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J. Biol. Chem., Vol. 275, Issue 27, 20431-20435, July 7, 2000
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From the New England BioLabs Inc.,
Beverly, Massachusetts 01915
Received for publication, January 10, 2000, and in revised form, April 17, 2000
Protein splicing is a self-catalytic process in
which an intervening sequence, termed an intein, is excised from a
protein precursor, and the flanking polypeptides are religated. The
conserved intein penultimate His facilitates this reaction by assisting in Asn cyclization, which results in C-terminal splice junction cleavage. However, many inteins do not have a penultimate His. Previous
splicing studies with 2 such inteins yielded contradictory results. To
resolve this issue, the splicing capacity of 2 more inteins without
penultimate His residues was examined. Both the Methanococcus
jannaschii phosphoenolpyruvate synthase and RNA polymerase
subunit A' inteins spliced. Splicing of the phosphoenolpyruvate synthase intein improved when its penultimate Phe was changed to His,
but splicing of the RNA polymerase subunit A' intein was inhibited when
its penultimate Gly was changed to His. We propose that inteins lacking
a penultimate His (i) arose by mutation from ancestors in which a
penultimate His facilitated splicing, (ii) that loss of this His
inhibited, but may not have blocked, splicing, and (iii) that selective
pressure for efficient expression of the RNA polymerase yielded an
intein that utilizes another residue to assist Asn cyclization,
changing the intein active site so that a penultimate His now inhibits splicing.
Protein splicing is a post-translational event analogous to RNA
splicing that involves the removal of an internal protein fragment
(intein) from a precursor protein and the joining of the two flanking
sequences (exteins) to produce an active extein protein
(1). As of January 2000, 100 putative inteins have been
identified in all three phylogenetic domains (see the Intein Registry
in InBase (2)). Inteins have 2 structural domains (Fig.
1A) as follows: a splicing
domain that is composed of the N-terminal and C-terminal splicing
regions, and a central region encoding a homing endonuclease (3, 4) or
a small linker. The structure of the intein splicing domain is
conserved among inteins, forming a protein fold termed the HINT module
(5-8). The homing endonuclease domain is dispensable. Residues
mediating or assisting the protein splicing reaction have been
identified by sequence comparison, mutation, and structural analysis
(6, 8-19) (Fig. 1A).
The protein splicing reaction requires the intein splicing domain plus
the first amino acid of the C-extein. The self-catalytic protein
splicing mechanism (reviewed in Noren et al. (20)) consists of the following four steps, each involving nucleophilic displacements (Fig. 2): (i) formation of a linear
(thio)ester by an acyl rearrangement of the conserved Cys or Ser at the
intein N terminus; (ii) formation of a branched intermediate by
transesterification when the thiol/hydroxyl group of the Ser, Thr, or
Cys at the beginning of the C-extein attacks the (thio)ester from
step 1, resulting in transfer of the N-extein to the side chain of the
first C-extein residue; (iii) resolution of the branched intermediate
by cyclization of the intein C-terminal Asn or Gln, resulting in
cleavage of the peptide bond between the intein and the C-extein; and
(iv) formation of a native peptide bond between the exteins by a
spontaneous S-N (or O-N) acyl rearrangement. Dead-end side reactions
are often observed when the intein is expressed in a heterologous
extein. N-terminal splice junction cleavage products are formed by
cleavage of the (thio)ester at either the N-terminal splice junction or at the branch point in the branched intermediate. C-terminal splice junction cleavage results when Asn or Gln cyclization precedes steps 1 or 2. Although inteins are not true enzymes in the sense that
they do not act on multiple substrates, they use the same mechanisms as
enzymes to facilitate splicing, including oxyanion holes at each splice
junction (6, 20).
Protein Splicing in the Absence of an Intein Penultimate
Histidine*
![]()
ABSTRACT
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
![]()
INTRODUCTION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES

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Fig. 1.
A, organization of a typical protein
splicing precursor. A precursor is depicted with an intein composed of
a homing endonuclease domain (black box) separating the
N-terminal and C-terminal splicing regions (white boxes)
that form the intein splicing domain. Mini inteins have a short linker
instead of an endonuclease domain. Intein motifs are shown
above the precursor, and conserved residues in selected
blocks are shown below the precursor. Block A
contains the conserved Ser or Cys at the N terminus of the intein,
although Ala is present at this position in 3 intein families.
Block G contains the conserved dipeptide His-Asn at the
intein C terminus and Ser, Thr, or Cys at the beginning of the
C-extein. Three inteins have Gln instead of Asn in block G
(2, 29). B, intein polymorphism at the penultimate residue.
As of January 2000, 10 families of intein alleles lack a penultimate
His. The number in parentheses is the total number of
residues in each intein. Abbreviations are as follows: Ceu, C. eugametos; CIV, Chilo iridescent virus;
Aae, Aquifex aeolicus; Spb,
Bacillus subtilis SP
phage; Ssp,
Synechocystis sp. PCC6803; Pab, Pyrococcus
abyssi; Pho, Pyrococcus horikoshii OT3;
Pfu, Pyrococcus furiosus; RIR1,
ribonucleoside-diphosphate reductase,
subunit; KlbA,
kilB operon orfA; LHR, large
helicase-related protein; Lon, ATP-dependent
protease LA; Moaa, molybdenum cofactor biosynthesis homolog.
C, schematic representation of the Rpol A' and PEP MEIEP
precursors. Splice junction residues, the position of the intein
penultimate amino acid (arrow), and the number of extein
residues are indicated. Native extein sequences are represented by
E, and H represents a 6-aa His tag.

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Fig. 2.
The self-catalytic protein splicing
reaction. The protein splicing mechanism is depicted with
X representing either the oxygen or the sulfur present in
the side chain of Ser, Thr, or Cys. In some inteins Asn is replaced by
Gln, which can similarly cyclize. All tetrahedral intermediates,
assisting groups and proton transfer steps are omitted for
clarity.
This paper focuses on the role of the intein penultimate residue, which is thought to facilitate C-terminal splice junction cleavage and Asn cyclization when His is present at this position. Inteins must increase the rate of Asn or Gln cyclization, since Asn cyclization takes several days at 37 °C, pH 7.4, in model peptides, and cyclization of Gln is even slower due to entropic factors (21). Moreover, in both proteins and peptides, the preferred reaction is the attack by the main chain nitrogen on the side chain carbonyl leading to deamidation, as opposed to the protein splicing reaction in which the side chain amide nitrogen attacks the main chain carbonyl (21). Inteins can increase the rate of Asn or Gln cyclization and direct the reaction toward peptide bond cleavage by aligning reactive groups and rendering the peptide bond more labile by generating an electrophilic center at the carbonyl carbon. The increased electrophilicity could be accomplished by (i) hydrogen bonding to the carbonyl oxygen, thereby stabilizing the developing negative charge on the tetrahedral intermediate of the cyclization reaction, and/or (ii) making the main chain amine a better leaving group by donating a proton. Inteins could also facilitate cyclization by increasing the nucleophilicity of the side chain amide group. The intein penultimate His is thought to assist Asn cyclization. Most inteins have a His in the penultimate position (2), and mutation of this His inhibits or blocks splicing (10, 11, 18). The crystal structures of the Mycobacterium xenopi gyrase subunit A (GyrA)1 intein (6) and the Saccharomyces cerevisiae vacuolar ATPase intein (8) in the absence of a C-extein reveal that the intein penultimate His is in hydrogen bonding distance to an Asn carboxylate oxygen. The penultimate His therefore facilitates Asn cyclization by making the Asn carbonyl carbon more electrophilic. Modeling of the M. xenopi GyrA intein suggests that the penultimate His may donate a proton to the main chain amine leaving group (6).
Seventeen inteins (10 families of intein alleles) have another residue
at the penultimate position (2), including Gly, Ala, and Phe which are
unlikely to assist in Asn or Gln cyclization (Fig. 1B). Are
these inteins capable of splicing? Previous studies of 2 such inteins
yielded contradictory results. The Chlamydomonas eugametos
ClpP intein failed to splice in Escherichia coli unless its
penultimate Gly was mutated to His (19), suggesting that inteins
lacking a penultimate His are inactive. On the other hand, the DnaE
intein of Synechocystis sp. PCC6803 spliced in E. coli (22), although more spliced product accumulated when its
penultimate Ala was mutated to His (23). To address this issue further, the Methanococcus jannaschii (Mja) phosphoenolpyruvate
synthase (PEP) and RNA polymerase subunit A' (Rpol A') inteins with Phe and Gly at the intein penultimate position, respectively, were tested
for their ability to splice with their native penultimate residue and
with a penultimate His.
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EXPERIMENTAL PROCEDURES |
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Construction of MEIEP Clones-- The Pyrococcus sp. GB-D DNA polymerase intein in pMIP21 (24) was replaced with either the Mja Rpol A' intein or the Mja PEP intein plus varying lengths of native N- and C-extein sequences (E) to generate MEIEP fusions (Fig. 1C). DNA encoding the M. jannaschii inteins was amplified by polymerase chain reaction (PCR) from genomic DNA using Mja Rpol A' primers, 5'-ATG CTC GAG CAC CAA ACT TAA TTA TTG AGG AT and 5'-ATT GAG GCC TTC AGC GTT GTA GGG CGG GCA ATT or Mja PEP primers 5'-ATG CTC GAG ACG ATG TTT GTT AAG GAT GAA AAA and 5'-ATT GAG GCC TCT AGA AAC GAT TGC CGC GTG GCA GTT. The Mja Rpol A' fragment included 200 native N-extein residues and 5 native C-extein residues. The Mja PEP intein fragment included 150 native N-extein residues and 7 native C-extein residues. The resultant PCR fragment was digested with XhoI and StuI, purified from agarose gels with a QIAEX II gel extraction kit (Qiagen Inc.) and ligated into gel-purified XhoI/StuI cut pMIP21 vector DNA. All mutants were constructed by substituting a restriction enzyme fragment in pMEIEP with a PCR fragment generated using the following primers containing the desired mutations: PEP intein F411H primers 5'-AAA TGG AAA CCA ATA AGG GT and 5'-GCG GCC CTA AAA CGA TTG CCG CGT GGC AGT TAT GTA CAA CTA TTGG; Rpol A' intein G451H primers 5'-GAA TTT GGT ATT GAA TTA AAG and 5'-ATT GAG GCC TTC AGC GTT GTA GGG CGG GCA ATT GTG TGT TAA AAA GCC; Rpol A' intein primers 5'-AAA GAG AAA TGC CTT AA GAA TGGA and 5'-CCT TCA GCG TTG TAG GGC GGG CAA TTX XXT GTT AAA AAG CC, in which XXX was TGC for G451A, AAA for G451F, TTT for G451K, and CCA for G451W. A His6 tag was incorporated at the end of paramyosin by insertion of a double-strand oligonucleotide into the SalI and PstI sites in the PEP intein clone and the SalI and HindIII sites in the Rpol A' intein clone.
The sequence of all PCR fragments was confirmed after sequencing both DNA strands by the NEB DNA sequencing core facility. All enzymes were obtained from New England BioLabs and used as described by the manufacturer.
MEIEP Production and Characterization--
E. coli
strain TB1 (New England BioLabs) cells containing pMEIEP plasmids were
grown at 30 °C to mid log phase and then further incubated in the
presence or absence of 0.4 mM
isopropyl-1-thio-
-D-galactopyranoside at 15 °C
overnight. Nickel column (Qiagen Inc.) purified proteins containing the
C-terminal His tag were prepared as described by the manufacturer with
the addition of 10% glycerol in all buffers. Induction of MEIEP
precursors in the presence of
isopropyl-1-thio-
-D-galactopyranoside resulted in
increased proteolytic cleavage within the intein and little or no
increase in precursor, spliced products, or single splice junction
cleavage products. Therefore, experiments were performed with purified
samples from uninduced cultures.
MEIEP precursors, spliced products, and cleavage products are
distinguishable by relative mobility in Coomassie Blue-stained SDS-PAGE
and by immunoreactivity in Western blots using anti-MBP and
anti-paramyosin sera (24). In order to obtain clear separation of MEEP
and IEP, samples were electrophoresed in 8% acrylamide SDS-PAGE, and
the 30-kDa EP product was run off the bottom of the gel. The same
samples were also electrophoresed in 12% acrylamide SDS-PAGE and
stained with Coomassie Blue for analysis of the EP product (data not
shown). Coomassie Blue-stained gels were digitized with a Microtek
Scanmaker III and quantitated with NIH Image 1.51 software as described
(25). The values for at least 3 independent experiments were averaged
for each sample and the standard deviation of the means calculated. The
increase or decrease in molar percent of spliced product (MEEP) or
N-terminal splice junction cleavage product (IEP) was calculated as
follows: percent increase = (mutant
wild type)/wild
type × 100 and percent decrease = (wild type
mutant)/wild type × 100.
N-terminal Sequencing by Edman Degradation--
Purified Mja
Rpol A' MEIEP samples were sequenced as described (24). Briefly,
protein samples were subjected to electrophoresis on a 8% Tris glycine
polyacrylamide gel (NOVEX) and transferred to a ProBlott polyvinylidene
difluoride membrane (PE Biosystems). The membrane was stained with
Coomassie Blue R-250, bands corresponding to the branched intermediate
(MEIEP*); the MEIEP precursor and the MEEP spliced product were
excised, and each was subjected to sequential Edman degradation. The
data were acquired and analyzed on an Applied Biosystems 610A Data System.
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RESULTS |
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Splicing of the Mja PEP and Mja Rpol A' Inteins in E. coli--
The well studied MIP in vitro protein splicing
system (18, 24-26) was used to examine whether a penultimate His is
required for splicing of the Mja Rpol A' and PEP inteins. The MIP
precursor consists of an intein (I) inserted in-frame between the
E. coli maltose-binding protein (MBP or M) and the
Sal
fragment of Dirofilaria immitis paramyosin (P). In this
study, native extein sequences (E) were included to improve splicing by
better mimicking the native precursor active site, generating the MEIEP
fusions (Fig. 1C). The Mja PEP intein has a penultimate Phe
at position 411 and the Mja Rpol A' intein has a penultimate Gly at
position 451. Size, immunoreactivity, and in some cases N-terminal
protein sequencing were used to identify precursor (MEIEP), spliced
product (MEEP), branched intermediate (MEIEP*), and N-terminal splice
junction (ME + IEP) or C-terminal splice junction (MEI + EP) cleavage
products. Cleared cell lysates were chromatographed over
nickel-chelating columns, resulting in purification of proteins
containing the C-terminal His tag and loss of ME and MEI. The Mja PEP
and Rpol A' MEIEP precursors spliced efficiently in E. coli
(Fig. 3), with 60% spliced MEEP product
observed with the Mja PEP intein and 68% with the Mja Rpol A' intein
(Table I). No C-terminal splice junction
cleavage product (EP) was observed when samples were electrophoresed in
12% SDS-PAGE (data not shown). No increase in spliced product was
observed if protein samples were incubated overnight in
vitro at 16 or 37 °C at pH 6.0 to 8.5 (data not shown). It is
not known why some proportion of precursors usually fail to splice in
heterologous systems, although it has most often been attributed to
misfolding or aggregation.
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Protein Splicing of Mja PEP and Mja Rpol A' Inteins in MEIEP after Mutation of the Penultimate Intein Residue to His-- Mutation of the Mja PEP intein penultimate Phe and the Mja Rpol A' intein penultimate Gly to His was performed to see if "reversion" to this normally conserved residue would improve splicing. There was a 43% increase in spliced MEEP product obtained from the F411H mutant Mja PEP intein samples as compared with the wild type samples (Fig. 3 and Table I). However, replacing the Mja Rpol A' intein penultimate Gly with His resulted in a 27% decrease in spliced product, a 57% increase in IEP N-terminal splice junction cleavage product, and an accumulation of a slowly migrating protein; amino acid sequencing of the latter protein indicated that it was the branched intermediate, since it had the predicted pair of amino acids present in each of 15 cycles of Edman degradation (Table II). One amino acid in each cycle corresponded to the MBP sequence, and the other residue in that cycle corresponded to the Mja Rpol A' intein sequence. The identities of the Mja Rpol A' precursor (MEIEP) and spliced product (MEEP) were also confirmed by protein sequencing (data not shown). The accumulation of branched intermediate and N-terminal splice junction cleavage products is indicative of inhibiting only the Asn cyclization step and not the acyl shift or transesterification steps (Fig. 2).
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Further Substitutions of the Mja Rpol A' Intein Penultimate
Residue--
The Mja Rpol A' intein penultimate residue, Gly-451, was
replaced with Ala, Lys, Phe, or Trp in the MEIEP context (Fig.
4 and Table
III). Ala, Lys, and Phe substitutions
resulted in a similar decrease in spliced product (~27%) as in the
G451H mutation. G451H and G451F resulted in an increase in N-terminal
splice junction cleavage products and branched intermediate, suggesting
that His and Phe substitutions only inhibited Asn cyclization. The
bulky penultimate Trp residue resulted in the largest reduction in
spliced product (59%) but still allowed N-terminal splice junction
cleavage and the accumulation of branched intermediate. No C-terminal
splice junction cleavage product (EP) was observed in any sample (data not shown).
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DISCUSSION |
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A His is present at the penultimate position in 83% of inteins (2). Mutagenesis and structural studies have demonstrated the importance of this residue in facilitating Asn cyclization and protein splicing (6, 8, 10-12, 18). Contradictory results were obtained when the first two inteins naturally lacking a penultimate His were tested for the ability to splice. The C. eugametos ClpP intein with a penultimate Gly (19) failed to splice in E. coli, whereas the Synechocystis sp. PCC6803 DnaE intein with a penultimate Ala did splice (22). The present study examined two more inteins that lack a penultimate His. Both the M. jannaschii PEP and Rpol A' inteins with a Gly or Phe at the penultimate position yielded >60% spliced product in E. coli despite the fact that neither Gly nor Phe can chemically participate in Asn cyclization. In experiments to be published elsewhere,2 we have also demonstrated splicing of the Pyrococcus sp. GB-D KlbA intein, which has a penultimate Ser. To date, half of the intein families that lack a penultimate His have been examined, and all but 1 are capable of splicing. We therefore suggest that the failure of the C. eugametos ClpP intein to splice in E. coli (19) is the exception, rather than the rule, and that most inteins that lack a penultimate His will probably be active. It is possible that the C. eugametos ClpP intein splices in its native organism, since there is precedent for failure of active inteins to splice in E. coli (27).
The splicing reaction requires that the two splice junctions are in close proximity. Inteins are thought to have a complex active site with two oxyanion holes as follows: one at the C-terminal splice junction that facilitates Asn or Gln cyclization and includes the intein penultimate His, and a second oxyanion hole at the N-terminal splice junction that facilitates the first two nucleophilic displacements and includes residues in intein block B (6, 20). Several substitutions in the penultimate position of the Mja Rpol A' intein had little effect on reactions at the N-terminal splice junction, since N-terminal splice junction cleavage products were observed and the branched intermediate accumulated. However, all of these mutations inhibited Asn cyclization as evidenced by the failure to rapidly resolve the branched intermediate and the absence of C-terminal splice junction cleavage products. Although these data support the presence of separable oxyanion holes at each splice junction, precursor and intermediate structures would help to determine whether they are distinct or overlapping.
Both the C. eugametos ClpP and Mja Rpol A' inteins have a penultimate Gly. Unlike the C. eugametos ClpP intein that is activated by a penultimate His (19), the Mja Rpol A' intein is inhibited by a penultimate His. A penultimate His in the Mja Rpol A' intein may cause steric inhibition at the intein active site or block access to the C-terminal splice junction by a new residue(s) that facilitates Asn cyclization. Four more mutations were made at Gly451 ranging from the second smallest amino acid, Ala, to the largest amino acid, Trp. Substituting Gly with Ala yielded a similar reduction in spliced product as His, Lys, and Phe, indicating that either packing at the C-terminal splice junction is so tight that substituting Gly with the slightly larger Ala will cause the same steric effect as substituting with Phe or that the conformational flexibility that Gly provides is critical for aligning active site residues at the Mja Rpol A' intein C-terminal splice junction.
We suggest that all inteins evolved from ancestors that had a
penultimate His that facilitated Asn or Gln cyclization. Mutation of
the intein penultimate His might have yielded an intein that still
spliced, although less efficiently (unless other compensatory mutations
occurred simultaneously). Asn or Gln cyclization would then become
rate-limiting. Enough active extein might still be synthesized to
permit survival of the host until further mutation increased splicing
proficiency. In support of this hypothesis, splicing of the C. eugametos ClpP (19), the Synechocystis sp. PCC6803 DnaE
(23), and the Mja PEP inteins improved when the intein penultimate
residue was "reverted" to His. These inteins may yet to have fully
compensated for the absence of a penultimate His. They may have
recently mutated or selective pressure may be low since they may
produce sufficient amounts of spliced extein despite inefficient
splicing. The more essential and highly expressed the gene product, the
stronger the selection for mutations that would improve splicing.
Although dnaE encodes an essential protein that is part of
the replicative DNA polymerase, splicing of Synechocystis sp. PCC6803 DnaE does not have to be very efficient, since only a few
molecules of replicative DNA polymerase are generally required per cell
(<20 molecules/cell in E. coli) (28). However, Rpol A' is
not only an essential protein, but it is a highly expressed protein,
comprising part of the archaeal RNA polymerase. Therefore, individuals
that acquired mutations that improved splicing of the Mja Rpol A'
intein would rapidly become fixed in the population. In fact, the Mja
Rpol A' intein has changed so much that splicing is now inhibited when
its penultimate residue is reverted back to His. The differences in
splicing capacity of inteins that naturally lack a penultimate His may
thus reflect inteins at different stages of evolving toward rapid
splicing after mutation of their penultimate His. The data also suggest
that splicing of inteins that naturally lack a penultimate His may
improve if the native penultimate residue is replaced by His.
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ACKNOWLEDGEMENT |
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We thank Gary Olsen and David Graham, University of Illinois, for kindly providing us with M. jannaschii genomic DNA. DNA sequencing was performed by the New England BioLabs Core Sequencing Facility, and protein sequencing was performed by Jack Benner. We thank Don Comb for support and encouragement and Maurice Southworth, Eric Adam, Karen Sandman, Tom Evans, and Chris Noren for helpful discussions and reading of the manuscript.
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FOOTNOTES |
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* The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
To whom correspondence should be addressed: New England BioLabs
Inc., 32 Tozer Rd., Beverly, MA 01915. Tel.: 978-927-5054; Fax:
978-921-1350; E-mail: perler@neb.com.
Published, JBC Papers in Press, April 18, 2000, DOI 10.1074/jbc.M000178200
2 M. W. Southworth and F. B. Perler, manuscript in preparation.
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ABBREVIATIONS |
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The abbreviations used are:
aa, amino acid;
Mja, M. jannaschii;
PEP, phosphoenolpyruvate synthase;
Rpol A', RNA polymerase subunit A';
GyrA, gyrase subunit A;
M and MBP, maltose-binding protein;
P, Dirofilaria immitis paramyosin
Sal fragment;
I, Rpol A' or PEP intein;
E, native extein;
MEIEP, a
chimeric precursor consisting of MBP, a partial native N-extein, an
intein, a partial native C-extein and D. immitis paramyosin
Sal fragment;
MEIEP*, the branched intermediate of the MEIEP
precursor;
MEEP, the spliced exteins from the MEIEP precursor;
IEP, an
N-terminal splice junction cleavage product of MEIEP;
PCR, polymerase
chain reaction;
PAGE, polyacrylamide gel electrophoresis.
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