Functional characterization of putative promoter elements from infectious hypodermal and hematopoietic necrosis virus (IHHNV) in shrimp and in insect and fish cell lines

Genome assembly of the Australian black tiger shrimp (Penaeus monodon) reveals a novel fragmented IHHNV EVE sequence

Shrimp are a valuable aquaculture species globally; however, disease remains a major hindrance to shrimp aquaculture sustainability and growth. Mechanisms mediated by endogenous viral elements have been proposed as a means by which shrimp that encounter a new virus start to accommodate rather than succumb to infection over time. However, evidence on the nature of such endogenous viral elements and how they mediate viral accommodation is limited. More extensive genomic data on Penaeid shrimp from different geographical locations should assist in exposing the diversity of endogenous viral elements. In this context, reported here is a PacBio Sequel-based draft genome assembly of an Australian black tiger shrimp (Penaeus monodon) inbred for 1 generation. The 1.89 Gbp draft genome is comprised of 31,922 scaffolds (N50: 496,398 bp) covering 85.9% of the projected genome size. The genome repeat content (61.8% with 30% representing simple sequence repeats) is almost the highest identified for any species. The functional annotation identified 35,517 gene models, of which 25,809 were protein-coding and 17,158 were annotated using interproscan. Scaffold scanning for specific endogenous viral elements identified an element comprised of a 9,045-bp stretch of repeated, inverted, and jumbled genome fragments of infectious hypodermal and hematopoietic necrosis virus bounded by a repeated 591/590 bp host sequence. As only near complete linear ∼4 kb infectious hypodermal and hematopoietic necrosis virus genomes have been found integrated in the genome of P. monodon previously, its discovery has implications regarding the validity of PCR tests designed to specifically detect such linear endogenous viral element types. The existence of joined inverted infectious hypodermal and hematopoietic necrosis virus genome fragments also provides a means by which hairpin double-stranded RNA could be expressed and processed by the shrimp RNA interference machinery.

Transcriptionally promiscuous "blurry" promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Background

We have recently described a peculiar feature of the promoters in two Drosophila Tc1-like elements, Bari1 and Bari3. The AT-richness and the presence of weak core-promoter motifs make these promoters, that we have defined “blurry”, able to activate transcription of a reporter gene in cellular systems as diverse as fly, human, yeast and bacteria. In order to clarify whether the blurry promoter is a specific feature of the Bari transposon family, we have extended this study to promoters isolated from three additional DNA transposon and from two additional LTR retrotransposons.

Results

Here we show that the blurry promoter is also a feature of two vertebrate transposable elements, Sleeping Beauty and Hsmar1, belonging to the Tc1/mariner superfamily. In contrast, this feature is not shared by the promoter of the hobo transposon, which belongs to the hAT superfamily, nor by LTR retrotransposon-derived promoters, which, in general, do not activate transcription when introduced into non-related genomes.

Conclusions

Our results suggest that the blurry promoter could be a shared feature of the members of the Tc1/mariner superfamily with possible evolutionary and biotechnological implications.

Electronic supplementary material

The online version of this article (10.1186/s13100-019-0155-6) contains supplementary material, which is available to authorized users.

Diversity of single-stranded DNA containing viruses in shrimp

Over the past four decades, shrimp aquaculture has turned into a major industry providing jobs for millions of people worldwide especially in countries with large coastal boundaries. While the shrimp industry continues to expand, the sustainability of shrimp aquaculture has been threatened by the emergence of diseases. Diseases caused by single-stranded DNA containing viruses, such as infectious hypodermal and hematopoietic necrosis virus (IHHNV) and hepatopancreatic parvovirus (HPV), have caused immense losses in shrimp aquaculture since the early 1980s. In fact, the disease outbreak in the blue shrimp (Penaeus stylirostris) caused by IHHNV in early 1980s ultimately led to the captive breeding program in shrimp being shifted from P. stylirostris to the white shrimp (Penaeus vannamei), and today P. vannamei is the preferred cultured shrimp species globally. To date, four single-stranded DNA viruses are known to affect shrimp; these include IHHNV, HPV, spawner-isolated mortality virus (SMV) and lymphoidal parvo-like virus (LPV). Due to the economic losses caused by IHHNV and HPV, most studies have focused on these two viruses, and only IHHNV is included in the OIE list of Crustacean Diseases. Hence this review will focus on IHHNV and HPV. IHHNV and HPV virions are icosahedral in morphology measuring 20-22 nm in size and contain a single-stranded DNA (ssDNA) of 4-6 kb in size. Both IHHNV and HPV are classified into the sub-order Brevidensoviruses, family Densovirinae. The genome architecture of both viruses are quite similar as they contain two completely (as in IHHNV) or partially overlapping (as in HPV) non-structural and one structural gene. Histopathology and polymerase chain reaction (PCR)-based methods are available for both viruses. Currently, there is no anti-viral therapy for any viral diseases in shrimp. Therefore, biosecurity and the use of genetically resistant lines remains as the corner stone in the management of viral diseases. In recent years, gene silencing using the RNA interference (RNAi) approach has been reported for both IHHNV and HPV via injection. However, the delivery of RNAi molecules via oral route remains a challenge, and the utility of RNAi-based therapy has yet to be materialized in shrimp aquaculture.

Engineered cell lines for fish health research

As fish farming continues to increase worldwide, the related research areas of fish disease and immunology are also expanding, aided by the revolution in access to genomic information and molecular technology. The genomes of most fish species of economic importance are now available and annotation based on sequence homology with characterised genomes is underway. However, while useful, functional homology is more difficult to determine, there being a lack of widely distributed and well characterised reagents such as monoclonal antibodies, traditionally used in mammalian studies, to help with confirming functions and cellular interactions of fish molecules. In this context, fish cell lines and the possibility of their genetic engineering offer good prospects for studying functional genomics with respect to fish diseases. In this review, we will give an overview of available permanently genetically engineered fish cell lines, as cell-based reporter systems or platforms for expression of endogenous immune or pathogen genes, to investigate interactions and function. The advantages of such systems and the technical challenge for their development will be discussed.

Cloning and comparative analysis the proximal promoter activities of arginase and agmatinase genes in Apostichopus japonicus

Our previous work demonstrated that Apostichopus japonicus arginase and agmatinase from l-arginine metabolism synergistically compete with NOS under pathogens challenge. Here we conducted a study to further investigate the mechanism in the regulation of arginase and agmatinase genes in l-arginine metabolism using EPC cell system. Luciferase analysis and progressive 5' deletion analysis suggested that Ajagmatinase promoter was a very robust promoter for its transcription, and the core region of Ajarginase promoter was located within -277 bp to -157 bp. Besides, their promoter activities were significantly activated by LPS and l-arginine challenge both in a time- and dose-dependent manners in EPC cells. When different truncated reporter vector and expression vector co-transfection experiment revealed transcription factor NF-κB/Rel and STAT5 could significantly inhibited Ajarginase promoter activity, but not Ajagmatinase. Our findings were provided novel insights into the transcriptional regulation of Ajarginase and Ajagmatinase, and selectively change their expressions might prevent pathogens infection.

Prevalence and genomic analysis of infectious hypodermal and hematopoietic necrosis virus (IHHNV) in Litopenaeus vannamei shrimp farmed in Shanghai, China

Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is prevalent among farmed shrimp and results in significant reductions in shrimp production. In order to gain a better understanding of the prevalence of IHHNV in the Litopenaeus vannamei shrimp population of Shanghai, China, samples were collected during two cultivation seasons and subjected to diagnostic PCR. The results of this study showed that 167 out of 200 shrimp were positive for IHHNV, indicating a high viral prevalence (83.5 %) in farmed shrimp populations. Our results also indicated that there was a moderate correlation between IHHNV prevalence and water temperature, salinity and pH and only a slight correlation with the concentration of dissolved oxygen (DO). A mathematical model was developed in order to predict the relationship between these four characteristics of water quality and IHHNV prevalence, ultimately resulting in an estimate of the best water quality criteria (IHHNV prevalence = 0) where T = 30 °C pH = 8.0, DO = 18.3 mg/L, and salinity = 1.5 ‰. Additionally, two IHHNV genotypes were identified, the sequencing of which revealed a high similarity to the known IHHNV genotypes based on a comparison of their nucleotide and amino acid sequences. Two types of repetitive sequences were detected at both the 5' and 3' ends of the non-coding regions, which are commonly found in other IHHNV genomic sequences. Phylogenetic analysis indicated that the IHHNV Shanghai genotypes were closely related to strains from Ganyu and Sheyang, but not to strains originating from Fujian, China. This finding suggests that IHHNVs have emerged independently several times in China.

Transgene expression in Penaeus monodon cells: evaluation of recombinant baculoviral vectors with shrimp specific hybrid promoters

It has been realized that shrimp cell immortalization may not be accomplished without in vitro transformation by expressing immortalizing gene in cells. In this process, efficiency of transgene expression is confined to the ability of vectors to transmit gene of interests to the genome. Over the years, unavailability of such vectors has been hampering application of such a strategy in shrimp cells. We report the use of recombinant baculovirus mediated transduction using hybrid promoter system for transgene expression in lymphoid cells of Penaeus monodon. Two recombinant baculovirus vectors with shrimp viral promoters (WSSV-Ie1 and IHHNV-P2) were constructed (BacIe1-GFP and BacP2-GFP) and green fluorescent protein (GFP) used as the transgene. The GFP expression in cells under the control of hybrid promoters, PH-Ie1 or PH-P2, were analyzed and confirmed in shrimp cells. The results indicate that the recombinant baculovirus with shrimp specific viral promoters (hybrid) can be employed for delivery of foreign genes to shrimp cells for in vitro transformation.

Biology, genome organization, and evolution of parvoviruses in marine shrimp

As shrimp aquaculture has evolved from a subsistent farming activity to an economically important global industry, viral diseases have also become a serious threat to the sustainable growth and productivity of this industry. Parvoviruses represent an economically important group of viruses that has greatly affected shrimp aquaculture. In the early 1980s, an outbreak of a shrimp parvovirus, infectious hypodermal and hematopoietic necrosis virus (IHHNV), led to the collapse of penaeid shrimp farming in the Americas. Since then, considerable progress has been made in characterizing the parvoviruses of shrimp and developing diagnostic methods aimed to preventing the spread of diseases caused by these viruses. To date, four parvoviruses are known that infect shrimp; these include IHHNV, hepatopancreatic parvovirus (HPV), spawner-isolated mortality virus (SMV), and lymphoid organ parvo-like virus. Due to the economic repercussions that IHHNV and HPV outbreaks have caused to shrimp farming over the years, studies have been focused mostly on these two pathogens, while information on SMV and LPV remains limited. IHHNV was the first shrimp virus to be sequenced and the first for which highly sensitive diagnostic methods were developed. IHHNV-resistant lines of shrimp were also developed to mitigate the losses caused by this virus. While the losses due to IHHNV have been largely contained in recent years, reports of HPV-induced mortalities in larval stages in hatchery and losses due to reduced growth have increased. This review presents a comprehensive account of the history and current knowledge on the biology, diagnostics methods, genomic features, mechanisms of evolution, and management strategies of shrimp parvoviruses. We also highlighted areas where research efforts should be focused in order to gain further insight on the mechanisms of parvoviral pathogenicity in shrimp that will help to prevent future losses caused by these viruses.

Spawning stress triggers WSSV replication in brooders via the activation of shrimp STAT

In the early days of shrimp aquaculture, wild-captured brooders usually spawned repeatedly once every 2-4days. However, since the first outbreaks of white spot disease (WSD) nearly 20years ago, captured female brooders often died soon after a single spawning. Although these deaths were clearly attributable to WSD, it has always been unclear how spawning stress could lead to an outbreak of the disease. Using real-time qPCR, we show here that while replication of the white spot syndrome virus (WSSV; the causative agent of WSD) is triggered by spawning, there was no such increase in the levels of another shrimp DNA virus, IHHNV (infectious hypodermal and hematopoietic necrosis virus). We also show that levels of activated STAT are increased in brooders during and after spawning, which is important because shrimp STAT is known to transactivate the expression of the WSSV immediate early gene ie1. Lastly, we used dsRNA silencing experiment to show that both WSSV ie1 gene expression and WSSV genome copy number were reduced significantly after shrimp STAT was knocked-down. This is the first report to demonstrate in vivo that shrimp STAT is important for WSSV replication and that spawning stress increases activated STAT, which in turn triggers WSSV replication in WSSV-infected brooders.

Genomics, Molecular Epidemiology and Diagnostics of Infectious hypodermal and hematopoietic necrosis virus

Infectious hypodermal and hematopoietic necrosis virus (IHHNV) is one of the major viral pathogens of penaeid shrimps worldwide, which has resulted in severe mortalities of up to 90 % in cultured Penaeus (Litopenaeus) stylirostris from Hawaii and hence designated Penaeus stylirostris densovirus (PstDNV). IHHNV is distributed in shrimp culture facilities worldwide. It causes large economic loss to the shrimp farming industry. Our knowledge about the natural reservoirs of IHHNV is still scarce. Recent studies suggest that there is sufficient sequence variation among the isolates from different locations in Asia, suggesting multiple geographical strains of the virus. Four complete genomes and several partial sequences of the virus are available in the GenBank. Complete genome information would be useful for assessing the specificity of diagnostics for viruses from different geographical areas. Comparisons of complete genome sequences will help us gain insights into point mutations that can affect virulence of the virus. In addition, because of unavailability of shrimp cell lines for culturing IHHNV in vitro, quantification of virus is difficult. The recent progress in research regarding clinical signs, geographical distribution, complete genome sequence and genetic variation, transmission has made it possible to obtain information on IHHNV. A comprehensive understanding of IHHNV infection process, pathogenesis, structural proteins and replication is essential for developing prevention measures. To date, no effective prophylactic measure for IHHNV infection is available for shrimp to reduce its impact. This review provides an overview of key issues regarding IHHNV infection and disease in commercially important shrimp species.

The interaction between viral protein and host actin facilitates the virus infection to host

Although the virus-host interaction has attracted extensive studies, the host proteins essential for virus infection remain largely unknown. To address this issue, the shrimp Penaeus stylirostris densovirus (PstDNV), belonging to the family Parvoviridae, was characterized. PstDNV, a single-stranded DNA virus with a 3.9-kb genome, encoded only three open reading frames (ORFs). Among the three viral proteins, the PstDNV ORF2-encoded protein was discovered to interact with the shrimp actin, suggesting that the host actin played a very important role in virus infection. The RNAi assays revealed that the ORF2-encoded protein was required for the PstDNV infection. The confocal evidence demonstrated that the interaction between the ORF2-encoded protein and actin was essential for the virus infection. Therefore our study indicated that the manipulation of the host actin cytoskeleton was a necessary strategy for viral pathogens to invade host cells.

Expression strategy of densonucleosis virus from the German cockroach, Blattella germanica

Blattella germanica densovirus (BgDNV) is an autonomous parvovirus that infects the German cockroach. BgDNV possesses three mRNAs for NS proteins, two of which are splice variants of the unspliced transcript. The unspliced variant encodes open reading frame 5 (ORF5) (NS3), while NSspl1 encodes ORF3 (NS1) and ORF4 (NS2) and NSspl2 encodes the C-proximal half of NS1. BgDNV possesses three VP transcripts, one of which (VP) is unspliced, while the other two (VPspl1 and VPspl2) are generated by alternative splicing. The unspliced VP transcript contains both ORF1 and ORF2, while in VPspl1, ORF1 and ORF2 are joined in frame. The transcription of NS genes begins at an earlier stage of the virus life cycle than the transcription of VP genes. NS and VP transcripts overlap by 48 nucleotides (nt). BgDNV is characterized by two additional NS transcripts overlapping by more than 1,650 nt with VP-coding transcripts. Four different bands (97, 85, 80, and 57 kDa) corresponding to three BgDNV capsid proteins were detected on SDS-PAGE. Mass spectrometry analysis showed that the amino acid composition of the 85-kDa and 80-kDa proteins is the same. Moreover, both of these proteins are ubiquitinated. The BgDNV PLA(2) domain, which is critical for cellular uptake of the virus, is located in ORF2 and is present only in VP1. In contrast to all of the parvoviruses studied in this respect, VP2 has a unique N terminus that is not contained within VP1 and VP3. In situ recognition with NS1- and VP-specific antibodies revealed an uneven pattern of NS1 expression resembling a halo within the nuclear membrane.

Identification of the core sequence elements in Penaeus stylirostris densovirus promoters

In silico analysis of three Penaeus stylirostris densovirus (PstDNV) promoters, designated P2, P11, and P61, revealed sequence motifs including the TATA box, downstream promoter element (DPE), GC- and A-rich regions, inverted repeat, activation sequence-1 like (ASL) box, and a conserved guanosine (G) at +24. To delineate the regulatory role of these motifs on promoter activity, deletion constructs were made in a promoter assay vector, pGL3 Basic, that contains a luciferase reporter gene. Luciferase assay showed that P2 had the highest promoter activity followed by P11 and P61 in Sf9 cells. The deletions of inverted repeat, DPE, and GC-rich regions in P2 had the highest negative impact on this promoter. Deletions of DPE, G at the +24, and ASL box in P11 had the highest negative impact on this promoter activity. In P61, DPE and G at +24 are the two key regulators of transcriptional activity. Identification of the key transcriptional regulators is important in understanding the PstDNV pathogenesis in shrimp. This information is also valuable in constructing shrimp viral promoter-based vectors for protein expression in insect cell culture system as well as in shrimp.

The infectious hypodermal and haematopoietic necrosis virus: a brief review of what we do and do not know

Given its high prevalence, its wide distribution and its remarkable capacity to cause severe mortality in shrimp, the infectious hypodermal and haematopoietic necrosis virus (IHHNV) may deserve far more attention than it has received, as it remains considered as one of the most serious problems plaguing the global shrimp farming industry. Furthermore, its real measurable impact over wild shrimp populations remains unknown. Undeniably, the progress that we have reached today on the knowledge of its geographical distribution, clinical signs, genetic diversity, transmission and virulence may help to identify and understand important aspects of its biology and pathogenesis. However, the information regarding the molecular events that occur during the infection process is scarce. Thus, it may not be surprising to find that there are no therapeutic options available for the prophylaxis or treatments to reduce the deleterious impact of this viral pathogen to date. The aim of this review is to integrate and discuss the current state of knowledge concerning several aspects of the biology of IHHNV and to highlight potential future directions for this area of research.

Transcriptional analysis of Penaeus stylirostris densovirus genes

Penaeus stylirostris densovirus (PstDNV) genome contains three open reading frames (ORFs), left, middle, and right, which encode a non-structural (NS) protein, an unknown protein, and a capsid protein (CP), respectively. Transcription mapping revealed that P2, P11 and P61 promoters transcribe the left, middle and right ORFs. NS transcript uses the D1/A1 donor/acceptor sites for splicing and has two alternate transcription termination sites (TTS) that were different from the previously predicted TTS. The transcription initiation site (TIS) and the TTS for the middle and the right ORFs conform to predicted sites. PstDNV transcript quantification in infected shrimp revealed that the NS and CP transcripts were expressed at an equivalent level and significantly higher than the middle ORF transcript. In vitro assay showed that P2 had the highest promoter activity followed by P11 and P61. Transcription mapping data provided new insights into PstDNV gene expression strategy.

Viral disease emergence in shrimp aquaculture: origins, impact and the effectiveness of health management strategies

Shrimp aquaculture has grown rapidly over several decades to become a major global industry that serves the increasing consumer demand for seafood and has contributed significantly to socio-economic development in many poor coastal communities. However, the ecological disturbances and changes in patterns of trade associated with the development of shrimp farming have presented many of the pre-conditions for the emergence and spread of disease. Shrimp are displaced from their natural environments, provided artificial or alternative feeds, stocked in high density, exposed to stress through changes in water quality and are transported nationally and internationally, either live or as frozen product. These practices have provided opportunities for increased pathogenicity of existing infections, exposure to new pathogens, and the rapid transmission and transboundary spread of disease. Not surprisingly, a succession of new viral diseases has devastated the production and livelihoods of farmers and their sustaining communities. This review examines the major viral pathogens of farmed shrimp, the likely reasons for their emergence and spread, and the consequences for the structure and operation of the shrimp farming industry. In addition, this review discusses the health management strategies that have been introduced to combat the major pathogens and the reasons that disease continues to have an impact, particularly on poor, small-holder farmers in Asia.