Table 2 Plasmids used in this study

pUC18

Ap^R; cloning vector

Yanisch-Perron et al. [56]

pRMJ1

Source of sacB-Km^R cassette

Jones and Williams [17]

pCR2.1-TOPO

Vector for cloning PCR products; Ap^R, Km^R

ThermoFisher (Invitrogen)

pBAC890

Engineered allele: ΔbenD5472

PCR fragment with this allele was constructed by SOEing (see “Materials and methods”). This fragment was cloned into pCR2.1-TOPO

This study

pBAC1565

Engineered allele: Δgcd52089

Carries ADP1 DNA upstream and downstream of the deleted gcd in pUC18; ADP1 region corresponds to genome positions 2,909,747–2,916,396^a with a deletion of 2,911,970 to 2,914,369^a. The deleted DNA is replaced by a BamHI recognition sequence (GGATCC)

This study

pBAC1566

Engineered allele: Δgcd::sacB-Km^R52069

The sacB-Km^R cassette, excised from pRMJ1 as a BamHI fragment was inserted in the corresponding restriction site of pBAC1565

This study