Christopher Surridge

Analysis of β-tubulin sequences reveals highly conserved, coordinated amino acid substitutions : evidence that these hot spots are directly involved in the conformational change required for dynamic instability

Vertebrate β‐tubulins have been classified into six classes on the basis of their C‐terminal sequences [(1987) J. Cell Biol. 105, 1707‐1720]. In particular, the sequences starting at residue 430 differ between isotypes of the same animal but are conserved between species. We extend this analysis and show that there are three ‘hot spots’, at residues 35, 55–57 and 124 which exhibit intra‐species heterogeneity but inter‐species conservation. There is a remarkable correlation between the identity of these residues and the C‐terminal sequences, and suggests that the vertebrate β‐tubulins fall into three broad types. This correlation extends to those non‐vertebrate organisms which have the Type 1 C‐terminal sequence. We propose that these three ‘hot spots’ and the C‐terminal peptide interact in the tertiary structure. We have also noted that the C‐terminal peptide almost always contains a single phenylalanine or tyrosine residue, and that there is a strong correlation between this residue and the amino acids at positions 217/218, in both the vertebrate and non‐vertebrate sequences. We propose that the C‐terminal aromatic amino acid interacts with residues 217/218 in the tertiary structure. Analysis of conditions which stabilise microtubules and/or lower the steady state critical concentration strongly suggests that these two sets of coordinated amino acid substitutions are directly involved in effecting the conformational change associated with GTP hydrolysis which results in dynamic instability. We propose that there is an interaction between the highly acidic sequence between residue 430 and the aromatic amino acid (termed peptide A) and conserved basic amino acids located close to the ‘hot spots’. We suggest that this interaction is altered in response to the assembly‐dependent GTP hydrolysis, with the consequential increase in the subunit dissociation rate constant.

Rice cultivation: feast or famine?

Proponents call it a miracle. Detractors call it smoke and mirrors. Will the System of Rice Intensification feed the hungry third world or needlessly divert farmers from tried and true techniques? Christopher Surridge investigates.

Agricultural biotech: the rice squad.

Feeding the world in the twenty-first century could require a second green revolution. But that may involve the most audacious feat of genetic engineering yet attempted, says Christopher Surridge.

Functional role of a consensus peptide which is common to α-, β-, and γ-tubulin, to actin and centractin, to phytochrome A, and to the TCP1α chaperonin protein

The TRiC (TCP1 Ring Complex) chaperonin complex participates in the functional folding of actin, centractin, α‐,β‐,γ‐tubulin, and phytochrome. Each of the cytoskeletal proteins contain a peptide, RK(A,C,T)F/KRAF, located towards the C‐terminus, which is homologous to a TCP1α peptide, while the equivalent phytochrome peptide (RLKAF in certain isoforms) is very similar to the KLRAF peptide of TCP1α. We propose that this TCP1α peptide binds to the nascent polypeptides as they emerge from the ribosome, that this binding restricts the folding pathway, and that the TCP1α peptide is subsequently displaced by the synthesis of the consensus peptide. This hypothesis is strongly supported by the crystallographic structure of actin.

Plant science: On the slide

Pitcher plants have highly effective ways of trapping their insect prey. Electron microscope studies of the pitcher of one species show how its surface features help to maximize the plant’s diet.

...And biologists' work on protein energy converters

londonThe 1997 Nobel prize for Chemistry has been awarded to three biologists for their work on proteins that interconvert chemical energy.

Molecular motors. Spotting the goods trains.

Microtubule-based motor proteins, such as dynein and kinesin, can transport organelles around the cell. But many of these motors were originally identified for reasons other than this. A direct assay for organelle transport has now been devised, however, and initial tests using it have identified two hitherto unknown kinesins in the slime mouldDicytostelium discoideum.

Plant development: A bunch of leaves

tems, but now appears clear in P. dominulus. Losers were more likely to suffer continuing aggression from the dominant female if they had a more broken (higher-rank) pattern. Going beyond correlation, Tibbetts and Dale manipulated the clypeus spots with yellow and black paint. To one member of a pair that had not previously interacted, the authors either added a spot, obliterated an existing spot, or added paint in ways that did not change the existing pattern. After these females had established a clear dominance relationship,dominant females continued to be aggressive towards subordinates whose painted marks indicated an increase in status. The result clearly supports the hypothesis that there are social costs to erroneously high status signals: cheating subordinates are punished. The study had several puzzling features, however. The key result discussed above relates to behaviour after dominance had been established. Surprisingly, though, manipulating the spot pattern had no effect on behaviour before rank was established. Also,females painted with high-status marks were no more likely to attain dominant status than were those painted with lowstatus marks, or controls. If extra marks give a badge of high status, then their owner should be more likely to become dominant. Another curiosity is that after dominance was established, the dominant females were also more aggressive towards subordinates painted to look even more subordinate. This is hard to explain in a two-female system.But wasps often begin nests in groups of more than two. A female with marks indicating very low rank that acted instead like a second-ranked female could plausibly be perceived by the dominant female as a threat and receive more aggression. A further unpredicted result is that unpainted subordinates were aggressive towards painted dominants,whether they were painted with a higheror a lower-status mark than that of their ‘true’ status. In ten cases, the unpainted subordinate female even overthrew the painted dominant; these cases were evenly divided between those in which the dominant was painted with a higheror a lowerstatus mark. Also interesting is that the correlation of spot number or brokenness with head width is very weak, accounting for only 7% or 3% of the variance, respectively. A reliable cue of condition should account for more of the variance. Perhaps head width is not the best measure of condition, and perhaps the clypeus marks are actually correlated with a better, as-yet-unknown measure. But the marks are fixed in the pupal stage,and are not altered by later feeding and overwintering, which are known to affect condition.It seems that if clypeus marks are status badges, they are not conventional ones. news and views

Animal behaviour: Guardian caterpillars

able to the molecule to overcome its reaction barrier. But some remarkable reactions occur without the need for thermal excitation, through a process known as quantum tunnelling. Schreiner et al. report that just such a process occurs for HCOH — when the molecule adopts a certain conformation, it decays to produce formaldehyde in a matter of minutes, even though the calculated barrier for the reaction is too high to be overcome at the temperatures used in the experiments. Instead, the hydrogen atom in the hydroxyl group (OH) of HCOH ‘tunnels’ through the barrier, in a process that relies on the wave–particle duality of the atom (Fig. 1). This unexpected reaction might explain why previous attempts to detect HCOH failed — the product decayed before it was found and analysed. The authors investigated the quantum tunnelling process by replacing the hydrogen atom of the hydroxyl group with deuterium (a heavy isotope of hydrogen). They found that the deuterated form of HCOH is essentially stable under their experimental conditions. This stabilizing effect occurs because the wave associated with the deuterium atom decays before reaching the exit of the barrier (unlike the wave for the hydrogen atom), and provides direct evidence of quantum-tunnelling. Turning again to theoretical predictions to validate their results, the authors modelled the tunnelling process computationally. The half-life for HCOH at close to zero kelvin was predicted to be 122 minutes, whereas that of deuterated HCOH was predicted to be more than 1,200 years, in good agreement with their experimental observations. The data provided by this study will be invaluable for those searching for HCOH under different conditions, for example in the gas phase, where it is expected to participate in many reactions. For such studies, it will be necessary to find out if the tunnelling process is similar in gases and solids — that is, does the matrix surrounding the HCOH molecules in Schreiner and colleagues’ experiments have some role in the mechanism? The findings also provide a well-defined system of small molecules that will be a perfect model for studying the mechanisms of tunnelling reactions in solids. Far from being yesterday’s news, small molecules still have much to teach us. ■

Taking after Grandma

People often talk about characters — hair colour, a hooked nose, a talent for the trombone — missing a generation. This is simply the result of recessive genes acting on complex traits. However, Susan Lolle, Robert Pruitt and colleagues now report in Nature that, for the plant Arabidopsis thaliana at least, this can be quite literally true.