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Team:UC-Santa Cruz/Project/Pumps
From 2013.igem.org
Ion Pumps
The goal of the ion pumps group was to find and obtain light driven sodium
and chloride pumps to be expressed in C. cresentus. Choice of ion pumps was based on ion selectivity and
structure simplicity.
Two pumps were used for this project. The first choice was
the widely studied Halorhodopsin (HR), an
inward pointing chloride conductor. For the sodium pump we chose the newly discovered
KR2, an outward facing pump.
First, we searched the iGEM
catalog for any parts containing the coding sequence for HR. We found
three parts; BBaK559000, BBaK9001 and BBaK559010 and
requested them for use in our project. After isolating and
sequencing these plasmids, we found them to contain incomplete versions
of the coding sequence of Halorhodopsin from N.pharaonis.
Another problem was that the sequence of the HR in the parts contained an extra
base which was not in agreement with the coding
sequence the team who made the part reported. With this we searched for a new
source to obtain the Halorhodopsin gene from.
The next attempt was to search other organisms that
contained the HR gene. We found that one of these organisms, Halobacterium
Salinarum (HS)
was in a frozen stock close by our lab on campus. Fortunately the codon usage of the wild-type HR for H. salinarum was very similar that of C. Cresentus,
therefore codon optimization was not required.
Specific primers were then designed to amplify the HR gene out of the HS
genome. The primers contain restriction sites for ligation into our plasmids.
(see tags section)
The second pump used in this project was a newly discovered light driven sodium pump KR2, from a lab in South Korea. The organism which contains the KR2 gene, Krokinobacter Eikastus, proved quite difficult to obtain. Additionally, the codon usage for K. eikastus was very different from C. cresentus. By entering the codon usage table for C. cresentus into an excel sheet with the KR2 DNA sequence we were able to identify the rare codons in the gene.
Using this information G-blocks were designed to be (codon optimized for C. Cresentus and assembled into the PSB1C3 standard plasmid backbone. A Gibson reaction was then performed with the G-Blocks and the plasmid backbone to create our submission to the registry.
Cloning of a Newly discovered Na pumping Halorhodopsin from marine flavobacterium Krokinobacter eikastus
Sequences:
DNA Sequence KR2 Na pumping halorhodopsin-
ATGACACAAGAACTAGGGAATGCCAATTTCGAAAATTTCATTGGAGCTACAG
AAGGATTTTCTGAAATTGCTTATCAATTTACATCACATATCCTTACGTTAGGGTACGCAGTGATGCTTGCAGGATT
ACTATACTTTATCCTTACCATCAAAAATGTAGATAAAAAATTCCAAATGTCGAACATATTATCAGCTGTGGTAATG
GTATCGGCATTTTTGCTATTATATGCGCAGGCACAAAACTGGACATCCAGTTTTACCTTTAATGAAGAAGTAGGAA
GATATTTTTTAGATCCGAGTGGTGATCTATTTAATAACGGATATCGCTATCTTAACTGGCTCATCGATGTACCTAT
GCTTCTCTTTCAAATTCTATTTGTAGTAAGTTTAACTACTTCAAAATTTAGCTCTGTACGTAACCAATTCTGGTTT
TCTGGGGCAATGATGATTATTACTGGGTACATTGGACAGTTTTATGAGGTAAGTAACTTGACTGCCTTTTTAGTAT
GGGGAGCTATTTCATCTGCTTTTTTCTTCCATATTTTATGGGTTATGAAGAAGGTAATTAATGAAGGAAAAGAGGG
GATTTCCCCAGCAGGACAAAAAATACTTTCTAATATCTGGATCTTATTTTTAATATCATGGACTTTATATCCAGGA
GCTTACTTAATGCCATACCTTACTGGAGTAGACGGATTTTTATATAGTGAAGATGGCGTGATGGCTAGACAACTAG
TATACACTATTGCAGATGTAAGTTCTAAAGTTATCTATGGTGTATTATTAGGTAACCTAGCAATTACATTAAGTAA
AAACAAAGAGTTGGTTGAAGCAAATAGCTAA
Protein Sequence KR2 Na pumping halorhodopsin-
MTQELGNANFENFIGATEGFSEIAYQFTSHILTLGYAVMLAGLLYFILTIKN
VDKKFQMSNILSAVVMVSAFLLLYAQAQNWTSSFTFNEEVGRYFLDPSGDLFNNGYRYLNWLIDVPMLLFQILFVV
SLTTSKFSSVRNQFWFSGAMMIITGYIGQFYEVSNLTAFLVWGAISSAFFFHILWVMKKVINEGKEGISPAGQKIL
SNIWILFLISWTLYPGAYLMPYLTGVDGFLYSEDGVMARQLVYTIADVSSKVIYGVLLGNLAITLSKNKELVEANS*
Length: 280
Molecular weight: 31.524 kDa
Isoelectric point: 4.96
The codon
Usage table for Caulobacter crescentus-
|
Amino Acid |
Codon |
Number/ Genome |
#/1000 |
Fraction |
|
Ala |
GCG |
57020 |
46.06 |
0.334895631 |
|
Ala |
GCA |
3967 |
3.2 |
0.023299386 |
|
Ala |
GCT |
10175 |
8.22 |
0.059760839 |
|
Ala |
GCC |
99100 |
80.04 |
0.582044144 |
|
Arg |
AGG |
2701 |
2.18 |
0.029839039 |
|
Arg |
AGA |
1059 |
0.86 |
0.011699201 |
|
Arg |
CGG |
19055 |
15.39 |
0.210508291 |
|
Arg |
CGA |
4608 |
3.72 |
0.05090644 |
|
Arg |
CGT |
10018 |
8.09 |
0.110672897 |
|
Arg |
CGC |
53078 |
42.87 |
0.586374131 |
|
Asn |
AAT |
5773 |
4.66 |
0.196547733 |
|
Asn |
AAC |
23599 |
19.06 |
0.803452267 |
|
Asp |
GAT |
16529 |
13.35 |
0.231087561 |
|
Asp |
GAC |
54998 |
44.42 |
0.768912439 |
|
Cys |
TGT |
1309 |
1.06 |
0.142732526 |
|
Cys |
TGC |
7862 |
6.35 |
0.857267474 |
|
End |
TGA |
1799 |
1.45 |
0.472550565 |
|
End |
TAG |
1247 |
1.01 |
0.327554505 |
|
End |
TAA |
761 |
0.61 |
0.19989493 |
|
Gln |
CAG |
34155 |
27.59 |
0.859829318 |
|
Gln |
CAA |
5568 |
4.5 |
0.140170682 |
|
Glu |
GAG |
47647 |
38.48 |
0.713289121 |
|
Glu |
GAA |
19152 |
15.47 |
0.286710879 |
|
Gly |
GGG |
13983 |
11.29 |
0.126510929 |
|
Gly |
GGA |
5358 |
4.33 |
0.048476404 |
|
Gly |
GGT |
11281 |
9.11 |
0.102064635 |
|
Gly |
GGC |
79906 |
64.54 |
0.722948031 |
|
His |
CAT |
6487 |
5.24 |
0.293343583 |
|
His |
CAC |
15627 |
12.62 |
0.706656417 |
|
Ile |
ATA |
790 |
0.64 |
0.014615555 |
|
Ile |
ATT |
3549 |
2.87 |
0.065658995 |
|
Ile |
ATC |
49713 |
40.15 |
0.91972545 |
|
Leu |
TTG |
8478 |
6.85 |
0.068407378 |
|
Leu |
TTA |
427 |
0.34 |
0.003445382 |
|
Leu |
CTG |
84529 |
68.27 |
0.68204851 |
|
Leu |
CTA |
1742 |
1.41 |
0.014055868 |
|
Leu |
CTT |
7698 |
6.22 |
0.062113706 |
|
Leu |
CTC |
21060 |
17.01 |
0.169929156 |
|
Lys |
AAG |
40138 |
32.42 |
0.924284991 |
|
Lys |
AAA |
3288 |
2.66 |
0.075715009 |
|
Met |
ATG |
26760 |
21.61 |
1 |
|
Phe |
TTT |
5212 |
4.21 |
0.119489213 |
|
Phe |
TTC |
38407 |
31.02 |
0.880510787 |
|
Pro |
CCG |
37265 |
30.1 |
0.552000474 |
|
Pro |
CCA |
2760 |
2.23 |
0.040883438 |
|
Pro |
CCT |
4338 |
3.5 |
0.064258099 |
|
Pro |
CCC |
23146 |
18.7 |
0.342857989 |
|
Ser |
AGT |
1687 |
1.36 |
0.026704447 |
|
Ser |
AGC |
20348 |
16.44 |
0.322099631 |
|
Ser |
TCG |
26206 |
21.17 |
0.41482912 |
|
Ser |
TCA |
2127 |
1.72 |
0.033669447 |
|
Ser |
TCT |
2144 |
1.73 |
0.03393855 |
|
Ser |
TCC |
10661 |
8.61 |
0.168758805 |
|
Thr |
ACG |
20611 |
16.65 |
0.318075896 |
|
Thr |
ACA |
1775 |
1.43 |
0.027392398 |
|
Thr |
ACT |
1768 |
1.43 |
0.027284372 |
|
Thr |
ACC |
40645 |
32.83 |
0.627247334 |
|
Trp |
TGG |
17312 |
13.98 |
1 |
|
Tyr |
TAT |
11882 |
9.6 |
0.459918715 |
|
Tyr |
TAC |
13953 |
11.27 |
0.540081285 |
|
Val |
GTG |
37323 |
30.15 |
0.397755611 |
|
Val |
GTA |
1517 |
1.23 |
0.016166848 |
|
Val |
GTT |
6714 |
5.42 |
0.07155189 |
|
Val |
GTC |
48280 |
39 |
0.514525652 |
Codon optimized sequence for KR2 Na pumping halorhodopsin
ATGACGCAAGAACTGGGGAATGCCAATTTCGAAAATTTCATCGGTGCGACCG
AAGGCTTTAGCGAAATCGCCTATCAATTTACGTCGCATATCCTCACGCTGGGGTACGCGGTGATGCTCGCCGGGCT
GCTCTACTTTATCCTGACCATCAAGAATGTCGATAAGAAGTTCCAAATGTCGAACATCCTCAGCGCGGTGGTCATG
GTGTCGGCCTTTCTGCTCCTGTATGCGCAGGCGCAAAACTGGACCTCCTCGTTTACCTTTAATGAAGAAGTCGGTC
GTTATTTTCTCGATCCGAGCGGTGATCTGTTTAATAACGGCTATCGCTATCTCAACTGGCTCATCGATGTGCCCAT
GCTGCTCTTTCAAATCCTGTTTGTCGTGTCGCTCACGACCAGCAAGTTTAGCTCGGTCCGTAACCAATTCTGGTTT
AGCGGGGCCATGATGATCATCACGGGGTACATCGGGCAGTTTTATGAGGTGTCGAACCTGACCGCCTTTCTCGTCT
GGGGTGCGATCAGCTCGGCCTTTTTCTTCCATATCCTGTGGGTGATGAAGAAGGTCATCAATGAAGGCAAGGAGGG
GATCTCCCCGGCGGGGCAAAAGATCCTCAGCAATATCTGGATCCTGTTTCTCATCTCGTGGACGCTGTATCCCGGT
GCCTACCTCATGCCGTACCTGACCGGCGTGGACGGGTTTCTCTATAGCGAAGATGGCGTGATGGCGCGCCAACTGG
TCTACACGATCGCCGATGTGTCGAGCAAGGTCATCTATGGTGTGCTCCTGGGTAACCTCGCGATCACCCTGTCGAA
GAACAAGGAGCTCGTCGAAGCCAATAGCTAA
Protein Sequence for codon
optimized KR2 Na pumping halorhodopsin-
MTQELGNANFENFIGATEGFSEIAYQFTSHILTLGYAVMLAGLLYFILTIKN
VDKKFQMSNILSAVVMVSAFLLLYAQAQNWTSSFTFNEEVGRYFLDPSGDLFNNGYRYLNWLIDVPMLLFQILFVV
SLTTSKFSSVRNQFWFSGAMMIITGYIGQFYEVSNLTAFLVWGAISSAFFFHILWVMKKVINEGKEGISPAGQKIL
SNIWILFLISWTLYPGAYLMPYLTGVDGFLYSEDGVMARQLVYTIADVSSKVIYGVLLGNLAITLSKNKELVEANS*
Alignment of two protein sequences,
one wild type and one codon optimized for Caulobacter (to confirm we have the same protein)
MTQELGNANFENFIGATEGFSEIAYQFTSHILTLGYAVMLAGLLYFILTIKN
VDKKFQMSNILSAVVMVSAFLLLYAQAQNWTSSFTFNEEVGRYFLDPSGDLFNNGYRYLNWLIDVPMLLFQILFVV
SLTTSKFSSVRNQFWFSGAMMIITGYIGQFYEVSNLTAFLVWGAISSAFFFHILWVMKKVINEGKEGISPAGQKIL
SNIWILFLISWTLYPGAYLMPYLTGVDGFLYSEDGVMARQLVYTIADVSSKVIYGVLLGNLAITLSKNKELVEANS
*
MTQELGNANFENFIGATEGFSEIAYQFTSHILTLGYAVMLAGLLYFILTIKN
VDKKFQMSNILSAVVMVSAFLLLYAQAQNWTSSFTFNEEVGRYFLDPSGDLFNNGYRYLNWLIDVPMLLFQILFVV
SLTTSKFSSVRNQFWFSGAMMIITGYIGQFYEVSNLTAFLVWGAISSAFFFHILWVMKKVINEGKEGISPAGQKIL
SNIWILFLISWTLYPGAYLMPYLTGVDGFLYSEDGVMARQLVYTIADVSSKVIYGVLLGNLAITLSKNKELVEANS
*
BioBrick pSB1C3 sequence with KR2 inserted- 2913 bp.
TACTAGTAGCGGCCGCTGCAGTCCGGCAAAAAAGGGCAAGGTGTCACCACCC
TGCCCTTTTTCTTTAAAACCGAAAAGATTACTTCGCGTTATGCAGGCTTCCTCGCTCACTGACTCGCTGCGCTCGG
TCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGC
AGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCAC
AGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAA
GATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTC
CGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTT
CGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTG
AGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGT
AGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTTGGTATCTGCGCT
CTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTG
GTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGG
GTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAG
ATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGCTCGAGGC
TTGGATTCTCACCAATAAAAAACGCCCGGCGGCAACCGAGCGTTCTGAACAAATCCAGATGGAGTTCTGAGGTCAT
TACTGGATCTATCAACAGGAGTCCAAGCGAGCTCGATATCAAATTACGCCCCGCCCTGCCACTCATCGCAGTACTG
TTGTAATTCATTAAGCATTCTGCCGACATGGAAGCCATCACAAACGGCATGATGAACCTGAATCGCCAGCGGCATC
AGCACCTTGTCGCCTTGCGTATAATATTTGCCCATGGTGAAAACGGGGGCGAAGAAGTTGTCCATATTGGCCACGT
TTAAATCAAAACTGGTGAAACTCACCCAGGGATTGGCTGAGACGAAAAACATATTCTCAATAAACCCTTTAGGGAA
ATAGGCCAGGTTTTCACCGTAACACGCCACATCTTGCGAATATATGTGTAGAAACTGCCGGAAATCGTCGTGGTAT
TCACTCCAGAGCGATGAAAACGTTTCAGTTTGCTCATGGAAAACGGTGTAACAAGGGTGAACACTATCCCATATCA
CCAGCTCACCGTCTTTCATTGCCATACGAAATTCCGGATGAGCATTCATCAGGCGGGCAAGAATGTGAATAAAGGC
CGGATAAAACTTGTGCTTATTTTTCTTTACGGTCTTTAAAAAGGCCGTAATATCCAGCTGAACGGTCTGGTTATAG
GTACATTGAGCAACTGACTGAAATGCCTCAAAATGTTCTTTACGATGCCATTGGGATATATCAACGGTGGTATATC
CAGTGATTTTTTTCTCCATTTTAGCTTCCTTAGCTCCTGAAAATCTCGATAACTCAAAAAATACGCCCGGTAGTGA
TCTTATTTCATTATGGTGAAAGTTGGAACCTCTTACGTGCCCGATCAACTCGAGTGCCACCTGACGTCTAAGAAAC
CATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCAGAATTTCAGATAAAAAAAATCCTTAGCT
TTCGCTAAGGATGATTTCTGGAATTCGCGGCCGCTTCTAGAG/ATGACGCAAGAACTGGGGAATGCCAATTTCGAA
AATTTCATCGGTGCGACCGAAGGCTTTAGCGAAATCGCCTATCAATTTACGTCGCATATCCTCACGCTGGGGTACG
CGGTGATGCTCGCCGGGCTGCTCTACTTTATCCTGACCATCAAGAATGTCGATAAGAAGTTCCAAATGTCGAACAT
CCTCAGCGCGGTGGTCATGGTGTCGGCCTTTCTGCTCCTGTATGCGCAGGCGCAAAACTGGACCTCCTCGTTTACC
TTTAATGAAGAAGTCGGTCGTTATTTTCTCGATCCGAGCGGTGATCTGTTTAATAACGGCTATCGCTATCTCAACT
GGCTCATCGATGTGCCCATGCTGCTCTTTCAAATCCTGTTTGTCGTGTCGCTCACGACCAGCAAGTTTAGCTCGGT
CCGTAACCAATTCTGGTTTAGCGGGGCCATGATGATCATCACGGGGTACATCGGGCAGTTTTATGAGGTGTCGAAC
CTGACCGCCTTTCTCGTCTGGGGTGCGATCAGCTCGGCCTTTTTCTTCCATATCCTGTGGGTGATGAAGAAGGTCA
TCAATGAAGGCAAGGAGGGGATCTCCCCGGCGGGGCAAAAGATCCTCAGCAATATCTGGATCCTGTTTCTCATCTC
GTGGACGCTGTATCCCGGTGCCTACCTCATGCCGTACCTGACCGGCGTGGACGGGTTTCTCTATAGCGAAGA
TGGCGTGATGGCGCGCCAACTGGTCTACACGATCGCCGATGTGTCGAGCAAGGTCATCTATGGTGTGCTCCTGGGT
AACCTCGCGATCACCCTGTCGAAGAACAAGGAGCTCGTCGAAGCCAATAGCTAA/
