Current Molecular Medicine (v.14, #10)

Outfielders Playing in the Infield: Functions of Aging-Associated "Nuclear" Proteins in the Mitochondria by P. Czypiorski, J. Altschmied, L.L. Rabanter, C. Goy, S. Jakob., J. Haendeler (1247-1251).
Over the past few years it has become clear that mitochondria are not merely the powerhouses ofcells. Proteome-analyses of mitochondria from different organisms and organs revealed that more than 1000proteins are localized in and/or on mitochondria. This by far exceeds the number of proteins required forclassical mitochondrial functions, e.g. the respiratory chain, the tricarboxylic acid cycle, fatty acid oxidation andapoptosis. This suggests that many of these proteins have other, as yet unknown functions. Several proteinswith well-described nuclear functions, like the transcription factor FoxO3A or the Telomerase ReverseTranscriptase, have recently been shown to be localized also within the mitochondria. This mini-review willfocus on the description of the functions of these two proteins in the nucleus and in the mitochondria - as twoexamples of many more proteins, which are yet to be uncovered. It will give insights into the role of theseproteins within different organelles of the cell and will reveal that the functions of the proteins are probably notthe same in the nucleus and the mitochondria. Therefore, these differences have to be considered whentargeting proteins for therapeutic approaches.

CD147 Interacts with NDUFS6 in Regulating Mitochondrial Complex I Activity and the Mitochondrial Apoptotic Pathway in Human Malignant Melanoma Cells by Z. Luo, W. Zeng, W. Tang, T. Long, J. Zhang, X. Xie, Y. Kuang, M. Chen, J. Su, X. Chen (1252-1264).
Malignant melanoma (MM) is one of the most lethal tumors and is characterized by highinvasiveness, frequent metastasis, and resistance to chemotherapy. The risk of metastatic MM is accompaniedby disordered energy metabolism involving the oxidative phosphorylation (OXPHOS) process, which is largelycarried out in mitochondrial complexes. Complex I is the first and largest mitochondrial enzyme complexassociated with this process. CD147 is a transmembrane glycoprotein mainly expressed on the cell surface,and also appears in the cytoplasm in some tumors. We found that CD147 is often translocated to thecytoplasm in metastatic MM specimens as compared to primary MM. We also demonstrated high expression ofCD147 in isolated mitochondrial fractions of A375 cells. The yeast two-hybrid (Y2H) assay identified NDUFS6(which encodes a subunit of mitochondrial respiratory chain complex I) as a candidate that interacts withCD147 and depletion of CD147 in A375 cells significantly decreased complex I enzyme activity. We alsoshowed that CD147 increased the viability of A375 cells exposed to berberine-induced mitochondrial damage,and protected them from apoptosis through a mitochondrial-dependent pathway. This finding was confirmed byadding exogenous Bcl-2 to A375 cell cultures. In summary, our results identify the existence of CD147 inhuman melanoma cell mitochondria. They indicate that CD147 appears to regulate complex I activity andapoptosis in MM by interacting with mitochondrial NDUFS6. Our findings provide new insight into the functionof CD147 and identify it as a promising therapeutic target in melanoma through disruption of the energymetabolism.

Evaluating the Susceptibility of Mitochondrial DNA Germline Mutations in Chinese Cancer Patients by J. Liu, L.-Y. Xu, R.-L. Li, E.-M. Li, Q.-P. Kong (1265-1272).
It has been suggested that impairment of mitochondrial oxidative phosphorylation (OXPHOS) is acommon character in cancer cells, urging attention to variation on mitochondrial DNA (mtDNA) that encodes 13units of the OXPHOS. However, most of mtDNA somatic mutations in cancer were suggested to result from therelaxed functional constrains and thus the byproducts of tumorigenesis. MtDNA germline mutations present notonly in the cancer tissue but also in the normal tissue. However, it remains unclear whether the cancerousmtDNA germline mutations suffered similar selective constraints as the somatic mutations did. To address thisquestion, we collected 153 whole mitochondrial genomes (including 20 newly obtained genomes in this study)from the normal tissues of cancer patients and compared with a number of 561 whole mtDNA sequences fromthe general population in China. Different from the observations on cancerous mtDNA somatic mutations, ourresults revealed that the germline mutations showed no significant difference between the cancer patients andthe general population in either the sub-haplogroup composition, mutation pattern or the potential pathogenicityof the private mutations. It then seems that regulation on cellular OXPHOS level, triggered by mtDNA variationto some extent, exerts little influence on the susceptibility of cancer, which echoes the opinion that aerobicglycolysis, not mitochondrial respiration, plays the key role in generating energy in cancer cells, thussuggesting the role of most mtDNA mutations in cancer likely being overestimated.

Reappraising the Relationship Between Mitochondrial DNA Variant m.16189T>C and Type 2 Diabetes Mellitus in East Asian Populations by L. Zhong, J. Tang, Q.-P. Kong, C. Sun, W.-P. Zhou, M. Yang, Y.-G. Yao, Y.-P. Zhang (1273-1278).
The role of mitochondrial DNA (mtDNA) variant 16189T>C in type 2 diabetes mellitus (T2DM)remains hotly debated in the past decade. If mutation 16189T>C indeed posed a risk to T2DM, as echoed bysome recent studies, correlation between this mutation and disease should be observed when carrying out asystematical study using data and samples collected in a large geographic region in China. To test thishypothesis, we first performed a linear regression analysis between the prevalence of T2DM and the allelefrequency of 16189C variant in 10 East Asian populations, and further genotyped this variant in two casecontrolcohorts from west Han Chinese (Kunming and Xining). Linear regression analysis showed that nosignificant correlation was observed (r2=0.211, P=0.181), and the genotyping results indicated that them.16189T>C frequency difference between case and control was not significant in either populations (P=0.38and 0.89 for Kunming and Xining, respectively). Matrilineal backgrounds constitution (in terms of haplogroups)analysis generated a similar haplogroup distribution in both populations (P>0.1). All results failed tosubstantiate that m.16189T>C may play an active role in the development of T2DM in East Asian populations.

Sinipercids are a group of freshwater perciform fish endemic in East Asia with the majority of speciesrecorded in China. In the present study, we analyzed the organizations of complete mitogenomes of the sixsinipercid fish populations from the Yangtze River and the Pearl River systems in China. The proportion of G wasrelatively low just at 16.2%-16.5% among the fish populations analyzed. The similarity and divergence analysisshowed that the populations from different drainages have more sequence similarities than those from differentspecies in the same drainages. The rate of point mutation was 0.39% and a total of 422 variable sites wereidentified in the 12 protein-coding genes (excluding the ND6) among the four S. scherzeri populations. Theanalysis of evolutionary relationship showed that the four S. scherzeri populations can be divided into two groupsof Yangtze River system and the Pearl River. Overall the data provide significant information for the genetic andevolutionary status of sinipercids upon adapting to different environments, and for genetic conservation andselective breeding of these fish species in fishery and aquaculture.

Complex Evolutionary Patterns Revealed by Mitochondrial Genomes of the Domestic Horse by T. Ning, J. Li, K. Lin, H. Xiao, S. Wylie, S. Hua, H. Li, Y.-P. Zhang (1286-1298).
The domestic horse is the most widely used and important stock and recreational animal, valued forits strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria viaoxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horsemitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. Tounderstand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencingapproach to obtain the complete sequences of 15 mitochondrial genomes, and four mitochondrial genesequences, ND6, ATP8, ATP6 and CYTB, collected from 509, 363, 363 and 409 domestic horses,respectively. Evidence of strong substitution rate heterogeneity was found at nonsynonymous sites across thegenomes. Signatures of recent positive selection on mtDNA of domestic horse were detected. Specifically, fiveamino acids in the four mitochondrial genes were identified as the targets of positive selection. Coalescentbasedsimulations imply that recent population expansion is the most probable explanation for the matrilinealpopulation history for domestic horse. Our findings reveal a complex pattern of non-neutral evolution of themitochondrial genome in the domestic horses.

Minifish mtDNA has Abundance of Repeat Sequences and Inefficient Replication In Vitro by J. Wang, L.-Y. Peng, C.-P. You, Q.-L. Li, M. Wen, S.-J. Liu, Y.-H. Hong (1299-1307).
Paedocypris is a newly described minifish genus endemic to Southeast Asia. Besides a tiny adultsize of ~8 mm in length, minifish feature fragmentary habitats of acidic peat blackwater swamps, an unusualreproduction mode, truncated development and one of the smallest known genomes. A complete sequence isabsent for the minifish mitochondrial DNA (mtDNA). Here we report the complete mtDNA sequence and itsunusual feature in the minifish P. progenetica (Pp). We show that the Pp mtDNA is a circular molecule of17,382 bp in length and has the same number of similarly oriented genes as in other vertebrates. Specifically,it comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 D-loop. Surprisingly, the D-loop iselusive for amplification by standard PCR conditions. The D-loop possesses a 28-bp dinucleotide TA repeatand more intriguingly, up to 25 copies of a 34-bp tandem repeat sequence. These tandem repeats predict theformation of paired regions. Hence, besides a generally conserved mtDNA with other vertebrates, the PpmtDNA features an unusual D-loop and compromised DNA replication in vitro.

Minifish Shows High Genetic Variation in mtDNA Size by X.-W. Chen, Q.-L. Li, X.-J. Hu, Y.-M. Yuan, M. Wen, L.-Y. Peng, S.-J. Liu, Y.-H. Hong (1308-1313).
The genus Paedocypris is a newly described taxon of minifish species that are characterized byextensive chromosome evolution and one of the smallest known vertebrate nuclear genomes. Paedocyprisfeatures a tiny adult size, a short generation time, low fecundity and fragmented tropical habitats, which arefactors that favor rapid speciation. Most recently, we have revealed that P. progenetica (Pp), the type speciesof the genus Paedocypris, has an unusual mtDNA bearing - within its D-loop - a tandem array of a 34-bprepeat sequence called the minifish repeat, which shows compromised replication efficiency in vitro. Here wereport that Pp exhibits high genetic variation in mtDNA size. The efficiency of D-loop amplification was found todepend upon primers. Interestingly, Pp individuals of one and the same population differed drastically inmtDNA size resulting from varying copy numbers of the minifish repeat. We conclude that minifish has a highmutation rate and perhaps represents a rapidly evolving taxon of vertebrates.

Analysis of Mitochondrial Respiratory-Related Genes Reveals Nuclear and Mitochondrial Genome Cooperation in Allotetraploid Hybrid by L.-Y. Peng, J. Wang, M. Tao, C.-P. You, L. Ye, J. Xiao, C. Zhang, Y. Liu, S.-J. Liu (1314-1321).
An allotetraploid hybrid lineage derived from the distant hybridization of red crucian carp (Carassiusauratus red var., ♀, 2n =100) x common carp (Cyprinus carpio L., ♂, 2n =100) was investigated for itsmitochondrial and nuclear genome inheritance patterns. Based on liver transcriptomic data for this hybrid, redcrucian carp, and common carp, we identified 94, 136, and 86 contigs corresponding to 41, 46, and 37mitochondrial respiratory chain nuclear genes, respectively. Mitochondrial respiratory chain nuclear genesequences from red crucian carp and common carp were both detected in the allotetraploid hybrid, indicatingthat both parental nuclear genomes were participated in the synthesis of mitochondrial respiratory proteincomplexes in the hybrid. For mitochondrial respiratory related genes, high sequence similarity (>90%) and alow nucleotide divergence rate (<0.2) between red crucian carp and common carp could be a critical factorallowing cooperation of the three genomes (red crucian carp mitochondrial genome, red crucian and commoncarp nuclear genomes) in the allotetraploid hybrid lineage. Interestingly, gene duplication events wereidentified in the allotetraploid hybrid, red crucian and common carp, as confirmed by analysis of orthologousgene trees for these fish. Our findings provide valuable information with which to study cooperation betweenthe nuclear and mitochondrial genomes of other hybrids, and will provide basic genetic information ofrelevance to mitochondrial-related diseases in humans and animals.

Inheritance of the Complete Mitochondrial Genomes in Three Different Ploidy Fishes by C.-P. You, R.-R. Zhao, J. Hu, S.-J. Liu, M. Tao, C. Zhang, Y.-B. Chen, Q.-B. Qin, J. Xiao, W. Duan, Y. Liu (1322-1330).
Diploid natural gynogenetic goldfish (2nGRCG), triploid hybrids (3nRB) and tetraploid hybrids(4nRB) are generated by distant hybridization of red common goldfish (RCG, Carassius auratus red var.) andblunt snout bream (BSB, Megalobrama amblycephala). In the present study, we obtained the completemitochondrial DNA (mtDNA) sequences of the hybrid offspring and compared them with the homologoussequences of RCG and BSB. All mtDNA sequences of these hybrids were 16,580bp in length, and the genesnumber, size, and order were quite similar to that of RCG. Genetic analysis revealed that the mtDNAsequences of these hybrids had high similarity (>99%) and low divergence (<2%) to their maternal RCG, yetlower similarities (84%) and higher divergences (16%) to their paternal BSB. The phylogenetic analysis alsoshowed that the sequences of 2nGRCG, 3nRB and 4nRB were clustered with RCG rather than with BSB.These results indicate that the mitochondrial genomes of 2nGRCG, 3nRB and 4nRB remain maternallyinherited after hybridization and polyploidization. Moreover, clade separation of hybrid offspring from theirpaternal BSB in the phylogenetic tree implies that phylogenetic analysis of mtDNA is incomplete for elucidatingthe true relationships between different species, particularly when they have undergone hybridization orallopolyploidization. Our study provides significant information for both evolution and genetic studies of mtDNAfor hybrid species and allopolyploidization species.

Allopolyploidization is Not So Simple: Evidence from the Origin of the Tribe Cyprinini (Teleostei: Cypriniformes) by W. Ma, Z.-H. Zhu, X.-Y. Bi, R.W. Murphy, S.-Y. Wang, Y. Gao, H. Xiao, Y.-P. Zhang, J. Luo (1331-1338).
The identification of allopolyploidization events benefits from molecular dating and divergenceassessments of progenitor genomes. Information on gene duplications only, either orthologs or paralogs,provides incomplete information. Analyses of mitochondrial DNA yield insights into matrilineal history, whichmay differ from patrilineal evolution. Two important food and pet fishes, the common carp (Cyprinus carpio)and goldfish (Carassius sp.), appear to have experienced allotetraploidization sometime from 12 to 20 millionyears ago (Ma). However, much work is necessary to detail the initial polyploidization event. Herein, we usethis group of fishes as a model system to investigate competing scenarios for allopolyploidization. We analyzeboth the nuclear genes encoding growth hormone (GH), recombination activating protein 1 (RAG1) andHOXA2B gene, and the maternal heredited 12 concatenated mitochondrial protein-coding gene in 19 speciesof cyprinids and use two species in Balitoridae as outgroup taxa. Our analyses clarify the phylogenetic positionof the paternal and maternal ancestors for the common carp and goldfish. The estimation of matrilinealdivergence (10.71-12.42 Ma) is significantly younger than the dates of the parental ancestor divergedthatobtained by nuclear genes (16.62-19.64 Ma). Analyses of both genomes date the allopolyploidization event ofthe common ancestor of Cy. carpio and Ca sp. to about 10.71-12.42 Ma, which is most likely represented bymaternal divergent time. The divergence of the two copies of the nuclear genes which was more ancient thanthe maternal markers might have been included the divergence of the progenitors' genome divergence whenthe allopolyploidization event occurred. Thus, the scenarios of allopolyploidzation for this group of fish can besuggested as the following: the matrilineal common ancestor of species in tribe Cyprinini might have doubledits genome by mating with a paternal ancestor in the subfamily Cyprininae, which was a sister-group thatdiverged around 4.20-8.93 Ma. Our work provides new evidence for the divergence dates ofallopolyploidization within the Cyprinini, and documents the necessity of considering both matrilineal andpatrilineal histories when investigating allopolyploidization.