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Table 1 Bacterial strains and plasmids used in this studya

From: The outer membrane protein Omp35 affects the reduction of Fe(III), nitrate, and fumarate by Shewanella oneidensis MR-1

Bacterial strain or plasmid Description Reference, Source
S. oneidensis strains   
MR-1 Manganese-reducing strain from Lake Oneida, N.Y. sediments [1]
OMP35-1 omp35 mutant derived from MR-1; omp35::Kmr This work
OMCA-1 omcA mutant derived from MR-1; omcA::Kmr [8]
OMCB-1 omcB mutant derived from MR-1; omcB::Kmr [8]
ETRA-153 etrA mutant derived from MR-1; etrA::Kmr [17]
CMA-1 menaquinone-minus mutant derived from MR-1 [6]
E. coli strains   
JM109 recA1 F' traD36 lacIqΔ(lacZ)M15 proA+B+/ e14-(McrA-) Δ(lac-proAB) thi gyrA96 (Nalr) endA1 hsdR17 (rK- mK+) relA1 supE44 [61]
S17-1λpir λ(pir) hsdR pro thi; chromosomally integrated RP4-2 Tc::Mu Km::Tn7; donor strain to mate pEP185.2-derived plasmids into MR-1 [62]
S17-1 C600::RP-4 2-Tc::Mu-Km::Tn7 hsdR hsdM recA thi pro; donor strain to mate pVK100- derived plasmids into MR-1 [62]
TOP10 F- mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZ ΔM15ΔlacX74 deoR recA1 araD139 Δ(ara-leu)7697 galU galK rpsL (Smr) endA1nupG; used as host for plasmids derived from pCR2.1-TOPO Invitrogen
pBCSK 3.4-kb vector; pUC ori; Cmr; used for complementation Stratagene
pBComp218F & R pBCSK with the MR-1 omp35 open reading frame plus associated 5' and 3' regions; 218 bp upstream sequence in the forward (F) and reverse (R) orientation This work
pBComp411F & R pBCSK with the MR-1 omp35 open reading frame plus associated 5' and 3' regions; 411 bp upstream sequence in F and R orientation This work
pCR2.1-TOPO 3.9-kb vector for cloning PCR products; Kmr Apr Invitrogen
pUT/mini-Tn5Km Apr; Tn5-based delivery plasmid; used as source of Kmrgene [63]
pTOPO/omp35 pCR2.1-TOPO with the MR-1 omp35 open reading frame plus associated 5' and 3' regions; 5.6 kb This work
pTOPO/omp35:Km pTOPO/omp35 with the Kmr gene replacing bases 458–850 of omp35; 7.3 kb This work
pEP185.2 4.28-kb mobilizable suicide vector derived from pEP184; oriR6K mobRP4 Cmr [64]
pDSEPomp35 Kmr-interrupted omp35 gene cloned into the Xho I site of pEP185.2; Cmr Kmr; 7.7 kb; used for gene replacement to generate strain OMP35-1 This work
  1. aNalr, Smr, Kmr, Apr, Tcr, and Cmr, resistance to nalidixic acid, streptomycin, kanamycin, ampicillin, tetracycline, and chloramphenicol, respectively. bThe vector pBCSK freely replicates in MR-1 while pEP185.2 does not.