How Fast Does a Signal Propagate through Proteins?

As the molecular basis of signal propagation in the cell, proteins are regulated by perturbations, such as mechanical forces or ligand binding. The question arises how fast such a signal propagates through the protein molecular scaffold. As a first step, we have investigated numerically the dynamics of force propagation through a single (Ala) protein following a sudden increase in the stretching forces applied to its end termini. The force propagates along the backbone into the center of the chain on the picosecond scale. Both conformational and tension dynamics are found in good agreement with a coarse-grained theory of force propagation through semiflexible polymers. The speed of force propagation of 50Å ps⁻¹ derived from these simulations is likely to determine an upper speed limit of mechanical signal transfer in allosteric proteins or molecular machines.     

Does GABA Act as a Signal in Plants?: Hints from Molecular Studies

GABA is a non-protein amino acid that accumulates rapidly in plant tissues in response to biotic and abiotic stress. There have been a number of suggestions as to the role that GABA might play in plants, ranging from a straightforward involvement in N metabolism to a signal mediating plant-animal and plant-microbe interactions. It has also been several proposed that it might function as an intracellular signalling molecule in plants. Here, we discuss recent evidence that plant cells respond at the molecular level to the presence of applied GABA. We argue that these data might serve as the basis for investigating the possible signalling role for GABA in plant development and stress responses in more detail.Key Words: 14-3-3 proteins, GABA, signalling, gene expression, stress, senescenceGABA (γ-aminobutyric acid), which comprises a significant fraction of the free amino acid pool in plant cells, was first identified in potato tubers over half a century ago, but its functions remained obscure for many years. In animal systems, GABA is present at high levels in the brain where it acts as an important neurotransmitter. GABA is synthesised in a pathway known as the GABA shunt, which operates not only in the animals, but in bacteria, fungi and plants too.^1,2 The function of GABA in plants has attracted renewed attention in the last decade following the discovery that intracellular and/or extracellular GABA concentrations increase rapidly in response to a range of stresses. Subsequently, a number of possible roles for GABA and the GABA shunt in plants have been suggested.^1,2 These include acting as a buffering mechanism in C and N metabolism, cytosolic pH regulation, protection against oxidative stress and defence against herbivorous pests. It has been proposed recently that one common function of GABA might be to mediate interactions between plants and other organisms, including bacterial and fungal pathogens, nematodes and insect pests.³ On the other hand, because of the rapid increases in GABA concentration in response to stress, it has sometimes been inferred that GABA might act as an intracellular signalling molecule in plants. However, few studies have adopted molecular approaches to GABA function, and molecular responses are largely unknown.     

Can Reindeer Overabundance Cause a Trophic Cascade?

Abstract The region Finnmark, in northernmost Europe, harbors dense populations of semi-domestic reindeer of which some exhibit characteristics of overabundance. Whereas overabundance is evident in terms of density-dependent reductions in reindeer body mass, population growth and abundance of forage plants, claims have been made that this reindeer overabundance also has caused a trophic cascade. These claims are based on the main premise that reindeer overgrazing negatively impacts small-sized, keystone tundra herbivores. We tested this premise by a large-scale study in which the abundance of small rodents, hares and ptarmigans was indexed across reindeer management districts with strong differences in stocking densities. We examined the scale-dependent relations between reindeer, vegetation and these small-sized herbivores by employing a spatially hierarchical sampling design within the management districts. A negative impact of reindeer on ptarmigan, probably as a result of browsing reducing tall Salix, was indicated. However, small rodents (voles and lemmings), which are usually the keystone herbivores in the plant-based tundra food web, were not negatively impacted. On the contrary, there was a strong positive relationship between small rodents and reindeer, both at the scale of landscape areas and local patches, with characteristics of snow-bed vegetation, suggesting facilitation between Norwegian lemmings and reindeer. We conclude that the recent dampening of the vole and lemming population cycle with concurrent declines of rodent predators in northernmost Europe were not caused by large herbivore overgrazing.     

Aluminum Inhibition of the Inositol 1,4,5-Trisphosphate Signal Transduction Pathway in Wheat Roots: A Role in Aluminum Toxicity?

In crop plants, aluminum (Al) rhizotoxicity is a major problem worldwide; however, the cause of Al toxicity remains elusive. The effects of Al on the inositol 1,4,5-trisphosphate (Ins[1,4,5]P3)-mediated signal transduction pathway were investigated in wheat roots. Exogenously applied Al (50 [mu]M) rapidly inhibited root growth (<2 hr) but did not affect general root metabolism. An Ins(1,4,5)P3 transient was generated in root tips, either before or after exposure to Al for 1 hr, by treating the roots with H2O2 (10 mM). Background (unstimulated) levels of Ins(1,4,5)P3 were similar in both Al-treated and Al-untreated root apices. However, H2O2-stimulated levels of Ins(1,4,5)P3 in root apices showed a significant (>50%) reduction after Al exposure in comparison with untreated controls, indicating that Al may be interfering with the phosphoinositide signaling pathway. When phospholipase C (PLC) was assayed directly in the presence of Al or other metal cations in microsomal membranes, AlCl3 and Al-citrate specifically inhibited PLC action in a dose-dependent manner and at physiologically relevant Al levels. Al exposure had no effect on inositol trisphosphate dephosphorylation or on a range of enzymes isolated from wheat roots, suggesting that Al exposure may specifically target PLC. Possible mechanisms of PLC inhibition by Al and the role of Ins(1,4,5)P3 in Al toxicity and growth are discussed. This study provides compelling evidence that the phytotoxic metal cation Al has an intracellular target site that may be integrally involved in root growth.     

Is There a Phylogenetic Signal in Prokaryote Proteins?

Using the sequence information from nine completely sequenced bacterial genomes, we extract 32 protein families that are thought to contain orthologous proteins from each genome. The alignments of these 32 families are used to construct a phylogeny with the neighbor-joining algorithm. This tree has several topological features that are different from the conventional phylogeny, yet it is highly reliable according to its bootstrap values. Upon closer study of the individual families used, it is clear that the strong phylogenetic signal comes from three families, at least two of which are good candidates for horizontal transfer. The tree from the remaining 29 families consists almost entirely of noise at the level of bacterial phylum divisions, indicating that, even with large amounts of data, it may not be possible to reconstruct the prokaryote phylogeny using standard sequence-based methods. Received: 22 November 1998 / Accepted: 17 February 1999     

Does Aging Have a Purpose?

Ideas of proponents and opponents of programmed aging concerning the expediency of this phenomenon for the evolution of living organisms are briefly considered. We think that evolution has no “gerontological” purpose, because the obligate restriction of cell proliferation during the development of multicellular organisms is a factor that “automatically” triggers aging due to the accumulation of various macromolecular lesions in cells as a result of the suppression, or even complete cessation of emergence of new, intact cells. This leads to the “dilution” of stochastic damage (the most important of which is DNA damage) at the level of the entire cellular population. Some additional arguments in favor of the inexpediency of aging for both species and individuals are also listed.     

Does Human Body Odor Represent a Significant and Rewarding Social Signal to Individuals High in Social Openness?

Across a wide variety of domains, experts differ from novices in their response to stimuli linked to their respective field of expertise. It is currently unknown whether similar patterns can be observed with regard to social expertise. The current study therefore focuses on social openness, a central social skill necessary to initiate social contact. Human body odors were used as social cues, as they inherently signal the presence of another human being. Using functional MRI, hemodynamic brain responses to body odors of women reporting a high (n = 14) or a low (n = 12) level of social openness were compared. Greater activation within the inferior frontal gyrus and the caudate nucleus was observed in high socially open individuals compared to individuals low in social openness. With the inferior frontal gyrus being a crucial part of the human mirror neuron system, and the caudate nucleus being implicated in social reward, it is discussed whether human body odor might constitute more of a significant and rewarding social signal to individuals high in social openness compared to individuals low in social openness process.     

Does zoo herpetology have a future?

Fifty-two North American zoo reptile and amphibian departments were surveyed to determine their contributions to recognized American Zoo and Aquarium Association (AZA)-sponsored programs and formalized research projects over the past 10 years. Surveys also requested information concerning the allocation of resources for conservation and research programs, staff educational background, and entry level salaries. Twenty-two institutions responded to the survey, collectively indicating a total of 164 technical papers, 16 field studies, and 101 non-technical articles completed between 1987 and 1997. Of the 164 technical papers published, 130 (79%) were contributed by three institutions. Of the 16 field studies, seven were outside the United States, whereas nine focused on native species and ecosystems. Six of the reported field studies involved only financial or logistical support. Of the 101 non-technical articles, 42 (42%) were contributed by a single institution. Twenty-one formalized in-house research projects were reported. However, only four appeared to have a clearly defined objective. Survey respondents also reported nine species of reptiles and one amphibian taxon are managed by Species Survival Plans (SSPs). There are currently 12 Taxon Advisory Group (TAG) coordinators, with four of the current coordinators having served on multiple TAG committees. There are 41 AZA-approved studbooks for reptiles and two for amphibians, with 29 having actually been published to date. The average starting salary reported in our survey for entry level keeper positions was $19,500 (range, $13,500–30,000). The average level of education reported was high school graduate. There was no correlation between productivity and higher wages, or level of education. Only one institution received funding specifically for research. We conclude that zoo herpetology departments are not realizing their potential for formalized research and conservation projects and propose recommendations for future involvement. Zoo Biol 17:453–462, 1998. © 1998 Wiley-Liss, Inc.     

Does FSH signaling have a gender?

FSH is the main endocrine control of mammalian reproduction. FSH triggers somatic cells of the gonads which support germ cells metabolically, i.e. Sertoli cells of the seminiferous tubules, and granulosa cells harboring the oocyte, within the ovarian follicle. FSH leads to similar biological responses in both cell types since it stimulates proliferation and differentiation, according to the developmental stage. However, FSH receptor knock-out female mice are infertile, unlike male mice. Hence, FSH is not equally important in both sexes. Nevertheless, does FSH induce distinct signalling mechanisms in its target cells ? Here, we compare the signalling mechanisms induced by FSH in ovarian and testicular physiology.     

Does Gonyaulax polyedra measure a week?

Cell communication was investigated in Gonyaulax polyedra by mixing two cultures grown on opposite lighting regimens, as reported in a companion paper. Herein, using the same data, 7-d (circaseptan) rhythms are also shown to characterize the luminescence of this cellular organism. A fraction of a culture of G. polyedra, grown in 12 h of light (L), alternating with 12 h of darkness (D), was exposed for 3 d to an LD-shift by 11 h. The circadian glow rhythm was compared under free-running conditions (LL) for cultures previously kept on the two differing LD regimens and for mixed cultures. A circaseptan modulation of the circadian amplitude is detected in cultures that had not undergone an LD shift and in some of the mixed cultures, but not in the shifted cultures. A statistically significantly lower circaseptan amplitude (less than 50%) and acrophase advance of over 120 degrees or 56 h (p less than 0.001) characterizes the mixed cultures, as compared to the original unshifted cultures, a finding that could mean that G. polyedra communicates along a circaseptan frequency. Whether a prior phase-shift known to affect circaseptan behavior in another unicell, Acetabularia mediterranea, led to an alteration of the time structure of G. polyedra remains an interesting subject for further study in this model, a model attractive to students of unicellular rhythms and underlying mechanisms that henceforth should be studied at multiple circadian and circaseptan frequencies. Circadian and circaseptan interrelations can both serve as markers for mechanisms of intercellular communication.     

How Does a Simplified-Sequence Protein Fold?

To investigate a putatively primordial protein we have simplified the sequence of a 56-residue α/β fold (the immunoglobulin-binding domain of protein G) by replacing it with polyalanine, polythreonine, and diglycine segments at regions of the sequence that in the folded structure are α-helical, β-strand, and turns, respectively. Remarkably, multiple folding and unfolding events are observed in a 15-μs molecular dynamics simulation at 330 K. The most stable state (populated at ∼20%) of the simplified-sequence variant of protein G has the same α/β topology as the wild-type but shows the characteristics of a molten globule, i.e., loose contacts among side chains and lack of a specific hydrophobic core. The unfolded state is heterogeneous and includes a variety of α/β topologies but also fully α-helical and fully β-sheet structures. Transitions within the denatured state are very fast, and the molten-globule state is reached in <1 μs by a framework mechanism of folding with multiple pathways. The native structure of the wild-type is more rigid than the molten-globule conformation of the simplified-sequence variant. The difference in structural stability and the very fast folding of the simplified protein suggest that evolution has enriched the primordial alphabet of amino acids mainly to optimize protein function by stabilization of a unique structure with specific tertiary interactions.     

Clomiphene and hypospadias on a detailed level: Signal or chance?

BACKGROUND: Clomiphene, a drug used to induce ovulation, is chemically related to diethylstilbestrol (DES). DES is associated with vaginal cancer and infertility among daughters and with hypospadias among second-generation male offspring. Because clomiphene has a long half-life and metabolites have been found in feces up to 6 weeks after administration, fetal exposure is possible if the mother took this drug prior to becoming pregnant. METHODS: Case-control analyses were performed to investigate the association between clomiphene exposure and hypospadias. Cases were all male subjects registered in the European Concerted Action on Congenital Anomalies and Twins (EUROCAT) Northern Netherlands registry for congenital anomalies with nonsyndromal hypospadias. Controls were all male children born without hypospadias, including those with chromosomal and monogenic defects. Logistic regression analyses were performed to calculate odds ratios (ORs) and 95% confidence intervals (CIs). RESULTS: Of 392 cases, 7 (1.8%) were exposed to clomiphene compared with 64 of 4538 controls (1.4%). For penoscrotal hypospadias, we found that the OR was significantly increased (6.08; 95% CI, 1.40-26.33); for the mild and moderate forms of hypospadias, the ORs were not increased. CONCLUSIONS: Because penoscrotal hypospadias is rare, the effect is diluted when all forms of hypospadias are studied as a group. Therefore, our study stresses the importance of studying birth defects on as detailed a level as possible. Other studies should be conducted to confirm our findings.     

Signal convergence in fruits: a result of selection by frugivores?

The Dispersal Syndrome hypothesis remains contentious, stating that apparently nonrandom associations of fruit characteristics result from selection by seed dispersers. We examine a key assumption under this hypothesis, i.e. that fruit traits can be used as reliable signals by frugivores. We first test this assumption by looking at whether fruit colour allows birds and primates to distinguish between fruits commonly dispersed by birds or primates. Second, we test whether the colours of fruits dispersed by primates are more contrasting to primates than the colours of bird‐dispersed fruits, expected if fruit colour is an adaptation to facilitate the detection by seed dispersers. Third, we test whether fruit colour has converged in unrelated plant species dispersed by similar frugivores. We use vision models based on peak sensitivities of birds’ and primates’ cone cells. We base our analyses on the visual systems of two types of birds (violet and ultraviolet based) and three types of primates (trichromatic primates from the Old and the New Worlds, and a dichromatic New World monkey). Using a Discriminant Function Analysis, we find that all frugivore groups can reliably discriminate between bird‐ and primate‐dispersed fruits. Fruit colour can be a reliable signal to different seed dispersers. However, the colours of primate‐dispersed fruits are less contrasting to primates than those of bird‐dispersed fruits. Fruit colour convergence in unrelated plants is independent of phylogeny and can be better explained by disperser type, which supports the hypothesis that frugivores are important in fruit evolution. We discuss adaptive and nonadaptive hypotheses that can potentially explain the pattern we found.     

Chemical Signal as a Rapid Long-Distance Information Messenger After Local Wounding of a Plant?

A series of works have described an important role of chemical signaling compounds in generation of the stress response of plants in both the wounded and distant undamaged plant tissues. However, pure chemical signals are often not considered in the fast (minutes) long-distance signaling (systemic response) because of their slow propagation speed. Physical signals (electrical and hydraulic) or a combination of the physical and chemical signals (hydraulic dispersal of solutes) have been proposed as possible linkers of the local wound and the rapid systemic response. We have recently demonstrated an evidence for involvement of chemical compounds (jasmonic and abscisic acids) in the rapid (within 1 hour) inhibition of photosynthetic rate and stomata conductance in distant undamaged tobacco leaves after local burning. The aim of this addendum is to discuss plausible mechanisms of a rapid long-distance chemical signaling and the putative interactions between the physical and chemical signals leading to the fast systemic response.Key Words: tobacco, local burning, systemic response, hydraulic surge, electrical signal, abscisic acid, jasmonic acidPlants have evolved an amazingly complex system of defence-related strategies to protect themselves upon local wounding.^1–7 Important characteristics of self-defence responses of plants are their velocity and ubiquity. Indeed, fast (minutes to hours) responses to injurious factors have been detected in the site of injury and in distant regions (systemic response) in various plants.^8–11 These findings suggest that a signal generated by an attack to one leaf is transmitted through a whole plant. Several kinds of chemical^3,6 and physical¹² signals induced by local wounding and even their combination¹³ have been implicated. However, a little is known about the interactions of these signals and about the mechanisms of initiation of the short-term systemic responses.We have used a model system—tobacco plants exposed to the local burning—to study the signals involved in rapid wound responses of photosynthetic apparatus.¹⁴ Local burning of an upper leaf of a tobacco plant induced rapid changes in surface electrical potential (within seconds) and a pronounced fast decline in the stomatal conductance, CO₂ assimilation and transpiration (within minutes) in the basipetal direction (Fig. 1). Moreover, we have detected a fast (within minutes) transient increase in levels of endogenous abscisic acid (ABA) followed by a huge rapid rise in endogenous jasmonic acid (JA) in the leaf below the burned one. ABA and jasmonates are known to be involved in signaling pathways leading to stomatal closure and downregulation of photosynthesis.^15,16 Increases in ABA and/or JA levels have only previously been detected in remote untreated tissues several hours after local wounding^8,9 suggesting that chemical signals are too slow to induce rapid systemic response. Previous works have reported that fast physical (electrical) signals play an essential role in short-term systemic photosynthetic responses.^11,17 However, a several-minutes delayed stomata closing response after the initiation of electrical potential changes has been reported in Mimosa¹⁸ and in our case in tobacco¹⁴ plants. Therefore, the guard cell deflation is most likely triggered not only by the electrical signal, but also by indirect factors. Based on close correlations, our results now provide a new evidence for the idea that chemical signals (ABA and mainly JA) participate in mediating the short-term systemic photosynthetic responses to local burning in tobacco plants.Open in a separate windowFigure 1The model of putative signalling pathways leading to the rapid systemic responses of tobacco plants to local burning. Hypothetical (dashed lines) local responses, generation of signals and transport processes and detected (full line) systemic responses are demonstrated. For details see the text.The question is how do the physical (electrical and/or hydraulic) and chemical signals act? They may independently induce specific elements of systemic responses. However, they are more likely to act in a coordinated, interactive fashion. In this scenario (see Fig. 1), within first minutes after the local burning, hydraulic surge transmitted basipetally and acropetally through the xylem would transport chemicals released at the wound site (hydraulic dispersal¹⁹) and evoke changes in the ion fluxes in surrounding living cells leading to the local electrical activity.^12,13 The hypothesis of hydraulic dispersal is supported by our preliminary experiments with the fluorescent dye Rhodamine B applied on cut petiole of the upper leaf of tobacco plants showing that solutes can be rapidly transported (within minutes) basipetally following wounding.The rapid kinetics and transient character of ABA accumulation¹⁴ suggest that the main transport mechanism is the hydraulic dispersal in xylem. The participation of ABA in the generation of systemic electrical activity and/or vice versa cannot be ruled out.^8,20A rapid hydraulically driven transport of chemicals in the xylem of wounded plant in a reversed (basipetal) direction^19,21 to transpiration stream is not generally accepted. Exposing of leaves of undamaged plants to radioactive labelled molecules to determine the speed of chemical signal transport could be misrepresent, because hydraulic signal is not generated in undamaged plants and then the detected transport speed is too slow. Moreover, previous work²² demonstrated that neither the mass flow itself, nor the associated pressure changes induce the systemic response (the proteinase inhibitor activity). Thus, the efficacy of chemical agents in rapid systemic signaling seems to depend on transport by the mass flows associated with hydraulic signals.¹⁹However, hydraulic dispersal acts only for minutes, until all water released at the wound site is exhausted.²¹ A requirement for hydraulic dispersal of any solute is its presence in the wounded tissue at the time of wounding.¹⁹ Detected slower kinetics of JA accumulation than in the case of ABA and the huge rise of JA levels¹⁴ indicate a systemic accumulation of JA also by some additional processes.Does additional JA accumulation result from de-novo synthesis in undamaged leaves as a response to physical signal or does it result from a JA transport from the wounded leaves? In the longer time-frame the phloem transport²³ should also be considered. Experiments with tomato plants have shown that de novo JA synthesis in distant leaves is not required for the systemic response and that biosynthesis of JA at the wound site is necessary for the generation of a systemic signal.⁷ Indeed, a short-term increase in endogenous concentrations of JA has been detected in wounded tissue in Nicotiana sylvestris⁹ and rice.¹⁰However, a rapid burst in the systemic JA accumulation found in our experiments¹⁴ would implicate an ultra-rapid and extreme JA accumulation at the wound site before its transport. The systemic JA accumulation (within 1 hour¹⁴) preceded the generation of enzymes involved in the JA biosynthesis in the wounded leaf.Thus, several processes are suggested to play a role in the ultra-rapid and huge JA accumulation:

1. initiation of JA accumulation by preexisting enzymes,²⁴
2. fast release of free JA from its storage pools in cells (e.g., JA-conjugates²⁵),
3. direct uptake of elicitors (JA) by the phloem of the wounded leaf and exchange between the xylem and phloem as a consequence of severe wounds,²⁶
4. the mass flow (containing remaining JA) driven mainly acropetally in the xylem by transpiration after damping the hydraulic surge,²¹
5. JA accumulation evoked by the fast transmitting physical (electrical or hydraulic) signal that leads to imbalances in ion fluxes,^8,12,27
6. JA accumulation (and subsequent transport) directly in the phloem, where JA biosynthetic enzymes are located (at least in tomato²⁴),
7. volatile chemical compounds (methylester of JA) spreading in the surrounding air of wounded leaf could serve as signaling molecules and sources of JA.^25,28

The relevance of the above mentioned mechanisms should be checked by further research. Complex quantitative and kinetic analysis of JA and ABA content, levels of its biosynthetic derivatives (also volatiles in the surrounding air) and simultaneous physical signal detection in wounded and distant unwounded tissues would fill the remaining void about their role and interactions in the wound signal transduction networks. In addition, a suppression of other signaling pathways with similar transport kinetics (e.g., volatile compounds transmission, systemin and oligosaccharides generation and/or transport, using mutant plants) would be useful.Substantial similarity between the rapid physical (electrical) signaling in animal nervous system compared with the physical (electrical) signaling in plants has already been reported.^29,30 Interaction of chemical and electrical signals is the process well documented for post-synaptic events in animals. Our data now strengthen the role of chemical signals next to the role of physical signals in plants in the rapid systemic wound response; such a role of chemicals in plants was often underestimated up to now.     

Does Rap1 deserve a bad Rap?

The Ras superfamily of small G proteins is remarkable for both its diversity and physiological functions. One member, Rap1, has been implicated in a particularly wide range of biological processes, from cell proliferation and differentiation to cell adhesion. But the diversity of Rap1 has lead to contradictory reports of its effects. Originally identified as an antagonist of Ras-induced transformation, Rap1 can oppose other actions of Ras including regulation of cell growth and differentiation, integrin-dependent responses and synaptic plasticity. Furthermore, recent evidence confirms that Rap1, like Ras, can activate the MAP kinase cascade (ERK) in several cell types. These diverse functions of Rap1 underscore that the activation and action of Rap1 are regulated by complex factors that are cell-type specific.