Mitochondria contain their own genome (mtDNA) which encodes some essential subunits of the oxidative phosphorylation complexes, as well as tRNAs and rRNAs required for mitochondrial protein synthesis. Mitochondrial translation requires nuclear-encoded factors and has adapted mechanisms to function within mitochondria. The mitochondrial ribosome (mitoribosome) is specialized for translation within this organelle, having evolved from bacterial ancestors. Translation in mitochondria involves initiation through IF2 and IF3 binding, elongation of the polypeptide chain, and termination. Adaptations allow for membrane insertion of proteins and regulation of mitochondrial protein synthesis.

1. ORGANIZATION AND
REGULATION OF
MITOCHONDRIAL PROTEIN
SYNTHESIS
HEENA
(L-2013-BS-33-IM)

2. PRESENTATION OUTLINE
 Basics about mitochondria-size structure and
functions
 Origin of Mitochondria
 Mitochondrial Genetic System
 Structure of mt-DNA
 Translational requirements of mitochondria
 Mitoribosomes
 Adaptation Of translation machinery To
operate within mitochondria
 Translation cycle in mitochondria
 Regulation Of mitochondrial translation

3. MITOCHONDRIA
The word
mitochondria comes
from Greek mitos
i.e,“thread” and
chondrion i.e.,
“granule
Rod shaped
Diameter between
.75-0.3µm
Size varies among
species
Double membrane
Present in all
eukaryotic organelle
except in RBC
The 5 enzyme
complexes of
oxidative
phosphorylation are
in the inner
mitochondrial
membrane
A number of
organisms have
reduced or
transformed their
mitochondria into
other structures

4. MITOCHONDRIAL ENZYMES
OUTER
MEMBERANE
Monoamine oxidase
NADH cyt c
reductase
Carnitine acyl
transferase I
Porin
Intermembrane
space
Adenylate
Kinase
Inner Membrane
Electron transport
chain
ATP synthase
Transporters
Matrix
TCACycle enzymes
Enzymes of β-
oxidation
Pyruvate
Dehydrogenase
Glutamate
dehydrogenase

5. Mitochondria:The Power house of cell
 Play central role in cellular energy provision
 Are the energy-transducing organelle of eukaryotic cells
 Converts fuel derived from cellular metabolism to ATP
through the process of oxidative phosphorylation.
Other Functions Of Mitochondria
In addition to supplying cellular energy, mitochondria are
involved in other tasks, such as
 Cell signaling
 Cellular differentiation
 Apoptosis
 Control of the cell cycle and cell growth

6. ORIGIN OF MITOCHONDRIA
 In the autogenous hypothesis, mitochondria were born by
splitting off a portion of DNA from the nucleus of the eukaryotic
cell at the time of divergence with the prokaryotes; this DNA
portion would have been enclosed by membranes, which could
not be crossed by proteins
Endosymbiotic
 The endosymbiotic hypothesis suggests that mitochondria were
originally prokaryotic cells, capable of implementing oxidative
mechanisms that were not possible for eukaryotic cells; they
became endosymbionts living inside the eukaryote
Autogenous

7. ENDOSYMBIOTIC THEORY
 Mitochondria evolved from eubacterial endosymbiont living
proteobacteria whose close contemporary relatives are free.
 Proof:
1. N formylmethionyl-t-RNA (fMet-tRna)
2. Antibiotics
3. Components of mitochondrial translation machinery
 The functional benefits conferred by the endosymbiont ,
notably the ability for compartmentalized energy conversion
by OXPHOS.

8.  During evolution, genetic information was either lost or
transferred from the endosymbiont to the nuclear
chromosomes through an incomplete process that has left
mitochondria with a vestigial genomes.
 This created highly disparate mitochondria genomes that
have retained coding capacity for both translated and
nontranslated RNA.
 In animals and fungi, mitochondrial DNA (mtDNA) encodes
for just a few messenger RNAs (mRNAs) that are translated
within mitochondria. This requires the existence of a
complete mitochondrial gene expression system that has
coevolved with the mitochondrial genome

9.  Mitochondrial genomes also contain genes for ribosomal RNA
(mt-rRNA) , transfer RNAs (mt-tRNAs)
 These alone are insufficient for protein synthesis and the
mitochondria-encoded components must be complemented with
factors encoded by the nuclear genome, including all of the
mitoribosomal protein subunit.
 The constraints of translating only a few mRNA typically those
encodes hydrophobic membrane subunits of OXPHOS
complexes , have driven the corresponding selection of
mitochondrial gene expression system.

10.  Mitochondrial translation mechanisms are highly specialized as
compared to bacteria and eukaryotic cytoplasmic ribosomes
 Species specific specialization of translation in mitochondria, was
compared by systems employed by yeast and mammals.
 Yeast is an important model organism to study
mitochondrial gene expression
why?
 Methods to manipulate its mtDNA are available .
 Most extensively studies are performed on Sachromyces
cerevisiae

11. MITOCHONDRIAL
GENETIC SYSTEM
Possess their own
genome
It is inherited
from female
germ line
Double stranded
circular
molecule
mtDNA can vary
in length from 6
to 24,000 kb
Nucleoids

12. Coding capacity of mtDNA
 The nucleotide sequence of Human mtDNA is highly conserved
among mammals.
 16569 BP
 37 genes coding for :
 mtDNA encoded polypeptides are all subunits of enzyme
complexes of inner membrane that are involved in respiration
and Oxidative phosphorylation.
 Coding capacity of mtDNA reaches from 100 genes in jackobids
to only a few in parasitic protists.
2rRNA 22 tRNA
13
POLYPEPTIDES

13.  Despite the vast diversity of mitochondrial genome at least 4
conserved and interconnected , principals are present.
1. Evolution of Mitochondrial genome is an ongoing process.
2. Biased toward high adenine-thymine content.
3. Evolutionary pressure to reduce the number of mitochondrial
encoded gene. There is no correlation between size of
mitochondrial genome and its coding capacity due to
intergenic region.
4. The loss of genes is non random , with mt-rRNA genes
universally retained.

14. WHY THESE GENES ARE NOT SUCCESSFULLY TRANSFERRED TO
NUCLEUS ?
 Size of products that are needed to be imported back into the mitochondrion.
In case of Cytb and Cox1 , it was hypothesized that highly hydrophobic
proteins are difficult to import across the outer membrane and sort to correct
location.
 Experiments have shown that if either Cytb or Cox1 is expressed from the
nucleus, import to mitochondria fails.

16. STRUCTURE OF mtDNA
 2 Strands
 Most information is encoded on Heavy (H) strand , it code for
 He light (l) strand codes for 8 tRNAs and a single polypeptide.
 Lack introns except for 1 regulatory region
 Intergenetic sequences are absent or limited to few bases.
 Some proteins genes are overlapping.
 In many cases part of termination codon are not encoded but
are generated post-trancriptionaly by polyadenylation of m-RNA
2 rRNA 14 tRNA 12 Polypeptides

17. D-LOOP
 Discovered in 1971 as the short segment of 3 strands
of the circular mt-DNA from growing cell.
 Third strand was a replicated segment of heavy strand or
H strand, which it displaced and was hydrogen bonded to
light strand.
 Initial segmented is generated by a replication of H-strand
that has been arrested shortly after initiation
 D-loop occurs in the main non coding area of mt-DNA , a
segment called the control region or D loop region.

18. THE TRANSLATIONAL REQUIREMENTS OF MITOCHONDRIA
the arginine codon AGG
and AGA in addition to UAA
and UAG for termination
UGA Serves as a codon for
tryptophan rather than as
stop codon.
AGR(R=A,G) specifies a
stop in mtDNA of
vertebrates , codes for
serine in mtDNA of
echinoderms and codes for
arginine in mtDNA of yeast
22 tRNA, instead of 31

19.  All RNA components for translation are supplied in
mitochondria, where as all protein components including
ribosomal proteins , translational factors and ammino acyl t-
RNA synthetases are encoded in nucleus and transported to
mitochondria for biogenesis of r-RNA and t-RNA.
mt-tRNA
 Both rRNA and tRNA molecules are unusually small.
 The number of mt-tRNA genes varies across eukaryotes.
 If mt-tRNA are absent from mitochondrial genome the import of nuclear
encoded t-RNAs has evolved.
 More than 90% of mt-tRNA in metazoan have conventional cloverleaf-shaped
secondary structure, truncated mt-tRNA do occur, resulting in minimal species
with only acceptor or anticodon arms.
 The genes encoding mt-tRNA are highly susceptible to point mutations, which
are primary cause of mitochondrial dysfunction.

20. MITORIBOSOMES
Acts as
riboprotein for
translating
mitochondrial
mRNA encoded
in mtDNA
The mitoribosomes and
OXPHOS complex have
coevolved with the
mitochondrial genomes.
Mammalian
and yeast
mitoriboso-
mes shares
common
attributes.
Length of mt-rRNA
varies from 600 in
flagellates , 950 in
mammals to 2000
nucleotides in plants
Smaller
sedimentation
coefficient than
cytoplasmic
ribosomes

21. MITOCHONDRIAL RIBOSOMES LIKE
CYTOPLASMIC RIBOSOMES HAVE 2 SUBUNITS

22. MAIN DIFFERENCE IN MITOCHONDRIAL
RIBOSOMES
 No 5S rRNA in mitochondrial genome except in plant
mitochondria.
Function of 5S rRNA
The central protuberance of ribosomal LSU is formed
around 5S rRNA , and the 5S rRNA is involved in
coordinating movement with the small subunit (SSU)
during translation cycle.
 Due to its structural and functional importance , its
absence was thought to be compensated by import of
nuclear encoded 5s rRNA.

24.  Loss of 5S is compensated by diff means
In human miotoribosomes
In procine
In yeast mitoribosomes
 Both m-rRNA flank the SSU rRNA with which they are
cotranscribed.
 This organization is highly conserved in metazoans. metazoans,
despite tRNA genes tending to be more mobile than other genes
within mitochondrial genome
tRNA-
val
tRNA-
phe
rRNA
expansion
segment

25. EVOLUTION OF RIBOSOMAL RNA GENES
 There is different evolutionary path for yeast and
mammalian mitoribosomes.
 The yeast is toward rRNA expansion has 4,944
nucleotides.
 Mammalian rRNA is toward reduction ,total length of
human mt-rRNA is just 2,513 nucleotides.
 There is evidence that up to divergence of metazoan
lineage they shared a trajectory in which rRNA
expanded

26.  Structures of yeast and human mitoribosomes share a
mitochondrial specific protein, mL44.
 In yeast mitoribosomes, this protein belongs to ribonuclease
III family of RNA binding proteins, it binds the 5’ expansion
of LSU rRNA .
 Human mitoribosomes, lacks this expansion segment but
maintains mL44 in similar position by protein-protein
interaction.
 This suggest at least for this region that rRNA expansion
occurred prior to rRNA contraction in mammalian
mitoribosomes.

27. MITORIBOSOMAL PROTEOME
 An enlarged mitoribosomal proteome occurred with expansion of
rRNA.
 Bacterial LSU has just 34 proteins
 Mammalian and Yeast mitochondria have approximately 53 and
46 .
 Which means proteome expansion in human was not
reversed upon subsequent contraction of rRNA.
 Therefore rRNA expansion alone cannot explain the gain of
mitochondrial-specific proteins.
 In case of mammalian mitoribosomes , additional proteins
have been found to stabilize the rRNA contraction.

28.  It appears that mitoribosomes has expanded their complexity
by recruiting proteins from the surrounding environment, these
proteins have lost their catalytic or ligand binding residues
and appeared to stabilize rRNA contraction
 These include;
 Nucleic acid binding proteins
 Other proteins share homology with lipid binding (yeast ML50)
and Oxidoreductase (human mL43) proteins

29. ADAPTATION OF TRANSLATION MACHINERY
TO OPERATE WITHIN MITOCHONDRIA
 Adaptation of the Polypeptide Exit Tunnel
It act as passageway that nascent polypeptide
must navigate to reach solvent or inner mitochondrial
membrane.
 During egress, nascent polypeptide starts folding inside by
influence of interaction between nascent chain and exit
tunnel.
 Wide range of polypeptides are accommodated in exit tunnel ,
this pressure is relieved as only few mRNAs are translated.

30.  KEY FEATURES OF ADAPTATIONS IN HUMAN
MITORIBOSOMES
 The rRNA lining the tunnel walls in bacterial and
cytoplasmic ribosomes is replaced by protein moieties
 These protein moieties are hydrophobic residues
Mimic the native environment of membrane
protein being synthesized
May help to slow the rate of translation to
help folding within the tunnel and interaction with
insertion machinary

31. MEMBRANE ATTACHMENT
 Mitochondria-encoded membrane proteins are
cotranslationally inserted into inner mitochondrial
membrane to reduce protein aggregation.
 Mammalian Mitoribosomes
 Yeast Mitoribosomes
Aligns with tunnel exit site
ML45
Mba1

33. COTRANSLATIONAL PROTEIN
INSERTION
 The first protein identified as a ligand of mitoribosomal
tunnel exit was Oxa1.
 In case of bacteria it is YidC .
 Yidc also facilitates folding and assembly in addition to
acting as protein insertase.
 A number of other cofactors are proposed to have role in
cotranslational protein insertion.

34. THE TRANSLATIONAL CYCLE IN
MITOCHONDRIA
Translation can be divided into 3 stages:
Initiation
mRNA is loaded
onto ribosome
and start codon
is selected
Elongation
Elongation of
polypeptide by
selective addition
of ammino acids
Termination
and recycling
of ribosomes

35. INITIATION OF TRANSLATION
 With AUG , AUA and AUU are also used as start codon.
 Like bacteria, there is no Shine-Dalgarno sequence .
 No 5’ 7-methylguanylate cap.
 No 5’ UTRs region.
 Maximum 3 nucleotides only before start codon.

36. Then how start codons are accurately specified
on mammalian mitochondrial transcript?
Mammalian mitoribosomes preferentially select AUG
codon closest to 5’ end of mRNA, facilitated by absence
of secondary structure around the start codon that allow
recognition by initiation complex.

37.  Only 2 of the 3 Ifs are there i.e...GTPase IF2met and IF3 mt.
 Through Low cryo-electron microscopy it was found that IF2met could
functionally replace IF2 and absence of IF1.
 Features of IF2
• 37 residue
• Bind to same location as IF1 on SSU.
• Varies in length in diff species.
• Conserved in different vertebrates.
ADDITIONAL MITOCHONDRIAL SPECIFIC ELEMENTS ARE:
 Pentatricopeptide repeat protein (PPR)
 Ms39 near to mRNA entrance Channel

38. INITIATION CYCLE
2. IF3 met promotes dissociation
of 55S.
3. IF2met bound GTP bind to SSU.
4. mRNA and fmet tRNA bind.
5. the mRNA is locked in place by
codon:anticodon interactions
to form the 28S initiation
complex. If fMet-tRNA binds
in the absence of mRNA, or if
the mRNA does not contain a
proper start codon, the
initiation step fails
6.the large subunit joins, and
along with the hydrolysis of
GTP to GDP and IF Leaves.

39.  mS29 mediates contact between head of SSU amd
central protuberance of LSU with a bound GDP
molecule
Differences In Yeast
 no mS29 is present
 Lack poly(A) tail.
 Mitochondrial mRNA contain 5’ UTRs (50-100 ntds)  target
of transcript specific translational activators
Partially replace missing shine delgerno
sequences , with these binds initiation factors

40. ELONGATION
 Most conserved phase of translation in mitochondria.
 E site tRNA is recognized by normal 3’ CCA-binding pocket.
 MAIN DIFFERENCES OF ELONGATION
 Reduced contact between mammalian mitoribosomes and
tRNAs than in case of bacteria.
 Highly variable elbow region of mtRNA held to LSU by
acceptor arm only.
 EFFECT OF REDUCED CONTACT
As mtRNA transverse the ribosome by adopting hybrid state it causes the
rotation of ribosome.
 Human mitoribosomes were also observed in state of rolling of SSU With
respect to LSU.

41. ELONGATION CYCLE  EF-Tu Delivers the amminoacyl-
tRNA to mitoribosomes with GTP
 EF-Ts regenerates the GTP-
bound form of EF-Tu
 EF-G1 catalyze the coordinated
movement of mRNA and tRNA
during translocation
 EF-Tu and EF-Ts appear as
heterodimers that dissociates
only in presence of
amminocylated tRNA and GTP.
 EF-Ts is absent in yeast

42. TERMINATION
 Reduced number of stop codons
 UGA codes for tryptophan due to which no RF2 is there.
 UAA and UAG terminates only 11 out of 13 ORF remaining are 2
terminates by AGA and AGG.
 This is not true for AGA/AGG terminated ORFs
 For these ICT1, a codon – independent peptidyl-tRNA hydrolase
terminates translation.
 ICT1 is incorporated into mitoribosomes with C terminal helix
anchored to it.

43. RECYCLING OF MITORIBOSOMES
 After the hydrolysis of peptidyl tRNA mitoribosomes
become substrate for ribosome recycling factor (RRF1).
 It splits ribosomes into individual subunits .
 RRF1 is assisted by EF-G homolog (EF-G2).
 While in bacteria, only EF-G is involved in recycling.
 Initiation factor, IF3 is also thought to have role in
termination by catalyzing the dissociation of
mitoribosome
.

45. REGULATION OF MITOCHONDRIAL
TRANSLATION
 OXPHOS complex are assembled from proteins synthesized by
2 distinct translation system
 Tight coordination is necessary to minimize accumulation of
harmful assembly intermediate.
TRANSLATIONAL ACTIVATORS
 Certain mechanisms act to coordinate mitochondrial and
nuclear gene expression through regulatory factors, known as
translational activators.
 In yeast , translation activators promotes synthesis of
proteins by interaction with 5’ UTR.
 In mammals TCAO1, is the only identified translation activator

46.  Other translational activators are those belonging to class of
RNA- binding PRP proteins
 Exact function of translational activators is unknown but
genetic interaction suggest that they play role in translation
initiation.
 Upregulation of translational activators occurs when cell switch from
anaerobic to aerobic metabolism which require more energy,

47. 2 MECHANISMS OF ACTION OF TRANSLATIONAL
ACTIVATORS
By regulation of abundance of
nuclear encoded mRNA which have
been transported to mitochondria
like Pet494 is translational activator
of COX3 mRNA
By regulating mitochondrial
encoded gene expression this
occurs by efficiency of OXPHOS
complex assembly.

48. TRANSLATION REGULATION OF COX1
SYNTHESIS
 Cytochrome oxidase is 14 subunit proton pumping enzyme.
 In yeast 3 mitochondrial encoded subunits have its own set of
translational activators.
Mam33 Pet111 Pet 122
Pet309 Pet 54
Mss51 Pet 494
COX1 COX2 COX3

49. FUNCTIONS OF DIFFERENT TRANSLATIONAL ACTIVATORS
 Mss51 – it is required for synthesis and assembly of Cox1
 Pet309 and Mam33 binds with mitoribosomes
Mss51 mediate the interaction
.

50. MECHANISM
 Therefore when cellular heme concentration are low ,the redox
cofactors for COX are not present, Mss 51 is inactivated
 Synthesis of Cox1 is repressed

51. COX1 synthesis require
Mam33,Pet309, Mss51 and
heme b
Newly synthesized Cox1
interact with Mss51 and
other assembly factors
Tight binding of Mss51
require Cox14 and Coa4
Binding of Coa1
to this traps
Mss51
Unknown signal release
Mss51
Mss1 stimulate further
round of Cox1
synthesis with heme b

52. TRANSLATION REGULATION OF CYTOCHROME B
In yeast, Cytochrome bc1 consist of 10 subunits , of
which only cyt b is encoded by mitochondrial
genome.
Cyt b expression depends upon maturation of
mRNA and 4 translational activators
1) Cbp1
2) Cbs1
3) Cbs2
4) Cbp3-Cbp6 complex

53.  In case if assembly is blocked or heme b is unavailable
activation of cyt b stops

54. Regulation of
cytb synthesis
Cyt b synthesis
require binding of
4 translational
activators
After synthesis
Cbp3-Cbp6
interacts with
protein and
detaches from
ribosomes.
Hemeb and
Cbp4 binds
cytb
andCbp3-
Cbp-6
detaches
Liberated
complex
activates
further
round of
cytb
synthesis.
Qcr7 and
Qcr8 and
heme b
associate
with cytb to
form bc1
complex