Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

The germline genome of the binucleated ciliate Tetrahymena thermophila undergoes programmed chromosome breakage and massive DNA elimination to generate the somatic genome. Here, we present a complete sequence assembly of the germline genome and analyze multiple features of its structure and its relationship to the somatic genome, shedding light on the mechanisms of genome rearrangement as well as the evolutionary history of this remarkable germline/soma differentiation. Our results strengthen the notion that a complex, dynamic, and ongoing interplay between mobile DNA elements and the host genome have shaped Tetrahymena chromosome structure, locally and globally. Non-standard outcomes of rearrangement events, including the generation of short-lived somatic chromosomes and excision of DNA interrupting protein-coding regions, may represent novel forms of developmental gene regulation. We also compare Tetrahymenas germline/soma differentiation to that of other characterized ciliates, illustrating the wide diversity of adaptations that have occurred within this phylum.</p

Local Admixture of Amplified and Diversified Secreted Pathogenesis Determinants Shapes Mosaic \u3cem\u3eToxoplasma gondii\u3c/em\u3e Genomes

Toxoplasma gondii is among the most prevalent parasites worldwide, infecting many wild and domestic animals and causing zoonotic infections in humans. T. gondii differs substantially in its broad distribution from closely related parasites that typically have narrow, specialized host ranges. To elucidate the genetic basis for these differences, we compared the genomes of 62 globally distributed T. gondii isolates to several closely related coccidian parasites. Our findings reveal that tandem amplification and diversification of secretory pathogenesis determinants is the primary feature that distinguishes the closely related genomes of these biologically diverse parasites. We further show that the unusual population structure of T. gondii is characterized by clade-specific inheritance of large conserved haploblocks that are significantly enriched in tandemly clustered secretory pathogenesis determinants. The shared inheritance of these conserved haploblocks, which show a different ancestry than the genome as a whole, may thus influence transmission, host range and pathogenicity

An integrated workflow for phenazine-modifying enzyme characterization

Increasing availability of new genomes and putative biosynthetic gene clusters (BGCs) has extended the opportunity to access novel chemical diversity for agriculture, medicine, environmental and industrial purposes. However, functional characterization of BGCs through heterologous expression is limited because expression may require complex regulatory mechanisms, specific folding or activation. We developed an integrated workflow for BGC characterization that integrates pathway identification, modular design, DNA synthesis, assembly and characterization. This workflow was applied to characterize multiple phenazine-modifying enzymes. Phenazine pathways are useful for this workflow because all phenazines are derived from a core scaffold for modification by diverse modifying enzymes (PhzM, PhzS, PhzH, and PhzO) that produce characterized compounds. We expressed refactored synthetic modules of previously uncharacterized phenazine BGCs heterologously in Escherichia coli and were able to identify metabolic intermediates they produced, including a previously unidentified metabolite. These results demonstrate how this approach can accelerate functional characterization of BGCs

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents â 1/475% of the genus-level bacterial and archaeal taxa present in the rumen. © 2018 Nature Publishing Group. All rights reserved

Minimum Information about a Biosynthetic Gene cluster

A wide variety of enzymatic pathways that produce specialized metabolites in bacteria, fungi and plants are known to be encoded in biosynthetic gene clusters. Information about these clusters, pathways and metabolites is currently dispersed throughout the literature, making it difficult to exploit. To facilitate consistent and systematic deposition and retrieval of data on biosynthetic gene clusters, we propose the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard.Chemistry and Chemical Biolog

The role of human beta defensins 2 and 3 in the second trimester amniotic fluid in predicting preterm labor and premature rupture of membranes

Aim Human beta defensins 2 (HBD2) and 3 (HBD3) are peptides expressed in the amnion and chorion. This is a matched case control study conducted in our Department to determine whether second trimester amniotic fluid HBD2 and HBD3 concentrations measured at the time of genetic amniocentesis could be potential markers of preterm labor prediction. Methods Amniotic fluid HBD2 and HBD3 were determined by an enzyme-linked immunosorbent assay (ELISA) Women with preterm labor were deWned as cases (N = 41) while for each case a woman matched for age delivering at term served as control (N = 41). Subgroup analysis was conducted to examine possible associations of HBD2 and HBD3 in cases of premature rupture of membranes. Nineteen women with preterm labor and premature rupture of membranes were deWned as cases while for every case a woman matched for maternal age delivering at term served as control (N1 = 19). Results were presented as odds ratios (OR) and 95% conWdence intervals. Statistical analysis used STATA 8.2 and SPSS 11.5 edition. A P-value of &lt;0.05 was considered statistically signiWcant. Results Amniotic fluid concentrations of HBD2 at the time of genetic amniocentesis were positively associated with preterm premature rupture of membranes (P = 0.028), but not with preterm labour. No association of HBD3 and preterm birth was documented. Conclusion Second trimester amniotic fluid HBD2 might be a predictor of premature rupture of membranes. © Springer-Verlag 2009

decRiPPter datasets - Integration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products

Datasets for decRiPPter, a genome mining tool for novel types of ribosomally synthesized and post-translationally modified peptides (RiPPs). 1) All training data for the SVM and the scripts used to generate them, 2) The output from the analysis of 1,295 Streptomyces genomes, passed through the 'mild' and the 'strict' filter

Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides

Microbial Biotechnolog

Experimental evidence for the role of domain swapping in the evolution of the histone fold

The histone fold forms the fundamental endoskeleton of the protein core of the nucleosome and is also found in several transcription factors. We have investigated the evolutionary origins of this ubiquitous protein motif, which is found soluble exclusively as an antiparallel (handshake motif) dimer. We introduced a three amino acid insertion into the middle of a homodimeric archaeal histone fold motif. The engineered molecule was found to be a soluble and stable monomer with properties consistent with a four-helix-bundle protein. The experimental evidence presented here support the hypothesis that the handshake association motif characteristic of present-day histone dimers is the evolutionary product of domain swapping between two four-helix bundle domains, each of which derived from the tandem duplication of a primitive helix–strand–helix unit