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Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115
| ABSTRACT |
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The mitochondrial genome of the peronosporomycete water mold Saprolegnia ferax has been characterized as a 46 930 bp circle containing an 8618 bp large inverted repeat (LIR). Eighteen reading frames encode identified subunits of respiratory complexes I, III, IV and V; 16 encode polypeptides of small and large mitoribosome subunits; and one encodes a subunit of the sec-independent protein translocation pathway. Of four additional putative reading frames three are homologues of those found in the related Phytophthora infestans genome. Protein encoding loci in the tightly compacted genome typically are arranged in operon-like clusters including three abutting and two overlapping pairs of reading frames. Translational RNAs include the mitochondrial small and large subunit rRNAs and 25 tRNA species. No tRNAs are encoded to enable translation of any threonine or the arginine CGR codons. The LIR separates the molecule into 19 274 bp large and 10 420 bp small single copy regions, and it encodes intact duplicate copies of four reading frames encoding known proteins, both rRNAs, and five tRNAs. Partial 3' sequences of three additional reading frames are duplicated at single copy sequence junctions. Active recombination between LIR elements generates two distinctive gene orders and uses the duplicated 3' sequences to maintain intact copies of the partially duplicated loci.
Key words: mitochondrial genes, mtDNA, Oomycetes, Peronosporomycetes, stramenopiles
| INTRODUCTION |
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The Peronosporomycetes (Oomycetes) are a class of fungal-like protists included in an assemblage of lower eukaryotes often referred to as stramenopiles (Patterson 1989
, Dick 2001
). Members of this lineage are unified taxonomically by the presence of tripartite tubular hairs (stramenopiles) at some stage of their life cycle. The diverse collection of organisms also includes autotrophic chromophytes (chlorophyll a + c containing algae such as chrysophytes, fucophytes, xanthophytes and diatoms), additional fungal-like heterotrophs (thraustochytrids, labyrinthulids and hyphochytriomycetes) and the heterotrophic bicosoecids. Complete mitochondrial DNA sequences have been determined for six of these organismsthe chromophytes Chrysodidymus synuroideus (Chesnick et al 2000
), Laminaria digitata (Oudot-LeSeq et al 2002
), Ochromonas danica (Burger et al 2002) and Pylaiella littoralis (Oudot-LeSeq et al 2001
); the heterotrophic bicosecid Cafeteria roenbergensis (Burger 1999
); and the peronosporomycete Phytophthora infestans (Paquin et al 1997
). Like most protists, mitochondrial genomes of peronosporomycetes typically are compact mtDNAs and encode at least 30 polypeptides of known function.
Two distinct mtDNA organizational patterns have emerged from restriction endonuclease analyses of a variety of peronosporomycete taxa. The more prevalent LIR pattern initially was described for Achlya ambisexualis (Hudspeth et al 1983
) and subsequently was found in at least some representatives from all other examined orders, with the exception of the Leptomitales. This pattern features a large inverted repeat, ranging from about 8.5 to 28.9 kb (Hudspeth and Hudspeth 1996
), which separates the molecule into small and large single copy regions. Intramolecular recombination events between the repeat elements in Achlya (Hudspeth et al 1983
, Boyd et al 1984
) were shown to generate two equimolar orientational genome isomers, each with its own gene order.
In the less prevalent non-LIR pattern, initially described for Phytophthora infestans (Klimczak and Prell 1984
) of the order Pythiales, the LIR is conspicuously absent. Non-LIR genomes subsequently have been described only for additional Phytophthora species (Forster et al 1987
, Shumard-Hudspeth and Hudspeth 1990
) and Apodachlya and Leptomitus of the Leptomitales (McNabb and Klassen 1988
, Hudspeth 1992
).
In this work we report the complete mtDNA sequence for the peronosporomycete Saprolegnia ferax, compare it with the non-LIR pattern P. infestans, and examine the consequences of active intramolecular recombination events between LIR elements.
| MATERIALS AND METHODS |
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Total DNA was prepared from late log-phase mycelia with purified mtDNA obtained as the upper band in bis-benzimide (Hoechst 33258; Calbiochem, La Jolla, California) CsCl gradients (Hudspeth et al 1980
, Shumard et al 1986
). Plasmid DNAs were isolated by the alkaline lysis method (Birnboim and Doly 1979
).
Cloning and DNA sequencing.
Before sequencing of the genome, a preliminary seven-enzyme restriction map was constructed to approximate the limits of the LIR. Initial DNAs for sequencing then were prepared from clones generated from a combination of mapped EcoRI or unmapped HindIII restriction fragments ligated into pUC19 and transformed into E. coli JM83 following established procedures (Maniatis et al 1982
). Clones were sequenced using sequence-generated primers prepared using either a 392 or PCRmate 391 DNA synthesizer (Applied Biosystems, Foster City, California) or were obtained commercially (MWG Biotech, High Point, North Carolina). Positions of abutting EcoRI or HindIII clones were confirmed by sequencing of mtDNA PCR products generated by crossing of presumptive adjacent restriction sites. Regions of sequence not included in the initial clones were generated by direct sequencing of purified mtDNA using primers derived from sequenced noncontiguous clones. Subsequent PCR products were generated and sequenced to include these regions. DNA sequence data were obtained using a 373 DNA Sequencer (Applied Biosystems, Foster City, California) or a Beckman Coulter CEQ 2000XL automated DNA sequencer (Beckman Coulter, Fullerton, California).
Sequence data were assembled using Sequencher (Gene Codes Corp., Ann Arbor, Michigan). Protein-encoding and rRNA loci were identified using the NCBI BLASTP and BLASTN similarity searches (Altschul et al 1990
). tRNAs were identified using tRNAscan-SE (Lowe and Eddy 1997
). Protein alignments were performed using the Clustal X program (Thompson et al 1997
).
The complete mtDNA sequence has been deposited in GenBank as accession number AY534144.
| RESULTS |
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Genetic organization and gene content.
The 66 intron-less genetic loci (77 including LIR duplicated sequences) encoded in the genome are shown in FIG. 1
and listed in TABLE I
. These loci, representing 92.1% of the genomic sequence, often are arranged in operon-like clusters and are densely packed in the genome. Two pairs of genes overlap (rps12-rps7, rpl2-rps19) and three pairs abut each other (rps2-rps4, rps13-rps11, rps19-rps3). Intergenic regions average only 47 bp with a range of 23 (overlapping loci) to 341 bp. The overall A+T content of 76.9% is significantly higher in intergenic regions (94.1%) than in protein-encoding (79.2%) sequences. Thirty-nine loci encode polypeptides of which 35 are readily assigned by similarity searches of the GenBank protein database. Eighteen of these are components of the mitochondrial respiratory chain, 16 are subunits of the mitoribosome, and one, secY, is a homolog of E. coli tatCa component of the sec-independent protein translocation pathway (Bogsch et al 1998
, Weiner et al 1998
). Three of four unassigned reading frames (orf64, orf143 and orf273) share regions of homology (FIG. 2
) with "unique" P. infestans ORFs (Paquin et al 1997
, below) of approximately equivalent sizes and the carboxyl region of rps4 shares homology with orf100 of P. infestans. The remaining 27 loci (exclusive of LIR duplicated sequences) encode RNA components of the mitochondrial translational apparatus. Twenty-five are tRNAs, and the remaining two encode the small (rns) and large (rnl) subunit rRNAs. The tRNAs include both initiator and elongator trnM plus cognate species for trnG, trnI, trnL, trnR, and trnS. No trnT was detected.
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| DISCUSSION |
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The overall genetic content and organization of the two genomes is similar. All 35 assignable reading frames, both rRNAs, and the 25 species of tRNAs are common to both genomes with differences reflected only in the numbers and types of ORFs.
Genome organization, with the exception of the LIR, also is strikingly similar, with the genes organized as compact blocks of loci. In S. ferax these blocks are suggestive of three major polycistronic transcripts. A 20-loci clockwise transcript (FIG. 1
) originates at nad6 in the small single copy region and terminates with rnl in the LIR, while a 22-loci anticlockwise transcript originates at rps13 in the large single copy region and terminates following rps7 in the LIR. Finally, a 33-loci clockwise transcript extends from secY in the large single copy region to rps7 in the other LIR. This latter transcript would overlap the anticlockwise transcript at its origin and duplicates transcription for nine of the LIR encoded loci.
Gene-order conservation.
Comparison of gene order and potential transcriptional units in the S. ferax and P. infestans genomes revealed two major blocks of colinear loci. With the inclusion of a newly identified orf68 in the P. infestans genome (see below) a colinear set of 26 loci extending from trnLUAG through rps4 (FIG. 1
) is apparent. Retained within this block are the remnants of the conserved prokaryotic ribosomal protein linkages including rps13-rps11, rpl2-rps19-rps3-rpl16 and rps14-rps8-rpl6, all previously noted for P. infestans (Lang et al 1999
). The presumptive stramenopile linkage of rps8-rpl6-rps2-rps4 (Chesnick et al 2000
) is similarly present. A second major block includes the eight LIR genes from nad2 through rps7.
The retention of large colinear blocks of loci in the Peronosporomycetes, even in distantly related taxa, is expected. This is based on the necessity of either retaining or acquiring promoter sites for the translocated loci. Due to the paucity of intergenic target sequences for translocation events that avoid disruption of other loci, the rate of viable translocations is expected to be low and the retention of genetic linkages to be high.
Unassigned reading frames.
Deduced amino acid sequences of the four unassigned Saprolegnia ORFs were compared with the five free-standing ORFs reported for P. infestans (Paquin et al 1997
). Two of the ORFs lie in the largest positionally conserved gene block with orf143 located between nad7 and trnHGUG, and orf273 between trnICAU and atp8. Each ORF shares obvious regions of amino acid similarity with its P. infestans equivalent. The orf143/orf142 pair (FIG. 2b
) encodes the more highly conserved deduced polypeptide with an amino acid identity of about 45%. The orf273/orf217 pair (FIG. 2c
) is significantly less conserved but still clearly retains three regions of conservationone centrally located and the others near the termini.
No homologue to Saprolegnia orf64 was identified previously in the P. infestans genome. However, because this ORF is included in a conserved 26 loci gene block (see above), and, because the corresponding block in the P. infestans genome contains an intergenic region of sufficient length to encode a comparable reading frame, we re-evaluated this region of the P. infestans genome. A short open reading frame, designated orf68, subsequently was located between secY and trnCGCA on the complementary strand as in S. ferax, but in P. infestans this ORF shares a 12-codon overlap with the carboxyl region of secY. The alignment of deduced amino acid sequences from this ORF pair revealed the conserved P. infestans polypeptide (48% identity) shown in FIG. 2a
.
Searches of the protein databases, using short regions of identity/similarity derived from each of the three ORF pairs noted above, failed to identify likely mitochondrial homologues. However, their positional and relative amino acid conservation in two distinct subclass peronosporomycete lineages strongly argues for their validity as functional, albeit highly derived, mitochondrial proteins.
Of the three P. infestans ORFs without obvious S. ferax homologues, orf100 is a candidate for a carboxyl extension of rps4. Similar to other protists and prokaryotes, this locus in S. ferax encodes a polypeptide with a carboxyl terminus about 75 amino acids longer than that reported for P. infestans. The proximity of orf100 five nucleotides downstream of rps4 in P. infestans prompted the inclusion of a concatenated rps4/orf100 sequence in an alignment with deduced rps4 polypeptides from the "jakobid" protist Reclinomonas americana (Lang et al 1997
), the brown alga Pylaiella littoralis (Oudot-LeSeq et al 2001
) and the peronosporomycete Saprolegnia (FIG. 3
). While it is apparent that the carboxyl region of rps4 is far less conserved than the remainder of the polypeptide among these representative taxa, orf100 and the rps4 carboxyl region of S. ferax clearly are homologous. It remains to be determined if the rps4/orf100 combination of P. infestans encodes a true frame shift, represents a genomically fragmented rps4 or is a sequencing artifact.
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Codon usage and tRNAs.
Twenty-five species of tRNAs with appropriate clover-leaf structures and unambiguous anticodons are encoded in S. ferax mtDNA, with five of these duplicated in the LIR. This set of tRNAs is identical to that encoded in the P. infestans genome (Paquin et al 1997
) and is insufficient to support mitochondrial protein synthesis. Notably absent are the tRNAs required for translation of arginine CGR and all threonine codons. The two-codon arginine AGR family is accounted for by trnRUCU (only AGA codons are used in S. ferax), but the use of trnRGCG in the four-codon arginine family in lieu of the more typical trnRACG with its wobble "A" deaminated to "I" (Pfitzinger et al 1990
) limits translation to CGY codons. Thus, as in P. infestans, it is necessary to postulate the import of cytosolic tRNAs enabling translation of arginine CGR and all threonine codons. Similarly, as originally observed in E. coli (Muramatsu et al 1988
) and inferred for P. infestans and other protists and plants (Gray et al 1998
), it is assumed that the wobble "C" of trnICAU is post-transcriptionally modified to lysidine to enable translation of the isoleucine AUA codon.
LIR recombination retains intact loci.
The primary architectural difference between S. ferax and P. infestans mtDNAs is the presence of the LIR. Size variation in LIR genomes has been well documented among peronosporomycete taxa and has been shown to be the major contributor to genome size variation (Hudspeth and Hudspeth 1996
, McNabb and Klassen 1988
). S. ferax contains the shortest described LIR, and the 8618 bp are shown here to encode intact copies of four polypeptides, five tRNAs and both rRNAs. It was a surprise to find partial protein-encoding sequences, rather than intergenic sequences, at the repeat termini. We had anticipated that, because an active recombination mechanism between repeat elements has been inferred for S. ferax and other members of the Saprolegniales (Hudspeth et al 1983
, Boyd et al 1984
), the LIR would terminate with intergenic sequences and thereby ensure intact encoded loci for both mtDNA orientational isomers.
The LIR ends encode 3' termini for three polypeptides but still maintain available intact copies for the three loci. At the small single copy junctions, the LIR terminates with 106 codons of nad5. When the genome assumes the orientational isomer presented in FIG. 1
, the right-handed repeat element generates an intact nad5 locus while the left-handed element retains only the carboxyl-encoding fragment. In the alternate configuration it is the left-handed repeat that forms the intact locus. A different approach to retaining intact loci is used for the large single copy junctions. Here the LIR termini encode two in-frame codonslysine and terminationthat are common to the flanking loci. These codons provide translational termination for both atp1 and cox1 in both mtDNA orientations. Thus, the extension of coding sequences into the LIR still provides intact nad5, atp1 and cox1 loci for either mtDNA isomer.
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 Corresponding author. E-mail: mykes{at}niu.edu
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