Genome sequence of proteorhodopsin-containing sea ice bacterium Glaciecola punicea ACAM 611T

Here, we report the draft genome sequence of Antarctic sea ice bacterium Glaciecola punicea ACAM 611(T), the type species of the genus Glaciecola. A blue-light-absorbing proteorhodopsin gene is present in the 3.08-Mb genome. This genome sequence can facilitate the study of the physiological metabolisms and ecological roles of sea ice bacteria.     

Complete genome sequence of the marine cellulose- and xylan-degrading bacterium Glaciecola sp. strain 4H-3-7+YE-5

Glaciecola sp. strain 4H-3-7+YE-5 was isolated from subseafloor sediments at Suruga Bay in Japan and is capable of efficiently hydrolyzing cellulose and xylan. The complete genome sequence of Glaciecola sp. 4H-3-7+YE-5 revealed several genes encoding putatively novel glycoside hydrolases, offering a high potential for plant biomass degradation.     

A complete genome assembly of Glaciecola mesophila sp. nov. sequenced by using BIGIS-4 sequencer system

Using a pyrosequencing-based custom-made sequencer BIGIS-4, we sequenced a Gram-negative bacterium Glaciecola mesophila sp. nov. (Gmn) isolated from marine invertebrate specimens. We generated 152043 sequencing reads with a mean high-quality length of 406 bp, and assembled them using the BIGIS-4 post-processing module. No systematic low-quality data was detected beyond expected homopolymer-derived errors. The assembled Gmn genome is 5144318 bp in length and harbors 4303 annotated genes. A large number of metabolic genes correspond to various nutrients from surface marine invertebrates. Its abundant cold-tolerant and cellular signaling and related genes reveal a fundamental adaptation to low-temperature marine environment.     

Physicochemical parameters for growth of the sea ice bacteria Glaciecola punicea ACAM 611(T) and Gelidibacter sp. strain IC158.

The water activity and pH ranges for growth of Glaciecola punicea (a psychrophile) were extended when this organism was grown at suboptimal rather than optimal temperatures. No such extension was observed for Gelidibacter sp. strain IC158 (a psychrotolerant bacterium) at analogous temperatures. Salinity and pH may be primary physicochemical parameters controlling bacterial community development in sea ice.     

Effect of polysaccharide extracted from Glaciecola polaris on the protection of mouse macrophages from oxidative injury

The effect of the protein-bound polysaccharide extracted from Glaciecola polaris (PSG) was investigated in vitro in the protection of oxidatively-injured mouse macrophages stressed by tert-butyl hydroperoxide (tbOOH) or by oxidatively modified low-density lipoprotein (Ox-LDL). The results showed that PSG treatments to protect the macrophages from oxidative injury was effective and the macrophage colony-stimulating factor (M-CSF) exhibited some similar effects. It was speculated that both M-CSF and PSG could protect macrophages from oxidative injury. The results suggested that the effects of PSG were associated with its capability of inducing M-CSF expression.     

Physicochemical Parameters for Growth of the Sea Ice Bacteria Glaciecola punicea ACAM 611T and Gelidibacter sp. Strain IC158

The water activity and pH ranges for growth of Glaciecola punicea (a psychrophile) were extended when this organism was grown at suboptimal rather than optimal temperatures. No such extension was observed for Gelidibacter sp. strain IC158 (a psychrotolerant bacterium) at analogous temperatures. Salinity and pH may be primary physicochemical parameters controlling bacterial community development in sea ice.     

Predominance of Roseobacter, Sulfitobacter, Glaciecola and Psychrobacter in seawater collected off Ushuaia, Argentina, Sub-Antarctica

Bacterial diversity in sub-Antarctic seawater, collected off Ushuaia, Argentina, was examined using a culture independent approach. The composition of the 16S rRNA gene libraries from seawater and seawater contaminated with the water soluble fraction of crude oil was statistically different (P value 0.001). In both libraries, clones representing the Alphaproteobacteria, Gammaproteobacteria, the Cytophaga-Flavobacterium-Bacteroidetes group and unculturable bacteria were dominant. Clones associated with the genera Roseobacter, Sulfitobacter, Staleya, Glaciecola, Colwellia, Marinomonas, Cytophaga and Cellulophaga were common to both the libraries. However, clones associated with Psychrobacter, Arcobacter, Formosa algae, Polaribacter, Ulvibacter and Tenacibaculum were found only in seawater contaminated with hydrocarbons (Table 1). Further, the percentage of clones of Roseobacter, Sulfitobacter and Glaceicola was high in seawater (43%, 90% and 12% respectively) compared to seawater contaminated with hydrocarbons (35%, 4% and 9% respectively). One of the clones F2C63 showed 100% similarity with Marinomonas ushuaiensis a bacterium identified by us from the same site.     

Improvement of the quality of wheat bread by addition of glycoside hydrolase family 10 xylanases

Although many xylanases are widely used in the baking industry, only one glycoside hydrolase family 10 (GH 10) xylanase has previously been reported to be effective in baking. In this study, we compared the effectiveness of two GH 10 xylanases, psychrophilic XynA from Glaciecola mesophila and mesophilic EX1 from Trichoderma pseudokoningii, in bread making. The optimal dosages needed to improve wheat flour dough and bread quality were 270-U/kg flour for EX1 and 0.9-U/kg flour for XynA. At their optimal dosage, both XynA and EX1 had significant dough-softening ability, resulting in a 50% reduction in Brabender units. XynA was more effective than EX1 in reducing the time to reach maximum consistency. XynA and EX1 showed similar effects in improving the bread volume (~30% increase). EX1 was more effective in reducing the initial crumb firmness. Although both enzymes exhibited similar anti-staling effects on the bread, based on a decrease in the bread firmness, XynA had a greater effect on reducing the firming rate, and EX1 showed an enhanced reduction in the initial firmness. These results show that these two GH 10 xylanases have unique advantages in improving dough and bread quality and indicate their potential in bread making.     

Characterization of facultative oligotrophic bacteria from polar seas by analysis of their fatty acids and 16S rDNA sequences

One hundred and seventy three bacterial strains, isolated previously after enrichment under oligotrophic, psychrophylic conditions from Arctic (98 strains) and Antarctic seawater (75 strains), were characterized by gas-liquid chromatographic analysis of their fatty acid compositions. By numerical analysis, 8 clusters, containing 2 to 59 strains, could be delineated, and 8 strains formed separate branches. Five clusters contained strains from both poles, two minor clusters were confined to Arctic isolates, and one cluster consisted of Antarctic isolates only. The 16S rRNA genes from 23 strains, representing the different fatty acid profile clusters and including the unclustered strains, were sequenced. The sequences grouped with the alpha and gamma Proteobacteria, the high percent G+C gram positives, and the Cytophaga-Flavobacterium-Bacteroides branch. The sequences of strains from 4 clusters and of 7 unclustered strains were closely related (sequence similarities above 97%) to reference sequences of Sulfitobacter mediterraneus, Halomonas variabilis, Alteromonas macleodii, Pseudoalteromonas species, Shewanella frigidimarina, and Rhodococcus fascians. Strains from the other four clusters and an unclustered strain showed sequence similarities below 97% with nearest named neighbours, including Rhizobium, Glaciecola, Pseudomonas, Alteromonas macleodii and Cytophaga marinoflava, indicating that the clusters which they represent form as yet unnamed taxa.     

Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice

A comprehensive assessment of bacterial diversity and community composition in arctic and antarctic pack ice was conducted through cultivation and cultivation-independent molecular techniques. We sequenced 16S rRNA genes from 115 and 87 pure cultures of bacteria isolated from arctic and antarctic pack ice, respectively. Most of the 33 arctic phylotypes were >97% identical to previously described antarctic species or to our own antarctic isolates. At both poles, the alpha- and gamma-proteobacteria and the Cytophaga-Flavobacterium group were the dominant taxonomic bacterial groups identified by cultivation as well as by molecular methods. The analysis of 16S rRNA gene clone libraries from multiple arctic and antarctic pack ice samples revealed a high incidence of closely overlapping 16S rRNA gene clone and isolate sequences. Simultaneous analysis of environmental samples with fluorescence in situ hybridization (FISH) showed that approximately 95% of 4',6'-diamidino-2-phenylindole (DAPI)-stained cells hybridized with the general bacterial probe EUB338. More than 90% of those were further assignable. Approximately 50 and 36% were identified as gamma-proteobacteria in arctic and antarctic samples,respectively. Approximately 25% were identified as alpha-proteobacteria, and 25% were identified as belonging to the Cytophaga-Flavobacterium group. For the quantification of specific members of the sea ice community, new oligonucleotide probes were developed which target the genera Octadecabacter, Glaciecola, Psychrobacter, Marinobacter, Shewanella, and Polaribacter: High FISH detection rates of these groups as well as high viable counts corroborated the overlap of clone and isolate sequences. A terrestrial influence on the arctic pack ice community was suggested by the presence of limnic phylotypes.     

Phylogenetic Diversity of Numerically Important Arctic Sea-Ice Bacteria Cultured at Subzero Temperature

Heterotrophic bacteria in sea ice play a key role in carbon cycling, but little is known about the predominant players at the phylogenetic level. In a study of both algal bands and clear ice habitats within summertime Arctic pack ice from the Chukchi Sea, we determined the abundance of total bacteria and actively respiring cells in melted ice samples using epifluorescence microscopy and the stains 4', 6'-diamidino-2-phenylindole 2HCl (DAPI) and 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), respectively. Organic-rich and -poor culturing media were used to determine culturable members by plating (at 0 degrees C and 5 degrees C) and most-probable-number (MPN) analyses (at -1 degrees C). Total bacterial counts ranged from 5.44 x 10(4) ml(-1) in clear ice to 2.41 x 10(6) ml(-1) in algal-band ice samples, with 2-27% metabolically active by CTC stain. Plating and MPN results revealed a high degree of culturability in both types of media, but greater success in oligotrophic media (to 62% of total abundance) and from clear ice samples. The bacterial enumeration anomaly, commonly held to mean 相似文献   

Evolutionary analysis identifies multiple genome expansions and contractions in Sepsidae (Diptera) and suggests targets for future genomic research

We here argue that data from comparative studies of genome size and karyotypes provide important information for planning comparative research on genome evolution. We document for 39 species of sepsids that there is a four‐fold difference in genome size (151–618 Mbp). Mapping genome sizes onto a phylogenetic hypothesis identifies that this range is the result of five genome expansions and four genome contractions that we here define as changes in genome size of more than 50 Mbp. We then generate karyotype data for 10 species and find no changes in chromosome number. The study reveals that the “Oriental” clade of sepsids is a promising system for studying genome evolution because it has experienced three genome expansion events. These events can be compared with an expansion in the “Neotropical” clade in order to reveal the mechanisms that underlie genome expansion in Sepsidae. A review of the literature on genome sizes and karyotypes reveals that they have been poorly documented in Metazoa. This means that researchers interested in the evolution of genome expansions and contractions are currently not being able to identify appropriate target taxa for genome sequencing. We thus argue for more comparative research on genome sizes and karyotypes and point out that historically species were chosen for genome sequencing for reasons not related to genome evolution (e.g. small genome size, model species status, phylogenetic position, interesting phenotypes). We believe that it is now time to use a more genome‐centric selection criterion, where species for whole genome sequencing are selected based on their importance for understanding genome evolution.     

A mitochondrial genome with a reversed transmission route in the Mediterranean mussel Mytilus galloprovincialis

Species of the marine mussel genus Mytilus are known to contain two mitochondrial genomes, one transmitted maternally (the F genome) and the other paternally (the M genome). The two genomes have diverged by more than 20% in DNA sequence. Here we present the complete sequence of a third genome, genome C, which we found in the sperm of a Mytilus galloprovincialis male. The coding part of the new genome resembles in sequence the F genome, from which it differs by about 2% on average, but differs from the M genome by as much as the F from the M. Its major control region (CR) is more than three times larger than that of the F or the M genome and consists of repeated sequence domains of the CR of the M genome flanked by domains of the CR of the F genome. We present a sequence of events that reconstruct most parsimoniously the derivation of the C genome from the F and M genomes. The sequence consists of a duplication of CR elements of the M genome and subsequent insertion of these tandemly repeated elements in the F genome by recombination. The fact that the C genome was found as the only mitochondrial genome in the sperm of the male from which it was extracted suggests that it is transmitted paternally.     

Reshuffling of the Bacillus subtilis 168 genome by multifold inversion

The genome of Bacillus subtilis 168 was modified to yield a genome vector for the cloning of DNA several Mb in size. Unlike contemporary plasmid-based vectors, this 4.2 Mb genome vector requires specific in vivo handling protocols because of its large size. Inversion mutagenesis, a method to modify local genome structure without gain or loss of genes, was applied intensively to the B. subtilis genome; this technique made possible both exchange and translocation of designated regions of the genome. This method not only reshuffles the genome of B. subtilis, but can provide insight into the biologic principles underlying genome plasticity.     

trans-dominant inhibition of human hepatitis delta virus genome replication.

Infection with hepatitis delta virus (HDV) is an important cause of acute and chronic liver disease and can be rapidly fatal. Sequencing of the HDV RNA genome has revealed variability at the C-terminal end of the delta antigen reading frame. One genome type (termed the S genome) synthesizes a 24-kDa protein thought to be required for genome replication. Another genome type (termed the L genome) extends the reading frame by 19 amino acids as a result of a single base change. Replication of the S and L genomes was studied in cultured fibroblasts. While the S genome efficiently initiated genome replication, the L genome did not. Moreover, in a codelivery experiment, L genome RNA inhibited replication of the S genome. Potent trans inhibition was also observed following cotransfection of the S genome and a plasmid encoding the larger delta antigen. Mutational analysis indicated that the inhibitory activity was not a simple function of the large delta antigen reading frame's extra length. Implications for the viral life cycle, clinical infection, and potential treatment are discussed.     

Whole genome engineering by synthesis

Whole genome engineering is now feasible with the aid of genome editing and synthesis tools. Synthesizing a genome from scratch allows modifications of the genomic structure and function to an extent that was hitherto not possible, which will finally lead to new insights into the basic principles of life and enable valuable applications. With several recent genome synthesis projects as examples, the technical details to synthesize a genome and applications of synthetic genome are addressed in this perspective. A series of ongoing or future synthetic genomics projects, including the different genomes to be synthesized in GP-write, synthetic minimal genome, massively recoded genome, chimeric genome and synthetic genome with expanded genetic alphabet, are also discussed here with a special focus on theoretical and technical impediments in the design and synthesis process. Synthetic genomics will become a commonplace to engineer pathways and genomes according to arbitrary sets of design principles with the development of high-efficient, low-cost genome synthesis and assembly technologies.     

杨树基因组中染色体基因丰度分化及EST序列对基因覆盖度的检测(英文)

高等植物基因组中,大部分序列为非表达序列,基因序列所占的比例很小,了解基因在基因组中的分布是研究基因组结构的一个重要方面。在美国能源部资助下,一个毛果杨无性系的基因组测序已经完成并对公众发布。杨树全基因组序列的完成,为我们了解林木基因组中基因的分布提供了一个特例。在本文中,我们利用泊松分析对杨树基因组中基因在各个染色体上的密度进行了检测,结果表明杨树基因组中各条染色体的基因含量存在显著差异。杨树全基因组测序项目揭示现代杨树基因组起源于一次古全基因组复制事件(称为杨柳科基因组复制),所以杨树基因组不同染色体间存在很大的同源复制片段。但是我们的研究显示,杨树基因组中大多数高度同源的染色体上基因的密度与染色体间的同源性没有明显关系,这说明杨柳科全基因组复制事件后,各个高度同源染色体上的基因发生了流失,且基因流失的速率是不一样的。同时本文还对近九万条毛果杨EST序列进行了比对分析,结果显示这些EST序列覆盖的基因仅占杨树基因组中基因总数的16.8%左右。EST测序虽然是发现基因的一个重要手段,但小规模EST测序对基因的覆盖度很低,所以小规模EST测序的应用价值是有限的。     

The ups and downs of genome size evolution in polyploid species of Nicotiana (Solanaceae)

BACKGROUND: In studies looking at individual polyploid species, the most common patterns of genomic change are that either genome size in the polyploid is additive (i.e. the sum of parental genome donors) or there is evidence of genome downsizing. Reports showing an increase in genome size are rare. In a large-scale analysis of 3008 species, genome downsizing was shown to be a widespread biological response to polyploidy. Polyploidy in the genus Nicotiana (Solanaceae) is common with approx. 40 % of the approx. 75 species being allotetraploid. Recent advances in understanding phylogenetic relationships of Nicotiana species and dating polyploid formation enable a temporal dimension to be added to the analysis of genome size evolution in these polyploids. METHODS: Genome sizes were measured in 18 species of Nicotiana (nine diploids and nine polyploids) ranging in age from <200,000 years to approx. 4.5 Myr old, to determine the direction and extent of genome size change following polyploidy. These data were combined with data from genomic in situ hybridization and increasing amounts of information on sequence composition in Nicotiana to provide insights into the molecular basis of genome size changes. KEY RESULTS AND CONCLUSIONS: By comparing the expected genome size of the polyploid (based on summing the genome size of species identified as either a parent or most closely related to the diploid progenitors) with the observed genome size, four polyploids showed genome downsizing and five showed increases. There was no discernable pattern in the direction of genome size change with age of polyploids, although with increasing age the amount of genome size change increased. In older polyploids (approx. 4.5 million years old) the increase in genome size was associated with loss of detectable genomic in situ hybridization signal, whereas some hybridization signal was still detected in species exhibiting genome downsizing. The possible significance of these results is discussed.     

小麦及其近缘种中基因组特异性DNA重复序列的研究进展

本文对小麦族植物中基因组特异性DNA重复序列的分类、基本特征、分离和鉴定方法、在小麦遗传改良中的应用以及未来研究的发展趋势进行了简述。综合已有的研究结果可以看出基因组特异性DNA重复序列是小麦族植物基因组特异性形成的重要构成部分。对基因组特异性DNA重复序列的研究是认识小麦族植物基因组的有效途径之一,基因组特异性DNA重复序列的应用将进一步促进小麦族植物分子细胞遗传学和普通小麦遗传改良研究的进展。 Advances in Studies of Genome-Specific Repetitive DNA Sequences in Wheat and Related Species BAI Jian-rong1,2,JIA Xu1,WANG Dao-wen1 1.The State Key Laboratory of Plant Cell and Chromosome Engineering,Institute of Genetics and Developmental Biology,The Chinese Academy of Sciences,Beijing 100101,China; 2.Crop Genetics Institute,Shanxi Academy of Agricultural Sciences,Taiyuan 030031,China Abstract:In this paper we review recent advances in studies of several aspects of genome specific repetitive DNA sequences in wheat and related species.The available results demonstrate that genome specific repetitive DNA sequences are important components of genome specificity in wheat and related species.Research on genome specific repetitive DNA sequences is essential to the elucidation of genome function.The application of genome specific repetitive DNA sequences will aid molecular cytogenetic studies in wheat and related species and contributes to genetic improvement of common wheat. Key words：wheat;genome specific repetitive DNA sequence;chromosome