Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system.

A circularly permuted streptavidin (CP51/46) has been designed to remove the flexible polypeptide loop that undergoes an open to closed conformational change when biotin is bound. The original termini have been joined by a tetrapeptide linker, and four loop residues have been removed, resulting in the creation of new N- and C-termini. Isothermal titration calorimetric studies show that the association constant has been reduced approximately six orders of magnitude below that of wild-type streptavidin to 10(7) M(-1). The deltaH degrees of biotin association for CP51/46 is reduced by 11.1 kcal/mol. Crystal structures of CP51/46 and its biotin complex show no significant alterations in the binding site upon removal of the loop. A hydrogen bond between Ser45 and Ser52 found in the absence of biotin is broken in the closed conformation as the side-chain hydroxyl of Ser45 moves to hydrogen bond to a ureido nitrogen of biotin. This is true in both the wild-type and CP51/46 forms of the protein, and the hydrogen bonding interaction might thus help nucleate closure of the loop. The reduced entropic cost of binding biotin to CP51/46 is consistent with the removal of this loop and a reduction in entropic costs associated with loop closure and immobilization. The reduced enthalpic contribution to the free energy of binding is not readily explainable in terms of the molecular structure, as the binding contacts are nearly entirely conserved, and only small differences in solvent accessible surfaces are observed relative to wild-type streptavidin.     

The role of experience and chemical alarm signalling in predator recognition by fathead minnows, Pimephales promelas

Young-of-the-year, predator-naive fathead minnows, Pimephales promelas , from a pikesympatric population did not respond to chemical stimuli from northern pike, Esox Indus , while wild-caught fish of the same age and size did. These results suggest that chemical predator recognition is a result of previous experience and not genetic factors, Wild young-of-the-year minnows responded to pike odour with a response intensity that was similar to that of older fish, demonstrating that the ability to recognize predators is learned within the first year. The intensity of response of wild minnows which had been maintained in a predator free environment for 1 year was similar to that of recently caught minnows of the same age, suggesting that reinforcement was not required for predator recognition to be retained. Naive minnows that were exposed simultaneously to chemical stimuli from pike (a neutral stimulus) and minnow alarm substance exhibited a fright response upon subsequent exposure to the pike stimulus alone. Predator-naive minnows exposed simultaneously to chemical stimuli from pike and glass-distilled water did not exhibit a fright response to the pike stimulus alone. These results demonstrate that fathead minnows can acquire predator recognition through releaserinduced recognition learning, thus confirming a known mechanism through which alarm substance may benefit the receivers of an alarm signal.     

Ribonuclease T2 represents a distinct circularly permutated version of the BECR RNases

Detection of homologous relationships among proteins and understanding their mechanisms of diversification are major topics in the fields of protein science, bioinformatics, and phylogenetics. Recent developments in sequence/profile-based and structural similarity-based methods have greatly facilitated the unification and classification of many protein families into superfamilies or folds, yet many proteins remain unclassified in current protein databases. As one of the three earliest identified RNases in biology, ribonuclease T2, also known as RNase I in Escherichia coli, RNase Rh in fungi, or S-RNase in plant, is thought to be an ancient RNase family due to its widespread distribution and distinct structure. In this study, we present evidence that RNase T2 represents a circularly permutated version of the BECR (Barnase-EndoU-Colicin E5/D-RelE) fold RNases. This subtle relationship cannot be detected by traditional methods such as sequence/profile-based comparisons, structure-similarity searches, and circular permutation detections. However, we were able to identify the structural similarity using rational reconstruction of a theoretical RNase T2 ancestor via a reverse circular permutation process, followed by structural modeling using AlphaFold2, and structural comparisons. This relationship is further supported by the fact that RNase T2 and other typical BECR RNases, namely Colicin D, RNase A, and BrnT, share similar catalytic site configurations, all involving an analogous set of conserved residues on the α0 helix and the β4 strand of the BECR fold. This study revealed a hidden root of RNase T2 in bacterial toxin systems and demonstrated that reconstruction and modeling of ancestral topology is an effective strategy to identify remote relationship between proteins.     

Change in the chemical signature of the ant leptothorax lichtensteini bondroit with time

The cuticular hydrocarbons of foraging workers of the ant Leptothorax lichtensteini have been identified by gas chromatography-mass spectrometry. Characterization of these compounds at regular intervals, by gas chromatography, has shown a change with time in the relative proportions of some of the hydrocarbons: n-hexacosane, 4-methylhexacosane, 4-methyloctacosane, 3-methylnoncosane. Some of which constitute a part of the colony signature. These changes occur in a synchronous manner, and in the same way for all the individuals of a colony tested at the same time. The changes also appear in queenless colonies; nevertheless, the presence of a queen seems to accelerate the change over the course of 1 yr. Certain hypotheses are formulated as to the mode of regulation of the synthesis of cuticular hydrocarbons responsible for these changes with time and as to the role played by the queen in this regulation. The implications of such a dynamic system for the process of nestmate recognition are discussed.     

模式识别在生物固体发酵技术中的应用

本文首次应用计算机模式识别技术,对啤酒糟固体发酵工艺进行优化,找到模式优化区。并在该区域内选择实验点进行工艺实验,证明优化结果可靠,模式识别可应用于生物固体发酵领域。     

Queen number and genetic relatedness in a neotropical wasp, Polybia occidentalis

We found that genetic relatedness among Polybia occidentalisworkers was .26±0.057, a value high enough to make altruisticbehavior by workers relatively easy to explain. This comparativelyhigh level of relatedness can be attributed to close relatednessamong queens of .57±0.077 and to great variation amongcolonies in numbers of queens. The harmonic mean of queen numberis 3.1 queens per colony, which is much lower than the arithmeticmean of 10.6 queens per colony. These results are consistentwith a colony cycle called cyclical oligogyny, that is characterizedby a reduction in queen number from colony initiation to colonyreproduction. We did not find any evidence that one or a fewqueens monopolized egg laying or that there was any inbreeding,both of which have been hypothesized to increase relatednessamong workers. Another factor that can increase relatednessamong workers and the brood they rear is withincolony segregationon the basis of relatedness. We found that combmate pupae aresignificantly more closely related to each other (r = .41) thanthey are to pupae in other combs (r = .33), but we have notinvestigated whether workers take advantage of these relatednesspatterns. This distribution of relatedness among combs willoccur if queens do not lay eggs randomly throughout the nest,but concentrate their egg laying on one or a subset of the availablecombs.     

Recognition of glycoside hydrolase 12 proteins by the immune receptor RXEG1 confers Fusarium head blight resistance in wheat

Fusarium head blight (FHB), caused by Fusarium graminearum, is a devastating disease in wheat (Triticum aestivum) that results in substantial yield losses and mycotoxin contamination. Reliable genetic resources for FHB resistance in wheat are lacking. In this study, we characterized glycoside hydrolase 12 (GH12) family proteins secreted by F. graminearum. We established that two GH12 proteins, Fg05851 and Fg11037, have functionally redundant roles in F. graminearum colonization of wheat. Furthermore, we determined that the GH12 proteins Fg05851 and Fg11037 are recognized by the leucine-rich-repeat receptor-like protein RXEG1 in the dicot Nicotiana benthamiana. Heterologous expression of RXEG1 conferred wheat responsiveness to Fg05851 and Fg11037, enhanced wheat resistance to F. graminearum and reduced levels of the mycotoxin deoxynivalenol in wheat grains in an Fg05851/Fg11037-dependent manner. In the RXEG1 transgenic lines, genes related to pattern-triggered plant immunity, salicylic acid, jasmonic acid, and anti-oxidative homeostasis signalling pathways were upregulated during F. graminearum infection. However, the expression of these genes was not significantly changed during infection by the deletion mutant ΔFg05851/Fg11037, suggesting that the recognition of Fg05851/Fg11037 by RXEG1 triggered plant resistance against FHB. Moreover, introducing RXEG1 into three other different wheat cultivars via crossing also conferred resistance to F. graminearum. Expression of RXEG1 did not have obvious deleterious effects on plant growth and development in wheat. Our study reveals that N. benthamiana RXEG1 remains effective when transferred into wheat, a monocot, which in turn suggests that engineering wheat with interfamily plant immune receptor transgenes is a viable strategy for increasing resistance to FHB.     

Chiral discrimination of the enantiomers of δ-phenyl-δ-valerolactone by cellulose triacetate: A chromatographic and microcalorimetric study of the thermodynamics

The resolution of racemic δ-phenyl-δ-valerolactone by chromatography on cellulose triacetate CTA I results in one of the best separations of optical antipodes observed so far on this chiral stationary phase. The thermodynamics of the stereoselective interaction of the enantiomers of δ-phenly-δ-valerolactone have been studied by chromatography at different temperatures and by direct microcalorimetric investigations of the complexation with CTA I. This analysis suggests that the separation process is mainly controlled thermodynamically and that kinetic effects, if any, play a minor role. Microcalorimetric titration experiments indicate that specific (optimum) complexation sites on CTA I for the stronger retained enantiomer of δ-phenly-δ-valerolactone are rapidly saturated, whereas the first eluted enantiomer seems to interact much less selectively with defined interaction sites on the chiral polymer matrix. © 1993 Wiley-Liss, Inc.     

Molecular correlates of neuronal specificity in the developing insect nervous system

The development of the nervous system in insects, as in most other higher animals, is characterized by the high degree of precision and specificity with which synaptic connectivity is established. Multiple molecular mechanisms are involved in this process. In insects a number of experimental methods and model systems can be used to analyze these mechanisms, and the modular organization of the insect nervous system facilitates this analysis considerably. Well characterized molecular elements involved in axogenesis are the cell-cell adhesion molecules that underlie selective fasciculation. These are cell-surface molecules that are expressed in a regional and dynamic manner on developing axon fascicles. Secreted molecules also appear to be involved in directing axonal navigation. Nonneuronal cells, such as glia, provide cellular and noncellular substrates that are important pathway cues for neuronal outgrowth. Once outgrowing processes reach their general target regions they make synapses with the appropriate postsynaptic cells. The molecular mechanisms that allow growth cones to recognize their correct target cells are essential for neuronal specificity and are being analyzed in neuromuscular and brain interneuron systems of insects. Candidate synaptic recognition molecules with remarkable and highly restricted expression patterns in the developing nervous system have recently been discovered.