The labdane-related diterpenoids (LRDs) are an important superfamily of natural products whose structural diversity critically depends on the hydrocarbon skeletal structures generated, in large part, by class I diterpene synthases. In the plant kingdom, where the LRDs are predominantly found, the relevant class I diterpene synthases are clearly derived from the ent-kaurene synthase (KS) required in all land plants for phytohormone biosynthesis and, hence, are often termed KS-like (KSL). Previous work, initiated by the distinct function of two alleles of a KSL from rice, OsKSL5, identified a single residue switch with a profound effect on not only OsKSL5 product outcome but also that of land plant KSs more broadly, specifically, replacement of a key isoleucine with threonine, which interrupts formation of the tetracyclic ent-isokaurene at the tricyclic stage, leading to production of ent-pimaradiene instead. Here, further studies of these alleles led to discovery of another, nearby residue that tunes product outcome. Substitution for this newly identified residue is additionally shown to exert an epistatic effect in KSs, altering product distribution only if combined with replacement of the key isoleucine. On the other hand, this pair of residues was found to exert additive effects on the product outcome mediated by distantly related KSLs from the eudicot castor bean. Accordingly, it was possible to use a rational combination of substitutions for this pair of residues to engineer significantly increased (dominant) selectivity for novel 8α-hydroxy-ent-pimar-15-ene product outcome in the KS from the dicot Arabidopsis thaliana, demonstrating the utility of these results.
The labdane-related diterpenoids (LRDs) are an important superfamily of natural products whose structural diversity critically depends on the hydrocarbon skeletal structures generated, in large part, by class I diterpene synthases. In the plant kingdom, where the LRDs are predominantly found, the relevant class I diterpene synthases are clearly derived from the ent-kaurene synthase (KS) required in all land plants for phytohormone biosynthesis and, hence, are often termed KS-like (KSL). Previous work, initiated by the distinct function of two alleles of a KSL from rice, OsKSL5, identified a single residue switch with a profound effect on not only OsKSL5 product outcome but also that of land plant KSs more broadly, specifically, replacement of a key isoleucine with threonine, which interrupts formation of the tetracyclic ent-isokaurene at the tricyclic stage, leading to production of ent-pimaradiene instead. Here, further studies of these alleles led to discovery of another, nearby residue that tunes product outcome. Substitution for this newly identified residue is additionally shown to exert an epistatic effect in KSs, altering product distribution only if combined with replacement of the key isoleucine. On the other hand, this pair of residues was found to exert additive effects on the product outcome mediated by distantly related KSLs from the eudicot castor bean. Accordingly, it was possible to use a rational combination of substitutions for this pair of residues to engineer significantly increased (dominant) selectivity for novel 8α-hydroxy-ent-pimar-15-ene product outcome in the KS from the dicot Arabidopsis thaliana, demonstrating the utility of these results.
The labdane-related
diterpenoids
(LRDs) form a large superfamily of natural products, with ∼7000
known compounds, which are characterized by a decalin core structure.[1] While this bicyclic core is generated from the
acyclic general diterpenoid precursor (E,E,E)-geranylgeranyl diphosphate (GGPP)
by class II diterpene cyclases, substantial additional structural
diversity is generated by the subsequently acting class I diterpene
synthases. In the plant kingdom, where the LRDs are predominantly
found, these enzymes seem to have most directly evolved via gene duplication and neo-functionalization of the ent-kaurene synthases (KSs) required in all vascular plants for gibberellin
hormone biosynthesis.[2] Accordingly, these
enzymes are often termed KS-like (KSL) and form a distinct subfamily
within the plant terpene synthase family.[3]Like class I terpene synthases more generally, the KS(L)s
carry
out catalysis in a highly conserved α-helical bundle domain
that contains two signature motifs. These DDxxD and NDxx(S/T)xxxE
sequences are involved in ligation of a trinuclear Mg2+ cluster to promote substrate binding and the subsequent initiating
ionization of the allylic diphosphate ester bond.[4,5] This
is typically followed by formation of a series of carbocation intermediates,
leading to the creation of distinct diterpene backbones, largely guided
by the initial configuration of the substrate imposed by the steric
confines of the active site.[6] Moreover,
terpene synthases additionally seem to utilize electrostatic interactions
to further guide these carbocation cascades, including not only the
pyrophosphate anion coproduct but also electron-rich amino acid side-chains.[7] Finally, the reaction is terminated by deprotonation,
most often using the pyrophosphate anion coproduct,[8] which generally yields an olefin, although prior addition
of water can occur, yielding a hydroxylated product. Notably, such
hydroxylation also is a key step in terpenoid biosynthesis, as this
increases both solubility and the ability to specifically bind molecular
targets, which is required for biological activity.[2,9]Particularly relevant here are various single residue “switches”
between aliphatic and hydroxylated side-chains at a key position,
which profoundly affects product outcome in KS(L)s. This “switch”
position was initially identified by discovery of two functionally
distinct alleles of the rice (Oryza sativa) OsKSL5,
which react with ent-copalyl diphosphate (1, ent-CPP), with that from subspecies japonica (OsKSL5j) producing ent-pimara-8(14),15-diene (2) and that from subspecies indica (OsKSL5i)
producing ent-(iso)kaur-15-ene (3) instead.[10,11] Subsequently, of the three differences in the active site between
these two orthologs, it was found that mutation of an isoleucine in 3 producing OsKSL5i to the threonine occupying that position
in 2 producing OsKSL5j was sufficient to completely switch
product outcome, with the resulting OsKSL5i:I664T mutant yielding
only 2. Furthermore, this Ile was noted as being conserved
across all the known plant KSs, and substitution of Thr was found
to similarly alter product outcome with the KS from not only rice
(OsKS) but also the eudicot Arabidopsis thaliana (AtKS),
leading to predominant production of 2 rather than ent-kaur-16-ene (4).[12] Later work demonstrated similar effects with both the KS from a
gymnosperm[13] as well as those from earlier
diverging bryophytes.[14] This effect on
product outcome represents abbreviation of the sequential bicyclization
and rearrangement required for formation of the tetracyclic ent-kaurane backbone found in 3 and 4 after initial cyclization to a tricyclic ent-pimar-15-en-8-yl+ intermediate, which is then directly deprotonated at carbon-14
to yield 2 (Scheme ). Notably, the importance of Thr at this position
to enable pimaradiene production was demonstrated in another riceKSL, OsKSL4, as substitution of the Thr at this position by Ile led
to predominant production of a tetracycle resulting from further cyclization
and rearrangement of the initially formed syn-pimar-15-8-yl+ intermediate that is otherwise directly deprotonated by the
wild-type enzyme.[15] However, most KSLs
do not contain such a hydroxyl containing residue at this position,
demonstrating that alternative mechanisms exist for altering product
outcome. In addition, even in the original work with OsKSL5,[12] it was noted that substitution of Ile for the
Thr found at this position in OsKSL5j did not lead to complete specificity
for production of 3, as the resulting OsKSL5j:T664I also
produces small amounts of 4, along with more substantial
amounts of ent-atiserene (5), resulting
from alternative rearrangement of the ent-beyeran-12-yl+ intermediate formed by the second cyclization step (Scheme ).
Scheme 1
Cyclization Mechanism
for KS(L)s Investigated Here
All KSs produce 4. OsKSL5j produces 5,
while OsKSL5i produces 2. RcKSL2 produces largely 8. RcKSL3 produces 10. RcKSL4 produces 9. Initial cyclization of ent-CPP (1) leads to the ent-pimar-15-en-8-yl+, as C13 epimers, which may be followed
by either direct deprotonation, addition of water, or secondary cyclization,
most often followed by further rearrangement, prior to terminating
deprotonation. Compound numbering corresponds to that defined in the
text.
Cyclization Mechanism
for KS(L)s Investigated Here
All KSs produce 4. OsKSL5j produces 5,
while OsKSL5i produces 2. RcKSL2 produces largely 8. RcKSL3 produces 10. RcKSL4 produces 9. Initial cyclization of ent-CPP (1) leads to the ent-pimar-15-en-8-yl+, as C13 epimers, which may be followed
by either direct deprotonation, addition of water, or secondary cyclization,
most often followed by further rearrangement, prior to terminating
deprotonation. Compound numbering corresponds to that defined in the
text.Here is reported further investigation
of OsKSL5 that led to identification
of a secondary residue switch that further tunes product outcome.
Notably, this residue also is conserved in plant KSs, where it seems
to exert an epistatic effect, only altering product outcome in the
context of changes to the originally identified key Ile. Interestingly,
the residues at both positions were found to exert additive effects
on product outcome in distantly related eudicot KSLs. Building on
the realization that these can act in an additive fashion, rational
engineering of AtKS was carried out to enable predominant production
of a novel hydroxylated diterpene.
Results and Discussion
Further
Investigation of OsKSL5
It was previously found
that of the three differences in active site residues between the
orthologous OsKSL5j and OsKSL5i, switching the Ile at position 664
in OsKSL5i to the Thr found in OsKSL5j was sufficient to “short
circuit” the production of 3, as OsKSL5i:I664T
specifically produces 2 instead. However, the reciprocal
residue switch led to production of a mixture of tetracycles 3–5 (i.e., by OsKSL5j:T664I),
rather than the almost exclusive production of 3 observed
with OsKSL5i.[12] Hypothesizing that changes
to the other active site residues that differ between these two orthologs
might be sufficient to increase catalytic specificity for the production
of 3, the corresponding double residue switch constructs,
OsKSL5j:T664I + L661V or V718I, were made. The product outcome of
these two double mutants was investigated by incorporation into a
previously described modular metabolic engineering system—i.e., these were expressed in E. coli also
engineered to produce their substrate 1.[16] Relative to the original OsKSL5j:T664I single residue switch
mutant, while the addition of V718I did not alter product outcome,
the addition of L661V led to much more specific production of 3 (Figure a). Indeed, the product outcome mediated by this OsKSL5j:L661V/T664I
double residue switch mutant is essentially identical to that mediated
by OsKSL5i. Moreover, the reciprocal single residue switch, OsKSL5i:V661L,
led to reduced catalytic specificity and production of a mixture of 3–5, closely resembling that mediated
by the OsKSL5j:T664I mutant, although it does not affect the specific
production of 2 by the originally reported OsKSL5i:I664T
residue switch (Figure b). Thus, these two residues together seem to fully account for the
specific production of 2 versus 3 catalyzed
by these two functionally distinct alleles of OsKSL5.
Figure 1
Epistatic effect of the
original/primary and newly identified/secondary
pair of residues on OsKSL5 product outcome. (a) Chromatograms from
GC–MS analysis of wild-type OsKSL5j and the indicated mutants.
(b) Chromatograms from GC–MS analysis of wild-type OsKSL5i
and the indicated mutants. (c) Punnett square representation of the
epistatic effect of the primary (664) and secondary (661) residues
on product outcome in OsKSL5. Numbers correspond to the chemical structures
defined in the text. Enzymatic products were identified by comparison
of both retention time and mass spectra to authentic standards (Figure S1).
Epistatic effect of the
original/primary and newly identified/secondary
pair of residues on OsKSL5 product outcome. (a) Chromatograms from
GC–MS analysis of wild-type OsKSL5j and the indicated mutants.
(b) Chromatograms from GC–MS analysis of wild-type OsKSL5i
and the indicated mutants. (c) Punnett square representation of the
epistatic effect of the primary (664) and secondary (661) residues
on product outcome in OsKSL5. Numbers correspond to the chemical structures
defined in the text. Enzymatic products were identified by comparison
of both retention time and mass spectra to authentic standards (Figure S1).However, as previously reported,[12] switching
this residue alone did not affect the production of 2 by OsKSL5j, nor did the reciprocal double residue switch further
affect product outcome (i.e., both OsKSL5j:L661V
and OsKSL5i:V661L/I664T still specifically produce 2).
Hence, the presence of the hydroxyl containing Thr at the original/primary
position (i.e., residue 664) masks the effect of the newly identified/secondary
position (i.e., residue 661) in OsKSL5, and this pair of residues
then seems to exhibit an epistatic interaction (Figure c). In particular, the presence of leucine
instead of valine at the secondary position (661) decreases the specific
production of 3 in the presence of Ile at the primary
position, although it does not affect progression of the reaction
through the second cyclization step (i.e., all the
products are tetracycles; see Scheme ). On the other hand, even in the closely related (89%
amino acid sequence identity) 3 producing OsKSL6, substitution
of Leu for the Val found at this secondary position only slightly
decreases catalytic fidelity. The resulting OsKSL6:V661L mutant still
predominantly produces 3, with only slight increases
in the relative amounts of 4 and 5 (Figure S2), leaving in question the broader impact
of this secondary position on product outcome.
Investigation of the Secondary
Position in KSs
Notably,
the newly identified/secondary position seems to be completely conserved
as a Leu in land plant KSs (Figure a), which are specific for the production of 4. This contrasts to the results reported above with OsKSL5
and -6, where Leu instead of Val at this position negatively impacts
catalytic specificity. Substitution of Val for this Leu has only a
minor effect on product outcome in either the rice OsKS or AtKS—i.e., both OsKS:L655 V and AtKS:L635V still produce almost
entirely 4 (Figure b,c). Nevertheless, when combined with substitution
of Thr for Ile at the primary position, such substitution more dramatically
impacts catalytic fidelity, leading to less specific production of 2, with small increases in the relative amounts of 4, as well as the double-bond isomer of 2, ent-pimara-7,15-diene (6), and a more significant increase
in the amount of 8α-hydroxy-ent-pimar-15-ene
(7; resulting from addition of water prior to terminating
deprotonation). Thus, the effect of Leu versus Val at the secondary
position is largely masked in these two KSs, with substantial changes
in product outcome only evident upon substitution for the Ile at the
primary position. Accordingly, the residues at these two positions
in the KSs seem to exhibit an essentially epistatic relationship as
well, albeit with opposite effect as observed with OsKSL5 (c.f., Figures c and 2d).
Figure 2
Epistatic effect of the original/primary and newly identified/secondary
pair of residues on KS product outcome. (a) Partial sequence alignment
of representative KSs and KSLs with an asterisk (*) above the primary
(original) position and a pound sign (#) above the secondary (new)
position. Residues are numbered as in the full-length proteins from
the NCBI database accession numbers given in the Materials section. (b) Chromatograms from GC–MS analysis
of wild-type OsKS and the indicated mutants. (c) Chromatograms from
GC–MS analysis of wild-type AtKS and the indicated mutants.
(d) Punnett square representation of the epistatic effect of the primary
(prim.) and secondary (sec.) residues on product outcome in KSs. Numbers
correspond to the chemical structures defined in the text. Enzymatic
products were identified by comparison of both retention time and
mass spectra to authentic standards (Figure S1).
Epistatic effect of the original/primary and newly identified/secondary
pair of residues on KS product outcome. (a) Partial sequence alignment
of representative KSs and KSLs with an asterisk (*) above the primary
(original) position and a pound sign (#) above the secondary (new)
position. Residues are numbered as in the full-length proteins from
the NCBI database accession numbers given in the Materials section. (b) Chromatograms from GC–MS analysis
of wild-type OsKS and the indicated mutants. (c) Chromatograms from
GC–MS analysis of wild-type AtKS and the indicated mutants.
(d) Punnett square representation of the epistatic effect of the primary
(prim.) and secondary (sec.) residues on product outcome in KSs. Numbers
correspond to the chemical structures defined in the text. Enzymatic
products were identified by comparison of both retention time and
mass spectra to authentic standards (Figure S1).
Application in Distant
Eudicot KSLs
While monocots
seem to have particularly expanded upon LRD biosynthesis, with multiple
KSLs present in these species,[2] there are
a number of eudicots that similarly contain small families of KSLs.
This includes castor bean (Ricinus communis), which
contains three KSLs only distantly related to those found in monocots
and that further exhibit an intriguing range of catalytic functionality.[17] In particular, all three RcKSLs react with 1. However, RcKSL2 produces a mixture of pentacyclic ent-trachylobane (8) with smaller amounts of
tetracyclic 4, while RcKSL3 produces essentially only
the tricyclic ent-sandaracopimaradiene (9), and RcKSL4 produces predominantly the tetracyclic ent-beyerene (10). As expected, the R. communis KS, RcKS, contains an Ile at the primary switch position (Figure a), and substitution
of Thr has a similar effect to that in other KSs, largely short-circuiting
the complex dual cyclization and rearrangement reaction leading to 4 (Figure S3). The resulting RcKS:I594T
mutant produces small amounts of 4, along with a mixture
of pimaradienes 2 and 6, as well as 7, plus the labdatriene double-bond isomers ent-sclarene (11) and (Z)-biformene (12), which result from immediate deprotonation of the allylic
carbocation formed upon initiating diphosphateionization (i.e., without any cyclization). The RcKSLs contain an Ile
(RcKSL2 and -3) or Val (RcKSL4) at the primary switch position (Figure a). Consistent with
the retained production of 4 following substitution of
Val for the corresponding Ile in AtKS,[14] substitution of Ile for the Val at this position in RcKSL4 did not
affect product outcome—i.e., the resulting
RcKSL4:V632I still predominantly produces 10 (Figure S4). Substitution of Thr at this primary
switch position seems to most significantly reduce catalytic activity,
as indicated by the reduced overall yield of diterpenes from expression
of the corresponding mutants in the metabolic engineering system,
not only with RcKS, but also RcKSL2–4. Nevertheless, such substitution
also still abbreviated the catalyzed cyclization reactions, although
it has a less dramatic effect. The resulting RcKSL2:I636T mutant still
produces substantial amounts of 8 and 4,
although the major products are the labdatrienes 11 and 12 (Figure b). Similarly, the resulting RcKSL4:V632T still produces substantial
amounts of 10 (Figure c). Even in the tricycle 9 producing RcKSL3,
the resulting I634T mutant still produces substantial amounts of 9, along with the labdatriene 11 (Figure d).
Figure 3
Additive effect of the
original/primary and newly identified/secondary
pair of residues on RcKSL product outcome. (a) Partial sequence alignment
of RcKS(L)s and OsKSLs with an asterisk (*) above the primary (original)
position and a pound sign (#) above the secondary (new) position.
Residues are numbered as in the full-length proteins from the NCBI
database accession numbers given in the Materials section. (b) Chromatograms from GC–MS analysis of wild-type
RcKSL2 and the indicated mutants. (c) Chromatograms from GC–MS
analysis of wild-type RcKSL4 and the indicated mutants. (d) Chromatograms
from GC–MS analysis of wild-type RcKSL3 and the indicated mutants.
Numbers correspond to the chemical structures defined in the text.
Enzymatic products were identified by comparison of both retention
time and mass spectra to authentic standards (Figure S1).
Additive effect of the
original/primary and newly identified/secondary
pair of residues on RcKSL product outcome. (a) Partial sequence alignment
of RcKS(L)s and OsKSLs with an asterisk (*) above the primary (original)
position and a pound sign (#) above the secondary (new) position.
Residues are numbered as in the full-length proteins from the NCBI
database accession numbers given in the Materials section. (b) Chromatograms from GC–MS analysis of wild-type
RcKSL2 and the indicated mutants. (c) Chromatograms from GC–MS
analysis of wild-type RcKSL4 and the indicated mutants. (d) Chromatograms
from GC–MS analysis of wild-type RcKSL3 and the indicated mutants.
Numbers correspond to the chemical structures defined in the text.
Enzymatic products were identified by comparison of both retention
time and mass spectra to authentic standards (Figure S1).Intriguingly, while the
other two RcKSLs contain Leu (as found
in KSs), RcKSL3 contains serine at the secondary switch position instead
(Figure a). Hypothesizing
that this residue might exert an effect on product outcome, this Ser
was substituted with Leu. Interestingly, the resulting RcKSL3:S631L
mutant produces a small amount of the tetracyclic 4,
along with a number of other diterpenes (9, 11, 13–17), although 9 is still the major product. However, also substituting Thr for the
Ile at the primary position restores almost exclusive production of 9 by the RcKSL3:S631L/I634T double mutant (Figure d). On the other hand, substituting
Ser for the Leu at this secondary position in RcKSL2 was more effective
at preventing the normally catalyzed second cyclization step, with
the resulting RcKSL2:L633S mutant producing less of 8 and 4 than RcKSL2:I636T. Notably, combining these changes
led to almost complete abbreviation of the catalyzed reaction after
initial cyclization, with the RcKSL2:L633S/I636T double mutant largely
producing pimaradienes 2 and 6, along with
the labdatriene 11 (Figure b). Similarly, such substitution in RcKSL4
also was more effective at abbreviating further cyclization, as the
resulting RcKSL4:L629S mutant produced less 10 than RcKSL4:V632T.
Again, combining these changes led to almost complete abbreviation
of catalysis, with the RcKSL4:L629S/V632T double mutant producing
mostly the tricyclic 2 and 6, along with
substantial amounts of the bicyclic 11 (Figure c). Given that substitution
of alanine for this Leu in both RcKSL2 and -4 has a lesser effect
than substitution of Ser, the observed change in product outcome seems
to depend more on the presence of the hydroxyl group than the change
in steric volume (Figure S5). Accordingly,
these two positions seem to have an additive effect on product outcome,
with the presence of residues with hydroxyl containing side-chains
promoting abbreviation of the normally catalyzed cyclization reaction.
Rational Combination in AtKS for Specific Generation of 8α-Hydroxy-ent-pimar-15-ene
It has previously been reported
that substitution of smaller residues (Ala or Ser) for the Ile in
the primary position in AtKS leads to increased production of the
hydroxylated pimarene 7, although 2 remains
the major product.[14] Given the additive
effects observed with the RcKSLs above, and the significant increase
in relative production of 7 by addition of the L635V
mutation to AtKS:I638T (i.e., by AtKS:L635V/I638T;
see Figure c), it
was hypothesized that a further optimized combination of changes at
these two positions might lead to even more specific production of 7. Indeed, combining the L635V change at the secondary position
with either Ala or Ser substitution for the Ile at the primary position
led to increased production of 7, with the AtKS:L635V/I638S
double mutant exhibiting the highest specificity, such that 7 is the dominant product (Figure ).
Figure 4
Application of the additive effect between the
original/primary
and newly identified/secondary pair of residues on AtKS product outcome
to engineer predominant production of a hydroxylated diterpene. Chromatograms
from GC–MS analysis of the wild-type AtKS and the indicated
mutants. Numbers correspond to the chemical structures defined in
the text. Enzymatic products were identified by comparison of both
retention time and mass spectra to authentic standards (Figure S1).
Application of the additive effect between the
original/primary
and newly identified/secondary pair of residues on AtKS product outcome
to engineer predominant production of a hydroxylated diterpene. Chromatograms
from GC–MS analysis of the wild-type AtKS and the indicated
mutants. Numbers correspond to the chemical structures defined in
the text. Enzymatic products were identified by comparison of both
retention time and mass spectra to authentic standards (Figure S1).
Conclusions
The results presented here demonstrate
that the residues at the original/primary and newly identified/secondary
switch positions interactively affect KS(L) product outcome. However,
the exact nature of the interaction differs, as does their effects.
These differences seem to reflect the phylogenetic relationships between
the various KS(L)s investigated here. Conservation of Leu at the secondary
position in KSs is consistent with both the ability of this residue
to increase the catalytic rate and specificity for production of 4, as well as functional conservation of KSs as representative
of the ancestral activity in the KS(L) subfamily. The more pronounced
effect on catalytic specificity observed with Val substitution for
the Leu at the secondary position in the presence of Thr substitution
for the Ile at the primary position provides some evidence for how
these residues interactively affect product outcome. Specifically,
substitution of the smaller Val for Leu at the secondary position
presumably opens up the active site, which seems to decrease the confinement
of the key ent-pimar-15-en-8-yl+ intermediate
within the active site. As a result, this carbocation is no longer
as precisely positioned relative to the residue at the primary position—e.g., for stabilization by the hydroxyl group of Thr, enabling
alternative product outcomes.By contrast, OsKSL5 belongs to
an early diverging KSL lineage within monocots[18] and is relatively distantly related to any KSs (Figure ). This is consistent
with the distinct effects on product outcome observed upon interchanging
Leu and Val at the secondary position (Figure d). Moreover, it seems likely that these
enzymes arose via parallel re-evolution of the ability
to produce the ent-kauranyl+ intermediate
relative to KSs (albeit with specific terminating deprotonation to
yield 3 rather than 4). In particular, there
seems to be distinct positioning of not only the ent-pimarenyl+ intermediate in the active site of these OsKSLs
relative to the KSs, as evidenced by the lack of effect of such interchange
on production of 2, but also of the ent-kauranyl+ intermediate, as evidenced by the observed
effect on production of 3 instead (Figures and 2).
Figure 5
Phylogenetic
tree for the KS(L)s biochemically characterized here
(constructed from protein sequence alignment with the Neighbor Joining
algorithm, 100 replicates, using CLC Sequence Viewer 6.9.1). The nonvascular
plant derived PpCPS/KS and gymnosperm derived PgKS serve as the outgroup
rooting the tree. For utilized sequences, see the NCBI protein database
accession numbers referred to in the Materials section.
Phylogenetic
tree for the KS(L)s biochemically characterized here
(constructed from protein sequence alignment with the Neighbor Joining
algorithm, 100 replicates, using CLC Sequence Viewer 6.9.1). The nonvascular
plant derived PpCPS/KS and gymnosperm derived PgKS serve as the outgroup
rooting the tree. For utilized sequences, see the NCBI protein database
accession numbers referred to in the Materials section.Similarly, RcKSL2–4 belong
to an early diverging KSL lineage
within eudicots[17] and also are relatively
distantly related to any KSs (Figure ). This is consistent with the clearly additive effect
of altering the residues at the primary and secondary position in
these KSLs. The presence of a hydroxylated side-chain containing residue
in either position seems to at least partially block progression of
the reaction past initial cyclization. In the case of RcKSL3, whose
product 9 is epimeric (at carbon-13) to the other pimarane
products reported here (i.e., 2, 6, 7), the presence of either Ser at the secondary position or
Thr at the primary position is sufficient for specific production
of 9, while a Leu/Ile pairing (respectively) enables
some further cyclization and rearrangement (at least to a small extent; Figure d). On the other
hand, in RcKSL2 and -4 the effect of the analogous substitution with
Ser/Thr (respectively) is only partial, with complete blockage of
further cyclization only observed if both are present (Figure b and c). This suggests that
the ent-pimar-15-en-8-yl carbocation is positioned
roughly equidistant from these residues, enabling this additive effect.Notably, realization that the effect of the residues at these two
positions can exert additive effects led to rational engineering.
Specifically, for production of the hydroxylated pimarene 7 by AtKS. Previous results had demonstrated that substitution of
Ala or Ser for the Ile at the primary switch position led to substantial
production of 7.[14] Given the
increase in relative amounts of 7 produced by the addition
of Val substitution for the Leu at the secondary switch position to
the original Thr for Ile primary switch (see Figure c), it seemed intuitively obvious that combining
these changes might lead to specific production of 7.
Indeed, the AtKS:L635V/I638S double mutant produces 7 as its major/predominant product (Figure ). Thus, the newly identified/secondary switch
position and interactive effect between this and the previously identified/primary
position has already been shown to have practical implications for
engineering product outcome. It will be of interest to further investigate
the utility of these residues for altering catalytic specificity in
other KSLs and plant terpene synthases more broadly.
Methods
Materials
Unless
otherwise noted, chemicals were purchased
from Fisher Scientific and molecular biology reagents from Invitrogen.
Sequence alignments and phylogenetic analysis were performed with
CLC sequence viewer 6.9.1 using the default parameters. The NCBI protein
database accession numbers of proteins included in this study: PpCPS/KS, Physcomitrella patens KS (BAF61135); PgKS, Picea
glauca KS (ADB55711); AtKS, Arabidopsis thaliana
ent-KS (AAC39443); RcKS, Ricinus communis ent-KS (XM_002533648); OsKS, Oryza sativa ent-KS (BAE72099);
HvKS, Hordeum vulgare ent-KS (Q673F9); OsKSL4, Oryza sativa kaurene synthase-like enzyme 4 (Q66QH3); OsKSL5i, Oryza sativa kaurene synthase-like enzyme 5i (A4KAG7); OsKSL5j, Oryza sativa kaurene synthase-like enzyme 5j (Q6Z5J6); OsKSL6, Oryza sativa kaurene synthase-like enzyme 6 (ABH10733);
RcKSL2, Ricinus communis kaurene synthase-like enzyme
2 (XM_002525795); RcKSL3, Ricinus communis kaurene
synthase-like enzyme 3 (XM_002525790); RcKSL4, Ricinus communis kaurene synthase-like enzyme 4 (XM_002525796).
Mutant Construction
The constructs utilized here encode
pseudomature enzymes suitable for recombinant expression in Escherchia coli (i.e., without the N-terminal
transit peptide sequence that leads to the necessary plastid import
in planta), although residue numbering is based on the full-length
proteins. Previous work has shown that RcKSL2 contains an Ala in the
“middle” position of the NDxx(S/T)xxxE motif, and that
the A676T mutant was observed previously to produce the same product
profiles with the wild type but with significantly higher efficiency
(about 60-fold increase) in our metabolic engineering system,[17] so in this study, all the relevant mutants were
generated in an RcKSL2:A676T background. Site-directed mutants were
constructed by whole-plasmid PCR amplification of the relevant pENTR/SD/d-TOPO
constructs using the relevant primers (Table S1) and AccuPrime Pfx DNA Polymerase. All mutants were verified by
complete gene sequencing and then transferred via directional recombination to the T7-based, N-terminal GST-fusion
expression vector pDEST15.
Enzymatic Analyses
To determine
catalyzed product outcome,
each pDEST15 based construct was cotransformed with a previously described
pGGeC vector containing both a GGPP synthase and ent-CPP synthase,[16] along with a previously
reported pIRS plasmid that increases metabolic flux toward terpenoids,[19] into the OverExpress C41 strain of E.
coli (Lucigen). The resulting recombinant strains were cultured
in 50 mL of TB medium (pH = 7.0), with appropriate antibiotics, in
250 mL Erlenmeyer flasks. These cultures were first grown by shaking
at 37 °C to mid log phase (OD600 ∼ 0.7); then
the temperature dropped to 16 °C for 0.5 h prior to induction
with 1 mM isopropylthiogalactoside (IPTG) and supplementation with
40 mM pyruvate and 1 mM MgCl2. The induced cultures were
further shaken at 16 °C for an additional 72 h before extraction
with an equal volume of hexanes, with the organic phase then separated,
and concentrated under N2 when necessary.
Product Analyses
Gas chromatography with mass spectral
detection (GC-MS) was carried out on a Varian 3900 GC with a Saturn
2100T ion trap mass spectrometer in electron ionization (70 eV) mode,
using an Agilent HP-5MS column (Agilent, 19091S-433) with 1.2 mL/min
helium flow rate. Samples (1 uL) were injected in splitless mode using
an 8400 autosampler, with the injection port set at 250 °C. The
following temperature program was used: the oven temperature started
at 50 °C, which was maintained for 3 min, and then increased
at a rate of 15 °C/min to 300 °C, where it was held for
another 3 min. The mass spectrum was recorded by mass-to-charge ratio
(m/z) values in a range from 90
to 650, starting from 13 min after sample injection until the end
of the run. Enzymatic products were identified by comparison of retention
time and mass spectra to those of authentic standards.
Authors: Travis A Pemberton; Mengbin Chen; Golda G Harris; Wayne K W Chou; Lian Duan; Mustafa Köksal; Alex S Genshaft; David E Cane; David W Christianson Journal: Biochemistry Date: 2017-03-31 Impact factor: 3.162