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DNA Sequence of the Serratia Marcescens Lipoprotein Gene

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DNA Sequence of the Serratia Marcescens Lipoprotein Gene Proc. NatI. Acad. Sci. USA Vol. 77, No. 3, pp. 1369-1373, March 1980 Biochemistry DNA sequence of the Serratia marcescens lipoprotein gene (promoter/A-T base pairs/secretion/signal peptide/loop model/gene evolution) KENZO NAKAMURA AND MASAYORI INOUYE Department of Biochemistry, State University of New York, Stony Brook, New York 11794 Communicated by Charles Yanofsky, December 12, 1979 ABSTRACT The Serratia marcescens gene for the outer gene of S. marcescens with that of E. coli revealed several in- membrane lipoprotein (lpp) was cloned in A phage vector teresting and unique features concerning the mechanism of Charon 14. The recombinant phage was very unstable, and the expression of this gene, the secretion of the lipoprotein across Ipp gene with a 300-base-pair deletion at the transcription ter- mination site was further cloned in pBR322. The DNA sequence the cytoplasmic membrane, and the evolution of the gene. of 834 base pairs encompassing the Ipp gene was determined and compared with that of the Escherichia coli ipp gene. The MATERIALS AND METHODS sequence comparisons exhibit several unique features. (i) The Materials. [y-32P]ATP (m9000 Ci/mmol; 1 Ci = 3.7 X 101O promoter region is highly conserved (84% homology) and has becquerels), prepared by the method of Johnson and Walseth an extremely high A+T content (78%) as in E. coli (80%). (ii) (8) from carrier-free The 5' nontranslated region of the lipoprotein mRNA is also [32P]orthophosphate (New England Nu- highly conserved (95% homology). (iii) In the DNA sequence clear) and ADP (Sigma), was used for 5'-end-labeling of DNA corresponding to the signal peptide of this secretory protein, fragments. Tac I and Alu I were obtained from Bethesda Re- there are three drastic changes, including addition of one base search (Rockville, MD); other restriction enzymes were from pair and deletion of four base pairs in S. marcescens as com- New England BioLabs. Nitrocellulose filters (BA85) were ob- pared to E. coli. The resultant alterations in the amino acid se- tained from Schleicher & Schuell. quence, however, do not change the basic properties of the Bacteria and Phage. S. marcescens (5), E. coli man signal peptide, which are assumed to be essential for its function JE5527 in the secretory mechanism. (iv) The DNA sequence from the 1pp-2 pps thi his rpsL gyrL recAl (9), E. coli K802 hsr- hsm + amino terminus to the 51st residue of the mature lipoprotein is galK sull lacY met, and A phage vector Charon 14 (ref. 10; highly conserved (95% homology) and there is no amino acid obtained from F. R. Blattner) were used. substitution. (v) The DNA sequence corresponding to the seven Construction of XlppSm-1. An 8.5-kilobase (kb) EcoRI amino acid residues at the carboxyl terminus has only 42% fragment of S. marcescens chromosomal DNA carrying the lpp homology, resulting in four amino acid substitutions. (v) Within gene (5) was cloned into Charon 14 vector phage by the method the section of 40 base pairs beginning with the termination used for the codon (UAA) and ending immediately before the oligo(T) tran- cloning of the E. coli lpp gene (4). High-titer lysates scription termination site in the E. coli Ipp gene, there is about were prepared by the plate lysate technique (ref. 10; E. coli 60% homology. However, after this section, there is no obvious K802 as host) with plaques that consistently gave positive hy- homology between the two sequences, probably because of a bridization with 5'-32P-labeled E. coli lipoprotein mRNA after deletion of 300 base pairs at this region. (vii) Seven stable plaque purification. Purification of X DNA from the plate lysate stem-and-loop structures could be formed in the mRNA region. has been described (4). (viii) Alterations in the third position of codons used in the Ipp Construction of pKEN221. gene suggest that the gene has evolved somewhat differently XlppSm-1 DNA (2.5 ,ug) and from other genes in S. marcescens. pBR322 DNA (1 ,g) were double-digested with EcoRI and BamHI and treated with 0.3 unit of T4 DNA ligase (Miles) in The outer membrane lipoprotein is the most abundant protein 75 ,l of 66 mM Tris-HCI, pH 7.5/10 mM MgCl2/10 mM di- in Escherichia coli and is one of the most extensively investi- thiothreitol/0.4 mM ATP at 12.5°C for 8 hr. E. coli JE5527 cells gated membrane proteins (for reviews, see refs. 1 and 2). The were transformed as described (11). Ampicillin-resistant, tet- complete nucleotide sequence of the lipoprotein mRNA (3) and racycline-sensitive transformants were grown on Whatman the DNA sequence of the lipoprotein gene of E. coli (4) have 3MM filter papers and screened for lpp clones by colony hy- been determined. A study of these sequences revealed many bridization (12). The 0.95-kb Msp I fragment of AlppEc-1 unique features concerning the expression of this gene. E. coli carrying the E. coli lpp gene (4) was nick-translated with [a- lipoprotein mRNA hybridizes with restriction enzyme frag- 32P]dATP and [a-32P]dCTP as described (13) and used as a 32p ments of chromosomal DNAs from nine different enterobac- probe. Hybridization conditions were the same as described for teria (5). Among these bacteria, Serratia marcescens is one of plaque hybridization (4). About 60% of the ampicillin-resistant those most distantly related to E. coli (5). S. marcescens DNA transformants were tetracycline sensitive, and 23% of them (31 has an A+T content of 42%, in contrast to 49% in E. coli DNA out of 135 colones examined) gave positive hybridization. (6). Furthermore, DNA-DNA hybridization experiments show DNA Sequence Determination. The sequence was deter- only 24% homology between the DNA of S. marcescens and mined by the method of Maxam and Gilbert (14). The cleaved E. coli (7). products were separated by the thin sequencing gel system (0.04 In this report, we describe the cloning and DNA sequence X 20 X 40 cm) with 20%, 10%, or 8% polyacrylamide in 7 M determination of the S. marcescens lipoprotein gene. E. coli urea. cells carrying this clone produced a large amount of S. mar- Other Procedures. Methods for the isolation of total DNA cescens lipoprotein. This foreign protein is apparently assem- or plasmid DNA, agarose gel electrophoresis, and Southern blot bled normally in the E. coli outer membrane (unpublished hybridization were as described (5). When 32P-labeled DNA data). A comparison of the DNA sequence of the lipoprotein fragments were used as hybridization probes, the hybridization medium contained 0.60 M NaCl/0.06 M sodium citrate instead The publication costs of this article were defrayed in part by page of 0.75 M NaCl/0.075 M sodium citrate and was heated at 90°C charge payment. This article must therefore be hereby marked "ad- for 3 min before hybridization. vertisement" in accordance with 18 U. S. C. §1734 solely to indicate this fact. Abbreviations: kb, kilobase; bp, base pairs. 1369 Downloaded by guest on September 29, 2021 1370 Biochemistry: Nakamura and Inouye Proc. Natl. Acad. Sci. USA 77 (1980) RESULTS on S. marcescens chromosomal DNA by Southern blot hy- Cloning of the S. marcescens Lipoprotein Gene. We pre- bridization with 5'-32P-labeled E. coli lipoprotein mRNA (data viously showed that 32P-labeled E. coli lipoprotein mRNA not shown). hybridizes with an 8.5-kb EcoRI fragment of S. marcescens Instability of the lpp Gene in XlppSm-1. The XlppSm-1 DNA (5). The 8.5-kb EcoRI fragment carrying the lpp gene was phage was propagated on solid medium. DNA isolated from cloned in X phage vector, Charon 14. Phage DNA was isolated these phages contained a 7.3-kb EcoRI fragment as a minor from a plaque that consistently gave positive hybridization with component (about one-fourth of the amount of the 8.3-kb 5'-32P-labeled lipoprotein mRNA after a two-step plaque pu- fragment), which also hybridized with 5'-32P-labeled E. coli rification. Upon digestion with EcoRI, this phage DNA gave lipoprotein mRNA (data not shown). This fragment appears three major bands of 20, 13.2, and 8.3 kb. The first two frag- to be generated by a deletion within the cloned fragment during ments were identical with the left and the right arm of Charon phage growth. Furthermore, none of the DNA prepared from 14 vector DNA, respectively (ref. 10; Fig. 1A). The 8.3-kb phages grown in liquid culture hybridized with the E. coli li- fragment, although somewhat shorter than the 8.5-kb chro- poprotein mRNA. These results indicate that the hybrid phage mosomal fragment, showed positive hybridization with 5'- carrying the Ipp gene is very unstable, readily losing a part of 32P-labeled E. coli lipoprotein mRNA by the Southern blotting or the whole Ipp gene during phage growth. technique (data not shown). This phage is designated XIppSm-1, and the restriction enzyme cleavage map of its DNA is shown Subcloning of the lpp Gene into pBR322. Using XlppSm-1 in Fig. 1A. Restriction enzyme cleavage sites within the cloned DNA, we subcloned the 4.2-kb EcoRI/BamHI fragment into 8.3-kb EcoRI fragment (Fig. 1A) agreed with those determined plasmid pBR322. One of the transformants isolated produced a large amount of the S. marcescens lipoprotein which was A assembled normally in the E. coli outer membrane (unpub- Choron 14 b1007 KH54 nin lished data). This clone was designated pKEN221 (Fig. 1B). O~77SR 80 Upon restriction enzyme analysis, we found that pKEN221 X /pp Sm-1 t ,~I I~ I I contained a 1.05-kb Hae III fragment that hybridized with the ° E- E L a W>sD 0 m0uD o co E.
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