Nucleotide sequence of a region of the mitochondrial genome of Aspergillus nidulans including the gene for ATPase subunit 6

A mitochondrial reading frame which may code for a second form of ATPase subunit 9 in Aspergillus nidulans

The nucleotide sequence of a 74 codon reading frame from the Aspergillus nidulans mitochondrial genome is presented. The derived amino acid sequence displays typical features of dicyclohexylcarbodiimide (DCCD) binding proteins and is 84% homologous with a mitochondrial reading frame that potentially encodes an ATPase subunit 9 polypeptide in Neurospora crassa. However, in A. nidulans, as in N. crassa, there is strong biochemical and genetic evidence that this subunit is in fact nuclearly-encoded. In both organisms the DCCD-binding protein found in the F0 complexes of mitochondria from actively-growing cultures is almost certainly the product of this nuclear gene, and definitely not that of the mitochondrial reading frame. The discovery of an intact open reading frame than can code for a DCCD-binding protein in the mitochondrial genome of a second species of filamentous fungus strenghthens the possibility that the presence of a mitochondrial version of this gene has some biological significance.

Organisation of the mitochondrial genome of Trichophyton rubrum. DNA sequence analysis of the ND4 gene, the ATPase subunit-6 gene, the ribosomal RNA small-subunit gene, the ND6 gene, the COXIII gene, the ATPase subunit-8 gene and six tRNA genes that correspond respectively to the tyrosine, lysine, glutamine, asparagine, isoleucine and tryptophan isoacceptors

We present the nucleotide sequence of a 5207-bp-long region of the mitochondrial genome of the dermatophyte Trichophyton rubrum. This represents about 1/5th of the total genome and extends a previous study. From the 5' end of the present sequence, the order of genes is as follows: the end of the ND4 gene, the gene coding for subunit 6 of ATPase, the gene coding for the small ribosomal RNA (SSU rRNA), the tyrosyl tRNA gene, the ND6 gene, the COXIII gene, the ATPase 8 subunit gene and a cluster of tRNAs genes corresponding respectively to the lysine, glutamine, asparagine, isoleucine and tryptophan isoacceptors. The interesting features of this region are its compact organisation, the presence of subunit 8 of the ATPase gene and the secondary structure of SSU rRNA which is close to that of Aspergillus nidulans. On the basis of the order of the genes, which is essentially similar to that of A. nidulans, we can also assume that the LSU rRNA subunit gene should be just upstream of this sequenced region.

Revision of the nucleotide sequence and RNA splicing pathway of the Neurospora mitochondrial gene encoding ATPase subunit 6

Previous sequence analysis of the Neurospora oli2 (ATP6) mitochondrial gene suggested that, in addition to a typical Group-I intron, it contained an unusual, mostly-palindromic, 93-nucleotide intron. We report here revisions of the nucleotide sequence and analysis of the size and sequence of reverse-transcriptase PCR products that show: (1) the Group-I intron splice sites are located as predicted by previous DNA sequence analysis; (2) the putative 93-nt intron is not excised from the mature mRNA, and most of this sequence is actually in the 5' untranslated region. We conclude that the Neurospora ATP6 gene contains only one intron. Analysis of the cDNA sequence also confirms the non-universal nature of the Neurospora mitochondrial genetic code: a TGA codon inferred from the DNA sequence is present as UGA in the mRNA. This provides direct evidence that this codon is not altered, for example by RNA editing, to conform to the universal code.

RNA editing of a chimeric maize mitochondrial gene transcript is sequence specific

RNA editing was analysed in the mitochondrial ATPase complex subunit 6 gene (atp6) transcripts of the C male-sterile cytoplasm (cms-C) of maize. The only copy of atp6 in cms-C, designated C-atp6, is a triple gene fusion product comprised of DNA sequences derived from atp9, atp6, and an unknown origin. Sequences of cDNAs revealed 19 C to U alterations resulting in 16 amino acid residue changes compared to the genomic sequence. The only C to U edit in the 39-nucleotide sequence similar to atp9 was comparable to a change in the complete atp9 mRNAs of Petunia, Oenothera, wheat, and sorghum. The 442 nucleotides of unknown origin were not edited. The 18 editing events within the atp6 homologous region were similar to those in the atp6 transcripts of sorghum. RNA editing in maize C-atp6 transcripts introduces a translational stop codon at the same position where it is created by editing in sorghum and Oenothera atp6 mRNAs and is already present in atp6 open reading frames of most other plant and non-plant organisms. Our results, along with other reports on editing in chimeric transcripts, indicate that RNA editing is not influenced by rearrangements but instead is sequence specific.

Prediction of transmembrane topology of F0 proteins from Escherichia coli F1F0 ATP synthase using variational and hydrophobic moment analyses

The a subunit, a membrane protein from the E. coli F1F0 ATP synthase has been examined by Fourier analysis of hydrophobicity and of amino-acid residue variation. The amino-acid sequences of homologous subunits from Vibrio alginolyticus, Saccharomyces cerevisiae, Neurospora crassa, Aspergillus nidulans, Schizosaccharomyces pombe and Candida parapsilosis were used in the variability analysis. By Fourier analysis of sequence variation, two transmembrane helices are predicted to have one face in contact with membrane lipids, while the other spans are predicted to be more shielded from the lipids by protein. By Fourier analysis of hydrophobicity, six amphipathic alpha-helical segments are predicted in extra-membrane regions, including the region from Glu-196 to Asn-214. Fourier analysis of sequence variation in the b- and the c-subunits of the Escherichia coli F1F0 ATP synthase indicates that the single transmembrane span of the b-subunit and the C-terminal span of the c subunit each have a face in contact with membrane lipids. On the basis of this analysis topographical models for the a- and c-subunits and for the F0 complex are proposed.

Recent evidence for evolution of the genetic code

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.

RNA editing in ATPase subunit 6 mRNAs in Oenothera mitochondria. A new termination codon shortens the reading frame by 35 amino acids

The open reading frame encoding ATPase subunit 6 in Oenothera mitochondria is edited at 21 positions in all cDNA clones investigated. Only one of these events is silent, all others improve similarity between the homologous polypeptides of other species. The introduction of a new UAA termination codon shortens the polypeptide by 35 amino acids to a carboxy terminus conserved in other species. In one of the cDNA clones, an additional editing event was observed resulting in a premature UAA termination codon in the amino terminal region.

Evolutionary relationships among the permease proteins of the bacterial phosphoenolpyruvate: sugar phosphotransferase system. Construction of phylogenetic trees and possible relatedness to proteins of eukaryotic mitochondria

The amino acid sequences of 15 sugar permeases of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (PTS) were divided into four homologous segments, and these segments were analyzed to give phylogenetic trees. The permease segments fell into four clusters: the lactose-cellobiose cluster, the fructose-mannitol cluster, the glucose-N-acetylglucosamine cluster, and the sucrose-beta-glucoside cluster. Sequences of the glucitol and mannose permeases (clusters 5 and 6, respectively) were too dissimilar to establish homology with the other permeases, but short regions of statistically significant sequence similarities were noted. The functional and structural relationships of these permease segments are discussed. Some of the homologous PTS permeases were found to exhibit sufficient sequence similarity to subunits 4 and 5 of the eukaryotic mitochondrial NADH dehydrogenase complex to suggest homology. Moreover, subunits 4 and 5 of this complex appeared to be homologous to each other, suggesting that these PTS and mitochondrial proteins comprise a superfamily. The integral membrane subunits of the evolutionarily divergent mannose PTS permease, the P and M subunits, exhibited limited sequence similarity to subunit 6 of the mitochondrial F1F0-ATPase and subunit 5b of cytochrome oxidase, respectively. These results suggest that PTS sugar permeases and mitochondrial proton-translocating proteins may be related, although the possibility of convergent evolution cannot be ruled out.

Isolation of the ATP synthase subunit 6 and sequence of the mitochondrial ATP6 gene of the yeast Candida parapsilosis

The mitochondrially translated product called subunit 6 was extracted from the yeast Candida parapsilosis mitochondria using an organic solvent mixture and purified by reverse-phase HPLC. The partial N-terminal sequence of subunit 6 reveals a post-translational cleavage site as in Saccharomyces cerevisiae. The structural mitochondrial gene ATP6 was isolated form a mitochondrial DNA library using the oligonucleotide probe procedure. The gene and the surrounding regions were cloned into M13tg130 and M13tg131 phage vectors. The insert contained an open reading frame 738-bp encoding a 246-amino-acid polypeptide. Mature subunit 6 contains 243 amino acid residues and the predicted molecular mass is 26,511 Da. The subunit shows 52% similarity with ATP synthase subunit 6 of the yeast S. cerevisiae. Comparison between protein and DNA sequences shows that the CUN codon family codes for a leucine in C. parapsilosis mitochondria.

Expression of the wheat chloroplast gene for CF0 subunit IV of ATP synthase

The nucleotide sequence of the wheat chloroplast atp I gene encoding CF0 subunit IV of ATP synthase has been determined. The gene encodes a polypeptide of 247 amino acid residues with high sequence similarity to subunit IV from other plant chloroplasts and from cyanobacteria. The polypeptide shows sequence homology to the C-terminus of the F0 alpha subunit of Escherichia coli ATP synthase and subunit 6 of mitochondrial ATP synthase. The atp I gene is co-transcribed with the atp H, atp F and atp A genes for other subunits of ATP synthase in wheat. A gene-fusion of most of the atp I coding region with cro'-lacI'-lacZ' has been constructed in pEX2 and the fusion-protein has been used to raise antibodies in rabbits. The antibodies react with a polypeptide of 17 kDa in wheat thylakoid membranes indicating that the wheat atp I gene is expressed at the protein level. A model for the organisation of the polypeptide in the thylakoid membrane with four membrane-spanning segments is proposed.

A broad bean mitochondrial atp6 gene with an unusually simple, non-conserved 5' region

A nucleotide sequence of broad bean mitochondrial DNA (mtDNA) that contains an atp6 gene of 876 ntp is presented. Relative to other plant atp6 genes, this broad bean gene comprises a 90 ntp non-conserved 5' region, a 759 ntp highly conserved central region and a 27 ntp non-conserved 3' region. The non-conserved, 5' region of the broad bean atp6 gene differs from the corresponding regions of most other plant atp6 genes in that it contains only one potential translation initiation codon and, following this codon, a 63 ntp segment that predicts an amino acid sequence with a predominance of alternating leucines.

Structural aspects of proton-pumping ATPases

ATP synthase is found in bacteria, chloroplasts and mitochondria. The simplest known example of such an enzyme is that in the eubacterium Escherichia coli; it is a membrane-bound assembly of eight different polypeptides assembled with a stoichiometry of alpha 3 beta 3 gamma 1 delta 1 epsilon 1 a1b2c10-12. The first five of these constitute a globular structure, F1-ATPase, which is bound to an intrinsic membrane domain, F0, an assembly of the three remaining subunits. ATP synthases driven by photosynthesis are slightly more complex. In chloroplasts, and probably in photosynthetic bacteria, they have nine subunits, all homologues of the components of the E. coli enzyme; the additional subunit is a duplicated and diverged relation of subunit b. The mammalian mitochondrial enzyme is more complex. It contains 14 different polypeptides, of which 13 have been characterized. Two membrane components, a (or ATPase-6) and A6L, are encoded in the mitochondrial genome in overlapping genes and the remaining subunits are nuclear gene products that are translated on cytoplasmic ribosomes and then imported into the organelle. The sequence of the proteins of ATP-synthase have provided information about amino acids that are important for its function. For example, amino acids contributing to nucleotide binding sites have been identified. Also, they provide the basis of models of secondary structure of membrane components that constitute the transmembrane proton channel. An understanding of the coupling of the transmembrane potential gradient for protons, delta mu H+, to ATP synthesis will probably require the determination of the structure of the entire membrane bound complex. Crystals have been obtained of the globular domain, F1-ATPase. They diffract to a resolution of 3-4 A and data collection is in progress. As a preliminary step towards crystallization of the entire complex, we have purified it from bovine mitochondria and reconstituted it into phospholipid vesicles.

Sequence analysis of the wheat mitochondrial atp6 gene reveals a fused upstream reading frame and markedly divergent N termini among plant ATP6 proteins

The nucleotide sequence of the wheat mitochondrial gene for subunit 6 (atp6) of the F1F0 ATPase complex has been determined. Unlike bacterial, chloroplast or animal/fungal mitochondrial atp6 counterparts, which encode proteins of about 230-270 amino acids, the wheat mitochondrial atp6 homologue comprises the latter part of an open reading frame (ORF) of 386 codons. The ATP6 protein may therefore by synthesized with a long N-terminal presequence. This is supported by the finding that the ORF is preceded by a conserved sequence block closely related to ones preceding several other actively transcribed wheat mitochondrial protein-coding genes. The fused upstream ORF is similar in length, but unrelated in sequence, to those preceding the maize and tobacco mitochondrial atp6 genes. In wheat, the atp6 gene is located on a recombinationally active repeated DNA element, whose length of 1.4 kb corresponds approximately to that of the atp6 mRNA. A comparison of the wheat and maize ATP6 sequences reveals unexpectedly high divergence in the region corresponding to the mature N-terminal domain and may reflect mitochondrial DNA rearrangements during atp6 gene evolution in monocotyledonous plants.

Bacterial adenosine 5'-triphosphate synthase (F1F0): purification and reconstitution of F0 complexes and biochemical and functional characterization of their subunits

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Polymorphism in mitochondrial DNA of several Trichophyton rubrum isolates from clinical specimens

Mitochondrial DNA from six isolates of Trichophyton rubrum (a fungal pathogen of humans) was isolated, purified and digested by restriction endonucleases HindIII, HaeIII, AluI and EcoR1. The isolates could be classified into two groups according to their characteristic fragment patterns. Electron microscopy indicated that T. rubrum mitochondrial DNA are circular molecules of different lengths, 26.85 microns and 21.60 microns respectively, according to the group.

The organization and sequence of the genes for ATP synthase subunits in the cyanobacterium Synechococcus 6301. Support for an endosymbiotic origin of chloroplasts

The nucleotide sequence has been determined of two regions of DNA cloned from the cyanobacterium Synechococcus 6301. The larger, 8890 base-pairs in length, contains a cluster of seven genes for subunits of ATP synthase. The order of the genes is a:c:b':b:delta:alpha:gamma, b' being a duplicated and diverged form of b. As in the Escherichia coli unc operon, the a gene is preceded by a gene for a small hydrophobic and basic protein. The hydrophobic profile of the potential gene product suggests that its secondary structure is similar to the uncI protein. The smaller DNA fragment, 4737 base-pairs in length, is separated from the larger by at least 15 X 10(3) base-pairs of DNA. It contains a cluster of two genes encoding ATP synthase subunits beta and epsilon. Both clusters of ATP synthase genes are preceded by sequences resembling the -10 (Pribnow) box of E. coli promoters and are followed by sequences able to form stable stem-loop structures that might serve to terminate transcription. These features and the small intergenic non-coding sequences suggest that the clusters are operons, for which the names atp1 and atp2 are proposed. The order of genes within the two clusters is very similar to the gene order in the E. coli unc operon. However, it is most closely related to the arrangement of genes for ATP synthetase subunits a:c:b:alpha and beta:epsilon in two clusters in pea chloroplast DNA. This close relationship between chloroplasts and the cyanobacterium is also evident from comparisons of the sequences of ATP synthase subunits; the Synechococcus proteins are much more closely related to chloroplast homologues than to those in other bacteria or in mitochondria. It is further supported by the cyanobacterial b and b' proteins which, in common with their chloroplast counterpart, subunit I, have extra amino-terminal extensions relative to the E. coli b protein. This extension is known to be removed by post-translational processing in the chloroplast, but its function is obscure. It also seems likely that the cyanobacterial and chloroplast ATP synthases have important similarities in subunit composition. For example, the presence of two related genes, b and b', in the cyanobacterium suggests that its ATP synthase is a complex of nine polypeptides, and that it may have single copies of related b and b' proteins rather than two copies of identical b subunits as found in the E. coli enzyme.4+off

The ATPase subunit 6 gene of tobacco mitochondria contains an unusual sequence

We have isolated and characterized the F0-ATPase subunit 6 gene (atp6) from tobacco mitochondria. The tobacco sequence exists as a single copy, is transcribed and contains an open reading frame (ORF) capable of encoding a peptide of 395 amino acids. The first 130 amino acids of the tobacco putative polypeptide show limited homology with the N terminus predicted for the maize ATPase subunit 6. Although poorly conserved at the sequence level, the tobacco and maize amino termini are hydrophilic and have a high percentage of charged amino acids. This portion of the predicted peptide may represent a presequence that is common to the ATPase subunit 6 of plants. Significant homology between tobacco and maize begins with amino acid 131, in a region that is highly conserved among fungal ATPase 6 subunits. In the remainder of the predicted protein, tobacco and maize share approximately 81% homology. A 41 bp sequence and a 175 bp conserved region found upstream from the tobacco atp6 coding region are homologous with sequence elements found in the 5' flanking regions of other plant mitochondrial genes and may be important for regulation and expression of the atp6 gene.

The ATP synthase subunit 9 gene of Aspergillus nidulans: sequence and transcription

We have determined the nucleotide sequence of the Aspergillus nidulans nuclear gene oliC31, which encodes subunit 9 of mitochondrial ATP synthase. The open reading frame contains no introns and specifies a predicted protein of 143 amino acids comprising a pre-sequence of 62 residues and a mature protein of 81 residues. The amino acid homology with the equivalent Neurospora crassa protein is 50% for the pre-sequence and 80% for the mature protein. A comparison with this and other imported mitochondrial proteins has revealed conserved regions which may be important for transport or subsequent processing. Multiple transcription initiation and polyadenylation sites have been identified. The promoter region of the oliC31 gene is characterised by long pyrimidine-rich tracts preceding the transcription initiation sites.

The pho1 mutation. A frameshift, and its compensation, producing altered forms of physiologically efficient ATPase in yeast mitochondria

The pho1 mutation belongs to the OL12 gene on mitochondrial DNA of Saccharomyces cerevisiae, which codes for a membrane factor subunit of the mitochondrial ATPase (apparent molecular mass 20 kDa). We analysed the ATPase complex from the pho1 mutant and from three revertants, after immunoprecipitation from mitochondrial extracts, by dodecyl sulphate/acrylamide gel electrophoresis. In two revertants the OL12 gene product appeared as an abundant slower migrating peptide, while in the pho mutant, two bands appeared in very low amounts. For the third revertant, a strong band appeared at the normal level. Sequencing of the OL12 gene from these strains gave the following results: the pho1 mutation is a frameshift, arising by insertion of an extra thymidine into a group of three. Two of the revertants contain the same group of four thymidines, but genetic compensation of the frameshift occurs 24 base pairs downstream by the loss of four bases, implying a deficit of one codon. The third revertant has recovered the normal three-thymidine sequence. There is excellent correlation between the modified sequences and electrophoretic migration of the peptide product. Owing to the leakiness of the pho1 phenotype (reduced but not nil growth rate on oxidizable carbon sources, 5-10% highly oligomycin-sensitive ATPase complex, low amounts of OL12 gene product peptides), some translational correction of the frameshift is bound to occur. Based on these results, the compatibility of abnormal ATPase architecture with modified energetic efficiency is discussed.

The Aspergillus nidulans mitochondrial genome

A brief description is provided of the overall organisation of the Aspergillus nidulans mitochondrial genome, as revealed by DNA sequence analysis.

Two intervening sequences in the ATPase subunit 6 gene of Neurospora crassa. A short intron (93 base-pairs) and a long intron that is stable after excision

A 3590 base-pair region of the mitochondrial genome of Neurospora crassa, including the gene for ATPase subunit 6 (oli2), has been sequenced. The oli2 gene is interrupted by two intervening sequences. The first intron, situated after the third codon of the gene, is 93 base-pairs long; two-thirds of this intron consist of a palindromic sequence. The second intron is 1370 base-pairs long and contains an extended open reading frame that is continuous and in frame with the upstream exon sequence. This intron has structural homology with most other fungal mitochondrial introns. Transcript analysis has yielded a complex pattern of RNA species and demonstrated that the second intron is quite stable after excision. An unknown reading frame (homologous to reading frames of other mitochondrial genomes) is located 1000 base-pairs upstream from the oli2 coding sequence.

Identification of the polypeptides encoded in the ATPase 6 gene and in the unassigned reading frames 1 and 3 of human mtDNA

Antibodies prepared against chemically synthesized peptides predicted from the DNA sequence have been used to identify the polypeptides encoded in the ATPase 6 gene and in unidentified reading frames (URFs) 1 and 3 of human mtDNA. In particular, antibodies directed against the COOH-terminal nonapeptide of the putative polypeptide encoded in the ATPase 6 reading frame immunoprecipitated specifically component 17 of the HeLa cell mitochondrial translation products, the reaction being inhibited by the specific peptide. Similarly, antibodies directed against the COOH-terminal undecapeptide of the putative URF1 product or against the COOH-terminal heptapeptide of the presumptive URF3 product were effective in immunoprecipitating specifically component 12 or, respectively, component 24 of the mitochondrial translation products. The sizes of proteins 17, 12, and 24, as estimated from their electrophoretic mobilities, are compatible with their being the products of the ATPase 6 gene, URF1, and URF3, respectively.

Mitochondrial transfer RNA genes from fungi (Aspergillus nidulans) and plants (Lupinus luteus) are transcribed in Xenopus laevis oocyte nuclei

Three plasmids containing Aspergillus nidulans mitochondrial transfer RNA genes were microinjected into the nucleus of Xenopus laevis oocytes. Plasmids that contained a single tRNACys gene or two tRNA genes (Arg and Asn) yielded tRNA-sized transcripts. Plasmids containing cloned Lupinus mitochondrial tRNA genes were also transcribed and processed in X. laevis nuclei.

Biogenesis of mitochondria: the mitochondrial gene (aap1) coding for mitochondrial ATPase subunit 8 in Saccharomyces cerevisiae

A mitochondrial gene (denoted aap1) in Saccharomyces cerevisiae has been characterized by nucleotide sequence analysis of a region of mtDNA between the oxi3 and oli2 genes. The reading frame of the aap1 gene specifies a hydrophobic polypeptide containing 48 amino acids. The functional nature of this reading frame was established by sequence analysis of a series of mit- mutants and revertants. Evidence is presented that the aap1 gene codes for a mitochondrially synthesized polypeptide associated with the mitochondrial ATPase complex. This polypeptide (denoted subunit 8) is a proteolipid whose size has been previously assumed to be 10 kilodaltons based on its mobility on SDS-polyacrylamide gels, but the sequence of the aap1 gene predicts a molecular weight of 5,815 for this protein.

DNA duplication has resulted in transfer of an amino-terminal peptide between two mitochondrial proteins

The mitochondrial genome of the ascomycete Aspergillus nidulans possesses at least nine unidentified reading frames (URFs). Two of these are particularly interesting in that the amino acid sequences of the derived translation products are very similar in the N-terminal regions. The first 36 residues of the URFx gene product are repeated at the start of a second reading frame, URFA3, with only six mismatches. Despite this similarity in their amino-termini, the latter parts of URFx and URFA3 are completely different. Closer examination of the nucleotide sequences at the 5' ends of the two genes shows that the conserved peptides are part of a 300-base pair (bp) duplication within the mitochondrial genome. This duplication also includes the tRNA gene for asparagine and a conserved 116-bp intergenic region.