Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis

Background

Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler's diarrhea. In this study, we performed an in-depth annotation of the genes in its genome related to the various steps in the infective process, drug resistance and mobile genetic elements.

Results

For acid and bile resistance, L. hongkongensis possessed a urease gene cassette, two arc gene clusters and bile salt efflux systems. For intestinal colonization, it possessed a putative adhesin of the autotransporter family homologous to those of diffusely adherent Escherichia coli (E. coli) and enterotoxigenic E. coli. To evade from host defense, it possessed superoxide dismutase and catalases. For lipopolysaccharide biosynthesis, it possessed the same set of genes that encode enzymes for synthesizing lipid A, two Kdo units and heptose units as E. coli, but different genes for its symmetrical acylation pattern, and nine genes for polysaccharide side chains biosynthesis. It contained a number of CDSs that encode putative cell surface acting (RTX toxin and hemolysins) and intracellular cytotoxins (patatin-like proteins) and enzymes for invasion (outer membrane phospholipase A). It contained a broad variety of antibiotic resistance-related genes, including genes related to β-lactam (n = 10) and multidrug efflux (n = 54). It also contained eight prophages, 17 other phage-related CDSs and 26 CDSs for transposases.

Conclusions

The L. hongkongensis genome possessed genes for acid and bile resistance, intestinal mucosa colonization, evasion of host defense and cytotoxicity and invasion. A broad variety of antibiotic resistance or multidrug resistance genes, a high number of prophages, other phage-related CDSs and CDSs for transposases, were also identified.     

Differential roles of RIPK1 and RIPK3 in TNF-induced necroptosis and chemotherapeutic agent-induced cell death

Apoptosis is a key mechanism for metazoans to eliminate unwanted cells. Resistance to apoptosis is a hallmark of many cancer cells and a major roadblock to traditional chemotherapy. Recent evidence indicates that inhibition of caspase-dependent apoptosis sensitizes many cancer cells to a form of non-apoptotic cell death termed necroptosis. This has led to widespread interest in exploring necroptosis as an alternative strategy for anti-cancer therapy. Here we show that in human colon cancer tissues, the expression of the essential necroptosis adaptors receptor interacting protein kinase (RIPK)1 and RIPK3 is significantly decreased compared with adjacent normal colon tissues. The expression of RIPK1 and RIPK3 was suppressed by hypoxia, but not by epigenetic DNA modification. To explore the role of necroptosis in chemotherapy-induced cell death, we used inhibitors of RIPK1 or RIPK3 kinase activity, and modulated their expression in colon cancer cell lines using short hairpin RNAs. We found that RIPK1 and RIPK3 were largely dispensable for classical chemotherapy-induced cell death. Caspase inhibitor and/or second mitochondria-derived activator of caspase mimetic, which sensitize cells to RIPK1- and RIPK3-dependent necroptosis downstream of tumor necrosis factor receptor-like death receptors, also did not alter the response of cancer cells to chemotherapeutic agents. In contrast to the RIPKs, we found that cathepsins are partially responsible for doxorubicin or etoposide-induced cell death. Taken together, these results indicate that traditional chemotherapeutic agents are not efficient inducers of necroptosis and that more potent pathway-specific drugs are required to fully harness the power of necroptosis in anti-cancer therapy.Cell death by apoptosis is a natural barrier to cancer development, as it limits uncontrolled proliferation driven by oncogenes.¹ Chemotherapeutic agents that target apoptosis have been successful in anti-cancer therapy. However, cancer cells, especially cancer stem cells, often evolve multiple mechanisms to circumvent growth suppression by apoptosis.² This resistance to apoptosis is a major challenge for many chemotherapeutic agents. Targeting other non-apoptotic cell death pathways is an attractive therapeutic alternative.A growing number of recent studies show that there are distinct genetic programmed cell death modes other than apoptosis.³ Necroptosis is mediated by receptor interacting protein kinase 3 (RIPK3).⁴ In the presence of caspase inhibition and cellular inhibitor of apoptosis proteins (cIAPs) depletion, tumor necrosis factor (TNF) receptor 1 triggers a signaling reaction that culminates in binding of RIPK3 with its upstream activator RIPK1 through the RIP homotypic interaction motif (RHIM).⁴ RIPK1 and RIPK3 phosphorylation stabilizes this complex and promotes its conversion to an amyloid-like filamentous structure termed the necrosome.⁵ Once activated, RIPK3 recruits its substrate mixed lineage kinase domain-like (MLKL).⁶ Phosphorylated MLKL forms oligomers that translocate to intracellular membranes and the plasma membrane, which eventually leads to membrane rupture.^{7, 8, 9, 10}In addition to phosphorylation, RIPK1 and RIPK3 are also tightly regulated by ubiquitination, a process mediated by the E3 ligases cIAP1, cIAP2, and the linear ubiquitin chain assembly complex.¹¹ The ubiquitin chains on RIPK1 act as a scaffold to activate nuclear factor-κB (NF-κB) and mitogen-activated protein kinase pathways and inhibit formation of the necrosome. As such, depletion of cIAP1/2 by second mitochondria-derived activator of caspase (Smac) mimetics or removal of the ubiquitin chains by the de-ubiquitinating enzyme cylindromatosis (CYLD) promotes necroptosis.^{12, 13, 14, 15} In addition, RIPK1 and RIPK3 are cleaved and inactivated by caspase 8.^{16, 17, 18} Mice deficient for caspase 8 or FADD, an essential adaptor protein of caspase 8, suffer from embryonic lethality due to extensive RIPK1- or RIPK3-dependent necroptosis.^{19, 20, 21} Hence, caspase inhibition and IAP depletion are key priming signals for necroptosis.The physiological functions of RIPK1 and RIPK3 have been extensively investigated in infectious and sterile inflammatory diseases.^{4, 22} By contrast, their roles in cancer cells'' response to chemotherapeutics are poorly understood. Here we show that RIPK1 and RIPK3 expression is significantly decreased in human colon cancer tissues, suggesting that suppression of RIPK1 or RIPK3 expression is advantageous for cancer growth. However, the loss of RIPK1 and RIPK3 expression in colon cancer was not due to epigenetic DNA modification. Interestingly, RIPK1 and RIPK3 expression in colon cancer cells is reduced by hypoxia, a hallmark of solid tumor. We found that chemotherapeutic agents did not effectively elicit RIPK1/RIPK3-dependent necroptosis in colon cancer cells. Moreover, caspase inhibition and Smac mimetics, which are potent sensitizers for necroptosis, also did not enhance chemotherapeutic agent-induced cell death. These results show that traditional chemotherapeutic agents are not strong inducers of classical necroptosis in colon cancers and suggest that development of pathway-specific drugs is needed to harness the power of necroptosis in anti-cancer therapy.     

Evidence for the phosphorylation of the type II insulin-like growth factor receptor in cultured cells

The ATP pools of monolayer cultures of rat embryo fibroblasts and rat liver cells (BRL-3A2) were labeled with [32P]H3PO4. The type II insulin-like growth factor (IGF) receptor was purified by affinity chromatography on wheat germ lectin-Sepharose and IGF-II-Sepharose columns. A phosphorylated species having the expected size of the type II receptor (Mr = 220,000 without reduction, Mr = 260,000 with reduction) was identified by sodium dodecyl sulfate polyacrylamide gel electrophoresis and autoradiography. IGF-II stimulated phosphorylation of the type II receptor in BRL-3A2 rat liver cells. Lability of the receptor phosphate bonds to alkaline pH suggests that the bulk of phosphorylation was occurring on serine residues.     

Differences in insulin-induced glucose uptake and enzyme activity in running rats

To evaluate the relationship between enhanced insulin action and level of exercise training, in vivo glucose uptake was assessed in the absence of added insulin and during insulin-stimulated conditions for three activity levels of voluntarily trained rats (low 2-5 km/day, medium 6-9 km/day, high 11-16 km/day). After rats rested for 24 h and fasted overnight, glucose uptake was estimated by comparing steady-state serum glucose (SSSG) levels at low insulin (SSSI) concentrations achieved during an insulin suppression test. In the absence of added insulin, SSSI averaged approximately 20 microU/ml and glucose uptake was similar for high runners and younger weight-matched controls. However, with insulin added to sustain SSSI at approximately 35 microU/ml, SSSG was significantly reduced in all runners (P less than 0.02), with the lowest value attained in high runners. Fasting serum triglycerides were also reduced in all runners (P less than 0.05), with the lowest values seen in medium and high runners. The concentration of glycogen in liver and select skeletal muscles at the start of the study was not different between trained and control rats, suggesting that enhanced insulin-stimulated glucose uptake was not the result of lower glycogen levels. In addition, glycogen synthase and succinate dehydrogenase activities in biceps femoris muscle were only elevated for high runners, but glycogen synthase activity was not enhanced in plantaris muscle and was decreased in soleus muscle. These findings indicate that enhanced insulin-stimulated glucose uptake and reduced serum triglyceride concentrations induced in exercise-trained rats at varying activity levels are dissociated from changes in glycogen synthase and oxidative enzyme activity for skeletal muscle.     

Darwin's Manufactory Hypothesis Is Confirmed and Predicts the Extinction Risk of Extant Birds

In the Origin of Species Darwin hypothesized that the “manufactory” of species operates at different rates in different lineages and that the richness of taxonomic units is autocorrelated across levels of the taxonomic hierarchy. We confirm the manufactory hypothesis using a database of all the world''s extant avian subspecies, species and genera. The hypothesis is confirmed both in correlations across all genera and in paired comparisons controlling for phylogeny. We also find that the modern risk of extinction, as measured by “Red List” classifications, differs across the different categories of genera identified by Darwin. Specifically, species in “manufactory” genera are less likely to be threatened, endangered or recently extinct than are “weak manufactory” genera. Therefore, although Darwin used his hypothesis to investigate past evolutionary processes, we find that the hypothesis also foreshadows future changes to the evolutionary tree.     

Responsiveness of dairy cows to human approach and novel stimuli

This study investigated intra-test and inter-test consistency of dairy cattle behavioural responses to a series of tests involving human approach and exposure to novelty. Thirty-six lactating Holstein–Friesian cows were each subjected to three human approach tests and three novel stimuli tests. Flight response score was assessed by an experimenter approaching cows when they were in the passageway of the home-pen (AP), lying down (AL) and at the feedface (FF). Each human approach test was repeated on each cow three times. The intra-animal repeatability estimates were 0.65, 0.40, 0.27 for AP, AL and FF tests, respectively. Repeatability evaluates an individual's consistency across tests by comparing it to the variation within the group. Cows showed moderate consistency in their flight response scores to the different approach tests (W₃₅ = 0.56, P < 0.01). Three novel stimuli (water spray, striped boards and flashing light) were individually presented once to each cow. Investigatory and reactivity behavioural responses were assessed. Cows showed the greatest reactivity response to the water spray compared to the striped boards (U₁ = 56, P < 0.001) and flashing light (U₁ = 66, P < 0.001). No statistically significant agreement existed between the novel stimuli reactivity and investigatory responses with the AP flight response scores. In conclusion, consistency over time was demonstrated over a relatively short period for the AP test and consistency between human approach situations was shown, however, consistency between human and novel situations was not found.     

Melatonin suppresses AOM/DSS-induced large bowel oncogenesis in rats

The inhibitory effects of exogenous melatonin (MEL) on colon oncogenesis were investigated using an azoxymethane (AOM)/dextran sodium sulfate (DSS) rat model. Male F344 rats initiated with a single intraperitoneal injection of AOM (20 mg/kg bw) were promoted by 1% (w/v) DSS in drinking water for 7 days. They were then given 0.4, 2 or 10 ppm MEL in drinking water for 17 weeks. At week 20, the development of colonic adenocarcinoma was significantly inhibited by the administration with MEL dose-dependently. MEL exposure modulated the mitotic and apoptotic indices in the colonic adenocarcinomas that developed and lowered the immunohistochemical expression of nuclear factor kappa B, tumor necrosis factor α, interleukin-1β and STAT3 in the epithelial malignancies. These results may indicate the beneficial effects of MEL on colitis-related colon carcinogenesis and a potential application for inhibiting colorectal cancer development in the inflamed colon.     

Anti-Insulin Receptor Autoantibodies Are Not Required for Type 2 Diabetes Pathogenesis in NZL/Lt Mice,a New Zealand Obese (NZO)-Derived Mouse Strain

The New Zealand obese (NZO) mouse strain shares with the related New Zealand black (NZB) strain a number of immunophenotypic traits. Among these is a high proportion of B-1 B lymphocytes, a subset associated with autoantibody production. Approximately 50% of NZO/HlLt males develop a chronic insulin-resistant type 2 diabetes syndrome associated with 2 unusual features: the presence of B lymphocyte–enriched peri-insular infiltrates and the development of anti-insulin receptor autoantibodies (AIRAs). To establish the potential pathogenic contributions ofBlymphocytes and AIRAs in this model, a disrupted immunoglobulin heavy chain gene (Igh-6) congenic on the NZB/BlJ background was backcrossed 4 generations into the NZO/HlLt background and was then intercrossed to produce mice that initially segregated for wild-type versus the mutant Igh-6 allele and thus permitted comparison of syndrome development. A new flow cytometric assay (AIRA binding to transfected Chinese hamster ovary cells stably expressing mouse insulin receptor) showed IgM and IgG subclass AIRAs in serum from Igh-6 intact males, but not in Igh6^null male serum. However, the absence of B lymphocytes and antibodies distinguishing mutant from wild-type males failed to significantly affect diabetes-free survival. The Igh6^nullmales gained weight less rapidly than wild-type males, probably accounting for a retardation, but not prevention, of hyperglycemia. Thus, AIRA and the Blymphocyte component of the peri-insulitis in chronic diabetics were not essential either to development of insulin resistance or to eventual pancreatic beta cell failure and loss. A new substrain, designated NZL, was generated by inbreeding Igh-6 wild-type segregants. Currently at the F10 generation, NZL mice exhibit the same juvenile-onset obesity as NZO/HlLt males, but develop type 2 diabetes at a higher frequency (> 80%). Also, unlike NZO/HlLt mice that are difficult to breed, the NZL/Lt strain breeds well and thus offers clear advantages to obesity/diabetes researchers.     

The Maintenance of Stable Dominance Hierarchies and the Pattern of Aggression: Support for the Suppression Hypothesis

Three hypotheses have been proposed to explain the development and maintenance of dominance hierarchies. According to the first hypothesis the dominance hierarchy is a result of the animals fighting once at their first encounter and then using the outcome of that fight to determine the rank order. The second hypothesis proposes that a dominance hierarchy reflects the fighting ability of the individuals in the group at each moment and is therefore relatively fluid with individuals continuously fighting for position. A third hypothesis, the suppression hypothesis, states that the dominance hierarchy is based to a large extent on the outcome of the first fight between the individuals but the dominant animal in each pair continuously attacks the subdominant individuals to condition them to lose in future encounters. We studied six well‐established flocks containing six adult hens each (Gallus gallus domesticus). Five of the flocks had linear hierarchies. The aggression was significantly more often directed towards the next low‐ranking individual. There was a good correlation between rank and comb size (height × width), but no significant correlation between rank and weight, or rank and level of fluctuating asymmetry. There was no significant correlation between levels of aggression and similarity of comb size for individuals of neighboring ranks. Our results tentatively support the suppression hypothesis for the maintenance of dominance hierarchies in the domestic hen.     

The effects of operant control over food and light on the behaviour of domestic hens

In intensive farming systems, the animals have little control over important elements in their environments. For instance, food of a pre-set type is delivered at set times, and the lighting schedule is controlled by the farmer. It has been suggested that low levels of environmental control over important events may reduce welfare by increasing passivity and stress. This study aimed to evaluate the effect of providing control over food and lighting additional to a restricted regime on the behaviour of small groups of laying hens (Gallus gallus domesticus). Twelve pens, each containing five birds, were paired to give six controlling and six non-controlling pens. These pairs of pens were yoked, such that birds in the controlling pens were able to make an operant response to gain access to extra food and light, whilst the yoked pens also received these outcomes but were unable to control their occurrence. The birds were kept continuously in the experimental conditions for 9 weeks. Records were made of general behaviour and activity, aggression and plumage damage scores, every 2 weeks. Data on key-pecking and egg production were continuously recorded throughout the experiment. The controlling birds used the operant keys to open the feeder for an average of 92min and to turn on the light for 46min per pen per day. The high number of key-pecks indicates that the birds were motivated to make use of the keys to control access to additional food and light. The non-controlling treatment pens showed significantly higher levels of preening and resting. Contrary to previous studies the use of operant feeders in this experiment did not induce a high level of feather pecking or aggressive interactions, as there was no significant difference between treatments. During the experiment the non-controlling hens laid significantly more eggs than the controlling hens. The results suggest that lack of control over these particular environmental events induced mild stress in the non-controlling pens of birds, and that further investigations into the effect of lack of control on welfare would be warranted.