Impact of Plant Functional Group, Plant Species, and Sampling Time on the Composition of nirK-Type Denitrifier Communities in Soil

We studied the influence of eight nonleguminous grassland plant species belonging to two functional groups (grasses and forbs) on the composition of soil denitrifier communities in experimental microcosms over two consecutive years. Denitrifier community composition was analyzed by terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified nirK gene fragments coding for the copper-containing nitrite reductase. The impact of experimental factors (plant functional group, plant species, sampling time, and interactions between them) on the structure of soil denitrifier communities (i.e., T-RFLP patterns) was analyzed by canonical correspondence analysis. While the functional group of a plant did not affect nirK-type denitrifier communities, plant species identity did influence their composition. This effect changed with sampling time, indicating community changes due to seasonal conditions and a development of the plants in the microcosms. Differences in total soil nitrogen and carbon, soil pH, and root biomass were observed at the end of the experiment. However, statistical analysis revealed that the plants affected the nirK-type denitrifier community composition directly, e.g., through root exudates. Assignment of abundant T-RFs to cloned nirK sequences from the soil and subsequent phylogenetic analysis indicated a dominance of yet-unknown nirK genotypes and of genes related to nirK from denitrifiers of the order Rhizobiales. In conclusion, individual species of nonleguminous plants directly influenced the composition of denitrifier communities in soil, but environmental conditions had additional significant effects.     

Expression of collier in the premandibular segment of myriapods: support for the traditional Atelocerata concept or a case of convergence?

Background  

A recent study on expression and function of the ortholog of the Drosophila collier (col) gene in various arthropods including insects, crustaceans and chelicerates suggested a de novo function of col in the development of the appendage-less intercalary segment of insects. However, this assumption was made on the background of the now widely-accepted Pancrustacea hypothesis that hexapods represent an in-group of the crustaceans. It was therefore assumed that the expression of col in myriapods would reflect the ancestral state like in crustaceans and chelicerates, i.e. absence from the premandibular/intercalary segment and hence no function in its formation.     

Leaf chlorophyll content as a proxy for leaf photosynthetic capacity

Improving the accuracy of estimates of forest carbon exchange is a central priority for understanding ecosystem response to increased atmospheric CO₂ levels and improving carbon cycle modelling. However, the spatially continuous parameterization of photosynthetic capacity (Vcmax) at global scales and appropriate temporal intervals within terrestrial biosphere models (TBMs) remains unresolved. This research investigates the use of biochemical parameters for modelling leaf photosynthetic capacity within a deciduous forest. Particular attention is given to the impacts of seasonality on both leaf biophysical variables and physiological processes, and their interdependent relationships. Four deciduous tree species were sampled across three growing seasons (2013–2015), approximately every 10 days for leaf chlorophyll content (Chl_Leaf) and canopy structure. Leaf nitrogen (N_Area) was also measured during 2014. Leaf photosynthesis was measured during 2014–2015 using a Li‐6400 gas‐exchange system, with A‐Ci curves to model Vcmax. Results showed that seasonality and variations between species resulted in weak relationships between Vcmax normalized to 25°C () and N_Area (R² = 0.62, P < 0.001), whereas Chl_Leaf demonstrated a much stronger correlation with (R² = 0.78, P < 0.001). The relationship between Chl_Leaf and N_Area was also weak (R² = 0.47, P < 0.001), possibly due to the dynamic partitioning of nitrogen, between and within photosynthetic and nonphotosynthetic fractions. The spatial and temporal variability of was mapped using Landsat TM/ETM satellite data across the forest site, using physical models to derive Chl_Leaf. TBMs largely treat photosynthetic parameters as either fixed constants or varying according to leaf nitrogen content. This research challenges assumptions that simple N_Area– relationships can reliably be used to constrain photosynthetic capacity in TBMs, even within the same plant functional type. It is suggested that Chl_Leaf provides a more accurate, direct proxy for and is also more easily retrievable from satellite data. These results have important implications for carbon modelling within deciduous ecosystems.     

Crystal structure of NblA from Anabaena sp. PCC 7120, a small protein playing a key role in phycobilisome degradation

Cyanobacterial light-harvesting complexes, the phycobilisomes, are proteolytically degraded when the organisms are starved for combined nitrogen, a process referred to as chlorosis or bleaching. Gene nblA, present in all phycobilisome-containing organisms, encodes a protein of about 7 kDa that plays a key role in phycobilisome degradation. The mode of action of NblA in this degradation process is poorly understood. Here we presented the 1.8-A crystal structure of NblA from Anabaena sp. PCC 7120. In the crystal, NblA is present as a four-helix bundle formed by dimers, the basic structural units. By using pull-down assays with immobilized NblA and peptide scanning, we showed that NblA specifically binds to the alpha-subunits of phycocyanin and phycoerythrocyanin, the main building blocks of the phycobilisome rod structure. By site-directed mutagenesis, we identified amino acid residues in NblA that are involved in phycobilisome binding. The results provided evidence that NblA is directly involved in phycobilisome degradation, and the results allowed us to present a model that gives insight into the interaction of this small protein with the phycobilisomes.     

Mutations in ACY1, the gene encoding aminoacylase 1, cause a novel inborn error of metabolism

N-terminal acetylation of proteins is a widespread and highly conserved process. Aminoacylase 1 (ACY1; EC 3.5.14) is the most abundant of the aminoacylases, a class of enzymes involved in hydrolysis of N-acetylated proteins. Here, we present four children with genetic deficiency of ACY1. They were identified through organic acid analyses using gas chromatography-mass spectrometry, revealing increased urinary excretion of several N-acetylated amino acids, including the derivatives of methionine, glutamic acid, alanine, leucine, glycine, valine, and isoleucine. Nuclear magnetic resonance spectroscopy analysis of urine samples detected a distinct pattern of N-acetylated metabolites, consistent with ACY1 dysfunction. Functional analyses of patients' lymphoblasts demonstrated ACY1 deficiency. Mutation analysis uncovered recessive loss-of-function or missense ACY1 mutations in all four individuals affected. We conclude that ACY1 mutations in these children led to functional ACY1 deficiency and excretion of N-acetylated amino acids. Questions remain, however, as to the clinical significance of ACY1 deficiency. The ACY1-deficient individuals were ascertained through urine metabolic screening because of unspecific psychomotor delay (one subject), psychomotor delay with atrophy of the vermis and syringomyelia (one subject), marked muscular hypotonia (one subject), and follow-up for early treated biotinidase deficiency and normal clinical findings (one subject). Because ACY1 is evolutionarily conserved in fish, frog, mouse, and human and is expressed in the central nervous system (CNS) in human, a role in CNS function or development is conceivable but has yet to be demonstrated. Thus, at this point, we cannot state whether ACY1 deficiency has pathogenic significance with pleiotropic clinical expression or is simply a biochemical variant. Awareness of this new genetic entity may help both in delineating its clinical significance and in avoiding erroneous diagnoses.     

Tandem duplication and divergence of a sea urchin protein belonging to the troponin C superfamily

The Spec1 and Spec2 proteins of the sea urchin Strongylocentrotus purpuratus are related to calmodulin, troponin C, and myosin light chains by sequence similarity in their four calcium binding domains. These domains, the EF-hands, are distinct helix-loop-helix structures of about 40 amino acids. The Spec1 and Spec2 genes are expressed specifically in aboral ectoderm cells of the developing embryo; however, the function of the Spec proteins in these cells is unknown. To find conserved regions of the proteins that might be important for structure and function, Spec homologues from Lytechinus pictus, a distantly related sea urchin, were sought. L. pictus embryos do not synthesize detectable amounts of the 14,000-17,000-Da Spec proteins as determined by two-dimensional gel electro-phoresis, but do synthesize three 34,000-Da proteins that cross-react with Spec1 antibodies and display a similar ontogenetic pattern of expression. cDNA clones were isolated by hybridization to a synthetic oligonucleotide corresponding to the EF-hand. One clone, LpS1, encodes an mRNA with developmental properties like those of the S. purpuratus Spec mRNAs. However, LpS1 contains an open reading frame for a protein of 34,000 Da rather than 17,000 Da, and antibodies raised against part of the LpS1 reading frame demonstrate that LpS1 encodes a 34,000-Da protein in L. pictus embryos. The sequence of LpS1 reveals the presence of eight EF-hand domains, which share structural homology with the Spec1 or Spec2 EF-hands; however, little else in the protein sequence is conserved. The results support the hypothesis that the LpS1 gene arose from a duplication of an ancestral Spec gene and that the overall structural features of the Spec family of proteins are more conserved than the amino acid sequences.     

Phototropism of rice (Oryza sativa L.) coleoptiles: fluence-response relationships, kinetics and photogravitropic equilibrium

Phototropism of rice (Oryza sativa L.) coleoptiles induced by unilateral blue light was characterized using red-light-grown seedlings. Phototropic fluence-response relationships, investigated mainly with submerged coleoptiles, revealed three response types previously identified in oat and maize coleoptiles: two pulse-induced positive phototropisms and a phototropism that depended on stimulation time. The effective ranges of fluences and fluence rates were comparable to those reported for maize. Compared with oats and maize, however, curvature responses in rice were much smaller and coleoptiles straightened faster after establishing the maximal curvature. When stimulated continuously, submerged coleoptiles developed curvature slowly over a period of 6 h, whereas air-grown coleoptiles, which showed smaller phototropic responsiveness, established a photogravitropic equilibrium from about 4 h of stimulation. The plot of the equilibrium angle against log fluence rates yielded a bell-shaped optimum curve that spanned over a relatively wide fluence-rate range; a maximal curvature of 25° occurred at a fluence rate of 1 μmol · m⁻² · s⁻¹. This optimum curve apparently reflects the light sensitivity of the steady-state phototropic response. Received: 28 June 1996 / Accepted: 30 July 1996