User:Nkuldell/mtDNA pt2

Modifications

Change to make	number of such changes	method for generating changes	comments
remove dubious ORF sequences, hypothetical proteins	11 ORFs,4781 bps total	txn' with linear DNA bearing flanking sequences?	Q0010, Q0017, Q0032, AI5_BETA, Q0092, Q0142, Q0143, Q0144, Q0182, Q0255, Q0297
remove introns
move all transcription to Watson strand
regulate promoters with alternative polymerase
what's left...

Summary of what's currently on mtDNA

• what's encoded on S. cerevisiae mtDNA:

Genes for	number	names	comments
proteins for oxidative phosphorylation	seven	apocytochrome b, subunits I-III of cytochrome oxidase, subunits 6, 8 and 9 of ATP synthase	COB is gene for cytochrome b and has six exons (B1-B6) and five introns (bI1-bI5) though some lab strains are missing first three introns, COX1 is gene for subunit I of cytochrome oxidase
protein for small subunit of mitochondrial ribosome	one	Var1p
mitochondrial tRNAs	24 or 25
tRNA maturation	one	9S
additional ORFs	about 20	within introns of large rRNA, COX1 and COB	can delete all 20 introns and strain is viable (Seraphin 1987) though deletion of individual introns can affect respiration

• yeast mtDNA is unlike other mt genomes in that it lacks subunits for NADH dehydrogenase
• yeast mtDNA has ORFs not found in other mt genomes. These ORFs thought to encode proteins that interact with nucleic acids to carry out excision of introns from mRNA, DNA transposition, DNA deletion, homologous recombination
• S. cerevisiae mt genome is ~ 5X the size of the human one

mt genetic material to keep / to cut

Info from SGD 05.31.06[[1]]
Genes in black are ??s for cutting
Seq info for intron-less mtDNA File:Macintosh HD-Users-nkuldell-Desktop-mtDNAseq coding 55features. Downloaded from SGD 05.31.06 Phenotype info for mtDNA File:Macintosh HD-Users-nkuldell-Desktop-phenotype mtDNA 55features. Downloaded from SGD 05.31.06

Gene name	alias	mt chromosomal coordinates	description
tP(UGG)Q		731 to 802	tRNA-Pro
Q0010	ORF6	3952 to 4338	Dubious mitochondrial open reading frame unlikely to encode a protein
Q0017	ORF7	4254 to 4415	Dubious mitochondrial open reading frame unlikely to encode a protein
15S_rRNA	15S_RRNA_2	6546 to 8194	Ribosomal RNA of the small mitochondrial ribosomal subunit;
tW(UCA)Q		9374 to 9447	tRNA-Trp1
Q0032	ORF8	11667 to 11957	Hypothetical protein
AI1	Q0050	13818 to 16322	Reverse transcriptase required for splicing of the COX1 pre-mRNA, encoded by a mobile group II intron within the mitochondrial COX1 gene
AI2	Q0055	13818 to 18830 CDS 13818 - 13986, and 16435 - 18830 Intron 13987 - 16434	Reverse transcriptase required for splicing of the COX1 pre-mRNA, encoded by a mobile group II intron within the mitochondrial COX1 gene
AI3	Q0060	13818 to 19996 CDS 13818 - 13986, 16435 - 16470, 18954 - 19996 Intron 13987 - 16434, 16471 - 18953	Endonuclease I-SceIII, encoded by a mobile group I intron within the mitochondrial COX1 gene
AI2	Q0055	13818 to 18830 CDS 13818 - 13986, and 16435 - 18830 Intron 13987 - 16434	Reverse transcriptase required for splicing of the COX1 pre-mRNA, encoded by a mobile group II intron within the mitochondrial COX1 gene
AI4	Q0065	13818 to 21935 CDS 13818 - 13986, 16435 - 16470, 18954 - 18991, 20508 - 21935 Intron 13987 - 16434, 16471 - 18953, 18992 - 20507	Endonuclease I-SceII, encoded by a mobile group I intron within the mitochondrial COX1 gene; intron is normally spliced by the BI4p maturase but AI4p can mutate to acquire the same maturase activity
AI5_ALPHA	Q0070, I-SceIV	13818 to 23167 CDS 13818 - 13986, 16435 - 16470, 18954 - 18991, 20508 - 20984, 21995 - 23167 Intron 13987 - 16434, 16471 - 18953, 18992 - 20507, 20985 - 21994	Endonuclease I-SceIV, involved in intron mobility; encoded by a mobile group I intron within the mitochondrial COX1 gene
COX1	Q0045 OXI3	13818 to 26701 CDS 13818 - 13986, 16435 - 16470, 18954 - 18991, 20508 - 20984, 21995 - 22246, 23612 - 23746, 25318 - 25342, 26229 - 26701 Intron 13987 - 16434, 16471 - 18953, 18992 - 20507, 20985 - 21994, 22247 - 23611, 23747 - 25317, 25343 - 26228	Subunit I of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; one of three mitochondrially-encoded subunits
AI5_BETA	Q0075	24156 to 25255 CDS 24156 - 24870, 24906 - 25255 Intron 24871 - 24905	Protein of unknown function, encoded within an intron of the mitochondrial COX1 gene; translational initiation codon is predicted to be ATA rather than ATG
ATP8	Q0080, AAP1	27666 to 27812	Subunit 8 of the F0 sector of mitochondrial inner membrane F1-F0 ATP synthase, encoded on the mitochondrial genome
ATP6	Q0085OLI2, OLI4, PHO1	28487 to 29266	Mitochondrially encoded subunit 6 of the F0 sector of mitochondrial F1F0 ATP synthase, which is a large, evolutionarily conserved enzyme complex required for ATP synthesis
Q0092	ORF5	30874 to 31014	Hypothetical protein
tE(UUC)Q		35373 to 35444	tRNA-Glu
BI2	Q0110	36540 to 38579 CDS 36540 - 36954, 37723 - 38579 Intron 36955 - 37722	Mitochondrial mRNA maturase with a role in splicing, encoded by both exon and intron sequences of partially processed COB mRNA
BI3	Q0115	36540 to 40265 CDS 36540 - 36954, 37723 - 37736, 39141 - 40265 Intron 36955 - 37722, 37737 - 39140	Mitochondrial mRNA maturase, forms a complex with Mrs1p to mediate splicing of the bI3 intron of the COB gene; encoded by both exon and intron sequences of partially processed COB mRNA
BI4	Q0120	36540 to 42251 CDS 36540 - 36954, 37723 - 37736, 39141 - 39217, 40841 - 42251 Intron 36955 - 37722, 37737 - 39140, 39218 - 40840	Mitochondrial mRNA maturase, forms a complex with Nam2p to mediate splicing of the bI4 intron of the COB gene; encoded by both exon and intron sequences of partially processed COB mRNA
COB	Q0105, COB1, CYTB	36540 to 43647 CDS 36540 - 36954, 37723 - 37736, 39141 - 39217, 40841 - 41090, 42508 - 42558, 43297 - 43647 Intron 36955 - 37722, 37737 - 39140, 39218 - 40840, 41091 - 42507, 42559 - 43296	Cytochrome b, mitochondrially encoded subunit of the ubiquinol-cytochrome c reductase complex which includes Cobp, Rip1p, Cyt1p, Cor1p, Qcr2p, Qcr6p, Qcr7p, Qcr8p, Qcr9p, and Qcr10p
OLI1	Q0130, ATP9, OLI3	46723 to 46953	F0-ATP synthase subunit 9 (ATPase-associated proteolipid), encoded on the mitochondrial genome; mutation confers oligomycin resistance; expression is specifically dependent on the nuclear genes AEP1 and AEP2
tS(UGA)Q2		48201 to 48290	tRNA-Ser
VAR1	Q0140, VARI	48901 to 50097	Mitochondrial ribosomal protein of the small subunit, mitochondrially-encoded; polymorphic in different strains due to variation in number of AAT (asparagine) codons; translated near the mitochondrial inner membrane
Q0142	ORF9	51052 to 51228	Hypothetical protein
Q0143	ORF10	51277 to 51429	Hypothetical protein
Q0144		54109 to 54438	Hypothetical protein
21S_rRNA	21S_rRNA_3, 21S_rRNA_4	58009 to 62447 Intron 60725 - 61867 Noncoding_exon 58009 - 60724, 61868 - 62447	Mitochondrial 21S rRNA; intron encodes the I-SceI DNA endonuclease
SCEI	Q0160OMEGA, I-SceI	61022 to 61729	I-SceI DNA endonuclease, encoded by the mitochondrial group I intron of the 21S_rRNA gene; mediates gene conversion that propagates the intron into intron-less copies of the 21S_rRNA gene
tT(UGU)Q1		63862 to 63937	tRNA-Thr
tC(GCA)Q		64415 to 64490	tRNA-Cys
tH(GUG)Q		64596 to 64670	tRNA-His
Q0182	ORF11	65770 to 66174	Hypothetical protein
tL(UAA)Q		66095 to 66179	tRNA-Leu
tQ(UUG)Q		66210 to 66285	tRNA-Gln
tK(UUU)Q		67061 to 67134	tRNA-Lys
tR(UCU)Q1		67309 to 67381	tRNA-Arg
tG(UCC)Q		67468 to 67542	tRNA-Gly
tD(GUC)Q		68322 to 68396	tRNA-Asp
tS(GCU)Q1		69203 to 69288	tRNA-Ser
tR(ACG)Q2		69289 to 69362	tRNA-Arg
tA(UGC)Q		69846 to 69921	tRNA-Ala
tI(GAU)Q		70162 to 70237	tRNA-Ile
tY(GUA)Q		70824 to 70907	tRNA-Tyr
tN(GUU)Q		71433 to 71503	tRNA-Asn
tM(CAU)Q1		72630 to 72705	tRNA-Met
COX2	Q0250, OXI1, OXII	73758 to 74513	Subunit II of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; one of three mitochondrially-encoded subunits
Q0255	ORF1, RF1	74495 to 75984 CDS 74495 - 75622, 75663 - 75872, 75904 - 75984 Intron 75623 - 75662, 75873 - 75903	Hypothetical protein
tF(GAA)Q		77431 to 77505	tRNA-Phe
tT(XXX)Q2		78162 to 78089 Note: this feature is encoded on the Crick strand.	tRNA-Thr
tV(UAC)Q		78533 to 78608	tRNA-Val
COX3	Q0275, OXI2	79213 to 80022	Subunit III of cytochrome c oxidase, which is the terminal member of the mitochondrial inner membrane electron transport chain; one of three mitochondrially-encoded subunits
tM(CAU)Q2		85035 to 85112	tRNA-fMet
RPM1		85295 to 85777	RNA component of mitochondrial RNase P, which also contains the protein subunit Rpm2p; Rnase P removes 5' extensions from tRNA precursors
Q0297	ORF12	85554 to 85709	Hypothetical protein