Scheffler Immo E. Mitochondria
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INDEX 461
Translation factors, 133–140
defi ciency of, 136
need for specifi c, 136
Transmembrane helices, 213–214
Transmembrane potential, 392–393
Trans-splicing, 116
Trichomonas vaginalis, 14, 15
TRMU gene, 373
tRNA genes, 66. See also Transfer
RNAs (tRNAs)
loss of, 368
tRNA
Lys
, 153
mutation in, 372
“tRNA punctuation model,” 114
tRNA structure, 126–128
Trypanosoma brucei, 76, 228
Trypanosoma cruzi, 76
Trypanosomatid genera, 116–117
Trypanosomes, 20
energy metabolism and NADH
oxidation m, 227–228
RNA editing in, 119–120
Tubular cristae, formation and
maintenance of, 29
Tumor cells, apoptosis in, 390
Turnover, mitochondrial, 54
12S rRNA gene, 372
23S rRNA, 129–130
Twinkle, 98, 101
Ubiquinol, biosynthesis of, 319–324
Ubiquinone (coenzyme Q), 175, 179
role in proton translocation, 237
structure of, 181
in succinate oxidation, 200
Ubiquinone–cytochrome c
oxidoreductase, 202–210
UCP-1 (thermogenin), 267–269, 271, 332
uncoupling by, 268
UCP-1 gene, cloning of, 268
UCP-1 mRNA, 268
UCP-2, 267, 269–271
functions for, 270
UCP-2 knockout mice, 270
UCP-3, 267, 269–271
functions for, 270
UCP-3 knockout mice, 270
UCP activation pathway, 270
UGA stop codon, 127
Ugo1p protein, 44
Uncoupling
in plants, 271–272
in Saccharomyces cerevisiae,
271
Uncoupling proteins, in warm-blooded
animals, 266–271
Unidentifi ed reading frames (URFs),
65
Uniporter, 337
Uniports, 336
Upstream activating sequence (UAS),
87
Upstream repressor sequence (URS),
87
UQCRB nuclear gene, 374
Urea cycle, 309, 310
Uridylate residues, 117, 118
Ustilago cynodontis, 72
UTP (uracil triphosphate), 118
3′UTRs, 132
5′UTRs, 132–133, 137
cis-acting sequences in, 138
VA R 1 gene, 73, 131, 140
VDAC proteins, 330–331. See also
Voltage-dependent anion channel
(VDAC)
Vectorial metabolism, 231
Vesicular membranes, 24
Voltage-dependent anion channel
(VDAC), 330–331
overexpression of, 338
V-type ATPases, 251
Warburg, O., 170–171
Warburg effect, 350
Warm-blooded animals, uncoupling
proteins in, 266–271
“Xenomitochondrial cybrids/hybrids,”
96, 428
Xenomitochondrial mice, 353
X-inactivation, 373
X-linked genes, 222–223
X-linked susceptibility locus, 370
Yarrowia lipolytica, 227, 348
genetic manipulation and, 221
462 INDEX
Y-chromosome
haplotype distributions of, 429
variation in, 428–430
Yeast (s)
complex I-like activity in, 227
generalizations about, 227
life-span research using, 398
mammalian UCP1 in, 269
meiosis and sporulation in, 50
as a model system, 86
molecular-genetic studies in,
280
NADH oxidation in, 226–227
nuclear genes of ATP synthase in,
258
post-transcriptional mechanisms in,
91
responses to glucose levels or oxygen
pressure, 87
Yeast cells
growth conditions for, 348–349
mitochondria in, 40
transformation of mitochondria in,
349
Yeast mitochondria, supercomplexes in,
183
Yeast mitochondrial cytochrome b gene,
125
Yeast mitochondrial genome map, 73
Yeast mitochondrial ribosomal protein
genes, 130
Yeast mutants, 83–84, 136
protein-import-defective, 145
Yeast nuclear genes, 213
Yeast ribosomal proteins, 130
Yeast strains, mating of, 138
Yeast translational activators, 139–140
yme mutants, 51
COLOR PLATES
Figure 3.5 (A) Mitochondria seen by electron microscope tomography. Cells were
derived from chick CNS. [The original fi gure was provided by G. Perkins, University
of California, San Diego; with permission from Academic Press (Perkins et al. (5) ).]
(B) The 3 - D reconstruction was achieved after the volume was segmented manually
contouring into the regions bounded by the outer, inner, and cristal membranes. [For
details the reader is referred to the original publication (Perkins et al. (5) .] In the
bottom of the fi gure, individual lamellar sections of crista are shown, together with the
tubular portions which connect the disks to the inner boundary membrane. (The pho-
tographs were generously provided by Dr. G. Perkins, University of California, San
Diego; with permission by Academic Press.)
A
B
COLOR PLATES
Figure 3.11 GFP targeted to the matrix in wild - type yeast cells and in various mutants:
fusion mutant ( fzo1 Δ ), fi ssion mutant ( dnm1 Δ ), tabulation mutant ( mmm1 Δ ); GFP
fl uorescence images were superimposed on images from a differential interference
contrast microscope. (From the review of Okamoto and Shaw (59) .)
Figure 4.3 Schematic representation of the yeast mitochondrial genome map, strain
FY1679, presented as a linearized map (35) . Exons of protein coding genes are indi-
cated in red (cox1, cox2, cox3, cob, atp9, var1), introns are gray; tRNA genes (green)
are labeled with the corresponding amino acid, 9S, 15S, and 21S RNA (yellow) are
labeled. Two signifi cant deletions are found in this strain, and fl ags indicate transcrip-
tion initiation sites. For details the original paper (35) should be consulted. (Repro-
duced from reference 35 , with permission.)
Thr2 Asp
Cys Ser2
His Arg2
Leu Ala
Gln Ile
Lys Tyr
Arg1 Asn
Gly Met
1,7 kb
f-Met
21S RNA
ori5
cox1
atp8
atp6
ori7
orf5
Glu
ori2
cob
atp9
Ser1
var1
ori8
ori6
Pro
ori1
15 S RNA
ori3
ori4
cox2
cox3
70
60
80
0
10
20
30
40
50
Trp
1,6 kb
9S RNA
orf1
SceI
Phe
Thr
Val
COLOR PLATES
Figure 4.9 RNA editing in Trypanosomes (see reference 201 for details). (A) Double transesterifi cation models, showing only the U -
insertions. (B) The modifi ed enzyme cascade model showing U - deletion, or U - addition or misedited U - addition as alternatives. In the
simplest version the U - tail of the guide RNA is shown as a free overhang, but it is also possible that it may pair with a purine - rich sequence
of the pre - edited RNA . The number of Us added to the 5 ′ fragment in the U - addition pathway (middle) is show as 13, but this number
is actually variable. If the trimming is precise, correct guided products are obtained. If trimming is incomplete or excessive, a misedited
product may result. (The fi gures were provided by Dr. L. Simpson. With permission from Oxford University Press.)
PP
i
first
transesterification
second
transesterification
Nucleophile:
UTP
Nucleophile:
oligo [U] tail
...3’
|||||||
-P-P-P...5’
5’...
anchor
guide RNA
pre-edited mRNA
UUU-
U
U
U
HO-UU
UTP-OH
|
|||||||
-P-P-P...5’
...3’5’...
-P-
UUU-
U
U
U
HO-UU
...3’
5’...
-OH
||||||
-P-P-P...5’
P-P-P-U-
|
UUU-
U
U
U
HO-UU
||||||
-P-P-P...5’
...3’
-U-
|
5’...
UUU-
U
U
U
HO-UU
||||||
-P-P-P...5’
...3’
-U-
|
5’...
UUU-
U
U
U
HO-U
5’...
-O
|||||||
-P-P-P...5’
...3’
|
|
|
U
U
U-
U
U
U
U
U
H
-P-
5’...
|||||||
-P-P-P...5’
...3’
|
U
U
U
U
U
U
U
OH
|
|
U
A
COLOR PLATES
Figure 4.9 ( Continued)
ligation
3’-5’ exonuclease
trimming
U-deletion
guided
U-addition
guided
UUU-
U
U
U
HO-U…UUU
UUU-
U
U
U
HO-U…UUU
PP
i
UTP
ATP
PP
i
+ AMP
||||||||
...3’
-P-P-P...5’
|
|
|
...3’
||||||
5’...
-UUU-
|
-P-P-P...5’
|
-U
U
U
UUUUUUU-OH
|
U
U
U
...3’
-P-P-P...5’
||||||||
5’...
UMP
-U
UU
-OH
|
|
|
UUU-
U
U
U
HO-U…UUU
5’...
...3’
|||||||
5’...
-
O
H
-P-P-P...5’
UUU-
U
U
U
HO-U…U
UMP
-
U
U
U
-
O
H
|||||||
...3’
5’...
|
-P-P-P...5’
|||||||
...3’
5’...
-
O
H
|
-P-P-P...5’
ATP
PP
i
+ AMP
UUU-
U
U
U
HO-U…UUU
UUU-
U
U
U
HO-U…UUU
...3’
|||||||
5’...
-
O
H
-P-P-P...5’
UUU-
U
U
U
HO-U…U
-UUU
|||||||
...3’
|
-P-P-P...5’
UUU-
U
U
U
HO-U…UUU
5’...
U-additions
UUU-
U
U
U
HO-U…UUU
UUU-
U
U
U
HO-U…UUU
PP
i
UTP
ATP
PP
i
+ AMP
||||||||
...3’
-P-P-P...5’
|
|
|
5’...
-UU
-U
UU
UUUUUUU-OH
U
U
U
...3’
-P-P-P...5’
||||||||
5’...
UMP
-U
UU
UU-OH
|
|
|
UUU-
U
U
U
HO-U…UUU
5’...
...3’
|||||||
5’...
-
O
H
-P-P-P...5’
UUU-
U
U
U
HO-U…U
U-addition
misedited
cleavage
|||||||
-P-P-P...5’
...3’
5’...
anchor
guide RNA
pre-edited mRNA
UUU-
U
U
U
HO-U…UUU
3’-5’ exonuclease
trimming
ligation
U
...3’
-P-P-P...5’
||||||
U
U
|
|
|
|
-
B
COLOR PLATES
Figure 5.2 Structure of cytochrome c showing the association of the heme with the
polypeptide chain.
AB
Figure 5.10 (A) Crystal structure of the peripheral subcomplex of respiratory complex
I (NADH – ubiquinone oxidoreductase) from Thermus thermophilus at 3.3 - Å resolution
(74, 76) . The subunits are labeled following the nomenclature for bacteria. (B) Location
and distances between the 9 Fe – S clusters in this subdomain. (Reproduced from refer-
ence 76 with permission.)
COLOR PLATES
Figure 5.14 Complex III. Schematic representation of the transmembrane helices in the dimeric complex seen from the
P and N (matrix) side (parts A and B, respectively) (82) .
A
B
COLOR PLATES
A
B
Figure 5.15 (A) Side view of complex III. The matrix side is at the bottom. Cyto-
chrome c1 extends into the intermembrane space. The membrane - spanning helices of
the various subunits are in the region indicated by the middle arrow (42 Å ). (B) Ste-
reoview of the transmembrane helices of a monomeric complex III. (C) Stereoview
from the outside showing the myxothiazol binding pocket. (D) Stereoview from the
matrix side showing the antimycin binding pocket. (From reference 147 with permis-
sion. The fi gure was generously provided by Dr. Yu.)
COLOR PLATES
C
D
Figure 5.15 (Continued)