Evolutionary analysis of species-specific duplications in flatworm genomes.

Platyhelminthes, also known as flatworms, is a phylum of bilaterian invertebrates infamous for their parasitic representatives. The classes Cestoda, Monogenea, and Trematoda comprise parasitic helminths inhabiting multiple hosts, including fishes, humans, and livestock, and are responsible for considerable economic damage and burden on human health. As in other animals, the genomes of flatworms have a wide variety of paralogs, genes related via duplication, whose origins could be mapped throughout the evolution of the phylum. Through in-silico analysis, we studied inparalogs, i.e., species-specific duplications, focusing on their biological functions, expression changes, and evolutionary rate. These genes are thought to be key players in the adaptation process of species to each particular niche. Our results showed that genes related with specific functional terms, such as response to stress, transferase activity, oxidoreductase activity, and peptidases, are overrepresented among inparalogs. This trend is conserved among species from different classes, including free-living species. Available expression data from Schistosoma mansoni, a parasite from the trematode class, demonstrated high conservation of expression patterns between inparalogs, but with notable exceptions, which also display evidence of rapid evolution. We discuss how natural selection may operate to maintain these genes and the particular duplication models that fit better to the observations. Our work supports the critical role of gene duplication in the evolution of flatworms, representing the first study of inparalogs evolution at the genome-wide level in this group.

Stage-specific transcriptomic analysis of the model cestode Hymenolepis microstoma.

Most parasitic flatworms go through different life stages with important physiological and morphological changes. In this work, we used a transcriptomic approach to analyze the main life-stages of the model tapeworm Hymenolepis microstoma (eggs, cysticercoids, and adults). Our results showed massive transcriptomic changes in this life cycle, including key gene families that contribute substantially to the expression load in each stage. In particular, different members of the cestode-specific hydrophobic ligand-binding protein (HLBP) family are among the most highly expressed genes in each life stage. We also found the transcriptomic signature of major metabolic changes during the transition from cysticercoids to adult worms. Thus, this work contributes to uncovering the gene expression changes that accompany the development of this important cestode model species, and to the best of our knowledge represents the first transcriptomic study with robust replicates spanning all of the main life stages of a tapeworm.

Full characterization of plasmids from Achromobacter ruhlandii isolates recovered from a single patient with cystic fibrosis (CF).

In the last decade Achromobacter spp. has been associated with chronic colonization in patients with cystic fibrosis (CF). Although Achromobacter xylosoxidans is the most frequent species recovered within this genus, other species such as A. ruhlandii have also been reported in these patients. Descriptions of mobile elements are scarce in Achromobacter and none of them have been originated in A. ruhlandii. The aim of this study was to report the full characterization of a plasmid which was maintained in four clonally related A. ruhlandii isolates. Between 2013 and 2015, nine A. ruhlandii isolates were recovered from a pediatric patient with CF at a hospital in Buenos Aires. Four selected clonally related isolates were sequenced by Illumina MiSeq, annotated using RAST and manually curated. The presence of a unique plasmid of 34096-bp and 50 CDS was observed in the four isolates, displaying only 1 nucleotide substitution translated into one amino acid change among them. These plasmids have a class 1 integron containing the aac-(6')-Ib gene, a mercury resistance operon region and the relE/stbE toxin/antitoxin system. Plasmids showed 79% similarity and 99% identity with pmatvim-7 from Pseudomonas aeruginosa. This is the first full description and characterization of a plasmid from A. ruhlandii which was maintained over time.

Bacillus natronophilus sp. nov., an alkaliphilic bacterium isolated from a soda lake.

An alkaliphilic, moderately halophilic, heterotrophic, rod-shaped, spore-forming bacterium (M30T) was isolated from a sediment sample collected from a soda lake (Lake Magadi, Tanzania). Strain M30T was strictly aerobic, catalase-positive, oxidase-negative and non-motile. Growth occurred at 12-43 °C (optimum, 25-30 °C), at pH 8.0-12 (optimum, pH 9.5-10) and at salinities of 0.5-15 % (w/v) NaCl (optimum 5 %). It utilized various sugars and organic acids as sole carbon sources and was positive for amylase, cellulase, gelatinase, protease and xylanase activities. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified lipid and one unidentified phospholipid. The DNA G+C content was 48.9 mol%. The predominant menaquinone was MK-7 and the major fatty acids (>10 %) comprised anteiso-C15 : 0, iso-C15 : 0, and anteiso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequence affiliated M30T to the genus Bacillus and showed the highest similarities to Bacillus populi FJAT-45347T (96.4 %) and Bacillus aurantiacus K1-5T (96.2 %). Based on the data from the current polyphasic study, M30T represents a novel species of the genus Bacillus, for which the name Bacillus natronophilus sp. nov. is proposed. The type strain is M30T (=JCM 32118T=CGMCC 1.16739T=MCC 3010T).

Nesterenkonia natronophila sp. nov., an alkaliphilic actinobacterium isolated from a soda lake, and emended description of the genus Nesterenkonia.

A Gram-stain-positive, alkaliphilic, moderately halophilic, cocci-shaped actinobacterium (strain M8T) was isolated from a sample of soda lake sediment (Lake Magadi, Tanzania). The isolate was heterotrophic, strictly aerobic, catalase-positive, oxidase-negative and formed orange-pigmented colonies in solid media. It utilized various sugars and organic acids as sole carbon sources. The organism grew at 10-38 °C, at pH 7.5-12.0 and in the presence of 1-12 % (w/v) NaCl, with optimal growth occurring at 30 °C, at pH 10 and in the presence of 5 % (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain M8T belonged to the genus Nesterenkonia, sharing the closest similarities to Nesterenkoniahalobia DSM 20541T, Nesterenkoniahalophila YIM 70179T and Nesterenkoniaaethiopica DSM 17733T (97.5, 97.5 and 97.1 %, respectively). The characteristic diamino acid of strain M8T was found to be lysine and the polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified glycolipids and two unidentified phospholipids. The DNA G+C content was 61.8 mol% (genome). The strain contained MK-7, MK-9 and MK-10 as the respiratory quinones, and the major fatty acids (>10 %) comprised anteiso-C17 : 0 and anteiso-C15 : 0. On the basis of phylogenetic analyses and phenotypic data, strain M8T is considered to represent a novel species, for which the name Nesterenkonianatronophila sp. nov. is proposed. The type strain is M8T (=JCM 32100T=CGMCC 1.16706T=MCC 3367T).

Membrane fusion and fission during eukaryogenesis.

All eukaryotes can be traced back to a single shared ancestral lineage that emerged from interactions between different prokaryotic cells. Current models of eukaryogenesis describe various selective forces and evolutionary mechanisms that contributed to the formation of eukaryotic cells. Central to this process were significant changes in cellular structure, resulting in the configuration of a new cell type characterized by internal membrane compartments. Additionally, eukaryogenesis results in a life cycle that relies on cell-cell fusion. We discuss the potential roles of proteins involved in remodeling cellular membranes, highlighting two critical stages in the evolution of eukaryotes: the internalization of symbiotic partners and a scenario wherein the emergence of sexual reproduction is linked to a polyploid ancestor generated by cell-cell fusion.

Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins.

Sexual reproduction consists of genome reduction by meiosis and subsequent gamete fusion. The presence of genes homologous to eukaryotic meiotic genes in archaea and bacteria suggests that DNA repair mechanisms evolved towards meiotic recombination. However, fusogenic proteins resembling those found in gamete fusion in eukaryotes have so far not been found in prokaryotes. Here, we identify archaeal proteins that are homologs of fusexins, a superfamily of fusogens that mediate eukaryotic gamete and somatic cell fusion, as well as virus entry. The crystal structure of a trimeric archaeal fusexin (Fusexin1 or Fsx1) reveals an archetypical fusexin architecture with unique features such as a six-helix bundle and an additional globular domain. Ectopically expressed Fusexin1 can fuse mammalian cells, and this process involves the additional globular domain and a conserved fusion loop. Furthermore, archaeal fusexin genes are found within integrated mobile elements, suggesting potential roles in cell-cell fusion and gene exchange in archaea, as well as different scenarios for the evolutionary history of fusexins.

Role of Fasciola hepatica Small RNAs in the Interaction With the Mammalian Host.

MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression being involved in many different biological processes and play a key role in developmental timing. Additionally, recent studies have shown that miRNAs released from parasites are capable of regulating the expression of host genes. In the present work, we studied the expression patterns of ncRNAs of various intra-mammalian life-cycle stages of the liver fluke, Fasciola hepatica, as well as those packaged into extracellular vesicles and shed by the adult fluke. The miRNA expression profile of the intra-mammalian stages shows important variations, despite a set of predominant miRNAs that are highly expressed across all stages. No substantial variations in miRNA expression between dormant and activated metacercariae were detected, suggesting that they might not be central players in regulating fluke gene expression during this crucial step in the invasion of the definitive host. We generated a curated pipeline for the prediction of putative target genes that reports only sites conserved between three different prediction approaches. This pipeline was tested against an iso-seq curated database of the 3' UTR regions of F. hepatica genes to detect miRNA regulation networks within liver fluke. Several functions related to the host immune response or modulation were enriched among the targets of the most highly expressed parasite miRNAs, stressing that they might be key players during the establishment and maintenance of infection. Additionally, we detected fragments derived from the processing of tRNAs, in all developmental stages analyzed, and documented the presence of novel long tRNA fragments enriched in vesicles. We confirmed the presence of at least 5 putative vault RNAs (vtRNAs), that are expressed across different stages and enriched in vesicles. The presence of tRNA fragments and vtRNAs in vesicles raise the possibility that they could be involved in the host-parasite interaction.

Draft Genome Sequence of Paraburkholderia sp. UYCP14C, a Rhizobium Strain Isolated from Root Nodules of Calliandra parvifolia.

Here, we present the draft genome sequence of strain UYCP14C, a rhizobium isolated from Calliandra parvifolia nodules. The assembled genome size was around 9.8 million bp, containing 9,031 predicted protein-coding sequences, including several symbiotic and nitrogen fixation genes. UYCP14C appears to be a novel species of the plant growth-promoting Paraburkholderia genus.

Full characterization of plasmids from Achromobacter ruhlandii isolates recovered from a single patient with cystic fibrosis (CF) / Caracterización completa de plásmidos provenientes de aislamientos de Achromobacter ruhlandii recuperados de un único paciente con fibrosis quística

Abstract In the last decade Achromobacter spp. has been associated with chronic colonizationin patients with cystic fibrosis (CF). Although Achromobacter xylosoxidans is the most frequentspecies recovered within this genus, other species such as A. ruhlandii have also been reportedin these patients. Descriptions of mobile elements are scarce in Achromobacter and none ofthem have been originated in A. ruhlandii. The aim of this study was to report the full char-acterization of a plasmid which was maintained in four clonally related A. ruhlandii isolates.Between 2013 and 2015, nine A. ruhlandii isolates were recovered from a pediatric patientwith CF at a hospital in Buenos Aires. Four selected clonally related isolates were sequencedby Illumina MiSeq, annotated using RAST and manually curated. The presence of a unique plas-mid of 34096-bp and 50 CDS was observed in the four isolates, displaying only 1 nucleotidesubstitution translated into one amino acid change among them. These plasmids have a class 1integron containing the aac-(6)-Ib gene, a mercury resistance operon region and the relE/stbEtoxin/antitoxin system. Plasmids showed 79% similarity and 99% identity with pmatvim-7 fromPseudomonas aeruginosa. This is the first full description and characterization of a plasmid fromA. ruhlandii which was maintained over time.

Resumen Durante la última década, Achromobacter spp. han sido asociadas con la colonización crónica en pacientes con fibrosis quística. Si bien Achromobacter xylosoxidans es la especie más frecuentemente recuperada, otras especies como Achromobacter ruhlandii también fueron reportadas en nuestra región. Sin embargo, pocos reportes se han centrado en la descripción de elementos móviles, y ninguno de ellos los documenta en A. ruhlandii. El objetivo de este estudio fue reportar la caracterización completa de un plásmido conservado en 4 aislamientos clonalmente relacionados de A. ruhlandii. Se recuperaron 9 aislamientos de A. ruhlandii entre 2013 y 2015 de un único paciente con fibrosis quística proveniente de un hospital pediátrico de Buenos Aires, Argentina. Se realizó la secuenciación completa del genoma de los 4 aislamientos seleccionados según el perfil de resistencia antibiótica en un equipo Illumina MiSeq. Estos fueron anotados mediante RAST y curados manualmente. Se detectó la presencia de un solo plásmido de 34.096 pb y 50CDS en los 4 aislamientos, observándose únicamente un cambio nucleotídico traducido en un cambio aminoacídico en un aislamiento. Los plásmidos ensamblados se caracterizaron por presentar un integrón de clase 1 que contenía el gen aac-(6')-Ib, un operón de resistencia a mercurio y el sistema de toxina-antitoxina relE/stbE. Cabe destacar que estos plásmidos poseen un 79% de similitud y un 99% de identidad con el plásmido pmatvim-7 de Pseudomonas aeruginosa. Esta es la primera descripción y caracterización completa de un plásmido proveniente de A. ruhlandii.