Source: After T. D. Fox, Annual Review of Genetics 21 (1987), p. 69.

Source: After T. D. Fox, Annual Review of Genetics 21 (1987), p. 69.

genes generally flank the protein and rRNA genes; so cleavage of the tRNAs releases mRNAs and rRNAs. In the mito-chondrial genomes of fungi, plants, and protists, there are multiple promoters, although genes are occasionally arranged and transcribed in operons.

Most mRNA molecules produced by the transcription of mtDNA are not capped at their 5' ends, unlike mRNA transcribed from nuclear genes (See Figure 14.6). Poly(A) tails are added to the 3' end of some mRNAs encoded by animal mtDNA, but poly(A) tails are missing from those encoded by mtDNA in fungi, plants, and protists. The poly(A) tails added to animal mitochondrial mRNAs are shorter than those attached to nuclear-encoded mRNA and are probably added by an entirely different mechanism.

Some of the genes in yeast and plant mitochondrial DNA contain introns, many of which are self-splicing. RNA encoded by some mitochondrial genomes undergoes extensive editing (see p. 000 in Chapter 14).

Translation in mitochondria has some similarities to eubacterial translation, but there are also important differences. In mitochondria, protein synthesis is initiated at AUG start codons by N-formylmethionine, just as in eubacterial initiation of translation. Mitochondrial translation also employs elongation factors similar to those seen in eubacte-ria, and the same antibiotics that inhibit translation in eubacteria also inhibit translation in mitochondria. However, mitochondrial ribosomes are variable in structure and are often different from those seen in both eubacterial and eukaryotic cells. Additionally, the initiation of translation in mitochondria must be different from that of both eubac-terial and eukaryotic cells, because animal mitochon-drial mRNA contains no Shine-Dalgarno ribosome-binding site and no 5' cap. (A Shine-Dalgarno sequence has been observed in mitochondrial mRNA of the protozoan Recli-nomonas americana, which has a very primitive, eubacter-ial-like mitochondrion.)

There is also much diversity in the tRNAs encoded by various mitochondrial genomes. Human mtDNA encodes 22 of the 32 tRNAs required for translation in the cytoplasm. (Only 32 are required in cytoplasmic translation because wobble at the third position of the codon allows tRNAs to pair with more than one codon; see p. 000 in Chapter 15.) In human mitochondrial translation, there is even more wobble than in cytoplasmic translation; many mitochondrial tRNAs will recognize any of the four nucleotides in the third position of the codon, permitting translation to take place with even fewer tRNAs. The increased wobble also means that any change in a DNA nucleotide at the third position of the codon will be a silent mutation (see p. 000 in Chapter 17) and will not alter the amino acid sequence of the protein. Thus more of the changes that occur in mtDNA are silent and accumulate over time, contributing to a higher rate of evolution. In some organisms, fewer than 22 tRNAs are encoded by mtDNA; in these organisms, nuclear-encoded tRNAs are imported from the cytoplasm to help carry out translation. In yet other organisms, the mitochondrial genome encodes a complete set of all 32 tRNAs.

Concepts 9

The processes of replication, transcription, and translation vary widely among mitochondrial genomes and exhibit a curious mix of eubacterial, eukaryotic, and unique characteristics.

Evolution of mtDNA

As already mentioned, comparisons of DNA sequences in mitochondrial genomes with homologous sequences in other organisms strongly support a common eubacterial origin for all mtDNA. Nevertheless, patterns of evolution seen in mtDNA vary greatly among different groups of organisms.

The sequences of vertebrate mtDNA exhibit an accelerated rate of change: mammalian mtDNA, for example, typically evolves from 5 to 10 times as fast as mammalian nuclear DNA. The gene content and organization of vertebrate mitochondrial genomes, however, is relatively constant. In contrast, sequences of plant mtDNA evolve slowly at a rate only one-tenth that of the nuclear genome, but their gene content and organization change rapidly. The reason for these basic differences in rates of evolution is not yet known.

One possible reason for the accelerated rate of evolution seen in vertebrate mtDNA is a high mutation rate in mtDNA, which would allow DNA sequences to change quickly. Increased errors associated with replication, the absence of DNA repair functions, and the frequent replication of mtDNA may increase the number of mutations. The large amount of wobble in mitochondrial translation may also allow mutations to accumulate over time, as discussed earlier. The use of mtDNA in evolutionary studies will be described in more detail in Chapter 23. __

Concepts B

All mtDNA appears to have evolved from a common eubacterial ancestor, but the patterns of evolution seen in different mitochondrial genomes varies greatly. Vertebrate mtDNA exhibits rapid change in sequence but little change in gene content and organization, whereas the mtDNA of plants exhibits little change in sequence but much variation in gene content and organization. Data on mitochondrial genomes that have been completely sequenced, and more information on human diseases and disorders caused by defects in mitochondria

Chloroplast DNA

Geneticists have long recognized that many traits associated with chloroplasts exhibit cytoplasmic inheritance, indicating that these traits are not encoded by nuclear genes. In 1963, chloroplasts were shown to have their own DNA (I Figure 20.11).

Among different plants, the chloroplast genome ranges in size from 80,000 to 600,000 bp, but most chloroplast genomes range from 120,000 to 160,000 bp (Table 20.3). Chloroplast DNA is usually contained on a single, double-stranded DNA molecule that is circular, is highly coiled, and lacks associated histone proteins. As in mtDNA, multiple copies of the chloroplast genome are found in each chloro-plast, and there are multiple organelles per cell; so there are several hundred to several thousand copies of cpDNA in a typical plant cell.

Gene Structure and Organization of cpDNA

The chloroplast genomes from a number of plant and algal species have been sequenced, and cpDNA is now recognized to be basically eubacterial in its organization: the order of some groups of genes is the same as that observed in E. coli,

Table 20.3 Size of the chloroplast genomes in

selected organisms

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