The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization

An analysis of the seven genes of the tryptophan pathway in the Sargasso Sea metagenome shows that the majority of contigs and scaffolds contain whole or split operons that are similar to previously analyzed trp gene organizations

Archaeal diversity in the Dead Sea: Microbial survival under increasingly harsh conditions

The Dead Sea is rapidly drying out. The lake is supersaturated with NaCl, and precipitated of halite from the water column has led to a decrease in sodium content, while concentrations of magnesium and calcium greatly increased, making the lake an ever more extreme environment for microbial life. In the past decades, blooms of algae (Dunaliella) and halophilic Archaea were twice observed in the lake (1980-1982 and 1992-1995), triggered by massive inflow of freshwater floods, but no conditions suitable for renewed microbial growth have occurred since. To examine whether the Death Sea in its current state (density 1.24 g ml-1, water activity about 0.67) still supports life of halophilic Archaea, we collected particulate matter from a depth of 5 m at an offshore station by means of tangential filtration. Presence of bacterioruberin carotenoids, albeit at low concentrations, in the particulate material showed the members of the Halobactericacae were still present in the lake\u27s water column. Amplification of 16S rRNA genes from the biomass yielded genes with less than 95% identify with environmental sequences reported from other environments and only 85-95% identity with cultivated Halobacteriaceae. It is thus shown that the Dead Sea, in spite of the ever more adverse conditions to life, supports a unique and varied community of halophilic Archaea. We have also isolated a number of strains of Halobacteriaceae from the samples collected, and their characterization is currently in progress

Microbial rhodopsins on leaf surfaces of terrestrial plants

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Environmental Microbiology 14 (2012): 140-146, doi:10.1111/j.1462-2920.2011.02554.x.The above-ground surfaces of terrestrial plants, the phyllosphere, comprise the main interface between the terrestrial biosphere and solar radiation. It is estimated to host up to 1026 microbial cells that may intercept part of the photon flux impinging on the leaves. Based on 454- pyrosequencing generated metagenome data, we report on the existence of diverse microbial rhodopsins in five distinct phyllospheres from tamarisk (Tamarix nilotica), soybean (Glycine max), Arabidopsis (Arabidopsis thaliana), clover (Trifolium repens) and rice (Oryza sativa). Our findings, for the first time describing microbial rhodopsins from non-aquatic habitats, point toward the potential coexistence of microbial rhodopsin-based phototrophy and plant chlorophyll-based photosynthesis, with the different pigments absorbing non-overlapping fractions of the light spectrum.This work was supported in part by a grant from Bridging the Rift Foundation (O.B. & S.B.), Israel Science Foundation grant 1203/06 (O.B.), the Gruss-Lipper Family Foundation at MBL (O.M.F., S.B. & A.F.P.), a US-Israel Binational Science Foundation grant 2006324 (S.B.), and DOE National Institutes of Health Grant R37GM27750, Department of Energy Grant DE-FG02-07ER15867, and endowed chair AU-0009 from the Robert A. Welch Foundation (J.L.S.)

The light-driven proton pump proteorhodopsin enhances bacterial survival tough times

Some microorganisms contain proteins that can interact with light and convert it into energy for growth and survival, or into sensory information that guides cells towards or away from light. The simplest energy-harvesting photoproteins are the rhodopsins, which consist of a single, membrane-embedded protein covalently bound to the chromophore retinal (a light-sensitive pigment) [1]. One class of archaeal photoproteins (called bacteriorhodopsin) was shown to function as a light-driven proton pump, generating biochemical energy from light [2,3]. For many years, these lightdriven proton pumps were thought to be found only in relatively obscure Archaea living in high salinity

Additional data for: Infection cycle and phylogeny of a Polinton-like virus with a virophage lifestyle infecting Phaeocystis globosa

The code is distributed via https://github.com/BejaLab/Gezelvirus. This repository contains the following items: * phylogeny-Gezel-PLVs - alignments and phylogenetic trees for the chosen set of proteins for Gezel-like PLVs * vcontact2 - results of the vcontact2 analysis * protein-homology-and-function - homology and function for proteins from mesomimiviral, NDDVs, lavidaviruses and other virophages and PLVs based on profile-profile searches. For each protein, the file mcl_genes_60.tsv lists MCL cluster ("Cluster"), cluster identity based on matches to Pfam ("Gene_Pfam", see genes_pfam.tsv for the corresponding manually curated rules), cluster identity based manually curated list of genes ("Gene_Cluster", see genes_cluster.tsv), best hhsearch hit for the particular protein ("Hit.ID", "Hit.Description", "Probab") and the final gene assigment ("Gene"). Functional assignments were checked mainly for proteins from Gezel-like PLVs and lavidaviruses - use with care for other groups. * alphafold-capsid-proteins - alphafold models of the MCP and mCP proteins of Gezel-14T * promoter-motifs - analysis of promoters in mesomimiviruses (meme) and location of PgV-16T-like early promoter motif among PLVs associated with P. globosa (fimo) * phylogeny-with-algae - phylogenetic analyses of the MCP genes from the Gezel-like group and NCLDV-like viruses. The files include alignment of MCPs ≥ 200 residues (*.a2m), trimmed alignment of unqiue long sequences (≥ 300 residues) used for phylogenetic analysis with iqtree2 (*.a2m.trim), iqtree2 output (*.treefile, *.log). In addition, for PLV MCP, short sequences were placed on the iqtree tree by re-evaluation of the iqtree2 trees with raxml-ng (*.raxml.bestTree, *..raxml.bestModel) and epa placement (*_epa). The final trees with metadata are provided in jtree format (*.jtree).</p

Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche

Recent advances in phylogenomic analyses and increased genomic sampling of uncultured prokaryotic lineages have brought compelling evidence in support of the emergence of eukaryotes from within the archaeal domain of life (eocyte hypothesis)1,2. The discovery of Asgardarchaeota and its supposed position at the base of the eukaryotic tree of life3,4 provided cues about the long-awaited identity of the eocytic lineage from which the nucleated cells (Eukaryota) emerged. While it is apparent that Asgardarchaeota encode a plethora of eukaryotic-specific proteins (the highest number identified yet in prokaryotes)5, the lack of genomic information and metabolic characterization has precluded inferences about their lifestyles and the metabolic landscape that favoured the emergence of the protoeukaryote ancestor. Here, we use advanced phylogenetic analyses for inferring the deep ancestry of eukaryotes, and genome-scale metabolic reconstructions for shedding light on the metabolic milieu of Asgardarchaeota. In doing so, we: (1) show that Heimdallarchaeia (the closest eocytic lineage to eukaryotes to date) are likely to have a microoxic niche, based on their genomic potential, with aerobic metabolic pathways that are unique among Archaea (that is, the kynurenine pathway); (2) provide evidence of mixotrophy within Asgardarchaeota; and (3) describe a previously unknown family of rhodopsins encoded within the recovered genomes

The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization-2

Ose from the Sargasso Sea metagenome. Full operons are written in bold whereas split operons are not.<p><b>Copyright information:</b></p><p>Taken from "The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization"</p><p>http://genomebiology.com/2008/9/1/R20</p><p>Genome Biology 2008;9(1):R20-R20.</p><p>Published online 27 Jan 2008</p><p>PMCID:PMC2395257.</p><p></p

The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization-3

Tinct groups; however a third group appears which consists of only environmental sequences and the Ple ((Candidatus)) sequence. The abbreviation of genes from known bacteria are listed in Table 8. For the environmental sequences abbreviation the NCBI accession numbers were taken. Bootstraps for the main groups are shown.<p><b>Copyright information:</b></p><p>Taken from "The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization"</p><p>http://genomebiology.com/2008/9/1/R20</p><p>Genome Biology 2008;9(1):R20-R20.</p><p>Published online 27 Jan 2008</p><p>PMCID:PMC2395257.</p><p></p

The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization-0

Gend, only pairs observed more than 30 times are shown). Pairs of genes composing the two split operons E→G→D→C and F→B→A are abundant while the pair C→F was rarely found. This may hint that the genes are usually organized as split operons rather than as full operons. The representation of classical full and split trp operons.<p><b>Copyright information:</b></p><p>Taken from "The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization"</p><p>http://genomebiology.com/2008/9/1/R20</p><p>Genome Biology 2008;9(1):R20-R20.</p><p>Published online 27 Jan 2008</p><p>PMCID:PMC2395257.</p><p></p

The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization-1

H unknown function; , the tRNA pseudouridine synthase; , a protein related to the molybdenum cofactor; , DNA or RNA helicases of superfamily II; , the SOS-response transcriptional repressor.<p><b>Copyright information:</b></p><p>Taken from "The tryptophan pathway genes of the Sargasso Sea metagenome: new operon structures and the prevalence of non-operon organization"</p><p>http://genomebiology.com/2008/9/1/R20</p><p>Genome Biology 2008;9(1):R20-R20.</p><p>Published online 27 Jan 2008</p><p>PMCID:PMC2395257.</p><p></p