GeneFIND web server for protein family identification and information retrieval

GENE FAMILY IDENTIFICATION NETWORK DESIGN FOR PROTEIN SEQUENCE ANALYSIS

With the exponential accumulation of sequence data, continued progress in the Human Genome Project will depend increasingly on advanced computational tools to manage and analyze the data. Utilizing information embedded within families of homologous sequences, a gene family identification approach may facilitate the understanding of gene functions. We have developed a GeneFIND (Gene Family Identification Network Design) system for database searching against gene families. It provides rapid and accurate protein family identification by combining global and motif sequence similarities and incorporating ProClass family information. Multi-level filters are used, starting with the MOTIFIND neural networks and BLAST search, followed by SSEARCH alignment, motif pattern match, hidden Markov modeling of motifs and ClustalW motif alignment. GeneFIND has been implemented as a full-scale system for the classification of more than 1200 ProSite and 6000 PIR families. It has been used to identify thousands of new family members and is well suited for genomic sequence analysis. The system is available for on-line family identification from our WWW server ().

A canonical FtsZ protein in Verrucomicrobium spinosum, a member of the Bacterial phylum Verrucomicrobia that also includes tubulin-producing Prosthecobacter species

Background

The origin and evolution of the homologous GTP-binding cytoskeletal proteins FtsZ typical of Bacteria and tubulin characteristic of eukaryotes is a major question in molecular evolutionary biology. Both FtsZ and tubulin are central to key cell biology processes – bacterial septation and cell division in the case of FtsZ and in the case of tubulins the function of microtubules necessary for mitosis and other key cytoskeleton-dependent processes in eukaryotes. The origin of tubulin in particular is of significance to models for eukaryote origins. Most members of domain Bacteria possess FtsZ, but bacteria in genus Prosthecobacter of the phylum Verrucomicrobia form a key exception, possessing tubulin homologs BtubA and BtubB. It is therefore of interest to know whether other members of phylum Verrucomicrobia possess FtsZ or tubulin as their FtsZ-tubulin gene family representative.

Results

Verrucomicrobium spinosum, a member of Phylum Verrucomicrobia of domain Bacteria, has been found to possess a gene for a protein homologous to the cytoskeletal protein FtsZ. The deduced amino acid sequence has sequence signatures and predicted secondary structure characteristic for FtsZ rather than tubulin, but phylogenetic trees and sequence analysis indicate that it is divergent from all other known FtsZ sequences in members of domain Bacteria. The FtsZ gene of V. spinosum is located within a dcw gene cluster exhibiting gene order conservation known to contribute to the divisome in other Bacteria and comparable to these clusters in other Bacteria, suggesting a similar functional role.

Conclusion

Verrucomicrobium spinosum has been found to possess a gene for a protein homologous to the cytoskeletal protein FtsZ. The results suggest the functional as well as structural homology of the V. spinosum FtsZ to the FtsZs of other Bacteria implying its involvement in cell septum formation during division. Thus, both bacteria-like FtsZ and eukaryote-like tubulin cytoskeletal homologs occur in different species of the phylum Verrucomicrobia of domain Bacteria, a result with potential major implications for understanding evolution of tubulin-like cytoskeletal proteins and the origin of eukaryote tubulins.

Thrombospondin-2 Is Essential for Myocardial Matrix Integrity

Cardiac hypertrophy can lead to heart failure (HF), but it is unpredictable which hypertrophied myocardium will progress to HF. We surmised that apart from hypertrophy-related genes, failure-related genes are expressed before the onset of failure, permitting molecular prediction of HF. Hearts from hypertensive homozygous renin-overexpressing (Ren-2) rats that had progressed to early HF were compared by microarray analysis to Ren-2 rats that had remained compensated. To identify which HF-related genes preceded failure, cardiac biopsy specimens were taken during compensated hypertrophy and we then monitored whether the rat progressed to HF or remained compensated. Among 48 genes overexpressed in failing hearts, we focused on thrombospondin-2 (TSP2). TSP2 was selectively overexpressed only in biopsy specimens from rats that later progressed to HF. Moreover, expression of TSP2 was increased in human hypertrophied hearts with decreased (0.19+/-0.01) versus normal ejection fraction (0.11+/-0.03 [arbitrary units]; P<0.05). Angiotensin II induced fatal cardiac rupture in 70% of TSP2 knockout mice, with cardiac failure in the surviving mice; this was not seen in wild-type mice. In TSP2 knockout mice, angiotensin II increased matrix metalloproteinase (MMP)-2 and MMP-9 activity by 120% and 390% compared with wild-type mice (P<0.05). In conclusion, we identify TSP2 as a crucial regulator of the integrity of the cardiac matrix that is necessary for the myocardium to cope with increased loading and that may function by its regulation of MMP activity. This suggests that expression of TSP2 marks an early-stage molecular program that is activated uniquely in hypertrophied hearts that are prone to fail.

Analyses of P-like transposable element sequences from the genome of Anopheles gambiae

We have identified 50 P element-homologous sequences in the genome of Anopheles gambiae by performing homology searches against the public genome database of A. gambiae using the canonical P element from Drosophila melanogaster as a query sequence. While most of these sequences belong to P subfamilies previously described from anopheline mosquitoes, at least four new subfamilies were identified. One of these A. gambiae P elements, which we termed AgPLS, was analysed in detail. AgPLS consists of three exons and does not have inverted terminal repeats. This element retains several of the structural features of other P-encoded peptides, such as motifs involved in DNA-protein and protein-protein interaction, and a motif involved in GTP utilization. Strong sequence and structural similarity to functional P elements, a number of nonsynonymous substitutions that is smaller than that of synonymous substitutions and the presence of putative nuclear localization signals suggest that the A. gambiae elements may retain the capacity for transposition or its repression. These sequences seem to be most closely related to P elements described from Musca domestica and Lucilia cuprina, the only P element hosts known outside the family Drosophilidae.

Primate epididymis-specific proteins: characterization of ESC42, a novel protein containing a trefoil-like motif in monkey and human

Epididymal secreted proteins promote sperm maturation and fertilizing capacity by interacting with sperm during passage through the epididymis. Here we investigate the molecular basis of sperm maturation by isolating cDNA clones for novel epididymis-specific expressed sequences. Thirty-six novel cDNAs were isolated and sequenced from a subtracted Macaca mulatta epididymis library. The clones encode proteins with a range of motifs characteristic of protein-modifying enzymes, protease inhibitors, hydrophobic ligand-binding and transport proteins, extracellular matrix-interacting proteins, and transcription regulatory factors. The full length coding sequences were obtained for 11 clones representing a range of abundance levels. Expression of each is regionally localized and androgen regulated. The most abundant, ESC42, contains a cysteine-rich region similar to the signature binding domain of the trefoil family of motogenic wound repair proteins. The monkey and human proteins are nearly 90% identical. Immunohistochemical staining revealed that the protein is most abundant in the epithelium of the caput and is also present in the lumen and bound to sperm. The ESC42 gene, located on chromosome 20q11, contains two exons encoding two nearly identical predicted signal peptides and a third exon encoding the rest of the protein.

The pdx genetic marker adjacent to the chloramphenicol biosynthesis gene cluster in Streptomyces venezuelae ISP5230: functional characterization

The pdx-4 mutation in Streptomyces venezuelae ISP5230 confers a growth requirement for pyridoxal (pdx) and is a marker for the genetically mapped cluster of genes associated with chloramphenicol biosynthesis. A gene regulating salvage synthesis of vitamin B6 cofactors in S. venezuelae was cloned by transforming a pdx-4 mutant host with the plasmid vector pDQ101 carrying a library of wild-type genomic DNA fragments, and by selecting for complementation of the host's pdx requirement. However, the corresponding replicative plasmid could not be isolated. Southern hybridizations and transduction analysis indicated that the complementing plasmid had integrated into the chromosome; after excision by a second crossover, the plasmid failed to propagate. To avoid loss of the recombinant vector, a pdx-dependent Streptomyces lividans mutant, KAA1, with a phenotype matching that of S. venezuelae pdx-4, was isolated for use as the cloning host. Introduction of pIJ702 carrying an S. venezuelae genomic library into S. lividans KAA1, and selection of prototrophic transformants, led to the isolation of a stable recombinant vector containing a 2.5 kb S. venezuelae DNA fragment that complemented requirements for pdx in both S. venezuelae and S. lividans mutants. Sequence analysis of the cloned DNA located an intact ORF with a deduced amino acid sequence that, in its central and C-terminal regions resembled type-I aminotransferases. The N-terminal region of the cloned DNA fragment aligned closely with distinctive helix-turn-helix motifs found near the N termini of GntR family transcriptional regulators. The overall deduced amino acid sequence of the cloned DNA showed 73% end-to-end identity to a putative GntR-type regulator cloned in cosmid 6D7 from the Streptomyces coelicolor A3(2) genome. This location is close to that of pdxA, the first pdx marker in S. coelicolor A3(2) identified and mapped genetically in Sir David Hopwood's laboratory. The S. venezuelae gene and S. coelicolor pdxA are postulated to be homologues regulating vitamin B6 coenzyme synthesis from pdx.

Mutation of human molybdenum cofactor sulfurase gene is responsible for classical xanthinuria type II

Drosophila ma-l gene was suggested to encode an enzyme for sulfuration of the desulfo molybdenum cofactor for xanthine dehydrogenase (XDH) and aldehyde oxidase (AO). The human molybdenum cofactor sulfurase (HMCS) gene, the human ma-l homologue, is therefore a candidate gene responsible for classical xanthinuria type II, which involves both XDH and AO deficiencies. However, HMCS has not been identified as yet. In this study, we cloned the HMCS gene from a cDNA library prepared from liver. In two independent patients with classical xanthinuria type II, we identified a C to T base substitution at nucleotide 1255 in the HMCS gene that should cause a CGA (Arg) to TGA (Ter) nonsense substitution at codon 419. A classical xanthinuria type I patient and healthy volunteers lacked this mutation. These results indicate that a functional defect of the HMCS gene is responsible for classical xanthinuria type II, and that HMCS protein functions to provide a sulfur atom for the molybdenum cofactor of XDH and AO.

Differential expression of house-keeping genes of Aspergillus nidulans during sexual development

The rpl3 gene and the rpl37 gene for Aspergillus nidulans ribosomal protein L3 (RPL3) and RPL37, which were identified as located on chromosome I and chromosome III, respectively, were isolated from chromosome-specific cosmid libraries. The nucleotide sequences of both of the rpl3 gene and the rpl37 gene identified the ORFs of 392 amino acids and 92 amino acids, respectively. Both of the two genes were present in a single copy. The expression of both genes together with two other house-keeping genes, the rps16 gene for RPS16 and the gene for gamma-actin, was analyzed during sexual development. All four genes showed nearly identical expression patterns in that each gene expression reached its maximum after 2 h, decreased thereafter, and increased again after 30-40 h of induction of sexual development.

Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics

Modern biomedical research greatly benefits from large-scale genome-sequencing projects ranging from studies of viruses, bacteria, and yeast to multicellular organisms, like Caenorhabditis elegans. Comparative genomic studies offer a vast array of prospects for identification and functional annotation of human ortholog genes. We presented a novel comparative proteomic approach for assembling human gene contigs and assisting gene discovery. The C. elegans proteome was used as an alignment template to assist in novel human gene identification from human EST nucleotide databases. Among the available 18,452 C. elegans protein sequences, our results indicate that at least 83% (15,344 sequences) of C. elegans proteome has human homologous genes, with 7,954 records of C. elegans proteins matching known human gene transcripts. Only 11% or less of C. elegans proteome contains nematode-specific genes. We found that the remaining 7,390 sequences might lead to discoveries of novel human genes, and over 150 putative full-length human gene transcripts were assembled upon further database analyses. [The sequence data described in this paper have been submitted to the

ProClass protein family database

ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PIR superfamilies and PROSITE patterns. By combining global similarities and functional motifs into a single classification scheme, ProClass helps to reveal domain and family relationships and classify multi-domain proteins. The database currently consists of >155 000 sequence entries retrieved from both PIR-International and SWISS-PROT databases. Approximately 92 000 or 60% of the ProClass entries are classified into approximately 6000 families, including a large number of new members detected by our GeneFIND family identification system. The ProClass motif collection contains approximately 72 000 motif sequences and >1300 multiple alignments for all PROSITE patterns, including >21 000 matches not listed in PROSITE and mostly detected from unique PIR sequences. To maximize family information retrieval, the database provides links to various protein family, domain, alignment and structural class databases. With its high classification rate and comprehensive family relationships, ProClass can be used to support full-scale genomic annotation. The database, now being implemented in an object-relational database management system, is available for online sequence search and record retrieval from our WWW server at http://pir.georgetown.edu/gfserver/proclass.html

Molecular cloning and characterization of a new fasting-inducible short-chain dehydrogenase/reductase from rat liver(1)

We have isolated a 668 bp cDNA from fasted rat liver, designated RLF98, by suppression subtractive hybridization (SSH). The full-length RLF98 cDNA, cloned by rapid amplification of cDNA ends (RACE), is 1113 bp long with an open reading frame of 912 bp. This cDNA encodes a protein of 303 amino acid residues with a calculated molecular weight of 32433 Da. In vitro transcription and translation of the full-length RLF98 cDNA produced a protein of about 33 kDa. The RLF98 protein shares strong amino acid sequence homology with members of the short-chain dehydrogenase/reductase (SDR) family. Northern analysis of RNA from rat liver revealed a transcript of 1.1 kb. Fasting increased this mRNA 2.7-fold. While the RLF98 gene is widely expressed in rat tissues, its level of expression is highly variable. Expression in liver and kidney is abundant and is more than 10 times that observed in other tissues. Our data indicate that the RLF98 is a new member of the SDR family that is upregulated by fasting. Additional experiments including purification of recombinant RLF98 protein are in progress to define the specific function of this protein and the role it plays during fasting-induced catabolism.

ProClass Protein Family Database

ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PROSITE patterns and PIR superfamilies. By combining global similarities and functional motifs into a single classification scheme, ProClass helps to reveal domain and family relationships and classify multi-domain proteins. The database currently consists of more than 120 000 sequence entries, approximately 60% of which is classified into about 3500 families. To maximize family information retrieval, the database provides links to various protein family/domain and structural class databases and contains multiple motif alignments of all PROSITE patterns as well as global alignments of PIR superfamilies. The motif sequences are retrieved from both PIR-International and SWISS-PROT databases, including a large number of new members detected by our GeneFIND family identification system. ProClass can be used to support full-scale genomic annotation, because of its high classification rate. The ProClass database is available for on-line search and record retrieval from our WWW server at http://diana.uthct.edu/proclass.html

Rhizobium (Sinorhizobium) meliloti phn genes: characterization and identification of their protein products

In Escherichia coli, the phn operon encodes proteins responsible for the uptake and breakdown of phosphonates. The C-P (carbon-phosphorus) lyase enzyme encoded by this operon which catalyzes the cleavage of C-P bonds in phosphonates has been recalcitrant to biochemical characterization. To advance the understanding of this enzyme, we have cloned DNA from Rhizobium (Sinorhizobium) meliloti that contains homologues of the E. coli phnG, -H, -I, -J, and -K genes. We demonstrated by insertional mutagenesis that the operon from which this DNA is derived encodes the R. meliloti C-P lyase. Furthermore, the phenotype of this phn mutant shows that the C-P lyase has a broad substrate specificity and that the organism has another enzyme that degrades aminoethylphosphonate. A comparison of the R. meliloti and E. coli phn genes and their predicted products gave new information about C-P lyase. The putative R. meliloti PhnG, PhnH, and PhnK proteins were overexpressed and used to make polyclonal antibodies. Proteins of the correct molecular weight that react with these antibodies are expressed by R. meliloti grown with phosphonates as sole phosphorus sources. This is the first in vivo demonstration of the existence of these hitherto hypothetical Phn proteins.