Screening human EST database for identification of candidate genes in respiratory chain deficiency

Disorders of mitochondrial oxidative phosphorylation (OXPHOS) are now recognized as major causes of human metabolic diseases and several mutations of mitochondrial and nuclear genes encoding respiratory chain components have been reported. Interestingly, mutations of nuclear genes involved in mitochondrial respiratory chain assembly, protein trafficking, and iron metabolism are also known to alter oxidative phosphorylation. While several hundred of these genes have been described in yeast, only a few nuclear genes have been hitherto identified in humans. Yeast gene databases present therefore an invaluable tool for identification of human homologues that should be regarded as candidate genes in OXPHOS diseases. In an attempt to identify the human counterparts of yeast genes, we developed a systematic comparison of yeast protein sequences to the GenBank dbEST database. Starting from 340 yeast protein sequences as templates, we searched the human dbEST counterparts using the BLAST similarity searching program and identified 102 groups of human EST likely to represent orthologues of yeast genes because of significant homology. This collection of human genes possibly related to mitochondrial OXPHOS may help identify nuclear genes responsible of mitochondrial disorders.     

利用辐射杂种板(GB4)精细定位人类新基因H-RalGDS于染色体9q34.1

目的 Ｈ－ＲａｌＧＤＳ基因是我们新近分离与克隆的人类新的Ｒａｓ相关基因,是鼠Ｒａｌ鸟嘌呤核苷酸解离刺激因子（ＲａｌＧＤＳ）在人类的同源基因。利用辐射杂种板（ｒａｄｉａｔｉｏｎ ｈｙｂｒｉｄ,ＲＨ）制图法进行该基因的精细定位。方法 根据Ｈ－ＲａｌＧＤＳ基因ｃＤＮＡ的３’不翻译区设计正反向引物,ＰＣＲ扩增人／鼠辐射体细胞杂种板（ｒａｄｉａｔｉｏｎ ｈｙｂｒｉｄ Ｇｅｎｂｒｉｄｇｅ ４ ｐａｎｅｌ）,并     

Comparative fluorescencein situ hybridization mapping of primate chromosomes withAlu polymerase chain reaction generated probes from human/rodent somatic cell hybrids

We have usedAlu polymerase chain reaction generated probes from rearranged human/rodent somatic cell hybrids for fluorescencein situ hybridization and comparative mapping of some intrachromosomal changes in the karyotypes of great apes (Pan troglodytes, P. paniscus, Gorilla gorilla Pongo pygmaeus), a gibbon (Hylobates lar), and an Old World monkey (Macaca fuscata). Probes containing chromosomes 2 and 18 fragments confirmed inversions already suggested by the banding pattern of great ape homologues. However, a chromosome 3 fragment showed complex rearrangements in the gibbon and macaque karyotype which were previously not well defined from banding. Subchromosomal painting will allow the identification of intrachromosomal changes on the basis of DNA homology and provides a powerful method to study karyological and genomic evolution.accepted for publication by M. SchmidInstitut für Anthropologie und Humangenetik, Universität München     

A study of 133 Chinese children with mitochondrial respiratory chain complex I deficiency

To investigate the clinical, enzymological and mitochondrial gene profiles of complex I deficiency in Chinese, clinical and laboratory data of the patients (79 boys, 54 girls) were retrospectively assessed. Activities of mitochondrial respiratory chain complexes in peripheral leucocytes were spectrophotometrically measured. The entire mitochondrial DNA (mtDNA) sequence was analyzed in 62 patients. Restriction fragment length polymorphism and gene sequencing analyses were performed in 15 families. Ninety‐one patients had isolated complex I deficiency; 42 had combined deficiencies of complex I and other complexes. The main clinical presentations were neuromuscular disorders (107 patients) and non‐neurological dysfunction (hepatopathy, renal damage and cardiomyopathy; 26 patients). In 32 of 62 patients who underwent mtDNA sequencing, 24 mutations were identified in 15 mitochondrial genes. The 12338T>C, 4833A>G and 14502T>C mutations were found in 12.9%, 11.3% and 4.8% patients, respectively. Seven patients had multiple mutations. Three novel mutations were identified. Chinese patients with complex I deficiency presented heterogeneous phenotypes and genotypes. Twenty‐four mutations were identified in 15 mitochondrial genes in 51.6% patients. mtDNA mutations were more common in isolated complex I deficiency than in combined complex deficiencies. The 12338T>C, 4833A>G and 14502T>C mutations were common.     

Identification of nucleotide-excision-repair genes on human chromosomes 2 and 13 by functional complementation in hamster-human hybrids

The CHO UV-sensitive mutants UV24 and UV135 (complementation groups 3 and 5, respectively) are defective in nucleotide excision repair. After fusing each mutant with human lymphocytes, resistant hybrid clones showing genetic complementation were isolated by repeated exposure to UV radiation. Using a combination of isozyme markers, DNA probes,and cytogenetic methods to analyze the primary hybrids and their subclones, correction of the repair defect was shown to be correlated with the presence of a specific human chromosome in each case. Chromosome 2 corrected UV24, and the gene responsible was designated ERCC3.Line UV135 was corrected by human chromosome 13 and the gene designated ERCC5.The UV-sensitive mouse cell line, Q31, was shown not to complement UV135 and thus appears to be mutated in the same genetic locus (homologous to ERCC5)as UV135. Breakage of complementing chromosomes with retention of the genes correcting repair defects allowed the following provisional assignments: regional localization of ERCC5to 13q14-q34, exclusion of ERCC3from the region of chromosome 2 distal to p23, and relief of the ambiguity of ACPlassignment (2p23 or 2p25) to 2p23 proximal to MDH1.     

1H MRS spectroscopy evidence of cerebellar high lactate in mitochondrial respiratory chain deficiency

Cerebellar ataxia is known to occasionally occur in the course of mitochondrial disorders. We report on MR spectroscopy (1H MRS) evidence of elevated brain lactate in the cerebellar area of 11 patients with cerebellar ataxia ascribed to mitochondrial respiratory chain deficiency (RCD). 1H MRS spectroscopy evidence of lactate peak was found in the cerebellum of 9/11 cases, while no lactate was detected in the putamen in 8/11. We suggest using 1H MRS in cerebellar atrophy in the diagnosis of mitochondrial RCD.     

Importance of muscle light microscopic mitochondrial subsarcolemmal aggregates in the diagnosis of respiratory chain deficiency

The purpose of this study was to evaluate relationships between subsarcolemmal mitochondrial aggregates and electron transport chain deficiencies in skeletal muscle with the objective of establishing an association between mitochondrial accumulation and electron transport chain complex deficiency. We conducted a large-scale, retrospective study to evaluate factors associated with subsarcolemmal mitochondrial aggregates (percent) in pediatric patients who received muscle biopsies for suspected respiratory chain disorders. Patients were included if they had histochemical stains for assessment of mitochondrial pathology and had biochemical testing for muscle electron transport chain complex activities. Significant positive bivariate correlations (n = 337) were found between subsarcolemmal mitochondrial aggregate percentage and electron transport chain complexes II, IV, I + III, and II + III activities. Evaluation showed that a cutoff value of > 2% subsarcolemmal mitochondrial aggregates had poor overall diagnostic accuracy (mean, 32%), compared with a < 5% cutoff (mean, 60%). To better evaluate the effects of subsarcolemmal mitochondrial aggregates percentages, patients were stratified according to lower one-third (group 1, n = 120 plus ties) and upper one-third (group 2, n = 115 plus ties) of subsarcolemmal mitochondrial aggregates values. Although only minor clinical and pathologic differences were observed, group 1 participants had significantly lower electron transport chain complex activities than group 2 for all enzymes except complex III. Logistic regression showed over 2-fold greater odds of deficiency for electron transport chain complexes I + III (P = .01) and II + III (P = .03) for group 1 participants compared with group 2. We conclude that, contrary to the previous > 2.0% subsarcolemmal mitochondrial aggregates cutoff for respiratory chain disorder, patients with a low subsarcolemmal mitochondrial aggregates percentage (≤4%) are significantly more likely to have electron transport chain complex deficiency than patients with increased subsarcolemmal mitochondrial aggregates percentage (≥10%). This morphological approach for assessment of mitochondrial proliferation may assist clinicians to select further testing to rule out an electron transport chain complex deficiency in children by other methods, including direct biochemical testing of electron transport chain complex activities, measurement of muscle coenzyme Q10 content, or evaluation for a mitochondrial DNA depletion syndrome.     

Autism associated to a deficiency of complexes III and IV of the mitochondrial respiratory chain

Autism is the prototype of generalized developmental disorders or what today are called autism spectrum disorders. In most cases it is impossible to detect a specific etiology. It is estimated that a causative diagnosis may be shown in approximately 10-37% of the cases, including, congenital rubella, tuberous sclerosis, chromosome abnormalities such as fragile X syndrome and 22q13.3 deletion syndrome, Angelman, Williams, Smith-Magenis, Sotos, Cornelia de Lange, M?bius, Joubert and Goldenhar syndromes, Ito's hypomelanosis, as well as certain cerebral malformations and several inherited metabolic disorders. The case of a 3-year old girl is described, who was considered as autistic according to the criteria established by the DSM-IV manual for psychiatric disorders. She showed a delay in psychomotor development since she was 18 months old; she pronounces very few words (10), points to some objects, does not look up and it is hard to establish eye contact with her. She has paradoxical deafness and therefore, does not respond when called or when she is given orders, she is beginning to walk. She has not convulsions. Laboratory tests showed an anion gap of 31.6 mEq/L, lactate: 2.55: mmol/L, pyruvate: 0.06 mmol/L, and elevated lactate to/pyruvate ratio: 42.5. Under optical microscopy a muscular biopsy showed a reduction of the diameter of muscular fibers. The study of energy metabolism showed a partial deficiency of complexes III and IV of the respiratory chain, which allowed us to conclude that this was a mitochondrial dysfunction with an autistic clinical spectrum.     

Quality improvement of mitochondrial respiratory chain complex enzyme assays using Caenorhabditis elegans

PurposeThe diagnosis of a mitochondrial disorder relies heavily on the enzymatic analysis of mitochondrial respiratory chain complexes in muscle or other tissues. However, considerable differences exist between clinical laboratories in the protocols or particular tests used for evaluation. In addition, laboratories can encounter difficulties in consistent technique, as well as procurement of adequate positive or negative controls. Currently, there is no external quality assurance for respiratory chain complex assays. In this study, we explored the use of Caenorhabditis elegans mitochondria as a potential aid to diagnostic centers that perform respiratory chain complex assays.MethodFive diagnostic test centers in the United States and one from Australia comparatively analyzed enzyme activities of mitochondria from C. elegans. The first survey consisted of three open-labeled samples including one normal control and two mutants; the second survey consisted of one open-labeled normal control and two blinded samples.ResultsThere was very good concordance among laboratories in detecting the majority of the defects present in the mutant specimens. Despite the ability to detect respiratory chain complex defects, the scatter between centers for certain enzymatic assays, particularly I + III, II, III, and IV, led to different diagnostic interpretations between the centers.ConclusionThe data strongly support the need for comparative testing of mitochondrial enzyme assays between multiple laboratories. Our overall results are encouraging for the use of nematode mitochondria as a tool that might provide a virtually inexhaustible supply of mitochondria with defined defects for development of assays and as a potential source of control specimens.     

无线粒体DNA的ρ°206细胞的培养及其呼吸链功能损害

培养无线粒体DNA的ρ°206细胞,观察其生长特性,应用电镜化学方法及检测MTT代谢率观察线粒体活性.结果发现ρ°206细胞具有嘧啶依赖性,血清中微量的嘧啶即可支持其生长增殖成克隆.在选择培养基中ρ°206细胞第5天大量死亡,第12天左右完全死亡,台盘蓝染色证实选择培养第6天以后已无活细胞存在.ρ°206细胞的MTT代谢率仅为143B·TK-细胞的20%左右,细胞色素氧化酶电镜细胞化学从形态学角度首次证实ρ°206细胞无细胞色素氧化酶活性,其线粒体数量及结构无明显异常改变.上述观察在转线粒体研究中具有一定的应用价值.     

Nuclear genes of human complex I of the mitochondrial electron transport chain: state of the art

The mitochondrial electron transport chain (mtETC) consists of four multi-subunit enzyme complexes. Complex I or NADH:ubiquinone oxidoreductase, the largest mtETC multisubunit complex, consists of approximately 41 subunits. Seven of these subunits are encoded by the mitochondrial genome, the remainder by the nuclear genome. Among the mitochondriocytopathies, complex I deficiencies are encountered frequently. Although some complex I deficiencies have been associated with mitochondrial DNA mutations, the genetic defect has not been elucidated in the majority of complex I-deficient patients. It is expected that many of these patients have mutations in the nuclear- encoded subunits of this complex, so vital for cellular energy production. After a brief summary of the current knowledge of complex I from cow, bacteria and fungi, this review presents the state of the art of the knowledge of the human nuclear-encoded complex I genes which, in the last 18 months, has made enormous progress. At present, the complete gene structure of four subunits and the cDNA structure of 18 of the 34 complex I nuclear-encoded subunits are known. Mapping of these subunits shows a random distribution over the chromosomes. The chromosomal localization is known for 14 complex I genes. Recently, the first mutation, a 5 bp duplication in the 18 kDa (AQDQ) subunit, has been reported. We expect that within 1 year all human nuclear-encoded complex I subunits will be cloned. Mutational analysis of these subunits is warranted in complex I-deficient patients and will not only be important for genetic counselling but will also extend the knowledge regarding the functional properties of the individual human complex I subunits.      

Genetic analysis of temperature-sensitive mutants of HSV-1: The combined use of complementation and physical mapping for cistron assignment

To date, mutations in mutants representing 19 of the 33 recognized HSV-1 complementation groups have been mapped. The physical map locations of mutations in 10 ts mutants of HSV-1 strain KOS representing 8 of the 19 complementation groups are reported herein. The mutations in three mutants were found to lie between coordinates 0.086 and 0.194—two of these were mapped finely to between coordinates 0.095 and 0.108—and in seven mutants, between 0.301 and 0.448. The mutation in 1 of the 10 mutants tsQ26, was mapped finely to a sequence between 500 and 1000 base pairs to the left of the 3′ end of the TK gene (0.301–0.304). The availability of physical mapping data has (1) confirmed the usefulness of the complementation test as a means of identifying viral gene functions, (2) facilitated the rapid assignment of mutants to new and recognized cistrons, and (3) prompted a reevaluation of previously ambiguous complementation for mutants in 2 complementation groups. Thus, the 10 mutants whose ts mutations were mapped in this study had been assigned previously to 8 complementation groups based on the assumption that complementation indices of 2 or greater signified that 2 mutants were in different genes. Combined with physical mapping data, however, the results of complementation tests now indicate that indices between 2 and 10 may reflect either inter- or intragenic complementation. Thus, the 10 mutants have now been assigned to 7 complementation groups. Although physical mapping data have confirmed the results of previous complementation tests for 6 of 8 groups analyzed, reevaluation of complementation data in the light of physical mapping data has resulted in a more precise genetic definition of the locus for viral DNA polymerase and of a locus (represented by mutants in complementation group 1–10) which maps in the left hand portion of U_L.     

Enrichment of human heterokaryons by ficoll gradient for complementation analysis of iduronate sulfatase deficiency

Ficoll gradients have been used to enrich for heterokaryons in cultures of human skin fibroblasts following polyethylene glycol (PEG) induced fusion. These gradients provide a simple and consistent method for obtaining populations of multinucleated cells, at least twofold greater than those resulting from fusion alone. Formation of glucose-6-phosphate dehydrogenase (G6PD) heteropolymers has been used as a functional assay for the presence of heterokaryons. Analysis of cell populations enriched for multinucleated cells has revealed complementation leading to iduronate sulfatase activity in heterokaryons derived from iduronate sulfatase-deficient fibroblasts expressing the Hunter and multiple sulfatase-deficiency mutations.     

Identification of novel mutations of the HADHA and HADHB genes in patients with mitochondrial trifunctional protein deficiency

Patients with long-chain 3-hydroxyacyl coenzyme A dehydrogenase (LCHAD) deficiency manifest hypoketotic hypoglycemia, hepatomegaly, hypotonia, lactic acidemia, acute renal failure, cardiomyopathy, and sudden death. We describe four novel mutations of the alpha- and beta-subunits of the mitochondrial trifunctional protein in four patients from three unrelated families. Their plasma acylcarnitine profiles suggested the presence of LCHAD deficiency by demonstrating highly elevated 3-hydroxyacyl carnitines by tandem mass spectrometry (MS/MS). Patients 1 and 2 had siblings who had died of lactic acidemia during the neonatal period. These patients also manifested lactic acidemia and died in the neonatal period. Patient 3 had a family history of Reye-like syndrome. She exhibited acute renal failure, rhabdomyolysis, pericardial effusion, and myopathy at the age of 12 years. DNA analysis of patients 1 and 2 revealed homozygosity for a c.1689+2T>G mutation of the HADHA gene, resulting in the skipping of exon 16 with an in-frame 69-bp deletion. Patient 3 was a compound heterozygosity of the HADHB gene, N307D/N389D. Patient 4, a 25-month-old baby, manifested recurrent episodes of lethargy, metabolic acidosis, elevated liver enzymes, and dark urine from the age of 10 months. Mutation analysis of the HADHB gene of patient 4 identified compound heterozygosity of N114D/N307D.     

A novel PCR-based technique using expressed sequence tags and gene homology for murine genetic mapping: localization of the complement genes

The complement system is a cascade of serum proteins and receptors which forms a vital arm of innate immunity and enhances the adaptive immune response. This work establishes the chromosomal localization of four key genes of the murine complement system. Mapping was performed using a novel and rapid PCR restriction length polymorphism method which was developed to exploit the murine expressed sequence tag (EST) database. This technique circumvents the laborious cDNA or genomic cloning steps of other mapping methods by relying on EST data and the prediction of exon-intron boundaries. This method can be easily applied to the genes of other systems, ranging from the interests of the individual researcher to large-scale gene localization projects. Here the complement system, probably one of the most well-characterized areas of immunology, was used as a model system. It was shown that the C3a receptor C1r and C1s genes form an unexpected complement gene cluster towards the telomeric end of chromosome 6. The second mannose binding lectin-associated serine protease gene was mapped to the telomeric end of chromosome 4, which is distinct from other complement-activating serine proteases. These results provide new insights into the evolution of this group of proteins.     

Regional mapping of human genes for hexosaminidase B and diphtheria toxin sensitivity on chromosome 5 using mouse × human hybrid cells

Mouse 3T3 (TK^–) cells were fused to human leukocytes containing a balanced translocation [ins(3;5) (q27;q13q15)] in which part of the long arm of a chromosome 5 has been inserted into the long arm of a chromosome 3. Two independent, primary hybrid clones (XVI-10C; XVI-18A) retained the deleted chromosome 5 [del(5) (q13q15)] translocation product and were informative for regional mapping on chromosome 5 of genes involved in expression of hexosaminidase B (HEX _B ) and diphtheria toxin sensitivity (DTS). Both XVI-10C and XVI-18A clones were sensitive to diphtheria toxin. Toxin-resistant derivatives of these clones (XVI-10C DTR; XVI-18A DTR) were analyzed for chromosome content and expression of Hex B activity, as were XVI-10C and XVI-18A cells which had not been exposed to diphtheria toxin. The results of this study provide evidence for localization ofDTS to region 5q155qter on the long arm of chromosome 5, and localization ofHEX _B to region 5pter5q13.     

Detection of mitochondrial DNA deletions in blood using the polymerase chain reaction: non-invasive diagnosis of mitochondrial myopathy

Southern hybridisation demonstrates deleted mitochondrial DNAs (mtDNAs) in muscle but not in blood in a subgroup of patients with mitochondrial myopathy. The polymerase chain reaction (PCR) was used to search for low levels of rearranged mitochondrial DNAs in blood in 24 patients with mitochondrial myopathy, and 15 asymptomatic relatives, all of whom have no detectable abnormality on restriction enzyme analysis of blood mitochondrial DNA. In eight patients and two of their relatives, PCR products were obtained consistent with deletions of mitochondrial DNA. The presence or absence of a deletion was correctly predicted in 10 out of 11 patients from whom information was available from muscle DNA. No false positives were obtained in 43 controls. PCR analysis of blood may be applicable as a non-invasive screening test of affected individuals and in carrier detection.     

The mitochondrial genome of the basidiomycete Agrocybe aegerita: molecular cloning,physical mapping and gene location

Summary The mtDNA of a wild-type strain of Agrocybe aegerita was purified from mitochondria isolated by cellular fractionation. A representative library was constructed in E. coli by molecular cloning at the HindIII restriction site of pBR322. Southern hybridizations between total DNA of the fungal strain and cloned mitochondrial insert probes were used to establish the restriction map of the mtDNA molecule. Its size was assessed at about 80 500 bp. Four structural genes (for Cox 1, Cox 2, Atp 6, and Atp 8) were located on the map by heterologous hybridizations with oligonucleote probes specific for yeast mitochondrial genes. The location of the genes coding for the large and the small RNAs of the mitochondrial ribosome was determined by hybridization with the E. coli rrnB operon. A comparison of A. aegerita mtDNA organization with that of both phylogenetically close and distant fungi is discussed.