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PubMed2004

FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression.

BACKGROUND: While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. RESULTS: We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. Steps are taken to ensure that the annotation is self-consistent and that the structure of GO is used to identify higher level functions that may not be annotated directly. An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. In a case study, a set of genes, that had statistically significant regression between gene expression levels and environmental temperature along the Atlantic Coast, shows a statistically significant (P < 0.001) enrichment in genes associated with amine metabolism. CONCLUSION: The methods described have application for functional genomics studies, particularly among non-model organisms. The web interface for FunnyBase can be accessed at http://genomics.rsmas.miami.edu/funnybase/super_craw4/. Data and source code are available by request at jpaschall@bioinfobase.umkc.edu.

Animals↗

PubMed1994

Assembly of 18-nucleotide primers by ligation of three hexamers: sequencing of large genomes by primer walking.

A novel method (SPEL-6) for sequencing large genomes permits 10-min synthesis of 18-mer primers and their immediate use in DNA sequencing by primer walking. Primers are ligated from three contiguous hexamers complementary to the single-stranded or denatured DNA (150:1 ratio), which is used both as the template for ligation and as the DNA to be sequenced. The complete library consists of 4096 hexamers, but sequencing remains very efficient with a fourfold smaller library composed of 1024 degenerate hexamers containing all four nucleotides at their position 3. The SSB protein (which binds to single-stranded DNA) greatly enhances the quality of sequencing ladders. The SPEL-6 method eliminates the need for subcloning, permits direct sequencing of large DNA fragments (of 50 kb or larger), is ideally suited for automation, and should accelerate the sequencing of large genomes by more than one order of magnitude.

Base Sequence↗

PubMed2002

Disruption of the RanBP17/Hox11L2 region by recombination with the TCRdelta locus in acute lymphoblastic leukemias with t(5;14)(q34;q11).

The t(5;14)(q33-34;q11) translocation constitutes a recurrent rearrangement in acute lymphoblastic leukemia involving the T cell receptor (TCR) delta locus on chromosome 14. Breakpoint sequences of the derivative chromosome 5 were isolated by application of a ligation-mediated PCR technique using TCR delta-specific primers to amplify genomic DNA from the leukemic cells of a patient with t(5;14). Through exon trap analysis, we identified various putative exons of the chromosome 5 target gene of the translocation; compilation of sequence information of trapped exons and available expressed sequence tags (ESTs) from the GenBank database allowed us to assemble 1.2 kb of the cDNA. Full-length cDNAs were isolated from a human testis cDNA library and sequence analysis predicted a putative Ran binding protein, a novel member of the importin-beta superfamily of nuclear transport receptors, called RanBP17. The t(5;14) breakpoint maps to the 3' coding region of the gene. The breakpoint of a second t(5;14) positive patient was mapped about 8 kb downstream of the most 3' RanBP17 exon and 2 kb upstream of the first exon of the orphan homeobox gene, Hox11L2. In both cases TCR delta enhancer sequences are juxtaposed downstream of the truncated or intact RanBP17 gene, respectively on the derivative chromosome.

Acute Disease↗

PubMed1984

Molecular cloning and nucleotide sequence of a variant wheat histone H4 gene.

To determine whether there is structural variation among histone H4 genes in wheat, one (TH091) of the H4 genes that had been cloned from a wheat genomic DNA library was sequenced and compared with another H4 gene (TH011) which we had described previously [Tabata et al., Nucl. Acids Res. 11 (1983) 5865-5865]. Nucleotide sequence analysis revealed that there are 17 nucleotide replacements in the protein-coding region of two H4 genes, causing only one amino acid substitution: a glycine at position 4 (from the N terminus) in TH011 was replaced by an aspartic acid in TH091. S1 mapping, using total nuclear RNA from germinated seeds, indicated that the H4 gene was transcribed in vivo.

Amino Acid Sequence↗

PubMedDate not supplied

Sequence analysis of Lys49 phospholipase A2 myotoxins: a highly conserved class of proteins.

A cDNA clone coding for a putative Lys49 phospholipase A2 myotoxin (ACL myotoxin) from Agkistrodon contortrix laticinctus was isolated from a venom gland library and sequenced. The sequence of the first 40 amino acid residues of the predicted protein matches exactly with the N-terminal sequence of the purified myotoxin. Sequence comparison of the predicted sequence of ACL myotoxin and other Lys49 and Asp49 phospholipase A2 enzymes shows that the Lys49 phospholipase toxins form a highly conserved protein family. In addition to the change at position 49, Lys49 myotoxins have several invariant residues not found in the Asp49 group, like Lys7, Glu12, Thr13, Lys16, Lys78, Lys80, Lys115, and Lys116. There are also some conserved residues in the Asp49 group that are not conserved in the Lys49 group: Tyr28, Gly32, Gly33. Gly53. Lys49 myotoxins also have a Lys-rich region in the C-terminus, which is not present in the Asp49 group. These differences clearly indicate that Lys49 myotoxins comprise a conserved and distinct class of phospholipase A2 enzymes.

Agkistrodon↗

PubMed2001

Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil.

The bacterial diversity assessed from clone libraries prepared from rRNA (two libraries) and ribosomal DNA (rDNA) (one library) from polychlorinated biphenyl (PCB)-polluted soil has been analyzed. A good correspondence of the community composition found in the two types of library was observed. Nearly 29% of the cloned sequences in the rDNA library were identical to sequences in the rRNA libraries. More than 60% of the total cloned sequence types analyzed were grouped in phylogenetic groups (a clone group with sequence similarity higher than 97% [98% for Burkholderia and Pseudomonas-type clones]) represented in both types of libraries. Some of those phylogenetic groups, mostly represented by a single (or pair) of cloned sequence type(s), were observed in only one of the types of library. An important difference between the libraries was the lack of clones representative of the Actinobacteria in the rDNA library. The PCB-polluted soil exhibited a high bacterial diversity which included representatives of two novel lineages. The apparent abundance of bacteria affiliated to the beta-subclass of the Proteobacteria, and to the genus Burkholderia in particular, was confirmed by fluorescence in situ hybridization analysis. The possible influence on apparent diversity of low template concentrations was assessed by dilution of the RNA template prior to amplification by reverse transcription-PCR. Although differences in the composition of the two rRNA libraries obtained from high and low RNA concentrations were observed, the main components of the bacterial community were represented in both libraries, and therefore their detection was not compromised by the lower concentrations of template used in this study.

Bacteria↗

PubMed1992

Sequence of the human factor VIII-associated gene is conserved in mouse.

cDNA and genomic clones corresponding to the human factor VIII-associated gene (F8A) were isolated from mouse cDNA and F8A-enriched genomic libraries. The sequences of these clones revealed an intronless gene coding for 380 amino acids, with 85% identity to the predicted human sequence. The single murine gene copy is genetically linked to factor VIII, but appears to lie outside the factor VIII gene by physical mapping. Like the human gene, the mouse F8A gene is highly expressed in a wide variety of tissues. This evolutionary comparison has helped to clarify the derived amino acid sequence in the human and strongly supports the hypothesis that the F8A gene encodes a protein.

Amino Acid Sequence↗

PubMed1992

cDNA sequence of a second fibrinogen alpha chain in lamprey: an archetypal version alignable with full-length beta and gamma chains.

The message for a second fibrinogen alpha chain has been cloned from a lamprey liver cDNA library. The sequence is unique in that the amino-terminal half is homologous to all other known alpha chains, including another from lamprey, but its carboxyl-terminal half is homologous to the carboxyl-terminal portions of beta and gamma chains, segments that compose the distal globular regions of fibrinogen. The structural pattern of this newly discovered alpha chain suggests that it could be a direct descendant of the archetypal chain that existed prior to the gene duplications that led to unique beta and gamma chains and before the dislocating events that gave rise to contemporary alpha chains.

Amino Acid Sequence↗

PubMed2000

Quantitative microscopy after fluorescence in situ hybridization - a comparison between repeat-depleted and non-depleted DNA probes.

Complex probes used in fluorescence in situ hybridization (FISH) usually contain repetitive DNA sequences. For chromosome painting, in situ suppression of these repetitive DNA sequences has been well established. Standard painting protocols require large amounts of an unlabeled 'blocking agent', for instance Cot-1 DNA. Recently, it has become possible to remove repetitive DNA sequences from library probes by means of magnetic purification and affinity PCR. Such a 'repeat depleted library probe' was hybridized to the q-arm of chromosome 15 of human metaphase spreads and interphase cell nuclei without any preannealing by Cot-1 DNA. Apart from this, 'standard' FISH conditions were used. After in situ hybridization, microscope images were obtained comparable to those achieved with the #15q library probe prior to depletion. The images were recorded by a true color CCD camera. By digital image analysis using 'line scan' and 'area scan' procedures, the painting efficiency expressed in terms of relative fluorescence signal intensity was quantitatively evaluated. The painting efficiency using the repeat depleted probe of chromosome 15q was compared to the painting efficiency after standard FISH. The results indicate that both types of probes are compatible to a high FISH efficiency. Using equivalent probe concentrations, no significant differences were found for FISH with standard painting probes and repeat depleted painting probes.

Cell Nucleus↗

PubMed2003

Molecular characterization of artemin and ferritin from Artemia franciscana.

Embryos of the brine shrimp, Artemia franciscana, exhibit remarkable resistance to physiological stress, which is temporally correlated with the presence of two proteins, one a small heat shock/alpha-crystallin protein termed p26 and the other called artemin, of unknown function. Artemin was sequenced previously by Edman degradation, and its relationship to ferritin, an iron storage protein, established. The isolation from an Artemia expressed sequence tag library of artemin and ferritin cDNAs extends this work. Artemin cDNA was found to contain an ORF of 693 nucleotides, and its deduced amino-acid sequence, except for the initiator methionine, was identical with that determined previously. Ferritin cDNA is 725 bp in length with an ORF of 516 nucleotides. Artemin amino-acid residues 32-185 are most similar to ferritin, but artemin is enriched in cysteines. The abundance of cysteines and their intramolecular spatial distribution suggest that artemin protects embryos against oxidative damage and/or that its function is redox regulated. The conserved regions in artemin and ferritin monomers are structurally similar to one another and both proteins assemble into oligomers. However, modeling of the quaternary structure indicated that artemin multimers lack the central space used for metal storage that characterizes ferritin oligomers, implying different roles for this protein. Probing of Northern blots revealed two artemin transcripts, one of 3.5 kb and another of 2.2 kb. These transcripts decreased in parallel and had almost disappeared by 16 h of development. The ferritin transcript of 0.8 kb increased slightly during reinitiation of development, then declined, and was almost completely gone by 16 h. Clearly, the loss of artemin and ferritin during embryo development is due to transcriptional regulation and proteolytic degradation of the proteins.

Amino Acid Sequence↗

PubMed1997

Propanediol utilization genes (pdu) of Salmonella typhimurium: three genes for the propanediol dehydratase.

The propanediol utilization (pdu) operon of Salmonella typhimurium encodes proteins required for the catabolism of propanediol, including a coenzyme B12-dependent propanediol dehydratase. A clone that expresses propanediol dehydratase activity was isolated from a Salmonella genomic library. DNA sequence analysis showed that the clone included part of the pduF gene, the pduABCDE genes, and a long partial open reading frame (ORF1). The clone included 3.9 kbp of pdu DNA which had not been previously sequenced. Complementation and expression studies with subclones constructed via PCR showed that three genes (pduCDE) are necessary and sufficient for propanediol dehydratase activity. The function of ORF1 was not determined. Analyses showed that the S. typhimurium propanediol dehydratase was related to coenzyme B12-dependent glycerol dehydratases from Citrobacter freundii and Klebsiella pneumoniae. Unexpectedly, the S. typhimurium propanediol dehydratase was found to be 98% identical in amino acid sequence to the Klebsiella oxytoca propanediol dehydratase; this is a much higher identity than expected, given the relationship between these organisms. DNA sequence analyses also supported previous studies indicating that the pdu operon was inherited along with the adjacent cobalamin biosynthesis operon by a single horizontal gene transfer.

Cobamides↗

PubMed1996

cDNA cloning and sequence analysis of a lysine-49 phospholipase A2 myotoxin from Agkistrodon contortrix laticinctus snake venom.

A cDNA clone (ACLPREMT1) for a K49 phospholipase A2 (PLA2) myotoxin from Agkistrodon contortrix laticinctus snake venom was isolated from a venom gland library and sequenced. The ACLPREMT1 cDNA is 734 bp in length and has an open reading frame of 414 bp. It codes for a K49 phospholipase A2 with 121 amino acid residues. The sequence of the first 20 amino acid residues of the predicted mature protein matches exactly with the N-terminal sequence of the purified myotoxin. Comparison of the ACLPREMT1 cDNA sequence with PLA2 cDNAs from Viperidae snakes shows that it has a similar organization: highly conserved 5' and 3' untranslated regions, a sequence encoding a 16-amino acid signal peptide, and the mature protein coding region. Comparison of the predicted sequence of ACL myotoxin and other K49 and D49 PLA2 myotoxins shows that, despite the homology (85-97%) at the nucleotide level, K49 PLA2 myotoxins are distinct from the D49 PLA2s and form a highly conserved protein family. In addition to the substitution of D49K, K49 myotoxins have several invariant residues not found in the D49 group, including K7, K78, K80, K115, and K116. There are also some conserved residues (E12, T13, K16, and N17) in all myotoxic proteins, including some neurotoxic and myotoxic PLA2s. Molecular modeling of ACL myotoxin shows that these residues are close together on the surface of one side of the molecule which suggests a potential site for binding to membranes and/or induction of toxicity.

Agkistrodon↗

PubMed1993

Identification of the nuclear-encoded chloroplast ribosomal protein L12 of the monocotyledonous plant Secale cereale and sequencing of two different cDNAs with strong codon bias.

Two different cDNA clones (SCL12-1 and SCL12-2) encoding precursors of a chloroplast ribosomal protein with homology to L12 from Escherichia coli were isolated from rye leaf cDNA libraries and sequenced. The corresponding polypeptide of rye chloroplast ribosomes was identified. The sequences for the mature proteins of M(r) 13,447 and 13,609 share 85% amino acid identity. The mature polypeptide of clone SCL12-1 has an amino acid identity of 71%, 72% or 44%, respectively, relative to L12 proteins from spinach, tobacco, or E. coli. Codon usage of the rye L12 cDNAs shows a high preference (97% and 82%) for G or C in the third base position.

Amino Acid Sequence↗

PubMed1996

Cloning and sequencing of cDNAs encoding plasma alpha-macroglobulin and murinoglobulin from guinea pig: implications for molecular evolution of alpha-macroglobulin family.

Several clones encoding plasma alpha-macroglobulin and murinoglobulin were isolated from guinea pig liver cDNA library and sequenced. The clones for alpha-macroglobulin contained overlapping sequences which together spanned a stretch of 4,546 nucleotides with one open reading frame coding for 1,476 amino acid residues. The clones for murinoglobulin contained overlapping sequences which together spanned a stretch of 4,578 nucleotides with one open reading frame coding for 1,464 amino acid residues. The phylogenetic analyses of 11 proteins of the alpha-macroglobulin family revealed that the mammalian tetrameric alpha-macroglobulins consist of two main branches: alpha M-1 subfamily (rat alpha 1- and mouse alpha-macroglobulins) and alpha M-2 subfamily (human alpha 2-, rat alpha 2-, and guinea pig alpha-macroglobulins). This dichotomy is in good accordance with their immunological, chemical, and physicochemical properties, and indicates that guinea pig alpha-macroglobulin is orthologous to human and rat alpha 2-macroglobulins but paralogous to rat alpha 1- and mouse alpha-macroglobulins. The divergence of the two subfamilies was a phylogenetically ancient event which occurred around the separation of metatherians and eutherians. The genes of the two subfamilies have been maintained in the rat, but either one became extinct in the mouse, guinea pig, or human. The tree also shows that guinea pig murinoglobulin forms one clade with mouse and rat murinoglobulins (alpha 1-inhibitor 3) prior to joining the alpha M-2 lineage, and suggests that murinoglobulin is not a primitive form of tetrameric alpha-macroglobulin, but rather has evolved under selective pressure which is different from that of the tetrameric paralogues.

Amino Acid Sequence↗

PubMed1993

Rabbit plasma alpha-1-antiproteinase S-1: cloning, sequencing, expression, and proteinase inhibitory properties of recombinant protein.

A cDNA clone coding for the isoform S-1 of alpha-1-antiproteinase (also called alpha-1-proteinase inhibitor or alpha-1-antitrypsin) was isolated from rabbit liver cDNA library and sequenced. The cDNA consists of 1,426 nucleotides including 5' and 3' noncoding regions and codes for 413 amino acid residues including a signal peptide of 24 residues. The nucleotide and deduced amino acid sequences show 95.5 and 95.2% homologies, respectively, with the F isoform which occurs more abundantly in the rabbit serum than the S isoform. Of the 20 amino acid differences between the two isoforms, nine are located in a stretch of 15 amino acids encompassing the reactive site region, suggesting that these genes have diverged from each other by a nonrandom mechanism. A hypothesis is proposed that the domestication of animal is responsible for the extremely high evolutionary rate in the serpin reactive site region. Prokaryotic expression plasmids were constructed from the cDNA, transfected into Escherichia coli, and expressed. Partially purified recombinant protein inhibited elastase, but did not inhibit trypsin when a small substrate was used. The recombinant S-1 form, however, protected trypsin from inactivation by soybean trypsin inhibitor, a property characteristic of alpha-macroglobulins or rodent murinoglobulins. It is known that there are two types of interaction between serpin and proteinase: (i) most serpins form a stable equimolar complex with the enzyme, resulting in the enzyme inhibition and (ii) some serpins act as a substrate rather than as an inhibitor, resulting in the loss of inhibitory activity.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1995

Human calgizzarin; one colorectal cancer-related gene selected by a large scale random cDNA sequencing and northern blot analysis.

A cDNA library was constructed from COLO 205 and 1056 clones randomly selected from this library were partially sequenced. Two hundred and two (38.4%) out of 526 independent genes had more than 80% similarity to the genes reported in GenBank. In Northern blot analysis, 96 out of 98 genes were shown to be expressed at the same level in colon and lung carcinoma cell lines and control fibroblasts. Only two clones, including human synovial phospholipase A-2 and a homologue to rabbit calgizzarin, were expressed at different levels among these cell lines. The full sequence of human calgizzarin was determined and its expression was remarkably elevated in colorectal cancers compared with that in normal colorectal mucosa.

Amino Acid Sequence↗

PubMed2006

Identification of genetic differences between two clinical isolates of Streptococcus mutans by suppression subtractive hybridization.

Streptococcus mutans is generally considered to be the principal aetiological agent for dental caries. Phenotypic variation in strains is often associated with differences in gene content, so the isolation of DNA fragments from these genes or associated regions is illuminating. The S. mutans strains 9-1 and 9-2, which both colonized the same oral cavity, were selected after screening for the possession of suspected virulence traits. Genomic DNA of strain 9-1 was used as the tester, and that of 9-2 was used as the driver. Suppression subtractive hybridization (SSH) was applied between the tester and the driver DNAs. The subtractive products were cloned into a pCR2.1 vector. Clone libraries representing sequence differences were obtained. The subtractive fragments that were found specifically in strain 9-1 but not in strain 9-2 were identified by dot blotting and then sequenced. BLASTn and BLASTx sequence homology analyses were subsequently performed. Twenty-seven sequences were found in the genome of strain 9-1 that were not in 9-2. Among them, three revealed no homology to published nucleotide sequences while the remaining sequences showed 81-100% homology to known genes of S. mutans strain UA159. These sequences are involved in competence development, signal transduction and transcriptional regulation, repairing stress damage, transport, carbohydrate catabolism, biochemical synthesis, or unknown functions. Differences exist in the genomes of different S. mutans isolates. SSH is effective in screening for S. mutans strain specific DNA sequences.

Adult↗

PubMedDate not supplied

A 63 kDa VSP9B10A-like protein expressed in a C-8 Giardia duodenalis Mexican clone.

BACKGROUND: It is well documented that Giardia duodenalis undergoes surface antigenic variation both in vivo and in vitro. Proteins involved have been characterized and referred to as VSP (variable surface protein). METHODS: Two cloned cDNA inserts of 0.45 and 1.95 kb were obtained from G. duodenalis expression library and sequenced. Comparison sequence analyses were made against Genbank. PCR analysis was performed on G. duodenalis isolates to identify isolates bearing genes encoding such a peptide. Specific antiserum was prepared against 450-bp encoded peptide and tested by Western blot, immunofluorescence, and inhibition of adhesion of G. duodenalis to target cells. RESULTS: We cloned and characterized a G. duodenalis 450-bp DNA fragment; its DNA sequence analysis revealed that this fragment displayed 99% identity with vsp9B10A gene. Predicted amino acid sequence for this fragment also had significant (99%) identity to VSP9B10A. A second 1.95-kb insert, which encompassed the 450-bp cDNA fragment, was also isolated; its DNA and amino acid sequence displayed 99.5% identity with vsp9B10A gene and 99.2% with the corresponding inferred protein, respectively. This inferred protein contained 24 Cys-X-X-Cys motifs and long ORF of 642 aminoacids. PCR analysis showed that DNA sequence encoding a fragment of this gene was present in P1, CIEA:0487:2-C-8 clone and in INP:180800-B2 G. duodenalis human isolates, while it was absent in sheep isolate of G. duodenalis INP:150593-J10. CONCLUSIONS: Immunofluorescence analysis using antibodies raised against the peptide encoded by 450-bp fragment showed that expression of this epitope varies on trophozoite surface of the C-8 Mexican clone and is involved in parasite adhesion to target epithelial cells.

Amino Acid Sequence↗