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At least 109 records · Page 6Linked to original sources

PubMed1993

Codon reading scheme in Mycoplasma pneumoniae revealed by the analysis of the complete set of tRNA genes.

The 33 genes encoding the complete set of tRNA species in Mycoplasma pneumoniae have been cloned and sequenced. They are organized into 5 clusters in addition to 9 single genes. No redundant gene was found, indicating that 33 tRNAs correspond to 32 different anticodons and decode all 62 codons used in this organism. There is only one single tRNA for each of the Ala, Leu, Pro, and Val family boxes. Therefore, a simplified decoding system resembling that recently described for Mycoplasma capricolum (1) has to also exist in M.pneumoniae. However, analysis of the anticodon set and codon usage revealed features characteristic of the latter: (i) there is no obvious preference toward AT rich synonymous codons, (ii) CGG codons are assigned for arginine and are translated by tRNA Arg(UCG), and (iii) CNN or GNN anticodons are encountered in the Ser, Thr, Arg, and Gly family boxes. We thus propose that this codon-anticodon recognition pattern has emerged in the 'M.pneumoniae cluster' under a genomic economization strategy but without the influence of AT pressure.

Amino Acid Sequence↗

PubMed1997

Proviral organization and sequence analysis of feline immunodeficiency virus isolated from a Pallas' cat.

The nucleotide sequence and genomic organization have been determined for a highly cytopathic feline immunodeficiency virus (FIV) isolated from a Pallas' cat. The 9747-bp provirus of this virus, FIV-Oma, has typical lentivirus organization with LTRs, gag, pol, and env open reading frames (ORFs), putative vif and rev ORFs, and an ORF similar to ORF2/ORFA of domestic cat FIV isolates. Although the FIV-Oma provirus is 300 to 600 bp longer than other FIV proviruses, these additional bases are distributed throughout the genome. Phylogenetic analysis of a conserved region of the pol gene suggests that FIV-Oma is more closely related to some of the puma and lion lentiviruses than it is to domestic cat FIV isolates; however, many regions of the genome exhibit extensive nucleotide sequence divergence. None of the eight molecular proviral clones isolated from a genomic library are infectious, but we have constructed an infectious, cytopathic clone of FIV-Oma from subcloned and PCR-amplified fragments of these proviral clones. This clone will be useful for identifying the genetic determinants of FIV-Oma's biological activities.

Amino Acid Sequence↗

PubMed1999

Sequence analysis and expression of a mRNA for a larval-specific cuticular protein, LCP1, from Helicoverpa armigera.

Several cDNA clones for a larval cuticular protein from Helicoverpa armigera were isolated and sequenced. The cDNA clones contain an open reading frame encoding a 109 residue protein which is homologous to other known cuticular proteins. The predicted protein appears to have a signal peptide which would be removed to give a mature protein of 91 amino acid residues with an Mr of 10 127. The mature protein, LCP1 (Larval Cuticular Protein), would be highly acidic, as is found for other cuticular proteins from flexible insect cuticles. The mRNA appears to be expressed throughout larval development although it is more highly expressed in the integument of the late final instar.

Amino Acid Sequence↗

PubMed1997

Genotypic analysis of the 5'-untranslated region of a pestivirus strain isolated from human leucocytes.

The 5'-untranslated genomic region of the pestivirus strain Europa, originated in human leucocytes and previously identified as bovine diarrhea virus (BVDV), was amplified by reverse transcription-PCR and sequenced. Analyses based on primary nucleotide sequence homology and on secondary palindromic sequence structures characteristic to genotypes revealed that this human isolate should be assigned to a novel genotype of pestivirus, type Ic. This newly emerged genotype was related to, but distinguishable from the three known BVDV genotypes, Ia, Ib and II. Three other bovine field isolates of BVDV originated from Germany were also found to belong to this new genotype Ic. Within pestivirus genotype Ic strains, the overall nucleotide sequence homology was 95-96%, and 88-92%, 88-90% and 77-79% with the other BVDV genotypes Ia, Ib and II, respectively. With the strains from border disease virus (genotype III) and hog cholera virus (genotype IV), homologies were less than 75%.

Animals↗

PubMed1997

Nucleotide sequence analysis of the large (L) genes of phocine distemper virus and canine distemper virus (corrected sequence).

This paper corrects the previously published sequence of the L gene of canine distemper virus (CDV). Errors in the published sequence (M. S. Sidhu et al., 1993, Virology 193, 50-65) led to frame shifts between residues 1021-1032, 1190-1219 and 1645-1650; a deletion of 21 amino acids between residues 1684-1705, and a single residue deletion at residue 1478. Residue 237 is now found to be glycine rather than tryptophan and residue 1626 proline instead of threonine. The sequence of the L gene of phocine distemper virus (PDV) was also determined. Alignment of the morbillivirus L proteins showed that PDV and CDV are more closely related to each other than to rinderpest virus and measles virus. Two regions of low identity are proposed to function as hinge regions between three highly conserved domains (I-III) in the morbillivirus L proteins. New sequence motifs have been identified on the basis of conservation in the morbilliviruses and the Paramyxovirinae.

Amino Acid Sequence↗

PubMed2005

Cactus mild mottle virus is a new cactus-infecting tobamovirus.

A new cactus-infecting tobamovirus, Cactus mild mottle virus (CMMoV), was isolated from diseased grafted cactus, Gymnocalycium mihanovichii and its molecular properties were characterized. CMMoV is distantly related to known species of the genus Tobamovirus on the basis of serological and sequence analyses. Western blot analysis showed that CMMoV is serologically unrelated to Sammon's Opuntia virus, which is the only known species of the genus Tobamovirus found in cactus plants. The 3'-terminal 2,910 nucleotides of CMMoV have been sequenced. The coat protein (CP) and movement protein (MP) genes encode 161 and 306 amino acids residues, respectively, and the 3' untranslated region (UTR) consists of 229 nucleotides long. The nucleotide and amino acid sequences of the CP of CMMoV were 39.6% to 49.2% and 25.8% to 40.3% identical to other seventeen tobamoviruses, respectively. The MP shared 34.9% to 40.6% and 16.3% to 27.0% and 44.6% to 63.4% identities, respectively, at the amino acid and nucleotide levels with other members of the genus. Percentage identities of nucleotides of the 3' UTR ranged from 42.5% to 63.4%. Phylogenetic tree analyses of the CP and MP suggest the existence of the fifth cactus-infecting subgroup in the genus Tobamovirus. Sequence analyses of these two viral proteins revealed that the highest amino acid sequence identity between the virus and seventeen other tobamoviruses was 40.6%, supporting the view that CMMoV is a new definite species of the genus Tobamovirus.

Cactaceae↗

PubMed1999

[The complete nucleotide sequences of A/Goose/Guangdong/2/96(H5N1) virus RNA segment 1-3 and 5].

OBJECTIVE: To determine the nucleotide and amino acid sequences of PB2, PB1, PA and NP genes and compared them with sequences of A/HK/156/97(H5N1) virus for revealing the relationship between A/Googs/Guangdong/2/96(H5N1) and A/HK/156/97(H5N1) viruses. METHODS: Virion RNA was transcribed into cDNA by reverse transcriptase, cDNA amplified by PCR, the productions of PCR were purified. Afterward, RNA sequence analysis was performed by the dideoxynucleotide chain termination method, using synthetic oligodeoxynucleotide primers. RESULTS: The lengths of A/Goose/Guangdong/2/96(H5N1) virus RNA segment 1-3 and 5 contain 2,341, 2,341, 2,233 and 1,565 nucleotides, respectively. They encode for PB2 (759 amino acids), PB1 (757 amino acids), PA (716 amino acids) and NP (498 amino acids) proteins. The homologies of amino acid sequences of PB2, PB1, PA and NP proteins between A/Goose/Guangdong/2/96 (H5N1) and A/HK/156/97 (H5N1) virus are 96.4%, 97.2%, 97.3% and 97.0%, respectively. CONCLUSION: The lengths of RNA segment 1-3 and 5 of Goose strain are 2,341, 2,341, 2,233 and 1,565 nucleotides, respectively. The nucleotide sequences of these genes are distinguish able from those of Hong Kong virus.

Amino Acid Sequence↗

PubMed1998

The simian T-lymphotropic virus STLV-PP1664 from Pan paniscus is distinctly related to HTLV-2 but differs in genomic organization.

We have isolated a highly divergent simian T-lymphotropic virus, STLV-PP1664, from a wild-caught bonobo (Pan paniscus). Previous phylogenetic analysis suggested that this virus represents an additional type of STLV but this has now become a matter of discussion. We have now obtained and analyzed the entire genome of STLV-PP1664. All major genes and their corresponding viral messengers were identified. Sequence comparison and phylogenetic analysis indicated that this virus, together with the closely related panp isolate, belongs to an early lineage within the PTLV-2 clade, differing from HTLV-2 by about 25%. In contrast to the HTLV-1 and HTLV-2 LTR, only two 21-bp repeats instead of three were found in the STLV-PP1664 LTR. Additional messengers, resulting from alternative splicing, potentially encode five different accessory proteins from open reading frames in the pX region: prorfI, porfII, ptorfV', and two isoforms of Rex. The amino acid sequences of these proteins are only distinctly related to the accessory proteins from HTLV-2. These data suggest a different genomic organization of the STLV-PP1664 pX region than that of HTLV-2. We conclude that STLV-PP1664, although related to HTLV-2, has some distinct features in the LTR and the pX regions, the impact of which needs further investigation. Although arguments pro and contra a distinct classification are nearly equally balanced, we propose to classify this virus as an STLV-2, designated STLV-2PP1664.

Amino Acid Sequence↗

PubMed2004

The impact of SNPs on the interpretation of SAGE and MPSS experimental data.

Serial Analysis of Gene Expression (SAGE) and Massively Parallel Signature Sequencing (MPSS) are powerful techniques for gene expression analysis. A crucial step in analyzing SAGE and MPSS data is the assignment of experimentally obtained tags to a known transcript. However, tag to transcript assignment is not a straightforward process since alternative tags for a given transcript can also be experimentally obtained. Here, we have evaluated the impact of Single Nucleotide Polymorphisms (SNPs) on the generation of alternative SAGE and MPSS tags. This was achieved through the construction of a reference database of SNP-associated alternative tags, which has been integrated with SAGE Genie. A total of 2020 SNP-associated alternative tags were catalogued in our reference database and at least one SNP-associated alternative tag was observed for approximately 8.6% of all known human genes. A significant fraction (61.9%) of these alternative tags matched a list of experimentally obtained tags, validating their existence. In addition, the origin of four out of five SNP-associated alternative MPSS tags was experimentally confirmed through the use of the GLGI-MPSS protocol (Generation of Long cDNA fragments for Gene Identification). The availability of our SNP-associated alternative tag database will certainly improve the interpretation of SAGE and MPSS experiments.

DNA Restriction Enzymes↗

PubMed1999

[Nucleotide sequence of A/Goose/Guangdong/2/96 (H5N1) virus M and NS RNA].

OBJECTIVE: To determine the nucleotide sequences of M and NS genes of A/Goose/Guangdong/2/96(H5N1) virus and also to compare them with the sequences of A/HK/156/97(H5N1) strain for revealing the relationship between the two viruses, as well as for setting up a solid base for studying M and NS genes of influenza A viruses in the future. METHODS: Virion RNA was transcribed into cDNA by reverse transcriptase, cDNA was amplified by PCR, the products of PCR were purified. Afterward, RNA sequence analysis was performed by the dideoxynucleotide chain termination method using synthetic oligodeoxynucleotide primers. RESULTS: The segment length of A/Goose/Guangdong/2/96(H5N1) virus RNA 7 is 1,027 nucleotides. It codes M1 (252 amino acids) and M2 (97 amino acids) proteins. However, the segment length of RNA 8 of A/Goose/Guangdong/2/96(H5N1) virus is 890 nucleotides coding NS1 (230 amino acids) and NS2 (121 amino acids) proteins. The amino acid sequence homologies of M1, M2, NS1 and NS2 protein molecules between A/Goose/Guangdong/2/9(H5N1) and A/HK/156/97 (H5N1) viruses are 97.6%, 92.8%, 65.7% and 76.9%, respectively. CONCLUSION: The lengths of A/Goose/Guangdong/2/96(H5N1) virus RNA 7 and RNA 8 and 1,027 are 890 nucleotides, respectively. These two RNA segments belong to those of avian influenza A virus. The A/HK/156/97(H5N1) virus RNA 7 and RNA 8 segments are not derived from those of A/Goose/Guangdong/2/96(H5N1) virus directly.

Amino Acid Sequence↗

PubMed1997

Nucleotide sequence and genomic organization of Acyrthosiphon pisum virus.

The nucleotide sequence of the genomic RNA of Acyrthosiphon pisum virus was determined. The APV genome is 10,016 nucleotides in length, excluding the 3'-end poly(A) track, and contains two large open reading frames (ORFs), encoding proteins of 296,340 and 63,279 Da. The ORF1 is preceded by an untranslated leader sequence of 267 nucleotides. The ORF1 product contains sequence motifs characteristic of RNA-dependent RNA polymerases, chymotrypsin-like proteases, and helicases. Interviral sequence comparison revealed significant similarities with viruses belonging to the so-called picornavirus superfamily. The ORF2 is most likely expressed by a -1 translational frameshift and is followed by an untranslated sequence of 222 nucleotides. Internal amino acid sequences of three capsid proteins (66K, 34K, 23/24K) were determined. Comparison of the obtained amino acid sequences with the APV sequence disclosed that the structural proteins are located in the 3'-terminal half of the genome. The 34K protein is encoded by the ORF1, while the 66K protein contains both ORF1-(34K) and ORF2-derived sequences and is probably expressed by a translational frameshift. The 23/24K proteins most likely arise by proteolytic breakdown of the 34K protein. Although the deduced APV genomic organization in some aspects resembles that of the picornaviruses, its overall genomic organization indicates that APV is a distinct species only distantly related to the Picornaviridae.

Amino Acid Sequence↗

PubMed1994

Predicted stem-loop structures and variation in nucleotide sequence of 3' noncoding regions among animal calicivirus genomes.

Caliciviruses are nonenveloped with a polyadenylated genome of approximately 7.6 kb and a single capsid protein. The "RNA Fold" computer program was used to analyze 3'-terminal noncoding sequences of five feline calicivirus (FCV), rabbit hemorrhagic disease virus (RHDV), and two San Miguel sea lion virus (SMSV) isolates. The FCV 3'-terminal sequences are 40-46 nucleotides in length and 72-91% similar. The FCV sequences were predicted to contain two possible duplex structures and one stem-loop structure with free energies of -2.1 to -18.2 kcal/mole. The RHDV genomic 3'-terminal RNA sequences are 54 nucleotides in length and share 49% sequence similarity to homologous regions of the FCV genome. The RHDV sequence was predicted to form two duplex structures in the 3'-terminal noncoding region with a single stem-loop structure, resembling that of FCV. In contrast, the SMSV 1 and 4 genomic 3'-terminal noncoding sequences were 185 and 182 nucleotides in length, respectively. Ten possible duplex structures were predicted with an average structural free energy of -35 kcal/mole. Sequence similarity between the two SMSV isolates was 75%. Furthermore, extensive cloverleaflike structures are predicted in the 3' noncoding region of the SMSV genome, in contrast to the predicted single stem-loop structures of FCV or RHDV.

Base Sequence↗

PubMed2006

The complete nucleotide sequence of a capsicum chlorosis virus isolate from Lycopersicum esculentum in Thailand.

The complete nucleotide sequence of a tospovirus isolated from Lycopersicum esculentum in Thailand was determined. The L RNA comprises of 8912 nt and codes for the RNA-dependent RNA-polymerase (RdRp) (2877 aa). Two ORFs are located on the M RNA (4823 nt) encoding the non-structural (NSm) protein (308 aa) and the viral glycoprotein precursors (Gn/Gc) (1121 aa) separated by an intergenic region of 433 nt. ORFs coding for the non-structural (NSs) and nucleocapsid (N) protein, 439 aa and 275 aa, respectively, were identified on the S RNA (3477 nt) separated by an intergenic region of 1202 nt. The N protein of the Thailand isolate was most closely related to that of capsicum chlorosis virus (CaCV), sharing an amino acid sequence identity of 92.7%. Additionally, multiple sequence analyses revealed significant similarities to tospoviruses of the species Watermelon silver mottle virus and to several putative tospovirus entries in GenBank. Based on these alignments it is proposed to refer to all these different viruses as isolates of CaCV.

Amino Acid Motifs↗

PubMed2006

Determination of the 5'- and 3'-terminal sequences completes the sequences of the two double-stranded RNAs of Penicillium stoloniferum virus S.

The two genomic segments of Penicillium Stoloniferum virus S (PsV-S), a member of the Partitiviridae, were recently sequenced and published. We independantly sequenced PsV-S and showed that the original sequence was missing nucleotides at both the 5' and 3' termini of both segments. We determined the correct sequence in three independent experiments and found the segments to be 1753 bp (encoding the RNA-dependant RNA polymerase) and 1581 bp (encoding the Capsid Protein). Homology was shown between the 5' and 3' ends of PsV-S and other members of the Partitiviridae.

Base Sequence↗

PubMed1996

Characterisation of Wongorr virus, an Australian orbivirus.

Sequence analyses of VP3 gene segments of Wongorr virus isolates from the Northern Territory of Australia were compared with the cognate gene segments from Picola and Paroo River viruses. Previous serological investigations had demonstrated some relationships between these viruses, however VP3 gene sequence and phylogenetic analyses placed these viruses within the same serogroup which was distinct from other described orbivirus serogroups. A polymerase chain reaction (PCR) was developed for the detection of this serogroup and used to identify and determine partial sequence data for other isolates of the virus. Wongorr virus and the other tick and mosquito-borne orbiviruses (Kemerovo and Corriparta), were more closely related than the Culicoides transmitted orbiviruses, such as bluetongue (BTV) and African horse sickness virus (AHSV) which were shown to be on a separate branch of the orbivirus phylogenetic tree.

Aedes↗

PubMed1997

Immunoglobulin heavy chain junctional diversity in young and aged humans.

The causes of observed deficiencies to the humoral immune response in aged humans are unknown. Since a major source of antibody diversity is generated at the VH-D-JH junctional regions of the immunoglobulin heavy chain, we determined whether differences in junctional diversity are manifested with aging. We compared the CDR3 regions of IgM heavy chain transcripts isolated from young adult and aged humans. A PCR assay that measures CDR3 length in the majority of mu-heavy chains showed the same average size and normal range of CDR3 length in aged individuals as observed in young adults. To characterize the features of junctional diversity of aged adults in more detail, we determined the CDR3 sequences of a subset of the mu-heavy chain repertoire that utilizes members of the VH 5 family. In general CDR3 length, D family usage, and JH gene usage were similar in aged compared to young adults. Thus, in contrast to dramatic changes in heavy chain junctional diversity associated with fetal to adult development, no major differences were found between young and aged adults. Since the CDR3 repertoire generated in aged individuals appears to be as diverse as that observed in younger adults, the decline in humoral immunocompetence with aging cannot be attributed to a restriction in heavy chain junctional diversification processes.

Adult↗

PubMed1999

In vitro selection of RNA aptamers that bind special elongation factor SelB, a protein with multiple RNA-binding sites, reveals one major interaction domain at the carboxyl terminus.

The SelB protein of Escherichia coli is a special elongation factor required for the cotranslational incorporation of the uncommon amino acid selenocysteine into proteins such as formiate dehydrogenases. To do this, SelB binds simultaneously to selenocysteyl-tRNA(Sec) and to an RNA hairpin structure in the mRNA of formiate dehydrogenases located directly 3' of the selenocysteine opal (UGA) codon. The protein is also thought to contain binding sites allowing its interaction with ribosomal proteins and/or rRNA. SelB thus includes specific binding sites for a variety of different RNA molecules. We used an in vitro selection approach with a pool completely randomized at 40 nt to isolate new high-affinity SelB-binding RNA motifs. Our main objective was to investigate which of the various RNA-binding domains in SelB would turn out to be prime targets for aptamer interaction. The resulting sequences were compared with those from a previous SELEX experiment using a degenerate pool of the wild-type formiate dehydrogenase H (fdhF) hairpin sequence (Klug SJ et al., 1997, Proc. Natl. Acad. Sci. USA 94:6676-6681). In four selection cycles an enriched pool of tight SelB-binding aptamers was obtained; sequencing revealed that all aptamers were different in their primary sequence and most bore no recognizable consensus to known RNA motifs. Domain mapping for SelB-binding aptamers showed that despite the different RNA-binding sites in the protein, the vast majority of aptamers bound to the ultimate C-terminus of SelB, the domain responsible for mRNA hairpin binding.

Bacterial Proteins↗

PubMed1998

Complete nucleotide sequence of the genomic RNA of tobacco mosaic virus strain Cg.

Tobacco mosaic virus (TMV)-Cg is a crucifer-infecting tobamovirus that was isolated from field-grown garlic. We determined the complete nucleotide sequence of the genomic RNA of TMV-Cg. The genomic RNA of TMV-Cg consists of 6303 nucleotides and encodes four large open reading frames, organized basically in the same way as that of other tobamoviruses. The nucleotide and deduced amino acid sequences are very similar to those of the other crucifer-infecting tobamoviruses that have been sequenced so far.

Amino Acid Sequence↗