scholarly journals Evolution and Characterization of Tetraonine Endogenous Retrovirus: a New Virus Related to Avian Sarcoma and Leukosis Viruses

2001 ◽  
Vol 75 (4) ◽  
pp. 2002-2009 ◽  
Author(s):  
Derek E. Dimcheff ◽  
Mallika Krishnan ◽  
David P. Mindell
Keyword(s):  
Southern Blotting ◽  
Phylogenetic Analyses ◽  
Endogenous Retrovirus ◽  
Pcr Analysis ◽  
Bonasa Umbellus ◽  
Long Terminal Repeats ◽  
Proviral Sequence ◽  
Reverse Transcription Pcr ◽  
Avian Sarcoma

ABSTRACT In a previous study, we found avian sarcoma and leukosis virus (ASLV) gag genes in 19 species of birds in the order Galliformes including all grouse and ptarmigan (Tetraoninae) surveyed. Our data suggested that retroviruses had been transmitted horizontally among some host species. To further investigate these elements, we sequenced a replication-defective retrovirus, here named tetraonine endogenous retrovirus (TERV), from Bonasa umbellus (ruffed grouse). This is the first report of a complete, replication-defective ASLV provirus sequence from any bird other than the domestic chicken. We found a replication-defective proviral sequence consisting of putative Gag and Env proteins flanked by long terminal repeats. Reverse transcription-PCR analysis showed that retroviral gagsequences closely related to TERV are transcribed, supporting the hypothesis that TERV is an active endogenous retrovirus. Phylogenetic analyses suggest that TERV may have arisen via recombination between different retroviral lineages infecting birds. Southern blotting usinggag probes showed that TERV occurs in tetraonines but not in chickens or ducks, suggesting that integration occurred after the earliest phasianid divergences but prior to the radiation of tetraonine birds.

scholarly journals Human Endogenous Retrovirus HERV-K14 Families: Status, Variants, Evolution, and Mobilization of Other Cellular Sequences

2005 ◽  
Vol 79 (5) ◽  
pp. 2941-2949 ◽  
Author(s):  
Aline Flockerzi ◽  
Stefan Burkhardt ◽  
Werner Schempp ◽  
Eckart Meese ◽  
Jens Mayer
Keyword(s):  
Human Genome ◽  
Germ Line ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retrovirus ◽  
Long Terminal Repeats ◽  
Essential Information ◽  
Human Endogenous Retroviruses ◽  
Consensus Sequences

ABSTRACT The human genome harbors many distinct families of human endogenous retroviruses (HERVs) that stem from exogenous retroviruses that infected the germ line millions of years ago. Many HERV families remain to be investigated. We report in the present study the detailed characterization of the HERV-K14I and HERV-K14CI families as they are represented in the human genome. Most of the 68 HERV-K14I and 23 HERV-K14CI proviruses are severely mutated, frequently displaying uniform deletions of retroviral genes and long terminal repeats (LTRs). Both HERV families entered the germ line ∼39 million years ago, as evidenced by homologous sequences in hominoids and Old World primates and calculation of evolutionary ages based on a molecular clock. Proviruses of both families were formed during a brief period. A majority of HERV-K14CI proviruses on the Y chromosome mimic a higher evolutionary age, showing that LTR-LTR divergence data can indicate false ages. Fully translatable consensus sequences encoding major retroviral proteins were generated. Most HERV-K14I loci lack an env gene and are structurally reminiscent of LTR retrotransposons. A minority of HERV-K14I variants display an env gene. HERV-K14I proviruses are associated with three distinct LTR families, while HERV-K14CI is associated with a single LTR family. Hybrid proviruses consisting of HERV-K14I and HERV-W sequences that appear to have produced provirus progeny in the genome were detected. Several HERV-K14I proviruses harbor TRPC6 mRNA portions, exemplifying mobilization of cellular transcripts by HERVs. Our analysis contributes essential information on two more HERV families and on the biology of HERV sequences in general.

scholarly journals Molecular Characterization of Bacteriophages for Microbial Source Tracking in Korea

2009 ◽  
Vol 75 (22) ◽  
pp. 7107-7114 ◽  
Author(s):  
Jung Eun Lee ◽  
Mi Young Lim ◽  
Sei Yoon Kim ◽  
Sunghee Lee ◽  
Heetae Lee ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Phylogenetic Analyses ◽  
Microbial Source Tracking ◽  
Group Iv ◽  
Source Tracking ◽  
Fecal Samples ◽  
Human Waste ◽  
Reverse Transcription Pcr ◽  
Group I

ABSTRACT We investigated coliphages from various fecal sources, including humans and animals, for microbial source tracking in South Korea. Both somatic and F+-specific coliphages were isolated from 43 fecal samples from farms, wild animal habitats, and human wastewater plants. Somatic coliphages were more prevalent and abundant than F+ coliphages in all of the tested fecal samples. We further characterized 311 F+ coliphage isolates using RNase sensitivity assays, PCR and reverse transcription-PCR, and nucleic acid sequencing. Phylogenetic analyses were performed based on the partial nucleic acid sequences of 311 F+ coliphages from various sources. F+ RNA coliphages were most prevalent among geese (95%) and were least prevalent in cows (5%). Among the genogroups of F+ RNA coliphages, most F+ coliphages isolated from animal fecal sources belonged to either group I or group IV, and most from human wastewater sources were in group II or III. Some of the group I coliphages were present in both human and animal source samples. F+ RNA coliphages isolated from various sources were divided into two main clusters. All F+ RNA coliphages isolated from human wastewater were grouped with Qβ-like phages, while phages isolated from most animal sources were grouped with MS2-like phages. UniFrac significance statistical analyses revealed significant differences between human and animal bacteriophages. In the principal coordinate analysis (PCoA), F+ RNA coliphages isolated from human waste were distinctively separate from those isolated from other animal sources. However, F+ DNA coliphages were not significantly different or separate in the PCoA. These results demonstrate that proper analysis of F+ RNA coliphages can effectively distinguish fecal sources.

scholarly journals Characterization of the Protocatechuate 4,5-Cleavage Pathway Operon in Comamonas sp. Strain E6 and Discovery of a Novel Pathway Gene

2010 ◽  
Vol 76 (24) ◽  
pp. 8093-8101 ◽  
Author(s):  
Naofumi Kamimura ◽  
Taichi Aoyama ◽  
Rieko Yoshida ◽  
Kenji Takahashi ◽  
Daisuke Kasai ◽  
...  
Keyword(s):  
Growth Defect ◽  
Pcr Analysis ◽  
Aromatic Acids ◽  
Transcription Start ◽  
Reverse Transcription Pcr ◽  
Degrading Bacterium ◽  
Pathway Gene ◽  
Insertional Inactivation ◽  
Dioxygenase Gene

ABSTRACT The protocatechuate (PCA) 4,5-cleavage (PCA45) pathway is the essential catabolic route for the degradation of various aromatic acids in the genus Comamonas. All of the PCA45 pathway genes, orf1-pmdKEFDABC, as well as another PCA 4,5-dioxygenase gene, pmdA II B II, were isolated from a phthalate-degrading bacterium, Comamonas sp. strain E6. Disruption of pmdB and pmdD in E6, which code for the β subunit of PCA 4,5-dioxygenase and 2-pyrone-4,6-dicarboxylate (PDC) hydrolase, respectively, resulted in a growth defect on PCA, indicating that these genes are essential for the growth of E6 on PCA. On the other hand, inactivation of pmdB II did not affect the growth of E6 on PCA. Disruption of pmdK, which is related to a 4-hydroxybenzoate/PCA transporter of Pseudomonas putida, resulted in growth retardation on PCA. The insertional inactivation of orf1 in E6, whose deduced amino acid sequence has no similarity with proteins of known function, led to the complete loss of growth on PCA and the accumulation of PDC and 4-oxalomesaconate (OMA) from PCA. These results indicated the involvement of orf1 in the PCA45 pathway, and this gene, designated pmdU, was suggested to code for OMA tautomerase. Reverse transcription-PCR analysis suggested that the pmdUKEFDABC genes constitute an operon. The transcription start site of the pmd operon was mapped at 167 nucleotides upstream of the initiation codon of pmdU. The pmd promoter activity was enhanced 20-fold when the cells were grown in the presence of PCA. Inducers of the pmd operon were found to be PCA and PDC, but PDC was the more effective inducer.

scholarly journals Molecular Identification of Enteroviruses from Cattle and Goat Feces and Environment in Thailand

2018 ◽  
Vol 85 (5) ◽  
Author(s):  
Nicharee Income ◽  
Nathamon Kosoltanapiwat ◽  
Sarawut Taksinoros ◽  
Pornsawan Leaungwutiwong ◽  
Pannamas Maneekan ◽  
...  
Keyword(s):  
Water Samples ◽  
Phylogenetic Analyses ◽  
Study Region ◽  
Reverse Transcription Pcr ◽  
Porcine Enterovirus ◽  
New Genotype ◽  
Mdbk Cells ◽  
Chicken Feces ◽  
Feces Analysis

ABSTRACTThe identification and characterization of viruses of the genusEnterovirusin healthy and infected livestock, including cattle and goats, have been increasing.Enterovirus E(EV-E) andEnterovirus F(EV-F) are commonly found in cattle, whereasEnterovirus G(EV-G) is found in goats. In this study, molecular and phylogenetic analyses were performed to determine the prevalence of EVs in cattle and goat feces from Kanchanaburi Province, Thailand. The presence of EVs in water samples and the feces of other animals collected from the areas surrounding cattle and goat farms was also investigated. By use of 5′-untranslated region (5′ UTR) real-time reverse transcription-PCR (RT-PCR), EVs were detected in 39.5% of cattle samples, 47% of goat samples, 35.3% of water samples, and one pool of chicken feces. Phylogenetic analysis revealed the presence of EV-E and EV-F in cattle, EV-E and EV-G in goats, and EV-F in water samples and chicken feces. Analysis of enteroviral VP1 sequences from cattle revealed that the EV-E genotypes circulating in the study region were EV-E1, with a possible new genotype that is closely related to EV-E2. Analysis of enteroviral VP1 sequences from goats suggested the circulation of EV-G5 and a possible new genotype that is closely related to EV-G20. Sequence analyses also suggested that although the VP1 sequences from goats were closely related to those of EV-G, which were considered porcine enterovirus sequences, their 5′ UTRs form a separated cluster with sequences of sheep and goat origin, suggesting a new classification of the ovine/caprine-specific enterovirus group.IMPORTANCEPossible new EV-E and EV-G genotypes were identified for EVs detected in this study. The EV-E viruses were also successfully isolated from MDBK cells. The goat EV sequence analysis suggested the presence of an ovine/caprine-specific EV group that is different from EV-G of porcine origin. The significance of our research is that it identifies and characterizes possible novel EVs, thereby indicating that enteroviruses in animals are continually evolving. The facts that enteroviruses can persist in the environment, contaminate it for long periods, and be transmitted between animals raise serious concerns regarding this group of viruses as emerging livestock pathogens.

scholarly journals Comprehensive Genomic Analysis and Expression Profiling of Diacylglycerol Kinase (DGK) Gene Family in Soybean (Glycine max) under Abiotic Stresses

2019 ◽  
Vol 20 (6) ◽  
pp. 1361 ◽  
Author(s):  
Kue Carther ◽  
Toi Ketehouli ◽  
Nan Ye ◽  
Yan-Hai Yang ◽  
Nan Wang ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Expression Profiling ◽  
Phylogenetic Analyses ◽  
Functional Characterization ◽  
Genomic Analysis ◽  
Diacylglycerol Kinase ◽  
Soybean Genome ◽  
Pcr Analysis

Diacylglycerol kinase (DGK) is an enzyme that plays a pivotal role in abiotic and biotic stress responses in plants by transforming the diacylglycerol into phosphatidic acid. However, there is no report on the characterization of soybean DGK genes in spite of the availability of the soybean genome sequence. In this study, we performed genome-wide analysis and expression profiling of the DGK gene family in the soybean genome. We identified 12 DGK genes (namely GmDGK1-12) which all contained conserved catalytic domains with protein lengths and molecular weights ranging from 436 to 727 amino acids (aa) and 48.62 to 80.93 kDa, respectively. Phylogenetic analyses grouped GmDGK genes into three clusters—cluster I, cluster II, and cluster III—which had three, four, and five genes, respectively. The qRT-PCR analysis revealed significant GmDGK gene expression levels in both leaves and roots coping with polyethylene glycol (PEG), salt, alkali, and salt/alkali treatments. This work provides the first characterization of the DGK gene family in soybean and suggests their importance in soybean response to abiotic stress. These results can serve as a guide for future studies on the understanding and functional characterization of this gene family.

scholarly journals Cloning and expression of a novel Mu class murine glutathione transferase isoenzyme

2002 ◽  
Vol 366 (3) ◽  
pp. 817-824 ◽  
Author(s):  
Jianxia GUO ◽  
Ludwika ZIMNIAK ◽  
Piotr ZIMNIAK ◽  
John L. ORCHARD ◽  
Shivendra V. SINGH
Keyword(s):  
Small Intestine ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Glutathione Transferase ◽  
Cloning And Expression ◽  
Pcr Analysis ◽  
Amino Acid Residues ◽  
Reverse Transcription Pcr ◽  
Mouse Small Intestine

The present study describes the cDNA cloning, expression and characterization of a novel Mu class murine glutathione transferase (GST) isoenzyme. Screening of a cDNA library from the small intestine of a female A/J mouse using consensus probes derived from Mu class murine GST genes (mGSTM1—mGSTM5) resulted in the isolation of a full-length cDNA clone of a previously unknown Mu class GST gene (designated as mGSTM7). The choice of tissue was based on our previous identification in female A/J mouse small intestine of a potentially novel Mu class GST isoenzyme. The deduced amino acid sequence of mGSTM7, which comprises of 218 amino acid residues, exhibited about 67—78% identity with other Mu class murine GSTs. Recombinant mGSTM7-7 cross-reacted with anti-(GST Mu) antibodies, but not with anti-(GST Alpha) or anti-(GST Pi) antibodies. The pI and the reverse-phase-HPLC elution profile of recombinant mGSTM7-7 were different from those of other Mu class murine GSTs. The substrate specificity of mGSTM7-7 was also different compared with other Mu class murine GSTs. Interestingly, mGSTM7 had a higher identity with the human Mu class isoenzyme hGSTM4 (87% identity and 94% similarity in the amino acid sequence) than with any of the known mouse Mu class GSTs. Specific activities of recombinant mGSTM7-7 and human GSTM4-4 were comparable towards several substrates. For example, similar to hGSTM4-4, recombinant mGSTM7-7 was poorly active in catalysing the GSH conjugation of 1-chloro-2,4-dinitrobenzene and ethacrynic acid, and lacked activity towards 1,2-dichloro-4-nitrobenzene and 1,2-epoxy-3-(p-nitrophenoxy)propane. These results suggested that hGSTM4-4 might be the human counterpart of mouse GSTM7-7. Reverse transcription-PCR analysis using mGSTM7-specific primers revealed that mGSTM7 is widely expressed in tissues of female A/J mice, including liver, forestomach, lung, kidney, colon and spleen.

scholarly journals Discovery of a Novel Murine Type C Retrovirus by Data Mining

2001 ◽  
Vol 75 (6) ◽  
pp. 3053-3057 ◽  
Author(s):  
Lindell Bromham ◽  
Francis Clark ◽  
Jeff J. McKee
Keyword(s):  
Leukemia Virus ◽  
Endogenous Retrovirus ◽  
Expression Data ◽  
Long Terminal Repeats ◽  
Mouse Tissues ◽  
Recombinant Type ◽  
Multiple Copies ◽  
Type C ◽  
Identification And Characterization

ABSTRACT Analysis of genomic and expression data allows both identification and characterization of novel retroviruses. We describe a recombinant type C murine retrovirus, similar to the Mus dunni endogenous retrovirus, with VL30-like long terminal repeats and murine leukemia virus-like coding sequences. This virus is present in multiple copies in the mouse genome and expressed in a range of mouse tissues.

scholarly journals Identification and Characterization of a Repeat-in-Toxin Gene Cluster in Vibrio anguillarum

2008 ◽  
Vol 76 (6) ◽  
pp. 2620-2632 ◽  
Author(s):  
Ling Li ◽  
Jessica L. Rock ◽  
David R. Nelson
Keyword(s):  
Atlantic Salmon ◽  
Gene Cluster ◽  
Vibrio Anguillarum ◽  
Hypothetical Protein ◽  
Pcr Analysis ◽  
Toxin Gene ◽  
Reverse Transcription Pcr ◽  
Hemolysin Gene ◽  
Negative Mutant

ABSTRACT Vibrio anguillarum is the causative agent of vibriosis in fish. Hemolysins of V. anguillarum have been considered virulence factors during infection. One hemolysin gene, vah1, has been previously identified but does not account for all hemolytic activity. The mini-Tn10Km mutagenesis performed with a vah1 mutant resulted in a hemolysin-negative mutant. The region surrounding the mutation was cloned and sequenced, revealing a putative rtx operon with six genes (rtxACHBDE), where rtxA encodes an exotoxin, rtxC encodes an RtxA activator, rtxH encodes a conserved hypothetical protein, and rtxBDE encode the ABC transporters. Single mutations in rtx genes did not result in a hemolysin-negative phenotype. However, strains containing a mutation in vah1 and a mutation in an rtx gene resulted in a hemolysin-negative mutant, demonstrating that the rtx operon is a second hemolysin gene cluster in V. anguillarum M93Sm. Reverse transcription-PCR analysis revealed that the rtxC and rtxA genes are cotranscribed, as are the rtxBDE genes. Additionally, Vah1 and RtxA each have cytotoxic activity against Atlantic salmon kidney (ASK) cells. Single mutations in vah1 or rtxA attenuate the cytotoxicity of V. anguillarum M93Sm. A vah1 rtxA double mutant is no longer cytotoxic. Moreover, Vah1 and RtxA each have a distinct cytotoxic effect on ASK cells, Vah1 causes cell vacuolation, and RtxA causes cell rounding. Finally, wild-type and mutant strains were tested for virulence in juvenile Atlantic salmon. Only strains containing an rtxA mutation had reduced virulence, suggesting that RtxA is a major virulence factor for V. anguillarum.

scholarly journals Endogenization of a Prosimian Retrovirus during Lemur Evolution

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 383
Author(s):  
Kathleen Apakupakul ◽  
Sharon L. Deem ◽  
Rabia Maqsood ◽  
Peeti Sithiyopasakul ◽  
David Wang ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Animal Health ◽  
Endogenous Retrovirus ◽  
Endogenous Retroviruses ◽  
Evolutionary Context ◽  
History Of ◽  
Clock Analysis ◽  
Host Virus Interactions ◽  
Virus Interactions

Studies of viruses that coevolved with lemurs provide an opportunity to understand the basal traits of primate viruses and provide an evolutionary context for host-virus interactions. Germline integration of endogenous retroviruses (ERVs) are fossil evidence of past infections. Hence, characterization of novel ERVs provides insight into the ancient precursors of extant viruses and the evolutionary history of their hosts. Here, we report the discovery of a novel endogenous retrovirus present in the genome of a lemur, Coquerel’s sifaka (Propithecus coquereli). Using next-generation sequencing, we identified and characterized the complete genome sequence of a retrovirus, named prosimian retrovirus 1 (PSRV1). Phylogenetic analyses indicate that PSRV1 is a gamma-type betaretrovirus basal to the other primate betaretroviruses and most closely related to simian retroviruses. Molecular clock analysis of PSRV1 long terminal repeat (LTR) sequences estimated the time of endogenization within 4.56 MYA (±2.4 MYA), placing it after the divergence of Propithecus species. These results indicate that PSRV1 is an important milestone of lemur evolution during the radiation of the Propithecus genus. These findings may have implications for both human and animal health in that the acquisition of a gamma-type env gene within an endogenized betaretrovirus could facilitate a cross-species jump between vertebrate class hosts.

Characterization of Partial Gene Deletions in Type III von Willebrand Disease with Alloantibody Inhibitors

1994 ◽  
Vol 72 (02) ◽  
pp. 180-185 ◽  
Author(s):  
David J Mancuso ◽  
Elodee A Tuley ◽  
Ricardo Castillo ◽  
Norma de Bosch ◽  
Pler M Mannucci ◽  
...  
Keyword(s):  
Von Willebrand Factor ◽  
Von Willebrand Disease ◽  
Pcr Analysis ◽  
Gene Deletions ◽  
Factor Gene ◽  
Type Iii ◽  
Large Deletions ◽  
Von Willebrand ◽  
Willebrand Factor

Summaryvon Willebrand factor gene deletions were characterized in four patients with severe type III von Willebrand disease and alloantibodies to von Willebrand factor. A PCR-based strategy was used to characterize the boundaries of the deletions. Identical 30 kb von Willebrand factor gene deletions which include exons 33 through 38 were identified in two siblings of one family by this method. A small 5 base pair insertion (CCTGG) was sequenced at the deletion breakpoint. PCR analysis was used to detect the deletion in three generations of the family, including two family members who are heterozygous for the deletion. In a second family, two type III vWD patients, who are distant cousins, share an -56 kb deletion of exons 22 through 43. The identification and characterization of large vWF gene deletions in these type III vWD patients provides further support for the association between large deletions in both von Willebrand factor alleles and the development of inhibitory alloantibodies.

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