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pTBR101-CM

Bifidobacterium longum–E. coli shuttle vector.

Catalog number RDB15972
Resource name pTBR101-CM
Clone info. Bifidobacterium longum–E. coli shuttle vector. Efficiently transform B. longum 105-A.
Comment For selection of E. coli transformants of this plasmid, the depositor recommends use of both Cm (2.5 microgram/mL) and Ap (100 microgram/mL) because Cm resistance conferred by this plasmid is not strong. For selection of B. longum 105-A transformants, the depositor uses Cm at a concentration of 2.5 microgram/mL. They can successfully select true transformants at this concentration, but it depends on the Bifidobacterium strain. If endogenous Cm resistance is higher than 2.5 microgram/mL in your strain, the depositor recommends change of the CmR marker to the other appropriate markers that you used might be necessary. CmR region can be easily removed from pTBR101-CM by HindIII digestion. Please refer Hirayama et al., AEM, 78, 4984-4994, 2012 for further information. B. longum 105-A (JCM 31944) is available from JCM as a host strain.
Vector backbone pTBR101-CM (Plasmid)
Size of vector backbone 8.4 kb
Selectable markers Cm^r, Amp^r
Reference of insert sequence AB688000 (DDBJ accession number)
Depositor|Developer Fukiya, Satoru | Kano, Yasunobu |
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External Database

            Reference sequence
              
             
            Sequence (full) RDB15972zzk01.seq provided by the depositor

            Distribution information

            Please check terms and conditions set forth by the depositor, which are specified in the RIKEN BRC Catalog and/or Web Catalog.
            Terms and conditions for distribution In publishing the research results obtained by use of the BIOLOGICAL RESOURCE, a citation of the following literature designated by the DEPOSITOR is requested. (Hirayama et al., Appl. Environ. Microbiol., 78(14):4984-4994 (2012)). The availability of the BIOLOGICAL RESOURCE is limited to a not-for-profit academic purpose.
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            提供条件 利用者は、研究成果の公表にあたって寄託者の指定する文献を引用する(Hirayama et al., Appl. Environ. Microbiol., 78(14):4984-4994 (2012))。本リソースは,非営利の学術研究に限って提供する。
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            RDB15972 pTBR101-CM DNA solution

            Please review the QC test results indicated by check icon below as well as clone information before placing your order.

            How to cite this biological resource

            Materials & Methods section:

            The pTBR101-CM was provided by the RIKEN BRC through the National BioResource Project of the MEXT, Japan (cat. RDB15972).

            Reference section:

            Hirayama, Y., Sakanaka, M., Fukuma, H., Murayama, H., Kano, Y., Fukiya, S., Yokota, A., Development of a double-crossover markerless gene deletion system in Bifidobacterium longum: functional analysis of the α-galactosidase gene for raffinose assimilation. Appl. Environ. Microbiol. 78 (14): 4984-4994 (2012). PMID 22582061. [link to RRC of NBRP]

            Further references such as user reports and related articles (go to bottom)


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            Featured content

            Featured content Bacteria host strains (en) (English text)
            Featured content Bacteria host strains (ja) (Japanese text)

            QC test results

            RIKEN BRC has sequenced portions of this material for quality test.
            Please review the QC test results indicated by check icon as well as clone information before placing your order.

            Test sheet RDB19984_B3Eip1-1.pdf check

            Nucleotide sequence of a portion of this resource (if available).

            Primer: tetA_mid_F (Pr1320)
            Region: insert(pTB4_p1 3')
            Sequence file: RDB19984_B3Eia.seq check
            >15972_19984_B3Ei_2_tetA_mid_F_A01_01_ABI08.ab1
                1 NNNNNNNNNN NNNNNNNNNN GGNNNCNNTA TCGNCTACGC GATCATGGCG NCCACACCCG
               61 TCCTGTGGAT CCTCATCAGC ACCACCCGCG ACACGAACGT ATTACATACG CAATCATATC
              121 AGTGTCACAC ATCAGGTACA ACCGTACCGC AACACGCTTC GAGCGGACGC AAGCGGCTTT
              181 TGCGCGGAGC ATTTCCGGCC ATTTGCCCAG CTTGTTCCGC GCTTCCGAGA AGGTGTGGAG
              241 TTGGGTTTTC TGTGATGCCG CGCGAGCGGT CTGGAGGCTC CGCCGACCAT GGGGCATGGG
              301 TCTTCCCGGC AAGCCGATTC GCACCGCGAA TCGAGTGATT GTAGCTACAA TCACGTCGCT
              361 TGCTACTCCG GCCTTCGGCA CTCGGGTTGT TGCTCCTGCG CCGAAGGGCG AGGGAGGCTG
              421 CGGGCTCGGT TCATGTACAT GAACCGTCTA GCTTGCTTAC CTTCGATTTG ATGGACATCT
              481 CCATGTGGAT GTCCATGGAG ATGTCCATGG AGATGTCCAT GGAGATGTCC ATGGAGATGT
              541 CCATGGAGAT GTCCATGTGG GTGTCCATGT GGGTGTCCAT GGATATATCC ATCTGAGCGC
              601 ATAGGAAAAC GCATGAGGGT GGATGATCGT TCGGGGTGAT GCCTTCTTCC NCGAACGGGA
              661 AGGGGCTCTT CCTTTTTCTG GAATGTCATC TTCCAGCGCC CTTCGCCTTG AGCTCCTTGA
              721 NCAGCATCGT CGCGTTGTCG CGGATGCTCG CGTCCGTGAN CGGGGANAGC TCGTCCGCAT
              781 ANGANCGGCA GANGANCGCG TACANNNNNT CCCGCACCCA GGCGCTGCGC GCGATGCCCA
              841 NCTTGAACGC GGCCCGGCNC ANCATCTCGT ATNCGTCGCC NNNGANCAGG NNNTTGANCT
              901 NGNGNNNAAA NNNGATTANN CNTGNCNNNN ATATACNNNC CGGGGNNNTT NNNNNNNNNN
            //
            Primer: lacIpro_R1 (Pr0762)
            Region: insert(pTB4_p3,pTB4_p2)
            Sequence file: RDB19984_B3Eib.seq check
            >15972_19984_B3Ei_2_lacIpro_R1_E01_05_ABI08.ab1
                1 NNNNNNNNNN NNNNNNNNNN NNNNNNACNN GCGCTCNTGA NCCCGAAGTG GCGAGCCCGA
               61 TCTTCCCCAT CGGTGANGTC GGCGATATAG GCGCCAGCAA CCGCACCTGT GGCGCCGGTG
              121 ATGCCGGCCA CGATGCGTCC GGCGTAGAGG ATCCAGGTGC TTGACAGGGT GATGGAGCGT
              181 CACCCAGAAC TGTCCGAGAA GGACGTGGTG ACCGCGTTCC GCAGCGTCAT GGTGGACGCG
              241 GAGCGCGAGT CCGGCGCGTG GATGGCGATA GGGCTCGACG GGCGCGGCAG GAACGTCGAG
              301 ATGCTGTACA GGGTCGTCGG CGACCTCGTG GTGATCTACC ACGCGTTCAC GCCGCCGACC
              361 AAGAAGTTCA GGCGCGAGAT AGACCGTCTG CGCGGCGATG GGAGGACGCT ATGAGTGATT
              421 TCAGCGAACG CGACAGGCAG TTGATGGCGC TGGTCGGGCT GACCGAGGAG CAGGTGCTGG
              481 AGGATGAGCG GATGGCCGAG TCCGAGACTG TCCCGGACGA CCTGACGGGG CGCGTGTACT
              541 ACGGGCTCCA TCTCGCCGAG CCCGACGAGC AGATGGTCAG CGTGTCCGTC CGCATGCCCA
              601 AGAGCACGCT GGACGGTCTG ACCGCGATGG CCAGGCGGTA CCACATCAGC CGCAGCGAGT
              661 ACATGCGCCG TAAGCTCGCT GGAGCGATCT GAGACCTGTC AGGCCGATGG TTCGAATCAC
              721 GTAACACCCG CGCACCACCG TGAGGATGTG CGGGTGTTAC GTGATGTGCC ACAGTCGTGG
              781 CACGATGCCG CGNGAGCGGT CTGGANGCTC TGCCGACTAN NGGGGCATGG GTCTTCCCNG
              841 CNNGCCGATT CNCACCNCNN NNCGAGNGNA NCGTATATNC GTNCACGTNN NTTGNNACNN
            901 CNNGNNNNNN NNNN
            //
            Primer: pBS423_seq3_3 (Pr0751)
            Region: insert(repA mid)
            Sequence file: RDB19984_B3Eic.seq check
            >15972_19984_B3Ei_2_pBS423_seq3_3_G01_07_ABI08.ab1
                1 NNNNNNNNNN NNNNNNNNNN NNNGNGNCTT CCCCNNCGTC CCCTGTGCTG CGNCGATGAC
               61 TACTCCCAGC TGGTGCNNNN GNNCCGCATC GACGCGCTCA GATGCAAGCA CATCGAGGCG
              121 AATCCGGCAG CGCAGGTGAA CATGCTCGTT GTTGACGTTG ATTCGTCTGA GGGCCGTTTA
              181 ATGAGCCTGT GGGGGCATCG GGACATGCCG CCCAACTTCA TCGCGGAGAA TCCGGCCAAC
              241 GGCCACTGCC ACGCGGGCTG GGTGCTCACC GAACCCGTCT GCCGCACCGA CATGGCCAGA
              301 CTCAAGCCCC TGAAGCTCCT GCACGCCGTC ACCGAGGGGC TGCGCCGCAG CGTGGACGGC
              361 GACGAGGGCT ATTCCGGCCT GCTCATGAAG AACCCGTTGA GCGACGCGTG GGACAGCGAC
              421 CTGTGCCGCG AGGACACCTA CGACCTGCCC GACCTCGTGG CCGCGCTCGA AGCGCACGGG
              481 GACATGCCGC CCAAGAGCTG GACGCGCACC AAACGCGCCC GCGAGGTCGG AGTGGGCCGC
              541 AACTGCACCC TGTTCGACGA GGCCCGCACC CTCGCCTACC GCGAGGTGCG CCGACTGCCT
              601 GACCGCACGC CCGCCTCCTC CGACCTGCTG CGCGAGTACG TGCGCCGCAC CTGCCACGAA
              661 ATCAACGCCT CGTTCCCCGA CCCGCTGCCC GTGCGCGAGG TCAACGACAC CGCCNAGAGC
              721 ATCCACAAGT GGATCACCAC GCGAAGCCGC ATGTGGCGAG ACGGTGCCGT CGCCNACGCC
              781 GCCACGTTCG TCGCCATCCA ATCCGCACGC GGAAAGAAAT CNGGGCNANG NCAGACAAAA
              841 CGNATTTGAA GANAAGTTCG CGNANTANGC GCANGNNGNG CNTGNNNNNN GANNNTCCNN
              901 ANNNNTCNNN AGNNNNNCCN ATTGCCNNNN NNNGNNNNNN NCNNANNNNN NNNGGNNNNN
            961 NNNNN
            //
            Primer: repA_F_rev2 (Pr1322)
            Region: insert(repA 5',pTB4_p1 5')
            Sequence file: RDB19984_B3Eid.seq check
            >15972_19984_B3Ei_2_repA_F_rev2_D01_04_ABI08.ab1
                1 NNNNNNNNNN NNNNNNNNNN NNNNNNNNGC CCTNNGANGA NCAACGTCAA CAACGAGCAT
               61 GTTCACCTGC GCTGNNNNNN NTCGCCTCGA TGTGCTTGCA TCTGAGCGCG TCGATGCGGC
              121 TCCGGCGCAC CAGCTGGGAG TAGTCATCGT CGCAGCACAG GGGACGCTGG GGAAGCCACC
              181 AGCCGTCGAA CGCCCGCGTC AGCTCCAGCG TCCCCTGCAC ATATTCGTTG CTCATAGCTC
              241 ACATCCTATT GCACATTTGT GCATTGCACA AGCGTGCGCC GAACCAAGTC AGATGGTTCA
              301 GCCCAGCGAA GCGTCGGCTG TTCCTTCCCG GAGTGGCCCA AAACTGTTGG AATCTGGCCG
              361 AAAACACCCC GGACGTATAT ACACGGCATG ACTAATCAAC TTTTGACGCC AGCTCAATGT
              421 CCTGCTCACC GGCGACGAAT ACGAGATGCT GTGCCGGGCC GCGTTCAAGC TGGGCATCGC
              481 GCGCAGCGCC TGGGTGCGGG AACGGGTGTA CGCGCTCCTC TGCCGCTCCT ATGCGGACGA
              541 GCTCTCCCCG CTCACGGACG CGAGCATCCG CGACAACGCG ACGATGCTGC TCAAGGAGCT
              601 CAAGGCGAAG GGCGCTGGAA GATGACATTC CAGAAAAAGG AAGAGCCCCT TCCCGTTCGT
              661 GGAAGAAGGC ATCACCCCGA ACGATCATCC ACCCTCATGC GTTTTCCTAT GCGCTCAGAT
              721 GGATATATCC ATGGACACCC ACATGGACAC CCACATGGAC ATCTCCATGG ACATCTCCAT
              781 GGACATCTCC ATGGNCATCT CCATGGACAT CTCCATGNAC ATCCACATGG AGATGTCCAT
              841 CAAATCNNAN NNTNNNCAAG CTAGANGGTN CATGTACNTG AANCGANCCC GCNNCCTCCN
            901 NNNNCNTNCN GNNNNNNNCN NCNNNCCNAN NGNCGAANNN NNNNNNN
            //
            Primer: repB_F_rev (Pr1321)
            Region: insert(repB 5',repA 3')
            Sequence file: RDB19984_B3Eie.seq check
            >15972_19984_B3Ei_2_repB_F_rev_E01_05_ABI08.ab1
                1 NNNNNNNNNN NNNNNNNNNN NNNNNNNANG CCTCGGCTAA CTCCTTGGCG GGCAATGGGC
               61 GCTTCTTGCG AATTGNNTGG ATGGTCATTG TCCAAGCACC TCCTGCGCGT ACTGCGCGAA
              121 CTTCTCTTCA AATGCGTTTT GTCTGGCCTC GCCCGATTTC TTTCCGCGTG CGGATTGGAT
              181 GGCGACGAAC GTGGCGGCGT TGGCGACGGC ACCGTCTCGC CACATGCGGC TTCGCGTGGT
              241 GATCCACTTG TGGATGCTCT TGGCGGTGTC GTTGACCTCG CGCACGGGCA GCGGGTCGGG
              301 GAACGAGGCG TTGATTTCGT GGCAGGTGCG GCGCACGTAC TCGCGCAGCA GGTCGGAGGA
              361 GGCGGGCGTG CGGTCAGGCA GTCGGCGCAC CTCGCGGTAG GCGAGGGTGC GGGCCTCGTC
              421 GAACAGGGTG CAGTTGCGGC CCACTCCGAC CTCGCGGGCG CGTTTGGTGC GCGTCCAGCT
              481 CTTGGGCGGC ATGTCCCCGT GCGCTTCGAG CGCGGCCACG AGGTCGGGCA GGTCGTAGGT
              541 GTCCTCGCGG CACAGGTCGC TGTCCCACGC GTCGCTCAAC GGGTTCTTCA TGAGCAGGCC
              601 GGAATAGCCC TCGTCGCCGT CCACGCTGCG GCGCAGCCCC TCGGTGACGG CGTGCANGAG
              661 CTTCAGGGGC TTGAGTCTGG CCATGTCGGT GCGGCAGACG GGTTCGGTGA GCACCCAGCC
              721 CGCGTGGCAG TGGCCGTTGG CCGGANTCTC CGCGATGAAG TTGGGCGGCA TGTCCCGATG
              781 CCCCCACANG CTCATTAAAC GGCCCTCAGA CNAATCANCG TCNACAACNA NCATGTTCAC
              841 CTGCGCNGNC NGNATTCNCC NCNATGNGCT NGNNTCTGAN CGCGNNNATG NNGNNNCNNG
            901 NNNANNNNCN GGGNNNANNN ATCNNCNNNN CNNNNGGNNN NNNNGGNNNN NNNNNN
            //
            Primer: pTBR101CM_seq7 (Pr0561)
            Region: insert(repB 3',pTB4_p2,pTB4_p3 3')
            Sequence file: RDB19984_B3Eif.seq check
            >15972_19984_B3Ei_2_pTBR101CM_seq7_F01_06_ABI08.ab1
                1 NNNNNNNNNN NNNNNNNTCC NNCGNCTNNN NCGNNNNNGN NGGCNNCTCG TGGNNCCAGA
               61 CCGCCGAACA CTTCAACNTG NCCCAAGGTG CCGTGCGCCA ACGCGCCTAC CGCGCCCGCA
              121 AGGAACGCGA GGCCGAGGCA AAAGCCGCAA GGCCGGAGTA GCAAGTGACG TGAACGTATA
              181 TACGTTCACT CGATTCGCGG TGCGAATCGG CTTGCCGGGA AGACCCATGC CCCATAGTCG
              241 GCAGAGCCTC CAGACCGCTC ACGCGGCATC GTGCCACGAC TGTGGCACAT CACGTAACAC
              301 CCGCACATCC TCACGGTGGT GCGCGGGTGT TACGTGATTC GAACCATCGG CCTGACAGGT
              361 CTCAGATCGC TCCAGCGAGC TTACGGCGCA TGTACTCGCT GCGGCTGATG TGGTACCGCC
              421 TGGCCATCGC GGTCAGACCG TCCAGCGTGC TCTTGGGCAT GCGGACGGAC ACGCTGACCA
              481 TCTGCTCGTC GGGCTCGGCG AGATGGAGCC CGTAGTACAC GCGCCCCGTC AGGTCGTCCG
              541 GGACAGTCTC GGACTCGGCC ATCCGCTCAT CCTCCAGCAC CTGCTCCTCG GTCAGCCCGA
              601 CCAGCGCCAT CAACTGCCTG TCGCGTTCGC TGAAATCACT CATAGCGTCC TCCCATCGCC
              661 GCGCAGACGG TCTATCTCGC GCCTGAACTT CTTGGTCGGC GGCGTGAACG CGTGGTAGAT
              721 CACCACGANG TCGCCGACGA NCCTGTACAG CATCTCGACG TTCCTGCCGC GCCCGTCGAN
              781 NCCTATCGCC ATCCACGCGC CGGANTCGCG CTCCGCGTCC ACCATGACGC TGCGGAACGC
              841 GGNCACCACG TCCTTCTCGG ANAGTTCTGG GNGANGCTNC ATCACCCNGN NNNGCNCCNN
              901 NNNTNCNCTA CNCCNNANGC NTCNNNNNCN NGNNTCACNN GCNNNNNNNG NNNNNGNNNN
            961 NNGNNNNNNN NNN
            //
            Primer: pBR_EcoRI_R (Pr0139)
            Region: CmR
            Sequence file: RDB19984_B3Eig.seq check
            >15972_19984_B3Ei_2_pBR_EcoRI_R_C01_03_ABI08.ab1
                1 NNNNNNNNNN NNNNNNNNNN NNCGCNNTGT NAGNNTTNNT ACACGGNGCC TGNNTGCGTT
               61 AGCAATTTAA CTGTGATANN NNACCGCATT AACAAGCTTG CGGCAATAGT TACCCTTATT
              121 ATCAAGATAA GAAAGAAAAG GATTTTTCGC TACGCTCAAA TCCTTTAAAA AAACACAAAA
              181 GACCACATTT TTTAATGTGG TCTTTTATTC TTCAACTAAA GCACCCATTA GTTCAACAAA
              241 CGAAAATTGG ATAAAGTGGG ATATTTTNAA AATATATATT TATGTTACAG TAATATTGAC
              301 TTTTAAAAAA GGATTGATTC TAATGAAGAA AGCAGACAAG TAAGCCTCCT AAATTCACTT
              361 TAGATAAAAA TTTAGGAGGC ATATCAAATG AACTTTAATA AAATTGATTT AGACAATTGG
              421 AAGAGAAAAG AGATATTTAA TCATTATTTG AACCAACAAA CGACTTTTAG TATAACCACA
              481 GAAATTGATA TTAGTGTTTT ATACCGAAAC ATAAAACAAG AAGGATATAA ATTTTACCCT
              541 GCATTTATTT TCTTAGTGAC AAGGGTGATA AACTCAAATA CAGCTTTTAG AACTGGTTAC
              601 AATAGCGACG GAGAGTTAGG TTATTGGGAT AAGTTAGAGC CACTTTATAC AATTTTTGAT
              661 GGTGTATCTA AAACATTCTC TGGTATTTGG ACTCCTGTAA AGAATGACTT CAAAGAGTTT
              721 TATGATTTAT ACCTTTCTGA NGTAGAGAAN TATAATGGTT CGGGGAAATT GTTTCCCNAA
              781 ACACCTATAC CTGAAAATGC TTTTTCTCTT TCTATTATTC CATGGACTTC ATTTACTGGG
              841 TTTAACTTAA ANTATCAATA ATAATANNAN NTNNCTTCTA CCCNTTATTA CAGCNNNAAA
              901 ANTCATTANN NAANGNAATT CNANNTATTT ANNNCTNTNT TTACNNGNNN NNTNNNNNNN
            961 NTNNNNNNNN NN
            //

            Please visit Sequencing and PCR primers for primer information.


            References

            Original, user report and related articles

            original Hirayama, Y., Development of a double-crossover markerless gene deletion system in Bifidobacterium longum: functional analysis of the α-galactosidase gene for raffinose assimilation. Appl. Environ. Microbiol. 78 (14): 4984-4994 (2012). PMID 22582061. [link to RRC of NBRP]
            reference Nishiyama, K., Bifidobacterium bifidum Extracellular Sialidase Enhances Adhesion to the Mucosal Surface and Supports Carbohydrate Assimilation. MBio 8 (5). pii: e00928-17 (2017). PMID 28974612.
            reference Fukiya, S., Development of practical gene-mutagenesis systems in bifidobacteria. (Japanese text) Seibutsu-kogaku 94 (3): 110-116 (2016).

            2024.03.26

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