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At least 649 records · Page 36Linked to original sources
PubMed1999

Tissue-specific and light-dependent expression within a family of nuclear-encoded sigma-like factors from Zea mays.

The principal transcription machinery functioning in chloroplasts of higher plants is encoded in two subcellular compartments. Subunits of the RNA polymerase catalytic core are plastid encoded, while sigma factors required for promoter recognition are encoded in the nucleus. We have isolated nuclear-encoded cDNAs, sig1, sig2, and sig3, specifying three sigma factors from maize (Zea mays). The three deduced polypeptides have extensive sequence identity with the principal sigma factors of eubacteria. Two of the maize cDNAs, sig1 and sig3, encode NH2-terminal transit peptides which direct the uptake of a heterologous protein into chloroplasts in vitro. Transcripts for the sig3 gene were more abundant in green leaves than in roots and in light-treated seedlings than in dark-grown seedlings. In contrast, sig1 transcripts were readily detectable in all tissues examined. Thus, at least two promoter-selectivity factors function with the maize chloroplast RNA polymerase, one of which is constitutively expressed and the other is light activated.

Amino Acid Sequence↗
PubMed2001

Transperceptual encoding and retrieval processes in memory: a PET study of visual and haptic objects.

An important objective of functional neuroimaging research is to identify neuroanatomical correlates of memory processes such as encoding and retrieval. In typical studies directed at this goal, however, the to-be-remembered information has been presented in a single perceptual modality. Under these conditions it is not known whether the observed brain activity reflects the studied memory process as such or only the memory process in the given modality. The positron emission tomography (PET) study reported here was designed to identify brain regions involved in encoding and retrieval processes specific to visual and haptic modalities, as well as those common to the two modalities. These latter, common regions, were assumed to be associated with "transperceptual" encoding and retrieval processes. Abstract three-dimensional objects, difficult to describe verbally, served as to-be-remembered materials. A multivariate partial least squares analysis of the PET data revealed that transperceptual encoding processes activated right medial temporal lobe, superior prefrontal cortex bilaterally, and posterior inferior temporal gyrus bilaterally. Transperceptual recognition activations were observed in two right orbitofrontal regions and in anterior cingulate. These results provide initial evidence that some processes involved in memory encoding and retrieval operate beyond perceptual processes and in that sense are transperceptual.

Adult↗
PubMed2002

Inversion and contrast polarity reversal affect both encoding and recognition processes of unfamiliar faces: a repetition study using ERPs.

Using ERPs in a face recognition task, we investigated whether inversion and contrast reversal, which seem to disrupt different aspects of face configuration, differentially affected encoding and memory for faces. Upright, inverted, and negative (contrast-reversed) unknown faces were either immediately repeated (0-lag) or repeated after 1 intervening face (1-lag). The encoding condition (new) consisted of the first presentation of items correctly recognized in the two repeated conditions. 0-lag faces were recognized better and faster than 1-lag faces. Inverted and negative pictures elicited longer reaction times, lower hit rates, and higher false alarm rates than upright faces. ERP analyses revealed that negative and inverted faces affected both early (encoding) and late (recognition) stages of face processing. Early components (N170, VPP) were delayed and enhanced by both inversion and contrast reversal which also affected P1 and P2 components. Amplitudes were higher for inverted faces at frontal and parietal sites from 350 to 600 ms. Priming effects were seen at encoding stages, revealed by shorter latencies and smaller amplitudes of N170 for repeated stimuli, which did not differ depending on face type. Repeated faces yielded more positive amplitudes than new faces from 250 to 450 ms frontally and from 400 to 600 ms parietally. However, ERP differences revealed that the magnitude of this repetition effect was smaller for negative and inverted than upright faces at 0-lag but not at 1-lag condition. Thus, face encoding and recognition processes were affected by inversion and contrast-reversal differently.

Brain↗
PubMed1998

Human herpesvirus-8 ORF K8.1 gene encodes immunogenic glycoproteins generated by spliced transcripts.

A cDNA library from phorbol ester-induced human herpesvirus-8 (HHV-8) carrying BCBL-1 cells was screened with an HIV+KS+ serum, and several cDNA clones encoding HHV-8 proteins were identified. Sequence analysis of two full-length cDNA clones show open reading frames (ORFs) encoded by spliced messages originating from the HHV-8 K8.1 gene. One cDNA encodes an ORF of 228 amino acids, designated K8. 1.A, with a cleavable signal sequence, a transmembrane domain, and four N-glycosylation sites. The splicing event generated the transmembrane domain in the ORF not seen in the genomic K8.1 ORF. Another cDNA encodes an ORF of 167 amino acids, designated K8.1.B, that shares similar amino and carboxyl termini with ORF K8.1.A but with an in-frame deletion. The primary translation products of ORF K8.1A (34 kDa) and K8.1B (20 kDa) in the in vitro-transcription-translation experiments shifted into glycosylated species of 43 and 32 kDa, respectively, in the presence of microsomal membranes. This suggested that the ORF K8.1A and K8.1B encode for glycoproteins. Riboprobes from the K8.1A cDNA insert hybridized with an HHV-8-specific 0.9-kb abundant transcript from BCBL-1 cells. Synthesis of this RNA was eliminated in the presence of a DNA synthesis inhibitor, suggesting that this RNA was a late gene transcript. Because ORFs K8.1A and K8.1B are unique for HHV-8, human sera were tested in Western blot reactions for antibodies against glutathione-S-transferase-ORF K8.1A fusion protein. All sera that were positive for HHV-8 antibodies in immunofluorescence assays with phorbol ester-induced BCBL-1 cells were also positive for anti-ORF K8.1A antibodies. This suggests that measurement of anti-ORF K8.1A antibodies would provide an HHV-8-specific serological assay. Further work is needed to define the biological role of the HHV-8 ORF K8.1A and K8.1B glycoproteins.

Amino Acid Sequence↗
PubMed1999

Immune responses and protection induced by DNA vaccines encoding bovine parainfluenza virus type 3 glycoproteins.

This study was designed to assess the parameters influencing the magnitude and type of immune responses generated to plasmids encoding the hemagglutinin/neuraminidase (HN) and fusion (F) proteins of bovine parainfluenzavirus type 3 (BPIV3). Mice immunized with plasmids expressing HN or F under control of the Rous sarcoma virus long terminal repeat promoter were primed, but they did not develop measurable immune responses. In contrast, strong humoral and cellular immune responses were induced with constructs containing the human cytomegalovirus immediate-early promoter and intron A. After immunization with both HN- and F-encoding plasmids, enhanced responses were observed. Analysis of in vitro protein synthesis confirmed that the presence of the intron is crucial for the expression of the BPIV3 HN gene. Plasmid encoding HN induced significantly higher serum antibody titers by intradermal injection than by intramuscular delivery, whereas antigen-specific T cell proliferation was stronger in intramuscularly injected mice. Both the isotype ratios and the cytokine profiles indicated a Th1-type response after intramuscular immunization and a mixed to Th2-type response in intradermally immunized mice. A plasmid encoding a truncated, secreted form of HN induced a Th2-type immune response, regardless of the route of delivery. In cotton rats, HN- and F-encoding plasmids conferred protection from BPIV3 challenge.

Animals↗
PubMed2001

Molecular and genetic evidence for a virus-encoded glycosyltransferase involved in protein glycosylation.

The major capsid protein, Vp54, of chlorella virus PBCV-1 is a glycoprotein that contains either one glycan of approximately 30 sugar residues or two similar glycans of approximately 15 residues. Previous analysis of PBCV-1 antigenic mutants that contained altered Vp54 glycans led to the conclusion that unlike other glycoprotein-containing viruses, most, if not all, of the enzymes involved in the synthesis of the Vp54 glycan are probably encoded by PBCV-1 (I.-N. Wang et al., 1993, Proc. Natl. Acad. Sci. USA 90, 3840-3844). In this report we used molecular and genetic approaches to begin to identify these virus genes. Comparing the deduced amino acid sequences of the putative 375 PBCV-1 protein-encoding genes to databases identified seven potential glycosyltransferases. One gene, designated a64r, encodes a 638-amino-acid protein that has four motifs conserved in "Fringe type" glycosyltransferases. Analysis of 13 PBCV-1 antigenic mutants revealed mutations in a64r that correlated with a specific antigenic variation. Dual-infection experiments with different antigenic mutants indicated that viruses that contained wild-type a64r could complement and recombine with viruses that contained mutant a64r to form wild-type virus. Therefore, we conclude that a64r encodes a glycosyltransferase involved in synthesizing the Vp54 glycan. This is the first report of a virus-encoded glycosyltransferase involved in protein glycosylation.

Amino Acid Sequence↗
PubMed2002

Identification and characterization of a baboon reovirus-specific nonstructural protein encoded by the bicistronic s4 genome segment.

All characterized orthoreoviruses encode a characteristic spike-like protein on their polycistronic S1 genome segments that mediates virus cell attachment. In the case of baboon reovirus (BRV), the polycistronic S-class genome segment corresponds to the smallest S4 segment. We recently determined that the 5'-proximal open reading frame (ORF) of the bicistronic S4 segment encodes a nonstructural protein responsible for virus-induced syncytium formation. Current analysis indicates that the p16 protein encoded by the 3'-proximal ORF of the BRV S4 genome segment shows no sequence similarity to any other protein encoded by the orthoreoviruses, including the well-characterized sigma1/sigmaC reovirus cell attachment protein. Results indicate that p16 is a BRV-specific nonstructural protein that is not required for virus infection in cell culture and is not involved in viral cell attachment. In conjunction with previous studies of the BRV S1, S2, and S3 genome segments, the current results indicate that, unlike all other orthoreoviruses, BRV does not encode a cell attachment protein in its S-class genome segments. Furthermore, cell binding and infectivity studies suggested BRV may not utilize a functional homolog of the prototypical reovirus sigma1/sigmaC cell receptor-binding protein to mediate endocytic uptake by cells.

Animals↗
PubMed2002

Intraepithelial DNA immunisation with a plasmid encoding a codon optimised COPV E1 gene sequence, but not the wild-type gene sequence completely protects against mucosal challenge with infectious COPV in beagles.

DNA plasmids encoding the open reading frames of canine oral papillomavirus (COPV) nonstructural early genes E1, E2, or E7 protein were delivered into both oral mucosal and cutaneous epithelial sites in beagle dogs using particle-mediated immunotherapeutic delivery (PMID) technology. Control dogs were vaccinated with plasmid encoding either hepatitis B virus surface antigen (HBVs) or COPV L1. Using a prophylactic immunisation protocol, a priming dose of plasmid DNA was followed by a booster dose 6 weeks later. Four weeks after boost, all dogs were challenged with infectious COPV particles. Following viral challenge, as shown previously (M. A. Stanley et al., 2001, Vaccine 19, 2783-2792), mucosal papillomas developed in the negative-control HBVs vaccinated dogs, but all animals in the COPV L1 group were fully protected from disease development. In the early gene-vaccinated groups five of six in the E1-vaccinated dogs, two of six in E2-vaccinated dogs, and three of six in the E7-vaccinated beagles developed oral papillomas. Compared to the HBVs negative-control group the oral papillomas that did develop in the early-gene vaccinated beagles were significantly smaller, shorter in duration, and fewer in number. Taken together the disease burden was markedly reduced and this was statistically significant. In a second experiment one group of animals was vaccinated with plasmid encoding the wild-type COPV E1 gene, and a separate group was vaccinated with plasmid encoding a synthetic codon-optimised COPV E1 gene sequence. None of the codon-optimised E1-vaccinated animals developed papillomas at any challenge site. However, all animals vaccinated with wild-type E1 had papillomas. These data suggest that immunisation by PMID with papillomavirus early genes can significantly impact upon subsequent disease development and that full protection can be achieved using improved vectors encoding codon-optimised gene sequences perhaps emphasizing the importance of antigen load in the generation of protective responses to papillomavirus proteins.

Animals↗
PubMed1998

Further characterisation of the coronavirus IBV ORF 1a products encoded by the 3C-like proteinase domain and the flanking regions.

Coronavirus IBV encodes a piconarvirus 3C-like proteinase. In a previous report, this proteinase was shown to undergo rapid degradation in vitro in reticulocyte lysate due to a posttranslational event involving ubiquitination of the protein. Several lines of evidence presented here indicate that the proteinase itself is stable. Translation of the IBV sequence from nucleotide 8864 to 9787 resulted in the synthesis of a 33 kDa protein, representing the full-length 3C-like proteinase. Pulse-chase and time-course experiments showed that this protein was stable in reticulocyte lysate for up to 2 hours. However, a 45 kDa protein encoded by the IBV sequence from nucleotide 8693 to 9911 underwent rapid degradation in reticulocyte lysate, but was stable in wheat germ extract, suggesting that an ATP-dependent protein degradation pathway may be involved in the turnover of the 45 kDa protein. To identify the IBV sequence responsible for the instability of this 45 kDa protein species, the region from nucleotide 8693 to 9787 was translated both in vitro and in vivo, leading to the synthesis of a stable 43 kDa protein. These results suggest that a destabilising signal may be located in the IBV sequences between the nucleotides 9787 and 9911. Meanwhile, protein aggregation was observed when the product encoded by the IBV sequence from nucleotide 9911 to 10,510 was boiled for 5 minutes before being analysed in SDS-PAGE; when the same product was treated at 37 degrees C for 15 minutes, however, protein aggregation was not detected. Deletion studies indicate that the presence of a hydrophobic domain downstream of the 3C-like proteinase-encoding region may be the cause for the aggregation of the product encoded by this region of ORF 1a.

Animals↗
PubMed1991

Circadian oscillations of nuclear-encoded chloroplast proteins in pea (Pisum sativum).

The diurnal and circadian expression of light-inducible chloroplast proteins, i.e. light-harvesting chlorophyll a/b protein (LHCP), early light-inducible protein (ELIP) and Fe-S Rieske, has been studied in young pea plantlets at the level of mRNA integrated into polysomal complexes and at the level of proteins. Under light-dark as well as constant light conditions the levels of the three nuclear-encoded chloroplast proteins oscillate while the investigated plastid-encoded proteins, large subunit of ribulose-1,5-bisphosphate carboxylase (LSU), reaction center protein D1 and cytochrome f, do not show oscillations at the protein level. The levels of the nuclear-encoded polysome-bound mRNAs fluctuate in parallel with the changes in the levels of poly(A) RNA which were described previously. Under constant light conditions the oscillation at the level of polysomal bound mRNA is readily dampened while the steady-state levels of the investigated nuclear-encoded proteins still fluctuate. We conclude that the extent of expression of the genes for the nuclear-encoded chloroplast proteins studied is controlled by a circadian ocillator primarily, but not exclusively, at the level of transcription.

Cell Nucleus↗
PubMed1994

The Dictyostelium discoideum mitochondrial genome: a primordial system using the universal code and encoding hydrophilic proteins atypical of metazoan mitochondrial DNA.

A 3,345-bp fragment of Dictyostelium discoideum mitochondrial DNA (mtDNA) has been sequenced. This fragment contained the 80-kDa subunit of complex I (NADH:ubiquinone oxidoreductase), encoding a predicted amino acid sequence of 688 residues and a molecular mass of 79,805 daltons which is nuclear encoded in other metazoa. The C-terminus of the D. discoideum complex I gene shared a 10-bp overlap with NADH:ubiquinone oxidoreductase chain 5 (ND5), while 21 bp 5' were three tRNA genes (two isoleucine and a histidine) and a further 25 bp 5' of these genes is the partial sequence (104 residues) of an unidentified open reading frame (ORF104). Both the 80-kDa subunit and the ORF104 were hydrophilic and highly charged, suggesting they are not membrane associated, unlike most mitochondrially encoded proteins in the metazoa. Sequence analysis of the 80-kDa subunit, its adjacent ND5 gene, and ORF104 indicates the universal stop codon TGA, which codes for tryptophan in nearly all nonplant mtDNA, is either unassigned or coding for a stop codon in D. discoideum. The large size of the mitochondrial genome (54 kb), the lack of intergenic sequence, and the apparent use of the universal code suggest D. discoideum mtDNA may encode many primitive genes that are nuclear encoded in higher organisms.

Amino Acid Sequence↗
PubMed1993

The medial temporal lobe in encoding, retention, retrieval and interhemispheric transfer of visual memory in primates.

Low-level electrical stimulation through electrodes in the medial temporal lobe (MTL) was used to disrupt the performance of chiasm-split macaques working in a delayed matching-to-sample (DMS) visual memory task. The stimulation was below afterdischarge threshold and did not distract the animals. Nonetheless, stimulation caused severe deficits when delivered either during encoding or retrieval stages. Substantially less deficit appeared when stimulation was delivered during the retention interval. Stimulation levels which led to significant disruption on the DMS task had no effect on a discrimination task using the same kinds of images. Unilateral electrical stimulation delivered to MTL in one hemisphere during encoding and to MTL in the other hemisphere during retrieval produced an effective disruption, suggesting that the unilateral stimulation during the encoding period disrupts the encoding on that side while unilateral stimulation delivered to the opposite side during the retrieval period prevents the retrieval of the (now unilateral) memory. This suggestion is supported by control experiments in which significantly less disruption was caused by unilateral electrical stimulation delivered during both the encoding and the retrieval period if the stimulation was delivered to the same side in both periods. The electrical stimulation was further used to determine that interhemispheric access by one hemisphere to memories placed in the other was excellent. This was done, in these split-chiasm monkeys, by using unilateral stimulation to limit memory formation to just one hemisphere, then testing interhemispheric access by routing the test through the "ignorant" hemisphere (using just the ipsilateral eye). Successful interhemispheric access was obtained with either the anterior commissure or with the splenium of the corpus callosum (the other interhemispheric forebrain pathways having been cut). The electrical stimulation was also used to determine that the visual inputs even though entering via just one eye and one hemisphere, lead to bilateral memory formation. In this case each hemisphere was tested separately during retrieval by delivering disruptive levels of the electrical stimulation to the MTL of the other hemisphere.

Animals↗
PubMed1987

Neuronal response thresholds to and encoding of thermal stimuli during carrageenin-hyperalgesic-inflammation in the ventro-basal thalamus of the rat.

This study analyzed neuronal encoding and response thresholds to thermal stimuli at the ventro-basal (V.B.) thalamus level during a hyperalgesic inflammation induced by intra-plantar injection of carrageenin in the rat. The threshold and the encoding capacity of the cells were studied during two phases of the inflammatory process, namely the "acute" phase (the first two hours following the injection), and "sub-acute" phase 24 h after). In this second phase the hyperalgesia was verified using a behavioral nociceptive test, just prior to the recording session. Only VB neurones with a receptive field that included the injected paw were considered. In the acute phase, neurones exclusively driven by noxious stimuli were studied before and during the first two hours following the induction of the inflammatory oedema. In the sub-acute phase two groups of neurones which, on the basis of our previous studies, were presumably involved in the transmission of messages giving rise to the hyperalgesia could be separated: a group of neurones which were driven by intense mechanical stimuli and another group driven by moderate mechanical stimulation applied to the inflamed joints and/or the surrounding cutaneous areas. In the "acute" phase there was a dramatic lowering (by about 4 degrees C) of the response threshold of the neurones when the thermal stimulus was applied to the injected paw, although their threshold to the mechanical stimulus was still high. A linear encoding of the bath temperature used as a stimulus was observed for both the injected and the non-injected paws. For a few neurones, a leftward shift of the stimulus-response curve was found for the inflamed limb. In the "sub-acute" phase, neurones with high thresholds to the mechanical indentations still exhibited a low response threshold to the thermal stimulation, not only from the injected but also from the non-injected paw. The other group of neurones responded with relatively low thresholds to the both stimulus modalities. By contrast to the acute phase, the two groups of neurones exhibited only a weak ability to encode the stimulus intensity especially when the stimulus was applied to the inflamed paw. Both peripheral and central mechanisms are likely to be involved in the modifications of response threshold and encoding capacity at the VB thalamus level seen in these conditions of hyperalgesic inflammation. The differential time course of the responses to a liminal or to a supra-liminal temperature during the inflammation, are discussed in reference to some of the mismatches occurring in clinical situations of hyperalgesia.

Action Potentials↗
PubMed1993

The organisation and expression of the genes encoding the mitochondrial glycine decarboxylase complex and serine hydroxymethyltransferase in pea (Pisum sativum).

Restriction fragment length polymorphisms have been used to determine the chromosomal location of the genes encoding the glycine decarboxylase complex (GDC) and serine hydroxymethyltransferase (SHMT) of pea leaf mitochondria. The genes encoding the H subunit of GDC and the genes encoding SHMT both show linkage to the classical group I marker i. In addition, the genes for the P protein of GDC show linkage to the classic group I marker a. The genes for the L and T proteins of GDC are linked to one another and are probably situated on the satellite of chromosome 7. The mRNAs encoding the five polypeptides that make up GDC and SHMT are strongly induced when dark-grown etiolated pea seedlings are placed in the light. Similarly, when mature plants are placed in the dark for 48 h, the levels of both GDC protein and SHMT mRNAs decline dramatically and then are induced strongly when these plants are returned to the light. During both treatments a similar pattern of mRNA induction is observed, with the mRNA encoding the P protein of GDC being the most rapidly induced and the mRNA for the H protein the slowest. Whereas during the greening of etiolated seedlings the polypeptides of GDC and SHMT show patterns of accumulation similar to those of the corresponding mRNAs, very little change in the level of the polypeptides is seen when mature plants are placed in the dark and then re-exposed to the light.

Amino Acid Oxidoreductases↗
PubMed1993

The Nicotiana tabacum genome encodes two cytoplasmic thioredoxin genes which are differently expressed.

A Nicotiana tabacum thioredoxin h gene (EMBL Accession No. Z11803) encoding a new thioredoxin (called h2) was isolated using thioredoxin h1 cDNA (X58527), and represents the first thioredoxin h gene isolated from a higher plant. It encodes a polypeptide of 118 amino acids with the conserved thioredoxin active site Trp-Cys-Gly-Pro-Cys. This gene comprises two introns which have lengths of 1071 and 147 bp respectively, and three exons which encode peptides of 29, 41 and 48 amino acids, respectively. This thioredoxin h shows 66% identity with the amino acid sequence of thioredoxin h1 (X58527) and only around 35% with the choroplastic thioredoxins. The two thioredoxins, h1 and h2, do not have any signal peptides and are most probably cytoplasmic. Using the 3' regions of the mRNAs, two probes specific for thioredoxins h1 and h2 have been prepared. Southern blot analysis shows that thioredoxin sequences are present in only two genomic EcoRI fragments: a 3.3 kb fragment encodes h1 and a 4.5 kb fragment encodes h2. Analysis of the ancestors of the allotetraploid N. tabacum shows that thioredoxin h2 is present in N. sylvestris and N. tomentosiformis but that thioredoxin h1 is absent from both putative ancestors. Thus, the thioredoxin h1 gene has probably been recently introduced in to N. tabacum as a gene of agronomic importance, or linked to such genes. Northern blot analysis shows that both genes are expressed in N. tabacum, mostly in organs or tissues that contain growing cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1995

Structure and expression of the gene encoding ribosomal protein S1 from the cyanobacterium Synechococcus sp. strain PCC 6301: striking sequence similarity to the chloroplast ribosomal protein CS1.

We isolated a 38 kDa ssDNA-binding protein from the unicellular cyanobacterium Synechococcus sp. strain PCC 6301 and determined its N-terminal amino acid sequence. A genomic clone encoding the 38 kDa protein was isolated by using a degenerate oligonucleotide probe based on the amino acid sequence. The nucleotide sequence and predicted amino acid sequence revealed that the 38 kDa protein is 306 amino acids long and homologous to the nuclear-encoded 370 amino acid chloroplast ribosomal protein CS1 of spinach (48% identity), therefore identifying it as ribosomal protein (r-protein) S1. Cyanobacterial and chloroplast S1 proteins differ in size from Escherichia coli r-protein S1 (557 amino acids). This provides an additional evidence that cyanobacteria are closely related to chloroplasts. The Synechococcus gene rps1 encoding S1 is located 1.1 kb downstream from psbB, which encodes the photosystem II P680 chlorophyll a apoprotein. An open reading frame encoding a potential protein of 168 amino acids is present between psbB and rps1 and its deduced amino acid sequence is similar to that of E. coli hypothetical 17.2 kDa protein. Northern blot analysis showed that rps1 is transcribed as a monocistronic mRNA.

Amino Acid Sequence↗
PubMed1995

Nucleotide sequence analysis of an infectious laryngotracheitis virus gene corresponding to the US3 of HSV-1 and a unique gene encoding a 67 kDa protein.

The DNA sequence of 4005 nucleotides from the Kpnl O and part of Kpnl K fragments in the short unique region of infectious laryngotracheitis virus (ILTV) was determined. The sequence contained two complete and one partial open reading frames (ORFs). The partial ORF was open at the 5' end of the sequence and represented the NH2-terminal 118 amino acids (aa) of a polypeptide. Its partial predicted protein product exhibited significant homology to the US2 gene product of HSV-1 (herpes simplex virus type 1) and it homologs in other herpesviruses. ORF 2 is 471 aa long and could encode a protein of 53.8 kDa which shared aa homology with the protein kinases encoded by HSV-1 US3 and its gene homologs. Analysis of the ORF 2 aa sequence revealed domains characteristic of protein-serine/threonine (S/T) kinases of cellular and viral origin. The ORF 3 encoded a predicted protein of 601 aa (M(r) 67.5 kDa) which exhibited limited homology (18% overall identity) with the UL47 protein (major tegument protein) of HSV-1. Northern (RNA) blot hybridization and metabolic inhibitors were used to characterize the ILTV protein kinase and the 67K mRNAs. The data revealed that protein kinase is a gamma-1 gene encoding a 1.6 mRNa, while the 67K ORF is a gamma-2 gene encoding a 2 kb mRNA.

Amino Acid Sequence↗
PubMed1996

Model of amino acid substitution in proteins encoded by mitochondrial DNA.

Mitochondrial DNA (mtDNA) sequences are widely used for inferring the phylogenetic relationships among species. Clearly, the assumed model of nucleotide or amino acid substitution used should be as realistic as possible. Dependence among neighboring nucleotides in a codon complicates modeling of nucleotide substitutions in protein-encoding genes. It seems preferable to model amino acid substitution rather than nucleotide substitution. Therefore, we present a transition probability matrix of the general reversible Markov model of amino acid substitution for mtDNA-encoded proteins. The matrix is estimated by the maximum likelihood (ML) method from the complete sequence data of mtDNA from 20 vertebrate species. This matrix represents the substitution pattern of the mtDNA-encoded proteins and shows some differences from the matrix estimated from the nuclear-encoded proteins. The use of this matrix would be recommended in inferring trees from mtDNA-encoded protein sequences by the ML method.

Amino Acids↗