Volume 4 Issue 12, December 2019

A newly discovered energy-linked carbonic anhydrase, DabBA2, is a two-protein complex responsible for inorganic carbon accumulation in the sulfur bacterium Halothiobacillus neapolitanus. DABs are present in a wide range of proteobacterial clades, suggesting that they function in diverse metabolic pathways.

Influenza vaccine strain selection is informed by international efforts to track antigenic change, focusing on the viral hemagglutinin protein. Recent research advocates monitoring neuraminidase for immune escape mutations that could reduce vaccine efficacy.

Culture-independent methods capable of connecting bacteriophages (phages) to their target host bacteria will help define the roles of phages in host-associated microbiotas. A recent study used fluorescently dyed intestinal phages to identify novel phage–bacterial interactions from the human intestine.

A comparative transcriptional analysis identifies human HLA-DR as a factor that mediates entry of bat influenza A-like H17-pseudotyped viral particles into mammalian cells.

Yang et al. discover a conjugative plasmid that can transfer high-level virulence to Klebsiella pneumoniae strains.

This study answers the long-standing question of why the interaction between cyclophilin A (CypA) and HIV-1 capsid (CA) protein stimulates HIV-1 infectivity in human cells. Disruption of the CA−CypA interaction renders HIV-1 susceptible to potent restriction by human TRIM5α in primary blood cells, which occurs before reverse transcription.

Cooked and raw plant diets cause different changes in gut microbiome composition and function, including mechanisms of starch digestibility and xenobiotic availability, and consequently impact host energy status.

The gut microbiota regulates levels of serotonin (5-HT) in the gut, affecting the mammalian nervous system. But does 5-HT affect the microbiota? Here, it is shown to increase the relative abundance of spore-forming members of the gut microbiota and enhance mouse colonization by Turicibacter sanguinis, a gut bacterium that can take up 5-HT and modulate systemic lipid homeostasis.

The structure of a transferrin receptor from the parasite Trypanosoma brucei in complex with human transferrin helps to understand how the parasite can use surface exposed receptors to acquire nutrients during infection while avoiding host immune detection.

The sialic acid, Neu5Gc, is present in red meat and can be incorporated into host cell surface glycans triggering an inflammatory response. Here, a Neu5Gc-containing diet alters the murine gut microbiota, and bacterial sialidases specific for Neu5Gc were identified in human and mouse gut metagenomes, with purified sialidases able to cleave Neu5Gc from red meat.

The recovery of metagenome-assembled genomes from the coral Porites lutea, its dinoflagellate symbiont, and its bacterial and archaeal populations, enabled comparative genomic identification of functions important for host–microbe interactions and nutritional associations.

The in vivo structure of a T2SS from Legionella pneumophila elucidates the structure and function of the different components of this macromolecular complex that exports a wide range of virulence factors.

Metabolic state and ATP levels are better predictors of antibiotic lethality across diverse bacterial species than growth rate.

The combination of single-molecule quantification of mRNA and gene loci in single Escherichia coli cells with mathematical models of mRNA dynamics reveals additional factors governing transcription, including contributions from the transcriptional state of another copy of the same gene present in the cell and from gene-replication events.

A type I interferon response mediated by IL-1Ra drives susceptibility to Mycobacterium tuberculosis infection, and neutralization of IL-1Ra provides therapeutic benefit.

Single-cell imaging analysis shows that translation-inhibiting antibiotics disrupt Vibrio cholerae biofilm structure and enable entry of bacteriophages and intruder cells.

Host mucin glycans downregulate virulence processes of Pseudomonas aeruginosa and can be used therapeutically to attenuate infection in vivo in a burn wound model.

An analysis of the distribution and phylogeny of the enzymes involved in the tetrahydromethanopterin methyl branch of the Wood–Ljungdahl pathway suggests that it evolved in Archaea and was then transferred to Bacteria, subsequently enabling aerobic methylotrophy.

Short-term exposure to a high-fat diet reduces colonization resistance to Salmonella Typhimurium infection in mice and is associated with increase bile salts and plasmid transfer; however, E. coli can provide a protective effect under these conditions.

A herpesvirus can tolerate DNA polymerase infidelity that generates highly diverse DNA virus populations. These diverse virus populations can coexist, maintain fitness and even induce disease faster than wild-type virus.

Using a multi-omics and modelling approach, the authors characterize the metabolic interactions in a phototrophic community consisting of an alga and a fungus and identify the factors driving collaboration and competition.

Single-cell viral tagging was used to identify uncharacterized bacterial host–phage pairs present in the human faecal microbiome, revealing a lack of phages targeting more than one host species and a high level of cross-reactivity between hosts and phages from different subjects, despite subject-specific pairings, which could have implications for faecal microbiota transplants.

A genome-wide transposon screen in Halothiobacillus neapolitanus identifies genes involved in CO₂ concentrating mechanisms, of which dabA and dabB encode a heterodimeric complex that works as an energy-coupled inorganic carbon pump. Dab homologues exist in multiple archaea and bacteria, including pathogens such as Bacillus anthracis and Vibrio cholerae.

The neuraminidase antigenicity of the circulating influenza A(H3N2) viruses differs from that of a recent A(H3N2) vaccine virus due to three amino acid substitutions, two of which introduce an N-linked glycosylation site that significantly reduces the binding of neuraminidase by antibodies.

Infection with Cryptosporidium parvum is a leading cause of severe diarrhoeal disease and childhood mortality worldwide. Using tools they recently developed to genetically engineer Cryptosporidium, the authors define life cycle stage-specific markers and generate reporter parasites, making life cycle progression and parasite sex tractable.

The cephamycin group of β-lactam antibiotics targets sporulation-associated penicillin-binding proteins across pathogens and can be repurposed as a cost-effective strategy to treat recurrent Clostridioides difficile infection.

An analysis of mRNA modifications in Plasmodium falciparum reveals m⁶A dynamics associated with parasite development within human red blood cells. m⁶A methylation is regulated by the methyltransferase PfMT-A70 and is linked to mRNA stability or translational efficiency.

Human cytomegalovirus antagonizes the antiviral activity of sterile alpha motif and histidine–aspartate domain-containing protein 1 (SAMHD1) in macrophages by deploying the viral kinase pUL97 and hijacking cellular kinases.

SAMHD1 inhibits murine cytomegalovirus replication in vivo and its activity is counteracted by the viral kinase M97. Phosphorylation of SAMHD1 by M97 correlates with reduced dNTP hydrolase activity and a loss of viral restriction in infected cells.

Using metagenomics, culture and machine learning approaches, the authors characterized the resistome of preterm infants that received antibiotics and found that they have an enriched gut antibiotic resistome with distinct assembly patterns and prolonged carriage of multidrug-resistant bacteria, compared with healthy infants that did not receive antibiotics.

Analysis of the genetic stability and replication potential of bat H18N11 influenza A viruses reveals that they are poorly adapted to ferrets and mice and that they transmit among bats only in presence of the full-length neuraminidase-like protein N11.

Geospatial modelling shows an overall decline in morbidity and mortality due to lower respiratory infections in Africa from 2000 to 2017, but also identifies subnational areas with residual high risk.

Peptostreptococcus anaerobius is enriched in the gut microbiota of patients with colorectal cancer (CRC). Here, the authors show that it can selectively bind to tumours and CRC cell lines and trigger downstream responses, resulting in chronic inflammation and tumour progression in a mouse model of CRC.

Hrd1 is an endoplasmic reticulum-localized E3 ubiquitin ligase that inactivates Usp15 to promote inflammation during bacterial infection, and depletion of Hrd1 in macrophages protects mice from septic shock.

How bacteria coordinate transcription and translation is incompletely understood. Here, ppGpp-dependent coordination between both processes is shown to occur under normal growth conditions and to be disrupted when translational elongation is slowed, a process that leads to premature transcriptional termination.

Bactofilins form cytoskeletal filaments in various bacteria where they mediate, for example, stalk formation and chromosome segregation. This work reports multiple structures of bactofilin filaments that disprove the current filamentation model. Filamentation is shown to be non-polar, and filaments interact with membranes directly through a conserved hydrophobic motif.

A survey of the cellular RNA-binding proteins (RBPs) that interact with dengue virus and Zika virus genomic RNA identifies ribosome-binding protein 1 and vigilin as bona fide RBPs able to promote viral RNA translation, replication and stability.

A survey of fungal genomes across a broad range of taxa identifies shared gene clusters irrespective of their encoded functions and sheds light on the mechanisms underlying the formation, maintenance and evolution of these clusters.

Ruminococcus gnavus is a mucus-associated gut commensal that can release the sialic acid, 2,7-anhydro-Neu5Ac. Here, the authors identify the pathway for its transportation and metabolism in R. gnavus, and show that this pathway is essential for its spatial localization in vivo.

The level of serum iron in blood meals influences the ability of Aedes aegypti mosquitoes to acquire dengue virus, suggesting that the iron status of human populations at risk of dengue virus infection may affect viral spreading via mosquitoes.

Flavivirus infection leads to a rearrangement of host cell ER membranes that creates an environment permissive to viral replication. The morphology of these membrane rearrangements is known, but the mechanisms involved are unclear. Here, atlastins—ER-resident membrane-bound GTPases of the dynamin family—are shown to be targeted by flaviviruses to establish their replication organelle and for virion maturation and secretion.

A multifaceted approach was used to shed light on the genetic factors behind the heterogeneity that is observed in vitro and in vivo in the colony morphology of Aspergillus fumigatus isolates and on the impact of such morphological variation on fungal fitness and pathogenesis.

A human antithrombin glycosylation isoform dampens inflammatory responses and protects mice against lethal bacterial infection.

Core microbial populations across distinct gut habitats and diets were identified in a European seabass model indicating that microbial generalists persist and coexist by maintaining low competition, beneficial interactions and strain variability.

Vibrio cholerae cells are taken up by protozoa and expelled in food vacuoles, enhancing bacterial environmental survival and infectiousness in mice.

The non-coding RNA EBER2 of the Epstein–Barr virus M81 strain potentiates virus lytic replication in B cells by generating a paracrine loop whereby the chemokine CXCL8 is released from infected cells via extracellular vesicles—which are taken up by neighbouring cells—thereby enhancing its own expression.

Using metagenomics and metatranscriptomics, up to 16 strains of intracellular, sulfur-oxidizing symbiotic bacteria were identified in individual mussels with different functions, indicating that high strain diversity is present in symbioses.

Chassis-independent recombinase-assisted genome engineering (CRAGE) enables the integration of plasmids encoding biosynthetic gene clusters into the chromosomes of diverse bacteria to optimize production of natural products in non-native strains.

A screen for Salmonella type 3 secreted effector targets finds an interaction between SifA and host BLOC-2 complex that is important for positioning and stability of Salmonella-containing vacuoles during infection.

The actin methyltransferase SETD3, by virtue of its ability to interact with the viral 2A protein and independently of its enzymatic activity, is necessary for RNA replication of several enteroviruses in cell culture and in vivo.

Rickettsia surface protein OmpB promotes host colonization by blocking host ubiquitylation of bacterial surface proteins, thereby evading destruction by host autophagic processes.

Depletion of SAMHD1 has been shown to generate DNA damage and trigger cGAS–STING-mediated immunity. How HIV-2 and SIV bypass this activation, given Vpx-mediated depletion of SAMHD1, is unknown. Vpx is now shown to efficiently inhibit cGAS–STING-induced innate immunity through association with a new STING domain.

The tetrameric neuraminidase (NA) of influenza virus H1N1 requires calcium at the centre of the tetramer for its activity. Substitutions that alter binding of NA to central calcium contribute to H1N1 virus diversification and adaptation over time.