Molecular and Phylogenetic Characterisation of a Highly Divergent Novel Parvovirus (Psittaciform Chaphamaparvovirus 2) in Australian Neophema Parrots

Parvoviruses under the genus Chaphamaparvovirus (subfamily Hamaparvovirinae) are highly divergent and have recently been identified in many animals. However, the detection and characterisation of parvoviruses in psittacine birds are limited. Therefore, this study reports a novel parvovirus, tentatively named psittaciform chaphamaparvovirus 2 (PsChPV-2) under the genus Chaphamaparvovirus, which was identified in Australian Neophema birds. The PsChPV-2 genome is 4371 bp in length and encompasses four predicted open-reading frames, including two major genes, a nonstructural replicase gene (NS1), and a structural capsid gene (VP1). The NS1 and VP1 genes showed the closest amino acid identities of 56.2% and 47.7%, respectively, with a recently sequenced psittaciform chaphamaparvovirus 1 from a rainbow lorikeet (Trichoglossus moluccanus). Subsequent phylogenetic analyses exhibited that the novel PsChPV-2 is most closely related to other chaphamaparvoviruses of avian origin and has the greatest sequence identity with PsChPV-1 (60.6%). Further systematic investigation is warranted to explore the diversity with many avian-associated parvoviruses likely to be discovered.

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Nightshade curly top virus: A possible new virus of the genus Topocuvirus infecting Solanum nigrum in China

Plant Disease ◽

10.1094/pdis-03-20-0572-re ◽

2020 ◽

Author(s):

Kai Sun ◽

Yan Liang ◽

Xueting Zhong ◽

Xuenan Hu ◽

Pengjun Zhang ◽

...

Keyword(s):

Amino Acid ◽

Phylogenetic Analyses ◽

Solanum Nigrum ◽

Open Reading Frames ◽

Small Interfering Rnas ◽

Protein Amino Acid ◽

Sequence Identity ◽

Pathogenic Viruses ◽

Leaf Deformation ◽

Symptomatic Sample

Virus-like symptoms, including leaf deformation and curling, were observed on nightshade (Solanum nigrum) in Zhejiang province, China. To identify possible pathogenic viruses or viroids, a symptomatic sample was subjected to deep sequencing of small interfering RNAs. Assembly of the resulting sequences led to identification of a novel geminivirus, provisionally designated nightshade curly top virus (NCTV). The complete genomic DNA sequence is 2,867 nucleotides that encodes seven open reading frames. NCTV shares 77.1 % overall nucleotide sequence identity, 86.3 % coat protein amino acid, and 78.9 % replication-associated protein amino acid sequence identity with Topocuvirus tomato pseudo-curly top virus (TPCTV). Polymerase chain reaction screening of nightshade field isolates indicated that NCTV is widely distributed in Zhejiang. Agrobacterium-mediated inoculation revealed that NCTV is highly infectious to Nicotiana benthamiana, Solanum nigrum, Solanum lycopersicum, and Solanum tuberosum. Based on pairwise comparisons and phylogenetic analyses, NCTV is proposed as a provisional member of the genus Topocuvirus.

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Genomic and phylogenetic characterization of ChPV2, a novel goat PV closely related to the Xi-PV1 species infecting bovines

Virology Journal ◽

10.1186/s12985-020-01440-9 ◽

2020 ◽

Vol 17 (1) ◽

Author(s):

Anouk Willemsen ◽

Alexander van den Boom ◽

Julienne Dietz ◽

Seval Bilge Dagalp ◽

Firat Dogan ◽

...

Keyword(s):

Amino Acid ◽

Phylogenetic Analyses ◽

Regulatory Elements ◽

Open Reading Frames ◽

Capra Hircus ◽

Phylogenetic Position ◽

Reading Frame ◽

Phylogenetic Characterization ◽

Ruminant Species ◽

Reading Frames

Abstract Background Papillomaviruses (PVs) infecting artiodactyls are very diverse, and only second in number to PVs infecting primates. PVs associated to lesions in economically important ruminant species have been isolated from cattle and sheep. Methods Potential PV DNA from teat lesions of a Damascus goat was isolated, cloned and sequenced. The PV genome was analyzed using bioinformatics approaches to detect open reading frames and to predict potential features of encoded proteins as well as putative regulatory elements. Sequence comparison and phylogenetic analyses using the concatenated E1E2L2L1 nucleotide and amino acid alignments was used to reveal the relationship of the new PV to the known PV diversity and its closest relevants. Results We isolated and characterized the full-genome of novel Capra hircus papillomavirus. We identified the E6, E7, E1, E2, L2, L1 open reading frames with protein coding potential and putative active elements in the ChPV2 proteins and putative regulatory genome elements. Sequence similarities of L1 and phylogenetic analyses using concatenated E1E2L2L1 nucleotide and amino acid alignments suggest the classification as a new PV type designated ChPV2 with a phylogenetic position within the XiPV genus, basal to the XiPV1 species. ChPV2 is not closely related to ChPV1, the other known goat PV isolated from healthy skin, although both of them belong confidently into a clade composed of PVs infecting cervids and bovids. Interestingly, ChPV2 contains an E6 open reading frame whereas all closely related PVs do not Conclusion ChPV2 is a novel goat PV closely related to the Xi-PV1 species infecting bovines. Phylogenetic relationships and genome architecture of ChPV2 and closely related PV types suggest at least two independent E6 losses within the XiPV clade.

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A novel cripavirus of an ectoparasitoid wasp increases pupal duration and fecundity of the wasp’s Drosophila melanogaster host

The ISME Journal ◽

10.1038/s41396-021-01005-w ◽

2021 ◽

Author(s):

Jiao Zhang ◽

Fei Wang ◽

Bo Yuan ◽

Lei Yang ◽

Yi Yang ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Phylogenetic Analyses ◽

Parasitoid Wasp ◽

Developmental Time ◽

Open Reading Frames ◽

The Novel ◽

Structural Protein ◽

Developmental Duration ◽

Novel Virus ◽

Reading Frames

AbstractWe identified a 9332-nucleotide-long novel picornaviral genome sequence in the transcriptome of an agriculturally important parasitoid wasp (Pachycrepoideus vindemmiae (Rondani, 1875)). The genome of the novel virus, Rondani’s wasp virus 1 (RoWV-1), contains two long open reading frames encoding a nonstructural and a structural protein, respectively, and is 3’-polyadenylated. Phylogenetic analyses firmly place RoWV-1 into the dicistrovirid genus Cripavirus. We detected RoWV-1 in various tissues and life stages of the parasitoid wasp, with the highest virus load measured in the larval digestive tract. We demonstrate that RoWV-1 is transmitted horizontally from infected to uninfected wasps but not vertically to wasp offspring. Comparison of several important biological parameters between the infected and uninfected wasps indicates that RoWV-1 does not have obvious detrimental effects on wasps. We further demonstrate that RoWV-1 also infects Drosophila melanogaster (Meigen, 1830), the hosts of the pupal ectoparasitoid wasps, and thereby increases its pupal developmental duration and fecundity, but decreases the eclosion rate. Together, these results suggest that RoWV-1 may have a potential benefit to the wasp by increasing not only the number of potential wasp hosts but also the developmental time of the hosts to ensure proper development of wasp offspring.

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Proteins encoded by Novel ORFs have increased disorder but can be biochemically regulated and harbour pathogenic mutations

10.1101/562835 ◽

2019 ◽

Cited By ~ 2

Author(s):

N. Suhas Jagannathan ◽

Narendra Meena ◽

Kethaki Prathivadi Bhayankaram ◽

Sudhakaran Prabakaran

Keyword(s):

Amino Acid ◽

Amino Acid Sequences ◽

Open Reading Frames ◽

The Novel ◽

Biological Functions ◽

Novel Proteins ◽

Coding Regions ◽

Disordered Structures ◽

Reading Frames ◽

Computational Predictions

AbstractRecent evidence has suggested that protein or protein-like products can be encoded by previously uncharacterized Open Reading Frames (ORFs) that we define as Novel Open Reading Frames (nORFs)1,2. These nORFs are present in both coding and non coding regions of the human genome and the novel proteins that they encode have increased the number and complexity of cellular proteome from bacteria to humans. It is a conundrum whether these protein or protein-like products could play any significant functional biological role. But hopes have been raised to target them for anticancer and antimicrobial therapy3,4. To infer whether these novel proteins can perform biological functions, we used computational predictions to systematically investigate whether their amino acid sequences can form ordered or disordered structures. Our results indicated that that these novel proteins have significantly higher predicted disorder structure compared to all known proteins, yet we do not find any correlation between the pathogenicity of the mutations and whether they are present in the ordered and disordered regions of these novel proteins. This study reveals that we should investigate these novel proteins more systematically as they may be important to understand complex diseases.

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Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽

10.3390/v13010027 ◽

2020 ◽

Vol 13 (1) ◽

pp. 27

Author(s):

Jun Kwon ◽

Sang Guen Kim ◽

Hyoun Joong Kim ◽

Sib Sankar Giri ◽

Sang Wha Kim ◽

...

Keyword(s):

Morphological Traits ◽

Open Reading Frames ◽

Genome Comparison ◽

The Novel ◽

Promising Alternative ◽

Isolation And Characterization ◽

Global Issue ◽

Reading Frames ◽

Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

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Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽

10.1093/genetics/159.3.1103 ◽

2001 ◽

Vol 159 (3) ◽

pp. 1103-1115 ◽

Cited By ~ 1

Author(s):

Hongguang Shao ◽

Zhijian Tu

Keyword(s):

Phylogenetic Analyses ◽

Mosquito Species ◽

Open Reading Frames ◽

Inverted Repeats ◽

Sequence Comparisons ◽

Wide Range ◽

Multiple Copies ◽

Catalytic Motif ◽

Open The Doors ◽

Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

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Evolutionary History of Cucumber Mosaic Virus Deduced by Phylogenetic Analyses

Journal of Virology ◽

10.1128/jvi.76.7.3382-3387.2002 ◽

2002 ◽

Vol 76 (7) ◽

pp. 3382-3387 ◽

Cited By ~ 155

Author(s):

Marilyn J. Roossinck

Keyword(s):

Cucumber Mosaic Virus ◽

Mosaic Virus ◽

Virus Isolate ◽

Phylogenetic Analyses ◽

Open Reading Frames ◽

Broad Host Range ◽

Nontranslated Region ◽

History Of ◽

Evolutionary Success ◽

Reading Frames

ABSTRACT Cucumber mosaic virus (CMV) is an RNA plant virus with a tripartite genome and an extremely broad host range. Previous evolutionary analyses with the coat protein (CP) and 5′ nontranslated region (NTR) of RNA 3 suggested subdivision of the virus into three groups, subgroups IA, IB, and II. In this study 15 strains of CMV whose nucleotide sequences have been determined were used for a complete phylogenetic analysis of the virus. The trees estimated for open reading frames (ORFs) located on the different RNAs were not congruent and did not completely support the subgrouping indicated by the CP ORF, indicating that different RNAs had independent evolutionary histories. This is consistent with a reassortment mechanism playing an important role in the evolution of the virus. The evolutionary trees of the 1a and 3a ORFs were more compact and displayed more branching than did those of the 2a and CP ORFs. This may reflect more rigid host-interactive constraints exerted on the 1a and 3a ORFs. In addition, analysis of the 3′ NTR that is conserved among all RNAs indicated that evolutionary constraints on this region are specific to the RNA component rather than the virus isolate. This indicates that functions other than replication are encoded in the 3′ NTR. Reassortment may have led to the genetic diversity found among CMV strains and contributed to its enormous evolutionary success.

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Sequence and domain organization of scruin, an actin-cross-linking protein in the acrosomal process of Limulus sperm.

The Journal of Cell Biology ◽

10.1083/jcb.128.1.51 ◽

1995 ◽

Vol 128 (1) ◽

pp. 51-60 ◽

Cited By ~ 46

Author(s):

M Way ◽

M Sanders ◽

C Garcia ◽

J Sakai ◽

P Matsudaira

Keyword(s):

Amino Acid ◽

Actin Filaments ◽

Limited Proteolysis ◽

Open Reading Frames ◽

Actin Binding ◽

Molar Ratio ◽

Domain Organization ◽

Ring Canals ◽

Drosophila Protein ◽

Reading Frames

The acrosomal process of Limulus sperm is an 80-microns long finger of membrane supported by a crystalline bundle of actin filaments. The filaments in this bundle are crosslinked by a 102-kD protein, scruin present in a 1:1 molar ratio with actin. Recent image reconstruction of scruin decorated actin filaments at 13-A resolution shows that scruin is organized into two equally sized domains bound to separate actin subunits in the same filament. We have cloned and sequenced the gene for scruin from a Limulus testes cDNA library. The deduced amino acid sequence of scruin reflects the domain organization of scruin: it consists of a tandem pair of homologous domains joined by a linker region. The domain organization of scruin is confirmed by limited proteolysis of the purified acrosomal process. Three different proteases cleave the native protein in a 5-kD Protease-sensitive region in the middle of the molecule to generate an NH2-terminal 47-kD and a COOH-terminal 56-kD protease-resistant domains. Although the protein sequence of scruin has no homology to any known actin-binding protein, it has similarities to several proteins, including four open reading frames of unknown function in poxviruses, as well as kelch, a Drosophila protein localized to actin-rich ring canals. All proteins that show homologies to scruin are characterized by the presence of an approximately 50-amino acid residue motif that is repeated between two and seven times. Crystallographic studies reveal this motif represents a four beta-stranded fold that is characteristic of the "superbarrel" structural fold found in the sialidase family of proteins. These results suggest that the two domains of scruin seen in EM reconstructions are superbarrel folds, and they present the possibility that other members of this family may also bind actin.

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Sixty years from the first disease description, a novel badnavirus associated with chestnut mosaic disease

Phytopathology ◽

10.1094/phyto-09-20-0420-r ◽

2020 ◽

Author(s):

Armelle Marais ◽

Sergio Murolo ◽

Chantal Faure ◽

Yoann Brans ◽

Clement Larue ◽

...

Keyword(s):

High Throughput Sequencing ◽

Molecular Detection ◽

Phylogenetic Analyses ◽

Epidemiological Studies ◽

Mosaic Disease ◽

Open Reading Frames ◽

Sequence Comparisons ◽

High Incidence ◽

The Usa ◽

Reading Frames

Although the chestnut mosaic disease (ChMD) was described several decades ago, its etiology is still not elucidated. Here, using classical approaches in combination with high throughput sequencing (HTS) techniques, we identify a novel Badnavirus that is a strong etiological candidate for ChMD. Two disease sources from Italy and France were submitted to HTS-based viral indexing. Total RNAs were extracted, ribodepleted and sequenced on an Illumina NextSeq500 (2x150 or 2x 75 nt). In each source, we identified a single contig of about 7.2 kilobases that corresponds to a complete circular viral genome and shares homologies with various badnaviruses. The genomes of the two isolates have an average nucleotide identity of 90.5% with a typical badnaviral genome organization comprising three open reading frames. Phylogenetic analyses and sequence comparisons show that this virus is a novel species for which we propose the name Chestnut mosaic virus (ChMV). Using a newly developed molecular detection test, we systematically detected the virus in symptomatic graft-inoculated indicator plants (chestnut and American oak), as well in chestnut trees presenting typical ChMD symptoms in the field (100% and 87% in France and Italy surveys, respectively). Datamining of publicly available chestnut SRA transcriptomic data allowed the reconstruction of two additional complete ChMV genomes from two Castanea mollissima sources from the USA, as well as ChMV detection in C. dentata from the USA. Preliminary epidemiological studies, performed in France and in Central Eastern Italy, showed that ChMV has a high incidence in some commercial orchards, with a low within-orchard genetic diversity.

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A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli

mBio ◽

10.1128/mbio.01855-16 ◽

2016 ◽

Vol 7 (6) ◽

Cited By ~ 8

Author(s):

Adi Oron-Gottesman ◽

Martina Sauert ◽

Isabella Moll ◽

Hanna Engelberg-Kulka

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Ribosomal Protein ◽

Genetic Code ◽

Open Reading Frames ◽

Translation Machinery ◽

E Coli ◽

Universal Characteristic ◽

Living Organisms ◽

Reading Frames

ABSTRACT Escherichia coli mazEF is an extensively studied stress-induced toxin-antitoxin (TA) system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM), composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant. This in-frame ACA cleavage of MazF seems to depend on MazF binding to an extracellular-death-factor (EDF)-like element in ribosomal protein bS1 (bacterial S1), apparently causing MazF to be part of STM ribosomes. Furthermore, due to the in-frame MazF cleavage of ACAs under stress, a bias occurs in the reading of the genetic code causing the amino acid threonine to be encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA. IMPORTANCE The genetic code is a universal characteristic of all living organisms. It defines the set of rules by which nucleotide triplets specify which amino acid will be incorporated into a protein. Our results represent the first existing report on a stress-induced bias in the reading of the genetic code. We found that in E. coli , under stress, the amino acid threonine is encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA. This is because under stress, MazF generates a stress-induced translation machinery (STM) in which MazF cleaves in-frame ACA sites of the processed mRNAs.

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