AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex

Bacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of anti-CRISPRs that suppress these immune systems. Here we report structures of anti-CRISPR protein IF9 (AcrIF9) in complex with the type I-F CRISPR RNA-guided surveillance complex (Csy). In addition to sterically blocking the hybridization of complementary dsDNA to the CRISPR RNA, our results show that AcrIF9 binding also promotes non-sequence-specific engagement with dsDNA, potentially sequestering the complex from target DNA. These findings highlight the versatility of anti-CRISPR mechanisms utilized by phages to suppress CRISPR-mediated immune systems.

Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry

Bacteria and archaea have evolved sophisticated adaptive immune systems that rely on CRISPR RNA (crRNA)-guided detection and nuclease-mediated elimination of invading nucleic acids. Here, we present the cryo-electron microscopy (cryo-EM) structure of the type I-F crRNA-guided surveillance complex (Csy complex) from Pseudomonas aeruginosa bound to a double-stranded DNA target. Comparison of this structure to previously determined structures of this complex reveals a ∼180-degree rotation of the C-terminal helical bundle on the "large" Cas8f subunit. We show that the double-stranded DNA (dsDNA)-induced conformational change in Cas8f exposes a Cas2/3 "nuclease recruitment helix" that is structurally homologous to a virally encoded anti-CRISPR protein (AcrIF3). Structural homology between Cas8f and AcrIF3 suggests that AcrIF3 is a mimic of the Cas8f nuclease recruitment helix.

Conformational Dynamics of DNA Binding and Cas3 Recruitment by the CRISPR RNA-Guided Cascade Complex

Bacteria and archaea rely on CRISPR (clustered regularly interspaced short palindromic repeats) RNA-guided adaptive immune systems for sequence specific elimination of foreign nucleic acids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble with Cas (CRISPR-associated) proteins into a 405-kilodalton multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade binds foreign DNA complementary to the crRNA guide and recruits Cas3, a trans-acting nuclease-helicase required for target degradation. Structural models of Cascade have captured static snapshots of the complex in distinct conformational states, but conformational dynamics of the 11-subunit surveillance complex have not been measured. Here, we use hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) to map conformational dynamics of Cascade onto the three-dimensional structure. New insights from structural dynamics are used to make functional predictions about the mechanisms of the R-loop coordination and Cas3 recruitment. We test these predictions in vivo and in vitro. Collectively, we show how mapping conformational dynamics onto static 3D-structures adds an additional dimension to the functional understanding of this biological machine.

Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex

Genetic conflict between viruses and their hosts drives evolution and genetic innovation. Prokaryotes evolved CRISPR-mediated adaptive immune systems for protection from viral infection, and viruses have evolved diverse anti-CRISPR (Acr) proteins that subvert these immune systems. The adaptive immune system in Pseudomonas aeruginosa (type I-F) relies on a 350 kDa CRISPR RNA (crRNA)-guided surveillance complex (Csy complex) to bind foreign DNA and recruit a trans-acting nuclease for target degradation. Here, we report the cryo-electron microscopy (cryo-EM) structure of the Csy complex bound to two different Acr proteins, AcrF1 and AcrF2, at an average resolution of 3.4 Å. The structure explains the molecular mechanism for immune system suppression, and structure-guided mutations show that the Acr proteins bind to residues essential for crRNA-mediated detection of DNA. Collectively, these data provide a snapshot of an ongoing molecular arms race between viral suppressors and the immune system they target.

Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli

In bacteria and archaea, short fragments of foreign DNA are integrated into Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci, providing a molecular memory of previous encounters with foreign genetic elements. In Escherichia coli, short CRISPR-derived RNAs are incorporated into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Recent structures of Cascade capture snapshots of this seahorse-shaped RNA-guided surveillance complex before and after binding to a DNA target. Here we determine a 3.2 Å x-ray crystal structure of Cascade in a new crystal form that provides insight into the mechanism of double-stranded DNA binding. Molecular dynamic simulations performed using available structures reveal functional roles for residues in the tail, backbone and belly subunits of Cascade that are critical for binding double-stranded DNA. Structural comparisons are used to make functional predictions and these predictions are tested in vivo and in vitro. Collectively, the results in this study reveal underlying mechanisms involved in target-induced conformational changes and highlight residues important in DNA binding and protospacer adjacent motif recognition.

Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli

Clustered regularly interspaced short palindromic repeats (CRISPRs) are essential components of RNA-guided adaptive immune systems that protect bacteria and archaea from viruses and plasmids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble into a 405-kilodalton multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Here we present the 3.24 angstrom resolution x-ray crystal structure of Cascade. Eleven proteins and a 61-nucleotide crRNA assemble into a seahorse-shaped architecture that binds double-stranded DNA targets complementary to the crRNA-guide sequence. Conserved sequences on the 3' and 5' ends of the crRNA are anchored by proteins at opposite ends of the complex, whereas the guide sequence is displayed along a helical assembly of six interwoven subunits that present five-nucleotide segments of the crRNA in pseudo-A-form configuration. The structure of Cascade suggests a mechanism for assembly and provides insights into the mechanisms of target recognition.

Cerebral vascular response to hemorrhagic hypotension in newborn lambs: the influence of developing anemia

The ability of newborn animals to autoregulate cerebral blood flow (CBF) has been documented. Most studies of the cerebral vascular response to hypotension utilize hemorrhage, generally confounded with anemia. We studied the cerebral blood flow and metabolic response of chloralose and urethane anesthetized newborn lambs to regulated hypotension. Lambs (< or = 7 days old) were catheterized for radioactive microsphere determinations of CBF. The dorsal sagittal sinus was catheterized to obtain cerebral blood samples for the calculation of oxygen uptake. Cerebral perfusion pressure was reduced in a step-wise fashion with hemorrhagic hypotension. Animals spontaneously became anemic with hypotension (AH; n = 8). In a group of animals (NH; n = 6), anemia was prevented by infusion of autologous red blood cells. Arterial pressure was reduced from control to 50, 40, and 30 mm Hg. In the AH group hematocrit fell 37% but was not different from control in the NH group. Total CBF was maintained in all groups. The lowest perfusion pressures studied were 25 +/- 1 and 22 +/- 1 mm Hg in AH and NH groups respectively. Oxygen delivery decreased (37%) only in the AH group, secondary to anemia. Calculated oxygen consumption was maintained in the AH group but increased (approximately 50%) in the NH group at 50 and 40 mm Hg. The ratio of oxygen uptake to oxygen delivery (fractional oxygen extraction) increased linearly in both groups as arterial pressure decreased. The major findings of these experiments are (i) The anesthetized newborn lamb can maintain CBF when perfusion pressure falls to 25 mm Hg and this autoregulatory capacity (classically defined) is not dependent on a change in hematocrit and, presumably, viscosity; (ii) Cerebral hypotension, anemic or not, appears to be accompanied by an increase in fractional extraction of oxygen.

Pharmacokinetics of intravenous immunoglobulin in neonates

Intravenous immunoglobulin (IVIG) may be a therapeutic adjunct to antibiotic treatment of neonatal infections. We examined the pharmacokinetics and safety of IVIG in human neonates. Thirty neonates with suspected sepsis were randomly assigned either to a treatment (receiving either 250, 500, or 1,000 mg/kg of IVIG plus antibiotics) or control (antibiotics alone) group. The 500 mg/kg dose produced a rise in total IgG for greater than 8 and in group B streptococcus (GBS) type-specific IgG for greater than 4-14 days. The type-specific antibody elevation varied with the amount of pathogen-specific antibody and dose of IVIG. Pharmacokinetic analysis suggests a Vdss of 42 ml/kg, Cl of 3.0 ml/kg/day, a biphasic elimination curve, and a terminal elimination half-life of 24.2 days. No toxicity was observed. These data may be valuable in determining optimal dosing schedules for IVIG in treating or preventing neonatal infections.

A group B streptococcal extract reduces neutrophil counts and induces neutrophil aggregation

The possibility that group B streptococci (GBS) may induce neonatal neutropenia by promoting neutrophil aggregation and the entrapment of aggregates in the lung was studied in vivo and in vitro utilizing a cell free GBS extract [(GBS)-trichloroacetic acid (TCA)]. The intravenous infusion of the extract into neonatal lambs induced reductions of circulating white blood cells (0 time, 3.1 X 10(3)/mm3 +/- 0.5 versus 2.2 X 10(3)/mm3 +/- 0.7) 5 min after infusion (p less than 0.01). At necropsy these lambs had prominent accumulation of polymorphonuclear leukocytes in their pulmonary interstitium. Subsequently, neutrophil aggregation was studied by incubating GBS-TCA in human serum or phosphate-buffered saline with subsequent addition to human polymorphonuclear leukocytes in an aggregometer. GBS-TCA incubated in human serum induced prompt polymorphonuclear leukocyte aggregation (mean delta T 12.3% +/- 2.8 in human serum versus delta T 2.5% +/- 2.1 in phosphate-buffered saline, p less than 0.001). Preincubation of GBS-TCA followed by incubation in human serum with human GBS hyperimmune IgG significantly reduced aggregation (GBS-TCA in serum mean delta T 14.9 +/- 2.44 versus 5.42 +/- 1.80, p = 0.002). Cell-free GBS products may induce polymorphonuclear leukocyte aggregation in the presence of whole serum. This phenomenon might contribute to the pulmonary injury experienced by infants with GBS pneumonia and sepsis.

Effect of maternal intravenous infusions on fetal extracellular fluid composition in pregnant ewes

Infusion of intravenous solutions to women in labor is common clinical practice. Since these infusions may change the volume and electrolyte balance between the mother and fetus, we investigated the influence of acute maternal volume expansion upon fetal and maternal fluid and electrolyte equilibrium in the chronically catheterized fetal lamb. Paired measurements of maternal and fetal plasma sodium and potassium concentrations, osmolality, and colloid osmotic pressure (COP), plus measurements in the fetal-placental plasma volume were obtained following rapid maternal infusions with saline, dextrose, and dextran solutions. Maternal infusions resulted in changes in fetal electrolyte concentrations as well as alterations in transplacental COP differences. Despite these changes, however, no changes in fetal plasma volume were noted.

Short-term responses in neonatal lambs after infusion of group B streptococcal extract

Short-term (0 to 30 minutes) physiologic responses of neonatal lambs infused with a trichloroacetic extract of a type III (strain 878) group B streptococcus (878-TCA) were studied. Bolus injections of 878-TCA were associated with pulmonary hypertension, peripheral arterial hypoxemia, and reductions in circulating white blood cell and platelet counts. These events were associated with a rise in plasma levels of prostaglandins F2 alpha and E and could be prevented by proper treatment with ibuprofen. Continuous infusions of 878-TCA were associated with a dose-dependent rise in systemic and pulmonary arterial pressures and a fall in arterial PO2. During infusion, inhibition of prostaglandin synthesis resulted in a return toward preinfusion values. The authors conclude that venous infusions of extracts of 878-TCA induce significant pulmonary and systemic arterial vascular perturbations in the neonatal lamb and that some of these alterations are associated with the release of prostaglandins or other arachidonic acid metabolites.

Endotoxemia in the neonatal lamb

Although gram-negative sepsis is a major cause of neonatal morbidity and mortality, our understanding of endotoxemia in the neonate has been hampered by the lack of experimental models. Previous studies have suggested neonatal hyporesponsiveness to endotoxin. We studied unanesthetized neonatal lambs which had been exposed to the environment prior to study. These animals demonstrated the classic early phase changes of endotoxemia including pulmonary hypertension which was dependent upon prostanoid production. This model allows further studies of endotoxemia in the neonate.

Interobserver and method variability in tuberculin skin testing

Accurate measurement and interpretation of tuberculin skin tests is essential both to avoid unnecessary prophylactic treatment with potentially hepatotoxic drugs and to ensure the proper institution of therapy in tuberculin-positive individuals. Although two methods are currently used for reading tuberculin skin tests, palpation and ballpoint, the optimal technique has not been established. We compared measurements obtained by each method on 101 patients tested with intermediate tuberculin purified protein derivative. Fifty-eight of these patients were also tested using Mono-Vacc. Excellent interobserver agreement among the five raters was demonstrated for both the palpation and ballpoint techniques. There was no significant difference between the two methods for any reader using the normal 10-mm cutoff point for a positive intermediate tuberculin purified protein derivative test. For any individual observer the decision as to whether the test was positive or negative was unaffected by the method in at least 93% of readings. We conclude that readings by physicians using palpation and ballpoint methods are comparable for clinical decision making.

Umbilical cord care. A study of bacitracin ointment vs. triple dye

Umbilical cord colonization rates were examined over a 4-year period following topical application of bacitracin (1978-1980) or triple dye (1980-1982). A total of 2402 cords were cultured: 1229 following bacitracin cord care and 1173 after triple dye application. Cords treated with bacitracin had significantly higher colonization rates when compared to triple dye prophylaxis. Bacterial colonization with Staphylococcus epidermidis and group B beta-hemolytic streptococcus was found only after bacitracin prophylaxis. Our data support the use of triple dye for routine cord care and suggest that bacitracin application may increase the rate of group B streptococcal colonization.

Effect of cephalic pressure on fetal cerebral blood flow

During vaginal delivery, the fetus is exposed to a variety of stresses including pressure applied to the fetal skull. In order to study the effects of this stress on fetal homeostasis, we monitored the response to external cephalic compression applied to the acutely prepared near-term fetal lamb. In response to cephalic pressure, we noted initial bradycardia followed by sustained tachycardia. Mean arterial pressure and pulse pressure rose during cephalic pressure and gradually returned to baseline levels. Cerebral blood flow fell approximately 95% early in the period of compression. This fall in total cerebral blood flow was accompanied by a redistribution of cerebral flow. During this time, a smaller percentage of cerebral blood flow was found in the cortex and a greater percentage was directed to the brainstem.

Studies of short-term pulmonary and peripheral vascular responses induced in oophorectomized sheep by the infusion of a group B streptococcal extract

Short-term (0-30 min) pulmonary and systemic vascular responses of oophorectomized ewes infused intravenously with a trichloroacetic acid (TCA) extract of a type III (strain 878) group B streptococcus (GBS) were studied. TCA-878 extract induced significant pulmonary hypertension, reduction in femoral artery pressure and reduced femoral artery PO2. These responses were similar to those observed after the infusion of sublethal doses of E. coli endotoxin and could be prevented by priming the animal with ibuprofen or indomethacin. Ewes rechallenged 48 h after their initial dose of TCA-878 extract experienced pulmonary arterial pressure significantly higher than those induced by the first infusion. Similar augmented responses were not seen after rechallenge with endotoxin. Larger doses of TCA-878 extract resulted in increasingly higher pulmonary arterial pressure. We conclude that the venous infusion of TCA extracts of GBS-878 induces significant pulmonary hypertension in sheep and that this response may be mediated by prostaglandins. The vasoactive substance extracted from these streptococci could play a role in promoting the vascular instability experienced by the human neonate with early onset GBS disease.

Effect of resuscitative fluids upon physical properties of blood perfusing the brain

Acute physiologic changes induced by the infusion of resuscitative fluids may be harmful, resulting in the clinical sequelae of pulmonary and intraventricular hemorrhage. Using a chronically catheterized lamb model, changes in plasma sodium concentration, osmolality, hematocrit, glucose, colloid osmotic pressure, and arterial pressure were quantified in blood directly perfusing the brain, following distal infusions of fluids commonly used during neonatal resuscitation: molar and .5M NaHCO3, D10W and D25W, and whole blood. Distal infusion of hypertonic solutions resulted in acute alterations in electrolyte and osmotic equilibrium in the common carotid artery. All infused solutions caused a brief elevation in mean blood pressure; whole blood transfusion resulted in a sustained increase in blood pressure.

Osmolality and oncotic pressure of volume expanding fluids for newborn administration

Resuscitation of the newborn frequently requires rapid expansion of the circulating volume and correction of metabolic acidosis and hypoglycemia. solutions commonly used for resuscitation contain various concentrations of NaHCO3, glucose, electrolytes, and albumin. We have demonstrated the wide range of osmolalities of solutions frequently available in nurseries and delivery rooms and the resultant osmolalities caused by the addition of NaHCO3. We have also shown the in vitro concentration of albumin needed to equal full-term cord blood colloid osmotic pressure (COP).

The influence of asphyxia on fetal lidocaine toxicity

Local anesthetics have played an important role in modern obstetrics. Although reasonably safe, these agents have been shown to have detrimental effects in some fetuses. In the present study we examined the influence of acute asphyxia in the fetal lamb on the distribution and cerebral uptake of maternally infused lidocaine. Results demonstrate that asphyxia is associated with higher lidocaine concentrations in the fetal plasma, increased presentation of the drug to the fetal brain, and increased cerebral lidocaine uptake. These findings underscore the importance of evaluation of fetal status when considering the risks and benefits of maternal drug use.

Skin craters--a complication of transcutaneous oxygen monitoring

Continuous transcutaneous oxygen monitoring has become standard practice in the management of infants who require supplemental oxygen. Previously described complications of tcPO2 monitoring consist of prolonged intense skin erythema or first degree burns. Two cases of premature infants who developed numerous, hyperpigmented skin craters following prolonged tcPO2 monitoring are reported. Although these lesions appear to be harmless, they have not resolved with time and long-term cosmetic implications are unknown.

Bilateral clinical anophthalmia: drugs as potential factors

This case of bilateral clinical anophthalmia presents a host of interrelated drug reactions and potential teratogenic factors. While none of the drugs ingested by the mother has a high teratogenic potential, drug interactions, toxic potentiation, and unknown incompatibilities cannot be excluded. Although a single etiologic agent is not incriminated, the drugs ingested during pregnancy and their toxic effects and interactions are discussed. Use of drugs during pregnancy should be limited to those clinically indicated.