Cloning of a human tRNA isopentenyl transferase

A cDNA of human origin is shown to encode a tRNA isopentenyl transferase (E.C. 2.5.1.8). Expression of the gene in a Saccharomyces cerevisiae mutant lacking the endogenous tRNA isopentenyl transferase MOD5 resulted in functional complementation and reintroduction of isopentenyladenosine into tRNA. The deduced amino acid sequence contains a number of regions conserved in known tRNA isopentenyl transferases. The similarity to the S. cerevisiae MOD5 protein is 53%, and to the Escherichia coli MiaA protein 47%. The human sequence was found to contain a single C2H2 Zn-finger-like motif, which was detected also in the MOD5 protein, and several putative tRNA transferases located by BLAST searches, but not in prokaryotic homologues.     

Modelling compensatory regrowth with bud dormancy and gradual activation of buds

Many plants show compensatory regrowth after herbivory and dormant buds often have an important role in compensatory responses. Theoretical models have shown that herbivore damage may select for a bud bank, i.e., a pool of dormant buds that are protected from herbivory and that are activated after herbivore damage. Earlier models assumed that undamaged plants cannot activate their dormant buds without damage, although they apparently have sufficient resources for successful seed production through the additional shoots dormant buds could produce. However, many plants are able to gradually activate buds over an extended period of time without any cue from damage. The aim of this study was to analyze how herbivory imposes selection for gradual mobilization of the bud bank. I assume that selection pressures that affect the fraction of buds active at each time point include damage by herbivores, time left to the end of season, and the opportunity costs of dormant buds. I modelled bud dynamics with gradual activation when there is a single damage event and (i) when the seed set of a shoot is not dependent on the time it is active, or (ii) when the seed set of a shoot diminishes with later activation. In addition, I analyzed how (iii) risk of repeated herbivory affects selection for gradual activation. Under these models, gradual activation is optimal over a wide range of herbivory pressures. Selection appears to favour activation of all buds at the beginning of the season only when herbivore pressure is weak and when early shoots have a higher seed set than late shoots. Alternatively, strong herbivore pressure and late damage may select for a large bud bank throughout the growing season, without gradual activation; the bud bank is only mobilized after damage. In this case, damaged plants can overcompensate, i.e. they have a higher seed set than undamaged plants with the same bud activation pattern. Selection for overcompensation demands a stronger herbivore pressure in this current model than in earlier bud bank models. The model never predicts selection for overcompensation when there is a risk of repeated herbivory. This revised version was published online in July 2006 with corrections to the Cover Date.     

Lack of collagen type specificity for lysyl hydroxylase isoforms

Lysyl hydroxylase is the enzyme catalyzing the formation of hydroxylysyl residues in collagens. Large differences in the extent of hydroxylysyl residues are found among collagen types. Three lysyl hydroxylase isoenzymes (LH1, LH2, LH3) have recently been characterized from human and mouse tissues. Nothing is known about the distribution of these isoforms within cells or whether they exhibit collagen type specificity. We measured mRNA levels of the three isoforms, as well as the mRNAs of the main collagen types I, III, IV, and V and the alpha subunit of prolyl 4-hydroxylase, another enzyme involved in collagen biosynthesis, in different human cell lines. Large variations were found in mRNA expression of LH1 and LH2 but not LH3. Immunoblotting was utilized to confirm the results of Northern hybridization. The levels of mRNA of LH1, LH2, and the alpha subunit of prolyl 4-hydroxylase showed significant correlations with each other. The LH3 mRNA levels did not correlate with those of LH1, LH2, or the alpa subunit of prolyl 4-hydroxylase, clearly indicating a difference in the regulation of LH3. No correlation was observed between LH isoforms and individual collagen types, indicating a lack of collagen type specificity for lysyl hydroxylase isoforms. Our observations suggest that LH1, LH2, and the alpha subunit of prolyl 4-hydroxylase are coregulated together with total collagen synthesis but not with the specific collagen types and indicate that LH3 behaves differently from LH1 and LH2, implying a difference in their substrates. These observations set the basis for further studies to define the functions of lysyl hydroxylase isoforms.     

Ammonium and nitrate uptake rates and rhizosphere pH in non-mycorrhizal roots of Norway spruce [Picea abies (L.) Karst.]

Summary Relationships between root zone temperature, concentrations and uptake rates of NH ₄ ⁺ and NO ₃ ^– were studied in non-mycorrhizal roots of 4-year-old Norway spruce under controlled environmental conditions. Additionally, in a forest stand NH ₄ ⁺ and NO ₃ ^– uptake rates along the root axis and changes in the rhizosphere pH were measured. In the concentration (C_min) range of 100–150 M uptake rates of NH ₄ ⁺ were 3–4 times higher than those of NO ₃ ^– The preference for NH ₄ ⁺ uptake was also reflected in the minimum concentration (C_min) values. Supplying NH₄NO₃, the rate of NO ₃ ^– uptake was very low until the NH ₄ ⁺ concentrations had fallen below about 100 M. The shift from NH ₄ ⁺ to NO ₃ ^– uptake was correlated with a corresponding shift from net H⁺ production to net H⁺ consumption in the external solution. The uptake rates of NH ₄ ⁺ were correlated with equimolar net production of H⁺. With NO ₃ ^– nutrition net consumption of H⁺ was approximately twice as high as uptake rates of NO ₃ ^– In the forest stand the NO ₃ ^– concentration in the soil solution was more than 10 times higher than the NH ₄ ⁺ concentration (<100 M), and the rhizosphere pH of non-mycorrhizal roots considerably higher than the bulk soil pH. The rhizosphere pH increase was particularly evident in apical root zones where the rates of water and NO ₃ ^– uptake and nitrate reductase activity were also higher. The results are summarized in a model of water and nutrient transport to, and uptake by, non-mycorrhizal roots of Norway spruce in a forest stand. Model calculations indicate that delivery to the roots by mass flow may meet most of the plant demand of nitrogen and calcium, and that non-mycorrhizal root tips have the potential to take up most of the delivered nitrate and calcium.     

Silicon supply modifies C:N:P stoichiometry and growth of Phragmites australis

Silicon is a non-essential element for plant growth. Nevertheless, it affects plant stress resistance and in some plants, such as grasses, it may substitute carbon (C) compounds in cell walls, thereby influencing C allocation patterns and biomass production. How variation in silicon supply over a narrow range affects nitrogen (N) and phosphorus (P) uptake by plants has also been investigated in some detail. However, little is known about effects on the stoichiometric relationships between C, N and P when silicon supply varies over a broader range. Here, we assessed the effect of silicon on aboveground biomass production and C:N:P stoichiometry of common reed, Phragmites australis, in a pot experiment in which three widely differing levels of silicon were supplied. Scanning electron microscopy (SEM) showed that elevated silicon supply promoted silica deposition in the epidermis of Phragmites leaves. This resulted in altered N:P ratios, whereas C:N ratios changed only slightly. Plant growth was slightly (but not significantly) enhanced at intermediate silicon supply levels but significantly decreased at high levels. These findings point to the potential of silicon to impact plant growth and elemental stoichiometry and, by extension, to affect biogeochemical cycles in ecosystems dominated by Phragmites and other grasses and sedges.     

Somatic progenitor cell vulnerability to mitochondrial DNA mutagenesis underlies progeroid phenotypes in Polg mutator mice

Somatic stem cell (SSC) dysfunction is typical for different progeroid phenotypes in mice with genomic DNA repair defects. MtDNA mutagenesis in mice with defective Polg exonuclease activity also leads to progeroid symptoms, by an unknown mechanism. We found that Polg-Mutator mice had neural (NSC) and hematopoietic progenitor (HPC) dysfunction already from embryogenesis. NSC self-renewal was decreased in vitro, and quiescent NSC amounts were reduced in vivo. HPCs showed abnormal lineage differentiation leading to anemia and lymphopenia. N-acetyl-L-cysteine treatment rescued both NSC and HPC abnormalities, suggesting that subtle ROS/redox changes, induced by mtDNA mutagenesis, modulate SSC function. Our results show that mtDNA mutagenesis affected SSC function early but manifested as respiratory chain deficiency in nondividing tissues in old age. Deletor mice, having mtDNA deletions in postmitotic cells and no progeria, had normal SSCs. We propose that SSC compartment is sensitive to mtDNA mutagenesis, and that mitochondrial dysfunction in SSCs can underlie progeroid manifestations.     

A Sexual Ornament in Chickens Is Affected by Pleiotropic Alleles at HAO1 and BMP2, Selected during Domestication

Domestication is one of the strongest forms of short-term, directional selection. Although selection is typically only exerted on one or a few target traits, domestication can lead to numerous changes in many seemingly unrelated phenotypes. It is unknown whether such correlated responses are due to pleiotropy or linkage between separate genetic architectures. Using three separate intercrosses between wild and domestic chickens, a locus affecting comb mass (a sexual ornament in the chicken) and several fitness traits (primarily medullary bone allocation and fecundity) was identified. This locus contains two tightly-linked genes, BMP2 and HAO1, which together produce the range of pleiotropic effects seen. This study demonstrates the importance of pleiotropy (or extremely close linkage) in domestication. The nature of this pleiotropy also provides insights into how this sexual ornament could be maintained in wild populations.     

Multiple DNA binding domains mediate the function of the ERCC1-XPF protein in nucleotide excision repair

ERCC1-XPF is a heterodimeric, structure-specific endonuclease that cleaves single-stranded/double-stranded DNA junctions and has roles in nucleotide excision repair (NER), interstrand crosslink (ICL) repair, homologous recombination, and possibly other pathways. In NER, ERCC1-XPF is recruited to DNA lesions by interaction with XPA and incises the DNA 5' to the lesion. We studied the role of the four C-terminal DNA binding domains in mediating NER activity and cleavage of model substrates. We found that mutations in the helix-hairpin-helix domain of ERCC1 and the nuclease domain of XPF abolished cleavage activity on model substrates. Interestingly, mutations in multiple DNA binding domains were needed to significantly diminish NER activity in vitro and in vivo, suggesting that interactions with proteins in the NER incision complex can compensate for some defects in DNA binding. Mutations in DNA binding domains of ERCC1-XPF render cells more sensitive to the crosslinking agent mitomycin C than to ultraviolet radiation, suggesting that the ICL repair function of ERCC1-XPF requires tighter substrate binding than NER. Our studies show that multiple domains of ERCC1-XPF contribute to substrate binding, and are consistent with models of NER suggesting that multiple weak protein-DNA and protein-protein interactions drive progression through the pathway. Our findings are discussed in the context of structural studies of individual domains of ERCC1-XPF and of its role in multiple DNA repair pathways.     

Impact of IL28B-related single nucleotide polymorphisms on liver histopathology in chronic hepatitis C genotype 2 and 3

Background and Aims

Recently, several genome-wide association studies have revealed that single nucleotide polymorphisms (SNPs) in proximity to IL28B predict spontaneous clearance of HCV infection as well as outcome following peginterferon and ribavirin therapy among HCV genotype 1 infected patients. The present study aimed to evaluate the impact of IL28B SNP variability on liver histology in the context of a phase III treatment trial (NORDynamIC) for treatment-naïve patients with chronic HCV genotype 2 or 3 infection, where pretreatment liver biopsies were mandatory.

Methods

Three hundred and thirty-nine Caucasian patients had samples available for IL28B genotyping (rs12979860) of whom 314 had pretreatment liver biopsies that were evaluated using the Ishak protocol, allowing for detailed grading and staging of liver histopathology.

Results

IL28B CC_rs12979860 genotype in HCV genotype 3 infected patients was associated with higher ALT levels (p<0.0001), higher AST to platelet ratio index (APRI; p = 0.001), and higher baseline viral load (p<0.0001) as compared to patients with the CT or TT genotypes. Additionally the CC_rs12979860 genotype entailed more pronounced portal inflammation (p = 0.02) and steatosis (p = 0.03). None of these associations were noted among HCV genotype 2 infected patients.

Conclusion

This study shows that the CC_rs12979860 SNP is associated with more pronounced liver histopathology in patients chronically infected with HCV genotype 3, which may be secondary to higher viral load. The finding that IL28B variability did not impact on liver pathology or viral load among genotype 2 infected patients implies that IL28B may differentially regulate the course of genotype 2 and 3 infection.