Three distinct messenger RNAs can encode the human immunosuppressant-binding protein FKBP12.

FKBP12 is an 11.8-kDa protein that binds the potent immunosuppressants FK506 and rapamycin. When bound to FK506, FKBP12 forms an inhibitory complex with calcineurin and interferes with signal transduction in activated T lymphocytes. In studying human FKBP12 cDNAs and the human FKBP12 gene, we found that three distinct transcripts can encode human FKBP12. The transcripts, which we designate FKBP 12A, 12B and 12C, contain identical open reading frames, but vary in abundance and are distinguished by unique 3' untranslated regions. The mature transcripts derive from either four or five exons and are generated by the differential use of one splice junction and three cleavage-polyadenylation sites within FKBP12. FKBP12A and 12B populations increase in abundance and/or stability when T-cell populations are mitogenically activated in vitro, implying that one result of T-cell stimulation is increased demand for the FKBP12 message. These transcripts are also present in a variety of human tissues, suggesting that FKBP12 and/or the mRNAs encoding it might affect physiological function(s) in a diverse array of cells.

Cloning, genomic organization and transcription of the Entamoeba histolytica alpha-tubulin-encoding gene.

We have isolated and characterized an Entamoeba histolytica alpha-tubulin (alpha Tub)-encoding gene (Eh alpha tub). A 700-bp DNA fragment was amplified by PCR using primers derived from consensus alpha- and beta-Tub amino acid (aa) sequences from different organisms and E. histolytica DNA as the template. These PCR fragments were used to screen both genomic DNA and cDNA libraries in order to isolate an Eh alpha tub structural gene. Two overlapping clones containing the complete alpha tub ORF (1392 bp) were isolated from the genome and cDNA libraries. The deduced aa sequence of Eh alpha Tub has 55.5, 50 and 52% identity to Plasmodium falciparum alpha Tub 2, Saccharomyces cerevisiae alpha Tub 2 and human alpha Tub, respectively. Interestingly, the predicted Eh alpha Tub protein lacks a poly-acidic motif at its C terminus which is involved in Tub polymerization and microtubule-associated protein binding in other organisms. This fact may indicate a difference in tubule assembly in this organism and could provide a potential key for the development of therapeutic agents. According to Southern blot experiments and the sequences of several clones, at least two non-adjacent copies of alpha tub are present in the E. histolytica genome. A 1.5-kb transcript corresponding to the alpha tub mRNA was detected in mRNA from asynchronous E. histolytica trophozoites.

Overexpression of p59-HBI (FKBP59), full length and domains, and characterization of PPlase activity.

It has been previously proposed that the rabbit p59-HBI (Heat shock protein Binding Immunophilin) or rFKBP59 (FK506 Binding Protein), found associated with the 90 kDa heat shock protein in nontransformed steroid receptor complexes, has three domains structurally related to hFKBP12 (Callebaut, I., Renoir, J.M., Lebeau, M.C., Massol, N., Burny, A., Baulieu, E.E. and Mornon, J.P. (1992) Proc. Natl. Acad. Sci., USA 89, 6270-6274). Here we report the overexpression, as fusion proteins in E. coli, of the full length p59-HBI and a series of p59-HBI mutants delimiting these domains and their respective peptidyl prolyl cis trans isomerase (PPlase) activity. The PPlase activity of p59-HBI is comparable to that of hFKBP12 and is due to domain p59-HBI I which displays the highest homology with this immunophilin. The residual enzymatic activity found in domain p59-HBI II is discussed.

Structure-based drug design: applications in immunopharmacology and immunosuppression.

Structure-based drug design (SBDD) combines the power of many scientific disciplines, such as X-ray crystallography, nuclear magnetic resonance, medicinal chemistry, molecular modeling, biology, enzymology and biochemistry, in a functional paradigm of drug development. The current strength of SBDD lies in parlaying enzyme inhibitors into drugs, but a variety of technological advances over the past few years now makes it possible to address complex biological targets, such as those regulating immunosuppression and immunoactivation. Manual Navia and Debra Peattie discuss the SBDD paradigm and consider several of its achievements and challenges in immunopharmacology, particularly as these apply to the design of novel, potent immunosuppressants.

Structure-based drug design: applications in immunopharmacology and immunosuppression.

Structure-based drug design (SBDD) combines the power of many scientific disciplines, such as X-ray crystallography, nuclear magnetic resonance, medicinal chemistry, molecular modeling, biology, enzymology and biochemistry, in a functional paradigm of drug development. The current strength of SBDD lies in parlaying enzyme inhibitors into drugs, but a variety of technological advances over the past few years now makes it possible to address complex biological targets, such as those regulating immunosuppression and immunoactivation. Manuel Navia and Debra Peattie discuss the SBDD paradigm and consider several of its achievements and challenges in immunopharmacology, particularly as these apply to the design of novel, potent immunosuppressants.

Identification and characterization of gamma-giardin and the gamma-giardin gene from Giardia lamblia.

The giardins are abundant cytoskeletal proteins that range in size from 29-38 kDa and are specific to the ventral disk of the intestinal protozoan parasite Giardia lamblia. The 29-kDa (beta and beta-1; refs. 8-10) and the 33-kDa (alpha-1 and alpha-2; refs. 3 and 7) giardins have been characterized previously. In this paper we extend the analysis of the giardins to include the 38-kDa giardin, which we have named gamma-giardin. After purifying gamma-giardin by two-dimensional electrophoresis, we raised polyclonal antibodies to the protein and used them to demonstrate that gamma-giardin shares at least one epitope with 9 other giardin polypeptides and that it localizes to the ventral disk of the parasite. We also determined an internal peptide sequence of 12 amino acid residues and used this information to construct oligonucleotide probes for the gamma-giardin gene. After cloning the gene, we determined the nucleotide sequence of its 933-bp open reading frame and 866 bp of 5' and 3' flanking sequence. We found the downstream AGTPuAAPy motif typical of all G. lamblia genes sequenced to date, and determined that the single copy of the gamma-giardin gene localizes to the same chromosome or chromosomal cluster as the alpha-giardins. Finally, we demonstrated by primer extension analysis that gamma-giardin transcripts contain a short untranslated leader characteristic of G. lamblia messenger RNAs.

Expression and characterization of human FKBP52, an immunophilin that associates with the 90-kDa heat shock protein and is a component of steroid receptor complexes.

Using an FK506 affinity column to identify mammalian immunosuppressant-binding proteins, we identified an immunophilin with an apparent M(r) approximately 55,000, which we have named FKBP52. We used chemically determined peptide sequence and a computerized algorithm to search GenPept, the translated GenBank data base, and identified two cDNAs likely to encode the murine FKBP52 homolog. We amplified a murine cDNA fragment, used it to select a human FKBP52 (hFKBP52) cDNA clone, and then used the clone to deduce the hFKBP52 sequence (calculated M(r) 51,810) and to express hFKBP52 in Escherichia coli. Recombinant hFKBP52 has peptidyl-prolyl cis-trans isomerase activity that is inhibited by FK506 and rapamycin and an FKBP12-like consensus sequence that probably defines the immunosuppressant-binding site. FKBP52 is apparently common to several vertebrate species and associates with the 90-kDa heat shock protein (hsp90) in untransformed mammalian steroid receptor complexes. The putative immunosuppressant-binding site is probably distinct from the hsp90-binding site, and we predict that FKBP52 has different structural domains to accommodate these functions. hFKBP52 contains 12 protein kinase phosphorylation-site motifs and a potential calmodulin-binding site, implying that posttranslational phosphorylation could generate multiple isoforms of the protein and that calmodulin and intracellular Ca2+ levels could affect FKBP52 function. FKBP52 transcripts are present in a variety of human tissues and could vary in abundance and/or stability.

Nucleotide sequence of a second alpha giardin gene and molecular analysis of the alpha giardin genes and transcripts in Giardia lamblia.

The giardins are a group of proteins with relative molecular masses (Mrs) between 29,000 and 38,000 that are specific to the ventral disk of the intestinal protozoan parasite Giardia lamblia. We previously have characterized alpha-giardin, renamed here alpha-1-giardin, as a novel 33-kDa protein located on the edges of the disk microribbons. Southern blot analysis of G. lamblia genomic DNA, followed by cloning and sequencing, revealed the existence of a related gene that we have called alpha-2-giardin. Sequence comparison of the alpha-giardin genes reveals 81% identity at the nucleotide level and 77% at the predicted amino acid level. The predicted alpha-giardins have similar Mrs of approximately 33,900 and are very rich in alpha-helix conformations. Each gene is present in single copy and, like many other known Giardia coding sequences, exhibits a strong preference for cytidine and guanosine in the third base position of each codon. Chromosome hybridization analysis indicates that both genes are either on the same chromosome or on chromosomes with similar mobility. Experiments utilizing primer extension and RNA sequencing provide evidence that both genes are transcribed. The stable transcripts have extremely short leader regions of only 3 nucleotides, and the downstream sequence of the alpha-2-giardin gene reveals that the sequence AGTPuAA remains a consistent element within G. lamblia protein-encoding genes.

cDNA encoding murine FK506-binding protein (FKBP): nucleotide and deduced amino acid sequence.

A FKBP cDNA encoding murine FK506 binding protein (FKBP) has been cloned, and its complete nucleotide sequence has been determined. The open reading frame within the 1556-bp cDNA segment encodes an 108 amino acid (aa) protein that differs from the human FKBP by three aa and from the bovine FKBP by five aa. Molecular modeling of the protein places the aa substitutions at positions not directly involved in drug binding or interaction with the potential drug target protein, calcineurin A.

Solution structure of the major binding protein for the immunosuppressant FK506.

The major FK506 binding protein (FKBP, relative molecular mass approximately 11,800; Mr 11.8K) and cyclophilin (Mr approximately 17K) belong to a class of proteins termed immunophilins. Although unrelated at the amino-acid sequence level, they both possess peptidyl-prolyl cis-trans isomerase activities which are inhibited by immunosuppressants that block signal transduction pathways leading to T-lymphocyte activation. FK506 and rapamycin strongly inhibit the peptidyl-prolyl cis-trans isomerase activity of FKBP, whereas cyclosporin A inhibits that of cyclophilin. The significance of this enzyme activity and the role of the immunophilins in immunoregulation is unknown. To understand better the function of the immunophilins and their interaction with inhibitors, we are investigating the solution structures of FKBP and FKBP-inhibitor complexes by multidimensional NMR methods. Here we report the solution conformation of FKBP, as generated by NMR, distance geometry and molecular dynamics methods. The regular secondary structure of FKBP is composed mainly of beta sheet (approximately 35%) with little helical structure (less than 10%). The hydrophobic core of the molecule, containing the buried side chains of six of the protein's nine aromatic amino acids, is enclosed by a five-stranded antiparallel beta sheet on one side, a loop and a short helix at residues 51-56 and 57-65, and an aperiodic loop at residues 81-95. Examination of the structure suggests a possible site of interaction with FK506.

Chromatin organization in Entamoeba histolytica.

The chromatin structure of Entamoeba histolytica was investigated. It was found that this protozoan organizes its chromatin in nucleosome-like particles 10 nm in diameter, but digestion of the chromatin with micrococcal nuclease did not render a regularly spaced DNA ladder in agarose gels. Southern blot analysis of the products of Entamoeba chromatin digestion using total amebic DNA and a non-transcribed repetitive sequence produced a banding pattern characteristic of eukaryotic chromatin with a repetitive size of approximately 130 bp. Conversely, hybridization with two active gene probes, actin and ribosomal RNA, showed that these sequences are not part of the chromatin organized in nucleosomes. It was also found that the basic nuclear proteins differ from histones of higher eukaryotes in electrophoretic mobility. Screening of an E. histolytica HM1-IMSS genomic library with Saccharomyces cerevisiae H3 and H4 genes and attempts to amplify E. histolytica sequences, homologous to these yeast histone genes, gave negative results suggesting that the Entamoeba proteins involved in chromatin organization are not typical histones.

In situ analyses reveal that the two nuclei of Giardia lamblia are equivalent.

The protozoan parasite Giardia lamblia has the unusual morphology of bearing two equal-sized nuclei. This organism probably represents the earliest diverging lineage of eukaryotes, suggesting that its biological tactics may be transitional. To begin to understand the role played by the two equal-sized nuclei in this organism, and perhaps the role this organism has played along the path to higher eukaryotes, we have analyzed the structure and function of these two nuclei. We show that the two nuclei are equivalent with respect to the amount of DNA harbored in each nucleus, the presence of ribosomal DNA sequences, and the transcriptional activity. We begin also to address the question of how these bilaterally symmetrical ancestors divide, by illustrating the mitotic plane of division.

The giardins of Giardia lamblia: genes and proteins with promise.

The unique evolutionary position of the genus Giardia recently came to light when Mitch Sogin and colleagues showed it to be the earliest diverging lineage in the eukaryotic line of descent by ribosomal RNA analysis. Similar in significance, the acquisition of a cytoskeleton was a pivotal occurrence in evolution. With an endoskeleton came an internal support structure for cells as well as the means to regulate dynamic phenomena such as muscle contraction, mitotic movement of chromosomes, ciliar and flagellar beating, and cell migration. Debra Peattie has been exploring genes that express proteins of the Giardia cytoskeleton, and from this work she presents predictions of their structure and some thoughts about their function.

Ultrastructural localization of giardins to the edges of disk microribbons of Giarida lamblia and the nucleotide and deduced protein sequence of alpha giardin.

The giardins are a group of 29-38-kD proteins in the ventral disk of the protozoan parasite Giardia lamblia. The disk attaches the parasite to the host's intestinal epithelium and is composed of parallel, coiled microtubules that are adjacent to the ventral plasma membrane and from which processes called microribbons extend into the cytoplasm; the microribbons are connected by crossbridges. G. lamblia cytoskeletons, consisting of disks and attached flagella, were isolated and used to show that the 29-38-kD proteins separate into five bands by one-dimensional electrophoresis and into 23 species by two-dimensional analysis. Rabbit antibodies raised against a 33-kD protein band, purified by one-dimensional gel electrophoresis and shown to contain three proteins by two-dimensional electrophoresis, recognized 17 proteins by two-dimensional immunoblot analysis. By immunofluorescence these antibodies reacted with the ventral disk but not with the flagella in isolated cytoskeletons. Electron microscopy revealed that the anti-giardin antibodies bound to the edges of the microribbons but not to the microtubules, crossbridges, or other, nondisk structures. Antibodies to tubulin reacted with both the disk and flagella in isolated cytoskeletons but bound only to the microtubules in these structures. The amino-terminal sequence of the 33-kD immunogen was determined and used to construct a DNA oligomer, and the oligomer was used to isolate the alpha giardin gene. The gene was used to hybrid select RNA, and the in vitro translation product from this RNA was precipitated by the antibodies against the 33-kD immunogen. The gene sequence was a single open reading frame of 885 nucleotides that predicted a protein of 33.8 kD. The protein sequence is unique, having no significant homology to two other giardin sequences or to any sequences within the Protein Identification Resource. It is predicted to be 82% alpha helical. The downstream sequence of the gene indicates that the sequence AGT-PuAA is located six to nine nucleotides beyond the stop codon in all protein-encoding genes of G. lamblia that have been sequenced and reported to date.

Structure and expression of a family of Ultrabithorax mRNAs generated by alternative splicing and polyadenylation in Drosophila.

The 77-kb primary transcript of the homeotic Ultrabithorax (Ubx) gene is alternatively spliced to yield at least five different coding regions. Each is restricted to either a 3.2- or a 4.3-kb size class generated by alternative polyadenylation. The pathways for splicing and polyadenylation are therefore coordinately regulated, and because the relative abundance of the respective mRNAs varies throughout development, these pathways also appear to be developmentally regulated. Translation of these mRNAs yields a family of Ubx proteins characterized by constant amino- and carboxy-proximal regions of 247 and 99 amino acid residues, respectively. Members of this family are distinguished by a short variable region that links the constant regions and consists of different combinations of three optional elements of 9, 17, and 17 residues. Only four amino acid residues separate this variable region from the 60-residue homeo domain of the carboxy-terminal constant region. This proximity suggests that functional differences among the Ubx proteins derive from the differential effects of their variable regions on the DNA-binding capacity of the homeo domain. An argument is made that these functional differences are tissue specific.

Phylogenetic meaning of the kingdom concept: an unusual ribosomal RNA from Giardia lamblia.

An analysis of the small subunit ribosomal RNA (16S-like rRNA) from the protozoan Giardia lamblia provided a new perspective on the evolution of nucleated cells. Evolutionary distances estimated from sequence comparisons between the 16S-like rRNAs of Giardia lamblia and other eukaryotes exceed similar estimates of evolutionary diversity between archaebacteria and eubacteria and challenge the phylogenetic significance of multiple eukaryotic kingdoms. The Giardia lamblia 16S-like rRNA has retained many of the features that may have been present in the common ancestor of eukaryotes and prokaryotes.

Novel transcripts from the Ultrabithorax domain of the bithorax complex.

We present a detailed analysis of the transcriptional products of the bithoraxoid (bxd) region of the Ultrabithorax domain in the bithorax complex of Drosophila melanogaster. This region is transcribed twice during development: between 3 and 6 hr of embryogenesis, a set of early transcripts, 1.1 to 1.3 kb in size, is synthesized; from the midthird larval instar through the adult stages, a late 0.8-kb transcript is synthesized. We have sequenced five cloned cDNAs representing early transcripts and three cDNAs representing the late transcript and have located their exons within the 40 kb of DNA comprising the bxd region. S1 nuclease protection and primer extension of both the early and late transcripts were used to further elucidate their structure. The early RNAs are produced by complex differential splicing of a series of exons derived from a 26-kb primary transcript. Curiously, these RNAs do not possess significant protein coding potential. The late bxd RNA comprises a single exon transcribed from an intronic region of the early transcription unit. This RNA, by contrast, possesses excellent coding potential and, if translated, would yield a 101-amino-acid polypeptide.