Structure of 1-aminocyclopropane-1-carboxylate synthase in complex with an amino-oxy analogue of the substrate: implications for substrate binding

The crystal structure of 1-aminocyclopropane-1-carboxylate (ACC) synthase in complex with the substrate analogue [2-(amino-oxy)ethyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium (AMA) was determined at 2.01-A resolution. The crystallographic results show that a covalent adduct (oxime) is formed between AMA (an amino-oxy analogue of the natural substrate S-adenosyl-L-methionine (SAM)) and the pyridoxal 5'-phosphate (PLP) cofactor of ACC synthase. The oxime formation is supported by spectroscopic data. The ACC synthase-AMA structure provides reliable and detailed information on the binding mode of the natural substrate of ACC synthase and complements previous structural and functional work on this enzyme.     

Modulation of the internal aldimine pK(a)'s of 1-aminocyclopropane-1-carboxylate synthase and aspartate aminotransferase by specific active site residues

The active sites of the homologous pyridoxal phosphate- (PLP-) dependent enzymes 1-aminocyclopropane-1-carboxylate (ACC) synthase and aspartate aminotransferase (AATase) are almost entirely conserved, yet the pK(a)'s of the two internal aldimines are 9.3 and 7.0, respectively, to complement the substrate pK(a)'s (S-adenosylmethionine pK(a) = 7.8 and aspartate pK(a) = 9.9). This complementation is required for maximum enzymatic activity in the physiological pH range. The most prominent structural difference in the active site is that Ile232 of ACC synthase is replaced by alanine in AATase. The I232A mutation was introduced into ACC synthase with a resulting 1.1 unit decrease (from 9.3 to 8.2) in the aldimine pK(a), thus identifying Ile232 as a major determinant of the high pK(a) of ACC synthase. The mutation also resulted in reduced k(cat) (0.5 vs 11 s(-1)) and k(cat)/K(m) values (5.0 x 10(4) vs 1.2 x 10(6) M(-1) s(-1)). The effect of the mutation is interpreted as the result of shortening of the Tyr233-PLP hydrogen bond. Addition of the Y233F mutation to the I232A ACC synthase to generate the double mutant I232A/Y233F raised the pK(a) from 8.2 to 8.8, because the Y233F mutation eliminates the hydrogen bond between that residue and PLP. The introduction of the retro mutation A224I into AATase raised the aldimine pK(a) of that enzyme from 6.96 to 7.16 and resulted in a decrease in single-turnover k(max) (108 vs 900 s(-1) for aspartate) and k(max)/K(m)(app) (7.5 x 10(4) vs 3.8 x 10(5) M(-1) s(-1)) values. The distance from the pyridine nitrogen of the cofactor to a conserved aspartate residue is 2.6 A in AATase and 3.8 A in ACC synthase. The D230E mutation introduced into ACC synthase to close this distance increases the aldimine pK(a) from 9.3 to 10.0, as would be predicted from a shortened hydrogen bond.     

Experimental Hydrodynamics and Evolution: Function of Median Fins in Ray-finned Fishes

The median fins of fishes consist of the dorsal, anal, and caudal fins and have long been thought to play an important role in generating locomotor force during both steady swimming and maneuvering. But the orientations and magnitudes of these forces, the mechanisms by which they are generated, and how fish modulate median fin forces have remained largely unknown until the recent advent of Digital Particle Image Velocimetry (DPIV) which allows empirical analysis of force magnitude and direction. Experimental hydrodynamic studies of median fin function in fishes are of special utility when conducted in a comparative phylogenetic context, and we have examined fin function in four ray-finned fish clades (sturgeon, trout, sunfish, and mackerel) with the goal of testing classical hypotheses of fin function and evolution. In this paper we summarize two recent technical developments in DPIV methodology, and discuss key recent findings relevant to median fin function. High-resolution DPIV using a recursive local-correlation algorithm allows quantification of small vortices, while stereo-DPIV permits simultaneous measurement of x, y, and z flow velocity components within a single planar light sheet. Analyses of median fin wakes reveal that lateral forces are high relative to thrust force, and that mechanical performance of median fins (i.e., thrust as a proportion of total force) averages 0.35, a surprisingly low value. Large lateral forces which could arise as an unavoidable consequence of thrust generation using an undulatory propulsor may also enhance stability and maneuverability. Analysis of hydrodynamic function of the soft dorsal fin in bluegill sunfish shows that a thrust wake is generated that accounts for 12% of total thrust and that the thrust generation by the caudal fin may be enhanced by interception of the dorsal fin wake. Integration of experimental studies of fin wakes, computational approaches, and mechanical models of fin function promise understanding of instantaneous forces on fish fins during the propulsive cycle as well as exploration of a broader locomotor design space and its hydrodynamic consequences.     

Experimental hydrodynamics of fish locomotion: functional insights from wake visualization

Despite enormous progress during the last twenty years in understandingthe mechanistic basis of aquatic animal propulsion—a taskinvolving the construction of a substantial data base on patternsof fin and body kinematics and locomotor muscle function—thereremains a key area in which biologists have little information:the relationship between propulsor activity and water movementin the wake. How is internal muscular force translated intoexternal force exerted on the water? What is the pattern offluid force production by different fish fins (e.g., pectoral,caudal, dorsal) and how does swimming force vary with speedand among species? These types of questions have received considerableattention in analyses of terrestrial locomotion where forceoutput by limbs can be measured directly with force plates.But how can forces exerted by animals moving through fluid bemeasured? The advent of digital particle image velocimetry (DPIV)has provided an experimental hydrodynamic approach for quantifyingthe locomotor forces of freely moving animals in fluids, andhas resulted in significant new insights into the mechanismsof fish propulsion. In this paper we present ten "lessons learned"from the application of DPIV to problems of fish locomotionover the last five years. (1) Three-dimensional DPIV analysisis critical for reconstructing wake geometry. (2) DPIV analysisreveals the orientation of locomotor reaction forces. (3) DPIVanalysis allows calculation of the magnitude of locomotor forces.(4) Swimming speed can have a major impact on wake structure.(5) DPIV can reveal interspecific differences in vortex wakemorphology. (6) DPIV analysis can provide new insights intothe limits to locomotor performance. (7) DPIV demonstrates thefunctional versatility of fish fins. (8) DPIV reveals hydrodynamicforce partitioning among fins. (9) DPIV shows that wake interactionamong fins may enhance thrust production. (10) Experimentalhydrodynamic analysis can provide insight into the functionalsignificance of evolutionary variation in fin design.     

An anthranilate synthase of the extreme aminase type in a species of blue-green bacteria (algae)

Anthranilate synthase of Agmenellum quadruplicatum, a unicellular species of blue-green bacteria, consists of two nonidentical subunits. A 72,000 dalton protein has aminase activity but is incapable of reaction with glutamine (amidotransferase) unless a second protein (18,000 molecular weight) is present. The small subunit was first detected through its ability to complement a partially purified aminase subunit from Bacillus subtilis to produce a hybrid complex capable of amidotransferase function. Conditions for the function of the heterologous complex were less stringent than for the homologous A. quadruplicatum complex. A reducing agent such as dithiothreitol stabilizes the A. quadruplicatum aminase subunit and is obligatory for amidotransferase function. L-Tryptophan feedback inhibits both the aminase and amidotransferase reactions of anthranilate synthase; Ki values of 6 X 10(-8) M for the amidotransferase activity and 2 X 10(-6) M for the aminase activity were obtained. The Km value calculated for ammonia (2.2 mM) was more favorable than the Km value glutamine (13 mM). Likewise, the Vmax of anthranilate synthase was greater with ammonia than with glutamine. Starvation of a tryptophan auxotroph results in a threefold derepression of the aminase subunit, but no corresponding increase in the small 18,000 M subunit occurs. While microbial anthranilate synthase complexes are remarkably similar overall, the relatively good aminase activity of the A. quadruplicatum enzyme may be of physiological significance in nature.     

Predicted climate change,sea-level rise and wetland management in the Australian wet-dry tropics

The vulnerability of coastal areas in the Alligator Rivers Region (northern Australia) to predicted climate change and potential sea level rise was assessed as part of a national study. The coastal area is composed of a number of estuarine and freshwater habitats that are intricately interlinked and can not be effectively managed in isolation of each other. The outcomes of the assessment focused on the floodplain environments of the region, but are also applicable to the broader wetland environments that occur across the northern Australian wet-dry tropics. The management regime in the region is based on traditional Aboriginal ownership of much of the land, which is leased to the federal government as a national park. Scientific research has been intensive; however, important questions have been raised about the collation and effective use of this information. The vulnerability assessment framework required effective use of this information and cooperation with the management authority to identify change scenarios and management and research responses. A climate change scenario was established as the basis for predicting biophysical change in the coastal and wetland environments. The predictions suggest that large-scale change will occur and many of the existing values derived from these areas (i.e., usage by traditional Aboriginal occupants, and nature conservation) could be degraded or even lost. Recommended management responses include the initiation of specific monitoring, empowerment of local bodies to take active management steps, and to increase awareness of the likely consequences of change. Further data coordination and review are needed to ascertain the validity of the predictions and the concomitant management responses.     

Seasonal-like plasticity of spontaneous firing rate in a songbird pre-motor nucleus

Many animals exhibit seasonal changes in behavior and its underlying neural substrates. In seasonally breeding songbirds, the brain nuclei that control song learning and production undergo substantial structural changes at the onset of each breeding season, in association with changes in song behavior. These changes are largely mediated by photoperiod-dependent changes in circulating concentrations of gonadal steroid hormones. Little is known, however, about whether changes in the electrophysiological activity of neurons accompany the dramatic morphological changes in the song nuclei. Here we induced seasonal-like changes in the song systems of adult white-crowned sparrows and used extracellular recording in acute brain slices from those individuals to study physiological properties of neurons in the robust nucleus of the arcopallium (RA), a pre-motor nucleus necessary for song production. We report that: RA neurons from birds in breeding condition show a more than twofold increase in spontaneous firing rate compared to those from nonbreeding condition; this change appears to require both androgenic and estrogenic actions; and this change is intrinsic to the RA neurons. Thus, neurons in the song circuit exhibit both morphological and physiological adult seasonal plasticity.     

Functional aspects of song learning in songbirds

The oscine passerines, or 'songbirds', are one of the few animal taxa in which individuals learn their vocal signals. Recent comparative studies reveal a remarkable diversity of song-learning strategies in the songbirds. Here, we discuss recent studies that shed light on the possible functional basis of different song-learning programs. We argue that further insights into the evolution and ecology of song learning will require that comparative data and functional hypotheses be analyzed in a phylogenetic context, and we review recent studies that we feel might be the first steps in this process.     

Influences of chronic and current season grazing by collared pikas on above-ground biomass and species richness in subarctic alpine meadows

We studied an alpine herbivory gradient established by collared pikas, a small central place foraging lagomorph, to examine the effects of multiple grazing levels on above-ground live biomass (AGB) and species richness (SR) in alpine tundra. The effects of within-season (four sampling periods), multi-season (across three summers) and longer-term dynamics (inferred from spatial location of vegetation with respect to pika haypiles) were examined. Along the grazing gradient, we found support for and against hypotheses that propose biphasic, increasing, or decreasing responses to herbivory, both in terms of AGB and SR. Our results suggest that plant–herbivore predictability is still weak. To further examine the impact of herbivory, we experimentally removed pikas using mesh exclosures placed at increasing distance from the edge of talus occupied by pikas. AGB after the second consecutive year of herbivore exclusion increased by 125% compared to control plots in highly grazed areas adjacent to talus (<1 m). In more lightly grazed sites at distances 1–6 m from talus, AGB increased by more than 40% after pikas were removed. No differences were observed in the ungrazed sites >6 m from talus. AGB was highest in meadow patches previously grazed by pikas compared to those with little grazing history, but this response was only observed after two seasons following release from herbivory. Grazed sites at distances of 1–6 m had the highest SR. These results indicate that multi-year measurements of growth are particularly relevant in ecosystems dominated by long-lived perennials in regions where productivity is low. Infrequent herbivore vacancies may provide local short-term release from pika grazing, thereby contributing to the persistence of productive, highly palatable vegetation.