Genome Sequence of
 Lentisphaera araneosa
 HTCC2155
 T
 , the Type Species of the Order
 Lentisphaerales
 in the Phylum
 Lentisphaerae

Thrash, J. Cameron; Cho, Jang-Cheon; Vergin, Kevin L.; Morris, Robert M.; Giovannoni, Stephen J.

doi:10.1128/jb.00208-10

Cited by 29 publications

(20 citation statements)

References 16 publications

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“…Involved in DNA recombination (143), neighborhood of metallopeptidases and MFS1 transporters+Bacteria (mostly γ-proteobacteria) Lentisphaera araneosa (Lentisphaere) in a Oceanospirillales (Proteobacterial) clade, forms a clade together with Neptuniibacter caesariensis . Both bacteria were isolated from a surface water sample (144,145)COG132290Uncharacterized conserved proteinCOG5482NewUnknown{2}+{1}Bacteria (mostly α-proteobacteria) & phages Ricinus communis (Plantae) forms a clade with a tumorogenic Agrobacterium radiobacter (Rhizobiales) within a Rhizobiales clade91Predicted transcriptional regulatorCOG1395NewThe function is unknown but it likely binds nucleic acids. Harbors a HTH motif, co-occurs with a two-domain protein consisting of DUF1743 and tRNA_anti (PF01336) nucleic acid-binding OB-fold domain.+ArchaeaNo HGT observed92DUF1052PF06319PfamCo-occurs with HisKA and Lactamase_B or YkuD (PF03734) which also gives β-lactam resistance.{1}+Bacteria (mostly α-proteobacteria) An uncultured Acidobacterium within a Rhizobiales clade with Nitrobacter , Bradyrhizobium and Rhodopseudomonas palustris .…”

Section: Resultsmentioning

confidence: 99%

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

Steczkiewicz¹,

Muszewska²,

Kniżewski³

et al. 2012

Nucleic Acids Research

148

146

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Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, DNA repair and tRNA–intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such efforts are complicated, because the superfamily exhibits extreme sequence and structural divergence. Using advanced homology detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses, we provide a comprehensive reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases span over 21 900 proteins, which can be classified into 121 groups of various families. Eleven of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI, HpaII and Replic_Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small numbers of organisms. We observed multiple horizontal gene transfers even between human pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles in Eukaryotes, like stress sensing and cell-cycle regulation. Our results may inspire further experimental studies aimed at identification of exact biological functions, specific substrates and molecular mechanisms of reactions performed by these highly diverse proteins.

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Section: Resultsmentioning

confidence: 99%

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

Steczkiewicz¹,

Muszewska²,

Kniżewski³

et al. 2012

Nucleic Acids Research

148

146

View full text Add to dashboard Cite

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“…Examples of sulfated polysaccharides include animal‐derived chondroitin sulfate, seaweed‐derived carrageenans, and algae‐derived fucoidan. High copy numbers of sulfatases appears to be a trait relatively widespread in the PVC‐superphylum ( Planctomycetes – Verrucomicrobia – Chlamydia‐Lentisphaerae‐Omnitrophica ) (Thrash et al ., ). Intriguingly, genome comparisons among marine versus freshwater strains of the Verrucomicrobia suggest expansions of sulfatase genes in marine strains, likely reflecting the prevalence of these organic molecules in marine environments (Spring et al ., ).…”

Section: Organo‐sulfur Molecule Transformationsmentioning

confidence: 97%

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

Wasmund

Mußmann

Loy

2017

Environ Microbiol Rep

309

266

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SummaryAlmost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular‐ and ecosystem‐level processes. Sulfur‐transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate‐rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep‐subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle.

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“…An indicator gene for capsular exopolysaccharide synthesis corroborates exopolymer formation activity. While there have been few phenotypic studies of Verrucomicrobia, particularly in aquatic environments, characterization of Lentisphaera araneosa from the sister phylum Lentisphaerae showed it too was an abundant producer of exopolysaccharides (Cho et al, 2004;Thrash et al, 2010). Indicator genes also encoded cell wall polymer degradation genes as well as homologs to myrosinases ( Table 5), genes that cleave glucose from glucosinolate plant secondary metabolites.…”

Section: Verrucomicrobiamentioning

confidence: 99%

Expression patterns reveal niche diversification in a marine microbial assemblage

et al. 2012

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Resolving the ecological niches of coexisting marine microbial taxa is challenging due to the high species richness of microbial communities and the apparent functional redundancy in bacterial genomes and metagenomes. Here, we generated over 11 million Illumina reads of protein-encoding transcripts collected from well-mixed southeastern US coastal waters to characterize gene expression patterns distinguishing the ecological roles of hundreds of microbial taxa sharing the same environment. The taxa with highest in situ growth rates (based on relative abundance of ribosomal protein transcripts) were typically not the greatest contributors to community transcription, suggesting strong top-down ecological control, and their diverse transcriptomes indicated roles as metabolic generalists. The taxa with low in situ growth rates typically had low diversity transcriptomes dominated by specialized metabolisms. By identifying protein-encoding genes with atypically high expression for their level of conservation, unique functional roles of community members emerged related to substrate use (such as complex carbohydrates, fatty acids, methanesulfonate, taurine, tartrate, ectoine), alternative energy-conservation strategies (proteorhodopsin, AAnP, V-type pyrophosphatases, sulfur oxidation, hydrogen oxidation) and mechanisms for negotiating a heterogeneous environment (flagellar motility, gliding motility, adhesion strategies). On average, the heterotrophic bacterioplankton dedicated 7% of their transcriptomes to obtaining energy by non-heterotrophic means. This deep sequencing of a coastal bacterioplankton transcriptome provides the most highly resolved view of bacterioplankton niche dimensions yet available, uncovering a spectrum of unrecognized ecological strategies.

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Genome Sequence of Lentisphaera araneosa HTCC2155 ^T , the Type Species of the Order Lentisphaerales in the Phylum Lentisphaerae

Cited by 29 publications

References 16 publications

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

Expression patterns reveal niche diversification in a marine microbial assemblage

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Genome Sequence of Lentisphaera araneosa HTCC2155 T , the Type Species of the Order Lentisphaerales in the Phylum Lentisphaerae

Cited by 29 publications

References 16 publications

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

The life sulfuric: microbial ecology of sulfur cycling in marine sediments

Expression patterns reveal niche diversification in a marine microbial assemblage

Contact Info

Product

Resources

About

Genome Sequence of Lentisphaera araneosa HTCC2155 ^T , the Type Species of the Order Lentisphaerales in the Phylum Lentisphaerae