Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.


BACKGROUND:Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents exploration of their genomic functions, including those that convey (human) health benefits. METHODS:PacBio SMRT sequencing was used to determine the whole genome seqeunces of two B. longum subsp. longum strains. The B. longum pan-genome was computed using PGAP v1.2 and the core B. longum phylogenetic tree was constructed using a maximum-likelihood based approach in PhyML v3.0. M.blmNCII was cloned in E. coli and an internal fragment if arfBarfB was cloned into pORI19 for insertion mutagenesis. RESULTS:In this study we present the complete genome sequences of two Bifidobacterium longum subsp. longum strains. Comparative analysis with thirty one publicly available B. longum genomes allowed the definition of the B. longum core and dispensable genomes. This analysis also highlighted differences in particular metabolic abilities between members of the B. longum subspecies infantis, longum and suis. Furthermore, phylogenetic analysis of the B. longum core genome indicated the existence of a novel subspecies. Methylome data, coupled to the analysis of restriction-modification systems, allowed us to substantially increase the genetic accessibility of B. longum subsp. longum NCIMB 8809 to a level that was shown to permit site-directed mutagenesis. CONCLUSIONS:Comparative genomic analysis of thirty three B. longum representatives revealed a closed pan-genome for this bifidobacterial species. Phylogenetic analysis of the B. longum core genome also provides evidence for a novel fifth B. longum subspecies. Finally, we improved genetic accessibility for the strain B. longum subsp. longum NCIMB 8809, which allowed the generation of a mutant of this strain.


BMC Genomics


BMC genomics


O'Callaghan A,Bottacini F,O'Connell Motherway M,van Sinderen D




Has Abstract


2015-10-21 00:00:00










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    abstract:BACKGROUND:In animals, signaling of Bone Morphogenetic Proteins (BMPs) is essential for dorsoventral (DV) patterning of the embryo, but how BMP signaling evolved with changes in embryonic DV differentiation is largely unclear. Based on the extensive knowledge of BMP signaling in Drosophila melanogaster, the morphologic...

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    pub_type: 杂志文章


    authors: Lemke S,Antonopoulos DA,Meyer F,Domanus MH,Schmidt-Ott U

    更新日期:2011-05-31 00:00:00

  • Origin of a novel protein-coding gene family with similar signal sequence in Schistosoma japonicum.

    abstract:BACKGROUND:Evolution of novel protein-coding genes is the bedrock of adaptive evolution. Recently, we identified six protein-coding genes with similar signal sequence from Schistosoma japonicum egg stage mRNA using signal sequence trap (SST). To find the mechanism underlying the origination of these genes with similar ...

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    authors: Mbanefo EC,Chuanxin Y,Kikuchi M,Shuaibu MN,Boamah D,Kirinoki M,Hayashi N,Chigusa Y,Osada Y,Hamano S,Hirayama K

    更新日期:2012-06-20 00:00:00

  • A systematic analysis of protein palmitoylation in Caenorhabditis elegans.

    abstract:BACKGROUND:Palmitoylation is a reversible post-translational protein modification which involves the addition of palmitate to cysteine residues. Palmitoylation is catalysed by the DHHC family of palmitoyl-acyl transferases (PATs) and reversibility is conferred by palmitoyl-protein thioesterases (PPTs). Mutations in gen...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Edmonds MJ,Morgan A

    更新日期:2014-10-02 00:00:00

  • Testis transcriptome analysis in male infertility: new insight on the pathogenesis of oligo-azoospermia in cases with and without AZFc microdeletion.

    abstract:BACKGROUND:About 10% of cases of male infertility are due to the presence of microdeletions within the long arm of the Y chromosome (Yq). Despite the large literature covering this critical issue, very little is known about the pathogenic mechanism leading to spermatogenesis disruption in patients carrying these microd...

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    pub_type: 杂志文章


    authors: Gatta V,Raicu F,Ferlin A,Antonucci I,Scioletti AP,Garolla A,Palka G,Foresta C,Stuppia L

    更新日期:2010-06-24 00:00:00

  • Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms.

    abstract:BACKGROUND:Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 h post fertilization, and it has been demonstrated that chang...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: De Wit P,Durland E,Ventura A,Langdon CJ

    更新日期:2018-02-22 00:00:00

  • Cross species comparison of C/EBPα and PPARγ profiles in mouse and human adipocytes reveals interdependent retention of binding sites.

    abstract:BACKGROUND:The transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and others have previously shown that binding sites of these two transcription factors show a high degr...

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    pub_type: 杂志文章


    authors: Schmidt SF,Jørgensen M,Chen Y,Nielsen R,Sandelin A,Mandrup S

    更新日期:2011-03-16 00:00:00

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    pub_type: 杂志文章


    authors: Wang K,Ubriaco G,Sutherland LC

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  • Comparative venom gland transcriptome analysis of the scorpion Lychas mucronatus reveals intraspecific toxic gene diversity and new venomous components.

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    pub_type: 杂志文章


    authors: Ruiming Z,Yibao M,Yawen H,Zhiyong D,Yingliang W,Zhijian C,Wenxin L

    更新日期:2010-07-28 00:00:00

  • Replication-biased genome organisation in the crenarchaeon Sulfolobus.

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    authors: Andersson AF,Pelve EA,Lindeberg S,Lundgren M,Nilsson P,Bernander R

    更新日期:2010-07-28 00:00:00

  • Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala × Culter alburnus.

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    authors: Ren L,Yan X,Gao X,Cui J,Yan P,Wu C,Li W,Liu S

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  • Transcriptional profiling of Actinobacillus pleuropneumoniae during the acute phase of a natural infection in pigs.

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    authors: Deslandes V,Denicourt M,Girard C,Harel J,Nash JH,Jacques M

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    authors: Magi A,Pippucci T,Sidore C

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    pub_type: 杂志文章


    authors: Guo S,Liu J,Zheng Y,Huang M,Zhang H,Gong G,He H,Ren Y,Zhong S,Fei Z,Xu Y

    更新日期:2011-09-21 00:00:00

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    authors: Zeng W,Wu M,Jiang R

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    authors: Luo X,Ma C,Yue Y,Hu K,Li Y,Duan Z,Wu M,Tu J,Shen J,Yi B,Fu T

    更新日期:2015-05-12 00:00:00

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    authors: Ge S,Danino V,He Q,Hinton JC,Granfors K

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    journal_title:BMC genomics

    pub_type: 杂志文章


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    pub_type: 杂志文章


    authors: Zhao K,Wohlhueter RM,Li Y

    更新日期:2016-08-31 00:00:00

  • A high throughput screen for active human transposable elements.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Kvikstad EM,Piazza P,Taylor JC,Lunter G

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    abstract:BACKGROUND:The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative ana...

    journal_title:BMC genomics

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    authors: Auvinet J,Graça P,Belkadi L,Petit L,Bonnivard E,Dettaï A,Detrich WH 3rd,Ozouf-Costaz C,Higuet D

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  • Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis.

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    pub_type: 杂志文章


    authors: Ye W,Long Y,Ji G,Su Y,Ye P,Fu H,Wu X

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  • Meta-analysis of expression signatures of muscle atrophy: gene interaction networks in early and late stages.

    abstract:BACKGROUND:Skeletal muscle mass can be markedly reduced through a process called atrophy, as a consequence of many diseases or critical physiological and environmental situations. Atrophy is characterised by loss of contractile proteins and reduction of fiber volume. Although in the last decade the molecular aspects un...

    journal_title:BMC genomics

    pub_type: 杂志文章,meta分析


    authors: Calura E,Cagnin S,Raffaello A,Laveder P,Lanfranchi G,Romualdi C

    更新日期:2008-12-23 00:00:00

  • Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants.

    abstract:BACKGROUND:Taraxacum kok-saghyz R. (Tks) is a promising alternative species to Hevea brasiliensis for production of high quality natural rubber (NR). A comparative transcriptome analysis of plants with differential production of NR will contribute to elucidate which genes are involved in the synthesis, regulation and a...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Panara F,Lopez L,Daddiego L,Fantini E,Facella P,Perrotta G

    更新日期:2018-12-04 00:00:00

  • De novo assembly of highly diverse viral populations.

    abstract:BACKGROUND:Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and as a backbo...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Yang X,Charlebois P,Gnerre S,Coole MG,Lennon NJ,Levin JZ,Qu J,Ryan EM,Zody MC,Henn MR

    更新日期:2012-09-13 00:00:00

  • Genetic architecture of kernel composition in global sorghum germplasm.

    abstract:BACKGROUND:Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop for dryland areas in the United States and for small-holder farmers in Africa. Natural variation of sorghum grain composition (protein, fat, and starch) between accessions can be used for crop improvement, but the genetic controls are still un...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rhodes DH,Hoffmann L Jr,Rooney WL,Herald TJ,Bean S,Boyles R,Brenton ZW,Kresovich S

    更新日期:2017-01-05 00:00:00

  • Population and sex differences in Drosophila melanogaster brain gene expression.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Catalán A,Hutter S,Parsch J

    更新日期:2012-11-21 00:00:00

  • Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cericola F,Portis E,Lanteri S,Toppino L,Barchi L,Acciarri N,Pulcini L,Sala T,Rotino GL

    更新日期:2014-10-14 00:00:00

  • A transcription map of the 6p22.3 reading disability locus identifying candidate genes.

    abstract:BACKGROUND:Reading disability (RD) is a common syndrome with a large genetic component. Chromosome 6 has been identified in several linkage studies as playing a significant role. A more recent study identified a peak of transmission disequilibrium to marker JA04 (G72384) on chromosome 6p22.3, suggesting that a gene is ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Londin ER,Meng H,Gruen JR

    更新日期:2003-06-30 00:00:00

  • Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu YC,Chen WL,Kung WH,Huang HD

    更新日期:2017-03-14 00:00:00

  • The developmental transcriptomes of two sea biscuit species with differing larval types.

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    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Armstrong AF,Grosberg RK

    更新日期:2018-05-18 00:00:00