1. Linear Mitochondrial Plasmids of F
Linear Mitochondrial Plasmids of F. oxysporum Are Novel, Telomere-like Retroelements 
Tobias C Walther, John C Kennell 
Molecular Cell 
Volume 4, Issue 2, Pages (August 1999)
DOI: /S (00)

2. Figure 1
Partial Restriction Maps of the Linear Mitochondrial DNA Plasmids, pFOXC2 and pFOXC3, of Fusarium oxysporum f. sp. raphani and F. oxysporum f. sp. matthioli, Respectively
The plasmids have a hairpin at one terminus and repeats of a 5 bp sequence at the other terminus (small boxes). Although the plasmids are a contiguous DNA molecule, the coding strand is labeled (+) sense and the complementary strand (−) sense for simplicity. Previous studies indicate that pFOXC2 is insensitive to 5′ → 3′ exonuclease, which suggests that the 5′ end may be modified (black circle with question mark; Kistler and Leong 1986). A single large open reading frame encoding a putative protein of 527 amino acids identified using the fungal mitochondrial genetic code is indicated below the restriction maps. Shaded regions of the ORFs indicate the location of blocks of amino acids characteristic of reverse transcriptases (1, 2, 2a, and A–E). Block 2a is characteristic of reverse transcriptases of non-LTR retroelements. The conserved regions are compared to the three closely related ORFs encoded by the mitochondrial plasmids pFOXC1 of Fusarium oxysporum, f. sp. conglutinans, Varkud retroplasmid of Neurospora intermedia, and Et2.0L of Epichloë typhina (only partial sequence information is available for pFOXC1 and Et2.0L). The numbers below each ORF indicate the percent amino acid identity and similarity (in parentheses) with the RT domain of the pFOXC2 ORF. Restriction enzyme sites: Bg, BglII; E, EcoRI; E5, EcoRV; P, PstI; Sa, SalI; s, Sau3AI; and X, XmaI.
Molecular Cell 1999 4, DOI: ( /S (00) )

3. Figure 2
Southern Hybridization of 32P-Labeled cDNAs to Total Genomic and mtDNA
The panel on the left is an EtBr-stained agarose gel containing uncut and HindIII-digested total DNA, as well as HindIII-digested mtDNA, isolated from strain 699. The panel on the right is a Southern hybridization using 32P-labeled products of endogenous reactions using mtRNP particles from strain 699 as probe. The arrow identifies a 1.85 kb HindIII plasmid band that migrates with undigested pFOXC2 DNA. The size of PstI restriction fragments of phage λ DNA is indicated on the left (in kilobases).
Molecular Cell 1999 4, DOI: ( /S (00) )

4. Figure 3 Gel Electrophoretic Separation of 32P-Labeled cDNA Products
Reverse transcriptase reactions using 699 mtRNP particles and DEAE-purified mtRNP particles were incubated under standard conditions with 0.3 μM [32P]dCTP for 10 min, prior to the addition of dCTP to 100 μM and incubation for 0–45 min, as indicated. Products were precipitated and separated in a 1.0% nondenaturing agarose gel. The closed arrow indicates the 1.95 kb cDNA reaction product, and the open arrow and asterisk indicate a band which is detected in reactions that retain endogenous RNA. The size of 5′ end–labeled PstI restriction fragments of phage λ DNA is indicated on the left (in kilobases).
Molecular Cell 1999 4, DOI: ( /S (00) )

5. Figure 4
Restriction Endonuclease Analysis of the Termini of pFOXC2 and pFOXC3
Gel-purified pFOXC2 and pFOXC3 were digested with SalI (Sa), PstI (P), Sau3AI (s), BglII (Bg), or EcoRV (E5) and PstI, Sau3AI, or BglII, respectively, and the restriction fragments were 5′ end labeled and separated by electrophoresis in a 6% polyacrylamide gel containing 8 M urea (denaturing, left panel). Digestion of pFOXC3 with PstI did not produce a fragment. SalI and BglII fragments of pFOXC2 and BglII fragments of pFOXC3 were also analyzed in a 6% nondenaturing polyacrylamide gel (right panel). The numbers at the right of the panels indicate the size (in nucleotides) of 32P-labeled molecular weight markers: a 100 bp ladder (M) and Sau3AI fragments of pBluescribe (M′). The numbers to the right of the panels indicate the size of the plasmid restriction fragments (identified by arrowheads in the gel). The Sau3AI restriction digests contain a number of partially cut bands. The bands corresponding to terminal fragments are indicated by black arrows, and an asterisk identifies an EcoRV fragment (E5) that corresponds to the 3′ end of pFOXC2. Equal amounts of restriction products were loaded in the gels, and differences in the intensity of the 32P-labeled products likely reflect the efficiency of kinase reactions that favor molecules having 5′ overhangs (SalI, Sau3AI, and BglII) over blunt-ended (EcoRV) and 3′ overhangs (PstI). A schematic diagram of pFOXC2, which indicates the location of restriction sites for PstI, SalI, BglII, and EcoRV, is shown at the bottom (Sau3AI sites are indicated in Figure 1). The exact distance of the PstI site to the plasmid terminus is unknown; however, the distance to downstream sites is indicated (in nucleotides). The predicted size of the restriction fragments in both denaturing and nondenaturing gels, relative to the estimated length of the PstI fragment of pFOXC2, is indicated, as well as the observed (obs) size.
Molecular Cell 1999 4, DOI: ( /S (00) )

6. Figure 5
Hypothetical Model for the Replication of Linear, Non-LTR Retroplasmids, pFOXC2 and pFOXC3
See text for details.
Molecular Cell 1999 4, DOI: ( /S (00) )