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The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem

The Yellowstone geothermal complex contains over 10,000 diverse geothermal features that host numerous phylogenetically deeply rooted and poorly understood archaea, bacteria, and viruses. Microbial communities in high-temperature environments are generally less diverse than soil, marine, sediment, or lake habitats and therefore offer a tremendous opportunity for studying the structure and function of different model microbial… [Read More]

Identification and characterization of functional centromeres of the common bean

In higher eukaryotes, centromeres are typically composed of megabase-sized arrays of satellite repeats that evolve rapidly and homogenize within a species’ genome. Despite the importance of centromeres, our knowledge is limited to a few model species. We conducted a comprehensive analysis of common bean (Phaseolus vulgaris) centromeric satellite DNA using genomic data, fluorescence in situ… [Read More]

Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes

Accurate detection of transcriptional regulatory elements is essential for high-quality genome annotation, metabolic reconstruction, and modeling of regulatory networks. We developed a computational approach for reconstruction of regulons operated by transcription factors (TFs) from large protein families and applied this novel approach to three TF families in 10 Desulfovibrionales genomes. Phylogenetic analyses of 125 regulators… [Read More]

PSimScan: algorithm and utility for fast protein similarity search

In the era of metagenomics and diagnostics sequencing, the importance of protein comparison methods of boosted performance cannot be overstated. Here we present PSimScan (Protein Similarity Scanner), a flexible open source protein similarity search tool which provides a significant gain in speed compared to BLASTP at the price of controlled sensitivity loss. The PSimScan algorithm… [Read More]

Structural, Mechanistic and Genomic Insights into OCP-Mediated Photoprotection

Until relatively recently, photoprotective mechanisms in cyanobacteria were poorly understood. Yet, they play a crucial role in the ecophysiology of cyanobacteria, which inhabit a range of environments, some of them are extreme where stresses such as high salinity, drought and temperature exacerbate the threat of photodamage. This review focuses on the OCP-mediated photoprotective mechanism, which… [Read More]

The Orange Carotenoid Protein: a blue-green light photoactive protein

This review focuses on the Orange Carotenoid Protein (OCP) which is the first photoactive protein identified containing a carotenoid as the photoresponsive chromophore. This protein is essential for the triggering of a photoprotective mechanism in cyanobacteria which decreases the excess absorbed energy arriving at the photosynthetic reaction centers by increasing thermal dissipation at the level… [Read More]

Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album Strain BG8

The complete genome sequence of Methylomicrobium album strain BG8, a methane-oxidizing gammaproteobacterium isolated from freshwater, is reported. Aside from a conserved inventory of genes for growth on single-carbon compounds, M. album BG8 carries a range of gene inventories for additional carbon and nitrogen transformations but no genes for growth on multicarbon substrates or for N… [Read More]

Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments

Six phototrophic microbial mat communities from different geothermal springs (YNP) were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may… [Read More]

Revised sequence and annotation of the Rhodobacter sphaeroides 2.4.1 genome

The DNA sequences of chromosomes I and II of Rhodobacter sphaeroides strain 2.4.1 have been revised, and the annotation of the entire genomic sequence, including both chromosomes and the five plasmids, has been updated. Errors in the originally published sequence have been corrected, and ~11% of the coding regions in the original sequence have been… [Read More]