Patterns of Nucleotide Substitution in Mitochondrial Protein Coding Genes of Vertebrates

Maximum likelihood methods were used to study the differences in substitution rates among the four nucleotides and among different nucleotide sites in mitochondrial protein-coding genes of vertebrates. In the 1st+2nd codon position data, the frequency of nucleotide G is negatively correlated with evolutionary rates of genes, substitution rates vary substantially among sites, and the transition/transversion rate bias (R) is two to five times larger than that expected at random. Generally, largest transition biases and greatest differences in substitution rates among sites are found in the highly conserved genes. The 3rd positions in placental mammal genes exhibit strong nucleotide composition biases and the transitional rates exceed transversional rates by one to two orders of magnitude. Tamura-Nei and Hasegawa-Kishino-Yano models with gamma distributed variable rates among sites (gamma parameter, α) adequately describe the nucleotide substitution process in 1st+2nd position data. In these data, ignoring differences in substitution rates among sites leads to largest biases while estimating substitution rates. Kimura's two-parameter model with variable-rates among sites performs satisfactorily in likelihood estimation of R, α, and overall amount of evolution for 1st+2nd position data. It can also be used to estimate pairwise distances with appropriate values of α for a majority of genes.     

人类线粒体DNA变异的检测方法和思路

基于线粒体DNA（mtDNA)的研究对于人群源流迁移、线粒体相关疾病病因的探讨和法医鉴定等具有重意义,就检测人线粒体突变的一些常用方法,如RFLP、SSO和控制区测序等作一小结和归纳,并重点介绍目前mtDNA突变的筛选方法和思路,另外,还总结了近年来对人mtDNA方面的研究结果,对世界人群中主要单倍型类群（haplogroup)特征变异位点和相应的酶切检测引物作了归纳。     

Ancient Out-of-Africa Mitochondrial DNA Variants Associate with Distinct Mitochondrial Gene Expression Patterns

Mitochondrial DNA (mtDNA) variants have been traditionally used as markers to trace ancient population migrations. Although experiments relying on model organisms and cytoplasmic hybrids, as well as disease association studies, have served to underline the functionality of certain mtDNA SNPs, only little is known of the regulatory impact of ancient mtDNA variants, especially in terms of gene expression. By analyzing RNA-seq data of 454 lymphoblast cell lines from the 1000 Genomes Project, we found that mtDNA variants defining the most common African genetic background, the L haplogroup, exhibit a distinct overall mtDNA gene expression pattern, which was independent of mtDNA copy numbers. Secondly, intra-population analysis revealed subtle, yet significant, expression differences in four tRNA genes. Strikingly, the more prominent African mtDNA gene expression pattern best correlated with the expression of nuclear DNA-encoded RNA-binding proteins, and with SNPs within the mitochondrial RNA-binding proteins PTCD1 and MRPS7. Our results thus support the concept of an ancient regulatory transition of mtDNA-encoded genes as humans left Africa to populate the rest of the world.     

噬菌体RB69 DNA聚合酶以不正确的核苷酸为底物的聚合反应的稳态动力学研究

测定了ＲＢ６９ ＤＮＡ 聚合酶以不正确的核苷酸（ｒＮＴＰ、ｄｄＮＴＰ以及碱基不配对的ｄＮＴＰ）为底物进行聚合反应的稳态动力学常数,并与Ｋｌｅｎｏｗ 酶进行了比较．结果表明,ＲＢ６９ ＤＮＡ 聚合酶在以不正确的核苷酸为底物进行聚合反应时,其Ｋｍ 值与正确底物参入时相比有大幅度提高,而ｋｃａｔ保持不变或下降幅度较小．而Ｋｌｅｎｏｗ 酶在利用不正确的核苷酸为底物时,与正确底物参入时相比,其ｋｃａｔ大幅度下降,而Ｋｍ （或ＫＤ）基本保持不变或上升较小幅度．两种酶不同的动力学特点反映出它们不同的底物选择机制．     

黄瓜线粒体DNA类质粒pC1的性质和核酸序列研究

津研四号黄瓜线粒体中除主环ＤＮＡ外,还有４种ＤＮＡ类质粒：ｐＣ１、ｐＣ２、ｐＣ３、ｐＣ４。将环形类质粒ｐＣ１ｌｐｋ ｇｃ ｐＵＣ１９的ＥｃｏＲⅠ位点上,克隆至Ｅ．ｃｏｌｉ ＪＭ１０９中。以克隆的ｐＣ１为探针,进行同源性检测,ｐＣ１与津研四号黄瓜的核基因组、叶绿体基因组、线粒体基因组和线粒体中其他类质粒不同源。对ｐＣ１进行序列测定和分析,ｐＣ１长度２ ８８９ｂｐ,含有多个正向和反向重复序列,有３个８     

Patterns of Mating and Mitochondrial DNA Inheritance in the Agaric Basidiomycete Coprinus Cinereus

Patterns of mating and mitochondrial DNA (mtDNA) inheritance were investigated for the Basidiomycete, Coprinus cinereus in order to better understand the relationship of reproductive biology and mtDNA evolution in fungi. Results showed that the unique mating system of basidiomycetes can lead to the formation of mitochondrial mosaics (i.e., colonies composed of sectors differing in mtDNA). Mitochondria do not migrate along with nuclei during mating. Intracellular mixed or recombinant mtDNA molecules were not observed. Interestingly, it was found that mating asymmetry, caused by nonreciprocal nuclear migration, may be an important part of the reproductive biology of C. cinereus.     

Role of Histidine 932 of the Human Mitochondrial DNA Polymerase in Nucleotide Discrimination and Inherited Disease

The human mitochondrial DNA polymerase (pol γ) is nuclearly encoded and is solely responsible for the replication and repair of the mitochondrial genome. The progressive accumulation of mutations within the mitochondrial genome is thought to be related to aging, and mutations in the pol γ gene are responsible for numerous heritable disorders including progressive external opthalmoplegia, Alpers syndrome, and parkinsonism. Here we investigate the kinetic effect of H932Y, a mutation associated with opthalmoplegia. Mutations H932Y and H932A reduce the specificity constant governing correct nucleotide incorporation 150- and 70-fold, respectively, without significantly affecting fidelity of incorporation or the maximum rate of incorporation. However, this leads to only a 2-fold reduction in rate of incorporation at a physiological nucleotide concentration (∼100 μm). Surprisingly, incorporation of T:T or C:T mismatches catalyzed by either H932Y or H932A mutants was followed by slow pyrophosphate release (or fast pyrophosphate rebinding). Also, H932Y readily catalyzed incorporation of multiple mismatches, which may have a profound physiological impact over time. His-932 is thought to contact the β-phosphate of the incoming nucleotide, so it is perhaps surprising that H932Y appears to slow rather than accelerate pyrophosphate release.     

Variability of Nucleotide Sequences of Mitochondrial DNA Cytochrome b Gene in Chars of the Genus Salvelinus

Nucleotide sequences of two (405- and 1050-bp) regions of mitochondrial DNA (mtDNA) cytochrome c gene were established in chars of the genus Salvelinus from Russian Far East and Siberia. Based on the divergence and phylogenetic analysis of nucleotide sequences of the mtDNA cytochrome b gene, S. laecomaenis was shown to carry the most ancient mitochondrial lineage, which is close to the ancestral one. The archaic mtDNA of S. levanidovi occupied an isolated position on the phylogenetic trees. The mtDNA lineage of the southern S. malma was close to the S. alpinus–S. malma malmacomplex group. Within the S. alpinus–S. m. malma complex, three groups of mtDNA types having particular geographic distributions were distinguished. The Kolyma–Chukotka group includes lake S. taranetzi, S. boganidae, andS. elgyticus from Chukotka, lake chars from Kolyma. The Okhotsk group is represented by northernS. malma, lake chars from northern Sea of Okhotsk, and anadromous S. taranetzi. The Siberian group is close to the Okhotsk one and consists of Taimyr and Baikal region chars as well as Arctic char from Finland. The divergence of char mitochondrial lineages was dated to the Pliocene–Pleistocene.     

Origins of Laboratory Mice Deduced from Restriction Patterns of Mitochondrial DNA

To determine the origins of laboratory mice, the restriction patterns of mitochondrial DNAs (mtDNAs) from various strains were compared with those of relevant subspecies and/or races of mus musculus . In most strains and substrains of laboratory mice examined (50/55), the cleavage patterns were identical to those of the European subspecies M. m. domesticus . Those that varied include two sublines of NZB, the strain NZC, and the Japanese strain RR. The NZB and NZC patterns were identical to that of the European subspecies M. m. brevirostris , which itself has restriction patterns similar to M. m. domesticus . On the other hand, the RR pattern was identical to M. m. molossinus -like mice trapped in Western China and slightly different from Japanese M. m. molossinus . These findings suggest that the strains NZB and NZC stemmed from a European founder stock which differed from the ancestral stocks of other laboratory strains and that the ancestral mice of the RR strain had been transported from China to Japan. Therefore, most laboratory strains of mice are derived from the European subspecies M. m. domesticus while M. m. brevirostris and M. m. molossinus have made minor contributions. M. m. musculus does not appear to have made any contribution.     

Sequence Characterization of a Unique Intergenic Spacer in Gadiformes Mitochondrial DNA

The nucleotide sequences of intergenic spacers located between the tRNA^Thr and tRNA^Pro genes in mitochondrial DNA of cod fishes (order Godiformes) were determined. Spacers from eight species representing two families of cod fishes were analyzed and found to vary in size from 25 to 99 bp. Each spacer sequence contains one or two copies of a conserved 17-bp motif. Four to five central nucleotides of this motif constitute a substitutional hot spot as observed from interspecific and intraspecific comparisons. The substitution rate of the spacer is approximately twice that of the variable part I of the mitochondrial DNA control region, making this sequence region interesting as a molecular marker in population studies or stock assessments of cod fishes. We propose that the spacer originated in a duplication event and evolved into a functional domain, perhaps by binding regulatory proteins. Accepted February 26, 1999     

The Influence of Social Systems on Patterns of Mitochondrial DNA Variation in Baboons

Behavior is influenced by genes but can also shape the genetic structure of natural populations. Investigating this link is of great importance because behavioral processes can alter the genetic diversity on which selection acts. Gene flow is one of the main determinants of the genetic structure of a population and dispersal is the behavior that mediates gene flow. Baboons (genus Papio) are among the most intensely studied primate species and serve as a model system to investigate the evolution of social systems using a comparative approach. The general mammalian pattern of male dispersal and female philopatry has thus far been found in baboons, with the exception of hamadryas baboons (Papio hamadryas). As yet, the lack of data on Guinea baboons (Papio papio) creates a taxonomic gap in genus-wide comparative analyses. In our study we investigated the sex-biased dispersal pattern of Guinea baboons in comparison to hamadryas, olive, yellow, and chacma baboons using sequences of the maternally transmitted mitochondrial hypervariable region I. Analyzing whole-range georeferenced samples (N = 777), we found strong evidence for female-biased gene flow in Guinea baboons and confirmed this pattern for hamadryas baboons, as shown by a lack of genetic-geographic structuring. In addition, most genetic variation was found within and not among demes, in sharp contrast to the pattern observed in matrilocal primates including the other baboon taxa. Our results corroborate the notion that the Guinea baboons’ social system shares some important features with that of hamadryas baboons, suggesting similar evolutionary forces have acted to distinguish them from all other baboons.     

Human Mitochondrial DNA Variation and Evolution: Analysis of Nucleotide Sequences from Seven Individuals

We have analyzed nucleotide sequence variation in an approximately 900-base pair region of the human mitochondrial DNA molecule encompassing the heavy strand origin of replication and the D-loop. Our analysis has focused on nucleotide sequences available from seven humans. Average nucleotide diversity among the sequences is 1.7%, several-fold higher than estimates from restriction endonuclease site variation in mtDNA from these individuals and previously reported for other humans. This disparity is consistent with the rapidly evolving nature of this noncoding region. However, several instances of convergent or parallel gain and loss of restriction sites due to multiple substitutions were observed. In addition, other results suggest that restriction site (as well as pairwise sequence) comparisons may underestimate the total number of substitutions that have occurred since the divergence of two mtDNA sequences from a common ancestral sequence, even at low levels of divergence. This emphasizes the importance of recognizing the large standard errors associated with estimates of sequence variability, particularly when constructing phylogenies among closely related sequences. Analysis of the observed number and direction of substitutions revealed several significant biases, most notably a strand dependence of substitution type and a 32-fold bias favoring transitions over transversions. The results also revealed a significantly nonrandom distribution of nucleotide substitutions and sequence length variation. Significantly more multiple substitutions were observed than expected for these closely related sequences under the assumption of uniform rates of substitution. The bias for transitions has resulted in predominantly convergent or parallel changes among the observed multiple substitutions. There is no convincing evidence that recombination has contributed to the mtDNA sequence diversity we have observed.     

The Effect of the Nucleotide Context on Induction of Mutations in Hypervariable Segment 1 of Human Mitochondrial DNA

The distribution of unstable nucleotide positions with a higher frequency of homoplastic mutations was analyzed in hypervariable segment 1 (HVS1) of the major noncoding region of human mtDNA. Three motifs (GTAC, ACCC, CCTC) proved to be associated with a higher rate of point substitutions at unstable positions. The motifs were often arranged in direct, including tandem, repeats. Motifs CCTC and ACCC were found in extended poly(C) tracts, which form direct repeats associated with deletions and tandem duplications. The results suggested that the inconstancy of the human mitochondrial genome is to a great extent determined by context-dependent mutations.     

Fine characterization of the Iceman's mtDNA haplogroup

Starting from specimens of the intestinal contents of the so-called Tyrolean Iceman or Otzi (5,350-5,100 years before present), it was possible by polymerase chain reaction to amplify fragments of the human mitochondrial DNA (mtDNA) control region that correspond to the sequence found in 1994 at the Munich and Oxford laboratories and which had been attributed to the original DNA of the mummy. The particularly favorable condition of the specimens, showing very low contamination levels, made it easier to extend the analyses to the coding region, which had not previously been considered. The mtDNA of the European population is currently divided into nine (H, T, U, V, W, X, I, J, and K) main groups (haplogroups). The K haplogroup, in particular, is composed of two (K1 and K2) subclusters. The results demonstrate that the Iceman's mtDNA belongs to the K1 subcluster, yet it does not fit any of the three known branches (a, b, and c) into which the K1 subcluster is presently divided. In addition, some other sites, reported to be linked to environmental adaptation or pathologies, were investigated.     

Characterization and Evolution of the Mitochondrial DNA Control Region in Hornbills (Bucerotiformes)

We determined the mitochondrial DNA control region sequences of six Bucerotiformes. Hornbills have the typical avian gene order and their control region is similar to other avian control regions in that it is partitioned into three domains: two variable domains that flank a central conserved domain. Two characteristics of the hornbill control region sequence differ from that of other birds. First, domain I is AT rich as opposed to AC rich, and second, the control region is approximately 500 bp longer than that of other birds. Both these deviations from typical avian control region sequence are explainable on the basis of repeat motifs in domain I of the hornbill control region. The repeat motifs probably originated from a duplication of CSB-1 as has been determined in chicken, quail, and snowgoose. Furthermore, the hornbill repeat motifs probably arose before the divergence of hornbills from each other but after the divergence of hornbills from other avian taxa. The mitochondrial control region of hornbills is suitable for both phylogenetic and population studies, with domains I and II probably more suited to population and phylogenetic analyses, respectively.     

Nucleotide Substitution Rate of Mammalian Mitochondrial Genomes

We present here for the first time a comprehensive study based on the analysis of closely related organisms to provide an accurate determination of the nucleotide substitution rate in mammalian mitochondrial genomes. This study examines the evolutionary pattern of the different functional mtDNA regions as accurately as possible on the grounds of available data, revealing some important ``genomic laws.' The main conclusions can be summarized as follows. (1) High intragenomic variability in the evolutionary dynamic of mtDNA was found. The substitution rate is strongly dependent on the region considered, and slow- and fast-evolving regions can be identified. Nonsynonymous sites, the D-loop central domain, and tRNA and rRNA genes evolve much more slowly than synonymous sites and the two peripheral D-loop region domains. The synonymous rate is fairly uniform over the genome, whereas the rate of nonsynonymous sites depends on functional constraints and therefore differs considerably between genes. (2) The commonly accepted statement that mtDNA evolves more rapidly than nuclear DNA is valid only for some regions, thus it should be referred to specific mitochondrial components. In particular, nonsynonymous sites show comparable rates in mitochondrial and nuclear genes; synonymous sites and small rRNA evolve about 20 times more rapidly and tRNAs about 100 times more rapidly in mitochondria than in their nuclear counterpart. (3) A species-specific evolution is particularly evident in the D-loop region. As the divergence times of the organism pairs under consideration are known with sufficient accuracy, absolute nucleotide substitution rates are also provided. Received: 11 May 1998 / Accepted: 2 September 1998     

Molecular Characterization of Lengthy Mitochondrial DNA Duplications from the Parasitic Nematode Romanomermis Culicivorax

Complete nucleotide sequences, precise endpoints and coding potential of several 3.0-kilobase mitochondrial DNA (mtDNA) repeating units derived from two isofemale lineages of the mermithid nematode Romanomermis culicivorax have been determined. Endpoint analysis has allowed us to infer deletion and inversion events that most likely generated the present day repeat configuration. Each amplified unit contains the genes for NADH dehydrogenase subunits 3 and 6 (ND3 and ND6), an open reading frame (ORF 1) that represents a cytochrome P450-like gene, and three additional unidentified open reading frames. The primary nucleotide sequences of the R. culicivorax mt-repeat copies within individual haplotypes are highly conserved; three nearly complete copies of the repeat unit vary by 0.01% at the nucleotide level. These observations suggest that concerted evolution mechanisms may be active, resulting in sequence homogenation of these lengthy duplications.     

Misincorporation rate and type on the leading and lagging strands of UV-damaged DNA.

We have examined the fidelity of replication of the leading and lagging strands of UV-irradiated DNA by using an EBV-derived shuttle vector system which contains as marker gene for mutation analysis the bacterial gpt gene in both orientations relative to the EBV oriP. Human cells stably transformed with this vector were UV irradiated and gpt mutation rate and type were analysed. An increased mutagenicity associated with UV irradiation was observed, but the average error frequency was unaffected by the direction of replication of the target gene. Some variability by position and sequence context of leading and lagging strand errors was detected, suggesting that the different architecture of the replication complex for the two strands might, to some extent, affect mutation spectra. The comparable fidelity of translesion replication on the leading and lagging strands is in agreement with the current model for eukaryotic replication that postulates the simultaneous synthesis of both strands by a DNA polymerase with a proof-reading exonuclease.     

Problems of Molecular Systematics of the Genus Salvelinus Based on Nucleotide Sequence Variability in the Major Noncoding Region of Mitochondrial DNA

Variability of the major noncoding mitochondrial DNA region of char (Salvelinus alpinus complex) was analyzed by the median network method on the basis of the literature data on nucleotide sequences of this region. A significant portion (21%) of the polymorphic sites of char mtDNA was shown to be evolutionarily unstable, which results in mutation homoplasia at these sites. Using median-joining analysis the chars were divided into three phylogeographical groups: Arctic, Beringian, and chars occurring in the vast region from Lake Baikal and Taimyr Peninsula to the Atlantic Ocean. The latter group includes three subgroups (Siberian, Atlantic, and Acadian), which diverged from a common ancestor. In the Arctic group, the branch of Taranetz char S. taranetzi is clearly separated. It diverged from the common ancestor earlier than S. boganidae andS. elgyticus occurring on the Chukotka Peninsula species and S. a. erythrinus occurring in Alaska. The Beringian group, which includes dolly varden char from various regions of Asia and America, is an intermediate between the two char groups. The main problems of char systematics inferred from the major noncoding mtDNA region variability arise from the high level of mutation homoplasia.     

Nucleotide Sequence of a 28-kbp Portion of Rice Mitochondrial DNA: the Existence of Many Sequences That Correspond to Parts of Mitochondrial Genes in Intergenic Regions

The nucleotide sequence of a 27,588-bp region of rice mitochondrialDNA was determined. This sequence contains putative genes thatencode initiator methionine tRNA (trnfM), subunits III (nad3)and IV (nad4) of the NADH dehydrogenase complex, and ribosomalproteins S3 (rps3), S12 (rps12) and L16 (rp116). An open readingframe that contains sequences homologous to parts of rps2 andatpA is also present. In addition to these regions, there aremany short sequences with homology to fragments of mitochondrialDNAs from rice or other plants. These sequences may be remnantsof multiple rearrangements of the genome and their presenceseems to explain, in part, the large sizes of the mitochondrialgenomes of higher plants. (Received July 15, 1994; Accepted September 26, 1994)