Complete Genome Sequence of Croceibacter Bacteriophage P2559S

Croceibacter atlanticus HTCC2559(T), a marine bacterium isolated from the Sargasso Sea, is a phylogenetically unique member of the family Flavobacteriaceae. Strain HTCC2559(T) possesses genes related to interaction with primary producers, which makes studies on bacteriophages infecting the strain interesting. Here we report the genome sequence of bacteriophage P2559S, which was isolated off the coast of the Republic of Korea and lytically infects HTCC2559(T). Many genes predicted in the P2559S genome had their homologs in Bacteroides phages.     

Complete genome sequence of strain HTCC2170, a novel member of the genus Maribacter in the family Flavobacteriaceae

Strain HTCC2170 was isolated from surface waters off the Oregon coast using dilution-to-extinction culturing. Here, we present the finished genome sequence of a marine bacterium, Maribacter sp. strain HTCC2170. Strain sp. HTCC2170 is predicted to be a facultatively aerobic chemoorganotroph that, based on genomic sequence analysis, is capable of macromolecule degradation and anaerobic respiration.     

Genome sequence of the marine alphaproteobacterium HTCC2150, assigned to the Roseobacter clade

Here we announce the genome sequence of a marine bacterium, HTCC2150, that was isolated off the Oregon coast using dilution-to-extinction culturing and that is affiliated with the Roseobacter clade. The 16S rRNA phylogeny showed that the strain was closely related to members of the RCA clade. The genome sequence suggests that strain HTCC2150 is an organoheterotroph carrying diverse metabolic potential, including a close relationship with phytoplankton.     

Genome sequence of the Marine Janibacter Sp. Strain HTCC2649

Janibacter sp. strain HTCC2649 is a novel marine member of the Actinobacteria, family Intrasporangiaceae, and is closely related to Janibacter melonis CM2104(T) and Knoellia sinensis HKI 0119(T). The organism was isolated from a sample collected at Hydrostation S south of Bermuda by using high-throughput culturing techniques. Here we present the genome sequence of Janibacter sp. strain HTCC2649.     

Genome sequence of Oceanicaulis sp. strain HTCC2633, isolated from the Western Sargasso Sea

The genus Oceanicaulis represents dimorphic rods that were originally isolated from a marine dinoflagellate. Here, we announce the genome sequence of Oceanicaulis sp. strain HTCC2633, isolated by dilution-to-extinction culturing from the Sargasso Sea. The genome information of strain HTCC2633 indicates a chemoorganotrophic way of life of this strain.     

The small genome of an abundant coastal ocean methylotroph

OM43 is a clade of uncultured β-proteobacteria that is commonly found in environmental nucleic acid sequences from productive coastal ocean ecosystems, and some freshwater environments, but is rarely detected in ocean gyres. Ecological studies associate OM43 with phytoplankton blooms, and evolutionary relationships indicate that they might be methylotrophs. Here we report on the genome sequence and metabolic properties of the first axenic isolate of the OM43 clade, strain HTCC2181, which was obtained using new procedures for culturing cells in natural seawater. We found that this strain is an obligate methylotroph that cannot oxidize methane but can use the oxidized C1 compounds methanol and formaldehyde as sources of carbon and energy. Its complete genome is 1304 428 bp in length, the smallest yet reported for a free-living cell. The HTCC2181 genome includes genes for xanthorhodopsin and retinal biosynthesis, an auxiliary system for producing transmembrane electrochemical potentials from light. The discovery that HTCC2181 is an extremely simple specialist in C1 metabolism suggests an unanticipated, important role for oxidized C1 compounds as substrates for bacterioplankton productivity in coastal ecosystems.     

Synergistic metabolism of a broad range of C1 compounds in the marine methylotrophic bacterium HTCC2181

The 1.3 Mbp genome of HTCC2181, a member of the abundant OM43 clade of coastal bacterioplankton, suggested it is an obligate methylotroph. Preliminary experiments demonstrated that methanol and formaldehyde, but not other common C1 compounds such as methylamine, could support growth. Methanol concentrations in seawater are reportedly < 100 nM, suggesting either that the flux of methanol through plankton pools is very rapid, or that methanol may not be the primary growth substrate for HTCC2181. Therefore, we investigated the apparent extreme substrate range restriction of HTCC2181 in greater detail. Growth rate and maximum cell density of HTCC2181 increased with methanol concentration, yielding a K(s) value of 19 μM. In contrast, no growth was observed in the presence of the methylated (C1) compounds, methyl chloride, trimethylamine-oxide (TMAO) or dimethylsulfoniopropionate (DMSP) when they were the sole substrates. However, growth rate, maximum cell density and cellular ATP content were significantly enhanced when any of these methylated compounds were provided in the presence of a limiting concentration of methanol. These observations fit a model in which the metabolic intermediate formaldehyde is required for net carbon assimilation, allowing C1 substrates that do not produce a formaldehyde intermediate to be oxidized for energy, but not assimilated into biomass. Rates of methanol and TMAO oxidation and assimilation were measured with (14)C-radiolabelled compounds in cultures of HTCC2181 and seawater microbial communities collected off the Oregon coast. The results indicated that in nature as well as in culture, C1 substrates are partitioned between those that are mainly oxidized to produce energy and those that are assimilated. These findings indicate that the combined fluxes of C1 compounds in coastal systems are sufficient to support significant populations of obligate methyltrophs by a metabolic strategy that involves the synergistic metabolism of multiple C1 compounds.     

Complete Genome Sequence of Croceibacter atlanticus HTCC2559T

Here we announce the complete genome sequence of Croceibacter atlanticus HTCC2559^T, which was isolated by high-throughput dilution-to-extinction culturing from the Bermuda Atlantic Time Series station in the Western Sargasso Sea. Strain HTCC2559^T contained genes for carotenoid biosynthesis, flavonoid biosynthesis, and several macromolecule-degrading enzymes. The genome confirmed physiological observations of cultivated Croceibacter atlanticus strain HTCC2559^T, which identified it as an obligate chemoheterotroph.The phylum Bacteroidetes comprises 6 to ∼30% of total bacterial communities in the ocean by fluorescence in situ hybridization (8-10). Most marine Bacteroidetes are in the family Flavobacteriaceae, most of which are aerobic respiratory heterotrophs that form a well-defined clade by 16S rRNA phylogenetic analyses (4). The members of this family are well known for degrading macromolecules, including chitin, DNA, cellulose, starch, and pectin (17), suggesting their environmental roles as detritus decomposers in the ocean (6). Marine Polaribacter and Dokdonia species in the Flavobacteriaceae have also shown to have photoheterotrophic metabolism mediated by proteorhodopsins (11, 12).Several strains of the family Flavobacteriaceae were isolated from the Sargasso Sea and Oregon coast, using high-throughput culturing approaches (7). Croceibacter atlanticus HTCC2559^T was cultivated from seawater collected at a depth of 250 m from the Sargasso Sea and was identified as a new genus in the family Flavobacteriaceae based on its 16S rRNA gene sequence similarities (6). Strain HTCC2559^T met the minimal standards for genera of the family Flavobacteriaceae (3) on the basis of phenotypic characteristics (6).Here we report the complete genome sequence of Croceibacter atlanticus HTCC2559^T. The genome sequencing was initiated by the J. Craig Venter Institute as a part of the Moore Foundation Microbial Genome Sequencing Project and completed in the current announcement. Gaps among contigs were closed by Genotech Co., Ltd. (Daejeon, Korea), using direct sequencing of combinatorial PCR products (16). The HTCC2559^T genome was analyzed with a genome annotation system based on GenDB (14) at Oregon State University and with the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (15, 16).The HTCC2559^T genome is 2,952,962 bp long, with 33.9 mol% G+C content, and there was no evidence of plasmids. The number of protein-coding genes was 2,715; there were two copies of the 16S-23S-5S rRNA operon and 36 tRNA genes. The HTCC2559^T genome contained genes for a complete tricarboxylic acid cycle, glycolysis, and a pentose phosphate pathway. The genome also contained sets of genes for metabolic enzymes involved in carotenoid biosynthesis and also a serine/glycine hydroxymethyltransferase, which is often associated with the assimilatory serine cycle (13). The potential for HTCC2559^T to use bacterial type III polyketide synthase (PKS) needs to be confirmed because this organism had a naringenin-chalcone synthase (CHS) or chalcone synthase (EC 2.3.1.74), a key enzyme in flavonoid biosynthesis. CHS initiates the addition of three molecules of malonyl coenzyme A (malonyl-CoA) to a starter CoA ester (e.g., 4-coumaroyl-CoA) (1) and takes part in a few bacterial type III polyketide synthase systems (1, 2, 5, 18).The complete genome sequence confirmed that strain HTCC2559^T is an obligate chemoheterotroph because no genes for phototrophy were found. As expected from physiological characteristics (6), the HTCC2559^T genome contained a set of genes coding for enzymes required to degrade high-molecular-weight compounds, including peptidases, metallo-/serine proteases, pectinase, alginate lyases, and α-amylase.     

Lentisphaera araneosa gen. nov., sp. nov, a transparent exopolymer producing marine bacterium, and the description of a novel bacterial phylum, Lentisphaerae

Two phylogenetically distinct marine strains producing transparent exopolymers (TEP), designated HTCC2155(T) and HTCC2160, were cultivated from Oregon coast seawater by dilution to extinction in a high throughput culturing format. When cultured in low-nutrient seawater media, these strains copiously produced Alcian Blue-stainable viscous TEP. Growing cells were attached to each other by the TEP in a three dimensional network. Polymerase chain reaction employing 16S rDNA primers specific for the novel isolates indicated that they are indigenous to the water column of the Atlantic and Pacific oceans. The abundance of the isolates as determined by 16S rRNA dot blots, however, indicated that they are less than 1% of the total bacterial community. In phylogenetic analyses, the strains consistently formed a new phylum-level lineage within the domain Bacteria, together with members of the candidate phylum VadinBE97, which consists of Victivallis, the first cultured genus in the candidate phylum, and 16S rRNA gene clones from DNA extracted from marine or anaerobic terrestrial habitats. Five putative subgroups were delineated within this phylum-level lineage, including a marine group and an anaerobic group. The isolates are Gram negative, strictly aerobic, chemoheterotrophic, and facultatively oligotrophic sphere-shaped bacteria. The DNA G+C content of strain HTCC2155(T) was 48.3 mol% and the genome size was 2.9 mb. It is proposed from these observations that the strains be placed into a new genus and a new species named Lentisphaera araneosa (type strain HTCC2155(T) = ATCC BAA-859(T) = KCTC 12141(T)) gen. nov., sp. nov., the cultured marine representative of the Lentisphaerae phyl. nov., and the phylum be divided into two novel orders named the Lentisphaerales ord. nov. and the Victivallales ord. nov.     

In vitro evaluation of the biomedical properties of chitosan and quaternized chitosan for dental applications

The aim of this study was to evaluate the potential dental applications of chitosan (CS) and N-[1-hydroxy-3-(trimethylammonium)propyl]chitosan chloride (HTCC). HTCC was prepared by reacting CS with glycidyltrimethylammonium chloride (GTMAC). CS and HTCC were characterized by infrared (FITR) and ¹H NMR spectroscopy. The antibacterial activity of CS and HTCC against oral pathogens, their proliferation activity and effects on the ultrastructure of human periodontal ligament cells (HPDLCs) were investigated. The results indicated that four oral strains were susceptible to CS and HTCC with minimum inhibitory concentrations (MICs) ranging from 0.25 to 2.5 mg/mL. The in vitro 3-(4,5-dimethyl-2-thizolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay determined that CS at 2000, 1000, 100, and 50 μg/mL could stimulate the proliferation of HPDLCs. Instead, HTCC inhibited the proliferation at the same concentrations but accelerated the proliferation of HPDLCs at relatively low concentrations (10, 3, 1.5, 1, and 0.3 μg/mL). Transmission electron microscopy (TEM) observations revealed that the ultra-architecture of HPDLC was seriously destroyed by HTCC treatment at 1000 μg/mL. Taken together, these results contribute information necessary to enhance our understanding of CS and HTCC in the dental field.     

Complete genome sequence of strain HTCC2503T of Parvularcula bermudensis, the type species of the order "Parvularculales" in the class Alphaproteobacteria

The order "Parvularculales" represents the seventh order in the class Alphaproteobacteria. Parvularcula bermudensis, the type species of the order, was isolated from the Sargasso Sea using dilution-to-extinction culturing. We present here the complete genome sequence of Parvularcula bermudensis HTCC2503(T), which contains genes for carotenoid biosynthesis, dimethylsulfoniopropionate demethylase, and transduction-like gene transfer agents.     

Genome sequence of strain IMCC3088, a proteorhodopsin-containing marine bacterium belonging to the OM60/NOR5 clade

Strain IMCC3088, cultivated from the Yellow Sea, is a novel isolate belonging to the OM60/NOR5 clade and is closely related to clone OM241, Congregibacter litoralis, and strain HTCC2080. Here, the genome sequence of strain IMCC3088 is presented, showing the absence of photosynthetic gene clusters and the presence of proteorhodopsin.     

Genome Sequence of Fulvimarina pelagi HTCC2506T,a Mn(II)-Oxidizing Alphaproteobacterium Possessing an Aerobic Anoxygenic Photosynthetic Gene Cluster and Xanthorhodopsin

Fulvimarina pelagi is a Mn(II)-oxidizing marine heterotrophic bacterium in the order Rhizobiales. Here we announce the draft genome sequence of F. pelagi HTCC2506^T, which was isolated from the Sargasso Sea by using dilution-to-extinction culturing. The genome sequence contained a xanthorhodopsin gene as well as a photosynthetic gene cluster, which suggests the coexistence of two different phototrophic mechanisms in a single microorganism.Besides being mediated by the well-known process of aerobic oxygenic photosynthesis, utilization of light energy in the marine carbon and nutrient cycling processes is usually mediated by aerobic anoxygenic phototrophic bacteria (AAPB) or prokaryotes containing microbial rhodopsin family proteins (18). AAPB comprise about 10% of total microbial cells in the euphotic zone of diverse marine regimes, with alpha-, beta-, and gammaproteobacteria as major constituents (8, 10). Rhodopsin family proteins, including bacteriorhodopsin, proteorhodopsin, and xanthorhodopsin (XR), have been shown to exist in 7 to 70% of marine prokaryotes and contribute photoheterotrophy in diverse phylogenetic groups such as Flavobacteria, Proteobacteria, and Archaea (15, 19). However, no single microorganism has been reported to contain the genes for both aerobic anoxygenic phototrophy (AAnP) and rhodopsin family proteins.F. pelagi HTCC2506^T was cultivated through a dilution-to-extinction approach (3) from the western Sargasso Sea and identified as a novel genus and species in the order Rhizobiales of the Alphaproteobacteria by polyphasic taxonomy (2). Later, three F. pelagi strains, including HTCC2506^T, were shown to have Mn(II)-oxidizing activity (1). The draft genome sequence of HTCC2506^T was determined by shotgun sequencing at the J. Craig Venter Institute as part of the Moore Foundation Microbial Genome Sequencing Project and analyzed by the GenDB annotation program (17) at the Center for Genome Research and Biocomputing at Oregon State University and the Joint Genome Institute IMG system (http://img.jgi.doe.gov) (14).The draft genome was 3,802,689 bp in length, distributed in 20 contigs with 61.2% G+C content, and contained 3,754 protein-coding genes, three copies of 16S-23S-5S rRNA genes, and 54 tRNA genes. Remarkably, HTCC2506^T possessed XR and a complete gene set for AAnP together. A gene cluster encoding the AAnP apparatus was composed of bchIDO-crtCDF-bchCXYZ-pufBALMC-puhE-acsF-puhCBA-lhaA-bchMLHBNF-aerR-ppsR-ubiA-pucC-bchP-hemT. Mu-like prophage sequences were located closely adjacent to the AAnP gene cluster, which might imply the possibility of the lateral gene transfer of the AAnP gene cluster. The XR gene was followed by blh, a gene involved in retinal biosynthesis (16). To our knowledge, this is the first report of a microbe possessing both an AAnP apparatus and a rhodopsin family protein, although the two gene sets in HTCC2506^T had been separately reported to be present (5, 13). The HTCC2506^T genome also encoded a bacteriophytochrome (6, 7), a light-regulated signal transduction histidine kinase. Overall, the existence of a diverse repertoire of genes for sensing or harvesting of light energy implicates the importance of phototrophic metabolism for HTCC2506^T.In addition to genes for phototrophy, the genome contained several genes with diverse metabolic potential. A lithotrophic mode of energy acquisition was predicted from the presence of the form II coxSLM genes, which encode aerobic-type carbon monoxide dehydrogenase (9). As expected from the Mn(II)-oxidizing activity of HTCC2506^T, the genome also encoded a multicopper oxidase (MCO) enzyme, suggesting a potential lithotrophy. In terms of carbon assimilation, genes encoding RuBisCO and phosphoribulokinase of the Calvin-Benson-Bassham cycle (11) were predicted, suggesting the possibility of autotrophic CO₂ fixation in HTCC2506^T. Serine transhydroxymethylase for formaldehyde assimilation (12) was predicted. A gene encoding dimethylsulfoniopropionate (DMSP) lyase, which conveys the production of dimethylsulfide from DMSP (4), was also found in the genome.Although HTCC2506^T was originally isolated as a chemoheterotroph (2), the genome sequence clearly shows the phototrophic potential of this bacterium. This finding, combined with the prediction of many genes related to lithotrophy, carbon fixation, C₁ compound assimilation, and DMSP lysis, suggests that F. pelagi HTCC2506^T may use a wide range of potential metabolic functions to survive in the marine euphotic environment.     

cDNA(EST)文库的高通量生物信息学分析体系的构建与应用

应用生物信息学方法,构建了一套针对cDNA或EST文库的高通量、自动化分析体系,CLASP(cDNA Library Analysis SystemPrimary)。CLASP基于Linux操作系统,主要由Perl程序构成。它以cDNA文库(ESTs)序列为分析对象,具有自动查找序列同源基因并进行染色体定位(包括细胞遗传学定位和SIS定位)、EST自动延伸等功能;并对不同来源序列进行聚类分析。应用该体系对3对肺癌相关抑制性消减杂交(SSH)cDNA文库进行了分析。结果在所有3对文库的2083条EST中有1492条找到了同源基因,其中1365条得到染色体定位。对所余591条未知基因的EST进行了电子延伸,其中有214条EST得到不同程度的延伸。对上述cDNA文库中已知基因的EST以及电子延伸后的EST再分别进行聚类分析,而后综合两个聚类分析的结果,由此可发现不同文库间的共同与差异表达基因,可用于特定性状相关的基因功能预测。     

Genome Sequence of the Oligotrophic Marine Gammaproteobacterium HTCC2143, Isolated from the Oregon Coast

Strain HTCC2143 was isolated from Oregon Coast surface waters using dilution-to-extinction culturing. Here we present the genome of strain HTCC2143 from the BD1-7 clade of the oligotrophic marine Gammaproteobacteria group. The genome of HTCC2143 contains genes for carotenoid biosynthesis and proteorhodopsin and for proteins that have potential biotechnological significance: epoxide hydrolases, Baeyer-Villiger monooxygenases, and polyketide synthases.Strain HTCC2143 was sampled and isolated from surface waters (depth, 10 m) off the Coastal Pacific Ocean, Newport, OR (44°36′0"N, 124°6′0"W). In the course of dilution-to-extinction culture studies on coastal microbial communities, strain HTCC2143 was isolated in a pristine seawater-based medium (2). Phylogenetic analysis of 16S rRNA gene sequences placed strain HTCC2143 in the BD1-7 clade of the oligotrophic marine Gammaproteobacteria (OMG) group (2) and indicated that it is related to Dasania marina, isolated from Arctic marine sediment (3, 8). The HTCC2143 16S rRNA gene sequence is 95.3% similar to that of D. marina ({"type":"entrez-nucleotide","attrs":{"text":"AY771747","term_id":"157384056","term_text":"AY771747"}}AY771747) and is 96.6% similar to that of environmental gene clone 20m-45 ({"type":"entrez-nucleotide","attrs":{"text":"GU061297","term_id":"262072220","term_text":"GU061297"}}GU061297), taken from intertidal beach seawater of the Yellow Sea, South Korea. Other closer relatives of HTCC2143 included uncultured gammaproteobacterial clones from seafloor lava (clone P0X3b5B06 from Hawaii South Point X3, {"type":"entrez-nucleotide","attrs":{"text":"EU491383","term_id":"169640639","term_text":"EU491383"}}EU491383; 96.3%) (9), deep-sea sediment (Ucp1554 from the South Atlantic Ocean, Cape Basin, {"type":"entrez-nucleotide","attrs":{"text":"AM997645","term_id":"283475537","term_text":"AM997645"}}AM997645; 95.9%) (10), Yellow Sea sediment (95.8%; D8S-33, {"type":"entrez-nucleotide","attrs":{"text":"EU652559","term_id":"186462116","term_text":"EU652559"}}EU652559), and Arctic sediment (from Kings Bay, Svalbard, Norway; clone SS1_B_07_55, {"type":"entrez-nucleotide","attrs":{"text":"EU050825","term_id":"156453922","term_text":"EU050825"}}EU050825; 95.7%).Genomic DNA was prepared at Oregon State University and sequenced by the J. Craig Venter Institute. The finished contigs were automatically annotated with a system based on the program GenDB (5) and manually annotated as described in previous reports (7, 12). The annotation is available at http://bioinfo.cgrb.oregonstate.edu/microbes/. The draft genome of strain HTCC2143 comprises 3,925,629 bases and 3,662 predicted coding sequences with a G+C content of 47.0%. The genome of HTCC2143 was predicted to contain 40 tRNAs, 1 16S rRNA, 2 5S rRNAs, and 2 23S rRNA genes. Four genes for selenocysteine metabolism were found, including a selenophosphate-dependent tRNA 2-selenouridine synthase and an l-seryl-tRNA(Sec) selenium transferase (EC 2.9.1.1).Strain HTCC2143 had genes for a complete tricarboxylic acid cycle, glycolysis, a pentose phosphate pathway, and an Entner-Doudoroff pathway. Genes were present for a high-affinity phosphate transporter and a pho regulon for sensing of environmental inorganic phosphate availability, as well as genes from the NUDIX (nucleoside diphosphate linked to some other moiety X) hydrolase domain family (1) that reflects the metabolic complexity of prokaryotes (4). Genes for ammonium transporters, nitrate reductase, and sulfate reductase were also present in the HTCC2143 genome.Carotenoid and proteorhodopsin genes were also found in the genome, as well as genes for polyketide synthase modules and related proteins. Carotenoid and proteorhodopsin genes were reported previously from another member of the OMG group, strain HTCC2207, a SAR92 clade isolate (11). HTCC2143 also encoded two epoxide hydrolases, two cyclohexanone monooxygenases (CHMOs) and a cyclododecanone monooxygenase (CDMO). CDMOs and CHMOs are members of the Baeyer-Villiger monooxygenase (BVMO) family. BVMOs are “green” alternatives to the chemically mediated Baeyer-Villiger reactions that allow the conversion of ketones into esters or of cyclic ketones into lactones (6).This genome provides further evidence that dilution-to-extinction culturing methods that make use of low-nutrient media that are similar to the conditions of the natural environment can result in the isolation of novel, environmentally significant organisms with potential biotechnological value (13).     

Designing a Cell Surface Display System of Protein Domains in Lactobacilli Based on S-Layer Proteins of <Emphasis Type="Italic">Lactobacillus brevis</Emphasis> ATCC 367

S-layer proteins of lactobacilli may be utilized for developing a surface display system in these bacteria. In this study, S-layer proteins of Lactobacillus brevis ATCC 367 were identified for the first time. Using the peptide fingerprint method, it was shown that the main protein of the S-layer of this strain, SlpE, having a mass of 52 kDa is the product of translation of the consecutive open reading frames LVIS_2086 and LVIS_2085. Repeated sequencing of a genome region of L. brevis ATCC 367, containing LVIS_2086 and LVIS_2085 loci, has showed that the LVIS_2086 sequence contains the TGG tryptophan codon instead of the TAG stop codon. Thus, LVIS_2085 and LVIS_2086 form a single slpE gene, the nucleotide sequence we deposited in the Genbank database under No. KY273133. The translation product of the slpE gene consists of 465 amino acids and has a calculated mass of 51.6 kDa, which corresponds to the experimentally obtained value. An S-layer protein with a mass of 56 kDa, identified as a form of the SlpE, is probably formed during the posttranslational modification. The concomitant 48 kDa S-protein was proven to be product of the LVIS- 2083 gene. The N-terminal domains of LVIS_2083 and SlpE have 70.7 and 96.5%, respectively, identity to the anchoring N-terminal domain of SlpA from L. brevis ATCC 8287, which is responsible for attachment to the cell wall. In this work, fusion proteins consisting of N-terminal domains of Lvis_2083 and SlpA proteins and the eGFP marker protein were obtained. The ability of fusion proteins SlpA_eGFP and Lvis_2083_eGFP, as well as the recombinant Lvis_2083 protein, to be specifically sorbed on the cell wall of L. brevis ATCC 8287, ATCC 367, and L. acidophilus ATCC 4356 strains has been demonstrated. It was shown that in the chimeric Lvis_2083_eGFP construction the N-terminal domain Lvis_2083 is responsible for an attachment to the cell wall and provides display of the functionally active eGFP protein on its surface. Thus, the N-terminal domain Lvis_2083 can be used as a basis of the protein display system on the cell surface of L. brevis strains in vitro.     

Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data

Background  

One objective of metagenomics is to reconstruct information about specific uncultured organisms from fragmentary environmental DNA sequences. We used the genome of an isolate of the marine alphaproteobacterium SAR11 ('Candidatus Pelagibacter ubique'; strain HTCC1062), obtained from the cold, productive Oregon coast, as a query sequence to study variation in SAR11 metagenome sequence data from the Sargasso Sea, a warm, oligotrophic ocean gyre.