The Homeodomain Resource: sequences, structures and genomic information

BarH1 regulates the expression of conserved odorant-binding protein 22 from Dastarcus helophoroides

Chemical signals are pivotal in establishing tritrophic interactions among host plants, herbivorous insects, and natural enemies. Previous studies have shown that evolutionarily conserved MaltOBPs in Monochamus alternatus and DhelOBPs in Dastarcus helophoroides contribute to the establishment of pine -pest - natural enemy tritrophic interactions by recognizing the same volatile emitted by the host during crucial developmental stages. We hypothesized that the transcriptional regulatory mechanisms of evolutionarily conserved OBPs respectively from pests and enemies are similar. In this study, we identified the promoter region of DhelOBP22 through chromosome walking and discovered that transcription factor BarH1, which have been proved to regulate the expression of MaltOBP19 in M. alternatus, regulates the expression of DhelOBP22 by binding to its promoter region, as evidenced by dual-luciferase assays and electrophoretic mobility shift assay (EMSA). When the BarH1 gene was silenced using RNAi, the expression of DhelOBP22 was inhibited, leading to the disappearance of the attracted behavior of mated female D. helophoroides adults towards camphene. This study underscores that conserved transcriptional regulation mechanisms play a role in regulating the expression of evolutionarily conserved OBPs respectively from herbivores and natural enemies.

Designing synthetic transcription factors: A structural perspective

In this chapter, we discuss different design strategies of synthetic proteins, especially synthetic transcription factors. Design and engineering of synthetic transcription factors is particularly relevant for the need-based manipulation of gene expression. With recent advances in structural biology techniques and with the emergence of other precision biochemical/physical tools, accurate knowledge on structure-function relations is increasingly becoming available. Besides discussing the underlying principles of design, we go through individual cases, especially those involving four major groups of transcription factors-basic leucine zippers, zinc fingers, helix-turn-helix and homeodomains. We further discuss how synthetic biology can come together with structural biology to alter the genetic blueprint of life.

Requirement for two nearly identical TGIF-related homeobox genes in Drosophila spermatogenesis

The genetic analysis of spermatogenesis in Drosophila melanogaster has led to the identification of several genes that control the onset of meiosis, spermatid differentiation, or both. We described two tightly linked and nearly identical homeobox genes of the TGIF (TG-interacting factor) subclass called vismay and achintya that are essential for spermatogenesis in Drosophila. In flies deficient for both genes, spermatogenesis is blocked prior to any spermatid differentiation and before the first meiotic division. This suggests that vismay and achintya function at the same step as two previously characterized meiotic arrest genes, always early and cookie monster. Consistent with this idea, both always early and cookie monster are still expressed in flies deficient in vismay and achintya. Conversely, Vismay and Achintya proteins are present in always early mutant testes. Co-immunoprecipitation experiments further suggest that Vismay and Achintya proteins exist in a complex with Always early and Cookie monster proteins. Because Vismay and Achintya are likely to be sequence-specific DNA binding factors, these results suggest that they help to specify the spermatogenesis program by recruiting or stabilizing Always early and Cookie monster to specific target genes that need to be transcriptionally regulated during testes development.

New insights in the transcriptional activity and coregulator molecules in the arterial wall

A number of vascular diseases are associated with abnormal expression of genes that contribute to their pathophysiological and clinical manifestations, but at the same time offer potential therapeutic targets. One of the promising therapeutic approaches targets the pathophysiological pathways leading to aberrant gene activation, namely transcriptional activity and its molecular modulators (agonists, antagonists, coregulators, and nuclear receptors). The transcription factors can be divided into four classes (I-IV) classified by structural elements, like basic leucine zipper (bZIP) or basic helix-loop-helix (bHLH), which mediate their DNA binding activity but also determine the classes of drugs that can affect their activity. For example, statins modulate activation of the class-I transcription factor sterol responsive element-binding protein (SREBP), whose target genes including hydroxyl-methyl-glutaryl acetyl Coenzyme-A (HMG-CoA) reductase, HMG-CoA synthase, and the low-density lipoprotein receptor, all of which are involved in cholesterol and fatty acid metabolism. Similarly, insulin-like drugs target the nuclear receptor peroxisome-proliferator-activator-receptor (PPAR)-gamma (class-II), several anti-inflammatory drugs inhibit activation of nuclear factor kappa B (NFkappaB) (class-IV), while others (e.g. flavopiridol, rapamycin, and paclitaxel) target regulation of cell-cycle proteins. Increased understanding of the genetic and molecular basis of disease (e.g. transcriptional activity and its coregulation) will potentially enhance future diagnosis, treatment, and prevention of vascular diseases.

Putative homeodomain proteins identified in prokaryotes based on pattern and sequence similarity

A putative homeodomain has been identified in eubacterial genomes, which include several pathogens. The domain is related in sequence to homeodomain, a component specific to transcription factors and playing a very important role in eukaryotes such as controlling the developmental processes of the organism. The putative homeodomain has been characterized utilizing the eukaryotic homeodomain protein sequence signature present in PROSITE as well as the sequence similarity search using BLAST suite for different eubacterial genomes. These findings provide evidence for the occurrence of DNA-binding motif in prokarya similar to that in eukarya.

An automated phylogenetic key for classifying homeoboxes

When novel gene sequences are discovered, they are usually identified, classified, and annotated based on aggregate measures of sequence similarity. This method is prone to errors, however. Phylogenetic analysis is a more accurate basis for gene classification and ortholog identification, but it is relatively labor-intensive and computationally demanding. Here we report and demonstrate a rapid new method for gene classification based on phylogenetic principles. Given the phylogeny of a minimal sample of gene family members, our method automatically identifies amino acids that are phylogenetically characteristic of each class of sequences in the family; it then classifies a novel sequence based on the presence of these characteristic attributes in its sequence. Using a subset of homeobox protein sequences as a test case, we show that our method approximates classification based on full-scale phylogenetic analysis with very high accuracy in a tiny fraction of the time.

Therapeutic modulation of transcription factor activity

Aberrant gene expression is a fundamental cause of many disease-associated pathophysiologies. The pharmacological modulation of transcription factor activity therefore represents an attractive therapeutic approach to such disorders. With the exception of nuclear receptors, which are the direct targets of pharmaceuticals, other known classes of transcription factors are largely regulated indirectly by drugs that impact upon those signal transduction cascades that alter transcription factor phosphorylation and dephosphorylation and/or nuclear import. However, recent advances in drug discovery technologies now enable high-throughput screens that can identify molecules that act directly at the level of transcription factor complexes.

Reprogrammable recognition codes in bicoid homeodomain-DNA interaction

We describe experiments to determine how the homeodomain of the Drosophila morphogenetic protein Bicoid recognizes different types of DNA sequences found in natural enhancers. Our chemical footprint analyses reveal that the Bicoid homeodomain makes both shared and distinct contacts with a consensus site A1 (TAATCC) and a nonconsensus site X1 (TAAGCT). In particular, the guanine of X1 at position 4 (TAAGCT) is protected by Bicoid homeodomain. We provide further evidence suggesting that the unique arginine at position 54 (Arg 54) of the Bicoid homeodomain enables the protein to recognize X1 by specifically interacting with this position 4 guanine. We also describe experiments to analyze the contribution of artificially introduced Arg 54 to DNA recognition by other Bicoid-related homeodomains, including that from the human disease protein Pitx2. Our experiments demonstrate that the role of Arg 54 varies depending on the exact homeodomain framework and DNA sequences. Together, our results suggest that Bicoid and its related homeodomains utilize distinct recognition codes to interact with different DNA sequences, underscoring the need to study DNA recognition by Bicoid-class homeodomains in an individualized manner.

Stereoselective deuterium labeling of proR beta-protons in the NMR structure determination of a helix-turn-helix turn peptide mimic

The NMR structure of a small, side-chain-cyclized tripeptide mimic of the turn in the helix-turn-helix (HTH) motif was determined. The four beta-protons were stereospecifically assigned by stereoselective deuterium replacement of only the proR beta-protons. All 24 of 30 NOESY cross-peaks not involving chemically defined or freely rotating protons, and six of seven coupling constants from the P.COSY were used as distance and angle constraints in molecular modeling. MacroModel found 33/1000 structures in the NMR constrained search and 263/1000 structures in the unconstrained search, indicating meaningful constraint by the NMR data. However, the 10 lowest-energy structures from the unconstrained and constrained searches are very similar, so modeling alone was able to find the experimentally determined structure.

The homeodomain resource: a prototype database for a large protein family

The Homeodomain Resource is an annotated collection of non-redundant protein sequences, three-dimensional structures and genomic information for the homeodomain protein family. Release 2.0 contains 765 full-length homeodomain-containing sequences, 29 experimentally derived structures and 116 homeobox loci implicated in human genetic disorders. Entries are fully hyperlinked to facilitate easy retrieval of the original records from source databases. A simple search engine with a graphical user interface is provided to query the component databases and assemble customized data sets. A new feature for this release is the addition of more automated methods for database searching, maintenance and implementation of efficient data management. The Homeodomain Resource is freely available through the WWW at http://genome.nhgri.nih.gov/homeodomain

Threading analysis of the Pitx2 homeodomain: predicted structural effects of mutations causing Rieger syndrome and iridogoniodysgenesis

Mutations in the homeobox gene PITX2 are responsible for a range of clinical phenotypes involving ocular and craniofacial development. Several mutations within the Pitx2 homeodomain region are specifically responsible for the development of the related autosomal-dominant disorders Rieger syndrome and iridogoniodysgenesis. To address the question of the structural effect of disease-causing mutations on the Pitx2 homeodomain, we used threading techniques to examine the tertiary structure of the Pitx2 wild-type and mutant homeodomain, using the crystal structure of Drosophila engrailed homeodomain bound with DNA as a template [Kissinger et al., 1990]. The threading analysis reveals that the wild-type Pitx2 homeodomain is indeed capable of forming the typical three-helical bundle-fold characteristic of homeodomain proteins. Energy calculations indicate that the homeodomain structure is stabilized primarily by hydrophobic interactions between residues at the helical interface. Point mutations responsible for the development of these genetic disorders were also examined; the results suggest that these mutations lead to the inability of Pitx2 to adopt its proper structure and bind to the regulatory sequences of its target gene(s), which in turn affects its metabolic role in the cell. Published 1999 Wiley-Liss, Inc.