Biomedical subjects
A Klug
Publications and source records attributed to A Klug.
Structural biology. A marvellous machine for making messages.
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Design of polyzinc finger peptides with structured linkers.
Zinc finger domains are perhaps the most versatile of all known DNA binding domains. By fusing up to six zinc finger modules, which normally recognize up to 18 bp of DNA, designer transcription factors can be produced to target unique sequences within large genomes. However, not all continuous DNA sequences make good zinc finger binding sites. To avoid having to target unfavorable DNA sequences, we designed multizinc finger peptides with linkers capable of spanning long stretches of nonbound DNA. Two three-finger domains were fused by using either transcription factor IIIA for the Xenopus 5S RNA gene (TFIIIA) finger 4 or a non-sequence-specific zinc finger as a "structured" linker. Our gel-shift results demonstrate that these peptides are able to bind with picomolar affinities to target sequences containing 0--10 bp of nonbound DNA. Furthermore, these peptides display greater sequence selectivity and bind with higher affinity than similar six-finger peptides containing long, flexible linkers. These peptides are likely to be of use in understanding the behavior of polydactyl proteins in nature and in the targeting of human, animal, or plant genomes for numerous applications. We also suggest that in certain polydactyl peptides an individual finger can "flip" out of the major groove to allow its neighbors to bind shorter, nontarget DNA sequences.
Improved DNA binding specificity from polyzinc finger peptides by using strings of two-finger units.
Multizinc finger peptides are likely to reach increased prominence in the search for the "ideal" designer transcription factor for in vivo applications such as gene therapy. However, for these treatments to be effective and safe, the peptides must bind with high affinity and, more importantly, with great specificity. Our previous research has shown that zinc finger arrays can be made to bind 18 bp of DNA with picomolar affinity, but also has suggested that arrays of fingers also may bind tightly to related sequences. This work addresses the question of zinc finger DNA binding specificity. We show that by changing the way in which zinc finger arrays are constructed--by linking three two-finger domains rather than two three-finger units--far greater target specificity can be achieved through increased discrimination against mutated or closely related sequences. These new peptides have the added capability of being able to span two short gaps of unbound DNA, although still binding with picomolar affinity to their target sites. We believe that this new method of constructing zinc finger arrays will offer greater efficacy in the fields of gene therapy and in the production of transgenic organisms than previously reported zinc finger arrays.
A rapid, generally applicable method to engineer zinc fingers illustrated by targeting the HIV-1 promoter.
DNA-binding domains with predetermined sequence specificity are engineered by selection of zinc finger modules using phage display, allowing the construction of customized transcription factors. Despite remarkable progress in this field, the available protein-engineering methods are deficient in many respects, thus hampering the applicability of the technique. Here we present a rapid and convenient method that can be used to design zinc finger proteins against a variety of DNA-binding sites. This is based on a pair of pre-made zinc finger phage-display libraries, which are used in parallel to select two DNA-binding domains each of which recognizes given 5 base pair sequences, and whose products are recombined to produce a single protein that recognizes a composite (9 base pair) site of predefined sequence. Engineering using this system can be completed in less than two weeks and yields proteins that bind sequence-specifically to DNA with Kd values in the nanomolar range. To illustrate the technique, we have selected seven different proteins to bind various regions of the human immunodeficiency virus 1 (HIV-1) promoter.
The Human Genome Project.
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The role of the central zinc fingers of transcription factor IIIA in binding to 5 S RNA.
In the nine-zinc finger Xenopus transcription factor TFIIIA the central group of fingers, fingers 4 to 7, have been shown to bind to 5 S RNA. In this study, we have attempted to assess the role of this region of the TFIIIA molecule in more detail than hitherto. High-resolution footprinting by RNases A and CV1 has been used to probe the binding to 5 S RNA of three TFIIIA peptides Tf(1-6), Tf(4-6) and Tf(4-7), consisting of fingers 1 to 6, 4 to 6, and 4 to 7, respectively, and of full-length TFIIIA. The results pinpoint the outer margins of binding of the central fingers within helices IV and II of TFIIIA. A comparison of the footprints reveals that the presence of finger 7 affords protection at positions C19 and U55, the distal portion of helix II and the proximal portion of loop B. In addition, our footprints suggest that the central fingers bind in the same manner, whether in an isolated group or in the intact TFIIIA molecule. In a companion study, we have determined the binding affinities of Tf(4-6) and Tf(4-7) for full-length and three truncated 5 S RNA molecules, the latter selected on the basis of the regions of the 5 S RNA molecule known to be important in the binding of TFIIIA. The analysis uses only fully active protein involved in the binding and the results are consistent with the corresponding footprinting results. This is the first time that a detailed study of the binding site of one particular zinc finger to RNA has been reported; the results should be of use in the design of 5 S RNA molecules and TFIIIA peptides for structural studies of the interaction between zinc fingers and RNA.
Genes: we can't expect full understanding yet.
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Latency as a function of intensity in auditory neurons: influences of central processing.
The response latencies of sensory neurons typically shorten with increases in stimulus intensity. In the central auditory system this phenomenon should have a significant impact on a number of auditory functions that depend critically on an integration of precisely timed neural inputs. Evidence from previous studies suggests that the auditory system not only copes with the potential problems associated with intensity-dependent latency change, but that it also modifies latency change to shape the response properties of many cells for specific functions. This observation suggests that intensity-dependent latency change may undergo functional transformations along the auditory neuraxis. The goal of our study was to explore these transformations by making a direct, quantitative comparison of intensity-dependent latency change among a number of auditory centers from the lower brainstem to the thalamus. We found two main ways in which intensity-dependent latency change transformed along the neuraxis: (1) the range of latency change increased substantially and (2) one particular type of latency change, which has been suggested to be associated with sensitivity to temporally segregated stimulus components, occurred only at the highest centers tested, the midbrain and thalamus. Additional testing in the midbrain (inferior colliculus) indicated that inhibitory inputs are involved in shaping latency change. Our findings demonstrate that the central auditory system modifies intensity-dependent latency changes. We suggest that these changes may be functionally incorporated, actively enhanced, or modified to suit specific functions of the auditory system.
Features of contralaterally evoked inhibition in the inferior colliculus.
Cells in the central nucleus of the inferior colliculus (ICc) receive a large number of convergent inputs that are not only excitatory but inhibitory as well. While the excitatory responses of ICc cells have been studied extensively, less attention has been paid to the effects that inhibitory inputs have on auditory processing in the ICc. The purpose of this study was to examine the role of contralaterally evoked inhibition in single ICc cells in awake Mexican free-tailed bats. To study the contralaterally evoked inhibition, we created background activity by the iontophoretic application of the excitatory neurotransmitters glutamate and aspartate and visualized the inhibition as a gap in the carpet of background activity. We found that 85% of ICc cells exhibit a contralaterally evoked excitation followed by a period of inhibition. The inhibition acts primarily through GABA(A)20 ms) tones in generating persistent inhibition. While the early inhibition has clear roles in the shaping of excitatory response properties to a stimulus, the later persistent component of the inhibition is more enigmatic. The fact that the persistent inhibition lasts well beyond the duration of excitatory inputs to the ICc cell implies that the persistent inhibition may be important for the temporal segregation of the responses to multiple sound sources.
Zinc finger peptides for the regulation of gene expression.
Zinc fingers are small DNA-binding peptide motifs that were discovered in this laboratory. These motifs can be used as modular building blocks for the construction of larger protein domains that recognise and bind to specific DNA sequences. Phage display has been used to create a large library of different zinc fingers from which selections were made for binding to a given DNA sequence. From this database there have been elucidated elements of recognition rules that relate the amino acid sequence of a finger to its preferred DNA binding site. Control of gene expression using designed zinc finger peptides has been demonstrated by the specific inhibition of an oncogene mouse cell line and also by switching on genes in expression plasmids. These experiments demonstrate that zinc finger DNA-binding domains can be engineered de novo to recognise given DNA sequences. Five to six individual zinc fingers linked together would recognise a DNA sequence 15-18 bp in length, sufficiently long to constitute a rare address in the human genome. By adding functional groups to the engineered DNA-binding domains, e.g. silencing domains, novel transcription factors can be generated to up- or downregulate expression of a target gene. Among potential applications are the repression of oncogene expression and the disruption of the reproductive cycle of virus infection.
Structure of tau exon 10 splicing regulatory element RNA and destabilization by mutations of frontotemporal dementia and parkinsonism linked to chromosome 17.
Coding region and intronic mutations in the tau gene cause frontotemporal dementia and parkinsonism linked to chromosome 17. Intronic mutations and some missense mutations increase splicing in of exon 10, leading to an increased ratio of four-repeat to three-repeat tau isoforms. Secondary structure predictions have led to the proposal that intronic mutations and one missense mutation destabilize a putative RNA stem-loop structure located close to the splice-donor site of the intron after exon 10. We have determined the three-dimensional structure of this tau exon 10 splicing regulatory element RNA by NMR spectroscopy. We show that it forms a stable, folded stem-loop structure whose thermodynamic stability is reduced by frontotemporal dementia and parkinsonism linked to chromosome 17 mutations and increased by compensatory mutations. By exon trapping, the reduction in thermodynamic stability is correlated with increased splicing in of exon 10.
The tobacco mosaic virus particle: structure and assembly.
A short account is given of the physical and chemical studies that have led to an understanding of the structure of the tobacco mosaic virus particle and how it is assembled from its constituent coat protein and RNA. The assembly is a much more complex process than might have been expected from the simplicity of the helical design of the particle. The protein forms an obligatory intermediate (a cylindrical disk composed of two layers of protein units), which recognizes a specific RNA hairpin sequence. This extraordinary mechanism simultaneously fulfils the physical requirement for nucleating the growth of the helical particle and the biological requirement for specific recognition of the viral DNA.
Interaural intensity difference processing in auditory midbrain neurons: effects of a transient early inhibitory input.
Interaural intensity differences (IIDs) are important cues that animals use to localize high-frequency sounds. Neurons sensitive to IIDs are excited by stimulation of one ear and inhibited by stimulation of the other ear, such that the response magnitude of the cell depends on the relative strengths of the two inputs, which in turn depends on the sound intensities at the ears. In the auditory midbrain nucleus, the inferior colliculus (IC), many IID-sensitive neurons have response functions that decline steeply from maximum to zero spikes as a function of IID. However, there are also many neurons with much more shallow response functions that do not decline to zero spikes. We present evidence from single-unit recordings in the Free-tailed bat's IC that this partially inhibited response pattern is a result of the inhibitory input to these cells being very brief ( approximately 2 msec). Of the cells sampled, 54 of 137 (40%) achieved partial inhibition when tested with 60 msec tones, and the inhibition to these 54 cells occurred primarily during the first few milliseconds of the excitatory response. Consequently, the initial component of the response was highly sensitive to IIDs, whereas the later component was primarily insensitive to IIDs. Each of the 54 "partially inhibited" cells was able to reach complete inhibition with very short stimuli, such as simulated bat echolocation calls that invoked only the initial, IID-sensitive component. Local application of inhibitory transmitter antagonists disabled the short inhibitory input, indicating that this response pattern is created within the IC.
Multiple components of ipsilaterally evoked inhibition in the inferior colliculus.
The central nucleus of the inferior colliculus (ICc) receives a large number of convergent inputs that are both excitatory and inhibitory. Although excitatory inputs typically are evoked by stimulation of the contralateral ear, inhibitory inputs can be recruited by either ear. Here we evaluate ipsilaterally evoked inhibition in single ICc cells in awake Mexican free-tailed bats. The principal question we addressed concerns the degree to which ipsilateral inhibition at the ICc suppresses contralaterally evoked discharges and thus creates the excitatory-inhibitory (EI) properties of ICc neurons. To study ipsilaterally evoked inhibition, we iontophoretically applied excitatory neurotransmitters and visualized the ipsilateral inhibition as a gap in the carpet of background activity evoked by the transmitters. Ipsilateral inhibition was seen in 86% of ICc cells. The inhibition in most cells had both glycinergic and GABAergic components that could be blocked by the iontophoretic application of bicuculline and strychnine. In 80% of the cells that were inhibited, the ipsilateral inhibition and contralateral excitation were temporally coincident. In many of these cells, the ipsilateral inhibition suppressed contralateral discharges and thus generated the cell's EI property in the ICc. In other cells, the ipsilateral inhibition was coincident with the initial portion of the excitation, but the inhibition was only 2-4 ms in duration and suppressed only the first few contralaterally evoked discharges. The suppression was so slight that it often could not be detected as a decrease in the spike count generated by increasing ipsilateral intensities. Twenty percent of the cells that expressed inhibition, however, had inhibitory latencies that were longer than the excitatory latencies. In these neurons, the inhibition arrived too late to suppress most or any of the discharges. Finally, in the majority of cells, the ipsilateral inhibition persisted for tens of milliseconds beyond the duration of the signal that evoked it. Thus ipsilateral inhibition has multiple components and one or more of these components are typically evoked in ICc neurons by sound received at the ipsilateral ear.
Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers.
Zinc fingers are small DNA-binding modules noted for their occurrence in a large number of eukaryotic transcription factors, and their use in protein engineering. Although it was expected that zinc fingers can bind to a wide diversity of DNA sequences, previous studies using model zinc finger domains from Zif268 (and Sp1) have revealed a potential limitation to the DNA-binding specificity. For example, phage display selection of individual zinc fingers to recognize trinucleotide DNA subsites returned fingers that bound specifically only to triplets of the form GNN, i.e., triplets with guanine at the 5' end. Following our recently reported work [Isalan, M., Choo, Y., and Klug, A. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 5617-5621], we now show that this limitation can be overcome by the concerted randomization of certain amino acid positions in adjacent zinc fingers that specify overlapping DNA subsites. This illustrates an important mechanism underlying DNA recognition by arrays of zinc fingers, and points the way to improved strategies for the design of highly specific zinc finger proteins that bind any given nucleotide sequence.
Mutation in the tau gene in familial multiple system tauopathy with presenile dementia.
Familial multiple system tauopathy with presenile dementia (MSTD) is a neurodegenerative disease with an abundant filamentous tau protein pathology. It belongs to the group of familial frontotemporal dementias with Parkinsonism linked to chromosome 17 (FTDP-17), a major class of inherited dementing disorders whose genetic basis is unknown. We now report a G to A transition in the intron following exon 10 of the gene for microtubule-associated protein tau in familial MSTD. The mutation is located at the 3' neighboring nucleotide of the GT splice-donor site and disrupts a predicted stem-loop structure. We also report an abnormal preponderance of soluble tau protein isoforms with four microtubule-binding repeats over isoforms with three repeats in familial MSTD. This most likely accounts for our previous finding that sarkosyl-insoluble tau protein extracted from the filamentous deposits in familial MSTD consists only of tau isoforms with four repeats. These findings reveal that a departure from the normal ratio of four-repeat to three-repeat tau isoforms leads to the formation of abnormal tau filaments. The results show that dysregulation of tau protein production can cause neurodegeneration and imply that the FTDP-17 gene is the tau gene. This work has major implications for Alzheimer's disease and other tauopathies.