Comparison of NSP4 protein between group A and B human rotaviruses: detection of novel diarrhea-causing sequences in group B NSP4

Diversity in VP3, NSP3, and NSP4 of rotavirus B detected from Japanese cattle

Bovine rotavirus B (RVB) is an etiological agent of diarrhea mostly in adult cattle. Currently, a few sequences of viral protein (VP)1, 2, 4, 6, and 7 and nonstructural protein (NSP)1, 2, and 5 of bovine RVB are available in the DDBJ/EMBL/GenBank databases, and none have been reported for VP3, NSP3, and NSP4. In order to fill this gap in the genetic characterization of bovine RVB strains, we used a metagenomics approach and sequenced and analyzed the complete coding sequences (CDS) of VP3, NSP3, and NSP4 genes, as well as the partial or complete CDS of other genes of RVBs detected from Japanese cattle. VP3, NSP3, and NSP4 of bovine RVBs shared low nucleotide sequence identities (63.3-64.9% for VP3, 65.9-68.2% for NSP3, and 52.6-56.2% for NSP4) with those of murine, human, and porcine RVBs, suggesting that bovine RVBs belong to a novel genotype. Furthermore, significantly low amino acid sequence identities were observed for NSP4 (36.1-39.3%) between bovine RVBs and the RVBs of other species. In contrast, hydrophobic plot analysis of NSP4 revealed profiles similar to those of RVBs of other species and rotavirus A (RVA) strains. Phylogenetic analyses of all gene segments revealed that bovine RVB strains formed a cluster that branched distantly from other RVBs. These results suggest that bovine RVBs have evolved independently from other RVBs but in a similar manner to other rotaviruses. These findings provide insights into the evolution and diversity of RVB strains.

Distribution of two distinct rotavirus B (RVB) strains in the north-central Bangladesh and evidence for reassortment event among human RVB revealed by whole genomic analysis

Human rotavirus B (RVB), a rare cause of diarrhea in several Asian countries, has been reported to be genetically highly conserved. However, 14 RVB strains with two distinct RNA electropherotypes E1 and E2 (11 and 3 strains, respectively) were detected in adult patients with diarrhea, in Mymensingh in the north-central Bangladesh in 2014. In this study, VP7 gene sequences of all the 14 strains and nearly full-length sequences of all the 11 RNA segments of four RVB (two strains each representing E1 and E2 types) were determined and analyzed phylogenetically. For all the gene segments, sequence identities among strains with the same RNA pattern were higher (99%-100%) than those between strains with different RNA patterns (94-98%). Although all the gene segments of RVB strains were grouped into Indian-Bangladeshi lineage, VP1-3, VP6, VP7, NSP1, NSP2 and NSP5 genes of strains with E1 and E2 types were assigned to distinct sublineages S1 and S2, respectively. E1-strains clustered with Bangladeshi RVB strains reported previously (e.g., Bang117), while E2-strains with those from India (e.g., NIV-1048101), Myanmar, and Nepal. In contrast, VP4, NSP3 and NSP4 genes of both E1 and E2 RVB strains were classified into sublineage S2. These findings indicated that two genetically distinct RVB strains were simultaneously circulating in Mymensingh, Bangladesh. RVB strains with E1 electropherotype were suggested to be reassortants acquiring three gene segments (VP4, NSP3 and NSP4 genes) from the foreign RVB in the genetic background of indigenous Bangladeshi RVB represented by the strain Bang117.

Full genome analysis of group B rotaviruses from western India: genetic relatedness and evolution

To date, full-genome sequences of only seven human group B rotavirus (RVBs) strains have been described. Such data on more RVBs are necessary to establish the evolutionary relationship and ecological features of RVBs from different geographical regions. The present study was aimed at determining the full-length sequences of all 11 genes of 13 human RVB strains detected during 1995-2010 in sporadic and outbreak cases of acute gastroenteritis from four different cities of western India. This study also included estimation of evolutionary rates and site-specific selection pressure analysis for all gene segments. Nucleotide/deduced amino acid sequence analyses of structural and non-structural genes showed 95.1-99.8/94.1-100 % identity with the counterparts of RVB strains isolated in India, Bangladesh and Myanmar. Phylogenetic analyses of all gene segments revealed formation of a monophyletic clade of the western Indian RVB strains, reflecting their highly conserved nature. All gene segments were also found to be under negative/purifying selection pressure. These data suggest that RVB is circulating in the natural host as a series of stable viral clones. Estimates of rates of nucleotide substitution in all RVBs ranged from 1.36-4.78×10(-3) substitutions per site per year. The rate for human RVB VP7 and NSP2 genes were comparable, respectively, with the evolution kinetics of genotype G9/G12 and N1 group A rotavirus strains. The time of the most recent common ancestor of the extant human RVBs was estimated to be during 1915-1974. Evolutionary and genetic analyses carried out in this study provide data that is useful for the elucidation of evolutionary relationship/timescale, stasis or dynamics existing in the RVB population.

Molecular characterization of VP4, VP6, VP7 and NSP4 genes of group B rotavirus strains from outbreaks of gastroenteritis

OBJECTIVE

To characterize VP4, VP6, VP7 and NSP4 genes of representative GBR strains (NIV-005625, NIV-04622 and NIV-094456) detected as the major etiologic agent in the outbreaks of gastroenteritis in western India.

METHODS

Fecal specimens collected during the outbreaks of gastroenteritis were processed for RNA isolation, RT-PCR using GBR VP4, VP6, VP7 and NSP4 gene specific primers, nucleotide sequencing of the amplicons and phylogenetic analysis of the sequences.

RESULTS

Phylogenetic analysis of all of the VP4, VP6, VP7 and NSP4 gene sequences revealed clustering of GBR strains in Indian-Bangladeshi lineage of genotype G2 with 95.8%-99.4% nucleotide and 97.3%-100.0% amino acid identities. However, all three strains showed the presence of unique amino acid substitutions in the VP4 protein suggesting alteration in the antigenicity of outbreak strains of GBR. The VP8* and VP5* regions of VP4 proteins showed respectively 0.5%-6.3% and 0.2%-1.1% amino acid divergence from human GBR strains of Indian-Bangladeshi lineage.

CONCLUSIONS

These data confirm the reported variability of VP8* region and suggest the possible role of this region in the perpetuation of GBR infections in the environment. This is the first study to document the phylogenetic relationship of VP4, VP6, VP7 and NSP4 genes of GBR strains detected in the outbreaks of gastroenteritis from India with the GBR strains from other parts of world.

Genetic divergence of rotavirus nonstructural protein 4 results in distinct serogroup-specific viroporin activity and intracellular punctate structure morphologies

Nonstructural protein 4 (NSP4) viroporin activity is critical for the replication and assembly of serogroup A rotavirus (RVA); however, the dramatic primary sequence divergence of NSP4s across serogroups raises the possibility that viroporin activity is not a common feature among RVs. We tested for NSP4 viroporin activity from divergent strains, including RVA (EC and Ty-1), RVB (IDIR), and RVC (Cowden). Canonical viroporin motifs were identified in RVA, RVB, and RVC NSP4s, but the arrangement of basic residues and the amphipathic α-helices was substantially different between serogroups. Using Escherichia coli and mammalian cell expression, we showed that each NSP4 tested had viroporin activity, but serogroup-specific viroporin phenotypes were identified. Only mammalian RVA and RVC NSP4s induced BL21-pLysS E. coli cell lysis, a classical viroporin activity assay. In contrast, RVA, RVB, and RVC NSP4 expression was universally cytotoxic to E. coli and disrupted reduction-oxidation activities, as measured by a new redox dye assay. In mammalian cells, RVB and RVC NSP4s were initially localized in the endoplasmic reticulum (ER) and trafficked into punctate structures that were mutually exclusive with RVA NSP4. The punctate structures partially localized to the ER-Golgi intermediate compartment (ERGIC) but primarily colocalized with punctate LC3, a marker for autophagosomes. Similar to RVA NSP4, expression of RVB and RVC NSP4s significantly elevated cytosolic calcium levels, demonstrating that despite strong primary sequence divergence, RV NSP4 has maintained viroporin activity across serogroups A to C. These data suggest that elevated cytosolic calcium is a common critical process for all rotavirus strains.

Analysis of genetic diversity and molecular evolution of human group B rotaviruses based on whole genome segments

Group B rotavirus (GBR) is a rare enteric pathogen that causes severe diarrhoea, primarily in adults. Nearly full-length sequences of all 11 RNA segments were determined for human GBRs detected recently in India (IDH-084 in 2007, IC-008 in 2008), Bangladesh (Bang117 in 2003) and Myanmar (MMR-B1 in 2007), and analysed phylogenetically with the sequence data of GBRs reported previously. All RNA segments of GBR strains from India, Bangladesh and Myanmar showed >95 % nucleotide sequence identities. Among the 11 RNA segments, the VP6 and NSP2 genes showed the highest identities (>98 %), whilst the lowest identities were observed in the NSP4 gene (96.1 %), NSP5 gene (95.6 %) and VP8*-encoding region of the VP4 gene (95.9 %). Divergent or conserved regions in the deduced amino acid sequences of GBR VP1-VP4 and NSP1-NSP5 were similar to those in group A rotaviruses (GARs), and the functionally important motifs and structural characteristics in viral proteins known for GAR were conserved in all of the human GBRs. These findings suggest that, whilst the degree of genetic evolution may be dependent on each RNA segment, human GBR may have been evolving in a similar manner to GAR, associated with the similar functional roles of individual viral proteins.

Integrins alpha1beta1 and alpha2beta1 are receptors for the rotavirus enterotoxin

Rotavirus NSP4 is a viral enterotoxin capable of causing diarrhea in neonatal mice. This process is initiated by the binding of extracellular NSP4 to target molecule(s) on the cell surface that triggers a signaling cascade leading to diarrhea. We now report that the integrins alpha1beta1 and alpha2beta1 are receptors for NSP4. NSP4 specifically binds to the alpha1 and alpha2 I domains with apparent K(d) = 1-2.7 muM. Binding is mediated by the I domain metal ion-dependent adhesion site motif, requires Mg(2+) or Mn(2+), is abolished with EDTA, and an NSP4 point mutant, E(120)A, fails to bind alpha2 integrin I domain. NSP4 has two distinct integrin interaction domains. NSP4 amino acids 114-130 are essential for binding to the I domain, and NSP4 peptide 114-135 blocks binding of the natural ligand, collagen I, to integrin alpha2. NSP4 amino acids 131-140 are not associated with the initial binding to the I domain, but elicit signaling that leads to the spreading of attached C2C12-alpha2 cells, mouse myoblast cells stably expressing the human alpha2 integrin. NSP4 colocalizes with integrin alpha2 on the basolateral surface of rotavirus-infected polarized intestinal epithelial (Caco-2) cells as well as surrounding noninfected cells. NSP4 mutants that fail to bind or signal through integrin alpha2 were attenuated in diarrhea induction in neonatal mice. These results indicate that NSP4 interaction with integrin alpha1 and alpha2 is an important component of enterotoxin function and rotavirus pathogenesis, further distinguishing this viral virulence factor from other microbial enterotoxins.

An NSP4-dependant mechanism by which rotavirus impairs lactase enzymatic activity in brush border of human enterocyte-like Caco-2 cells

Lactase-phlorizin hydrolase (LPH, EC 3.2.1.23-62) is a brush border membrane (BBM)-associated enzyme in intestinal cells that hydrolyse lactose, the most important sugar in milk. Impairing in lactase activity during rotavirus infection has been described in diseased infants but the mechanism by which the functional lesion occurs remains unknown. We undertook a study to elucidate whether rotavirus impairs the lactase enzymatic activity in BBM of human enterocyte cells. In this study we use cultured human intestinal fully differentiated enterocyte-like Caco-2 cells to demonstrate how the lactase enzymatic activity at BBM is significantly decreased in rhesus monkey rotavirus (RRV)-infected cells. We found that the decrease in enzyme activity is not dependent of the Ca(2+)- and cAMP-dependent signalling events triggered by the virus. The LPH biosynthesis, stability, and expression of the protein at the BBM of infected cells were not modified. We provide evidence that in RRV-infected cells the kinetic of lactase enzymatic activity present at the BBM was modified. Both BBM(control) and BBM(RRV) have identical K(m) values, but hydrolyse the substrate at different rates. Thus, the BBM(RRV) exhibits almost a 1.5-fold decreased V(max) than that of BBM(control) and is therefore enzymatically less active than the latter. Our study demonstrate conclusively that the impairment of lactase enzymatic activity at the BBM of the enterocyte-like Caco-2 cells observed during rotavirus infection results from an inhibitory action of the secreted non-structural rotavirus protein NSP4.

Rotavirus nonstructural glycoprotein NSP4 is secreted from the apical surfaces of polarized epithelial cells

NSP4, a nonstructural glycoprotein encoded by rotavirus, is involved in the morphogenesis of virus particles in the endoplasmic reticulum of infected cells. NSP4 is also implicated in the pathophysiology of rotavirus-induced diarrhea by acting as an enterotoxin. To mediate enterotoxic effects in vivo, NSP4 must be secreted or released from rotavirus-infected cells in a soluble form; however, previous studies have indicated that NSP4 is a transmembrane glycoprotein localized within endomembrane compartments in infected cells. In this study, we examined the fate of NSP4 synthesized in Caco-2 cells infected with bovine rotavirus. Our studies reveal that NSP4 is actively secreted into the culture medium, preferentially from the infected-cell apical surface. The secretion of NSP4 is dramatically inhibited by brefeldin A and monensin, suggesting that a Golgi-dependent pathway is involved in release of the protein. In agreement with the proposed involvement of the Golgi apparatus during secretion, secreted NSP4 appears to undergo additional posttranslational modification compared to its cell-associated counterpart and is partially resistant to deglycosylation by endoglycosidase H. Our experiments identify a novel, soluble form of NSP4 secreted from virus-infected cells with the potential to carry out the enterotoxigenic role previously attributed to recombinant forms of the protein.