at 5.77 and 5.19 ppm arising from unsaturated protons. These latter protons are due to the formation of unsaturated 4-deoxy-L-erythro-hex-4-enepyranosyluronate
residues (
) by a
-elimination reaction (19). AlgE7
thus exhibits both epimerase and lyase activities, a property not
previously reported for any other enzyme. From the intensities of the
resonance signals of the end groups, the average size of the
unsaturated oligouronide was estimated (6) to represent a
pentasaccharide containing approximately 40% guluronic acid residues,
of which 50% are internal G and the other half represent the G
residues at the reducing ends. The lyase activity is apparently highly
specific since the G residues predominates at the reducing end, while
the unsaturated nonreducing end exclusively is
-M-.

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|
FIG. 6.
1H NMR spectrum of alginate epimerized by
AlgE7 (same alginate substrate as in Fig. 5). In the spectrum,
G, M, Gred,
Mred, and denote internal G
residues, internal M residues, reducing G and M residues and
4-deoxy-L-erythro-hex-4-enepyranosyluronate
residues, respectively; each numbers refer to the position of the
proton in the pyranosyl ring, and the nonunderlined M and G refer to
the neighbor residues. The spectrum was recorded as explained in the
legend to Fig. 5.
|
|
The NMR spectrum of alginate epimerized by the active AlgE4-AlgY hybrid
shows that this enzyme is an epimerase that predominantly produces
alginate with MG blocks, similar to AlgE4 (Fig.
7 and Table 3). Whether this
epimerization pattern is a direct result of the presence of the
N-terminal part of the AlgE4 A module is not known.

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|
FIG. 7.
1H NMR spectrum of alginate epimerized by
the AlgE4-AlgY hybrid (same alginate substrate as in Fig. 5). The
spectrum was recorded as explained in the legend to Fig. 5.
|
|
Southern blot analyses of genomic A. vinelandii
DNA.
Since all known algE-type epimerase genes have now
been sequenced, we were able to carry out a Southern blot analysis to
see if all hybridizing signals could be assigned to algE1 to
-7 or algY. Genomic A. vinelandii DNA
was digested with BglII, NcoI, and
HindIII (or combinations thereof) and subjected to
Southern blot analysis using the A fragment as a probe (Fig.
8). All of the hybridization signals
obtained in this analysis could be explained by the predicted
hybridizing fragments shown in Fig. 1. These results therefore indicate
that all algE-type genes present in the A. vinelandii genome have now been identified (see also Discussion).

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|
FIG. 8.
Southern blot analysis of genomic A. vinelandii DNA hybridized against the A probe. The DNA was
digested with BglII (lane 1),
BglII-NcoI (lane 2), NcoI (lane 3),
BglII-HindII (lane 4), and
NcoI-HindIII (lane 5). Numbers on the left
represent a -HindIII standard (in kilobases). Sizes
of the hybridizing DNA fragments should be compared to those predicted
in Fig. 1. Note that the signal intensities are strongly influenced by
the number of A modules in a given fragment and by the extent of
homology to the probe.
|
|
 |
DISCUSSION |
The A. vinelandii algE gene family represents an
unusually complex system with respect to both gene structure and
functional role, at least for a prokaryotic organism. Multicopy genes
(20, 24, 42, 44) and proteins with repeated homologous
sequences (10, 16, 25, 43) have previously been reported for
some bacteria, but a chromosomal arrangement combining these elements as in the epimerase gene family appears to be rather unique. The reason
why A. vinelandii has evolved at least seven structurally and functionally related genes to control the structure of its alginates is not fully understood. However, it seems very likely that
the existence of these genes is strongly related to the ability of
A. vinelandii to form metabolically dormant cysts, in which alginates of different structures presumably play a crucial role. In
the cyst stage, the modified vegetative cells are surrounded by a
capsule consisting of a thin outer layer (exine) and a thicker inner
layer (intine). Alginates account for 40 and 72% of the exine and
intine carbohydrates, respectively, and while the intine material
resembles the alginates in the vegetative cell capsule (mostly MM and
MG blocks; M/G ratio = 1.8), the alginates in the exine layer are
richer in polyguluronic acid (M/G ratio = 0.45), and 42% of the
diads are GG (28). If the predicted role of the epimerase
system in cyst formation is correct, it also implies that the epimerase
gene family can probably be seen as important components in a microbial
differentiation process, analogous to the extensively studied spore
formation in other bacteria.
If the above hypothesis is correct, it seems probable that each
epimerase catalyzes the formation of alginates with different physical
properties, as was previously shown for AlgE2 (G-block formation) and
AlgE4 (MG-block formation). The NMR analyses of the AlgE6 product
indicate that this enzyme is functionally related to AlgE2, but this
does not necessarily mean that their reaction products are structurally
or functionally equivalent. It could, for instance, be that the lengths
of the G blocks and the spacing between them are different, and such
differences might affect the properties of the corresponding alginates
significantly. In fact, currently available data indicate that AlgE6 is
capable of forming alginates with G blocks longer than those formed by AlgE2. It is well established in the literature that the alginate gel
strength increases with increasing G-block length (38, 41), and the observations described above therefore also may be significant with respect to the use of in vitro-epimerized alginates in industry and biotechnology.
Interestingly, AlgE7 displays both epimerase and lyase activities.
Gacesa (15) has proposed that the reaction mechanisms of
these two types of enzymes are very similar. Both enzyme activities includes removal of the proton at C-5 in the uronic acid, but instead
of replacing the C-5 proton in the final reaction step (epimerization),
the lyase activity catalyzes a
elimination of the 4-O-glycosidic
bond, producing unsaturated sugar derivatives at the nonreducing end.
According to this proposal, it seems probable that the same active site
is involved for both reactions with AlgE7. Whether the lyase reaction
can be viewed as an abortive epimerization or as an
epimerase-independent reaction is not clear. If the former is true, the
apparent specificity for the G-
-G-M or G-
-M-M glycosidic linkage
provides information about the direction of the epimerase action. A
more thorough study of epimerase-lyase coupling is under way in our
laboratory. The biological significance, if any, of the AlgE7 lyase
activity is not known. It is possible, however, that cyst formation
needs a fraction of shorter alginate oligomers and that AlgE7
contributes to this. A role in cyst germination also cannot be excluded.
The inability of algY to encode an active epimerase in
E. coli was surprising, as all other enzymes belonging to
this family are active after expression in this host. A Western blot
analysis (antibody kindly provided by Hilde Kristin Høidal) showing
that AlgY is produced in IPTG-induced E. coli cells excluded
the possibility that the lack of activity is caused by some expression
problems. The significance of this is unknown, but it could be that the enzyme is synthesized in an inactive form in E. coli, that
it needs an unknown cofactor, or that it displays some activity other than epimerization. It could, for instance, be that it is a lyase with
a substrate specificity not detected in our analyses. Concerning the
latter hypothesis, it should be emphasized that some of the nonconserved amino acids are similar in AlgE7A and AlgYA. These particular residues are located in the N-terminal part of the enzyme,
which when exchanged with the corresponding part from AlgE4 leads to an
active epimerase.
The Southern blot analysis of genomic A. vinelandii DNA
indicated that the chromosome does not contain any other genes
hybridizing to the A sequence. Recent experiments have shown that the A
module is responsible for the epimerization reaction (8),
and it is therefore likely that all active AlgE proteins encoded by
A. vinelandii have now been identified. The epimerase genes
appear to be localized in three separate physical locations, in which
algE5 and algY are localized separately.
Moreover, algE7 is separated by approximately 5 kb from the
main block containing algE1 to -4 and
algE6. All of the enzymes therefore clearly do not originate
from the same transcript. An operon organization in the block of six
genes seems also unlikely, since the length of the region (25 kb) and
the spacing between the genes are larger than expected for an operon structure (Fig. 1A and reference 7). By combining
transcriptional and Western blot analyses of A. vinelandii
cell cultures prepared during vegetative growth and at different stages
in the encystment process, it should be possible to approach these
problems in the near future.
 |
ACKNOWLEDGMENTS |
We thank Wenche Iren Strand for performing the NMR analyses.
This work was supported by grants from the Norwegian Research Council
and Pronova Biopolymers AS.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Unigen Center of
Molecular Biology, Medisinsk Teknisk Senter, N-7005 Trondheim, Norway. Phone: 47 73598680. Fax: 47 3598705. E-mail:
svein.valla{at}unigen.ntnu.no.
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