Functional characterization of the prokaryotic mobile genetic element IS26

Summary IS26L and IS26R are the 820 bp long elements found as direct repeats at both ends of the kanamycin resistance transposon Tn2680. They can mediate cointegration in E. coli K12 which contains no IS26 in its chromosome. Cointegration occurs in rec ⁺ or recA ^- strains with similar frequency. Upon cointegration mediated by either IS26R or IS26L, the element is duplicated and integrated into one of many different sites. Both IS26L and IS26R carry 14 bp perfect terminal inverted repeats and generate 8 bp direct repeats at their target sequences. Deletion formation mediated by IS26R was also observed. These functional and structural features of IS26 are characteristic of a prokaryotic mobile genetic element.     

Microbial Oxidation of the Isoprenoid Alkane Pristane

Microorganisms capable of utilizing pristane (2,6,10,14-tetramethylpentadecane) as a sole source of carbon and energy were isolated from soil specimens. A strain BPM 1613, tentatively classified in the genus Nocardia, accumulated several oxidation products of pristane in the culture fluid. Silica gel chromatography of the ethyl ether extract from the culture fluid yielded pristanol and pristanic acid as major products and pristyl pristanate and pristyl aldehyde as minor products. The confirmations on the estimated structures of these oxidation products are described in detail.     

A biochemical and genetic study on all non-synonymous single nucleotide polymorphisms of the gene encoding human deoxyribonuclease I potentially relevant to autoimmunity

A reduction of deoxyribonuclease I (DNase I) activity levels in the serum of patients with autoimmune diseases has been reported. The objectives of this study were to clarify genetic and biochemical aspects of 12 non-synonymous SNPs in the human gene (DNASE1), potentially giving rise to an alteration in the in vivo DNase I activity levels. Genotyping of all the non-synonymous SNPs was performed in healthy subjects of three ethnic groups including 15 populations using newly developed methods. Among them, only four SNPs, R-21S, Y95S, G105R, and Q222R were polymorphic in all or some populations; Asian group showed a relatively low genetic diversity of these SNPs. Furthermore, the distribution pattern of the common SNP Q222R was classified into three ethnic groups. The activity levels of the amino acid-substituted DNase I forms derived from SNPs R-21S, G105R, P132A, and P197S were significantly high compared with that of the wild-type; the polymorphic SNPs R-21S and G105R gave rise to a high activity-harboring DNase I isoform. On the other hand, activity levels from Q35H, R85G, V89M, C209Y, Q222R, and A224P were significantly low, but these SNPs, except Q222R, were not distributed in any of the populations. However, since these SNPs may produce potentially low levels of in vivo DNase I activity, a minor allele in each SNP will be served as a genetic risk factor for autoimmune diseases. These findings on non-synonymous SNPs in DNASE1 may provide a biochemical-genetic basis for the clarification of a possible relationship between DNase I and the diseases.     

Effects of life history strategies and tree competition on species coexistence in a sub-boreal coniferous forest of Japan

We examined the effects of different life history strategies and tree competition on species coexistence in a northern coniferous forest. We investigated the growth and demography of trees with stems ≥1 cm dbh in a 2-ha study plot in the Taisetsu Mountains of northern Japan. Three species, Abies sachalinensis, Picea jezoensis, and Picea glehnii, were found to be dominant in the forest. A. sachalinensis was the most dominant species in the understory, while the two Picea spp. were more abundant in the larger dbh size classes. The turnover rate of A. sachalinensis was about twice that of the Picea spp. The relative growth rate of understory trees in each species did not differ between different canopy conditions (closed canopy or canopy gap). The competitive advantage between A. sachalinensis and P. glehnii switched as they grew from understory (A. sachalinensis superior competitor) to canopy trees (P. glehnii superior competitor). Meanwhile, A. sachalinensis and P. jezoensis exhibited different environmental preferences. We propose that reversal in competitive superiority between different growth stages and trade-off between longevity and turnover are more important factors to promote their coexistence than regeneration niche differentiation related to canopy gaps in this sub-boreal coniferous forest.     

Molecular Adaptation of rbcL in the Heterophyllous Aquatic Plant Potamogeton

Background

Heterophyllous aquatic plants show marked phenotypic plasticity. They adapt to environmental changes by producing different leaf types: submerged, floating and terrestrial leaves. By contrast, homophyllous plants produce only submerged leaves and grow entirely underwater. Heterophylly and submerged homophylly evolved under selective pressure modifying the species-specific optima for photosynthesis, but little is known about the evolutionary outcome of habit. Recent evolutionary analyses suggested that rbcL, a chloroplast gene that encodes a catalytic subunit of RuBisCO, evolves under positive selection in most land plant lineages. To examine the adaptive evolutionary process linked to heterophylly or homophylly, we analyzed positive selection in the rbcL sequences of ecologically diverse aquatic plants, Japanese Potamogeton.

Principal Findings

Phylogenetic and maximum likelihood analyses of codon substitution models indicated that Potamogeton rbcL has evolved under positive Darwinian selection. The positive selection has operated specifically in heterophyllous lineages but not in homophyllous ones in the branch-site models. This suggests that the selective pressure on this chloroplast gene was higher for heterophyllous lineages than for homophyllous lineages. The replacement of 12 amino acids occurred at structurally important sites in the quaternary structure of RbcL, two of which (residue 225 and 281) were identified as potentially under positive selection.

Conclusions/Significance

Our analysis did not show an exact relationship between the amino acid replacements and heterophylly or homophylly but revealed that lineage-specific positive selection acted on the Potamogeton rbcL. The contrasting ecological conditions between heterophyllous and homophyllous plants have imposed different selective pressures on the photosynthetic system. The increased amino acid replacement in RbcL may reflect the continuous fine-tuning of RuBisCO under varying ecological conditions.