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PubMed2006

Mutational analysis of the flagellar protein FliG: sites of interaction with FliM and implications for organization of the switch complex.

The switch complex at the base of the bacterial flagellum is essential for flagellar assembly, rotation, and switching. In Escherichia coli and Salmonella, the complex contains about 26 copies of FliG, 34 copies of FliM, and more then 100 copies of FliN, together forming the basal body C ring. FliG is involved most directly in motor rotation and is located in the upper (membrane-proximal) part of the C ring. A crystal structure of the middle and C-terminal parts of FliG shows two globular domains connected by an alpha-helix and a short extended segment. The middle domain of FliG has a conserved surface patch formed by the residues EHPQ(125-128) and R(160) (the EHPQR motif), and the C-terminal domain has a conserved surface hydrophobic patch. To examine the functional importance of these and other surface features of FliG, we made mutations in residues distributed over the protein surface and measured the effects on flagellar assembly and function. Mutations preventing flagellar assembly occurred mainly in the vicinity of the EHPQR motif and the hydrophobic patch. Mutations causing aberrant clockwise or counterclockwise motor bias occurred in these same regions and in the waist between the upper and lower parts of the C-terminal domain. Pull-down assays with glutathione S-transferase-FliM showed that FliG interacts with FliM through both the EHPQR motif and the hydrophobic patch. We propose a model for the organization of FliG and FliM subunits that accounts for the FliG-FliM interactions identified here and for the different copy numbers of FliG and FliM in the flagellum.

Amino Acid Motifs↗

PubMed1983

Interactions of DNA replication factors in vivo as detected by introduction of suppressor alleles of dnaA into other temperature-sensitive dna mutants.

Suppressor mutations located within dnaA can suppress the temperature sensitivity of a dnaZ polymerization mutant, indicating in vivo interaction of the products of these genes. The suppressor allele of dnaA [designated dnaA(SUZ, Cs)] could not be introduced, even at the permissive temperature, by transduction into temperature-sensitive (Ts) dnaC or dnaG recipients; it was transduced into dnaB(Ts) and dnaE(Ts) strains but at very low frequency. Recipient cells which were dnaA+ dnaE(Ts) were killed by the incoming dnaA(SUZ, Cs) allele, and it is presumed that combinations of dnaA(SUZ, Cs) with dnaB(Ts), dnaC(Ts), or dnaG(Ts) are lethal also. In one specific case, the lethality required the presence of three alleles: the incoming dnaA suppressor mutation, the resident dnaA+ gene, and the dnaB(Ts) gene. This was shown by the fact that dnaB(Ts) could readily be introduced into a dnaA(SUZ, Cs) dnaB+ recipient. That is, in the absence of dnaA+, the dnaA suppressor and dnaB(Ts) double mutant was stable. One model to explain these results proposes that the dnaA protein functions not only in initiation but also in the replication complex which contains multiple copies of dnaA and other replication factors.

Bacterial Proteins↗

PubMed2005

Overexpression of mitochondrial transcription factor a ameliorates mitochondrial deficiencies and cardiac failure after myocardial infarction.

BACKGROUND: Mitochondrial DNA (mtDNA) copy number is decreased not only in mtDNA-mutation diseases but also in a wide variety of acquired degenerative and ischemic diseases. Mitochondrial transcription factor A (TFAM) is essential for mtDNA transcription and replication. Myocardial mtDNA copy number and TFAM expression both decreased in cardiac failure. However, the functional significance of TFAM has not been established in this disease state. METHODS AND RESULTS: We have now addressed this question by creating transgenic (Tg) mice that overexpress human TFAM gene and examined whether TFAM could protect the heart from mtDNA deficiencies and attenuate left ventricular (LV) remodeling and failure after myocardial infarction (MI) created by ligating the left coronary artery. TFAM overexpression could ameliorate the decrease in mtDNA copy number and mitochondrial complex enzyme activities in post-MI hearts. Survival rate during 4 weeks of MI was significantly higher in Tg-MI than in wild-type (WT) littermates (WT-MI), although infarct size was comparable. LV cavity dilatation and dysfunction were significantly attenuated in Tg-MI. LV end-diastolic pressure was increased in WT-MI, and it was also reduced in Tg-MI. Improvement of LV function in Tg-MI was accompanied by a decrease in myocyte hypertrophy, apoptosis, and interstitial fibrosis as well as oxidative stress in the noninfarcted LV. CONCLUSIONS: Overexpression of TFAM inhibited LV remodeling after MI. TFAM may provide a novel therapeutic strategy of cardiac failure.

Animals↗

PubMed2025

Bayesian classification of OXPHOS deficient skeletal myofibres.

Mitochondria are organelles in most human cells which release the energy required for cells to function. Oxidative phosphorylation (OXPHOS) is a key biochemical process within mitochondria required for energy production and requires a range of proteins and protein complexes. Mitochondria contain multiple copies of their own genome (mtDNA), which codes for some of the proteins and ribonucleic acids required for mitochondrial function and assembly. Pathology arises from genetic defects in mtDNA and can reduce cellular abundance of OXPHOS proteins, affecting mitochondrial function. Due to the continuous turn-over of mtDNA, pathology is random and neighbouring cells can possess different OXPHOS protein abundance. Estimating the proportion of cells where OXPHOS protein abundance is too low to maintain normal function is critical to understanding disease severity and predicting disease progression. Currently, one method to classify single cells as being OXPHOS deficient is prevalent in the literature. The method compares a patient's OXPHOS protein abundance to that of a small number of healthy control subjects. If the patient's cell displays an abundance which differs from the abundance of the controls then it is deemed deficient. However, due to the natural variation between subjects and the low number of control subjects typically available, this method is inflexible and often results in a large proportion of patient cells being misclassified. These misclassifications have significant consequences for the clinical interpretation of these data. We propose a single-cell classification method using a Bayesian hierarchical mixture model, which allows for inter-subject OXPHOS protein abundance variation. The model accurately classifies an example dataset of OXPHOS protein abundances in skeletal muscle fibres (myofibres). When comparing the proposed and existing model classifications to manual classifications performed by experts, the proposed model results in estimates of the proportion of deficient myofibres that are consistent with expert manual classifications.

Oxidative Phosphorylation↗

PubMed2006

Proteomic dissection of DNA polymerization.

DNA polymerases replicate the genome by associating with a range of other proteins that enable rapid, high-fidelity copying of DNA. This complex of proteins and nucleic acids is termed the replisome. Proteins of the replisome must interact with other networks of proteins, such as those involved in DNA repair. Many of the proteins involved in DNA polymerization and the accessory proteins are known, but the array of proteins they interact with, and the spatial and temporal arrangement of these interactions, are current research topics. Mass spectrometry is a technique that can be used to identify the sites of these interactions and to determine the precise stoichiometries of binding partners in a functional complex. A complete understanding of the macromolecular interactions involved in DNA replication and repair may lead to discovery of new targets for antibiotics against bacteria and biomarkers for diagnosis of diseases, such as cancer, in humans.

Animals↗

PubMed1991

Neuropsychological deficits in chronic cocaine abusers.

A basic neuropsychological assessment battery was given to thirty-seven chronic freebase cocaine ("crack") abusers. The following tests were used: Wechsler Memory Scale (Wechsler, 1945), Rey-Osterrieth Complex Figure (Osterrieth, 1944) (copy and immediate reproduction), Verbal Fluency (semantic and phonologic), Boston Naming Test (Goodglass, Kaplan, & Weintrab, 1983), Wisconsin Card Sorting Test (Heaton, 1981) and Digit-symbol from the WISC (Wechsler, 1974). In general, performance was lower than expected according to their age and educational level. Subjects showed significant impairment in short-term verbal memory and attention subtests. Neuropsychological test scores were correlated with lifetime amount of cocaine used, suggesting a direct relationship between cocaine abuse and cognitive impairment. A pattern of cognitive decline is proposed.

Adult↗

PubMed1983

The Chinese hamster cell emetine resistance gene. Analysis of cDNA and genomic sequences encoding ribosomal protein S14.

We used an intersecting pool strategy to recognize chimeric plasmids containing Chinese hamster ribosomal protein cDNAs. The screening procedure involved hybridization-selection of messenger RNAs, cell-free translation of selected mRNAs, and electrophoresis of polypeptide products on one- and two-dimensional polyacrylamide gels. The protocol was designed to recognize ribosomal protein S14 cDNAs specifically. Of 500 chimeric plasmids screened, two possessed cDNAs complementary to S14 mRNA and 18 contained sequences complementary to other ribosomal protein messages. Previously we demonstrated that mutations affecting Chinese hamster ovary cell ribosomal protein S14 are responsible for genetic resistance to the translational inhibitor emetine (emt b). Because emetine-resistant mutant and wild type Chinese hamster ovary cells elaborate mRNAs that encode electrophoretically distinguishable forms of S14 protein, we were able to identify S14 cDNA clones unambiguously. The data described here indicate that: 1) clone pCS14-1 contains most, if not all, of the S14 coding sequence as a cDNA; 2) S14 mRNA is approximately 0.01% of a Chinese hamster cell's polyadenylated messenger RNA; and 3) genomic DNA-encoding ribosomal protein S14 is a low, perhaps single, copy sequence with a complex structure, including several, long intervening sequences.

Animals↗

PubMed1998

Human mitochondrial function during cardiac growth and development.

Little information is presently available concerning mitochondrial respiratory and oxidative phosphorylation function in the normal human heart during growth and development. We investigated the levels of specific mitochondrial enzyme activities and content during cardiac growth and development from the early neonatal period (10-20 days) to adulthood (67 years). Biochemical analysis of enzyme specific activities and content and mitochondrial DNA (mtDNA) copy number was performed with left ventricular tissues derived from 30 control individuals. The levels of cytochrome c oxidase (COX) and complex V specific activity, mtDNA copy number and COX subunit II content remained unchanged in contrast to increased citrate synthase (CS) activity and content. The developmental increase in CS activity paralleled increasing CS polypeptide content, but was neither related to overall increases in mitochondrial number nor coordinately regulated with mitochondrial respiratory enzyme activities. Our findings of unchanged levels of cardiac mitochondrial respiratory enzyme activity during the progression from early childhood to older adult contrasts with the age-specific regulation found with CS, a Krebs cycle mitochondrial enzyme.

Adenosine Triphosphatases↗

PubMed1979

Post-transcriptional control of messenger RNA diversity in frog embryos.

The control of mRNA diversity during frog development has been investigated. Nuclear and messenger RNA from the early neurula and larval stages of Rana pipiens were hybridized in vast excess to labeled single-copy DNA and resistance to S1 nuclease was measured. Mixtures of RNA populations were also hybridized with single-copy DNA as a measurement of sequence overlap. Neurula and larval nuclear RNA hybridize to 11.3% and 12.1% of the single copy DNA. A mixture of both nuclear RNA populations hybridizes to 10.8% of the DNA, indicating a great amount of sequence overlap between the two populations. The mRNA complexity almost doubles during this developmental period from 4.7% of the single-copy DNA complexity at the early neurula to 8.7% at the larval stage. Mixtures of nuclear and messenger RNA were used to hybridize single-copy DNA and the results indicate that mRNA sequences present on neurula polysomes, but not on larval polysomes, are found in larval nuclei. Furthermore, mRNA sequences found on larval polysomes, but not on neurula polysomes, are found in the neurula nuclei. The data indicate that post-transcriptional events appear to play a role in the qualitative control of mRNA diversity during development.

Animals↗

PubMed1999

Genome dynamics of the major histocompatibility complex: insights from genome paralogy.

It has recently become apparent that the human genome contains at least three regions that are paralogous to the major histocompatibility complex (MHC). The number of gene families with copies in the MHC and these paralogous regions is increasing steadily as genome analysis progresses. This review presents the updated listing of the human gene families that constitute the MHC paralogous group. When genes with multiple copies within the MHC, such as class I and class II genes, are counted as single entities, nearly one-third of the genes residing in the HLA complex have paralogous copies in at least one of the three paralogous regions. The review also discusses the long-term genome dynamics of the MHC, taking into account the rapidly accumulating information on the genomic organizations of the MHCs in various model organisms.

Animals↗

PubMed2002

The fate of duplicated major histocompatibility complex class Ia genes in a dodecaploid amphibian, Xenopus ruwenzoriensis.

The dodecaploid anuran amphibian Xenopus ruwenzoriensis represents the only polyploid species of Xenopus in which the full silencing of the extra copies of the major histocompatibility complex (MHC) has not occurred. Xenopus ruwenzoriensis is a recent polyploid that has evolved within one of the two tetraploid groups of Xenopus through allopolyploidization. Family studies of its MHC haplotype suggested a polysomic inheritance of the MHC class I and II genes. Four class Ia bands can be detected per individual in Southern blot analysis and, similarly, four different cDNA sequences are expressed per individual. The Xenopus class Ia sequences we analyzed belong to only one of the old class I lineages and show a homogenization of their alpha3 domain sequences. This homogenization occurred after speciation within the Xenopus ruwenzoriensis species, either due to gene conversion or inter-alleles/loci recombination.A re-evaluation of the polymorphism of class Ia in Xenopus, by looking at the rate of non-synonymous versus synonymous substitutions, suggests that Xenopus MHC class Ia genes are not under strong overdominant selection. This is a rare situation among vertebrates. The observed polymorphism is most likely due to the interlocus genetic exchanges related to the peculiar mode of speciation of the genus.

Alleles↗

PubMed2002

The fate of duplicated major histocompatibility complex class Ia genes in a dodecaploid amphibian, Xenopus ruwenzoriensis.

Alleles↗

PubMed1991

A stochastic model for gene induction.

Expression levels of individual copies of an inducible gene have been presumed to be identical to the averaged level of many copies and to change in a smooth and predictable way according to the concentration of an inducing molecule. However, our recent experiments using a steroid-inducible system showed that the expression levels of individual copies are very heterogeneous and do not necessarily coincide with the averaged expression level of many copies (Ko et al., 1990, EMBO J. 9, 2835-2842). To explain this result, I present a stochastic model for gene induction here and its analysis using computer simulation. Stochasticity in the model is derived from the randomness corresponding to the random timing of molecular collisions and dissociations between transcription factors and a gene copy, since at any instant each copy is thought to be either "switched on" by having a transcription complex bound to it, or "switched off" by not having a transcription complex bound. This model can produce two types of gene induction that depend on the stability of the transcription complex on the regulatory region of the gene. An unstable transcription complex causes a homogeneous level of gene induction among individual copies, while a stable transcription complex causes a heterogeneous level. Since the recent consensus formed by in vitro transcription experiments is that the transcription complex is generally very stable, the latter case (the non-deterministic one) is highly possible. Since typical eukaryotic cells have just two copies for any gene in a single cell, this possibility of heterogeneous gene induction indicates that the phenotypes of individual cells cannot be precisely determined by just environmental signals, such as inducers. This may prompt us to reconsider many problems related to gene induction, including morphogenesis.

Animals↗

PubMed1990

Purification of the multienzyme complex for fatty acid oxidation from Pseudomonas fragi and reconstitution of the fatty acid oxidation system.

The multienzyme complex for fatty acid oxidation was purified from Pseudomonas fragi, which was grown on oleic acid as the sole carbon source. This complex exhibited enoyl-CoA hydratase [EC 4.2.1.17], 3-hydroxyacyl-CoA dehydrogenase [EC 1.1.1.35], 3-oxoacyl-CoA thiolase [EC 2.3.1.16], cis-3,trans-2-enoyl-CoA isomerase [EC 5.3.3.3], and 3-hydroxyacyl-CoA epimerase [EC 5.1.2.3] activities. The molecular weight of the native complex was estimated to be 240,000. Two types of subunits, with molecular weights of 73,000 and 42,000, were identified. The complex was composed of two copies each of the 73,000- and 42,000-Da subunits. The beta-oxidation system was reconstituted in vitro using the multienzyme complex, acyl-CoA synthetase and acyl-CoA oxidase. This reconstituted system completely oxidized saturated fatty acids with acyl chains of from 4 to 18 carbon atoms as well as unsaturated fatty acids having cis double bonds extending from odd-numbered carbon atoms. However, unsaturated fatty acids having cis double bonds extending from even-numbered carbon atoms were not completely oxidized to acetyl-CoA: about 5 mol of acetyl-CoA was produced from 1 mol of linoleic or alpha-linolenic acid, and about 2 mol of acetyl-CoA from 1 mol of gamma-linolenic acid. These results suggested that the 3-hydroxyacyl-CoA epimerase in the complex was not operative. When the epimerase was by-passed by the addition of 2,4-dienoyl-CoA reductase to the reconstituted system, unsaturated fatty acids with cis double bonds extending from even-numbered carbon atoms were also completely degraded to acetyl-CoA.

Animals↗

PubMed2006

Characterization and phylogenetic analysis of a cnidarian LMP X-like cDNA.

Proteasomes are multisubunit protease complexes which are partly responsible for metabolism of intracellular, ubiquitinylated proteins. Vertebrates have adapted a second and specialized structure responsible for the generation of peptides presented to the adaptive immune system and is thus, commonly referred to as the immunoproteasome. This complex is assembled from paralogous copies of subunits belonging to the constitutive, housekeeping proteasome. The immunoproteasome is more efficient in the generation of peptides for display on major histocompatibility complex (MHC) molecules. Important components of this complex are the paralogous members, LMP X and 7; where the latter replaces the former in the assembly of the immunoproteasome of vertebrates. In this report, we describe an LMP X-like cDNA from an endosymbiont-free gorgonian coral, Swiftia exserta. Cnidarians predate the phylogenetic divergence of protostomes and deuterostomes (P-D split), and are becoming an essential model for our comprehension of immune system evolution. Phylogenetic analyses of available sequences indicates that invertebrate LMP X-like sequences are outgroups to vertebrate LMP X and LMP 7, and is in agreement with previous observations that the duplication event giving rise to the two rapidly diverging lineages of proteasomal subunits occurred before jawed fished divergence.

Amino Acid Sequence↗

PubMed1983

Biosynthesis of the ubiquinol-cytochrome c reductase complex in yeast. Discoordinate synthesis of the 11-kd subunit in response to increased gene copy number.

In wild-type yeast cells, steady-state concentrations of subunits of the ubiquinol-cytochrome c reductase complex (complex III) and the levels of their translatable mRNAs change coordinately in response to the need for mitochondrial function. Despite this, re-introduction of the cloned gene for one of the subunits (11 kd) into cells by transformation with a free-replicating plasmid results in the discoordinate synthesis of this subunit only, without effects on either the synthesis or degradation of the other subunits. The overproduced subunit is associated with the mitochondrial fraction, yet does not interfere with mitochondrial function, as judged by the growth of transformed cells on nonfermentable media. Quantitative analysis of both mRNA and protein levels suggests that both translational controls and elevated turnover of excess protein contribute to a partial compensation for the effects of increased gene dosage in transformed cells. These contain approximately 30 copies of the cloned gene and 15-30 times the normal level of its mRNA. Nevertheless, synthesis of the 11-kd protein is only 6- to 8-fold higher than normal, and steady-state levels are increased only 5- to 10-fold. These findings imply that synthesis of the various subunits of complex III is not tightly coupled and that for the 11-kd subunit at least, the level of mRNA is likely to be the most important means of regulating protein level. Fine-tuning may be additionally achieved by control of translation and degradation of excess protein which is not assembled in the complex.

Electron Transport Complex III↗

PubMed1995

Reliability of the Rey-Osterrieth Complex Figure in use with memory-impaired patients.

Rater reliability was evaluated for the system most widely used to assess copy and recall of the Rey Complex Figure: the Osterrieth (1944) 18-item scoring system. The study sample consisted of 95 subjects (49 males, 46 females), most of whom were elderly individuals (M = 59.83, SD = 15.21 years) suffering from memory impairment. Four raters rated copy and delayed-recall protocols, and three raters re-rated the protocols after an interval of 3 months. Results revealed excellent inter- and intra-rater reliability coefficients (.85-.97) for total scores. However, reliabilities for the 18 individual items ranged from poor (.14) to excellent (.96). Differences in both reliability and level of subject performance were observed as a function of item and conditions of copy versus recall. It is concluded that the Osterrieth scoring system supports excellent reliability in use with memory-impaired patients using total scores. Nevertheless, individual-item reliability would benefit from enhancement, for example, via amplified delineation of relevant decision criteria.

Adult↗

PubMed2002

Imaging of procollagen transport reveals COPI-dependent cargo sorting during ER-to-Golgi transport in mammalian cells.

We have examined the ER-to-Golgi transport of procollagen, which, when assembled in the lumen of the ER, is thought to be physically too large to fit in classically described 60-80 nm COPI- and COPII-coated transport vesicles. We found that procollagen exits the ER via COPII- coated ER exit sites and is transported to the Golgi along microtubules in defined transport complexes. These procollagen-containing transport complexes are, however, distinct from those containing other cargo proteins like ERGIC-53 and ts-045-G. Furthermore, they do not label for the COPI coat complex in contrast to those containing ts-045-G. Inhibition of COPII or COPI function before addition of ascorbate, which is required for the folding of procollagen, inhibits export of procollagen from the ER. Inactivation of COPI coat function after addition of ascorbate results in the localisation of procollagen to transport complexes that now also contain ERGIC-53 and are inhibited in their transport to the Golgi complex. These data reveal the existence of an early COPI-dependent, pre-Golgi cargo sorting step in mammalian cells.

Animals↗