Type IV Pilin Post-Translational Modifications Modulate Material Properties of Bacterial Colonies

Bacterial type 4 pili (T4P) are extracellular polymers that initiate the formation of microcolonies and biofilms. T4P continuously elongate and retract. These pilus dynamics crucially affect the local order, shape, and fluidity of microcolonies. The major pilin subunit of the T4P bears multiple post-translational modifications. By interfering with different steps of the pilin glycosylation and phosphoform modification pathways, we investigated the effect of pilin post-translational modification on the shape and dynamics of microcolonies formed by Neisseria gonorrhoeae. Deleting the phosphotransferase responsible for phosphoethanolamine modification at residue serine 68 inhibits shape relaxations of microcolonies after perturbation and causes bacteria carrying the phosphoform modification to segregate to the surface of mixed colonies. We relate these mesoscopic phenotypes to increased attractive forces generated by T4P between cells. Moreover, by deleting genes responsible for the pilin glycan structure, we show that the number of saccharides attached at residue serine 63 affects the ratio between surface tension and viscosity and cause sorting between bacteria carrying different pilin glycoforms. We conclude that different pilin post-translational modifications moderately affect the attractive forces between bacteria but have severe effects on the material properties of microcolonies.     

Comprehensive analysis of nuclear export of herpes simplex virus type 1 tegument proteins and their Epstein‐Barr virus orthologs

Morphogenesis of herpesviral virions is initiated in the nucleus but completed in the cytoplasm. Mature virions contain more than 25 tegument proteins many of which perform both nuclear and cytoplasmic functions suggesting they shuttle between these compartments. While nuclear import of herpesviral proteins was shown to be crucial for viral propagation, active nuclear export and its functional impact are still poorly understood. To systematically analyze nuclear export of tegument proteins present in virions of Herpes simplex virus type 1 (HSV1) and Epstein‐Barr virus (EBV), the Nuclear EXport Trapped by RAPamycin (NEX‐TRAP) was applied. Nine of the 22 investigated HSV1 tegument proteins including pUL4, pUL7, pUL11, pUL13, pUL21, pUL37d11, pUL47, pUL48 and pUS2 as well as 2 out of 6 EBV orthologs harbor nuclear export activity. A functional leucine‐rich nuclear export sequence (NES) recognized by the export factor CRM1/Xpo1 was identified in six of them. The comparison between experimental and bioinformatic data indicates that experimental validation of predicted NESs is required. Mutational analysis of the pUL48/VP16 NES revealed its importance for herpesviral propagation. Together our data suggest that nuclear export is an important feature of the herpesviral life cycle required to co‐ordinate nuclear and cytoplasmic processes.      

Fine grinding or expanding of feed as pre-treatment for pelleting in dependence on dietary rapeseed expeller proportion: Nutritional consequences for broilers

Although commercial broiler feed is usually differently conditioned before pelleting, the nutritional consequences of fine grinding or expanding as pre-pelleting treatments are poorly defined so far. Therefore, the effects of these two pre-treatments on nutrient digestibility, broiler performance and digestive tract of broilers were tested. In order to investigate possible interactions between pre-treatments and diet composition two diets differing in rapeseed expeller proportion were tested in a two by two factorial design. Thus, four diets were designed including two diets containing 6% rapeseed expeller (RSE) which were pre-treated by fine grinding (6%FgP) or expanding (6%ExP), and two corresponding diets containing 12% RSE (12%FgP and 12%ExP). For the experiments, 864 male broilers were used. There was a significant diet-by-technical feed treatment (TFT) interaction in case of the digestibility of all considered crude nutrients (p < 0.05). Diet 6%ExP showed higher crude protein digestibility compared to other feeds (p < 0.001). The highest digestibility of organic matter, ether extract, crude fibre and N-free extractives achieved diet 12%FgP. Diets 6%ExP and 12%FgP showed higher N-corrected metabolisable energy content (p < 0.001). TFT affected daily feed intake (DFI) and body weight (BW) gain in a diet-dependent manner (p < 0.001). Feeding of 6%FgP enhanced DFI and BW gain compared to other feeds but 6%ExP reduced both parameters (p < 0.001). Weights of proventriculi and gizzards of animals fed 6%ExP were increased compared with 6%FgP (p < 0.01). In contrast, proventricular length in animals fed 6%FgP was increased compared with diet 6%ExP (p = 0.042). Moreover, animals fed 6%FgP had wider proventriculi than animals fed 12%FgP (p = 0.023). Feed 6%ExP increased proventricular weight compared to 12%ExP (p = 0.001). With regard to the strong relationships between diet and TFT no specific processing method can be recommended according to considered nutritional aspects. A marked prevention of proventricular dilatation due to pellet feeding could not be realised by various used TFT or feed formulations. Used amounts of RSE had no obvious adverse effects on considered nutritional aspects.     

Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species

Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool‐seq data to generate a de novo genome assembly for mining exons, upon which Pool‐seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual‐based single nucleotide polymorphisms [SNPs]) and from mapping the Pool‐seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (F_ST) between the two introduced populations exceeds that of the naturally sympatric populations (F_ST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ ( ≈ 0.002 and  ≈ 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high‐quality reference assembly from a divergent species. We conclude that the Pool‐seq‐only approach can be suitable for detecting and quantifying genome‐wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.     

Heat Stability of Differently Stabilized Solid Lipid Nanoparticles in the Presence of Excess Bulk Phase Protein

In order to apply emulsion-based delivery systems to food, they have to be stable in a protein rich environment. This study investigated the stability of solid lipid nanoparticles (SLN) during heat treatment in the presence or absence of β-lactoglobulin (BLG). SLN were stabilized either by Tween 20 (TS) or by the protein itself (BS) and were enriched to a total BLG content of 56 mg/mL. The sizes of both types of SLN were initially in the range of 170 nm. The amount of free protein was determined before and after enrichment with BLG. As revealed by particle size and zeta potential measurements, a protein layer of BLG (hard corona) adsorbed on BS but not on TS. By contrast, a soft corona was formed around both BS and TS. SLN were heat treated in the presence and absence of protein and were characterized regarding size and zeta potential. According to transmission electron microscopy imaging, heating did not affect the shape of TS and BS: TS were platelets, whereas BS exhibited a spherical or platelet like shape. Upon heat treatment, the particle size of TS increased to about 3.5 fold of the initial size (to appr. 600 nm) in the presence and in the absence of excess protein. The cloudy protein layer (soft corona) around TS could thus not prevent coalescence of TS. By contrast, BS did not experience a change in particle size. Hence, by the choice of emulsifier, an encapsulation system that is stable against heat treatment can be obtained.

     

An Active Immune Defense with a Minimal CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) RNA and without the Cas6 Protein

The prokaryotic immune system CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) is a defense system that protects prokaryotes against foreign DNA. The short CRISPR RNAs (crRNAs) are central components of this immune system. In CRISPR-Cas systems type I and III, crRNAs are generated by the endonuclease Cas6. We developed a Cas6b-independent crRNA maturation pathway for the Haloferax type I-B system in vivo that expresses a functional crRNA, which we termed independently generated crRNA (icrRNA). The icrRNA is effective in triggering degradation of an invader plasmid carrying the matching protospacer sequence. The Cas6b-independent maturation of the icrRNA allowed mutation of the repeat sequence without interfering with signals important for Cas6b processing. We generated 23 variants of the icrRNA and analyzed them for activity in the interference reaction. icrRNAs with deletions or mutations of the 3′ handle are still active in triggering an interference reaction. The complete 3′ handle could be removed without loss of activity. However, manipulations of the 5′ handle mostly led to loss of interference activity. Furthermore, we could show that in the presence of an icrRNA a strain without Cas6b (Δcas6b) is still active in interference.     

Ammonium Metabolism Enzymes Aid Helicobacter pylori Acid Resistance

The gastric pathogen Helicobacter pylori possesses a highly active urease to support acid tolerance. Urea hydrolysis occurs inside the cytoplasm, resulting in the production of NH₃ that is immediately protonated to form NH₄⁺. This ammonium must be metabolized or effluxed because its presence within the cell is counterproductive to the goal of raising pH while maintaining a viable proton motive force (PMF). Two compatible hypotheses for mitigating intracellular ammonium toxicity include (i) the exit of protonated ammonium outward via the UreI permease, which was shown to facilitate diffusion of both urea and ammonium, and/or (ii) the assimilation of this ammonium, which is supported by evidence that H. pylori assimilates urea nitrogen into its amino acid pools. We investigated the second hypothesis by constructing strains with altered expression of the ammonium-assimilating enzymes glutamine synthetase (GS) and glutamate dehydrogenase (GDH) and the ammonium-evolving periplasmic enzymes glutaminase (Ggt) and asparaginase (AsnB). H. pylori strains expressing elevated levels of either GS or GDH are more acid tolerant than the wild type, exhibit enhanced ammonium production, and are able to alkalize the medium faster than the wild type. Strains lacking the genes for either Ggt or AsnB are acid sensitive, have 8-fold-lower urea-dependent ammonium production, and are more acid sensitive than the parent. Additionally, we found that purified H. pylori GS produces glutamine in the presence of Mg²⁺ at a rate similar to that of unadenylated Escherichia coli GS. These data reveal that all four enzymes contribute to whole-cell acid resistance in H. pylori and are likely important for assimilation and/or efflux of urea-derived ammonium.     

Deleted in Breast Cancer 1 (DBC1) Protein Regulates Hepatic Gluconeogenesis

Liver gluconeogenesis is essential to provide energy to glycolytic tissues during fasting periods. However, aberrant up-regulation of this metabolic pathway contributes to the progression of glucose intolerance in individuals with diabetes. Phosphoenolpyruvate carboxykinase (PEPCK) expression plays a critical role in the modulation of gluconeogenesis. Several pathways contribute to the regulation of PEPCK, including the nuclear receptor Rev-erbα and the histone deacetylase SIRT1. Deleted in breast cancer 1 (DBC1) is a nuclear protein that binds to and regulates both Rev-erbα and SIRT1 and, therefore, is a candidate to participate in the regulation of PEPCK. In this work, we provide evidence that DBC1 regulates glucose metabolism and the expression of PEPCK. We show that DBC1 levels decrease early in the fasting state. Also, DBC1 KO mice display higher gluconeogenesis in a normal and a high-fat diet. DBC1 absence leads to an increase in PEPCK mRNA and protein expression. Conversely, overexpression of DBC1 results in a decrease in PEPCK mRNA and protein levels. DBC1 regulates the levels of Rev-erbα, and manipulation of Rev-erbα activity or levels prevents the effect of DBC1 on PEPCK. In addition, Rev-erbα levels decrease in the first hours of fasting. Finally, knockdown of the deacetylase SIRT1 eliminates the effect of DBC1 knockdown on Rev-erbα levels and PEPCK expression, suggesting that the mechanism of PEPCK regulation is, at least in part, dependent on the activity of this enzyme. Our results point to DBC1 as a novel regulator of gluconeogenesis.