scholarly journals Comparison of genomic and predicted amino acid sequences of respiratory and enteric bovine coronaviruses isolated from the same animal with fatal shipping pneumonia

2001 ◽  
Vol 82 (12) ◽  
pp. 2927-2933 ◽  
Author(s):  
Vladimir N. Chouljenko ◽  
X. Q. Lin ◽  
J. Storz ◽  
Konstantin G. Kousoulas ◽  
Alexander E. Gorbalenya
Keyword(s):  
Amino Acid ◽  
Hepatitis Virus ◽  
Mouse Hepatitis Virus ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Single Amino Acid ◽  
Untranslated Regions ◽  
Genome Sequences ◽  
Shipping Fever ◽  
Reading Frames

The complete genome sequences are reported here of two field isolates of bovine coronavirus (BCoV), which were isolated from respiratory and intestinal samples of the same animal experiencing fatal pneumonia during a bovine shipping fever epizootic. Both genomes contained 31028 nucleotides and included 13 open reading frames (ORFs) flanked by 5′- and 3′-untranslated regions (UTRs). ORF1a and ORF1b encode replicative polyproteins pp1a and pp1ab, respectively, that contain all of the putative functional domains documented previously for the closest relative, mouse hepatitis virus. The genomes of the BCoV isolates differed in 107 positions, scattered throughout the genome except the 5′-UTR. Differences in 25 positions were non-synonymous and were located in all proteins except pp1b. Six replicase mutations were identified within or immediately downstream of the predicted largest pp1a-derived protein, p195/p210. Single amino acid changes within p195/p210 as well as within the S glycoprotein might contribute to the different phenotypes of the BCoV isolates.

scholarly journals Isolation and Characterization of Genes Responsible for Naphthalene Degradation from Thermophilic Naphthalene Degrader, Geobacillus sp. JF8

2019 ◽  
Vol 8 (1) ◽  
pp. 44 ◽  
Author(s):  
Daisuke Miyazawa ◽  
Le Thi Ha Thanh ◽  
Akio Tani ◽  
Masaki Shintani ◽  
Nguyen Hoang Loc ◽  
...  
Keyword(s):  
Amino Acid ◽  
Thermophilic Bacterium ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Pcr Analysis ◽  
Naphthalene Degradation ◽  
Isolation And Characterization ◽  
Dihydrodiol Dehydrogenase ◽  
Reading Frames

Geobacillus sp. JF8 is a thermophilic biphenyl and naphthalene degrader. To identify the naphthalene degradation genes, cis-naphthalene dihydrodiol dehydrogenase was purified from naphthalene-grown cells, and its N-terminal amino acid sequence was determined. Using a DNA probe encoding the N-terminal region of the dehydrogenase, a 10-kb DNA fragment was isolated. Upstream of nahB, a gene for dehydrogenase, there were two open reading frames which were designated as nahAc and nahAd, respectively. The products of nahAc and nahAd were predicted to be alpha and beta subunit of ring-hydroxylating dioxygenases, respectively. Phylogenetic analysis of amino acid sequences of NahB indicated that it did not belong to the cis-dihydrodiol dehydrogenase group that includes those of classical naphthalene degradation pathways. Downstream of nahB, four open reading frames were found, and their products were predicted as meta-cleavage product hydrolase, monooxygenase, dehydrogenase, and gentisate 1,2-dioxygenase, respectively. A reverse transcriptase-PCR analysis showed that transcription of nahAcAd was induced by naphthalene. These findings indicate that we successfully identified genes involved in the upper pathway of naphthalene degradation from a thermophilic bacterium.

scholarly journals Relapsing Fever Spirochetes Contain Chromosomal Genes with Unique Direct Tandemly Repeated Sequences

2005 ◽  
Vol 73 (5) ◽  
pp. 3025-3037 ◽  
Author(s):  
Cyril Guyard ◽  
Earl M. Chester ◽  
Sandra J. Raffel ◽  
Merry E. Schrumpf ◽  
Paul F. Policastro ◽  
...  
Keyword(s):  
Amino Acid ◽  
Human Infection ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Relapsing Fever ◽  
Serum Samples ◽  
Borrelia Hermsii ◽  
Reading Frames ◽  
Antigenic Heterogeneity

ABSTRACT Genome sequencing of the relapsing fever spirochetes Borrelia hermsii and Borrelia turicatae identified three open reading frames (ORFs) on the chromosomes that contained internal, tandemly repeated amino acid sequences that were absent in the Lyme disease spirochete Borrelia burgdorferi. The predicted amino acid sequences of these genes (BH0209, BH0512, and BH0553) have hydrophobic N termini, indicating that these proteins may be secreted. B. hermsii transcribed the three ORFs in vitro, and the BH0512- and BH0553-encoded proteins (PBH-512 and PBH-553) were produced in vitro and in experimentally infected mice. PBH-512 and PBH-553 were on the spirochete's outer surface, and antiserum to these proteins reduced the adherence of B. hermsii to red blood cells. PCR analyses of 28 isolates of B. hermsii and 8 isolates of B. turicatae demonstrated polymorphism in each gene correlated with the number of repeats. Serum samples from relapsing fever patients reacted with recombinant PBH-512 and PBH-553, suggesting that these proteins are produced during human infection. These polymorphic proteins may be involved in the pathogenicity of these relapsing fever spirochetes and provide a mechanism for antigenic heterogeneity within their populations.

Incorporation of iron-sulphur clusters in membrane-bound proteins

2001 ◽  
Vol 29 (4) ◽  
pp. 418-421 ◽  
Author(s):  
A. Seidler ◽  
K. Jaschkowitz ◽  
M. Wollenberg
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Synechocystis Pcc 6803 ◽  
Membrane Bound ◽  
Nif Proteins ◽  
Reading Frames ◽  
Pcc 6803

The completely sequenced genome of the cyano-bacterium Synechocystis PCC 6803 contains several open reading frames, of which the deduced amino acid sequences show similarities to proteins known to be involved in FeS cluster synthesis of nitrogenase (Nif proteins) and other FeS proteins (Isc proteins). In this article, the results of our studies on these proteins are summarized and discussed with respect to their relevance in FeS cluster incorporation in chloroplasts. In cyanobacteria, there appears to exist several pathways for FeS cluster synthesis.

scholarly journals Characterization of pRGO1, a Plasmid from Propionibacterium acidipropionici, and Its Use for Development of a Host-Vector System in Propionibacteria

2000 ◽  
Vol 66 (11) ◽  
pp. 4688-4695 ◽  
Author(s):  
Pornpimon Kiatpapan ◽  
Yoshiteru Hashimoto ◽  
Hisako Nakamura ◽  
Yong-Zhe Piao ◽  
Hisayo Ono ◽  
...  
Keyword(s):  
Amino Acid ◽  
Shuttle Vector ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Vector System ◽  
Propionibacterium Acidipropionici ◽  
Rep Protein ◽  
Gram Positive Bacteria ◽  
High Degree ◽  
Reading Frames

ABSTRACT The complete nucleotide sequence of pRGO1, a cryptic plasmid fromPropionibacterium acidipropionici E214, was determined. pRGO1 is 6,868 bp long, and its G+C content is 65.0%. Frame analysis of the sequence revealed six open reading frames, which were designated Orf1 to Orf6. The deduced amino acid sequences of Orf1 and Orf2 showed extensive similarities to an initiator of plasmid replication, the Rep protein, of various plasmids of gram-positive bacteria. The amino acid sequence of the putative translation product of orf3 exhibited a high degree of similarity to the amino acid sequences of DNA invertase in several bacteria. For the putative translation products of orf4,orf5, and orf6, on the other hand, no homologous sequences were found. The function of these open reading frames was studied by deletion analysis. A shuttle vector, pPK705, was constructed for shuttling between Escherichia coli and a Propionibacterium strain containingorf1 (repA), orf2(repB), orf5, and orf6 from pRGO1, pUC18, and the hygromycin B-resistant gene as a drug marker. Shuttle vector pPK705 successfully transformed Propionibacterium freudenreichii subsp. shermanii IFO12426 by electroporation at an efficiency of 8 × 106 CFU/μg of DNA under optimized conditions. Transformation of various species of propionibacteria with pPK705 was also performed at efficiencies of about 104 to 107 CFU/μg of DNA. The vector was stably maintained in strains of P. freudenreichiisubsp. shermanii, P. freudenreichii, P. pentosaceum, and P. freudenreichii subsp.freudenreichii grown under nonselective conditions. Successful manipulation of a host-vector system in propionibacteria should facilitate genetic studies and lead to creation of genes that are useful industrially.

scholarly journals Genome Sequences of Two GH Clade SARS-CoV-2 Strains Isolated from Patients with COVID-19 in South Korea

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Minwoo Kim ◽  
Youn-Jung Lee ◽  
Jae Sun Yoon ◽  
Jin Young Ahn ◽  
Jung Ho Kim ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
South Korea ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Genome Sequences ◽  
Nonsynonymous Substitutions ◽  
Sequence Identity ◽  
Reading Frames

ABSTRACT We report the genome sequences of two GH clade severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains isolated from nasopharyngeal swabs from patients with coronavirus disease 2019 (COVID-19) in South Korea. These strains had two mutations in the untranslated regions and seven nonsynonymous substitutions in open reading frames, compared with Wuhan/Hu-1/2019, showing 99.96% sequence identity.

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

2019 ◽  
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.

scholarly journals Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp.

2006 ◽  
Vol 87 (3) ◽  
pp. 723-733 ◽  
Author(s):  
Yoshitake Takao ◽  
Kazuyuki Mise ◽  
Keizo Nagasaki ◽  
Tetsuro Okuno ◽  
Daiske Honda
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Rna Virus ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Genome Database ◽  
Virus Family ◽  
Translation Mechanism ◽  
Reading Frames

The complete nucleotide sequence of the genomic RNA of a marine fungoid protist-infecting virus (Schizochytrium single-stranded RNA virus; SssRNAV) has been determined. The viral RNA is single-stranded with a positive sense and is 9018 nt in length [excluding the 3′ poly(A) tail]. It contains two long open reading frames (ORFs), which are separated by an intergenic region of 92 nt. The 5′ ORF (ORF1) is preceded by an untranslated leader sequence of 554 nt. The 3′ large ORF (ORF2) and an additional ORF (ORF3) overlap ORF2 by 431 nt and are followed by an untranslated region of 70 nt [excluding the 3′ poly(A) tail]. The deduced amino acid sequences of ORF1 and ORF2 products show similarity to non-structural and structural proteins of dicistroviruses, respectively. However, Northern blot analysis suggests that SssRNAV synthesizes subgenomic RNAs to translate ORF2 and ORF3, showing that the translation mechanism of downstream ORFs is distinct from that of dicistroviruses. Furthermore, although considerable similarities were detected by using a blast genome database search, phylogenetic analysis based on both the nucleotide and amino acid sequences of the putative RNA-dependent RNA polymerase (RdRp) and the RNA helicase suggests that SssRNAV is phylogenetically distinct from other virus families. Therefore, it is concluded that SssRNAV is not a member of any currently defined virus family and belongs to a novel, unrecognized virus group.

scholarly journals Regulated Expression of the Streptococcus mutans dltGenes Correlates with Intracellular Polysaccharide Accumulation

1999 ◽  
Vol 181 (8) ◽  
pp. 2363-2372 ◽  
Author(s):  
Grace A. Spatafora ◽  
Megan Sheets ◽  
Rebecca June ◽  
David Luyimbazi ◽  
Katherine Howard ◽  
...  
Keyword(s):  
Amino Acid ◽  
Streptococcus Mutans ◽  
Growth Phase ◽  
Lactobacillus Rhamnosus ◽  
Constitutive Expression ◽  
Sole Source ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Phosphotransferase System ◽  
Reading Frames

ABSTRACT Intracellular polysaccharides (IPS) are glycogen-like storage polymers which contribute significantly to Streptococcus mutans-induced cariogenesis. We previously identified and cloned a locus from the S. mutans chromosome which is required for the accumulation of IPS. Sequencing of this locus revealed at least four contiguous open reading frames, all of which are preceded by a common promoter region and are transcribed in the same direction. Analysis of the amino acid sequence deduced from the first of these open reading frames (ORF1) revealed domains which are highly conserved among d-alanine-activating enzymes (DltA) inLactobacillus rhamnosus (formerlyLactobacillus casei) and Bacillus subtilis. The deduced amino acid sequences derived from ORF2, -3, and -4 also exhibit extensive similarity to DltB, -C, and -D, respectively, in these microorganisms. However, Southern hybridization experiments indicate that this operon maps to a locus on the S. mutanschromosome which is separate from the glgP,glgA, and glgD genes, whose products are known mediators of bacterial IPS accumulation. We therefore assigned a newdlt designation to the locus which we had formerly calledglg. We maintain that the dlt genes are involved in S. mutans IPS accumulation, however, since they complement a mutation in trans which otherwise rendersS. mutans IPS deficient. In this study, we found that expression of the S. mutans dlt genes is growth phase dependent and is modulated by carbohydrates internalized via the phosphoenolpyruvate phosphotransferase system (PTS). We demonstrated that the S. mutans dlt genes are expressed constitutively when non-PTS sugars are provided as the sole source of carbohydrate. Consistent with a role for the PTS in dltexpression is a similar constitutive expression of the dltgenes in an S. mutans PTS mutant grown in a chemically defined medium supplemented with glucose. In summary, these findings support a novel role for the dlt gene products inS. mutans IPS accumulation and suggest thatdlt expression in this oral pathogen is subject to complex mechanisms of control imposed by growth phase, dietary carbohydrate, and other factors present in the plaque environment.

scholarly journals Hepatitis C virus complete genome sequences identified from China representing subtypes 6k and 6n and a novel, as yet unassigned subtype within genotype 6

2006 ◽  
Vol 87 (3) ◽  
pp. 629-634 ◽  
Author(s):  
Ling Lu ◽  
Tatsunori Nakano ◽  
Chunhua Li ◽  
Yongshui Fu ◽  
Steve Miller ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Complete Genome ◽  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Untranslated Regions ◽  
Genome Sequences ◽  
Entire Genome ◽  
Reading Frames ◽  
Distinct Subtype

Here, the complete genome sequences for three hepatitis C virus (HCV) variants identified from China and belonging to genotype 6 are reported: km41, km42 and gz52557. Their entire genome lengths were 9430, 9441 and 9448 nt, respectively; the 5′ untranslated regions (UTRs) contained 341, 342 and 339 nt, followed by single open reading frames of 9045, 9045 and 9057 nt, respectively; the 3′ UTRs, up to the poly(U) tracts, were 41, 51 and 52 nt, respectively. Phylogenetic analyses showed that km41 is classified into subtype 6k and km42 into subtype 6n. Although gz52557 clustered distantly with subtype 6g, it appeared to belong to a distinct subtype. Analysis with 53 and 105 partial core and NS5B region sequences, respectively, representing 17 subtypes from 6a to 6q and three unassigned isolates of genotype 6 in co-analyses demonstrated that gz52557 was equidistant from all of these isolates, indicating that it belongs to a novel subtype. However, based on a recent consensus that three or more examples are required for a new HCV subtype designation, it is suggested that gz52557 remains unassigned to any subtype.

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