FAS: assessing the similarity between proteins using multi-layered feature architectures.

MOTIVATION: Protein sequence comparison is a fundamental element in the bioinformatics toolkit. When sequences are annotated with features such as functional domains, transmembrane domains, low complexity regions or secondary structure elements, the resulting feature architectures allow better informed comparisons. However, many existing schemes for scoring architecture similarities cannot cope with features arising from multiple annotation sources. Those that do fall short in the resolution of overlapping and redundant feature annotations. RESULTS: Here, we introduce FAS, a scoring method that integrates features from multiple annotation sources in a directed acyclic architecture graph. Redundancies are resolved as part of the architecture comparison by finding the paths through the graphs that maximize the pair-wise architecture similarity. In a large-scale evaluation on more than 10 000 human-yeast ortholog pairs, architecture similarities assessed with FAS are consistently more plausible than those obtained using e-values to resolve overlaps or leaving overlaps unresolved. Three case studies demonstrate the utility of FAS on architecture comparison tasks: benchmarking of orthology assignment software, identification of functionally diverged orthologs, and diagnosing protein architecture changes stemming from faulty gene predictions. With the help of FAS, feature architecture comparisons can now be routinely integrated into these and many other applications. AVAILABILITY AND IMPLEMENTATION: FAS is available as python package: https://pypi.org/project/greedyFAS/.

Acinetobacter equi sp. nov., isolated from horse faeces.

The taxonomic position of five strains isolated from horse faeces, and which shared identical 16S rRNA gene sequences, were studied. Cells of all isolates are Gram-stain-negative, obligately aerobic and have a rod-shaped appearance. The strains show highest 16S rRNA gene sequence similarities to Acinetobacter lwoffii (98.3 %), Acinetobacter haemolyticus (98.0 %), Acienetobacter johnsonii (97.9 %) and Acinetobacter brisouii (97.9 %). Whole-genome sequencing of strain 114T and phylogeny reconstruction based on a core set of 1061 Acinetobacter genes indicated that A. bouvetii CIP 107468T was the closest relative among species of the genus Acinetobacter for which whole genome sequences are available. The genomic DNA G+C content of strain 114T is 34.9 mol%, which is lower than any other value reported for the genus Acinetobacter. The predominant polyamine is 1,3-diaminopropane, which is typical for the genus Acinetobacter. The most abundant fatty acids are C16 : 1ω7c and/or iso-C15 : 0 2-OH (36 %) and C16 : 0 (28 %). The proportion of C18 : 1ω9c (7 %) is distinctively low compared to most species of the genus. The major ubiquinone of strain 114T is Q-9. Microscopic studies revealed the presence of pili and the absence of flagella. The capability of all five strains to utilize l-arabinose and gentisate as well as their lack of growth at temperatures of 41 °C and above provide sufficient criteria to distinguish the isolates from all species of the genus Acinetobacter with validly published names. Based on these combined data, the five isolates represent a novel species of the genus Acinetobacter, for which the name Acinetobacter equi sp. nov. is proposed. The type strain is 114T ( = DSM 27228T = CCUG 65204T).

Acinetobacter baumannii Virulence Is Mediated by the Concerted Action of Three Phospholipases D.

Acinetobacter baumannii causes a broad range of opportunistic infections in humans. Its success as an emerging pathogen is due to a combination of increasing antibiotic resistance, environmental persistence and adaptation to the human host. To date very little is known about the molecular basis of the latter. Here we demonstrate that A. baumannii can use phosphatidylcholine, an integral part of human cell membranes, as sole carbon and energy source. We report on the identification of three phospholipases belonging to the PLD superfamily. PLD1 and PLD2 appear restricted to the bacteria and display the general features of bacterial phospholipases D. They possess two PLDc_2 PFAM domains each encompassing the HxKx4Dx6GS/GGxN (HKD) motif necessary for forming the catalytic core. The third candidate, PLD3, is found in bacteria as well as in eukaryotes and harbours only one PLDc_2 PFAM domain and one conserved HKD motif, which however do not overlap. Employing a markerless mutagenesis system for A. baumannii ATCC 19606T, we generated a full set of PLD knock-out mutants. Galleria mellonella infection studies as well as invasion experiments using A549 human lung epithelial cells revealed that the three PLDs act in a concerted manner as virulence factors and are playing an important role in host cell invasion.

Evolutionary imprint of catalytic domains in fungal PKS-NRPS hybrids.

Fungal hybrid enzymes consisting of a polyketide synthase (PKS) and a nonribosomal peptide synthetase (NRPS) module are involved in the biosynthesis of a vast array of ecologically and medicinally relevant natural products. Whereas a dozen gene clusters could be assigned to the requisite PKS-NRPS pathways, the programming of the multifunctional enzymes is still enigmatic. Through engineering and heterologously expressing a chimera of PKS (lovastatin synthase, LovB) and NRPS (cytochalasin synthase, CheA) in Aspergillus terreus, we noted the potential incompatibility of a fungal highly reducing PKS (hrPKS) with the NRPS component of fungal PKS-NRPS hybrids. To rationalize the unexpected outcome of the gene fusion experiments, we conducted extensive bioinformatic analyses of fungal PKS-NRPS hybrids and LovB-type PKS. From motif studies and the function of the engineered chimeras, a noncanonical function of C-terminal condensation (C) domains in truncated PKS-NRPS homologues was inferred. More importantly, sequence alignments and phylogenetic trees revealed an evolutionary imprint of the PKS-NRPS domains, which reflect the evolutionary history of the entire megasynthase. Furthermore, a detailed investigation of C and adenylation (A) domains provides support for a scenario in which not only the A domain but also the C domain participates in amino acid selection. These findings shed new light on the complex code of this emerging class of multifunctional enzymes and will greatly facilitate future combinatorial biosynthesis and pathway engineering approaches towards natural product analogues.

Infantile postural asymmetry and osteopathic treatment: a randomized therapeutic trial.

The aim of this study was to assess the therapeutic efficacy of osteopathic treatment in infants with postural asymmetry. A randomized clinical trial of efficacy with blinded videoscoring was performed. Sixty-one infants with postural asymmetry aged 6 to 12 weeks (mean 9wks) were recruited. Thirty-two infants (18 males, 14 females) with a gestational age of at least 36 weeks were found to be eligible and randomly assigned to the intervention groups, 16 receiving osteopathic treatment and 16 sham therapy. After a treatment period of 4 weeks the outcome was measured using a standardized scale (4-24 points). With sham therapy, five infants improved (at least 3 points), eight infants were unchanged (within 3 points), and three infants deteriorated (not more than -3 points); the mean improvement was 1.2 points (SD 3.5). In the osteopathic group, 13 infants improved and three remained unchanged; the mean improvement was 5.9 points (SD 3.8). The difference was significant (p=0.001). We conclude that osteopathic treatment in the first months of life improves the degree of asymmetry in infants with postural asymmetry.

Patterns of postural asymmetry in infants: a standardized video-based analysis.

Cervical rotation deficit (CRD) and trunk convexity (TC) constitute the diagnosis of infantile postural asymmetry (IPA), which is often associated with further asymmetric features. However, very little data on the entire symptom complex are currently available. The aim of this study was to analyse the entire clinical spectrum of IPA based on a standardized video documentation. Forty-five infants (27 male) with an asymmetry score of > or = 12 points (scale: 4-24) at a median post-term age of 10 weeks (range: 6-16) were selected from two previously studies using predefined criteria. CRD and TC as reactive movements to an orienting head turn in the prone and supine position were assessed from video recordings by three independent observers. Plagiocephaly, oblique body position and asymmetric foot position were descriptively assessed by consent of the same observers. Hip dysplasia data were derived from sonography charts. The assessment of the reactive movements showed a "scoliosis" pattern in sox infants, a "torticollis" pattern in nine infants, a "mixed prone" pattern in 13 infants and a "mixed" pattern in 26 infants. Side agreement in the prone and supine position of TC and CRD was seen in 27 infants, with a left-sided convexity and left-sided head rotation deficit in two-thirds of the infants. Plagiocephaly was present in 27 infants, oblique body position in 13 infants, hip dysplasia in 4 infants and calcaneus foot in 11 infants. In conclusion, infantile asymmetry pattern analysis showed that morphological and functional anomalies are intricately linked and that infants with only a single apparent sign of asymmetry have actually a much more generalized disturbance.

Idiopathic infantile asymmetry, proposal of a measurement scale.

UNLABELLED: To evaluate the development of idiopathic infantile asymmetry and the efficacy of therapeutic interventions, spinal scoliosis can be quantified on the basis of radiographs. For obvious reasons, use of this technique is limited. Here we present a clinical method to describe and quantify infantile asymmetry. For item selection, spontaneous movements (SMs), reactive movements (RMs) and length differences were video recorded in 30 infants (median age 10 weeks, range 6-16) with variable degrees of asymmetry. Within these three categories, reactive movements elicited by head turns to the right and left side in the prone and supine position emerged as reliable parameters reflecting trunk convexity and cervical rotation deficits. Six-point scales were developed for both measurements and added to form final scales. Consistency and interobserver reliability were evaluated in another 20 infants (median age 9 weeks, range 6-15) with variable degrees of asymmetry. Statistical analysis indicated good reliability and consistency of the testing method with an intraclass correlation coefficient of 91.5% (Cronbach alpha 0.84). CONCLUSION: During the first months of life, idiopathic infantile asymmetry can be clinically assessed using a highly consistent and reliable measurement scale describing degrees of trunk convexity and cervical rotations deficit.