Pervasive migration of organellar DNA to the nucleus in plants

A surprisingly large number of plant nuclear DNA sequences inferred to be remnants of chloroplast and mitochondrial DNA migration events were detected through computer-assisted database searches. Nineteen independent organellar DNA insertions, with a median size of 117 by (range of 38 to >785 bp), occur in the proximity of 15 nuclear genes. One fragment appears to have been passed through a RNA intermediate, based on the presence of an edited version of the mitochondrial gene in the nucleus. Tandemly arranged fragments from disparate regions of organellar genomes and from different organellar genomes indicate that the fragments joined together from an intracellular pool of RNA and/or DNA before they integrated into the nuclear genome. Comparisons of integrated sequences to genes lacking the insertions, as well as the occurrence of coligated fragments, support a model of random integration by end joining. All transferred sequences were found in noncoding regions, but the positioning of organellar-derived DNA in introns, as well as regions 5 and 3 to nuclear genes, suggests that the random integration of organellar DNA has the potential to influence gene expression patterns. A semiquantitative estimate was performed on the amount of organellar DNA being transferred and assimilated into the nucleus. Based on this database survey, we estimate that 3–7% of the plant nuclear genomic sequence files contain organellar-derived DNA. The timing and the magnitude of genetic flux to the nuclear genome suggest that random integration is a substantial and ongoing process for creating sequence variation.Correspondence to: J.L. Blanchard     

Presence and abundance of CENP-B box sequences in great ape subsets of primate-specific α-satellite DNA

CENP-B, a highly conserved centromere-associated protein, binds to -satellite DNA, the centromeric satellite of primate chromosomes, at a 17-bp sequence, the CENP-B box. By fluorescence in situ hybridization (FISH) with an oligomer specific for the CENP-B box sequence, we have demonstrated the abundance of CENP-B boxes on all chromosomes (except the Y) of humans, chimpanzee, pygmy chimpanzee, gorilla, and orangutan. This sequence motif was not detected in the genomes of other primates, including gibbons, Old and New World monkeys, and prosimians. Our results indicate that the CENP-B box containing subtype of -satellite DNA may have emerged recently in the evolution of the large-bodied hominoids, after divergence of the phylogenetic lines leading to gibbons and apes; the box is thus on the order of 15–25 million years of age. The rapid process of dispersal and fixation of the CENP-B box sequence throughout the human and great ape genomes is thought to be a consequence of concerted evolution of -satellite subsets on both homologous and nonhomologous chromosomes.Correspondence to: T. Haaf     

Regulation, replication, and integration functions of the Vibrio cholerae CTXφ are encoded by region RS2

CTXφ is a filamentous phage that encodes cholera toxin, one of the principal virulence factors of Vibrio cholerae . CTXφ is unusual among filamentous phages because it can either replicate as a plasmid or integrate into the V. cholerae chromosome at a specific site. The CTXφ genome has two regions, the 'core' and RS2. Integrated CTXφ is frequently flanked by an element known as RS1 which is related to RS2. The nucleotide sequences of RS2 and RS1 were determined. These related elements contain three nearly identical open reading frames (ORFs), which in RS2 were designated rstR , rstA2 and rstB2 . RS1 contains an additional ORF designated rstC . Functional analyses indicate that rstA2 is required for CTXφ replication and rstB2 is required for CTXφ integration. The amino terminus of RstR is similar to the amino termini of other phage-encoded repressors, and RstR represses the expression of rstA2 . Although genes with related functions are clustered in the genome of CTXφ in a way similar to those for other filamentous phages, the CTXφ RS2-encoded gene products mediating replication, integration and repression appear to be novel.     

Origin of deoxycorticosterone sulfate (DOC-SO4) in plasma of pregnant women: Pregnenolone-3,21-disulfate is a placental precursor of DOC-SO4

The plasma levels of deoxycorticosterone sulfate (DOC-SO₄) in near-term pregnant women are 100 times those in plasma of men or non-pregnant women. Yet, neither the tissue site of synthesis nor the precursor of DOC-SO₄ that enters maternal plasma is known. Several potential sources have been excluded: plasma DOC-SO₄ is not derived from plasma DOC; and the secretion of C₂₁-steroids (other than aldosterone) from the maternal adrenals during human pregnancy is not increased. Similarly, the transfer of DOC-SO₄ from fetal plasma cannot account for the high level of DOC-SO₄ in the maternal compartment, and a reduced clearance of plasma DOC-SO₄ during pregnancy cannot account for the high levels of DOC-SO₄. Indeed, the rate of clearance of DOC-SO₄ from plasma is 10–100 times that of most other steroid sulfates. To address this question further, we evaluated the possibility that fetal plasma pregnenolone-3,21-disulfate serves as a precursor for DOC-SO₄ formation in the placenta. The preferential hydrolysis of the 3β-sulfate of pregnenolone-3,21-disulfate in placenta would give rise to pregnenolone-21-monosulfate, which, if acted upon by placental 3β-hydroxysteroid dehydrogenase/Δ^{5 → 4} isomerase, could give DOC-SO₄. [³H]Pregnenolone-3,21-disulfate was incubated with minces of human placental tissue for 5, 20, 60 and 120 min. Radiolabelled DOC-SO₄, DOC, and pregnenolone-21-monosulfate were isolated from the incubation media and quantified. After a 5 min incubation, 7.5% of substrate was converted to DOC-SO₄; and after 20, 60 and 120 min 30% of the [³H]pregnenolone-3,21-disulfate was recovered from the media of these incubations as [³H]DOC-SO₄. [³H]DOC was also present in the incubation media and the concentrations of this product increased as a function of incubation time. Therefore, pregnenolone-3,21-disulfate, which is present in very high concentrations in fetal plasma (1000 ng/ml), is metabolized in the placenta to DOC-SO₄. Because of the fetal and maternal vascular arrangements of the hemochorioendothelial placenta of human pregnancy, steroids produced in syncytiotrophoblasts preferentially enter the intervillous space; thus, fetal plasma pregnenolone-3,21-disulfate may serve as a placental precursor of maternal plasma DOC-SO₄.     

Of mice and wrens: the relation between abundance and geographic range size in British mammals and birds

We examine the relation between population size and geographic range size for British breeding birds and mammals. As for most other assemblages studied, a strong positive interspecific correlation is found in both taxa. The relation is also recovered once the phylogenetic relatedness of species has been controlled for using an evolutionary comparative method. The slope of the relation is steeper for birds than for mammals, but this is due in large part to two species of mammals that have much higher population sizes than expected from their small geographic ranges. These outlying mammal species are the only ones in Britain to be found only on small offshore islands, and so may be exhibiting density compensation effects. With them excluded, the slope of the abundance–range size relation for mammals is not significantly different to that for birds. However, the elevation of the relation is higher for mammals than for birds, indicating that mammals are approximately 30 times more abundant than birds of equivalent geographic range size. An earlier study of these assemblages showed that, for a given body mass, bats had abundances more similar to birds than to non-volant mammals, suggesting that the difference in abundance between mammals and birds might be due to constraints of flight. Our analyses show that the abundance–range size relation for bats is not different for that from other mammals, and that the anomalously low abundance of bats for their body mass may result because they have smaller than expected geographic extents for their size. Other reasons why birds and mammals might have different elevations for the relation between population size and geographic range size are discussed, together with possible reasons for why the slopes of these relations might be similar.     

Intratracheal instillation of a novel NO/nucleophile adduct selectively reduces pulmonary hypertension

Brilli, Richard J., Brian Krafte-Jacobs, Daniel J. Smith,Dominick Roselle, Daniel Passerini, Amos Vromen, Lori Moore, CsabaSzabó, and Andrew L. Salzman. Intratracheal instillation ofa novel NO/nucleophile adduct selectively reduces pulmonary hypertension. J. Appl. Physiol. 83(6):1968-1975, 1997.We examined the pulmonary and systemichemodynamic effects of administering soluble nitric oxide (NO) donorcompounds (NO/nucleophile adducts, i.e., NONOates) directly into thetrachea of animals with experimentally induced pulmonary hypertension.Steady-state pulmonary hypertension was created by using thethromboxane agonist U-46619. Yorkshire pigs were randomly assigned toone of four groups: group 1,intratracheal saline (control; n = 8);group 2, intratracheal sodiumnitroprusside (n = 6);group 3, intratracheal ethylputreanineNONOate (n = 6); andgroup 4, intratracheal2-(dimethylamino)-ethylputreanine NONOate (DMAEP/NO;n = 6). Pulmonary and systemichemodynamics were monitored after drug instillation.Group 4 had significant reductions in pulmonary vascular resistance index (PVRI) at all time points comparedwith steady state and compared with group1 (P < 0.05), whereas systemic vascular resistance index did not change. The meanchange in mean pulmonary arterial pressure in group4 was 33.1 ± 1.2% compared with +6.4 ± 1.3% in group 1 (P < 0.001), and the mean change inmean arterial pressure was 9.3 ± 0.7% compared with acontrol value of 0.9 ± 0.5%(P < 0.05). Groups 2 and 3 hadsignificant decreases in both PVRI and systemic vascular resistanceindex compared with steady state and with group1. In conclusion, intratracheal instillation of apolar-charged tertiary amine NONOate DMAEP/NO results in the selectivereduction of PVRI. Intermittent intratracheal instillation of selectiveNONOates may be an alternative to continuously inhaled NO in thetreatment of pulmonary hypertension.

     

Nonsyndromic cleft lip with or without cleft palate: evidence of linkage to BCL3 in 17 multigenerational families.

Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common craniofacial developmental defect. Recent segregation analyses have suggested that major genes play a role in the etiology of CL/P. Linkage to 22 candidate genes was tested in 11 multigenerational families with CL/P, and 21 of these candidates were excluded. APOC2, 19q13.1, which is linked to the proto-oncogene BCL3, gave suggestive evidence for linkage to CL/P. The study was expanded to include a total of 39 multigenerational CL/P families. Linkage was tested in all families, using an anonymous marker, D19S178, and intragenic markers in BCL3 and APOC2. Linkage was tested under two models, autosomal dominant with reduced penetrance and affecteds only. Homogeneity testing on the two-point data gave evidence of heterogeneity at APOC2 under the affecteds-only model. Both models showed evidence of heterogeneity, with 43% of families linked at zero recombination to BCL3 when marker data from BCL3 and APOC2 were included. A maximum multipoint LOD score of 7.00 at BCL3 was found among the 17 families that had posterior probabilities > = 50% in favor of linkage. The transmission disequilibrium test provided additional evidence for linkage with the 3 allele of BCL3 more often transmitted to affected children. These results suggest that BCL3, or a nearby gene, plays a role in the etiology of CL/P in some families.     

GENETIC VARIATION IN TRAGOPOGON SPECIES: ADDITIONAL ORIGINS OF THE ALLOTETRAPLOIDS T. MIRUS AND T. MISCELLUS (COMPOSITAE)

Genetic diversity in the introduced diploids Tragopogon dubius, T. porrifolius, and T. pratensis and their neoallotetraploid derivatives T. mirus and T. miscellus was estimated to assess the numbers of recurrent, independent origins of the two tetraploid species in the Palouse region of eastern Washington and adjacent Idaho. These tetraploid species arose in this region, probably within the past 50–60 yr, and provide one of the best models for the study of polyploidy in plants. The parental species of both T. mirus and T. miscellus have been well documented, and each tetraploid species has apparently formed multiple times. However, a recent survey of the distributions of these allotetraploids revealed that both tetraploid species have expanded their ranges considerably during the past 50 yr, and several new populations of each species were discovered. Therefore, to evaluate the possibility that these recently discovered populations are of recent independent origin, a broad analysis of genetic diversity in T. mirus, T. miscellus, and their diploid progenitors was conducted. Analyses of allozymic and DNA restriction site variation in all known populations of T. mirus and T. miscellus in the Palouse and several populations of each parental diploid species revealed several distinct genotypes in each tetraploid species. Four isozymic multilocus genotypes were observed in T. mirus, and seven were detected in T. miscellus. Tragopogon mirus possesses a single chloroplast genome, that of T. porrifolius, and two distinct repeat types of the 18S-26S ribosomal RNA genes. Populations of T. miscellus from Pullman, Washington, have the chloroplast genome of T. dubius; all other populations of T. miscellus have the chloroplast DNA of T. pratensis. All populations of T. miscellus combine the ribosomal RNA repeat types of T. dubius and T. pratensis, as demonstrated previously. When all current and previously published data are considered, both T. mirus and T. miscellus appear to have formed numerous times even within the small geographic confines of the Palouse, with estimates of five to nine and two to 21 independent origins, respectively. Such recurrent polyploidization appears to characterize most polyploid plant species investigated to date (although this number is small) and may contribute to the genetic diversity and ultimate success of polyploid species.     

Molecular phylogeny and divergence times of drosophilid species

The phylogenetic relationships and divergence times of 39 drosophilid species were studied by using the coding region of the Adh gene. Four genera--Scaptodrosophila, Zaprionus, Drosophila, and Scaptomyza (from Hawaii)--and three Drosophila subgenera--Drosophila, Engiscaptomyza, and Sophophora--were included. After conducting statistical analyses of the nucleotide sequences of the Adh, Adhr (Adh-related gene), and nuclear rRNA genes and a 905-bp segment of mitochondrial DNA, we used Scaptodrosophila as the outgroup. The phylogenetic tree obtained showed that the first major division of drosophilid species occurs between subgenus Sophophora (genus Drosophila) and the group including subgenera Drosophila and Engiscaptomyza plus the genera Zaprionus and Scaptomyza. Subgenus Sophophora is then divided into D. willistoni and the clade of D. obscura and D. melanogaster species groups. In the other major drosophilid group, Zaprionus first separates from the other species, and then D. immigrans leaves the remaining group of species. This remaining group then splits into the D. repleta group and the Hawaiian drosophilid cluster (Hawaiian Drosophila, Engiscaptomyza, and Scaptomyza). Engiscaptomyza and Scaptomyza are tightly clustered. Each of the D. repleta, D. obscura, and D. melanogaster groups is monophyletic. The splitting of subgenera Drosophila and Sophophora apparently occurred about 40 Mya, whereas the D. repleta group and the Hawaiian drosophilid cluster separated about 32 Mya. By contrast, the splitting of Engiscaptomyza and Scaptomyza occurred only about 11 Mya, suggesting that Scaptomyza experienced a rapid morphological evolution. The D. obscura and D. melanogaster groups apparently diverged about 25 Mya. Many of the D. repleta group species studied here have two functional Adh genes (Adh-1 and Adh-2), and these duplicated genes can be explained by two duplication events.