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PubMed2006

Toll-like receptor 3 and TICAM genes in catfish: species-specific expression profiles following infection with Edwardsiella ictaluri.

Toll-like receptors (TLRs) are a family of transmembrane proteins that recognize specific pathogen-associated molecular patterns and use conserved signaling pathways to activate proinflammatory cytokines and type-1 interferons to fight infection. TLR3 in mammals is best known for its recognition of dsRNA as ligand and its MyD88-independent signaling. TLR3, upon recognition of dsRNA, recruits and binds its adaptor protein TIR domain-containing adapter molecule (TICAM) 1. Here we report the genomic sequences and structures of TLR3 and a TICAM adaptor from channel catfish (Ictalurus punctatus). Whereas a partial TLR3 cDNA sequence has been reported from channel catfish, and complete TLR3 genes are known from other teleost fish species, a complete TICAM sequence has not been previously reported from a nonmammalian species. Analysis of catfish TLR3 and TICAM expression after infection with Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish (ESC), suggested a conserved TLR3-TICAM receptor-adaptor relation in catfish. Comparison of TLR3 and TICAM expression profiles in channel catfish with those from the closely related blue catfish species (Ictalurus furcatus), which exhibits strong resistance to ESC, revealed a striking pattern of species-specific expression. A dramatic downregulation of TLR3 and TICAM gene expression was observed in blue catfish head kidney and spleen, which we speculate may be the result of maturation and migration of different cell types to and from the lymphoid tissues following infection.

Adaptor Proteins, Signal Transducing↗
PubMed1997

Understanding species-specific differences in substrate recognition by Escherichia coli and human prolyl-tRNA synthetases.

Class II human prolyl-tRNA synthetase (ProRS) aminoacylates in vitro transcribed human tRNA(Pro) with kinetic parameters that are similar to those previously determined for aminoacylation of Escherichia coli tRNA(Pro) by its cognate synthetase. As in the bacterial system, large decreases in aminoacylation by human ProRS occur upon mutating anticodon positions G35 and G36 of human tRNA(Pro). The N73 'discriminator' base and the first and third base pairs of the acceptor stem vary between the E.coli and human isoacceptor groups. In contrast to the E. coli synthetase, the human enzyme does not appear to recognize these elements, since mutations at these positions do not significantly affect cognate synthetase charging. E. coli ProRS does not cross-aminoacylate human tRNA(Pro), and the bacterial tRNA(Pro) is a poor substrate for the human enzyme. Mutations in both the tRNAs and the synthetases have been made in an effort to identify elements in each system responsible for blocking cross-species aminoacylation. Alignment of all known ProRS primary sequences from different species reveals particularly low overall sequence homology, as well as two distinct groups of enzymes. The sequence divergence between E. coli and human ProRSs helps to explain the species-specific differences in the RNA code for aminoacylation of tRNA(Pro).

Amino Acid Sequence↗
PubMed1998

Analysis of bHLH and MYB domain proteins: species-specific regulatory differences are caused by divergent evolution of target anthocyanin genes.

The regulatory anthocyanin loci, an1, an2, an4 and an11 of Petunia hybrida, and r and c1 from Zea mays, control transcription of different sets of target genes. Both an2 and c1 encode a MYB-type protein. This study reports the isolation of a P. hybrida gene, jaf13, encoding a basic helix-loop-helix protein that, on the basis of sequence homology and intron/exon structure, represents the P. hybrida orthologue of the Z. mays r genes. Ectopic expression of an2 and jaf13 is sufficient for activation of the dihydroflavonol 4-reductase-A (dfrA) promoter and enhanced pigment accumulation in P. hybrida. This indicates that an2 and jaf13 play a key role in determining the tissue-specific expression pattern of structural genes. However, because chalcone synthase (chs) and flavanone-3-hydroxylase (f3h) are not activated, the pattern of pigmentation is not fundamentally altered. Expression of an2 in Z. mays complements a mutation in pl, a c1 paralogue, indicating that an2 activates a wider set of target genes in this host. Transient expression assays in Z. mays and P. hybrida tissues showed that C1 and R or AN2 and JAF13 can activate the promoter of the c2 gene, encoding Z. mays CHS, but not the chsA promoter from P. hybrida. These results indicate that regulatory anthocyanin genes are conserved between species and that divergent evolution of the target gene promoters is responsible for the species-specific differences in regulatory networks.

Amino Acid Sequence↗
PubMed1996

A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences.

DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5'-TTTAGGG-3'. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31 digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature.

Base Sequence↗
PubMed2026

Pathogen Species-Specific Differences in Induction of the Maize Polyubiquitin Gene Promoter in Transgenic Wheat.

The maize polyubiquitin promoter (ZmUbi) is a mainstay in molecular biology for transgene expression and is used for constitutive expression of defense-related gene products. Transgenic wheat lines were produced expressing a ZmUbi-RUBY reporter gene that produces the red pigment betalain. Some lines showed transgene silencing with reduced RUBY transcript accumulation and chimeric sectors of betalain. Infection of these plants with Blumeria graminis, Puccinia graminis f. sp. tritici (Pgt), or P. triticina (Pt) each resulted in localized betalain accumulation at infection sites and increased RUBY transcript accumulation. In contrast, two isolates of P. striiformis f. sp. tritici (Pst) caused no detectable RUBY transcript accumulation and no visible betalain accumulation at infection sites, although a modest betalain increase was detected in infected tissue extracts. Compared with Pst, Pgt more strongly induced host genes involved in transcriptional and post-transcriptional regulatory processes, although no obvious pathogen-induced changes in ZmUbi promoter methylation were observed. ZmUbi-GUS transgenic wheat plants were also pathogen challenged, and, unlike Pst, both Pgt and Pt induced localized GUS staining at infection sites. Database mining showed that the endogenous maize polyubiquitin gene from which ZmUbi is derived was pathogen inducible, albeit in a species-specific fashion. These pathogen differences in ZmUbi induction have implications when using this regulatory element to express defense-related transgenes in wheat. Comparing the resistance efficacy of transgenes against different pathogens using this promoter is potentially influenced by significant, localized expression differences occurring at infection sites of different pathogen species. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Promoter Regions, Genetic↗
PubMed1994

Species specificity and interspecies relatedness in VP4 genotypes demonstrated by VP4 sequence analysis of equine, feline, and canine rotavirus strains.

We determined the nucleotide and deduced amino acid sequences of the VP4 genes of five equine, two feline, and two canine rotavirus strains. A high degree of homology (> 97.0%) was found among the VP4 amino acid sequences of the equine strains H2, FI-14, and FI23. Equine strain L338 has a distinct VP4 amino acid sequence from those of the other equine strains (78.1% or less homology), and the L338 VP4 exhibited more than 17.0% divergence at the amino acid level from those of rotavirus strains published so far. The VP4 amino acid sequence of equine strain H1, which showed low homology with those of other equine strains, shares > 95.4% homology to those of porcine strains OSU and YM. VP4 amino acid sequences of feline strain Cat97 and canine strains CU-1 and K9 showed a high degree of homology (96.8 to 97.2%) to one another, and were found to be quite similar (96.0-97.0% homology) to that of a human HCR3 strain recently characterized. Feline strain Cat2, whose VP4 sequence is distinct from that of strain Cat97, has a VP4 similar to those of human strains K8 and AU-1 (97.8 and 97.5% homologies at amino acid level, respectively). Thus, the VP4 sequences of rotaviruses showed species specificity and interspecies relatedness.

Amino Acid Sequence↗
PubMed1994

Human glycyl-tRNA synthetase. Wide divergence of primary structure from bacterial counterpart and species-specific aminoacylation.

Several class I and class II human tRNA synthetases are clearly related to their bacterial counterparts. We report here the cloning, cDNA sequence, deduced primary structure, and expression in bacteria of a class II human glycyl-tRNA synthetase. While the human sequence aligns well with a Bombyx mori and a Saccharomyces cerevisiae sequence for glycyl-tRNA synthetase, particularly in the region of the class II-defining sequence motifs, it diverges widely from that of the Escherichia coli enzyme. The divergence is so great that from the sequences alone we cannot conclude that the human and E. coli proteins are descended from homologous genes. Moreover, even though the human and E. coli class II alanyl-tRNA synthetases cross-acylate their respective tRNAs, aminoacylations by the recombinant human and E. coli glycyl-tRNA synthetases are restricted to their homologous tRNAs. The species-specific aminoacylations correlate with a nucleotide sequence difference at a location in the acceptor stem that is known to be critical for aminoacylations by the E. coli enzyme. Thus, glycyl-tRNA synthetase may have followed a path of historical development different in at least some respects from that of several other tRNA synthetases.

Acylation↗
PubMed1995

The myxoma virus-soluble interferon-gamma receptor homolog, M-T7, inhibits interferon-gamma in a species-specific manner.

The myxoma virus M-T7 protein contains significant sequence similarity to the ligand binding domain of the mammalian interferon-gamma receptors, and functions as a soluble homolog which can bind and inhibit the biological activities of rabbit interferon-gamma (Upton, C., Mossman, K., and McFadden, G. (1992) Science 258:1369-1372). M-T7, the most abundantly secreted protein from myxoma virus-infected cells, was shown to be expressed in significant biological amounts as a typical poxvirus early gene product, efficiently secreted at early times of infection to levels that exceed 5 x 10(7) molecules/cell, and function as a stable inhibitory protein in infected cell supernatants until late times of infection. M-T7 was specific in binding and inhibiting rabbit interferon-gamma, and did not bind either human or murine interferon-gamma. Scatchard analysis of rabbit interferon-gamma binding curves yielded a single high affinity binding site on M-T7, with a Kd of 1.2 x 10(-9) M, which is comparable to the affinity between soluble forms of cellular interferon-gamma receptors and their cognate ligands. In comparison, rabbit interferon-gamma was shown to bind its cellular receptor with a Kd of 5.9 x 10(-10) M, again comparable to the affinity of membrane bound forms of other mammalian interferon-gamma receptors for interferon-gamma. Thus, the myxoma virus M-T7 protein is a functional soluble interferon-gamma receptor homolog which binds and inhibits interferon-gamma with high affinity in a species-specific manner.

Amino Acid Sequence↗
PubMed2004

Susceptibility of Borna disease virus to the antiviral action of gamma-interferon: evidence for species-specific differences.

Borna disease virus (BDV) infection in its predominant natural host - horses and sheep - leads to fatal meningoencephalomyelitis. The immune-mediated disease can also be induced experimentally in rats following intra- cerebral BDV infection. Despite a vigorous immune response, BDV persists in the central nervous system (CNS) in surviving rats. However, immunization of rats with BDV-specific T-cells prior to challenge with BDV prevents neurological disease and results in virus clearance from the CNS. To analyze whether interferon gamma (IFNgamma) might contribute to viral clearance in the rat brain, we tested the susceptibility of BDV to the antiviral action of rat IFNgamma using different rat cell lines. Even at high concentrations of IFNgamma, BDV infection of astrocyte and fibroblast cell lines as well as of rat embryo cells could not be inhibited efficiently. Similarly, infection of cultured rat hippocampal slices with BDV was not inhibited by rat IFNgamma. In contrast, de novo BDV infection of monkey kidney cells as well as human oligodendroglial cells was blocked by preincubation with human IFNgamma. Furthermore, IFNgamma reduced the BDV load in persistently BDV-infected human oligodendroglial cells but not in infected rat astrocytes. These data suggest species-specific differences in the susceptibility of BDV to the antiviral action of IFNgamma.

Animals↗
PubMed1988

Laboratory- and species-specific interpretive breakpoints for disk diffusion tests of chloramphenicol susceptibility of Haemophilus influenzae.

A total of 601 clinical isolates of Haemophilus influenzae isolated in six different regions of Sweden were tested for chloramphenicol susceptibility by using agar dilution MIC determinations and disk diffusion tests. For seven strains MICs were 4 micrograms/ml or higher, and for one strain the MIC was 2 micrograms/ml. All eight strains produced chloramphenicol acetyltransferase. For the remaining 593 strains, MICs were less than or equal to 1 microgram/ml, and the MICs for 50% and 90% of the strains were both 0.5 microgram/ml. Disk diffusion tests carried out by using revised interpretive criteria introduced in 1984 by the Swedish Reference Group for Antibiotics correctly identified the 593 strains as susceptible and the 8 strains as resistant. Quality assessments were performed in 29 clinical microbiology laboratories. The revised criteria for chloramphenicol disk diffusion testing gave rise to false resistance results in some laboratories. The interpretive accuracy improved when the interlaboratory variation was compensated for by using adjusted breakpoints. Such revision was possible through peak correction, single-strain regression analysis, and standard curve regression analysis. Peak-corrected breakpoints improved the accuracy from an overall incidence of false-resistant isolates of 4.4% to 2.3%. Single-strain regression analysis and standard curve regression analysis provided laboratory- and species-specific breakpoints which reduced false resistance rates of 0.14% and 0%, respectively.

Chloramphenicol↗
PubMedDate not supplied

Differential intertectal delay between Rana pipiens and Xenopus laevis: implications for species-specific visual plasticity.

In the frog Xenopus laevis, the isthmotectal projection, which relays input from the ipsilateral eye, exhibits anatomical reorganization following surgical eye rotation performed during tadpole stages while the isthmotectal projection in the frog Rana pipiens fails to show reorganization. This plasticity has been shown to be dependent upon activation of the N-methyl-D-aspartate (NMDA) receptor located on tectal cell dendrites. The reorganization process in Xenopus is hypothesized to employ a Hebbian mechanism requiring correlated firing of ipsilateral and contralateral inputs to a given tectal cell; when an ipsilateral axon synapses onto a tectal cell that receives input from a contralateral axon with a matching receptive-field location, the correlation in activity triggers stabilization of the ipsilateral synapse. However, in neither Xenopus nor Rana do ipsilateral and contralateral inputs begin to fire simultaneously in response to a given visual stimulus; the ipsilateral input is delayed because it reaches the tectum indirectly, through a polysynaptic relay via the opposite tectum and nucleus isthmi. The objective of this experiment was to test whether there is a significant difference in this intertectal delay between Xenopus laevis and Rana pipiens in order to determine whether intertectal delay could be a contributing factor in this species-specific ability to exhibit visual plasticity. We have found that intertectal delay is 26.16 ms longer in Rana pipiens (36.53 ms) than in Xenopus laevis (10.37 ms).

Animals↗
PubMed2006

The molecular origins of species-specific facial pattern.

The prevailing approach within the field of craniofacial development is focused on finding a balance between tissues (e.g., facial epithelia, neuroectoderm, and neural crest) and molecules (e.g., bone morphogenetic proteins, fibroblast growth factors, Wnts) that play a role in sculpting the face. We are rapidly learning that neither these tissues nor molecular signals are able to act in isolation; in fact, molecular cues are constantly reciprocating signals between the epithelia and the neural crest in order to pattern and mold facial structures. More recently, it has been proposed that this crosstalk is often mediated and organized by discrete organizing centers within the tissues that are able to act as a self-contained unit of developmental potential (e.g., the rhombomere and perhaps the ectomere). Whatever the molecules are and however they are interpreted by these tissues, it appears that there is a remarkably conserved mechanism for setting up the initial organization of the facial prominences between species. Regardless of species, all vertebrates appear to have the same basic bauplan. However, sometime during mid-gestation, the vertebrate face begins to exhibit species-specific variations, in large part due to differences in the rates of growth and differentiation of cells comprising the facial prominences. How do these differences arise? Are they due to late changes in molecular signaling within the facial prominences themselves? Or are these late changes a reflection of earlier, more subtle alterations in boundaries and fields that are established at the earliest stages of head formation? We do not have clear answers to these questions yet, but in this chapter we present new studies that shed light on this age-old question. This chapter aims to present the known signals, both on a molecular and cellular level, responsible for craniofacial development while bringing to light the events that may serve to create difference in facial morphology seen from species to species.

Animals↗
PubMed1995

Structural basis for species-specific differences in the phosphorylation of Na,K-ATPase by protein kinase C.

There is considerable evidence that protein kinases play a role in regulation of the activity of the Na,K-ATPase, but the characteristics of direct kinase phosphorylation of Na,K-ATPase subunits are still not well understood. There are 36 sites that could qualify as protein kinase C motifs in rat alpha 1. Here we have used protein fragmentation with trypsin to localize the site of phosphorylation of the rat Na,K-ATPase alpha 1 subunit to within the first 32 amino acids of the N terminus and then used direct sequencing of the phosphorylated protein to determine which of two candidate serine residues was modified. The result was that at most 25% of the 32P was found on Ser-11, a site that is well conserved in Na,K-ATPase alpha 1 subunits. The remaining 75% or more of the 32P was found on Ser-18, a site that is absent in many Na,K-ATPase alpha subunit sequences. This accounts for the observation that dog and pig alpha 1 subunits can be phosphorylated by protein kinase C only to much lower levels than can rat alpha 1. It is also likely to be relevant to other known species-specific effects of protein kinase C on Na,K-ATPase.

Amino Acid Sequence↗
PubMed1996

Species-specific and interspecies relatedness of NSP1 sequences in human, porcine, bovine, feline, and equine rotavirus strains.

We have sequenced gene 5 encoding NSP1 for three human, two porcine, two bovine, one feline, and five equine rotavirus strains, and compared the nucleotide and deduced amino acid sequences with the published sequences for other various strains. Subgroup I human strains L26, 69M, and DS-1 were found to have a similar NSP1 sequence despite their different G serotypes, VP4 genotypes, and RNA patterns. The NSP1 sequence of the human strain K8 showed a high degree of homology to those of porcine strains OSU and YM. A high degree of homology was found among three equine strains (H2, FI-14, and FI23), but they differed from the other equine strains L338 and H1. The strain H1 was similar to the porcine strains. The feline strain Cat2 showed a high homology to bovine strains UK, RF, and A44. Thus, species-specific and interspecies relatedness of NSP1 sequences among human, porcine, bovine, feline and equine rotaviruses was found. Overall genomic relatedness of strains L26 and YM to various human and animal strains was also examined by RNA-RNA hybridization assay. The present and previous hybridization results showed that there is a good correlation in most strains between overall genomic property (or genogroup) and NSP1 sequence homology.

Amino Acid Sequence↗
PubMed1986

Conformational energy calculations and electrostatic potentials of dihydrofolate reductase ligands: relevance to mode of binding and species specificity.

Classical potential energy calculations are reported for a series of 11 structurally diverse substrates, products, and inhibitors of dihydrofolate reductase. In almost every case, the calculations reveal a range of potential biologically active conformations accessible to the molecule, and geometry optimization with molecular mechanics and molecular orbital calculations further expands the range of accessible conformations. The energy calculations are supplemented with electrostatic potential energy surfaces for the heterocyclic components of each molecule. These data are used in conjunction with the energy calculations and the crystallographically determined enzyme structures to compare two alternative proposed binding modes of folates known to bind with their pteridine rings inverted relative to that of methotrexate. It is shown that the conformational flexibility of the connecting chain between the benzoyl glutamate and pteridine moieties in the folates actually allows the pteridine ring to shift between these alternative binding modes, a combination of which may offer the best explanation for the observed activity. The electrostatic potentials and conformational energy data are also used in an attempt to account for the species specificity of inhibitors of mammalian, bacterial, and protozoal dihydrofolate reductases. The results show that while these techniques can be used to explain many of the observed results, others require recourse to the observed crystal structures to provide a satisfactory explanation.

Aminopterin↗
PubMed1998

Sp1 activation of a TATA-less promoter requires a species-specific interaction involving transcription factor IID.

Sp1 is a ubiquitous activator of numerous TATA-containing and TATA-less promoters within the human genome. This transcription factor is distinct from several other mammalian activators because it cannot stimulate transcription of reporter genes when ectopically expressed in Saccharomyces cerevisiae . Here we report that in cultured cells from Drosophila melanogaster human Sp1 efficiently activates transcription from synthetic promoters containing TATA boxes, but not from promoters that contain an initiator instead of a TATA box. The inability of Sp1 to activate initiator-mediated transcription did not result from inactivity of the consensus initiator element used for the experiments, as other initiator functions were conserved in Drosophila cells. Interestingly, a difference between the Drosophila and human TFIID complexes was found to be responsible for the selective inability of Sp1 to activate initiator-mediated transcription in Drosophila; in a complementation assay with a TFIID-depleted HeLa cell extract both the Drosophila and human TFIID complexes supported TATA-mediated transcription, but only the human complex supported initiator-mediated transcription. These results suggest that a species-specific interaction is required for activation of TATA-less promoters by Sp1, revealing a difference in transcriptional activation mechanisms between vertebrates and invertebrates.

Animals↗
PubMed2002

Identification of residues in the PXR ligand binding domain critical for species specific and constitutive activation.

The cytochrome P450 family of enzymes has long been known to metabolize a wide range of compounds, including many of today's most common drugs. A novel nuclear receptor called PXR has been established as an activator of several of the cytochrome P450 genes, including CYP3A4. This enzyme is believed to account for the metabolism of more than 50% of all prescription drugs. PXR is therefore used as a negative selector target and discriminatory filter in preclinical drug development. In this paper we describe the design, construction and characterization by transient transfection of mutant receptors of the human and mouse PXR ligand binding domains. By modeling the human PXR ligand binding domain we have identified and mutated two polar residues in the putative ligand binding pocket which differ between the human and the mouse receptor. The first residue (Q285 in human/I282 in mouse) was mutated between the two species with the corresponding amino acids. These mutants showed that this residue is important for the species specific activation of PXR by the ligand pregnenolone-16alpha-carbonitrile (PCN), while having a less pronounced role in receptor activation by rifampicin. The second residue to be mutated (H407 in human/Q404 in mouse) unexpectedly proved to be important for the basal level of activation of PXR. The H407A mutant of the human receptor showed a high level of constitutive activity, while the Q404H mutant of the mouse receptor demonstrated a sharply decreased basal activity compared to wild-type.

Animals↗
PubMedDate not supplied

Species-specific regulation of the alpha-2(I) procollagen gene by proximal promoter elements.

Transcriptional regulation of the human alpha 2(I) procollagen proximal promoter involves the interaction of trans-acting factors at the inverted CCAAT box (G/CBE) located at position -80 and an adjacent GGAGGCCC-box at -70. Both these elements have previously been shown to be essential for activity of the human promoter. This study investigated nucleotide differences at three sites (-74, -72 and -71) between the human and mouse promoters that were sufficient to abolish trans-acting factor binding with the mouse sequence (GGAGACGT). Two distinct DNA-protein interactions were detected on the human -107/+54 promoter fragment while a single interaction was observed at the equivalent mouse promoter. One of these factors is the CCAAT-binding factor (CBF) and it's binding was observed on both the human and mouse promoters. Although the GGAGGCCC DNA-binding element was not detected on the mouse promoter, GGAGGCC-binding proteins were present in mouse nuclear extracts as observed by their interaction with the human promoter. Functional analysis of the human and mouse -343/+54 and -107/+54 promoter regions revealed significant differences between species; the human constructs having higher activity than the mouse. The differences in promoter activity between species may in part be a result of the nucleotide differences in the GGAGGCCC-box. Mutations in this region of the human -107/+54 promoter prevented DNA-protein interaction and lowered promoter activity. These results support the hypothesis that the GGAGGCCC-box in the human alpha 2(1) procollagen promoter has a regulatory function and that there exists a species-specific difference in transcription factor binding and regulation of the gene.

Amino Acid Motifs↗