Microbes, from the smallest viruses to the largest unicellular protists, dominate our oceans, playing a central role in ocean food webs and as key drivers of biogeochemical processes, yet the complex interactions and ecological significance of these relationships within and between biomes are largely unknown. Describing and studying the hosts (prokaryotes and eukaryote assemblages) alongside their viruses can help improve our understanding of the roles of microbes in a holistic way.
A Pelagic Microbiome (Viruses to Protists) from a Small Cup of Seawater. Viruses 2017, 9(3): 47 doi: 10.3390/v9030047
The aquatic microbiome is composed of a multi-phylotype community of microbes, ranging from the numerically dominant viruses to the phylogenetically diverse unicellular phytoplankton. They influence key biogeochemical processes and form the base of marine food webs, becoming food for secondary consumers. Due to recent advances in next-generation sequencing, this previously overlooked component of our hydrosphere is starting to reveal its true diversity and biological complexity. We report here that 250 mL of seawater is sufficient to provide a comprehensive description of the microbial diversity in an oceanic environment. We found that there was a dominance of the order Caudovirales (59%), with the family Myoviridae being the most prevalent. The families Phycodnaviridae and Mimiviridae made up the remainder of pelagic double-stranded DNA (dsDNA) virome. Consistent with this analysis, the Cyanobacteria dominate (52%) the prokaryotic diversity. While the dinoflagellates and their endosymbionts, the superphylum Alveolata dominates (92%) the microbial eukaryotic diversity. A total of 834 prokaryotic, 346 eukaryotic and 254 unique virus phylotypes were recorded in this relatively small sample of water. We also provide evidence, through a metagenomic-barcoding comparative analysis, that viruses are the likely source of microbial environmental DNA (meDNA). This study opens the door to a more integrated approach to oceanographic sampling and data analysis.
The spread of viruses among cells, organs, and hosts is often mediated by structures that carry multiple viral genome copies, such as polyploid virions, virion aggregates, occlusion bodies, virus-containing lipid vesicles, and virological synapses. These structures increase the multiplicity of infection, defined as the number of viral genomes that initiate infection. High multiplicities of infection may promote the emergence of social-like virus–virus interactions, such as cooperation to evade immunity and/or antiviral treatments and division of labor, but also of noncooperative interactions such as negative dominance and interference. Collective infectious units may be exploited for retarding drug-resistance evolution, for producing attenuated viruses, or for codelivering different genetic variants of a virus to target cells/hosts.
Collective Infectious Units in Viruses. Trends Microbiol. 02 March 2017 doi: 10.1016/j.tim.2017.02.003
Increasing evidence indicates that viruses do not simply propagate as independent virions among cells, organs, and hosts. Instead, viral spread is often mediated by structures that simultaneously transport groups of viral genomes, such as polyploid virions, aggregates of virions, virion-containing proteinaceous structures, secreted lipid vesicles, and virus-induced cell-cell contacts. These structures increase the multiplicity of infection, independently of viral population density and transmission bottlenecks. Collective infectious units may contribute to the maintenance of viral genetic diversity, and could have implications for the evolution of social-like virus-virus interactions. These may include various forms of cooperation such as immunity evasion, genetic complementation, division of labor, and relaxation of fitness trade-offs, but also noncooperative interactions such as negative dominance and interference, potentially leading to conflict.
miRNAs play significant roles in different diseases. By binding to target genes, miRNAs post-transcriptionally regulate gene expression. During viral infections, miRNAs manipulate the activities of viruses and host cells. Some viral miRNAs mimic cellular miRNAs, and interfere with cellular activities.
Kaposi’s sarcoma-associated herpesvirus (KSHV) encodes 25 mature miRNAs and all play essential roles in the viral life cycle and cellular activities. Recent studies have focused on the roles of KSHV miRNAs in KSHV induced-tumorigenesis and KS development. Identification of the targets, and delineation of the functions of KSHV miRNAs, could provide novel strategies for treatment and prevention of KSHV-associated malignancies.
KSHV microRNAs: Tricks of the Devil. Trends Microbiol. March 02 2017 doi: 10.1016/j.tim.2017.02.002
Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi’s sarcoma (KS), a vascular tumor frequently found in immunodeficient individuals. KSHV encodes 12 pre-microRNAs (pre-miRNAs), which are processed into 25 mature microRNAs (miRNAs). KSHV miRNAs maintain KSHV latency, enhance angiogenesis and dissemination of the infected cells, and interfere with the host immune system by regulating viral and cellular gene expression, ultimately contributing to KS development. This review describes the biogenesis of miRNAs and recent advances in defining the roles and mechanisms of action of KSHV miRNAs in KS development.
Zika virus (ZIKV) causes microcephaly, whereas other related pathogenic flaviviruses do not. To reach the fetal brain, a virus must be transported from the maternal to the fetal circulation, which requires crossing of the placental barrier. This study demonstrates that ZIKV, but not two other globally relevant flaviviruses, efficiently infects fetal endothelial cells, a key component of the placental barrier, because only ZIKV can efficiently use the cell-surface receptor AXL. This paper also shows that AXL, a receptor tyrosine kinase, is the primary ZIKV entry cofactor on human umbilical vein endothelial cells.
AXL-dependent infection of human fetal endothelial cells distinguishes Zika virus from other pathogenic flaviviruses. PNAS doi: 10.1073/pnas.1620558114
Although a causal relationship between Zika virus (ZIKV) and microcephaly has been established, it remains unclear why ZIKV, but not other pathogenic flaviviruses, causes congenital defects. Here we show that when viruses are produced in mammalian cells, ZIKV, but not the closely related dengue virus (DENV) or West Nile virus (WNV), can efficiently infect key placental barrier cells that directly contact the fetal bloodstream. We show that AXL, a receptor tyrosine kinase, is the primary ZIKV entry cofactor on human umbilical vein endothelial cells (HUVECs), and that ZIKV uses AXL with much greater efficiency than does DENV or WNV. Consistent with this observation, only ZIKV, but not WNV or DENV, bound the AXL ligand Gas6. In comparison, when DENV and WNV were produced in insect cells, they also infected HUVECs in an AXL-dependent manner. Our data suggest that ZIKV, when produced from mammalian cells, infects fetal endothelial cells much more efficiently than other pathogenic flaviviruses because it binds Gas6 more avidly, which in turn facilitates its interaction with AXL.
Seems like a great idea – the widespread use of insecticide coate bednets to cut the spread of malaria by mosquitoes (mostly active at night). Unfortunately nature is rarely that simple. Widespread use has driven mosquitoes to evolve resistance to the insecticides used. By identifying genetic patterns that predict when and where resistance will evolve, scientists hope to curb resistance.
Genomic Footprints of Selective Sweeps from Metabolic Resistance to Pyrethroids in African Malaria Vectors Are Driven by Scale up of Insecticide-Based Vector Control. (2017) PLoS Genet 13(2): e1006539. doi: 10.1371/journal. pgen.1006539
Malaria control currently relies heavily on insecticide-based vector control interventions. Unfortunately, resistance to insecticides threatens the continued effectiveness of these measures. Metabolic resistance, caused by increased detoxification of insecticides, presents the greatest threat to vector control, yet it remains unclear how these mechanisms are linked to underlying genetic changes driven by the massive selection pressure from these interventions, such as the widespread use of Long Lasting Insecticide Nets (LLINs) across Africa. Therefore, understanding the direction and speed at which this operationally important form of resistance spreads through mosquito populations is essential if we are to get ahead of the ‘resistance curve’ and avert a public health catastrophe. Here, using microsatellite markers, whole genome sequencing and fine-scale sequencing at a major resistance locus, we elucidated the Africa-wide population structure of Anopheles funestus, a major African malaria Vector, and detected a strong selective sweep occurring in a genomic region controlling cytochrome P450-based metabolic pyrethroid resistance in this species. Furthermore, we demonstrated that this selective sweep is driven by the scale-up of insecticide-based malaria control in Africa, highlighting the risk that if this level of selection and spread of resistance continues unabated, our ability to control malaria with current interventions will be compromised.
Zika virus cannot replicate in mice – unless you knock out the mouse type I interferon with antibodies. As we know, Zika can replicate all too well in humans, but the pathogenesis and cell tropism of this troubling virus is not well understood. This new paper shows that there are important differences in the original African strains of Zika virus and the strains which have spread around the world recently. Understanding these differences might help us explain why this troublesome virus seemingly emerged out of nowhere to cause so much grief.
Zika Virus Antagonizes Type I Interferon Responses during Infection of Human Dendritic Cells. (2017) PLoS Pathog 13(2): e1006164. doi: 10.1371/journal.ppat.1006164
Zika virus (ZIKV) is an emerging mosquito-borne flavivirus that, upon congenital infection, can cause severe neonatal birth defects. To better understand the early innate immune response to ZIKV, we compared infection of human dendritic cells (DCs) between a contemporary Puerto Rican isolate and historic isolates from Africa and Asia. Human DCs supported productive replication following infection with the contemporary strain and exhibited donor variability in viral replication, but not viral binding. While contemporary and historic Asian lineage viruses replicated similarly, the African strains displayed more rapid replication kinetics with higher infection magnitude and uniquely induced cell death. Minimal DC activation and antagonism of type I interferon (IFN) translation was observed during ZIKV infection, despite strong induction of IFNB1 transcription and translation of other antiviral effector proteins. Treatment with a RIG-I agonist potently blocked ZIKV replication in human DCs, while type I IFN treatment was significantly less effective. Mechanistically, all ZIKV strains inhibited type I IFN receptor signaling through blockade of STAT1 and STAT2 phosphorylation. Altogether, we found that while ZIKV efficiently evades type I IFN responses during infection of human DCs, RIG-I signaling remains capable of inducing a strong antiviral state.
Historically, bacteria have been thought of as simple cells whose only aim is to replicate. However, research over the past two decades has revealed that many types of bacteria are able to develop into communities that contain several types of cells, with different cell types performing particular roles. Streptomyces bacteria employ a newly-discovered cell type, the “explorer” cell, to rapidly colonize new areas in the face of competition. For decades, researchers have described Streptomyces colonies in terms of vegetative cells, aerial hyphae and spores. The explorer cells offer Streptomyces an alternative means of escape from their normal life cycle and local environment in the face of competition. This makes sens, given that Streptomyces lack the ability to move (“motility”) in the traditional sense (for example, by swimming or gliding). This discovery demonstrates a surprisingly dynamic strategy in which a ‘non-motile’ bacterium can use cues from other microbes, long-range signaling, and multicellularity to make a graceful exit when times get tough.
Bacteria: Exploring new horizons. (2017) eLife 6: e23624. doi: 10.7554/eLife.23624
Streptomyces exploration is triggered by fungal interactions and volatile signals. (2017) eLife 6: e21738. doi: 10.7554/eLife.21738
Dengue has represented a significant public health burden for a number of decades. Given the lack of dengue-specific drugs and limited availability of licensed vaccine, new methods for prevention and control are urgently needed. Researchers investigated whether genetic manipulation of the mosquitoes’ native JAK/STAT pathway-mediated anti-DENV defense system could be used to render mosquitoes more resistant to infection. They generated Aedes aegypti mosquitoes overexpressing the JAK/STAT pathway components Dome and Hop under the control of a bloodmeal-inducible, fat body-specific vitellogenin promoter. These genetically modified mosquitoes showed an increased resistance to DENV infection, likely because of higher expression of DENV restriction factors and lower expression of DENV host factors, as indicated by transcriptome analyses. Expression of the transgenes had a minimal impact on mosquito longevity; however, it significantly impaired the mosquitoes’ fecundity. Bloodmeal-inducible fat body-specific overexpression of either Hop or Dome did not affect mosquito permissiveness to either ZIKV or CHIKV infection, suggesting a possible specialization of JAK/STAT pathway antiviral defenses. This is the first to provide a proof-of-concept that genetic engineering of the mosquitoes’ JAK/STAT immune pathway can be used to render this host more resistant to DENV infection.
Engineered Aedes aegypti JAK/STAT Pathway-Mediated Immunity to Dengue Virus. (2017) PLoS Negl Trop Dis 11(1): e0005187. doi: 10.1371/journal.pntd.0005187
We have developed genetically modified Ae. aegypti mosquitoes that activate the conserved antiviral JAK/STAT pathway in the fat body tissue, by overexpressing either the receptor Dome or the Janus kinase Hop by the blood feeding-induced vitellogenin (Vg) promoter. Transgene expression inhibits infection with several dengue virus (DENV) serotypes in the midgut as well as systemically and in the salivary glands. The impact of the transgenes Dome and Hop on mosquito longevity was minimal, but it resulted in a compromised fecundity when compared to wild-type mosquitoes. Overexpression of Dome and Hop resulted in profound transcriptome regulation in the fat body tissue as well as the midgut tissue, pinpointing several expression signatures that reflect mechanisms of DENV restriction. Our transcriptome studies and reverse genetic analyses suggested that enrichment of DENV restriction factor and depletion of DENV host factor transcripts likely accounts for the DENV inhibition, and they allowed us to identify novel factors that modulate infection. Interestingly, the fat body-specific activation of the JAK/STAT pathway did not result in any enhanced resistance to Zika virus (ZIKV) or chikungunya virus (CHIKV) infection, thereby indicating a possible specialization of the pathway’s antiviral role.
Siderophores are small molecular iron chelators that are produced by microbes and whose most notable function is to sequester iron from the host and provide this essential metal nutrient to microbes. Recent studies have proposed additional, noncanonical roles for siderophores, including the acquisition of noniron metals and modulation of host functions. Recently, siderophores secreted by Klebsiella pneumoniae during lung infection have been shown to induce stabilization of the transcription factor HIF-1α, increase the expression of proinflammatory cytokines in the lung, and promote dissemination of K. pneumoniae to the spleen. Thus, their study demonstrated novel roles for siderophores in vivo, beyond iron sequestration. The interaction of siderophores with host cells further promotes the pathogenicity of K. pneumoniae and is likely relevant for other pathogens that also secrete siderophores in the host.
Siderophores: More than Stealing Iron. MBio. 2016 Nov 15;7(6). pii: e01906-16. doi: 10.1128/mBio.01906-16