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Nuclear Genome (nuclear + genome)

Distribution by Scientific Domains

Life Sciences	82%
Medical Sciences	14%

Distribution within Life Sciences

Plant Science	17%
Microbiology & Virology	8%

Selected Abstracts

CYTO-NUCLEAR EPISTASIS: TWO-LOCUS RANDOM GENETIC DRIFT IN HERMAPHRODITIC AND DIOECIOUS SPECIES

EVOLUTION, Issue 4 2006
Michael J. Wade
Abstract We report the findings of our theoretical investigation of the effect of random genetic drift on the covariance of identity-by-descent (ibd) of nuclear and cytoplasmic genes. The covariance in ibd measures of the degree to which cyto-nuclear gene combinations are heritable, that is, transmitted together from parents to offspring. We show how the mating system affects the covariance of ibd, a potentially important aspect of host-pathogen or host-symbiont coevolution. The magnitude of this covariance influences the degree to which the evolution of apparently neutral cytoplasmic genes, often used in molecular phylogenetics, might be influenced by selection acting on unlinked nuclear genes. To the extent that cyto-nuclear gene combinations are inherited together, genomic conflict is mitigated and intergenomic transfer it facilitated, because genes in both organelle and nuclear genomes share the same evolutionary fate. The covariance of ibd also affects the rate at which cyto-nuclear epistatic variance is converted to additive variance necessary for a response to selection. We find that conversion is biased in species with separate sexes, so that the increment of additive variance added to the nuclear genome exceeds that added to the cytoplasmic genome. As a result, the host might have an adaptive advantage in a coevolutionary arms race with vertically (maternally) transmitted pathogens. Similarly, the nuclear genome could be a source of compensatory mutations for its organellar genomes, as occurs in cytoplasmic male sterility in some plant species. We also discuss the possibility that adaptive cytoplasmic elements, such as favorable mitochondrial mutations or endosymbionts (e.g., Wolbachia), have the potential to release heritable nuclear variation as they sweep through a host population, supporting the view that cytoplasmic introgression plays an important role in adaptation and speciation. [source]

Development of microsatellite markers for Pythium helicoides

FEMS MICROBIOLOGY LETTERS, Issue 1 2009
Yin-Ling
Abstract A strategy combining dual-suppression PCR and thermal asymmetric interlaced PCR was used to determine sequences flanking microsatellite regions in Pythium helicoides. The primer pairs were designed to amplify loci containing (AC)n, (GA)n, (AGC)n, (CAC)n(CAA)n, (TCA)n and (CTTT)n repeats from the P. helicoides nuclear genome. The PCR products of each primer pair, amplified from three representative isolates collected from different hosts and locations, were cloned and sequenced. Different degrees of polymorphism were detected among these microsatellite markers. The numbers of alleles were 6, 2, 4, 11, 4 and 4 in YL-AC, YL-AGC, YL-CAA, YL-CTTT, YL-GA and YL-TCA, respectively. Allele analysis of 30 P. helicoides isolates showed length polymorphisms in all loci, except for YL-AC, using capillary electrophoresis. Thus, we have developed a simple method for designing PCR primers to amplify microsatellite markers from P. helicoides. [source]

Mitochondrial preprotein translocases as dynamic molecular machines

FEMS YEAST RESEARCH, Issue 6 2006
Martin Van Der Laan
Abstract Proteomic studies have demonstrated that yeast mitochondria contain roughly 1000 different proteins. Only eight of these proteins are encoded by the mitochondrial genome and are synthesized on mitochondrial ribosomes. The remaining 99% of mitochondrial precursors are encoded within the nuclear genome and after their synthesis on cytosolic ribosomes must be imported into the organelle. Targeting of these proteins to mitochondria and their import into one of the four mitochondrial subcompartments , outer membrane, intermembrane space (IMS), inner membrane and matrix , requires various membrane-embedded protein translocases, as well as numerous chaperones and cochaperones in the aqueous compartments. During the last years, several novel protein components involved in the import and assembly of mitochondrial proteins have been identified. The picture that emerges from these exciting new findings is that of highly dynamic import machineries, rather than of regulated, but static protein complexes. In this review, we will give an overview on the recent progress in our understanding of mitochondrial protein import. We will focus on the presequence translocase of the inner mitochondrial membrane, the TIM23 complex and the presequence translocase-associated motor, the PAM complex. These two molecular machineries mediate the multistep import of preproteins with cleavable N-terminal signal sequences into the matrix or inner membrane of mitochondria. [source]

Protein Import Into Mitochondria

IUBMB LIFE, Issue 3-5 2001
Stefan A. Paschen
Abstract Most mitochondrial proteins are encoded by the nuclear genome and thus have to be imported into mitochondria from the cytosol. Protein translocation across and into the mitochondrial membranes is a multistep process facilitated by the coordinated action of at least four specialized translocation systems in the outer and inner membranes of mitochondria. The outer membrane contains one general translocase, the TOM complex, whereas three distinct translocases are located in the inner membrane, which facilitates translocation of different classes of preproteins. The TIM23 complex mediates import of matrix-targeted preproteins with N -terminal presequences, whereas hydrophobic preproteins with internal targeting signals are inserted into the inner membrane via the TIM22 complex. The OXA translocase mediates the insertion of preproteins from the matrix space into the inner membrane. This review focuses on the structural organization and function of the import machinery of the model organisms of Saccharomyces cerevisiae and Neurospora crassa . In addition, the molecular basis of a new human mitochondrial disorder is discussed, the Mohr-Tranebjaerg syndrome. This is the first known disease, which is caused by an impaired mitochondrial protein import machinery leading to progressive neurodegeneration. [source]

Distribution of nuclear mitochondrial DNA in cattle nuclear genome

JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 5 2007
Y. Liu
Summary The nuclear mitochondrial pseudogenes (numts), originated from mtDNA insertions into the nuclear genome, have been detected to exist in many species. However, the distribution of numts in cattle nuclear genome yet has not been fully reported. By referring to the whole cattle mtDNA sequence and to the recently released cattle nuclear genome by Human Genome Sequencing Center (HGSC), 303 numts were identified by BLAST with 55 numts unmapped to cattle nuclear genome. Further analysis found that the size of the numts ranges from 37 to 1932 bp, and the homologous identity between numts and their corresponding mtDNA fragments varies from 73 to 98%. Furthermore, the identified cattle numts cover nearly all the mitochondrial genes including mtDNA control region, distributing over all the chromosomes with the exception of the chromosome 23 and Y chromosome (in the latter the sequence data are not available). In the discovered numts, 29 relatively complete mitochondrial genes, which were distributed in 72 numts, were detected. Undoubtedly, this research would provide some valuable information for successive research related to mitochondrial genes and the evolution of cattle. [source]

Fish mitochondrial genomics: sequence, inheritance and functional variation

JOURNAL OF FISH BIOLOGY, Issue 2 2008
K. H. Brown
Mitochondrial genomic research currently primarily focuses on the analysis and understanding of how mitochondrial mutations produce detrimental phenotypes in humans. Reasons for this focus on negative impacts include the large number of human diseases that are known to result from specific mitochondrial genomes, and the long held belief that mitochondria change only through the accumulation of mutations due to its clonal, maternal inheritance. Recent studies are beginning to challenge these preconceptions and have shown that mitochondrial genomes can have significant positive impacts. Although the number of studies using fishes as models in mitochondrial research is limited, many fish model species provide excellent opportunity for furthering the understanding of mitochondrial genomes, their interactions with the nuclear genome, the potential for understanding the mechanisms of how functional variation effects organisms and how selection for positive functional variation effects population variation. [source]

PHYLOGENY OF AULACOSEIRA (BACILLARIOPHYTA) BASED ON MOLECULES AND MORPHOLOGY,

JOURNAL OF PHYCOLOGY, Issue 4 2004
Stacy M. Edgar
The phylogeny of 67 populations representing 45 species of Aulacoseira Thwaites was estimated by maximum parsimony methods using a combination of nucleotide sequence data and qualitative and quantitative morphological characteristics of the silica cell wall gathered primarily from original observation by LM and SEM. A new type of character using continuous quantitative variables that describe the ontogenetic-allometric trajectories of cell wall characteristics over the life cycle (size range) of diatoms is introduced. In addition to the 45 Aulacoseira species, the phylogeny also incorporated one Miosira Krammer, Lange-Bertalot, and Schiller species and two outgroup species (Melosira varians Agardh and Stephanopyxis nipponica Gran & Yendo). Fifteen species, represented by 24 populations, also contained molecular data from the nuclear genome (18S rDNA), and 11 of these species (18 populations) contained data from the chloroplast genome (rbcL) as well, which were sequenced or downloaded from GenBank. The phylogeny of Aulacoseira is composed of five major clades: 1) an A. crenulata (Ehrenburg) Thwaites and A. italica (Ehrenburg) Simonsen clade, which is the most basal; 2) an A. granulata (Ehrenburg) Simonsen complex clade; 3) an A. ambigua (Grunow) Simonsen clade; 4) an A. subarctica (O. Müller) Haworth and A. distans (Ehrenburg) Simonsen clade; and 5) an A. islandica (O. Müller) Simonsen clade that also contained endemic species from Lake Baikal, Siberia and many extinct Aulacoseira taxa. Monophyly of Aulacoseira can only be achieved if Miosira is no longer given separate generic status. [source]

EXCHANGES OF INFORMATION, ENERGY & MATERIALS IN SYMBIOSES

JOURNAL OF PHYCOLOGY, Issue 2000
J.A. Raven
Symbiosis is important in the cell and environmental biology of algae. Some examples involving the author and numerous collaborators include: 1) chloroplasts of eukaryotic algae arose from endosymbioses. Plastids are incapable of independent existence; most of the genes of the cyanobacterial photobiont have been lost, and the majority of the rest have been transferred to the nuclear genome. Some of the genes retained by the plastid are those whose transcription is controlled by environmental cues transduced by the organelle. The general trend is for organelle genes to be transferred to the nucleus, escaping plastid redox activities generating mutagenic free radicals; 2) symbioses involving potentially free-living photobionts include marine lichens and sponges with cyanobacterial symbionts. For the lichen, Lichina, inorganic carbon acquisition appears to involve inorganic carbon transport by the mycobiont, and for the sponge, Cymbastella, the flagellar activity of the sponge is probably important for inorganic carbon supply to the photobiont; 3) the Australasian fucalean, Notheia, is an obligate epiphyte on the fucaleans, Hormosira and Xiphophora; the four species involved all contain the hexitol, altritol. Notheia anomala is known to be phyletically-distant from the other five altritol-containing species. Can Notheia synthesize altritol, or is it obtained from the phorophyte?; 4) Sacoglossan gastropods retain kleptoplastids (not strictly symbionts) from ulvophycean (or rhodophycean) marine algae. Analyses of the natural abundance of stable carbon isotopes suggest significant contribution of kleptoplastid photosynthesis to the carbon and energy budget of the mollusks. [source]

Rangewide population genetic structure of the African malaria vector Anopheles funestus

MOLECULAR ECOLOGY, Issue 14 2005
A. P. MICHEL
Abstract Anopheles funestus is a primary vector of malaria in Africa south of the Sahara. We assessed its rangewide population genetic structure based on samples from 11 countries, using 10 physically mapped microsatellite loci, two per autosome arm and the X (N = 548), and 834 bp of the mitochondrial ND5 gene (N = 470). On the basis of microsatellite allele frequencies, we found three subdivisions: eastern (coastal Tanzania, Malawi, Mozambique and Madagascar), western (Burkina Faso, Mali, Nigeria and western Kenya), and central (Gabon, coastal Angola). A. funestus from the southwest of Uganda had affinities to all three subdivisions. Mitochondrial DNA (mtDNA) corroborated this structure, although mtDNA gene trees showed less resolution. The eastern subdivision had significantly lower diversity, similar to the pattern found in the codistributed malaria vector Anopheles gambiae. This suggests that both species have responded to common geographic and/or climatic constraints. The western division showed signatures of population expansion encompassing Kenya west of the Rift Valley through Burkina Faso and Mali. This pattern also bears similarity to A. gambiae, and may reflect a common response to expanding human populations following the development of agriculture. Due to the presumed recent population expansion, the correlation between genetic and geographic distance was weak. Mitochondrial DNA revealed further cryptic subdivision in A. funestus, not detected in the nuclear genome. Mozambique and Madagascar samples contained two mtDNA lineages, designated clade I and clade II, that were separated by two fixed differences and an average of 2% divergence, which implies that they have evolved independently for ,1 million years. Clade I was found in all 11 locations, whereas clade II was sampled only on Madagascar and Mozambique. We suggest that the latter clade may represent mtDNA capture by A. funestus, resulting from historical gene flow either among previously isolated and divergent populations or with a related species. [source]

Huge populations and old species of Costa Rican and Panamanian dirt frogs inferred from mitochondrial and nuclear gene sequences

MOLECULAR ECOLOGY, Issue 10 2003
A. J. Crawford
Abstract Molecular genetic data were used to investigate population sizes and ages of Eleutherodactylus (Anura: Leptodactylidae), a species-rich group of small leaf-litter frogs endemic to Central America. Population genetic structure and divergence was investigated for four closely related species surveyed across nine localities in Costa Rica and Panama. DNA sequence data were collected from a mitochondrial gene (ND2) and a nuclear gene (c- myc). Phylogenetic analyses yielded concordant results between loci, with reciprocal monophyly of mitochondrial DNA haplotypes for all species and of c- myc haplotypes for three of the four species. Estimates of genetic differentiation among populations (FST) based upon mitochondrial data were always higher than nuclear-based FST estimates, even after correcting for the expected fourfold lower effective population size (Ne) of the mitochondrial genome. Comparing within-population variation and the relative mutation rates of the two genes revealed that the Ne of the mitochondrial genome was 15-fold lower than the estimate of the nuclear genome based on c- myc. Nuclear FST estimates were , 0 for the most proximal pairs of populations, but ranged from 0.5 to 1.0 for all other pairs, even within the same nominal species. The nuclear locus yielded estimates of Ne within localities on the order of 105. This value is two to three orders of magnitude larger than any previous Ne estimate from frogs, but is nonetheless consistent with published demographic data. Applying a molecular clock model suggested that morphologically indistinguishable populations within one species may be 107 years old. These results demonstrate that even a geologically young and dynamic region of the tropics can support very old lineages that harbour great levels of genetic diversity within populations. The association of high nucleotide diversity within populations, large divergence between populations, and high species diversity is also discussed in light of neutral community models. [source]

Microsatellite variation within and among North American lineages of Phragmites australis

MOLECULAR ECOLOGY, Issue 7 2003
K. Saltonstall
Abstract Over the past century, the spread of the common reed (Phragmites australis) has had a dramatic impact on wetland communities across North America. Although native populations of Phragmites persist, introduced invasive populations have dominated many sites and it is not clear if the two types can interbreed. This study compares patterns of differentiation in 10 microsatellite loci among North American and European Phragmites individuals with results obtained from sequencing of noncoding chloroplast DNA. Three population lineages (native, introduced and Gulf Coast) were previously identified in North America from chloroplast DNA and similar structuring was found in the nuclear genome. Each lineage was distinguished by unique alleles and allele combinations and the introduced lineage was closely related to its hypothesized source population in Europe. Size homoplasy and diagnostic base substitutions distinguishing lineages were evident at several loci, further emphasizing that native, introduced and Gulf Coast North American Phragmites lineages are genetically distinct. Gene flow between lineages was low and invasive introduced populations do not represent a hybrid population type. [source]

Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects

MOLECULAR ECOLOGY, Issue 3 2003
De-Xing Zhang
Abstract Population-genetic studies have been remarkably productive and successful in the last decade following the invention of PCR technology and the introduction of mitochondrial and microsatellite DNA markers. While mitochondrial DNA has proven powerful for genealogical and evolutionary studies of animal populations, and microsatellite sequences are the most revealing DNA markers available so far for inferring population structure and dynamics, they both have important and unavoidable limitations. To obtain a fuller picture of the history and evolutionary potential of populations, genealogical data from nuclear loci are essential, and the inclusion of other nuclear markers, i.e. single copy nuclear polymorphic (scnp) sequences, is clearly needed. Four major uncertainties for nuclear DNA analyses of populations have been facing us, i.e. the availability of scnp markers for carrying out such analysis, technical laboratory hurdles for resolving haplotypes, difficulty in data analysis because of recombination, low divergence levels and intraspecific multifurcation evolution, and the utility of scnp markers for addressing population-genetic questions. In this review, we discuss the availability of highly polymorphic single copy DNA in the nuclear genome, describe patterns and rate of evolution of nuclear sequences, summarize past empirical and theoretical efforts to recover and analyse data from scnp markers, and examine the difficulties, challenges and opportunities faced in such studies. We show that although challenges still exist, the above-mentioned obstacles are now being removed. Recent advances in technology and increases in statistical power provide the prospect of nuclear DNA analyses becoming routine practice, allowing allele-discriminating characterization of scnp loci and microsatellite loci. This certainly will increase our ability to address more complex questions, and thereby the sophistication of genetic analyses of populations. [source]

Haploid chromosomes in molecular ecology: lessons from the human Y

MOLECULAR ECOLOGY, Issue 7 2001
Matthew E. Hurles
Abstract We review the potential use of haploid chromosomes in molecular ecology, using recent work on the human Y chromosome as a paradigm. Chromosomal sex-determination systems, and hence constitutively haploid chromosomes, which escape from recombination over much of their length, have evolved multiple times in the animal kingdom. In mammals, where males are the heterogametic sex, the patrilineal Y chromosome represents a paternal counterpart to mitochondrial DNA. Work on the human Y chromosome has shown it to contain the same range of polymorphic markers as the rest of the nuclear genome and these have rendered it the most informative haplotypic system in the human genome. Examples from research on the human Y chromosome are used to illustrate the common interests of anthropologists and ecologists in investigating the genetic impact of sex-specific behaviours and dispersals, as well as patterns of global diversity. We present some methodologies for extracting information from these uniquely informative yet under-utilized loci. [source]

Discrepancies in population differentiation at microsatellites, mitochondrial DNA and plumage colour in the pied flycatcher , inferring evolutionary processes

MOLECULAR ECOLOGY, Issue 8 2000
J. Haavie
Abstract Genetic differentiation between three populations of the pied flycatcher Ficedula hypoleuca (Norway, Czech Republic and Spain, respectively) was investigated at microsatellite loci and mitochondrial DNA (mtDNA) sequences and compared with the pattern of differentiation of male plumage colour. The Czech population lives sympatrically with the closely related collared flycatcher (F. albicollis) whereas the other two are allopatric. Allopatric populations are on average more conspicuously coloured than sympatric ones, a pattern that has been explained by sexual selection for conspicuous colour in allopatry and a character displacement on breeding plumage colour in sympatry that reduces the rate of hybridization with the collared flycatcher. The Czech population was genetically indistinguishable from the Norwegian population at microsatellite loci and mtDNA sequences. Recent isolation and/or gene flow may explain the lack of genetic differentiation. Accordingly, different selection on plumage colour in the two populations is either sufficiently strong so that gene flow has little impact on the pattern of colour variation, or differentiation of plumage colour occurred so recently that the (presumably) neutral, fast evolving markers employed here are unable to reflect the differentiation. Genetically, the Spanish population was significantly differentiated from the other populations, but the divergence was much more pronounced at mtDNA compared to microsatellites. This may reflect increased rate of differentiation by genetic drift at the mitochondrial, compared with the nuclear genome, caused by the smaller effective population size of the former genome. In accordance with this interpretation, a genetic pattern consistent with effects of small population size in the Spanish population (genetic drift and inbreeding) were also apparent at the microsatellites, namely reduced allelic diversity and heterozygous deficiency. [source]

The identification of circular extrachromosomal DNA in the nuclear genome of Trypanosoma brucei

MOLECULAR MICROBIOLOGY, Issue 2 2003
N. S. Alsford
Summary Nuclear extrachromosomal DNA elements have been identified in several kinetoplastids such as Leishmania and Trypanosoma cruzi, but never in Trypanosoma brucei. They can occur naturally or arise spontaneously as the result of sublethal drug exposure of parasites. In most cases, they are represented as circular elements and are mitotically unstable. In this study we describe the presence of circular DNA in the nucleus of Trypanosoma brucei. This novel type of DNA was termed NR-element (NlaIII repeat element). In contrast to drug-induced episomes in other kinetoplastids, the T. brucei extrachromosomal NR-element is not generated by drug selection. Furthermore, the element is stable during mitosis over many generations. Restriction analysis of tagged NR-element DNA, unusual migration patterns during pulsed field gel electrophoresis (PFGE) and CsCl/ethidium bromide equilibrium centrifugation demonstrates that the NR-element represents circular DNA. Whereas it has been found in all field isolates of the parasites we analysed, it is not detectable in some laboratory strains notably the genome reference strain 927. The DNA sequence of this element is related to a 29 bp repeat present in the subtelomeric region of VSG-bearing chromosomes of T. brucei. It has been suggested that this subtelomeric region is part of a transition zone on chromosomes separating the relatively stable telomeric repeats from the recombinationaly active region downstream of VSG genes. Therefore, we discuss a functional connection between the occurrence of this circular DNA and subtelomeric recombination events in T. brucei. [source]

Approaches to achieve high-level heterologous protein production in plants

PLANT BIOTECHNOLOGY JOURNAL, Issue 1 2007
Stephen J. Streatfield
Summary Plants offer an alternative to microbial fermentation and animal cell cultures for the production of recombinant proteins. For protein pharmaceuticals, plant systems are inherently safer than native and even recombinant animal sources. In addition, post-translational modifications, such as glycosylation, which cannot be achieved with bacterial fermentation, can be accomplished using plants. The main advantage foreseen for plant systems is reduced production costs. Plants should have a particular advantage for proteins produced in bulk, such as industrial enzymes, for which product pricing is low. In addition, edible plant tissues are well suited to the expression of vaccine antigens and pharmaceuticals for oral delivery. Three approaches have been followed to express recombinant proteins in plants: expression from the plant nuclear genome; expression from the plastid genome; and expression from plant tissues carrying recombinant plant viral sequences. The most important factor in moving plant-produced heterologous proteins from developmental research to commercial products is to ensure competitive production costs, and the best way to achieve this is to boost expression. Thus, considerable research effort has been made to increase the amount of recombinant protein produced in plants. This research includes molecular technologies to increase replication, to boost transcription, to direct transcription in tissues suited for protein accumulation, to stabilize transcripts, to optimize translation, to target proteins to subcellular locations optimal for their accumulation, and to engineer proteins to stabilize them. Other methods include plant breeding to increase transgene copy number and to utilize germplasm suited to protein accumulation. Large-scale commercialization of plant-produced recombinant proteins will require a combination of these technologies. [source]

The Arabidopsis thaliana ATP-binding cassette proteins: an emerging superfamily

PLANT CELL & ENVIRONMENT, Issue 5 2000
T. G. E. Davies
ABSTRACT Solute transport systems are one of the major ways in which organisms interact with their environment. Typically, transport is catalysed by integral membrane proteins, of which one of the largest groups is the ATP-binding cassette (ABC) proteins. On the basis of sequence similarities, a large family of ABC proteins has been identified in Arabidopsis. A total of 60 open reading frames (ORFs) encoding ABC proteins were identified by BLAST homology searching of the nuclear genome. These 60 putative proteins include 89 ABC domains. Based on the assignment of transmembrane domains (TMDs), at least 49 of the 60 proteins identified are ABC transporters. Of these 49 proteins, 28 are full-length ABC transporters (eight of which have been described previously), and 21 are uncharacterized half-transporters. Three of the remaining proteins identified appear to be soluble, lacking identifiable TMDs, and most likely have non-transport functions. The eight other ORFs have homology to the nucleotide-binding and transmembrane components of multi-subunit permeases. The majority of ABC proteins found in Arabidopsis can, on the basis of sequence homology, be assigned to subfamilies equivalent to those found in the yeast genome. This assignment of the Arabidopsis ABC proteins into easily recognizable subfamilies (with distinguishable subclusters) is an important first step in the elucidation of their functional role in higher plants. [source]

Transcription of plastid genes is modulated by two nuclear-encoded , subunits of plastid RNA polymerase in the moss Physcomitrella patens

THE PLANT JOURNAL, Issue 4 2007
Yukihiro Kabeya
Summary In general, in higher plants, the core subunits of a bacterial-type plastid-encoded RNA polymerase (PEP) are encoded by the plastid rpoA, rpoB, rpoC1 and rpoC2 genes. However, an rpoA gene is absent from the moss Physcomitrella patens plastid genome, although the PpRpoA gene (renamed PpRpoA1) nuclear counterpart is present in the nuclear genome. In this study, we identified and characterized a second gene encoding the plastid-targeting , subunit (PpRpoA2). PpRpoA2 comprised 525 amino acids and showed 59% amino acid identity with PpRpoA1. Two PpRpoA proteins were present in the PEP active fractions separated from the moss chloroplast lysate, confirming that both proteins are , subunits of PEP. Northern blot analysis showed that PpRpoA2 was highly expressed in the light, but not in the dark, whereas PpRpoA1 was constitutively expressed. Disruption of the PpRpoA1 gene resulted in an increase in the PpRpoA2 transcript level, but most plastid gene transcript levels were not significantly altered. This indicates that transcription of most plastid genes depends on PpRpoA2-PEP rather than on PpRpoA1-PEP. In contrast, the transcript levels of petN, psbZ and ycf3 were altered in the PpRpoA1 gene disruptant, suggesting that these are PpRpoA1-PEP-dependent genes. These observations suggest that plastid genes are differentially transcribed by distinct PEP enzymes with either PpRpoA1 or PpRpoA2. [source]

The role of mitochondria in ageing and carcinogenesis

CLINICAL & EXPERIMENTAL DERMATOLOGY, Issue 4 2006
M. A. Birch-Machin
Summary Mitochondria can perform multiple cellular functions including energy production, cell proliferation and apoptosis. These organelles contain their own genetic material, mitochondrial DNA (mtDNA), which is maternally inherited. Although much smaller than the nuclear genome, mtDNA is equally important, as it has been hypothesized to play a crucial role in ageing and carcinogenesis. This is partly due to the fact that mitochondria represent the major site for the generation of cellular oxidative stress and play a key role in mediating programmed cell death (apoptosis). Damage to mtDNA is therefore an important contributor to human ageing, cancer and neurodegenerative diseases. The most relevant footprints of mtDNA damage are point mutations of single bases, or deletions of the 16.5-kb mitochondrial genome. This review will focus on the key roles of mitochondrial function and mtDNA in oxidative stress production and as a mediator of apoptosis, and on the use of mtDNA as a biomarker of sun exposure. This will be related to the contribution of mitochondria and mtDNA in the ageing process and cancer, with a specific focus on human skin. In conclusion, it is likely that the interplay between nuclear and mitochondrial genes may hold the final understanding of the mitochondrial role in these disease processes. [source]

CYTONUCLEAR INTERACTIONS CAN FAVOR THE EVOLUTION OF GENOMIC IMPRINTING

EVOLUTION, Issue 5 2009
Jason B. Wolf
Interactions between cytoplasmic (generally organelle) and nuclear genomes may be relatively common and could potentially have major fitness consequences. As in the case of within-genome epistasis, this cytonuclear epistasis can favor the evolutionary coadaptation of high-fitness combinations of nuclear and cytoplasmic alleles. Because cytoplasmic factors are generally uniparentally inherited, the cytoplasmic genome is inherited along with only one of the nuclear haplotypes, and therefore, coadaptation is expected to evolve through the interaction of these coinherited (usually maternally inherited) genomes. Here I show that, as a result of this coinheritance of the two genomes, cytonuclear epistasis can favor the evolution of genomic imprinting such that, when the cytoplasmic factor is maternally inherited, selection favors maternal expression of the nuclear locus and when the factor is paternally inherited selection favors paternal expression. Genomic imprinting evolves in this model because it leads to a pattern of gene expression in the nuclear haplotype that is coadapted with (i.e., adaptively coordinated with) gene expression in the coinherited cytoplasmic genome. [source]

INTERPOPULATION HYBRID BREAKDOWN MAPS TO THE MITOCHONDRIAL GENOME

EVOLUTION, Issue 3 2008
Christopher K. Ellison
Hybrid breakdown, or outbreeding depression, is the loss of fitness observed in crosses between genetically divergent populations. The role of maternally inherited mitochondrial genomes in hybrid breakdown has not been widely examined. Using laboratory crosses of the marine copepod Tigriopus californicus, we report that the low fitness of F3 hybrids is completely restored in the offspring of maternal backcrosses, where parental mitochondrial and nuclear genomic combinations are reassembled. Paternal backcrosses, which result in mismatched mitochondrial and nuclear genomes, fail to restore hybrid fitness. These results suggest that fitness loss in T. californicus hybrids is completely attributable to nuclear,mitochondrial genomic interactions. Analyses of ATP synthetic capacity in isolated mitochondria from hybrid and backcross animals found that reduced ATP synthesis in hybrids was also largely restored in backcrosses, again with maternal backcrosses outperforming paternal backcrosses. The strong fitness consequences of nuclear,mitochondrial interactions have important, and often overlooked, implications for evolutionary and conservation biology. [source]

CYTO-NUCLEAR EPISTASIS: TWO-LOCUS RANDOM GENETIC DRIFT IN HERMAPHRODITIC AND DIOECIOUS SPECIES

The role of mitochondria in inherited neurodegenerative diseases

JOURNAL OF NEUROCHEMISTRY, Issue 6 2006
Jennifer Q. Kwong
Abstract In the past decade, the genetic causes underlying familial forms of many neurodegenerative disorders, such as Huntington's disease, Parkinson's disease, Alzheimer's disease, amyotrophic lateral sclerosis, Friedreich ataxia, hereditary spastic paraplegia, dominant optic atrophy, Charcot-Marie-Tooth type 2A, neuropathy ataxia and retinitis pigmentosa, and Leber's hereditary optic atrophy have been elucidated. However, the common pathogenic mechanisms of neuronal death are still largely unknown. Recently, mitochondrial dysfunction has emerged as a potential ,lowest common denominator' linking these disorders. In this review, we discuss the body of evidence supporting the role of mitochondria in the pathogenesis of hereditary neurodegenerative diseases. We summarize the principal features of genetic diseases caused by abnormalities of mitochondrial proteins encoded by the mitochondrial or the nuclear genomes. We then address genetic diseases where mutant proteins are localized in multiple cell compartments, including mitochondria and where mitochondrial defects are likely to be directly caused by the mutant proteins. Finally, we describe examples of neurodegenerative disorders where mitochondrial dysfunction may be ,secondary' and probably concomitant with degenerative events in other cell organelles, but may still play an important role in the neuronal decay. Understanding the contribution of mitochondrial dysfunction to neurodegeneration and its pathophysiological basis will significantly impact our ability to develop more effective therapies for neurodegenerative diseases. [source]

Conserving the evolutionary potential of California valley oak (Quercus lobata Née): a multivariate genetic approach to conservation planning

MOLECULAR ECOLOGY, Issue 1 2008
DELPHINE GRIVET
Abstract California valley oak (Quercus lobata Née) is a seriously threatened endemic oak species in California and a keystone species for foothill oak ecosystems. Urban and agricultural development affects a significant fraction of the species' range and predicted climate change is likely to dislocate many current populations. Here, we explore spatial patterns of multivariate genotypes and genetic diversity throughout the range of valley oak to determine whether ongoing and future patterns of habitat loss could threaten the evolutionary potential of the species by eradicating populations of distinctive genetic composition. This manuscript will address three specific questions: (i) What is the spatial genetic structure of the chloroplast and nuclear genetic markers? (ii) What are the geographical trends in the distribution of chloroplast and nuclear genotypes? (iii) Is there any part of the species' range where allelic diversity in either the chloroplast or nuclear genomes is particularly high? We analysed six chloroplast and seven nuclear microsatellite genetic markers of individuals widespread across the valley oak range. We then used a multivariate approach correlating genetic markers and geographical variables through a canonical trend surface analysis, followed by GIS mapping of the significant axes. We visualized population allelic richness spatially with GIS tools to identify regions of high diversity. Our findings, based on the distribution of multivariate genotypes and allelic richness, identify areas with distinctive histories and genetic composition that should be given priority in reserve network design, especially because these areas also overlap with landscape change and little degree of protection. Thus, without a careful preservation plan, valuable evolutionary information will be lost for valley oak. [source]

OsNOA1/RIF1 is a functional homolog of AtNOA1/RIF1: implication for a highly conserved plant cGTPase essential for chloroplast function

NEW PHYTOLOGIST, Issue 1 2010
Hongjia Liu
Summary ,The bacterial protein YqeH is a circularly permuted GTPase with homologs encoded by plant nuclear genomes. The rice homolog OsNOA1/RIF1 is encoded by the single-copy gene Os02g01440. OsNOA1/RIF1 is expressed in different tissues and is light-inducible. The OsNOA1/RIF1-EYFP fusion protein was targeted to chloroplasts in transgenic Arabidopsis plants. In addition, the rice homolog was able to rescue most of the growth phenotypes in an Arabidopsis rif1 mutant. ,Rice (Oryza sativa) OsNOA1/RIF1 RNAi mutant seedlings were chlorotic with reduced pigment contents and lower photosystem II (PSII) efficiency. However, the expressions of the chloroplast-encoded genes rbcL, atpB, psaA and psbA were not affected. By contrast, reduced abundance of the chloroplast 16S rRNA was observed in the mutant. ,Quantitative iTRAQ-LC-MS/MS proteomics investigations revealed proteome changes in the rice mutant consistent with the expected functional role of OsNOA1/RIF1 in chloroplast translation. The RNAi mutant showed significantly decreased expression levels of chloroplast-encoded proteins as well as nuclear-encoded components of chloroplast enzyme complexes. Conversely, upregulation of some classes of nonchloroplastic proteins, such as glycolytic and phenylpropanoid pathway enzymes, was detected. ,Our work provides independent indications that a highly conserved nuclear-encoded cGTPase of likely prokaryotic origin is essential for proper chloroplast ribosome assembly and/or translation in plants. [source]

Mitochondrial DNA-based analysis of genetic variation and relatedness among Sri Lankan indigenous chickens and the Ceylon junglefowl (Gallus lafayetti)

ANIMAL GENETICS, Issue 1 2009
P. Silva
Summary Indigenous chickens (IC) in developing countries provide a useful resource to detect novel genes in mitochondrial and nuclear genomes. Here, we investigated the level of genetic diversity in IC from five distinct regions of Sri Lanka using a PCR-based resequencing method. In addition, we investigated the relatedness of IC to different species of junglefowls including Ceylon (CJF; Gallus lafayetti), a subspecies that is endemic to Sri Lanka, green (Gallus varius), grey (Gallus sonneratii) and red (Gallus gallus) junglefowls. A total of 140 birds including eight CJF were used to screen the control region of the mitochondrial DNA sequence for single nucleotide polymorphisms (SNPs) and other variants. We detected and validated 44 SNPs, which formed 42 haplotypes and six haplogroups in IC. The SNPs observed in the CJF were distinct and the D-loop appeared to be missing a 62-bp segment found in IC and the red junglefowl. Among the six haplogroups of IC, only one was region-specific. Estimates of haplotype and nucleotide diversities ranged from 0.901 to 0.965 and from 0.011 to 0.013 respectively, and genetic divergence was generally low. Further, variation among individuals within regions accounted for 92% of the total molecular variation among birds. The Sri Lankan IC were more closely related to red and grey junglefowls than to CJF, indicating multiple origins. The molecular information on genetic diversity revealed in our study may be useful in developing genetic improvement and conservation strategies to better utilize indigenous Sri Lankan chicken resources. [source]