scholarly journals The transcriptional and translational landscape of equine torovirus

2018 ◽  
Author(s):  
Hazel Stewart ◽  
Katherine Brown ◽  
Adam M. Dinan ◽  
Nerea Irigoyen ◽  
Eric J. Snijder ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Rna Synthesis ◽  
Gastrointestinal Disease ◽  
Genomic Analysis ◽  
Ribosome Profiling ◽  
Amino Acid Sequences ◽  
Comparative Genomic ◽  
Human Pathogens ◽  
Animal Virus ◽  
Subgenomic Rnas

AbstractThe genusTorovirus(subfamilyTorovirinae, familyCoronaviridae, orderNidovirales) encompasses a range of species that infect domestic ungulates including cattle, sheep, goats, pigs and horses, causing an acute self-limiting gastroenteritis. Using the prototype species equine torovirus (EToV) we performed parallel RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) to analyse the relative expression levels of the known torovirus proteins and transcripts, chimaeric sequences produced via discontinuous RNA synthesis (a characteristic of the nidovirus replication cycle) and changes in host transcription and translation as a result of EToV infection. RNA sequencing confirmed that EToV utilises a unique combination of discontinuous and non-discontinuous RNA synthesis to produce its subgenomic RNAs; indeed, we identified transcripts arising from both mechanisms that would result in sgRNAs encoding the nucleocapsid. Our ribosome profiling analysis revealed that ribosomes efficiently translate two novel CUG-initiated ORFs, located within the so-called 5’ UTR. We have termed the resulting proteins U1 and U2. Comparative genomic analysis confirmed that these ORFs are conserved across all available torovirus sequences and the inferred amino acid sequences are subject to purifying selection, indicating that U1 and U2 are functionally relevant. This study provides the first high-resolution analysis of transcription and translation in this neglected group of livestock pathogens.ImportanceToroviruses infect cattle, goats, pigs and horses worldwide and can cause gastrointestinal disease. There is no treatment or vaccine and their ability to spill over into humans has not been assessed. These viruses are related to important human pathogens including severe acute respiratory syndrome (SARS) coronavirus and they share some common features, however the mechanism that they use to produce subgenomic RNA molecules differs. Here we performed deep sequencing to determine how equine torovirus produces subgenomic RNAs. In doing so, we also identified two previously unknown open reading frames “hidden” within the genome. Together these results highlight the similarities and differences between this domestic animal virus and related pathogens of humans and livestock.

scholarly journals Transcriptional and Translational Landscape of Equine Torovirus

2018 ◽  
Vol 92 (17) ◽  
Author(s):  
Hazel Stewart ◽  
Katherine Brown ◽  
Adam M. Dinan ◽  
Nerea Irigoyen ◽  
Eric J. Snijder ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Rna Synthesis ◽  
Gastrointestinal Disease ◽  
Ribosome Profiling ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Human Pathogens ◽  
Content Type ◽  
Reading Frames

ABSTRACT The genus Torovirus (subfamily Torovirinae, family Coronaviridae, order Nidovirales) encompasses a range of species that infect domestic ungulates, including cattle, sheep, goats, pigs, and horses, causing an acute self-limiting gastroenteritis. Using the prototype species equine torovirus (EToV), we performed parallel RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) to analyze the relative expression levels of the known torovirus proteins and transcripts, chimeric sequences produced via discontinuous RNA synthesis (a characteristic of the nidovirus replication cycle), and changes in host transcription and translation as a result of EToV infection. RNA sequencing confirmed that EToV utilizes a unique combination of discontinuous and nondiscontinuous RNA synthesis to produce its subgenomic RNAs (sgRNAs); indeed, we identified transcripts arising from both mechanisms that would result in sgRNAs encoding the nucleocapsid. Our ribosome profiling analysis revealed that ribosomes efficiently translate two novel CUG-initiated open reading frames (ORFs), located within the so-called 5′ untranslated region. We have termed the resulting proteins U1 and U2. Comparative genomic analysis confirmed that these ORFs are conserved across all available torovirus sequences, and the inferred amino acid sequences are subject to purifying selection, indicating that U1 and U2 are functionally relevant. This study provides the first high-resolution analysis of transcription and translation in this neglected group of livestock pathogens. IMPORTANCE Toroviruses infect cattle, goats, pigs, and horses worldwide and can cause gastrointestinal disease. There is no treatment or vaccine, and their ability to spill over into humans has not been assessed. These viruses are related to important human pathogens, including severe acute respiratory syndrome (SARS) coronavirus, and they share some common features; however, the mechanism that they use to produce sgRNA molecules differs. Here, we performed deep sequencing to determine how equine torovirus produces sgRNAs. In doing so, we also identified two previously unknown open reading frames “hidden” within the genome. Together these results highlight the similarities and differences between this domestic animal virus and related pathogens of humans and livestock.

scholarly journals Sequence and expression divergence of an ancient duplication of the chaperonin groESEL operon in Vibrio species

Microbiology ◽  
2014 ◽  
Vol 160 (9) ◽  
pp. 1953-1963
Author(s):  
Nityananda Chowdhury ◽  
Joseph J. Kingston ◽  
W. Brian Whitaker ◽  
Megan R. Carpenter ◽  
Analuisa Cohen ◽  
...  
Keyword(s):  
Vibrio Vulnificus ◽  
Genomic Analysis ◽  
Duplication Event ◽  
Comparative Genomic ◽  
Human Pathogens ◽  
Additional Species ◽  
Evolutionary Advantage ◽  
Shock Proteins ◽  
Chromosome Ii ◽  
Chromosome I

Heat-shock proteins are molecular chaperones essential for protein folding, degradation and trafficking. The human pathogen Vibrio vulnificus encodes a copy of the groESEL operon in both chromosomes and these genes share <80 % similarity with each other. Comparative genomic analysis was used to determine whether this duplication is prevalent among Vibrionaceae specifically or Gammaproteobacteria in general. Among the Vibrionaceae complete genome sequences in the database (31 species), seven Vibrio species contained a copy of groESEL in each chromosome, including the human pathogens Vibrio cholerae, Vibrio parahaemolyticus and V. vulnificus. Phylogenetic analysis of GroEL among the Gammaproteobacteria indicated that GroESEL-1 encoded in chromosome I was the ancestral copy and GroESEL-2 in chromosome II arose by an ancient gene duplication event. Interestingly, outside of the Vibrionaceae within the Gammaproteobacteria, groESEL chromosomal duplications were rare among the 296 genomes examined; only five additional species contained two or more copies. Examination of the expression pattern of groEL from V. vulnificus cells grown under different conditions revealed differential expression between the copies. The data demonstrate that groEL-1 was more highly expressed during growth in exponential phase than groEL-2 and a similar pattern was also found in both V. cholerae and V. parahaemolyticus. Overall these data suggest that retention of both copies of groESEL in Vibrio species may confer an evolutionary advantage.

scholarly journals Interaction of two strongly divergent archaellins stabilizes the structure of the Halorubrum archaellum

2019 ◽  
Author(s):  
Mikhail G. Pyatibratov ◽  
Alexey S. Syutkin ◽  
Tessa E.F. Quax ◽  
Tatjana N. Melnik ◽  
R. Thane Papke ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Genomic Analysis ◽  
Halophilic Archaea ◽  
Amino Acid Sequences ◽  
Comparative Genomic ◽  
Low Salinity ◽  
Additional Stabilization ◽  
External Conditions ◽  
Thermal Stability Of

SUMMARYThe archaellum is a unique motility structure that has only functional similarity to its bacterial counterpart, the flagellum. Archaellar filaments consist of thousands of copies of the protein protomer archaellin. Most euryarchaeal genomes encode multiple homologous archaellins. The role of these multiple archaellin genes remains unclear. Halophilic archaea from the genus Halorubrum possess two archaellin genes, flaB1 and flaB2. Amino acid sequences of the corresponding protein products are extraordinarily diverged (identity of ∼ 40%). To clarify roles for each archaellin, we compared archaella from two natural Halorubrum lacusprofundi strains: the DL18 strain, which possesses both archaellin genes, and the type strain ACAM 34 whose genome contains the flaB2 gene only. Both strains synthesize functional archaella; however, the DL18 strain, where both archaellins are present in comparable amounts, is more motile. In addition, we expressed these different Hrr. lacusprofundi archaellins in a Haloferax volcanii strain from which the endogenous archaellin genes were deleted. Three Hfx. volcanii strains expressing Hrr. lacusprofundi archaellins flaB1, flaB2 or flaB1-flaB2 produced archaellum filaments consisting of only one (FlaB1 or FlaB2) or both (FlaB1/B2) archaellins. All three recombinant Hfx. volcanii strains were motile, although there were profound differences in the efficiency of motility. The recombinant filaments resemble the natural filaments of Hrr. lacusprofundi. Electron microscopy showed that FlaB1 FlaB2-archaella look like typical supercoiled filaments, while with the shape of the FlaB1- and FlaB2-archaella is more variable. Both native and recombinant FlaB1 FlaB2-filaments have greater thermal stability and are more resistant to low salinity stress than single-component filaments. This shows that thermal stability of archaellins depends on the presence of both archaellin types, indicating a close interaction between these subunits in the supramolecular structure. Functional helical Hrr. lacusprofundi archaella can be composed of either single archaellin: FlaB2 or FlaB1; however, the two divergent archaellin subunits in combination provide additional stabilization to the archaellum structure and thus adaptation to a wider range of external conditions. A comparative genomic analysis of archaellins suggests that the described combination of divergent archaellins is not restricted to Hrr. lacusprofundi, but is occurring also in organisms from other haloarchaeal genera.

scholarly journals Whole Genome Sequencing Based Taxonomic Classification, and Comparative Genomic Analysis of Potentially Human Pathogenic Enterobacter spp. Isolated from Chlorinated Wastewater in the North West Province, South Africa

2021 ◽  
Vol 9 (9) ◽  
pp. 1928
Author(s):  
Tawanda E. Maguvu ◽  
Cornelius C. Bezuidenhout
Keyword(s):  
Bacterial Species ◽  
Genomic Analysis ◽  
Gene Clusters ◽  
Comparative Genomic Analysis ◽  
Taxonomic Classification ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Human Pathogens ◽  
Wastewater Treatment Process ◽  
North West

Comparative genomics, in particular, pan-genome analysis, provides an in-depth understanding of the genetic variability and dynamics of a bacterial species. Coupled with whole-genome-based taxonomic analysis, these approaches can help to provide comprehensive, detailed insights into a bacterial species. Here, we report whole-genome-based taxonomic classification and comparative genomic analysis of potential human pathogenic Enterobacter hormaechei subsp. hoffmannii isolated from chlorinated wastewater. Genome Blast Distance Phylogeny (GBDP), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) confirmed the identity of the isolates. The algorithm PathogenFinder predicted the isolates to be human pathogens with a probability of greater than 0.78. The potential pathogenic nature of the isolates was supported by the presence of biosynthetic gene clusters (BGCs), aerobactin, and aryl polyenes (APEs), which are known to be associated with pathogenic/virulent strains. Moreover, analysis of the genome sequences of the isolates reflected the presence of an arsenal of virulence factors and antibiotic resistance genes that augment the predictions of the algorithm PathogenFinder. The study comprehensively elucidated the genomic features of pathogenic Enterobacter isolates from wastewaters, highlighting the role of wastewaters in the dissemination of pathogenic microbes, and the need for monitoring the effectiveness of the wastewater treatment process.

scholarly journals Comparative Genomics, Evolutionary and Gene Regulatory Regions Analysis of Casein Gene Family in Bubalus bubalis

2021 ◽  
Vol 12 ◽  
Author(s):  
Saif ur Rehman ◽  
Tong Feng ◽  
Siwen Wu ◽  
Xier Luo ◽  
An Lei ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Amino Acid Sequences ◽  
Comparative Genomic ◽  
Milk Traits ◽  
Casein Gene ◽  
Swamp Buffalo ◽  
Casein Genes

Buffalo is a luxurious genetic resource with multiple utilities (as a dairy, draft, and meat animal) and economic significance in the tropical and subtropical regions of the globe. The excellent potential to survive and perform on marginal resources makes buffalo an important source for nutritious products, particularly milk and meat. This study was aimed to investigate the evolutionary relationship, physiochemical properties, and comparative genomic analysis of the casein gene family (CSN1S1, CSN2, CSN1S2, and CSN3) in river and swamp buffalo. Phylogenetic, gene structure, motif, and conserved domain analysis revealed the evolutionarily conserved nature of the casein genes in buffalo and other closely related species. Results indicated that casein proteins were unstable, hydrophilic, and thermostable, although αs1-CN, β-CN, and κ-CN exhibited acidic properties except for αs2-CN, which behaved slightly basic. Comparative analysis of amino acid sequences revealed greater variation in the river buffalo breeds than the swamp buffalo indicating the possible role of these variations in the regulation of milk traits in buffalo. Furthermore, we identified lower transcription activators STATs and higher repressor site YY1 distribution in swamp buffalo, revealing its association with lower expression of casein genes that might subsequently affect milk production. The role of the main motifs in controlling the expression of casein genes necessitates the need for functional studies to evaluate the effect of these elements on the regulation of casein gene function in buffalo.

scholarly journals Integrated exome and RNA sequencing of dedifferentiated liposarcoma

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Makoto Hirata ◽  
Naofumi Asano ◽  
Kotoe Katayama ◽  
Akihiko Yoshida ◽  
Yusuke Tsuda ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Clinical Features ◽  
Large Scale ◽  
Genomic Analysis ◽  
Dedifferentiated Liposarcoma ◽  
Comparative Genomic ◽  
Sequencing Analysis ◽  
Genomic Alterations ◽  
Whole Exome ◽  
Well Differentiated

AbstractThe genomic characteristics of dedifferentiated liposarcoma (DDLPS) that are associated with clinical features remain to be identified. Here, we conduct integrated whole exome and RNA sequencing analysis in 115 DDLPS tumors and perform comparative genomic analysis of well-differentiated and dedifferentiated components from eight DDLPS samples. Several somatic copy-number alterations (SCNAs), including the gain of 12q15, are identified as frequent genomic alterations. CTDSP1/2-DNM3OS fusion genes are identified in a subset of DDLPS tumors. Based on the association of SCNAs with clinical features, the DDLPS tumors are clustered into three groups. This clustering can predict the clinical outcome independently. The comparative analysis between well-differentiated and dedifferentiated components identify two categories of genomic alterations: shared alterations, associated with tumorigenesis, and dedifferentiated-specific alterations, associated with malignant transformation. This large-scale genomic analysis reveals the mechanisms underlying the development and progression of DDLPS and provides insights that could contribute to the refinement of DDLPS management.

scholarly journals Nucleotide Sequence and Evolution of the Five-Plasmid Complement of the Phytopathogen Pseudomonas syringae pv. maculicola ES4326

2004 ◽  
Vol 186 (15) ◽  
pp. 5101-5115 ◽  
Author(s):  
John Stavrinides ◽  
David S. Guttman
Keyword(s):  
Nucleotide Sequence ◽  
Pseudomonas Syringae ◽  
Genomic Analysis ◽  
Type Iv Secretion ◽  
Comparative Genomic ◽  
Human Pathogens ◽  
Plasmid Evolution ◽  
Type Iv ◽  
Wide Range ◽  
Genomic Analyses

ABSTRACT Plasmids are transmissible, extrachromosomal genetic elements that are often responsible for environmental or host-specific adaptations. In order to identify the forces driving the evolution of these important molecules, we determined the complete nucleotide sequence of the five-plasmid complement of the radish and Arabidopsis pathogen Pseudomonas syringae pv. maculicola ES4326 and conducted an intraspecific comparative genomic analysis. To date, this is the most complex fully sequenced plasmid complement of any gram-negative bacterium. The plasmid complement comprises two pPT23A-like replicons, pPMA4326A (46,697 bp) and pPMA4326B (40,110 bp); a pPS10-like replicon, pPMA4326C (8,244 bp); and two atypical, replicase-deficient replicons, pPMA4326D (4,833 bp) and pPMA4326E (4,217 bp). A complete type IV secretion system is found on pPMA4326A, while the type III secreted effector hopPmaA is present on pPMA4326B. The region around hopPmaA includes a shorter hopPmaA homolog, insertion sequence (IS) elements, and a three-element cassette composed of a resolvase, an integrase, and an exeA gene that is also present in several human pathogens. We have also identified a novel genetic element (E622) that is present on all but the smallest plasmid (pPMA4326E) that has features of an IS element but lacks an identifiable transposase. This element is associated with virulence-related genes found in a wide range of P. syringae strains. Comparative genomic analyses of these and other P. syringae plasmids suggest a role for recombination and integrative elements in driving plasmid evolution.

scholarly journals A hidden gene in astroviruses encodes a cell-permeabilizing protein involved in virus release

2019 ◽  
Author(s):  
Valeria Lulla ◽  
Andrew E. Firth
Keyword(s):  
Genomic Analysis ◽  
Purifying Selection ◽  
Ribosome Profiling ◽  
Comparative Genomic ◽  
Virus Release ◽  
Structural Protein ◽  
Functional Protein ◽  
Cell Permeabilization ◽  
Virus Growth ◽  
Human Astroviruses

ABSTRACTHuman astroviruses are small nonenveloped viruses with positive-sense single-stranded RNA genomes that contain three main open reading frames: ORF1a, ORF1b and ORF2. Astroviruses cause acute gastroenteritis in children worldwide and have been associated with encephalitis and meningitis in immunocompromised individuals. Through comparative genomic analysis of >400 astrovirus sequences, we identified a conserved “ORFX” overlapping the capsid-encoding ORF2 in genogroup I, III and IV astroviruses. ORFX appears to be subject to purifying selection, consistent with it encoding a functional protein product, termed XP. Using ribosome profiling of cells infected with human astrovirus 1, we confirm initiation at the ORFX AUG. XP-knockout astroviruses are strongly attenuated and after passaging can partly restore viral titer via pseudo-reversions, thus demonstrating that XP plays an important role in virus growth. To further investigate XP, we developed an astrovirus replicon system. We demonstrate that XP has only minor effects on RNA replication and structural protein production. Instead, XP associates with the plasma membrane with an extracellular N-terminus topology and promotes efficient virus release. Using two different assays, we show that expression of human or related astrovirus XPs leads to cell permeabilization, suggesting a viroporin-like activity. The discovery of XP advances our knowledge of these important human viruses and opens a new direction of research into astrovirus replication and pathogenesis.

Sign in / Sign up

Export Citation Format

Share Document