Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “rate of evolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23Linked to original sources
PubMed1995

Tandem sequence duplications functionally complement deletions in the D1 protein of photosystem II.

Obligate photoheterotrophic mutants of the cyanobacterium Synechocystis sp. PCC 6803 that carry deletions of conserved residues in the plastoquinone-binding niche of the D1 protein were used to select for spontaneous mutations that restore photoautotrophic growth. Spontaneous pseudorevertants emerged from two deletion mutants, delta YNIV246-9 and delta NN266-7, when the cultures were maintained long after the carbon source (glucose) had been depleted from the medium and cells had reached stationary phase. Most pseudorevertants were found to contain tandem duplications of 6-45-base pair DNA sequences located close to the domain carrying the deletion; none of them restored the wild-type sequence. Three pseudorevertants isolated from the delta YNIV246-9 mutant contained a duplication (7-15 codons) of the DNA sequence immediately downstream of the deletion; the protein region encoded by this DNA may include part of the putative de helix, an important constituent of the plastoquinone-binding niche. Three pseudorevertants isolated from the delta NN266-7 mutant contained duplications corresponding to 2-8 amino acid residues adjacent to the site of the deletion. In all six pseudorevertants carrying duplications, the length of the D1 protein in the modified regions was restored to at least the length present in wild type, suggesting that a minimal length of these protein domains may be required for functional integrity. In another photoautotrophic strain isolated from delta NN266-7, no secondary mutations could be identified in the gene coding for the D1 protein; such mutations apparently reside on another protein subunit of the photosystem II complex. Photosystem II function in the pseudorevertants was altered as compared with wild type in terms of growth and oxygen evolution rates, photosystem II concentration, the semiquinone equilibrium at the acceptor side, and thermostability. A mechanism leading to tandem sequence duplication may involve DNA damage followed by DNA synthesis, strand displacement, and ligation.

Amino Acid Sequence↗
PubMed1999

Alterations in carboxylate ligation at the active site of photosystem II.

Photosystem II (PSII) is the photosynthetic enzyme catalyzing the oxidation of water and reduction of plastoquinone (Q). This reaction occurs at a catalytic site containing four manganese atoms and cycling among five oxidation states, the Sn states, where n refers to the number of oxidizing equivalents stored. Biochemical and spectroscopic techniques have been used previously to conclude that aspartate 170 in the D1 subunit influences the structure and function of the PSII active site (Boerner, R. J., Nguyen, A. P., Barry, B. A., and Debus, R. J. (1992) Biochemistry 31, 6660-6672). Substitution of glutamate for aspartate 170 resulted in an assembled manganese cluster, which was capable of enzymatic turnover, but at lower steady-state oxygen evolution rates. Here, we obtained the difference (light-minus-dark) Fourier transform IR spectrum associated with the S2Q--minus-S1Q transition by illumination of oxygen-evolving wild-type and DE170D1 PSII preparations at 200 K. These spectra are known to be dominated by contributions from carboxylic acid and carboxylate residues that are close to or ligating the manganese cluster. Substitution of glutamate for aspartate 170 results in alterations in the S2Q--minus-S1Q spectrum; the alterations are consistent with a change in carboxylate coordination to manganese or calcium. In particular, the spectra are consistent with a shift from bridging/bidentate carboxylates in wild-type PSII to unidentate carboxylate ligation in DE170D1 PSII.

Binding Sites↗
PubMed2001

A regulatory role of the PetM subunit in a cyanobacterial cytochrome b6f complex.

To investigate the function of the PetM subunit of the cytochrome b6f complex, the petM gene encoding this subunit was inactivated by insertional mutagenesis in the cyanobacterium Synechocystis PCC 6803. Complete segregation of the mutant reveals a nonessential function of PetM for the structure and function of the cytochrome b6f complex in this organism. Photosystem I, photosystem II, and the cytochrome b6f complex still function normally in the petM- mutant as judged by cytochrome f re-reduction and oxygen evolution rates. In contrast to the wild type, however, the content of phycobilisomes and photosystem I as determined from 77 K fluorescence spectra is reduced in the petM- strain. Furthermore, whereas under anaerobic conditions the kinetics of cytochrome f re-reduction are identical, under aerobic conditions these kinetics are slower in the petM- strain. Fluorescence induction measurements indicate that this is due to an increased plastoquinol oxidase activity in the mutant, causing the plastoquinone pool to be in a more oxidized state under aerobic dark conditions. The finding that the activity of the cytochrome b6f complex itself is unchanged, whereas the stoichiometry of other protein complexes has altered, suggests an involvement of the PetM subunit in regulatory processes mediated by the cytochrome b6f complex.

Cloning, Molecular↗
PubMed2006

The PsbQ protein is required in Arabidopsis for photosystem II assembly/stability and photoautotrophy under low light conditions.

RNA interference was used to simultaneously suppress the expression of the two genes that encode the PsbQ proteins of Photosystem II (PS II) in Arabidopsis thaliana, psbQ-1 (At4g21280) and psbQ-2 (At4g05180). Two independent PsbQ-deficient plant lines were examined. These plant lines produced little detectable PsbQ protein. Under normal growth light conditions, the wild type and mutant plants were visually indistinguishable. Additionally, analysis of steady state oxygen evolution rates and chlorophyll fluorescence characteristics indicated little alteration of photosynthetic capacity in the mutant plants. No loss of other PS II proteins was evident. Interestingly, flash oxygen yield analysis performed on thylakoid membranes isolated from the mutant and wild type plants indicated that the oxygen-evolving complex was quite unstable in the mutants. Furthermore, the lifetime of the S2 state of the oxygen-evolving complex appeared to be increased in these plants. Incubation of the wild type and mutant plants under low light growth conditions led to a significantly stronger observed phenotype in the mutants. The mutant plants progressively yellowed (after 2 weeks) and eventually died (after 3-4 weeks). The wild type plants exhibited only slight yellowing after 4 weeks under low light conditions. The mutant plants exhibited a large loss of a number of PS II components, including CP47 and the D2 protein, under low light conditions. Additionally, significant alterations of their fluorescence characteristics were observed, including an increased FO and decreased FV, yielding a large loss in PS II quantum efficiency (FV/FM). Analysis of QA- decay kinetics in the absence of 3-(3,4-dichlorophenyl)-1,1-dimethyl urea indicated a defect in electron transfer from QA- to QB, whereas experiments performed in the presence of this herbicide indicated that the recombination rate between QA- and the S2 state was strongly retarded. These results indicate that the loss of the PsbQ protein induces significant changes in Photosystem II function, particularly in low light-grown plants, and that the PsbQ protein is required for photoautotrophic growth under low light conditions.

Animals↗
PubMed2001

Partial recovery of light-independent chlorophyll biosynthesis in the chlL-deletion mutant of Synechocystis sp. PCC 6803.

A chlL-deletion mutant of Synechocystis sp. PCC 6803 designated as chlL- was unable to make significant amounts of chlorophyll in darkness. However, an apparent pseudorevertant has been generated spontaneously that can synthesize an increased amount of chlorophyll under light-activated heterotrophic growth conditions. Under these conditions, the chlorophyll content in this pseudorevertant was about 20% of that in the wild-type strain and about 4 times more than that in the original and in the recently recreated chlL-deletion mutant. This is paralleled by increased performance of dark-grown cells in terms of chlorophyll fluorescence induction and oxygen evolution rates in the pseudorevertant versus in the original mutant. PCR analysis confirmed that the chlL- -pseudorevertant mutant still lacked the chlL gene. These results imply that the light-independent chlorophyll biosynthesis pathway was partly recovered.

Bacterial Proteins↗
PubMed2002

Involvement of state transitions in the switch between linear and cyclic electron flow in Chlamydomonas reinhardtii.

The energetic metabolism of photosynthetic organisms is profoundly influenced by state transitions and cyclic electron flow around photosystem I. The former involve a reversible redistribution of the light-harvesting antenna between photosystem I and photosystem II and optimize light energy utilization in photosynthesis whereas the latter process modulates the photosynthetic yield. We have used the wild-type and three mutant strains of the green alga Chlamydomonas reinhardtii--locked in state I (stt7), lacking the photosystem II outer antennae (bf4) or accumulating low amounts of cytochrome b6f complex (A-AUU)--and measured electron flow though the cytochrome b6f complex, oxygen evolution rates and fluorescence emission during state transitions. The results demonstrate that the transition from state 1 to state 2 induces a switch from linear to cyclic electron flow in this alga and reveal a strict cause-effect relationship between the redistribution of antenna complexes during state transitions and the onset of cyclic electron flow.

Animals↗
PubMed2002

A photosystem II-associated carbonic anhydrase regulates the efficiency of photosynthetic oxygen evolution.

We show for the first time that Cah3, a carbonic anhydrase associated with the photosystem II (PSII) donor side in Chlamydomonas reinhardtii, regulates the water oxidation reaction. The mutant cia3, lacking Cah3 activity, has an impaired water splitting capacity, as shown for intact cells, thylakoids and PSII particles. To compensate this impairment, the mutant overproduces PSII reaction centres (1.6 times more than wild type). We present compelling evidence that the mutant has an average of two manganese atoms per PSII reaction centre. When bicarbonate is added to mutant thylakoids or PSII particles, the O2 evolution rates exceed those of the wild type by up to 50%. The donor side of PSII in the mutant also exhibits a much higher sensitivity to overexcitation than that of the wild type. We therefore conclude that Cah3 activity is necessary to stabilize the manganese cluster and maintain the water-oxidizing complex in a functionally active state. The possibility that two manganese atoms are enough for water oxidation if bicarbonate ions are available is discussed.

Animals↗
PubMed1996

Genetic divergence and fitness convergence under uniform selection in experimental populations of bacteria.

Replicate populations of bacteria were propagated for 1000 generations in the laboratory. The growth substrate was periodically renewed, so that during most generations (cell doublings) it was not limiting. The final clones demonstrated about a 40% fitness increase when competed against their common ancestor. This increase was uniform both among and within populations despite extensive differentiation in correlated traits: cell size, resistance to starvation and dry mass of culture. It is suggested that genetic diversity developed because selection promoted any changes directing cell activity toward a higher maximum growth rate. Evolution of this trait halted at a similar level when some basic constraints on bacterial metabolism were met. The selective values of emerging mutations must have depended on the genetic background. They would be beneficial early in evolution but ineffective near the limit of adaptation. This hypothesis was tested for one mutation that affected both fitness and colony morphology. In some clones it was the first adaptive mutation and provided a third of the total fitness increase, but it was not assimilated by the clones that reached the adaptive ceiling in some other way. Near the limit of adaptation, epistasis levels off the fitnesses of genetically variable clones.

Bacteria↗
PubMed2003

Continuous exchange of sequence information between dispersed Tc1 transposons in the Caenorhabditis elegans genome.

In a genome-wide analysis of the active transposons in Caenorhabditis elegans we determined the localization and sequence of all copies of each of the six active transposon families. Most copies of the most active transposons, Tc1 and Tc3, are intact but individually have a unique sequence, because of unique patterns of single-nucleotide polymorphisms. The sequence of each of the 32 Tc1 elements is invariant in the C. elegans strain N2, which has no germline transposition. However, at the same 32 Tc1 loci in strains with germline transposition, Tc1 elements can acquire the sequence of Tc1 elements elsewhere in the N2 genome or a chimeric sequence derived from two dispersed Tc1 elements. We hypothesize that during double-strand-break repair after Tc1 excision, the template for repair can switch from the Tc1 element on the sister chromatid or homologous chromosome to a Tc1 copy elsewhere in the genome. Thus, the population of active transposable elements in C. elegans is highly dynamic because of a continuous exchange of sequence information between individual copies, potentially allowing a higher evolution rate than that found in endogenous genes.

Animals↗
PubMed2000

Endogenous ABA maintains shoot growth in tomato independently of effects on plant water balance: evidence for an interaction with ethylene.

To examine whether the reduced shoot growth of abscisic acid (ABA)-deficient mutants of tomato is independent of effects on plant water balance, flacca and notabilis were grown under controlled-humidity conditions so that their leaf water potentials were equal to or higher than those of well-watered wild-type plants throughout development. Most parameters of shoot growth remained markedly impaired and root growth was also greatly reduced. Additional experiments with flacca showed that shoot growth substantially recovered when wild-type levels of ABA were restored by treatment with exogenous ABA, even though improvement in leaf water potential was prevented. The ability of applied ABA to increase growth was greatest for leaf expansion, which was restored by 75%. The ethylene evolution rate of growing leaves was doubled in flacca compared to the wild type and treatment with silver thiosulphate to inhibit ethylene action partially restored shoot growth. The results demonstrate that normal levels of endogenous ABA are required to maintain shoot development, particularly leaf expansion, in well-watered tomato plants, independently of effects on plant water balance. The impairment of shoot growth caused by ABA deficiency is at least partly attributable to ethylene.

Abscisic Acid↗
PubMed1995

Gene for cytochrome c oxidase subunit II in the mitochondrial DNA of Culex quinquefasciatus and Aedes aegypti (Diptera: Culicidae).

The cytochrome c oxidase subunit II (COII) gene between transfer RNA for Leu and Lys in the mitochondrial DNA of Culex quinquefasciatus Say and Aedes aegypti (L.) was amplified by the polymerase chain reaction (PCR) technique. Both the gene order and direction of transcription were identical to Anopheles and Drosophila. Nucleotide sequences of the PCR-amplified COII genes in these two mosquitoes exhibited 88% homology, and the frequency of transition was very close to that of transversion. The homology of deduced amino acid sequences of COII between these two mosquitoes was 95%. Two highly conserved segments of COII proteins were found in mosquitoes, fruit flies, locust, and honeybee. These segments contain the major amino acid residues of cytochrome c oxidase involved in electron transport and ligand binding. The amino acid residues are located at the positions similar to those of the mammalian enzymes. Two sets of the phylogenetic trees of a similar pattern were generated by comparing the divergences of nucleotide and amino acid sequences of COII. The branch lengths of the trees estimated by amino acid and nucleotide sequences showed different evolution rates of Aedes and Culex from their common ancestor.

Aedes↗
PubMed2000

A half-type ABC transporter TAPL is highly conserved between rodent and man, and the human gene is not responsive to interferon-gamma in contrast to TAP1 and TAP2.

TAPL is a half-type ABC transporter with sequence similarity to TAP1 and TAP2 that is transcribed in various rat tissues [Yamaguchi, Y., Kasano, M., Terada, T., Sato, R., and Maeda, M. (1999) FEBS Lett. 457, 231-236]. Primary structures of the human and mouse orthologous counterparts were deduced from cDNAs cloned by means of polymerase chain reaction, and they were compared with that of the rat. The mammalian TAPLs (rat, mouse, and human) are highly conserved, since about 95% of the amino acid residues are identical between rodents and man. Phylogenetic analysis demonstrated that the evolutional rate of TAPL is much slower than those of TAP1 and TAP2, although TAPL could have diverged from an ancestor of TAP1 or that of TAP1 and TAP2. The TAPL-GFP fusion protein transiently expressed in Cos-1 cells was co-localized with PDI, suggesting that TAPL is inserted into endoplasmic reticulum membrane. The conservation of the peptide-binding motifs of TAP proteins in TAPL raises the possibility that the TAPL might be a peptide transporter. The gene for human TAPL is assigned to chromosome 12q24.31-q24.32, while those for TAP1 and TAP2 are located at the MHC locus of chromosome 6p21.!3. Furthermore, the transcription of TAPL gene is not responsive to interferon-gamma, in contrast to TAP1 and TAP2. These results indicate that the gene regulation of TAPL is different from those of TAP1 and TAP2.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2004

Enhancement of cyclic electron flow around PSI at high light and its contribution to the induction of non-photochemical quenching of chl fluorescence in intact leaves of tobacco plants.

Non-photochemical quenching (NPQ) of Chl fluorescence is a mechanism for dissipating excess photon energy and is dependent on the formation of a DeltapH across the thylakoid membranes. The role of cyclic electron flow around photosystem I (PSI) (CEF-PSI) in the formation of this DeltapH was elucidated by studying the relationships between O2-evolution rate [V(O2)], quantum yield of both PSII and PSI [Phi(PSII) and Phi(PSI)], and Chl fluorescence parameters measured simultaneously in intact leaves of tobacco plants in CO2-saturated air. Although increases in light intensity raised V(O2) and the relative electron fluxes through both PSII and PSI [Phi(PSII) x PFD and Phi(PSI) x PFD] only Phi(PSI) x PFD continued to increase after V(O2) and Phi(PSII) x PFD became light saturated. These results revealed the activity of an electron transport reaction in PSI not related to photosynthetic linear electron flow (LEF), namely CEF-PSI. NPQ of Chl fluorescence drastically increased after Phi(PSII) x PFD became light saturated and the values of NPQ correlated positively with the relative activity of CEF-PSI. At low temperatures, the light-saturation point of Phi(PSII) x PFD was lower than that of Phi(PSI) x PFD and NPQ was high. On the other hand, at high temperatures, the light-dependence curves of Phi(PSII) x PFD and Phi(PSI) x PFD corresponded completely and NPQ was not induced. These results indicate that limitation of LEF induced CEF-PSI, which, in turn, helped to dissipate excess photon energy by driving NPQ of Chl fluorescence.

Chlorophyll↗
PubMed2005

Distinct roles of the cytochrome pathway and alternative oxidase in leaf photosynthesis.

In illuminated leaves, mitochondria are thought to play roles in optimizing photosynthesis. However, the roles of the cytochrome pathway (CP) and alternative oxidase (AOX) in photosynthesis, in particular in the redox state of the photosynthetic electron transport chain, are not separately characterized. We examined the effects of specific inhibition of two respiratory pathways, CP and AOX, on photosynthetic oxygen evolution and the redox state of the photosynthetic electron transport chain in broad bean (Vicia faba L.) leaves under various light intensities. Under saturating photosynthetic photon flux density (PPFD; 700 micromol photon m(-2) s(-1)), inhibition of either pathway caused a decrease in the steady-state levels of the photosynthetic O(2) evolution rate and the PSII operating efficiency, Phi(II). Because these inhibitors, at the concentrations applied to the leaves, had little effect on photosynthesis in the intact chloroplasts, two respiratory pathways are essential for maintenance of high photosynthetic rates at saturating PPFD. CP or AOX inhibition affected to Chl fluorescence parameters (e.g. photochemical quenching and non-photochemical quenching) differently, suggesting that CP and AOX contribute to photosynthesis in different ways. At low PPFD (100 micromol photon m(-2) s(-1)), only the inhibition of AOX, not CP, lowered the photosynthetic rate and Phi(II). AOX inhibition also decreased the Phi(II)/Phi(I) ratio even at low PPFD levels. These data suggest that AOX inhibition caused the over-reduction of the photosynthetic electron transport chain and induced the cyclic electron flow around PSI (CEF-PSI) even at the low PPFD. Based on these results, we discuss possible roles for CP and AOX in the light.

Antimycin A↗
PubMed1991

Genomic diversity and antigenic variation of HIV-1: links between pathogenesis, epidemiology and vaccine development.

Recent analysis of primate lentivirus genomes indicates that lentiviruses have infected primates for hundreds of years. The pathogenicity of such viruses may fluctuate due to the high evolution rate of some parts of the viral genome. Fixed nucleic acid substitutions in the gag gene appear to be caused by random fixation of selectively neutral mutants, whereas nonrandom fixation of selectively advantageous mutants, as has been observed for MHC molecules and serine protease inhibitors, appears to be operational for some hypervariable env gene regions. The former is characterized by an excess of silent mutations independent of the rate of change, the latter by an excess of nonsilent mutations. This latter type of selection may especially characterize the third variable region of the external HIV envelope (V3), which contains the principal neutralization domain.

Acquired Immunodeficiency Syndrome↗
PubMed1999

Rapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host.

Viroids, small single-stranded circular RNAs endowed with autonomous replication, are unique systems to conduct evolutionary studies of complete RNA genomes. The primary structure of 36 progeny variants of peach latent mosaic viroid (PLMVd), evolved from inoculations of the peach indicator GF-305 with four individual PLMVd cDNAs differing in their pathogenicity, has been determined. Most progeny variants had unique sequences, revealing that the extremely heterogeneous character of PLMVd natural isolates most probably results from the intrinsic ability of this RNA to accumulate changes, rather than from repeated inoculations of the same individual trees under field conditions. The structure of the populations derived from single PLMVd sequences differed according to the observed phenotype. Variant gds6 induced a reproducible symptomatic infection and gave rise to a more uniform progeny that preserves some parental features, whereas variant gds15, which induced a variable phenotype, showed a more complex behaviour, generating two distinct progenies in symptomatic and asymptomatic individual plants. Progenies derived from variants esc10 and Is11, which incited latent infections, followed a similar evolutionary pattern, leading to a population structure consisting of two main groups of variants, one of which was formed by variants closely related to the parental sequence. The evolution rate exhibited by PLMVd, considerably higher than that reported for potato spindle tuber viroid, may contribute to the fluctuating symptomatology of the severe PLMVd natural isolates. However, the polymorphism observed in PLMVd progenies does preserve some structural and functional elements previously proposed for this viroid, supporting the fact that they act as constraints limiting the genetic divergence of PLMVd quasispecies generated de novo.

Base Sequence↗
PubMed2005

A three-nucleotide mutation altering the Maize streak virus Rep pRBR-interaction motif reduces symptom severity in maize and partially reverts at high frequency without restoring pRBR-Rep binding.

Geminivirus infectivity is thought to depend on interactions between the virus replication-associated proteins Rep or RepA and host retinoblastoma-related proteins (pRBR), which control cell-cycle progression. It was determined that the substitution of two amino acids in the Maize streak virus (MSV) RepA pRBR-interaction motif (LLCNE to LLCLK) abolished detectable RepA-pRBR interaction in yeast without abolishing infectivity in maize. Although the mutant virus was infectious in maize, it induced less severe symptoms than the wild-type virus. Sequence analysis of progeny viral DNA isolated from infected maize enabled detection of a high-frequency single-nucleotide reversion of C(601)A in the 3 nt mutated sequence of the Rep gene. Although it did not restore RepA-pRBR interaction in yeast, sequence-specific PCR showed that, in five out of eight plants, the C(601)A reversion appeared by day 10 post-inoculation. In all plants, the C(601)A revertant eventually completely replaced the original mutant population, indicating a high selection pressure for the single-nucleotide reversion. Apart from potentially revealing an alternative or possibly additional function for the stretch of DNA that encodes the apparently non-essential pRBR-interaction motif of MSV Rep, the consistent emergence and eventual dominance of the C(601)A revertant population might provide a useful tool for investigating aspects of MSV biology, such as replication, mutation and evolution rates, and complex population phenomena, such as competition between quasispecies and population turnover.

Base Sequence↗
PubMed2005

Surface transport in premelted films with application to grain-boundary grooving.

We present a new model of surface transport in premelted films that is applicable to a wide range of materials close to their melting points. We illustrate its use by applying it to the evolution of a grain-boundary groove in a high vapor pressure material and show that Mullins's classical equation describing transport driven by gradients in surface curvature is reproduced asymptotically. The microscopic contact angle at the groove root is found to be modified over a thin boundary layer, and the apparent contact angle is determined. An explicit transport coefficient is derived that governs the evolution rate of systems controlled by surface transport through premelted films. The transport coefficient is found to depend on temperature and diverges as the bulk melting temperature is approached.

Journal Article↗