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Originally published In Press as doi:10.1074/jbc.M309575200 on September 15, 2003

J. Biol. Chem., Vol. 278, Issue 47, 46826-46831, November 21, 2003
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Four Inteins and Three Group II Introns Encoded in a Bacterial Ribonucleotide Reductase Gene*

Xiang-Qin Liu{ddagger}, Jing Yang, and Qing Meng

From the Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada

Received for publication, August 28, 2003 , and in revised form, September 12, 2003.


   ABSTRACT
TOP
 ABSTRACT
INTRODUCTION
 EXPERIMENTAL PROCEDURES
 RESULTS
 DISCUSSION
 REFERENCES
 
A bacterial ribonucleotide reductase gene was found to encode four inteins and three group II introns in the oceanic N2-fixing cyanobacterium Trichodesmium erythraeum. The 13,650-bp ribonucleotide reductase gene is divided into eight extein- or exon-coding sequences that together encode a 768-amino acid mature ribonucleotide reductase protein, with 83% of the gene sequence encoding introns and inteins. The four inteins are encoded on the second half of the gene, and each has conserved sequence motifs for a protein-splicing domain and an endonuclease domain. These four inteins, together with known inteins, define five intein insertion sites in ribonucleotide reductase homologues. Two of the insertion sites are 10 amino acids apart and next to key catalytic residues of the enzyme. Protein-splicing activities of all four inteins were demonstrated in Escherichia coli. The four inteins coexist with three group II introns encoded on the first half of the same gene, which suggests a breakdown of the presumed barrier against intron insertion in this bacterial conserved protein-coding gene.


   INTRODUCTION
TOP
 ABSTRACT
 INTRODUCTION
EXPERIMENTAL PROCEDURES
 RESULTS
 DISCUSSION
 REFERENCES
 
Inteins are intervening protein sequences embedded in precursor proteins and catalyze a protein-splicing reaction that excises the intein and joins the flanking sequences (N- and C-exteins) with a peptide bond (1–4). Inteins and intein-like sequences have been found in various host proteins in bacteria, archaea, and eukaryotes (5, 6). A typical intein is ~400 amino acid long and has two structural domains, with its N- and C-terminal parts forming the protein-splicing domain and its middle part forming the endonuclease domain (7, 8). The protein-splicing function ensures self-removal of intein from the host protein, and the endonuclease function initiates an intein homing (gene conversion) process and promotes maintenance and spread of the intein coding sequence (9–11). Inteins appear similar in overall structure and splicing mechanism, although they generally show low levels of sequence conservation (12–14).

Group II introns have properties of both catalytic RNAs and retroelements and are the presumed progenitors of eukaryotic nuclear spliceosomal introns (15–19). But unlike spliceosomal introns that are abundant in protein-coding genes, bacterial group II introns are strongly excluded from protein-coding genes outside mobile DNA (20, 21). Group II intron RNAs fold into a conserved structure with six domains, and most bacterial group II introns also encode a reverse-transcriptase-like (RTL)1 protein involved in intron mobility (22). Group II intron mobility includes efficient retrohoming (site-specific insertion) into homologous intron-less allele and less frequent retrotransposition into non-cognate sites (23, 24). Both retrohoming and retrotransposition are initiated and catalyzed by a ribonucleoprotein complex consisting of the excised intron RNA and the intron-encoded RTL protein (25, 26). Group II introns are rare in bacterial (and archaeal) protein genes and were found mostly in mobile DNAs such as transposon-like insertion sequence elements (21). Nearly half of bacterial group II introns are outside of any gene (27), despite the ~90% gene density of bacterial genomes, suggesting selection against insertion into genes. Among bacterial group II introns inside genes, few are inside conserved protein-coding genes, indicating extremely strong selection against insertion into "housekeeping" protein genes (20, 21). It was suggested that bacterial group II introns function primarily as retroelements, not as introns (21).

Only a few completely sequenced bacterial genomes encode both intein and intron. The only known example of coexistence of an intein and a group I intron in the same gene, a bacteriophage ribonucleotide reductase gene (28), was likened to lightning striking twice in the same place; it was reasoned to be an unlikely event of pure chance (29). Coexistence of intein and group II intron in one gene has not been reported before. Here we report the coexistence of four inteins and three group II introns in a bacterial ribonucleotide reductase gene. To our knowledge, this is the first report of coexistence of multiple inteins and multiple introns (any intron) in the same gene, which has interesting implications regarding the evolution and possible function of inteins and introns.


   EXPERIMENTAL PROCEDURES
TOP
 ABSTRACT
 INTRODUCTION
 EXPERIMENTAL PROCEDURES
RESULTS
 DISCUSSION
 REFERENCES
 
Gene Cloning and Sequence Analysis—GenBank searches, sequence alignments, and intron RNA folding were performed using the BLAST search program (30), the ClustalW program (31), and the MFOLD program (32), respectively. Parts of the ribonucleotide reductase gene were amplified by doing PCR from total genomic DNA of Trichodesmium erythraeum (Ter) strain IMS101, using the high fidelity Pfu DNA polymerase. DNA fragments were cloned in a pDrive plasmid vector (Qiagen), and DNA sequences were determined through automated DNA sequencing.

Protein-splicing Analysis in Escherichia coli Cells—To construct gene expression plasmids, intein coding sequences were inserted in the previously described pMST plasmid (33) between XhoI and AgeI sites, replacing the Ssp DnaB intein coding sequence of pMST. Protein production in E. coli cells, gel electrophoresis, and Western blot analysis were performed as described previously (33). Briefly, cells containing the expression plasmid were grown in liquid LB medium at 37 °C to late log phase (A600, 0.5). Isopropyl-1-thio-{beta}-D-galactopyranoside was added to a final concentration of 0.8 mM to induce production of the recombinant protein, and the induction was continued at 37 °C for 3 h or at 25 °C overnight. Cells were then harvested, and cellular proteins were dissolved in SDS- and dithiothreitol-containing gel loading buffer in a boiling water bath before electrophoresis in SDS-polyacrylamide gel. Western blots were carried out using anti-thioredoxin antibody (Invitrogen) and the enhanced chemiluminescence detection kit (ECL). Intensity of protein band was estimated by using a gel documentation system (Gel Doc 1000 coupled with Molecular Analyst software, Bio-Rad).


   RESULTS
TOP
 ABSTRACT
 INTRODUCTION
 EXPERIMENTAL PROCEDURES
 RESULTS
DISCUSSION
 REFERENCES
 
Identification of Ter RIR Gene Encoding Multiple Introns and Inteins—A search for new intein sequences led us to a DNA sequence in the GenBank (accession no. AABK02000003) that had been deposited by the U.S. Department of Energy Joint Genome Institute and was from the genome of the oceanic N2-fixing cyanobacterium T. erythraeum strain IMS101. Our initial analysis indicated that this DNA sequence has a ribonucleotide reductase (RIR) gene containing inteins as well as introns. Subsequent DNA cloning and sequence determination confirmed this analysis and also corrected a small deletion error in the above GenBank sequence. This revealed the complete T. erythraeum RIR gene as illustrated in Fig. 1. The 13,560-bp long Ter RIR gene is divided into eight exon- or extein-coding sequences by the presence of three intron- and four intein-coding sequences. The eight extein/exon-coding sequences are 252, 141, 306, 126, 396, 30, 390, and 663 bp long, respectively, and together they encode a 768-amino acid mature RIR protein that is highly similar to homologous but intein/intron-less RIR of other bacteria (Fig. 2A). Specifically, the mature RIR sequence of T. erythraeum is 69% identical and 80% similar to its homologue in the cyanobacterium Nostoc sp. strain PCC7120 (Nsp), and this level of RIR sequence identity is normal among cyanobacterial species. The Nsp RIR (also known as Asp RNR) has been functionally characterized as a class II B12-dependent ribonucleotide reductase (34). The mature RIR sequence of T. erythraeum is also 24% identical and 40% similar to the RIR sequence of the distantly related bacterium Lactobacillus leichmannii (Lle). The Lle RIR is also a class II (coenzyme B12-dependent) ribonucleoside triphosphate reductase with a known crystal structure (35). The 13,560-bp Ter RIR gene is much larger than other bacterial RIR genes because of the presence of intein and intron coding sequences, with just 17% of its coding sequences for exteins and exons and the remaining 83% for inteins and introns.



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  		FIG. 1.
Illustration of T. erythraeum RIR gene and predicted expression products. Black boxes represent the eight exons/exteins. I1, I2, and I3 (pink lines) represent the three introns named T.er.I2, T.er.I3, and T.er.I4 intron, respectively. I4, I5, I6, and I7 (red boxes) represent the four inteins named Ter RIR-1, Ter RIR-2, Ter RIR-3, and Ter RIR-4 intein, respectively. Green boxes inside I1 and I3 represent coding sequences for intron RTL proteins.

 



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  		FIG. 2.
Protein sequence comparisons. A, predicted mature RIR protein sequence of Ter is aligned with RIR sequences of Nostoc sp. strain PCC7120 (Nsp) and Lactobacillus leichmannii (Lle). Only sequences proximal to the insertion sites of the Ter introns and inteins are shown, and amino acid positions in the Ter sequence are numbered. Intron and intein insertion sites (I1 through I7) in the Ter sequence are marked with arrowheads, and the corresponding intron and intein names are shown in parentheses. The Nsp RIR sequence also has an intein at the I1 insertion site. B, four intein sequences predicted from the Ter RIR gene are aligned, and putative intein sequence motifs (blocks A through H) are underlined. Less conserved sequences are omitted, the numbers of omitted residues are shown in parentheses, and the length of each sequence is shown at the end. Symbols represent gaps introduced to optimize the alignment.

 
Identification and Sequence Analysis of the Inteins—The four intein-coding sequences are located on the second half of the gene (Fig. 1), are named Ter RIR-1, Ter RIR-2, Ter RIR-3, and Ter RIR-4 intein, according to nomenclature of known inteins, and are 394, 373, 323, and 381 amino acids long, respectively. Insertion positions of the four inteins are before amino acid residues Ser-276, Cys-408, Cys-418, and Thr-548 of the mature RIR protein, respectively. Boundaries of the four inteins were readily identified by comparison of extein sequences with intein-less homologues such as Nsp RIR (Fig. 2A) and by location of conserved intein sequence blocks A and G marking the ends of each intein (Fig. 2B). Each of the four inteins begins with a nucleophilic residue (Cys), ends with Asn, and is followed immediately by another nucleophilic residue (Ser, Cys, or Thr), as expected for the protein-splicing function of the intein (2). Each intein also has sequence motifs for protein-splicing function (sequence blocks A, B, F, and G) as well as putative sequence motifs for intein endonuclease function (sequence blocks C, E, and H) (36). The Ter RIR-1 intein and the Ter RIR-2 intein are also homologous to previously identified Nsp RIR intein and Pfu RIR1–2 intein, respectively, based on significant (>30%) sequence similarities and the same corresponding insertion site (data not shown). Protein-splicing function has been demonstrated for both the Nsp RIR intein (34) and the Pfu RIR1–2 intein (37). The four Ter RIR inteins showed only low levels (less than 15%) of sequence identity among themselves, and their insertion sites have no apparent sequence similarity, indicating that they are not closely related. Insertion sites of Ter RIR-2 and Ter RIR-3 inteins are just 10 amino acids apart and inside the catalytic center of ribonucleotide reductase, according to sequence comparison to the structurally determined Lle ribonucleotide reductase (35) (Fig. 2A). The Ter RIR-2 intein is inserted at Cys-408 that acts with metallocofactor to generate the active-site thiyl radical (S*), whereas the Ter RIR-3 intein is inserted at Cys-418 (Ter numbering) that forms a redox-active disulfide with another Cys residue. The four Ter RIR inteins, together with known RIR inteins in other organisms, define five distinct intein insertion sites in the RIR protein.

Protein-splicing Activity of the Inteins—To determine whether the four inteins are functional, we tested their protein-splicing activity in E. coli cells. For each intein, a plasmidborne fusion gene was constructed to produce a fusion protein in which the intein (plus 5 amino acids of its native extein sequence on each side) was fused to an N-terminal maltose binding protein and a C-terminal thioredoxin (Fig. 3). Similar fusion protein constructs had been used in previous studies of other inteins (33, 38), so that the protein-splicing products can readily be identified using SDS-polyacrylamide gel electrophoresis and Western blotting. Precursor protein, spliced protein, and excised intein were identified by their predicted sizes, and the first two were further identified using anti-thioredoxin antibody. To estimate the efficiency of protein splicing, the intensity of individual protein bands on Western blots was measured to estimate the amount of that protein, and protein-splicing efficiency was calculated as the amount of spliced protein divided by the sum of spliced protein and precursor protein. At 37 °C, the Ter RIR-1 intein and the Ter RIR-3 intein showed efficient protein splicing, as indicated by the strong bands corresponding to the spliced protein and the excised intein. In contrast, the Ter RIR-2 intein and Ter RIR-4 intein showed little or no protein splicing at 37 °C. At 25 °C, which is closer to the natural growth condition of T. erythraeum, all four inteins showed efficient protein splicing. The protein-splicing efficiency was estimated to be 100%, 76%, 100%, and 95% for Ter RIR-1, -2, -3, and -4 intein, respectively.



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  		FIG. 3.
Protein splicing of Ter RIR inteins. Top, schematic illustration of the fusion-protein construct consisting of maltose-binding protein sequence (M), intein sequence (black box), and thioredoxin sequence (T). Middle, predicted sizes of protein products from different fusionprotein constructs containing the specified inteins. Fusion-protein construct containing the Ssp DnaB mini-intein was included as a known standard for identifying the spliced protein (33). Bottom, observation of protein splicing. Total cellular proteins of E. coli producing the specified fusion-protein were resolved by SDS-PAGE and visualized by Coomassie Blue staining (left panel) or Western blot using an anti-thioredoxin antibody (right panel). The fusion-protein contains either the Ter RIR-1 intein (lanes 1, 2, and 10), the Ter RIR-2 intein (lanes 3, 4, and 11), the Ter RIR-3 intein (lanes 5, 6, and 12), the Ter RIR-4 intein (lanes 7, 8, and 13), or the Ssp DnaB mini-intein (lanes 9 and 14). The fusion protein was produced either at 37 °C (lanes 1, 3, 5, 7, 9, and 14) or at 25 °C (lanes 2, 4, 6, 8, and 10–13). Position of the precursor protein is marked with letter P, the spliced protein with letter S, and the excised intein with a black dot.

 
Identification and Analysis of the Introns—The three introns are located in the first half of the gene and are named T.er.I2, T.er.I3, and T.er.I4 intron, according to nomenclature of known introns; they are 2,524, 1,757, and 2,554 nucleotides long, respectively (Fig. 1). Boundaries of these introns were defined by comparison of exon sequences with intron-less homologues such as Nsp RIR and by sequence comparison to known introns. Each intron can be folded into a typical secondary structure of group II introns, which includes the six helical domains and the exon-binding sequences. Predicted secondary structure of the T.er.I2 intron is shown in Fig. 4A. The T.er.I3 and T.er.I4 introns are very similar to the previously identified T.er.I1 intron both in sequence (Fig. 4B) and in predicted secondary structure (not shown). The T.er.I1 intron is listed as T.sp.I1 intron in the database for mobile group II introns and located in an intergenic sequence of this organism. These three introns are over 80% identical to each other in the ~680-nucleotide folded RNA sequence and over 70% identical in overall sequence, although the T.er.I3 intron lacks a 754-nucleotide sequence present in the other two introns. These three introns are ~50% identical to the T.er.I2 intron. The T.er.I2 intron, T.er.I4 intron, and the intergenic T.er.I1 intron each encode an RTL protein in domain IV, and their RTL protein sequences are over 60% similar to each other (data not shown). But the T.er.I2 RTL lacks a domain Zn, and the T.er.I1 RTL coding sequence has at least two single-base deletions causing frameshifts and is likely not functional.



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  		FIG. 4.
Intron structure and sequence comparisons. A, predicted secondary structure of the T.er.I2 intron is shown, flanking exon nucleotides are shown in lowercase letters, and the exon-intron boundaries are marked with arrowheads. Typical group II intron features are indicated, which include the six helical domains (I to VI), the exon binding sequences (EBS1 and EBS2), and the intron binding sequences (IBS1 and IBS2). Open reading frame in domain IV represents RTL coding sequence. B, sequence of the T.er.I3 and T.er.I4 introns are aligned with sequence of the previously identified T.er.I1 intron. Only the folded RNA sequences are shown, omitted sequences (some encoding RTL) are indicated in parentheses, and the total length of each intron is shown at the end.

 

   DISCUSSION
TOP
 ABSTRACT
 INTRODUCTION
 EXPERIMENTAL PROCEDURES
 RESULTS
 DISCUSSION
REFERENCES
 
The T. erythraeum RIR gene was found to encode four inteins and three group II introns, which predicts three RNA splicing events followed by four protein-splicing events in producing the mature ribonucleotide reductase (Fig. 1). The Ter RIR gene is believed to be functional in vivo despite its seven intervening sequences, based on the following considerations. The Ter RIR gene, after excluding its intein and intron coding sequences, predicts a complete and normal looking class II ribonucleotide reductase. The non-intron parts of the Ter RIR gene, totaling 6,717 bp, are maintained as open reading frames, whereas its non-coding frames have numerous termination codons, which would be extremely unlikely if the Ter RIR gene were not functional. All of the four inteins are functional in protein splicing when tested in E. coli and are predicted to be functional in vivo. The group II introns are also predicted to be functional in vivo, based on their normal looking structure and high levels of sequence identity to known group II introns. Ribonucleotide reductase is an essential housekeeping enzyme in all organisms, and there are at least three known classes of ribonucleotide reductase with very different amino acid sequences for different classes. We can not exclude the possible existence of an additional copy or class of RIR gene in T. erythraeum, although no other class II RIR gene was found through a Blast search of the nearly complete genome sequence of this organism.

Four inteins in the Ter RIR protein represent the largest number of inteins found so far in one host protein, and their coexistence with three group II introns in the same gene adds to the novelty. A gene encoding a single intein and a single intron has been reported before (28), but that gene is a bacteriophage ribonucleotide reductase gene not similar to the Ter RIR gene, and that single intron is a group I intron frequently found in bacteriophage genes (20, 39). The Ter RIR gene is apparently a chromosomal gene, not a phage or plasmid gene, because it was found on a large sequence contig (~225 kb) of the incomplete Ter genome sequence that encodes numerous other known chromosomal genes. It is interesting to see the high levels of sequence identity among the T.er.I3, T.er.I4, and the intergenic T.er.I1 introns. If these introns are related through relatively recent retrotranspositions, the T.er.I4 intron may be the closest to the presumed progenitor, because it alone encodes an intact RTL protein for retrotransposition. It may also be possible for RTL protein of T.er.I4 intron to act on the other introns in RNA splicing and in retrotransposition. Furthermore, T.er.I3 and T.er.I4 introns in the same gene may possibly cause exon skipping during splicing, as was found with certain bacterial phage group I introns (40).

It is novel to see three group II introns in one bacterial gene, especially in a chromosomal conserved housekeeping proteincoding gene, although multiple group I introns in one gene have been reported previously for bacterial phage and prophage protein-coding genes (40, 41). Bacterial and archaeal group II introns are strongly excluded from conserved protein-coding genes, even in organisms with relatively large numbers of introns. For example, among the 28 group II introns in the cyanobacterium Thermosynechococcus elongatus (42), 26 are outside of gene or inside mobile elements (insertion sequence, other group II introns), and 1 is inside a tRNA gene. The remaining intron is inside a hypothetical protein gene but in reverse orientation to transcription and therefore not functional. Preliminary searches in the nearly complete genome sequence of T. erythraeum did not reveal exceptional abundance of intron or intron in protein genes. Therefore, the presence of three group II introns in the ribonucleotide reductase gene represents a striking departure from known patterns of bacterial intron distribution.

It is extremely unlikely that by pure chance the four inteins and three group II introns inserted in the T. erythraeum ribonucleotide reductase gene, considering the rarity of intein and intron. Ribonucleotide reductase and other DNA metabolism proteins are more likely than other proteins to have intein and phage group I intron, which has generated many discussions regarding possible reasons (12–14, 20, 29, 43). In these highly conserved genes, an intein or group I intron may spread more easily in a population, because the recognition sequences of the intein-contained or group I intron-encoded homing endonucleases would be better preserved. It may also be more difficult for these genes to lose an intein or intron, because any imprecise deletion of the intein or intron will likely inactivate the essential gene. Consistent with this argument, the four Ter RIR inteins are inserted in the more conserved parts of the RIR protein, and two of them (Ter RIR-2 and Ter RIR-3) are next to critical catalytic residues of the enzyme. It is more difficult to explain the existence of three group II introns in the Ter RIR gene, considering the apparently strong selection against intron insertions in bacterial conserved protein genes (20, 21, 29). In bacteria, protein translation starts before completion of transcription and may, therefore, interfere with RNA splicing (20, 44), and it remains to be determined whether or how the Ter RIR gene avoided this problem. Interestingly, there is a translation termination codon just 3, 15, and 18 nt after the beginning of the T.er.I2, T.er.I3, and T.er.I4 introns, respectively, which may help to pause translation before RNA splicing is complete, as has been suggested for some group I introns (20, 44). For whatever reason, barriers against intron insertion were broken in the Ter RIR gene, and multiple insertions through retrotransposition could have happened within a relatively short period of time. This may be reminiscent of what happened in the proliferation of introns in eukaryotes (45–47). Another interesting possibility is that the multiple inteins and introns may help to regulate the production of ribonucleotide reductase in T. erythraeum. This enzyme catalyzes the conversion of ribonucleotides to deoxyribonucleotides, and its production is intricately regulated in other organisms in response to DNA synthesis, cell cycle, and DNA damages (48). A regulatory role of the inteins and introns would confer selective advantage on the host organism and explain the existence of the inteins and introns against all odds.


   FOOTNOTES
 
* This work was supported by research grants from the National Science and Engineering Research Council of Canada and the Canadian Institute of Health Research. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. Back

{ddagger} To whom correspondence should be addressed. Tel.: 902-494-1208; Fax: 902-494-1355; E-mail: pxqliu{at}dal.ca.

1 The abbreviations used are: RTL, reverse transcriptase-like; RIR, ribonucleotide reductase; Ter, Trichodesmium erythraeum. Back


   ACKNOWLEDGMENTS
 
We thank Dr. J. B. Waterbury for the gift of T. erythraeum cells used in this study.



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 ABSTRACT
 INTRODUCTION
 EXPERIMENTAL PROCEDURES
 RESULTS
 DISCUSSION
 REFERENCES
 

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