Sialotranscriptomics of the argasid tick Ornithodoros moubata along the trophogonic cycle

The argasid tick Ornithodoros moubata is the main vector of human relapsing fever (HRF) and African swine fever (ASF) in Africa. Salivary proteins are part of the host-tick interface and play vital roles in the tick feeding process and the host infection by tick-borne pathogens; they represent interesting targets for immune interventions aimed at tick control. The present work describes the transcriptome profile of salivary glands of O. moubata and assesses the gene expression dynamics along the trophogonic cycle using Illumina sequencing. De novo transcriptome assembling resulted in 71,194 transcript clusters and 41,011 annotated transcripts, which represent 57.6% of the annotation success. Most salivary gene expression takes place during the first 7 days after feeding (6,287 upregulated transcripts), while a minority of genes (203 upregulated transcripts) are differentially expressed between 7 and 14 days after feeding. The functional protein groups more abundantly overrepresented after blood feeding were lipocalins, proteases (especially metalloproteases), protease inhibitors including the Kunitz/BPTI-family, proteins with phospholipase A2 activity, acid tail proteins, basic tail proteins, vitellogenins, the 7DB family and proteins involved in tick immunity and defence. The complexity and functional redundancy observed in the sialotranscriptome of O. moubata are comparable to those of the sialomes of other argasid and ixodid ticks. This transcriptome provides a valuable reference database for ongoing proteomics studies of the salivary glands and saliva of O. moubata aimed at confirming and expanding previous data on the O. moubata sialoproteome.

Posttranslational lysine 2-hydroxyisobutyrylation of human sperm tail proteins affects motility

STUDY QUESTION Does lysine 2-hydroxyisobutyrylation, a newly identified protein posttranslational modification (PTM), occur in human sperm and affect human sperm function? SUMMARY ANSWER Lysine 2-hydroxyisobutyrylation mainly occurs in human sperm tail proteins, and excessive lysine 2-hydroxyisobutyrylation affects human sperm motility. WHAT IS KNOWN ALREADY PTM is regarded as an important pathway in regulating sperm function since mature sperm are almost transcriptionally silent. However, only phosphorylation was extensively studied in mature sperm to date. Lysine 2-hydroxyisobutyrylation, a newly characterised PTM, is broadly conserved in both eukaryotic and prokaryotic cells. Although histone lysine 2-hydroxyisobutyrylation has been shown to be associated with active gene expression in spermatogenic cells, the presence, regulatory elements and function of lysine 2-hydroxyisobutyrylation have not been characterised in mature sperm. STUDY DESIGN, SIZE, DURATION Sperm samples were obtained from normozoospermic men and asthenozoospermic men who visited the reproductive medical centre at Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi, China, between May 2017 and November 2018. In total, 58 normozoospermic men and 65 asthenozoospermic men were recruited to participate in this study. PARTICIPANTS/MATERIALS, SETTING, METHODS Lysine 2-hydroxyisobutyrylation was examined using immunoblotting and immunofluorescence assays using a previously qualified pan anti-lysine 2-hydroxyisobutyrylation antibody. The immunofluorescence assay was imaged using super-resolution structured illumination microscopy. Sperm viability was examined by using the eosin staining method, and sperm motility parameters were assessed by computer-assisted sperm analysis. Sperm penetration ability was determined by evaluating the ability of the sperm to penetrate a 1% (w/v) methylcellulose solution. The level of intracellular adenosine triphosphate (ATP) was detected using a rapid bioluminescent ATP assay kit. MAIN RESULTS AND THE ROLE OF CHANCE Lysine 2-hydroxyisobutyrylation was present in several proteins (20–100 kDa) mainly located in the tail of human sperm. Sperm lysine 2-hydroxyisobutyrylation was derived from 2-hydroxyisobutyrate (2-Hib) and was regulated by acyltransferase P300 and nicotinamide adenine dinucleotide-dependent lysine deacylase sirtuins. Elevation of sperm lysine 2-hydroxyisobutyrylation by 2-Hib decreased total motility, progressive motility, penetration ability and ATP level of human sperm. Interestingly, the level of sperm lysine 2-hydroxyisobutyrylation was higher in asthenozoospermic men than that in normozoospermic men and was negatively correlated with the progressive motility of human sperm. Furthermore, high levels of lysine 2-hydroxyisobutyrylation in asthenozoospermic men accompanied decreased ATP levels. LIMITATIONS, REASONS FOR CAUTION Although the present study indicated the involvement of sperm lysine 2-hydroxyisobutyrylation in regulating human sperm motility, the underlying mechanism needs to be further illustrated. WIDER IMPLICATIONS OF THE FINDINGS The findings of this study provide insight into the novel role of lysine 2-hydroxyisobutyrylation in human sperm and suggest that abnormality of sperm lysine 2-hydroxyisobutyrylation may be one of the causes for asthenozoospermia. STUDY FUNDING/COMPETING INTEREST(S) National Natural Science Foundation of China (81771644 to T.L. and 81871207 to H.C.); Natural Science Foundation of Jiangxi province (20171ACB21006). The authors have no conflicts of interest to declare.

Evolution of BACON Domain Tandem Repeats in crAssphage and Novel Gut Bacteriophage Lineages

The human gut contains an expanse of largely unstudied bacteriophages. Among the most common are crAss-like phages, which were predicted to infect Bacteriodetes hosts. CrAssphage, the first crAss-like phage to be discovered, contains a protein encoding a Bacteroides-associated carbohydrate-binding often N-terminal (BACON) domain tandem repeat. Because protein domain tandem repeats are often hotspots of evolution, BACON domains may provide insight into the evolution of crAss-like phages. Here, we studied the biodiversity and evolution of BACON domains in bacteriophages by analysing over 2 million viral contigs. We found a high biodiversity of BACON in seven gut phage lineages, including five known crAss-like phage lineages and two novel gut phage lineages that are distantly related to crAss-like phages. In three BACON-containing phage lineages, we found that BACON domain tandem repeats were associated with phage tail proteins, suggestive of a possible role of these repeats in host binding. In contrast, individual BACON domains that did not occur in tandem were not found in the proximity of tail proteins. In two lineages, tail-associated BACON domain tandem repeats evolved largely through horizontal transfer of separate domains. In the third lineage that includes the prototypical crAssphage, the tandem repeats arose from several sequential domain duplications, resulting in a characteristic tandem array that is distinct from bacterial BACON domains. We conclude that phage tail-associated BACON domain tandem repeats have evolved in at least two independent cases in gut bacteriophages, including in the widespread gut phage crAssphage.

DeepCapTail: A Deep Learning Framework to Predict Capsid and Tail Proteins of Phage Genomes

The capsid and tail proteins are considered the main structural proteins for phages and also their footprint since they exist only in phage genomes. These proteins are known to lack sequence conservation, making them extremely diverse and thus posing a major challenge to identify and annotate them in genomic sequences. In this study, we aim to overcome this challenge and predict these proteins by using deep neural networks with composition-based features. We develop two models trained with k-mer features to predict capsid and tail proteins respectively. Evaluating the models on two different testing sets shows that they outperform state-of-the-art methods with improved F-1 scores.

Bacteria defend against phages through type IV pilus glycosylation

ABSTRACTBacterial surface structures such as type IV pili are common receptors for phage. Strains of the opportunistic pathogenPseudomonas aeruginosaexpress one of five different major type IV pilin alleles, two of which are glycosylated with either lipopolysaccharide O-antigen units or polymers of D-arabinofuranose. Here we show that both these post-translational modifications protectP. aeruginosafrom a variety of pilus-specific phages. We identified a phage capable of infecting strains expressing both non-glycosylated and glycosylated pilins, and through construction of a chimeric phage, traced this ability to its unique tail proteins. Alteration of pilin sequence, or masking of binding sites by glycosylation, both block phage infection. The energy invested by prokaryotes in glycosylating thousands of pilin subunits is thus explained by the protection against phage predation provided by these common decorations.SIGNIFICANCEPost-translational modification of bacterial and archaeal surface structures such as pili and flagella is widespread, but the function of these decorations is not clear. We propose that predation by bacteriophages that use these structures as receptors selects for strains that mask potential phage binding sites using glycosylation. Phages are of significant interest as alternative treatments for antibiotic-resistant pathogens, but the ways in which phage interact with host receptors are not well understood. We show that specific phage tail proteins allow for infection of strains with glycosylated pili, providing a foundation for the creation of designer phages that can circumvent first-line bacterial defenses.