Identification and genomic characterization of a novel fish reovirus, Hubei grass carp disease reovirus, isolated in 2009 in China

2013 ◽  
Vol 94 (10) ◽  
pp. 2266-2277 ◽  
Author(s):  
Yuding Fan ◽  
Shujing Rao ◽  
Lingbing Zeng ◽  
Jie Ma ◽  
Yong Zhou ◽  
...  
Keyword(s):  
Amino Acid ◽  
Grass Carp ◽  
Sequence Similarity ◽  
Amino Acid Level ◽  
Amino Acid Sequences ◽  
Full Genome Sequence ◽  
Total Size ◽  
The Family ◽  
Genomic Characterization

A novel fish reovirus, Hubei grass carp disease reovirus (HGDRV; formerly grass carp reovirus strain 104, GCRV104), was isolated from diseased grass carp in China in 2009 and the full genome sequence was determined. This reovirus was propagated in a grass carp kidney cell line with a typical cytopathic effect. The total size of the genome was 23 706 bp with a 51 mol% G+C content, and the 11 dsRNA segments encoded 12 proteins (two proteins encoded by segment 11). A nucleotide sequence similarity search using blastn found no significant matches except for segment 2, which partially matched that of the RNA-dependent RNA polymerase (RdRp) from several viruses in the genera Aquareovirus and Orthoreovirus of the family Reoviridae. At the amino acid level, seven segments (Seg-1 to Seg-6, and Seg-8) matched with species in the genera Aquareovirus (15–46 % identities) and Orthoreovirus (12–44 % identities), while for four segments (Seg-7, Seg-9, Seg-10 and Seg-11) no similarities in these genera were found. Conserved terminal sequences, 5′-GAAUU----UCAUC-3′, were found in each HGDRV segment at the 5′ and 3′ ends, and the 5′-terminal nucleotides were different from any known species in the genus Aquareovirus. Phylogenetic analysis based on RdRp amino acid sequences from members of the family Reoviridae showed that HGDRV clustered with aquareoviruses prior to joining a branch common with orthoreoviruses. Based on these observations, we propose that HGDRV is a new species in the genus Aquareovirus that is distantly related to any known species within this genus.

scholarly journals Identification and genome characterization of Heliothis armigera cypovirus types 5 and 14 and Heliothis assulta cypovirus type 14

2006 ◽  
Vol 87 (2) ◽  
pp. 387-394 ◽  
Author(s):  
Yang Li ◽  
Li Tan ◽  
Yanqiu Li ◽  
Wuguo Chen ◽  
Jiamin Zhang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Heliothis Armigera ◽  
Amino Acid Sequences ◽  
Nucleotide Sequencing ◽  
Sequencing Analysis ◽  
Electrophoretic Patterns ◽  
The Family ◽  
Genomic Characterization

Genomic characterization of Heliothis armigera cypovirus (HaCPV) isolated from China showed that insects were co-infected with several cypoviruses (CPVs). One of the CPVs (HaCPV-5) could be separated from the others by changing the rearing conditions of the Heliothis armigera larvae. This finding was further confirmed by nucleotide sequencing analysis. Genomic sequences of segments S10–S7 from HaCPV-14, S10 and S7 from HaCPV-5, and S10 from Heliothis assulta CPV-14 were compared. Results from database searches showed that the nucleotide sequences and deduced amino acid sequences of the newly identified CPVs had high levels of identity with those of reported CPVs of the same type, but not with CPVs of different types. Putative amino acid sequences of HaCPV-5 S7 were similar to that of the protein from Rice ragged stunt virus (genus Oryzavirus, family Reoviridae), suggesting that CPVs and oryzaviruses are related more closely than other genera of the family Reoviridae. Conserved motifs were also identified at the ends of each RNA segment of the same virus type: type 14, 5′-AGAAUUU…CAGCU-3′; and type 5, 5′-AGUU…UUGC-3′. Our results are consistent with classification of CPV types based on the electrophoretic patterns of CPV double-stranded RNA.

scholarly journals Identification and Molecular Characterization of a Novel Partitivirus from Trichoderma atroviride NFCF394

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 578 ◽  
Author(s):  
Jeesun Chun ◽  
Han-Eul Yang ◽  
Dae-Hyuk Kim
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Molecular Characteristics ◽  
Trichoderma Atroviride ◽  
Double Stranded Rna ◽  
Reading Frame ◽  
Viral Particles ◽  
The Family ◽  
Isogenic Strains

An increasing number of novel mycoviruses have been described in fungi. Here, we report the molecular characteristics of a novel bisegmented double-stranded RNA (dsRNA) virus from the fungus Trichoderma atroviride NFCF394. We designated this mycovirus as Trichoderma atroviride partitivirus 1 (TaPV1). Electron micrographs of negatively stained, purified viral particles showed an isometric structure approximately of 30 nm in diameter. The larger segment (dsRNA1) of the TaPV1 genome comprised 2023 bp and contained a single open reading frame (ORF) encoding 614 amino acid (AA) residues of RNA-dependent RNA polymerase (RdRp). The smaller segment (dsRNA2) consisted of 2012 bp with a single ORF encoding 577 AA residues of capsid protein (CP). The phylogenetic analysis, based on deduced amino acid sequences of RdRp and CP, indicated that TaPV1 is a new member of the genus Alphapartitivirus in the family Partitiviridae. Virus-cured isogenic strains did not show significant changes in colony morphology. In addition, no changes in the enzymatic activities of β-1,3-glucanase and chitinase were observed in virus-cured strains. To the best of our knowledge, this is the first report of an Alphapartitivirus in T. atroviride.

Characterization of a type D1A EUL-related lectin from rice expressed in Pichia pastoris

2014 ◽  
Vol 395 (4) ◽  
pp. 413-424 ◽  
Author(s):  
Bassam Al Atalah ◽  
Dieter Vanderschaeghe ◽  
Yehudi Bloch ◽  
Paul Proost ◽  
Kirsten Plas ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Recombinant Proteins ◽  
Sequence Similarity ◽  
Full Length ◽  
Carbohydrate Binding ◽  
Terminal Sequence ◽  
The Family ◽  
Carbohydrate Binding Site

Abstract OrysaEULD1A is one of the five EUL genes in rice (Oryza sativa) encoding a putative carbohydrate-binding protein belonging to the family of Euonymus related lectins (EUL). The OrysaEULD1A sequence comprises two highly similar EUL domains (91% sequence similarity and 72% sequence identity) separated by a 23 amino acid linker sequence and preceded by a 19 amino acid N-terminal sequence. In the present study, the full-length protein OrysaEULD1A as well as its individual domains OrysaEULD1A domain 1 and 2 were expressed in Pichiapastoris. After purification of the recombinant proteins, their carbohydrate-binding specificity was analyzed and compared. Interestingly, all recombinant lectins showed clear specificity towards galactosylated structures. Furthermore, all recombinant proteins agglutinated red blood cells, indicating that the full-length protein OrysaEULD1A and its domains are true lectins. These results taken together with data previously reported for single-domain EUL proteins indicate that although the amino acids – responsible for the formation of the carbohydrate-binding site – are identical for all EUL proteins in rice, these lectins show different carbohydrate specificities. This promiscuity of the carbohydrate-binding site can be attributed to gene divergence.

scholarly journals First Report on Co-isolation and Whole-genomic Characterization of Mammalian Orthorubulavirus 5 and Mammalian Orthoreovirus Type-3 From Domestic Pigs in India

2022 ◽  
Author(s):  
Fateh Singh ◽  
Katherukamem Rajukumar ◽  
Dhanapal Senthilkumar ◽  
Govindarajulu Venkatesh ◽  
Deepali Srivast ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genetic Analysis ◽  
Amino Acid Sequences ◽  
Nucleotide Identity ◽  
Domestic Pigs ◽  
S1 Gene ◽  
Mammalian Orthoreovirus ◽  
Genomic Characterization ◽  
Type 3

Abstract During a surveillance study to monitor porcine epidemic diarrohoea virus and transmissible gastroenteritis virus in India, a total of 1043 swine samples including faeces (n=264) and clotted blood (n=779) were collected and tested. Five samples (four faecal and one serum) showed cytopathic effects in Vero cells. Transmission electron microscopy of infective cell supernatant revealed the presence of two types of virions. Next generation sequencing (de novo) enabled complete genome assembly of Mammalian orthorubulavirus 5 (MRuV5; 15246 bp) and all 10 gene segments of Mammalian orthoreovirus (MRV; 22219 bp and 20512 bp). Genetic analysis of the MRuV5 revealed grouping of the Indian MRuV5 with those isolated from various mammalian species in South Korea and China, sharing more than 99% nucleotide identity. Deduced amino acid sequences of the HN, NP and F genes of MRuV5 isolates showed three (92L, 111R, 447H), two (86S, 121S) and two (139T, 246T) amino acid substitutions, respectively, compared to previously reported virus strains. The Indian MRV isolates were identified as MRV type-3 based on genetic analysis of S1 gene, showing the highest nucleotide identity (97.73%) with the MRV3 strain ZJ2013 isolated from pigs in China. Deduced amino acid sequences of MRV3 S1 gene revealed amino acid residues 198-204NLAIRLP, 249I, 340D, 419E known for sialic acid binding and neurotropism. We report the co-isolation and whole-genomic characterization of MRuV5 and MRV3 recorded incidentally for the first time from domestic pigs in India. It attracts attention to perform detailed surveillance studies and continuous monitoring of evolution and spread of emerging viruses, which may have pathogenic potential in animal and human hosts.

scholarly journals Isolation, Identification, and Genomic Analysis of a Novel Reovirus from Healthy Grass Carp and Its Dynamic Proliferation In Vitro and In Vivo

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 690
Author(s):  
Ke Zhang ◽  
Wenzhi Liu ◽  
Yiqun Li ◽  
Yong Zhou ◽  
Yan Meng ◽  
...  
Keyword(s):  
Cell Lines ◽  
Grass Carp ◽  
Amino Acid Sequences ◽  
Gibel Carp ◽  
Fish Cell ◽  
Fish Cell Lines ◽  
Total Size ◽  
Sequence Comparisons ◽  
Grass Carp Reovirus

A new grass carp reovirus (GCRV), healthy grass carp reovirus (HGCRV), was isolated from grass carp in 2019. Its complete genome sequence was determined and contained 11 dsRNAs with a total size of 23,688 bp and 57.2 mol% G+C content, encoding 12 proteins. All segments had conserved 5' and 3' termini. Sequence comparisons showed that HGCRV was closely related to GCRV-873 (GCRV-I; 69.57–96.71% protein sequence identity) but shared only 22.65–45.85% and 23.37–43.39% identities with GCRV-HZ08 and Hubei grass carp disease reovirus (HGDRV), respectively. RNA-dependent RNA-polymerase (RdRp) protein-based phylogenetic analysis showed that HGCRV clustered with Aquareovirus-C (AqRV-C) prior to joining a branch common with other aquareoviruses. Further analysis using VP6 amino acid sequences from Chinese GCRV strains showed that HGCRV was in the same evolutionary cluster as GCRV-I. Thus, HGCRV could be a new GCRV isolate of GCRV-I but is distantly related to other known GCRVs. Grass carp infected with HGCRV did not exhibit signs of hemorrhage. Interestingly, the isolate induced a typical cytopathic effect in fish cell lines, such as infected cell shrank, apoptosis, and plague-like syncytia. Further analysis showed that HGCRV could proliferate in grass carp liver (L28824), gibel carp brain (GiCB), and other fish cell lines, reaching a titer of up to 7.5 × 104 copies/μL.

scholarly journals Characterization of the Gallate Dioxygenase Gene: Three Distinct Ring Cleavage Dioxygenases Are Involved in Syringate Degradation by Sphingomonas paucimobilis SYK-6

2005 ◽  
Vol 187 (15) ◽  
pp. 5067-5074 ◽  
Author(s):  
Daisuke Kasai ◽  
Eiji Masai ◽  
Keisuke Miyauchi ◽  
Yoshihiro Katayama ◽  
Masao Fukuda
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Terminal Region ◽  
Ring Cleavage ◽  
Sphingomonas Paucimobilis ◽  
Acid Protein ◽  
Demethylation Pathway ◽  
Dioxygenase Gene ◽  
Amino Acid Protein

ABSTRACT Sphingomonas paucimobilis SYK-6 converts vanillate and syringate to protocatechuate (PCA) and 3-O-methylgallate (3MGA) in reactions with the tetrahydrofolate-dependent O-demethylases LigM and DesA, respectively. PCA is further degraded via the PCA 4,5-cleavage pathway, whereas 3MGA is metabolized via three distinct pathways in which PCA 4,5-dioxygenase (LigAB), 3MGA 3,4-dioxygenase (DesZ), and 3MGA O-demethylase (LigM) are involved. In the 3MGA O-demethylation pathway, LigM converts 3MGA to gallate, and the resulting gallate appears to be degraded by a dioxygenase other than LigAB or DesZ. Here, we isolated the gallate dioxygenase gene, desB, which encodes a 418-amino-acid protein with a molecular mass of 46,843 Da. The amino acid sequences of the N-terminal region (residues 1 to 285) and the C-terminal region (residues 286 to 418) of DesB exhibited ca. 40% and 27% identity with the sequences of the PCA 4,5-dioxygenase β and α subunits, respectively. DesB produced in Escherichia coli was purified and was estimated to be a homodimer (86 kDa). DesB specifically attacked gallate to generate 4-oxalomesaconate as the reaction product. The Km for gallate and the V max were determined to be 66.9 ± 9.3 μM and 42.7 ± 2.4 U/mg, respectively. On the basis of the analysis of various SYK-6 mutants lacking the genes involved in syringate degradation, we concluded that (i) all of the three-ring cleavage dioxygenases are involved in syringate catabolism, (ii) the pathway involving LigM and DesB plays an especially important role in the growth of SYK-6 on syringate, and (iii) DesB and LigAB are involved in gallate degradation.

An intergenic G-rich region in Leishmania tarentolae kinetoplast maxicircle DNA is a pan-edited cryptogene encoding ribosomal protein S12

1992 ◽  
Vol 12 (1) ◽  
pp. 56-67
Author(s):  
D A Maslov ◽  
N R Sturm ◽  
B M Niner ◽  
E S Gruszynski ◽  
M Peris ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Sequence Similarity ◽  
Rich Region ◽  
Leishmania Tarentolae ◽  
Significant Sequence Similarity ◽  
The Family ◽  
Intergenic Regions ◽  
Ribosomal Protein S12

Six short G-rich intergenic regions in the maxicircle of Leishmania tarentolae are conserved in location and polarity in two other kinetoplastid species. We show here that G-rich region 6 (G6) represents a pan-edited cryptogene which contains at least two domains edited independently in a 3'-to-5' manner connected by short unedited regions. In the completely edited RNA, 117 uridines are added at 49 sites and 32 uridines are deleted at 13 sites, creating a translated 85-amino-acid polypeptide. Similar polypeptides are probably encoded by pan-edited G6 transcripts in two other species. The G6 polypeptide has significant sequence similarity to the family of S12 ribosomal proteins. A minicircle-encoded gRNA overlaps 12 editing sites in G6 mRNA, and chimeric gRNA/mRNA molecules were shown to exist, in agreement with the transesterification model for editing.

Complete Genome Sequence of a Novel Ourmia-like Mycovirus Infecting the Phytopathogenic Fungus Botryosphaeria Dothidea

2021 ◽  
Author(s):  
Liying Sun ◽  
Ziqian Lian ◽  
Subha Das ◽  
Jingxian Luo ◽  
Ida Bagus Andika
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Amino Acid Sequences ◽  
Shanxi Province ◽  
Phytopathogenic Fungus ◽  
Botryosphaeria Dothidea ◽  
Reading Frame ◽  
Ring Rot ◽  
Ssrna Virus ◽  
The Family

Abstract In this study, we describe the full-length genome sequence of a novel ourmia-like mycovirus, tentatively designated Botryosphaeria dothidea ourmia-like virus 1 (BdOLV1), isolated from the phytopathogenic fungus, Botryosphaeria dothidea strain P8, associated with apple ring rot in Shanxi province, China. The complete BdOLV1 genome is comprised of 2797 nucleotides, a positive-sense (+) single-stranded RNA (ssRNA) with a single open reading frame (ORF). The ORF putatively encodes a 642-amino acid polypeptide with conserved RNA-dependent RNA polymerase (RdRp) motifs, related to viruses of the family Botourmiaviridae. Phylogenetic analysis based on the RdRp amino acid sequences showed that BdOLV1 is grouped with oomycete-infecting unclassified viruses closely related to the genus Botoulivirus in Botourmiaviridae. This is the first report of a novel (+)ssRNA virus in B. dothidea related to the genus Botoulivirus in the family Botourmiaviridae.

Muriicola soli sp. nov., isolated from soil

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Hye Jeong Kang ◽  
Min-Kyeong Kim ◽  
Su Gwon Roh ◽  
Seung Bum Kim
Keyword(s):  
Related Species ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Optimum Ph ◽  
Genomic Characterization

A Gram-stain-negative, oxidase-positive, catalase-positive, aerobic, orange-pigmented, rod-shaped and non-motile bacterium designated strain MMS17-SY002T was isolated from island soil. The isolate grew at 20–37 °C (optimum, 30 °C), at pH 6.0–9.5 (optimum, pH 7) and in the presence of 0.5–4.0 % (w/v) NaCl (optimum, 2.0 %). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain MMS17-SY002T was mostly related to the genus Muriicola of the family Flavobacteriaceae and had highest sequence similarity of 96.82 % to Muriicola marianensis A6B8T and Muriicola jejuensis EM44T, but formed a distinct phylogenetic line within the genus. Chemotaxonomic analyses showed that menaquinone 6 was the predominant isoprenoid quinone, the major fatty acids were iso-C15 : 1 G and iso-C15 : 0, and the diagnostic polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 42.4 mol%. Strain MMS17-SY002T could be distinguished from related species by the combination of trypsin, α-chymotrypsin, acid phosphatase, naphthol-AS-BI-phosphohydrolase, α-galactosidase, β-galactosidase and β-glucosidase activities. The orthologous average nucleotide identity between the genomes of strain MMS17-SY002T and M. jejuensis and that between the strain and M. marianensis A6B8T were 73.26 and 73.33%, respectively, thus confirming the separation of the strain from related species at species level. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic characterization, MMS17-SY002T should be recognized as a novel species of the genus Muriicola , for which the name Muriicola soli sp. nov. is proposed. The type strain is MMS17-SY002T (=KCTC 62790T=JCM 32370T).

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