Ridges and rivers: a test of competing hypotheses of Amazonian diversification using a dart-poison frog (Epipedobates femoralis). (49/1463)

Mitochondrial DNA cytochrome b sequence data from a dart-poison frog, Epipedobates femoralis, were used to test two hypotheses of Amazonian diversification: the riverine barrier and the ridge hypotheses. Samples were derived from sites located on both banks of the Rio Jurua and on both sides of the Iquitos Arch in western Amazonia. The phylogeographic structure was inconsistent with predictions of the riverine barrier hypothesis. Haplotypes from opposite river banks did not form monophyletic clades in any of our phylogenetic analyses, nor was the topology within major clades consistent with the riverine hypothesis. Further, the greatest differentiation between paired sites on opposite banks was not at the river mouth where the strongest barrier to gene flow was predicted to occur. The results instead were consistent with the hypothesis that ancient ridges (arches), no longer evident on the landscape, have shaped the phylogeographic relationships of Amazonian taxa. Two robustly supported clades map onto opposite sides of the Iquitos Arch. The mean haplotypic divergence between the two clades, in excess of 12%, suggests that this cladogenic event dates to between five and 15 million years ago. These estimates span a period of major orogenesis in western South America and presumably the formation of these ancient ridges.  (+info)

Neisseria gonorrhoeae bacterioferritin: structural heterogeneity, involvement in iron storage and protection against oxidative stress. (50/1463)

The iron-storage protein bacterioferritin (Bfr) from Neisseria gonorrhoeae strain F62 was identified in cell-free extracts and subsequently purified by column chromatography. Gonococcal Bfr had an estimated molecular mass of 400 kDa by gel filtration; however, analysis by SDS-PAGE revealed that it was composed of 18 kDa (BfrA) and 22 kDa (BfrB) subunits. DNA encoding BfrB was amplified by PCR using degenerate primers derived from the N-terminal amino acid sequence of BfrB and from a C-terminal amino acid sequence of Escherichia coli Bfr. The DNA sequence of bfrA was subsequently obtained by genome walking using single-specific-primer PCR. The two Bfr genes were located in tandem with an intervening gap of 27 bp. A potential Fur-binding sequence (12 of 19 bp identical to the consensus neisserial fur sequence) was located within the 5' flanking region of bfrA in front of a putative -35 hexamer. The homology between the DNA sequences of bfrA and bfrB was 55.7%; the deduced amino acid sequences of BfrA (154 residues) and BfrB (157 residues) showed 39.7% identity, and showed 41.3% and 56.1% identity, respectively, to E. coli Bfr. Expression of recombinant BfrA and BfrB in E. coli strain DH5alpha was detected on Western blots probed with polyclonal anti-E. coli Bfr antiserum. Most Bfrs are homopolymers with identical subunits; however, the evidence presented here suggests that gonococcal Bfr was composed of two similar but not identical subunits, both of which appear to be required for the formation of a functional Bfr. A Bfr-deficient mutant was constructed by inserting the omega fragment into the BfrB gene. The growth of the BfrB-deficient mutant in complex medium was reduced under iron-limited conditions. The BfrB-deficient mutant was also more sensitive to killing by H2O2 and paraquat than the isogenic parent strain. These results demonstrate that gonococcal Bfr plays an important role in iron storage and protection from iron-mediated oxidative stress.  (+info)

Targeted inactivation of the smallest plastid genome-encoded open reading frame reveals a novel and essential subunit of the cytochrome b(6)f complex. (51/1463)

The smallest conserved open reading frame in the plastid genome, ycf6, potentially specifies a hydrophobic polypeptide of only 29 amino acids. In order to determine the function of this reading frame we have constructed a knockout allele for ycf6. This allele was introduced into the tobacco plastid genome by chloroplast transformation to replace the wild-type ycf6 allele. Homoplasmic Deltaycf6 plants display a photosynthetically incompetent phenotype. Whereas the two photosystems are intact and physiologically active, we found that the electron transfer from photosystem II to photosystem I is interrupted in Deltaycf6 plants. Molecular analyses revealed that this block is caused by the complete absence of the cytochrome b(6)f complex, the redox-coupling complex that interconnects the two photosystems. Analysis of purified cytochrome b(6)f complex by mass spectroscopy revealed the presence of a protein that has exactly the molecular mass calculated for the Ycf6 protein. This suggests that Ycf6 is a genuine subunit of the cytochrome b(6)f complex, which plays a crucial role in complex assembly and/or stability. We therefore propose to rename the ycf6 reading frame petN.  (+info)

Cytochrome b evolution in birds and mammals: an evaluation of the avian constraint hypothesis. (52/1463)

Patterns of molecular evolution in birds have long been considered anomalous. Compared with other vertebrates, birds have reduced levels of genetic divergence between groups of similar taxonomic ranks for a variety of nuclear and mitochondrial markers. This observation led to the avian constraint hypothesis, which identifies increased functional constraint on avian proteins as the cause for the reduction in genetic divergence. Subsequent investigations provided additional support for the avian constraint hypothesis when rates of molecular evolution were found to be slower in birds than in mammals in a variety of independent calibrations. It is possible to test the avian constraint hypothesis as an explanation for this avian slowdown by comparing DNA sequence data from protein-coding regions in birds and homologous regions in mammals. The increased selective constraints should lead to a reduction in the proportion of amino acid replacement substitutions. To test for such a decrease, we calculated the numbers of amino acid replacement substitutions per replacement site (dN) and silent substitutions per silent site (dS) for the complete mitochondrial cytochrome b gene using 38 avian and 43 mammalian comparisons that were phylogenetically independent. We find that dN/dS is significantly smaller in birds than in mammals. This difference cannot be explained by differences in codon bias affecting dS values. We suggest that the avian slowdown can be explained, at least in part, by a decreased tolerance for amino acid substitutions in avian species relative to mammalian species.  (+info)

State transitions, cyclic and linear electron transport and photophosphorylation in Chlamydomonas reinhardtii. (53/1463)

The relationship between state transitions and the kinetic properties of the electron transfer chain has been studied in Chlamydomonas reinhardtii. The same turnover rate of cytochrome f was found in state 1 and 2. However, while DBMIB was inhibitory in both states, DCMU was effective only in state 1. These observations suggest that linear electron transport was active only in state 1, while a cyclic pathway around photosystem (PS) I operated in state 2. The reversible shift from linear to cyclic electron transport was modulated by changes of PSII antenna size, which inactivated the linear pathway, and by oxygen, which inhibited the cyclic one. Attainment of state 2, under anaerobiosis in the dark, was associated with the decline of the ATP/ADP ratio in the cells and the dark reduction of the intersystem carriers. Upon illumination of the cells, the ATP/ADP ratio increased in a few seconds to the aerobic level. Then, several minutes later, the F(m) returned to the state 1 level, and O(2) evolution was reactivated. This suggests that ATP, though required for photosynthesis, is not the rate-limiting factor in the reactivation of photosynthetic O(2) evolution, which is rather controlled by the redox state of the electron carriers.  (+info)

Turnover of the aggregates and cross-linked products of the D1 protein generated by acceptor-side photoinhibition of photosystem II. (54/1463)

It is known that the reaction-center binding protein D1 in photosystem (PS) II is degraded significantly during photoinhibition. The D1 protein also cross-links covalently or aggregates non-covalently with the nearby polypeptides in PS II complexes by illumination. In the present study, we detected the adducts between the D1 protein and the other reaction-center binding protein D2 (D1/D2), the alpha-subunit of cyt b(559) (D1/cyt b(559)), and the antenna chlorophyll-binding protein CP43 (D1/CP43) by SDS/urea-polyacrylamide gel electrophoresis and Western blotting with specific antibodies. The adducts were observed by weak and strong illumination (light intensity: 50-5000 microE m(-2) s(-1)) of PS II membranes, thylakoids and intact chloroplasts from spinach, under aerobic conditions. These results indicate that the cross-linking or aggregation of the D1 protein is a general phenomenon which occurs in vivo as well as in vitro with photodamaged D1 proteins. We found that the formation of the D1/D2, D1/cyt b(559) and D1/CP43 adducts is differently dependent on the light intensity; the D1/D2 heterodimers and D1/cyt b(559) were formed even by illumination with weak light, whereas generation of the D1/CP43 aggregates required strong illumination. We also detected that these D1 adducts were efficiently removed by the addition of stromal components, which may contain proteases, molecular chaperones and the associated proteins. By two-dimensional SDS/urea-polyacrylamide gel electrophoresis, we found that several stromal proteins, including a 15-kDa protein are effective in removing the D1/CP43 aggregates, and that their activity is resistant to SDS.  (+info)

Skull morphology and mitochondrial DNA sequence analysis in the lesser Japanese mole (Mogera imaizumii) from the Imperial Palace (Tokyo, Japan). (55/1463)

Since about 1630, the Imperial Palace has been biologically isolated from other habitats by the development and urbanization of Tokyo. We morphologically examined the skulls of the lesser Japanese mole (Mogera imaizumii) from the Imperial Palace and compared them with those from Kanto District, while the sequences of the cytochrome b and 12S rRNA genes were also analyzed to clarify the genetic status of this isolated population. The skulls from the Imperial Palace were much larger than those from Kanto District in the length items. We suggest that the Imperial Palace skulls morphologically may compose a cluster as a large body-sized type in Kanto District within the dots of Mogera imaizumii in charts of principal component analysis. The mitochondrial DNA sequences of the Imperial Palace population were highly homologous to those of other Tokyo population at the level of 98.5% in cytochrome b and 98.7% in 12S rRNA genes.  (+info)

The energy landscape for ubihydroquinone oxidation at the Q(o) site of the bc(1) complex in Rhodobacter sphaeroides. (56/1463)

Activation energies for partial reactions involved in oxidation of quinol by the bc(1) complex were independent of pH in the range 5. 5-8.9. Formation of enzyme-substrate complex required two substrates, ubihydroquinone binding from the lipid phase and the extrinsic domain of the iron-sulfur protein. The activation energy for ubihydroquinone oxidation was independent of the concentration of either substrate, showing that the activated step was in a reaction after formation of the enzyme-substrate complex. At all pH values, the partial reaction with the limiting rate and the highest activation energy was oxidation of bound ubihydroquinone. The pH dependence of the rate of ubihydroquinone oxidation reflected the pK on the oxidized iron-sulfur protein and requirement for the deprotonated form in formation of the enzyme-substrate complex. We discuss different mechanisms to explain the properties of the bifurcated reaction, and we preclude models in which the high activation barrier is in the second electron transfer or is caused by deprotonation of QH(2). Separation to products after the first electron transfer and movement of semiquinone formed in the Q(o) site would allow rapid electron transfer to heme b(L). This would also insulate the semiquinone from oxidation by the iron-sulfur protein, explaining the efficiency of bifurcation.  (+info)