Replication and maintenance of linear phage-plasmid N15

The lambdoid phage N15 of Escherichia coli is very unusual among temperate phages in that its prophage is not integrated into the chromosome but is a linear plasmid molecule with covalently closed ends (telomeres). Upon infection, the phage DNA circularizes via cohesive ends, and then a special phage enzyme of the tyrosine recombinase family, protelomerase, cuts at another site and joins the ends, forming hairpin telomeres of the linear plasmid prophage. Replication of the N15 prophage is initiated at an internally located ori site and proceeds bidirectionally, resulting in the formation of duplicated telomeres. The N15 protelomerase cuts them, generating two linear plasmid molecules with hairpin telomeres. Stable inheritance of the plasmid prophage is ensured by a partitioning operon similar to the F factor sop operon. Unlike the F centromere, the N15 centromere consists of four inverted repeats dispersed in the genome. The multiplicity and dispersion of centromeres are required for efficient partitioning of a linear plasmid. The centromeres are located in the N15 genome regions involved in phage replication and control of lytic development, and binding of partition proteins at these sites regulates these processes. The family of N15-like linear phage-plasmids includes lambdoid phages φKO2 and pY54, as well as Myoviridae phages ΦHAP-1, VHML, VP882, Vp58.5, and vB_VpaM_MAR of marine gamma-proteobacteria. The genomes of these phages contain similar protelomerase genes, lysogeny control modules, and replication genes, suggesting that these phages may belong to a group diverged from a common ancestor. © 2015 American Society for Microbiology

Comparative Study of Methanogenic Pathways in the Sediments of Thermokarst and Polygenetic Yamal Lakes

Comparative study of methanogen diversity and potential activity of different methanogenic pathways in the sediments of young thermokarst and mature polygenetic Yamal lakes was carried out. The hydrogenotrophic pathway of methanogenesis played an important role in methane formation in thermokarst lakes. The acetoclastic and methylotrophic pathways were also revealed there. In a polygenetic lake with a dissolved organic matter content closest to that of the thermokarst lakes, methanogenesis proceeded more intensively, and the relative abundance of methanogens, especially acetoclastic ones, was higher than in thermokarst lakes. The activity of methyl-reducing methanogens was also assumed there. Methanogens of the genera Methanothrix and Methanoregula, as well as representatives of the family Methanomassiliicoccaceae were identified in the sediments of all lakes. Methane-oxidizing bacteria (Methylobacter, Candidatus "Methylomirabilis") and archaea (Ca. "Methanoperedens") were also detected

Songs of Love and Marriage in \u22Shijing Guofeng (詩經國風)\u22 and Ancient Courtship through Song and Dance

Anaerobic enrichment from sediments of hypersaline alkaline lakes in Wadi el Natrun(Egypt) with chitin resulted in the isolation of a fermentative haloalkaliphilic bacterium,strain ACht6-1, growing exclusively with insoluble chitin as the substrate in a sodiumcarbonate-based medium at pH 8.5–10.5 and total NaC concentrations from 0.4 to1.75 M. The isolate had a Gram-negative cell wall and formed lipid cysts in old cultures.The chitinolytic activity was associated with cells. Analysis of the 4.4 Mb draft genomeidentified pathways for chitin utilization, particularly, secreted chitinases linked to the cellsurface, as well as genes for the hydrolysis of other polysaccharides and fermentationof sugars, while the genes needed for aerobic and anaerobic respiration were absent.Adaptation to a haloalkaliphilic lifestyle was reflected by the gene repertoire encodingsodium rather than proton-dependent membrane-bound ion pumps, including the Rnftypecomplex, oxaloacetate decarboxylase, V-type ATPase, and pyrophosphatase. Thephylogenetic analysis using 16S rRNA gene and ribosomal proteins indicated thatACht6-1 forms a novel deep lineage at the class level within the bacterial candidatedivision TG3. Based on phylogenetic, phenotypic and genomic analyses, the novelchitinolytic bacterium is described as Chitinispirillum alkaliphilum gen. nov., sp. nov.

Genome analysis of <i>Chitinivibrio alkaliphilus</i> gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3

Anaerobic enrichments from hypersaline soda lakes with chitin as substrate yielded five closely related anaerobic haloalkaliphilic isolates growing on insoluble chitin by fermentation at pH10 and salinities up to 3.5M. The chitinolytic activity was exclusively cell associated. To better understand the biology and evolutionary history of this novel bacterial lineage, the genome of the type strain ACht1 was sequenced. Analysis of the 2.6Mb draft genome revealed enzymes of chitin-degradation pathways, including secreted cell-bound chitinases. The reconstructed central metabolism revealed pathways enabling the fermentation of polysaccharides, while it lacks the genes needed for aerobic or anaerobic respiration. The Rnf-type complex, oxaloacetate decarboxylase and sodium-transporting V-type adenosine triphosphatase were identified among putative membrane-bound ion pumps. According to 16S ribosomal RNA analysis, the isolates belong to the candidate phylum Termite Group 3, representing its first culturable members. Phylogenetic analysis using ribosomal proteins and taxonomic distribution analysis of the whole proteome supported a class-level classification of ACht1 most probably affiliated to the phylum Fibribacteres. Based on phylogenetic, phenotypic and genomic analyses, the novel bacteria are proposed to be classified as Chitinivibrio alkaliphilus gen. nov., sp. nov., within a novel class Chitinivibrione