High Degree Of Sequence Identity Research Articles

The N-terminal domain is required for cell surface localisation of VapA, a member of the Vap family of Rhodococcus equi virulence proteins.

Rhodococcus equi pneumonia is an important cause of mortality in foals worldwide. Virulent equine isolates harbour an 80-85kb virulence plasmid encoding six virulence-associated proteins (Vaps). VapA, the main virulence factor of this intracellular pathogen, is known to be a cell surface protein that creates an intracellular niche for R. equi growth. In contrast, VapC, VapD and VapE are secreted into the intracellular milieu. Although these Vaps share very high degree of sequence identity in the C-terminal domain, the N-terminal domain (N-domain) of VapA is distinct. It has been proposed that this domain plays a role in VapA surface localization but no direct experimental data provides support to such hypothesis. In this work, we employed R. equi 103S harbouring an unmarked deletion of vapA (R. equi ΔvapA) as the genetic background to express C-terminal Strep-tagged Vap-derivatives integrated in the chromosome. The surface localization of these proteins was assessed by flow cytometry using the THE2122;-NWSHPQFEK Tag FITC-antibody. We show that VapA is the only cell surface Vap encoded in the virulence plasmid. We present compelling evidence for the role of the N-terminal domain of VapA on cell surface localization using fusion proteins in which the N-domain of VapD was exchanged with the N-terminus of VapA. Lastly, using an N-terminally Strep-tagged VapA, we found that the N-terminus of VapA is exposed to the extracellular environment. Given the lack of a lipobox in VapA and the exposure of the N-terminal Strep-tag, it is possible that VapA localization on the cell surface is mediated by interactions between the N-domain and components of the cell surface. We discuss the implications of this work on the light of the recent discovery that soluble recombinant VapA added to the extracellular medium functionally complement the loss of VapA.

Functions of the sulfatase‐modifying factor 1 (HaSumf1) in the development and host glucosinolate adaptation of Helicoverpa armigera

AbstractThe system of gulcosinoalte sulfatase–sulfatase‐modifying factors (Sumfs) in herbivorous insects fulfils an essential function in defending host plant glucosinolates (GLSs)—the compounds of cruciferous plants—by swiftly desulfurising them. Previously, eight HaSulfs and one HaSumf1 were identified in Helicoverpa armigera. GLSs have a significant impact on the growth and development of H. armigera larvae. They can induce the expression of HaSulf in the midgut of H. armigera at both gene and protein levels. In the present study, we utilised RNAi technology to silence the HaSumf1 gene and explored its potential impact on the growth, development, and adaptation of GLSs. The sequence analysis has indicated that the HaSumf1 gene in H. armigera shares a high degree of sequence identity with other insect genes and is expressed at its highest level in the fifth‐instar phase. Additionally, the qRT‐PCR results reveal that the expression of HaSumf1 was upregulated by 1.26 and 0.07 times in third‐instar and 1.65 and 0.19 times in fifth‐instar when fed with 0.004% and 0.04% GLS, respectively. The effectiveness of dsSumf1 silencing was observed in both third‐ and fifth‐instar stages, with silencing rates of 65.5%–88.9% and 61.3%–74.6%, respectively (p < 0.05). The findings of the bioassay indicate that H. armigera's body weight at fifth‐instar significantly increased after treatment with 0.004% GLS and 0.04% GLS, while the larval survival rate, pupation rate, and pupa weight decreased. Notably, when feeding dsRNA‐encapsulated carbon quantum dots (CQD‐dsRNA), this trend was significantly strengthened (p < 0.05). Taken together, these findings provide evidence supporting HaSumf1's conservation involvement in the adaptation of host plant GLSs during lepidopteran insect evolution. Therefore, it plays a critical role in the growth and development of H. armigera, offering molecular targets for developing novel pesticides and targeted control measures against this vital pest.

Twelve toll-like receptor (TLR) genes in the family Equidae - comparative genomics, selection and evolution.

Toll-like receptors (TLRs) represent an important part of the innate immune system. While human and murine TLRs have been intensively studied, little is known about TLRs in non-model species. The order Perissodactyla comprises a variety of free-living and domesticated species exposed to different pathogens in different habitats and is therefore suitable for analyzing the diversity and evolution of immunity-related genes. We analyzed TLR genes in the order Perissodactyla with a focus on the family Equidae. Twelve TLRs were identified by bioinformatic analyses of online genomic resources; their sequences were confirmed in equids by genomic DNA re-sequencing of a panel of nine species. The expression of TLR11 and TLR12 was confirmed in the domestic horse by cDNA sequencing. Phylogenetic reconstruction of the TLR gene family in Perissodactyla identified six sub-families. TLR4 clustered together with TLR5; the TLR1-6-10 subfamily showed a high degree of sequence identity. The average estimated evolutionary divergence of all twelve TLRs studied was 0.3% among the Equidae; the most divergent CDS were those of Equus caballus and Equus hemionus kulan (1.34%) in the TLR3, and Equus africanus somaliensis and Equus quagga antiquorum (2.1%) in the TLR1 protein. In each TLR gene, there were haplotypes shared between equid species, most extensively in TLR3 and TLR9 CDS, and TLR6 amino acid sequence. All twelve TLR genes were under strong negative overall selection. Signatures of diversifying selection in specific codon sites were detected in all TLRs except TLR8. Differences in the selection patterns between virus-sensing and non-viral TLRs were observed.

Specific Nucleotides in the Common Region of the Begomovirus Tomato Rugose Mosaic Virus (ToRMV) Are Responsible for the Negative Interference over Tomato Severe Rugose Virus (ToSRV) in Mixed Infection.

Mixed infection between two or more begomoviruses is commonly found in tomato fields and can affect disease outcomes by increasing symptom severity and viral accumulation compared with single infection. Viruses that affect tomato include tomato severe rugose virus (ToSRV) and tomato rugose mosaic virus (ToRMV). Previous work showed that in mixed infection, ToRMV negatively affects the infectivity and accumulation of ToSRV. ToSRV and ToRMV share a high degree of sequence identity, including cis-elements in the common region (CR) and their specific recognition sites (iteron-related domain, IRD) within the Rep gene. Here, we investigated if divergent sites in the CR and IRD are involved in the interaction between these two begomoviruses. ToSRV clones were constructed containing the same nucleotides as ToRMV in the CR (ToSRV-A(ToR:CR)), IRD (ToSRV-A(ToR:IRD)) and in both regions (ToSRV-A(ToR:CR+IRD)). When plants were co-inoculated with ToRMV and ToSRV-A(ToR:IRD), the infectivity and accumulation of ToSRV were negatively affected. In mixed inoculation of ToRMV with ToSRV-A(ToR:CR), high infectivity of both viruses and high DNA accumulation of ToSRV-A(ToR:CR) were observed. A decrease in viral accumulation was observed in plants inoculated with ToSRV-A(ToR:CR+IRD). These results indicate that differences in the CR, but not the IRD, are responsible for the negative interference of ToRMV on ToSRV.

Commonality of Virulence-Promoting Function in Rhodococcus equi Virulence Associated Proteins (Vaps)

Rhodococcus equi is a Gram-positive facultative intracellular pathogen associated with life-threatening bronchopneumonial disease in foals. Key to R. equi’s intracellular survival in host macrophages is the production of virulence associated proteins (Vaps). Numerous vap genes are found on virulence plasmids isolated from different species, and the Vaps share a high degree of sequence identity. VapA has been extensively studied, and although vapK and vapN genes from other R. equi virulence plasmids have been shown to be essential for R. equi intracellular survival, their mode of action is less characterised. We, therefore, examined whether VapK and VapN worked mechanistically in the same way as VapA. Indeed, like VapA, VapK and VapN neutralised lysosomal pH and reduced lysosomal hydrolase activity. A loss of VapA and R. equi virulence could be regained by the presence of either VapK or VapN. The acid-neutralisation activity was also observed to a lesser extent with VapB. There was a differential activity across these virulence-promoting Vaps with the most “acid-neutralising” activity found with VapN, then VapA and K, and finally VapB. These data suggest that VapA production, which is often found in equine infections, can be substituted by VapK and B (produced by plasmids often found in porcine species) or VapN (produced by plasmids often isolated in bovine and human samples). These data imply that the molecular mechanism(s) that VapA uses to neutralise lysosomal acidity should also be seen in VapN and K which will help guide researchers in identifying their precise mode of action and aid the future development of targeted therapeutics.

The extant immunoglobulin superfamily, member 1 gene results from an ancestral gene duplication in eutherian mammals

Immunoglobulin superfamily, member 1 (IGSF1) is a transmembrane glycoprotein with high expression in the mammalian pituitary gland. Mutations in the IGSF1 gene cause congenital central hypothyroidism in humans. The IGSF1 protein is co-translationally cleaved into N- and C-terminal domains (NTD and CTD), the latter of which is trafficked to the plasma membrane and appears to be the functional portion of the molecule. Though the IGSF1-NTD is retained in the endoplasmic reticulum and has no apparent function, it has a high degree of sequence identity with the IGSF1-CTD and is conserved across mammalian species. Based upon phylogenetic analyses, we propose that the ancestral IGSF1 gene encoded the IGSF1-CTD, which was duplicated and integrated immediately upstream of itself, yielding a larger protein encompassing the IGSF1-NTD and IGSF1-CTD. The selective pressures favoring the initial gene duplication and subsequent retention of a conserved IGSF1-NTD are unresolved.

Detection of Small CYP11B1 Deletions and One Founder Chimeric CYP11B2/CYP11B1 Gene in 11β-Hydroxylase Deficiency.

Objective11β-Hydroxylase deficiency (11β-OHD) caused by mutations in the CYP11B1 gene is the second most common form of congenital adrenal hyperplasia. Both point mutations and genomic rearrangements of CYP11B1 are important causes of 11β-OHD. However, the high degree of sequence identity between CYP11B1 and its homologous gene CYP11B2, presents unique challenges for molecular diagnosis of suspected 11β-OHD. The aim of this study was to detect the point mutation, indel, small deletion of CYP11B1 and chimeric CYP11B2/CYP11B1 gene in a one-tube test, improving the genetic diagnosis of 11β-OHD.MethodsOptimized custom-designed target sequencing strategy was performed in three patients with suspected 11β-OHD, in which both the coverage depth of paired-end reads and the breakpoint information of split reads from sequencing data were analysed in order to detect genomic rearrangements covering CYP11B1. Long-range PCR was peformed to validate the speculated CYP11B1 rearrangements with the breakpoint-specifc primers.ResultsUsing the optimized target sequencing approach, we detected two intragenic/intergenic deletions of CYP11B1 and one chimeric CYP11B2/CYP11B1 gene from three suspected patients with 11β-OHD besides three pathogenic heterozygous point mutation/indels. Furthermore, we mapped the precise breakpoint of this chimeric CYP11B2/CYP11B1 gene located on chr8:143994517 (hg19) and confirmed it as a founder rearrangement event in the Chinese population.ConclusionsOur optimized target sequencing approach improved the genetic diagnosis of 11β-OHD.

First Report of the Cactus Cyst Nematode, Cactodera cacti, Infecting Cereus jamacaru (Cactaceae) in Brazil.

During a survey in 2018 for plant nematodes associated with roots and soil in cactus cultivation areas in Ceará State (3°44'48"S, 38°34'29"W), cysts were found on roots of mandacaru, Cereus jamacaru DC. This cactus is native to Brazil, can grow to 6-10 meters in height, and is widely distributed in the Northeast region (Romeiro-Brito et al. 2016) where it is used in construction, in disease remedies, as forage, and as an ornamental (Sales et al. 2014). Several cysts, second-stage juveniles (J2) and eggs extracted from the soil and roots, using sucrose centrifugation, were examined by scanning electron microscopy (SEM) and light microscopy (LM) to determine morphological and morphometric characteristics. Molecular characteristics were determined by DNA extraction from J2 and embryonated eggs using a protocol specific for Heteroderidae (Subbotin et al., 2018). The internal transcribed spacer sequence (ITS) region of the rDNA and D2-D3 regions of the 28S rDNA were amplified using the universal primers TW81 (5'-GTTTCCGTAGGTGAACCTGC-3') and AB28 (5'-ATATGCTTAAGTTCAGCGGGT-3'), D2A(5'-ACAAGTACCGTGAGGGAAAGTTG-3') and D3B(5'-TCGGAAGGAACCAGCTACTA-3'), respectively. To confirm that mandacaru is a host for C. cacti, six plantlets of mandacaru were inoculated with 1,800 eggs of the nematode, and kept in a greenhouse at 31 ± 3 ºC and irrigated daily. Six non inoculated mandacaru plantlets served as control treatment. Morphometric characteristics of cysts (n=35) were body length, excluding neck, 555.8 ± 87.8 (354,9 - 727,6) μm, body width 392.1 ± 63.4 (297.9 - 553.7) μm, neck length 63.5 ± 25.8 (49.8-105.0) μm, length to width ratio 1.4 ± 0.2 (1.0-1.8) μm and vulval cone length 48.4 ± 15.2 (40.7 -53.6) μm. Cysts had a rough surface, were lemon-shaped to rounded and had a zigzag cuticular pattern with a protruding vulval cone. They were circumfenestrate without underbridge and bullae, but with the presence of vulval denticles. Measurements of second-stage juveniles (n = 13) included the body length 511.2 ± 33.7 (452.7 - 551.5) μm, stylet length 28.0 ± 2.8 (25.4 - 34.0) μm, tail length 50.7 ± 5.1 (40.6 - 57.4) μm, tail hyaline region 22.7 ± 2.2 (18.9 - 27.1), with a = 20.9 ± 2.2 (17.7-24.3) μm, b = 5.4 ± 0.4 (5.1-5.8) μm, b'= 3.4 ± 0.4 (3.1-3.9) μm, c = 10.2 ± 1.3 (8.9-13.3) μm and c' = 3.8 ± 0.4 (3.0-4.5) μm. The observations of essential morphological characteristics for identification indicated that the species found on C. jamacaru was Cactodera cacti (Filipjev & Schuurmans-Stekhoven, 1941) Krall & Krall, 1978. The sequences of the studied rDNA regions were submitted to GenBank (ITS: MW562829 and D2-D3 regions of 28S: MW562830). The samples used for molecular analysis showed a high degree of sequence identity (99.59%) with C. cacti, from China, Iran and USA for the ITS region. The identity of the D2-D3 regions of 28S sequence was 99.54% with C. cacti isolates from Germany and 99.41% with isolates from USA. Phylogenetic analyses were performed using Maximum likelihood (ML) method for both individual loci, confirming the species as Cactodera cacti. All inoculated mandacaru plantlets showed C. cacti cysts on the roots after 60 days, confirming that mandacaru is a host for C. cacti. This species was reported in São Paulo State, in 2001, associated with ornamental cactus cultivated in pots, but plant species were not identified (Santos et al., 2001). The second report in Brazil was to Schlumbergera sp., an ornamental plant (Oliveira et al. 2007). In both studies, the nematode was not morphologically nor molecularly characterized. Cactodera cacti has been commonly associated with cactus worldwide (Esser, 1992). It has been reported in association with C. jamacaru was first reported in 2011 in China (Duan et al. 2012). This is the first report of the occurrence of C. cacti on C. jamacaru in field conditions in Brazil, and its presence in cactus cultivation areas with agricultural importance represents a threat to cactus production in the country.

Evaluation of Porcine and Aspergillus oryzae α-Amylases as Possible Model for the Human Enzyme

α-amylases are ubiquitous enzymes belonging to the glycosyl hydrolase (GH13) family, whose members share a high degree of sequence identity, even between distant organisms. To understand the determinants of catalytic activity of α-amylases throughout evolution, and to investigate the use of homologous enzymes as a model for the human one, we compared human salivary α-amylase, Aspergillus oryzae α-amylase and pancreatic porcine α-amylase, using a combination of in vitro and in silico approaches. Enzyme sequences were aligned, and structures superposed, whereas kinetics were spectroscopically studied by using commercial synthetic substrates. These three enzymes show strikingly different activities, specifically mediated by different ions, despite relevant structural homology. Our study confirms that the function of α-amylases throughout evolution has considerably diverged, although key structural determinants, such as the catalytic triad and the calcium-binding pocket, have been retained. These functional differences need to be carefully considered when α-amylases, from different organisms, are used as a model for the human enzymes. In this frame, particular focus is needed for the setup of proper experimental conditions.

A Novel Glucocorticoid and Androgen Receptor Modulator Reduces Viral Entry and Innate Immune Inflammatory Responses in the Syrian Hamster Model of SARS-CoV-2 Infection.

Despite significant research efforts, treatment options for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain limited. This is due in part to a lack of therapeutics that increase host defense to the virus. Replication of SARS-CoV-2 in lung tissue is associated with marked infiltration of macrophages and activation of innate immune inflammatory responses that amplify tissue injury. Antagonists of the androgen (AR) and glucocorticoid (GR) receptors have shown efficacy in models of COVID-19 and in clinical studies because the cell surface proteins required for viral entry, angiotensin converting enzyme 2 (ACE2) and the transmembrane protease, serine 2 (TMPRSS2), are transcriptionally regulated by these receptors. We postulated that the GR and AR modulator, PT150, would reduce infectivity of SARS-CoV-2 and prevent inflammatory lung injury in the Syrian golden hamster model of COVID-19 by down-regulating expression of critical genes regulated through these receptors. Animals were infected intranasally with 2.5 × 104 TCID50/ml equivalents of SARS-CoV-2 (strain 2019-nCoV/USA-WA1/2020) and PT150 was administered by oral gavage at 30 and 100 mg/Kg/day for a total of 7 days. Animals were examined at 3, 5 and 7 days post-infection (DPI) for lung histopathology, viral load and production of proteins regulating the progression of SARS-CoV-2 infection. Results indicated that oral administration of PT150 caused a dose-dependent decrease in replication of SARS-CoV-2 in lung, as well as in expression of ACE2 and TMPRSS2. Lung hypercellularity and infiltration of macrophages and CD4+ T-cells were dramatically decreased in PT150-treated animals, as was tissue damage and expression of IL-6. Molecular docking studies suggest that PT150 binds to the co-activator interface of the ligand-binding domain of both AR and GR, thereby acting as an allosteric modulator and transcriptional repressor of these receptors. Phylogenetic analysis of AR and GR revealed a high degree of sequence identity maintained across multiple species, including humans, suggesting that the mechanism of action and therapeutic efficacy observed in Syrian hamsters would likely be predictive of positive outcomes in patients. PT150 is therefore a strong candidate for further clinical development for the treatment of COVID-19 across variants of SARS-CoV-2.

AzuR From the SmtB/ArsR Family of Transcriptional Repressors Regulates Metallothionein in Anabaena sp. Strain PCC 7120.

Metallothioneins (MTs) are cysteine-rich, metal-sequestering cytosolic proteins that play a key role in maintaining metal homeostasis and detoxification. We had previously characterized NmtA, a MT from the heterocystous, nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 and demonstrated its role in providing protection against cadmium toxicity. In this study, we illustrate the regulation of Anabaena NmtA by AzuR (Alr0831) belonging to the SmtB/ArsR family of transcriptional repressors. There is currently no experimental evidence for any functional role of AzuR. It is observed that azuR is located within the znuABC operon but in the opposite orientation and remotely away from the nmtA locus. Sequence analysis of AzuR revealed a high degree of sequence identity with Synechococcus SmtB and a distinct α5 metal binding site similar to that of SmtB. In order to characterize AzuR, we overexpressed it in Escherichia coli and purified it by chitin affinity chromatography. Far-UV circular dichroism spectroscopy indicated that the recombinant AzuR protein possessed a properly folded structure. Glutaraldehyde cross-linking and size-exclusion chromatography revealed that AzuR exists as a dimer of ∼28 kDa in solution. Analysis of its putative promoter region [100 bp upstream of nmtA open reading frame (ORF)] identified the presence of a 12–2–12 imperfect inverted repeat as the cis-acting element important for repressor binding. Electrophoretic mobility shift assays (EMSAs) showed concentration-dependent binding of recombinant dimeric AzuR with the promoter indicating that NmtA is indeed a regulatory target of AzuR. Binding of AzuR to DNA was disrupted in the presence of metal ions like Zn2+, Cd2+, Cu2+, Co2+, Ni2+, Pb2+, and Mn2+. The metal-dependent dissociation of protein–DNA complexes suggested the negative regulation of metal-inducible nmtA expression by AzuR. Overexpression of azuR in its native strain Anabaena 7120 enhanced the susceptibility to cadmium stress significantly. Overall, we propose a negative regulation of Anabaena MT by an α5 SmtB/ArsR metalloregulator AzuR.

Baltetin: a new C-type lectin-like isolated from Bothrops alternatus snake venom which act as a platelet aggregation inhibiting

C-type lectin-like proteins found in snake venom, known as snaclecs, have important effects on hemostasis through targeting membrane receptors, coagulation factors and other hemostatic proteins. Here, we present the isolation and functional characterization of a snaclec isolated from Bothrops alternatus venom, designated as Baltetin. We purified the protein in three chromatographic steps (anion-exchange, affinity and reversed-phase chromatography). Baltetin is a dimeric snaclec that is approximately 15 and 25 kDa under reducing and non-reducing conditions, respectively, as estimated by SDS-PAGE. Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry and Edman degradation sequencing revealed that Baltetin is a heterodimer. The first 40 amino acid residues of the N-terminal region of Baltetin subunits share a high degree of sequence identity with other snaclecs. Baltetin had a specific, dose-dependent inhibitory effect on epinephrine-induced platelet aggregation in human platelet-rich plasma, inhibiting up to 69% of platelet aggregation. Analysis of the infrared spectra suggested that the interaction between Baltetin and platelets can be attributed to the formation of hydrogen bonds between the PO32- groups in the protein and PO2- groups in the platelet membrane. This interaction may lead to membrane lipid peroxidation, which prevents epinephrine from binding to its receptor. The present work suggests that Baltetin, a new C-type lectin-like protein isolated from B. alternatus venom, is the first snaclec to inhibit epinephrine-induced platelet aggregation. This could be of medical interest as a new tool for the development of novel therapeutic agents for the prevention and treatment of thrombotic disorders.

Molecular and functional characaterization of the novel odorant-binding protein gene AccOBP10 from Apisceranacerana.

Odorant-binding proteins (OBPs) play an important role in odour perception and transport in insects. However, little is known about whether OBPs perform other functions in insects, particularly in Apis cerana cerana. Within this study, an OBP gene (AccOBP10) was isolated and identified from A. c. cerana. Both homology and phylogenetic relationship analyses indicated that the amino acid sequence of AccOBP10 had a high degree of sequence identity with other members of the gene family. Analysis of quantitative real-time PCR (qRT-PCR) showed that AccOBP10 mRNA was expressed at higher levels in the venom gland than in other tissues. The mRNA transcript expression of AccOBP10 was upregulated by low temperature (4°C), hydrogen peroxide (H2O2), pyridaben, methomyl and imidacloprid but downregulated by heat (42°C), ultraviolet light, vitamin C, mercuric chloride, cadmium chloride, paraquat and phoxim. Expression of AccOBP10 under abiotic stress was analysed by western blotting, and the results were consistent with those of qRT-PCR. And as a further study of AccOBP10 function, we demonstrated that knockdown of AccOBP10 by RNA interference could slightly increase the expression levels of some stress-related genes. Collectively, these results suggest that AccOBP10 is mainly involved in the response to stress conditions.

Three neuroparsin genes from oriental river prawn, Macrobrachium nipponense, involved in ovary maturation.

In this study, we identified three neuroparsin (NP) genes in Macrobrachium nipponense: Mn-NP1, Mn-NP2, and Mn-NP3, encoding 99, 100, and 101 amino acid proteins, respectively. Multiple sequence alignments showed that these genes contained 12 cysteine residues, of which 11 were at conserved positions. The total sequence identity between the genes was 47.5%, and they showed a high degree of sequence identity (> 54% similarity) with other crustacean genes. Phylogenetic tree analysis showed that Mn-NPs were clustered at different branches, indicating that Mn-NPs may have different functions. Tissue distribution data revealed that the three genes were present in males and females during the breeding and nonbreeding season, but their expression patterns differed. Mn-NP1 was highly expressed in the breeding season, in the male testis, and highly expressed in the nonbreeding season, in the female ovary. Mn-NP3 exhibited biased female expression in the breeding and nonbreeding season, with dominant expression in the ovary. All Mn-NPs were detected during embryo development, but with different expression patterns. These data indicated that Mn-NP1 may function during embryonic development, and that Mn-NP2 may be expressed during early embryo cell division, and late larval development. Mn-NP3 expression patterns reflected maternal inheritance, and may be associated with ovarian maturation. These expression data suggested that Mn-NP1 and Mn-NP2 are negatively correlated with ovarian development, with inhibition roles during this development. Mn-NP3 may be involved in vitellogenesis.

A quick and sensitive diagnostic tool for detection of Maize streak virus

Maize streak virus disease (MSVD), caused by Maize streak virus (MSV; genus Mastrevirus), is one of the most severe and widespread viral diseases that adversely reduces maize yield and threatens food security in Africa. An effective control and management of MSVD requires robust and sensitive diagnostic tests capable of rapid detection of MSV. In this study, a loop-mediated isothermal amplification (LAMP) assay was designed for the specific detection of MSV. This test has shown to be highly specific and reproducible and able to detect MSV in as little as 10 fg/µl of purified genomic DNA obtained from a MSV-infected maize plant, a sensitivity 105 times higher to that obtained with polymerase chain reaction (PCR) in current general use. The high degree of sequence identity between Zambian and other African MSV isolates indicate that this LAMP assay can be used for detecting MSV in maize samples from any region in Africa. Furthermore, this assay can be adopted in minimally equipped laboratories and with potential use in plant clinic laboratories across Africa strengthening diagnostic capacity in countries dealing with MSD.

Characterization of Avian Influenza Virus H10-H12 Subtypes Isolated from Wild Birds in Shanghai, China from 2016 to 2019.

H10, H11 and H12 (H10–H12) subtypes of the avian influenza virus (AIV) are associated with waterfowl. Although these subtypes of AIV are infrequently detected in nature, they can undergo reassortment with other AIV subtypes. Few H10–H12 subtypes of AIV have been isolated from wild birds in China. In this study, 12 AIV isolates of H10–H12 subtypes were identified via routine surveillance of wild birds in Shanghai, China from 2016 to 2019, including two H10, three H11 and seven H12 isolates. Sequence and phylogenetic analyses revealed that the genomic segments of the 12 isolates are highly diverse. These 12 isolates are closely related to those in the Eurasian lineage and share a high degree of sequence identity with those from wild birds and domestic ducks in countries in the East Asian–Australasian Flyway, including Japan, Korea, Bangladesh, Vietnam and China. However, parts of the genomic segments of two H12N2 isolates (NH112319-H12N2 and NH101807-H12N2) belong to the North American lineage, suggesting intercontinental reassortment among H12 AIVs in Eurasia and North American. To better understand the ecological and phylodynamic features of H10–H12 subtypes in wild birds, a large-scale surveillance of AIVs in wild birds is warranted.

Structural and Biochemical Characterization of Botulinum Neurotoxin Subtype B2 Binding to Its Receptors.

Botulinum neurotoxins (BoNTs) can be used therapeutically to treat a wide range of neuromuscular and neurological conditions. A collection of natural BoNT variants exists which can be classified into serologically distinct serotypes (BoNT/B), and further divided into subtypes (BoNT/B1, B2, …). BoNT subtypes share a high degree of sequence identity within the same serotype yet can display large variation in toxicity. One such example is BoNT/B2, which was isolated from Clostridium botulinum strain 111 in a clinical case of botulism, and presents a 10-fold lower toxicity than BoNT/B1. In an effort to understand the molecular mechanisms behind this difference in potency, we here present the crystal structures of BoNT/B2 in complex with the ganglioside receptor GD1a, and with the human synaptotagmin I protein receptor. We show, using receptor-binding assays, that BoNT/B2 has a slightly higher affinity for GD1a than BoNT/B1, and confirm its considerably weaker affinity for its protein receptors. Although the overall receptor-binding mechanism is conserved for both receptors, structural analysis suggests the lower affinity of BoNT/B2 is the result of key substitutions, where hydrophobic interactions important for synaptotagmin-binding are replaced by polar residues. This study provides a template to drive the development of future BoNT therapeutic molecules centered on assessing the natural subtype variations in receptor-binding that appears to be one of the principal stages driving toxicity.

IκB kinase α-1 and -2 regulate cytokine expression in the orange-spotted grouper (Epinephelus coioides)

IκB kinase (IKK) is the core regulator of the nuclear factor-κB (NF-κB) pathway, which is involved in cellular development and proliferation, as well as the inflammatory response. IKKα is an important subunit of the IKK complex. In this study, two IKKαs (EcIKKα-1 and -2) were characterized in E. coioides. Similar to IKKα of other species, EcIKKα-1 and -2 contained a kinase domain, a leucine zipper, a helix-loop-helix domain and a beta NF-κB essential modulator-binding domain. Sequence alignment indicated that EcIKKα-1 and -2 shared high degrees of sequence identity with IKKs from other species (about 63%–96%). EcIKKα-1 and -2 are widely expressed in all tissues, but have different expression profiles in normal groupers. Additionally, EcIKKα-1 and -2 responded rapidly to Cryptocaryon irritans infection at the local infection site (i.e., gill tissue), but there was no significant change in EcIKKα-2 expression. In GS cells, EcIKKα-1 was uniformly distributed in the cytoplasm, while EcIKKα-2 was observed uniformly both in the cytoplasm and nucleus. Both EcIKKα-1 and -2 were found to activate NF-κB, but the luciferase activity of EcIKKα-2 was twice that of EcIKKα-1. In addition, EcIKKα-1 and -2 can regulate the expression of immune-related cytokines (IL-1β, IL-6, IL-8, IL-12 [p35 subunit], and TNF-α). These findings should prove helpful to further elucidate the innate immunity function of IKKα in fish.

Sequence homology of Suppressor of IKKepsilon and Wound Inducible Transcript 3.0 confound co‐localization studies

Wounds created in the oral cavity heal at a rapid rate and leave minimal to no scarring. During the healing process of these wounds, expression of a gene, wound inducible transcript 3.0 (WIT3), was activated. The mechanism of how WIT3 affects the healing process is not known, but may involve an interaction between WIT3 and cytoskeleton structures. WIT3 shares 51% sequence identity with Suppressor of IKKe (SIKE). The function of SIKE is also unknown, but this protein was first identified as part of the innate immune response to viral infection. In this response, SIKE was shown to be phosphorylated following a viral infection and form an association with cytoskeletal proteins. As WIT3 shares a high degree of sequence identity and potential interactions with the cytoskeleton, the primary goal of this work was to determine if WIT3 is associated with the same cytoskeletal proteins as SIKE and/or even directly with SIKE. To assess localization and colocalization, immunofluorescence assays in four cell lines, epithelial ovarian cancer (DOV13), chronic myelogenous leukemia (HAP1), HAP1 cells with CRISPR/Cas9 knockouts of SIKE (SIKE‐CR), or WIT3 (WIT3‐CR), were completed using commercial SIKE or WIT3 specific antibodies. For SIKE in DOV13 cells, fluorescence was observed in actin‐like structures at the leading edge of the cells, in cytosolic puncta, and at the plasma membrane, similar to previously published data. The HAP1 cells formed cell clusters without apparent leading cell edges. Without lamellipodia, no staining of actin‐like or stress fiber‐like structures were observed, but staining at the plasma membrane and cytosolic puncta were identified in HAP1 and WIT3‐CR cell lines. For WIT3, two antibodies were tested, A and B. Antibody A showed that WIT3 was in the cytoplasm, whereas Antibody B showed that WIT3 was in mitochondrial‐like networks surrounding the nucleus and extending throughout the cytoplasm. The differences between the WIT3 antibodies in the same cell lines suggested that one or other of the antibodies was not specific to WIT3. As a control, staining for SIKE or WIT3 in their respective knockout cell lines was completed. Surprisingly, these negative controls yielded positive results. Knockout status of the cell line was confirmed via immunoblot. Cross reactivity was tested via immunoblot with purified SIKE and WIT3 recombinant protein. Together, these data were consistent with cross reactivity of the antibodies for SIKE and WIT3. To overcome this issue, stable cell lines introducing fluorescently tagged SIKE or WIT3 into their respective knockout cell lines were created. N‐terminal mTurquoise or C‐terminal sYFP2 tagged SIKE or WIT3 was transfected into their respective knockout cells and stable transfectants selected via geneticin. Colocalization using IFA and FRET (e.g mTurquoise‐SIKE to WIT3‐sYFP2) should resolve the issue of cross reactivity between SIKE and WIT3 antibodies observed in standard IFA assays. Our studies highlight the potential limitations of tools developed for highly homologous proteins and alternative approaches.

Determination of the crystal structure and substrate specificity of ananain

Ananain (EC 3.4.22.31) accounts for less than 10% of the total enzyme in the crude pineapple stem extract known as bromelain, yet yields the majority of the proteolytic activity of bromelain. Despite a high degree of sequence identity between ananain and stem bromelain, the most abundant bromelain cysteine protease, ananain displays distinct chemical properties, substrate preference and inhibitory profile compared to stem bromelain. A tripeptidyl substrate library (REPLi) was used to further characterize the substrate specificity of ananain and identified an optimal substrate for cleavage by ananain. The optimal tripeptide, PLQ, yielded a high kcat/Km value of 1.7 x 106 M−1s−1, with cleavage confirmed to occur after the Gln residue. Crystal structures of unbound ananain and an inhibitory complex of ananain and E−64, solved at 1.73 and 1.98 Å, respectively, revealed a geometrically flat and open S1 subsite for ananain. This subsite accommodates diverse P1 substrate residues, while a narrow and deep hydrophobic pocket-like S2 subsite would accommodate a non-polar P2 residue, such as the preferred Leu residue observed in the specificity studies. A further illustration of the atomic interactions between E−64 and ananain explains the high inhibitory efficiency of E−64 toward ananain. These data reveal the first in depth structural and functional data for ananain and provide a basis for further study of the natural properties of the enzyme.