- Short genome report
- Open Access
Genome sequences of two closely related strains of Escherichia coli K-12 GM4792
Standards in Genomic Sciencesvolume 10, Article number: 125 (2015)
Escherichia coli lab strains K-12 GM4792 Lac+ and GM4792 Lac- carry opposite lactose markers, which are useful for distinguishing evolved lines as they produce different colored colonies. The two closely related strains are chosen as ancestors for our ongoing studies of experimental evolution. Here, we describe the genome sequences, annotation, and features of GM4792 Lac+ and GM4792 Lac-. GM4792 Lac+ has a 4,622,342-bp long chromosome with 4,061 protein-coding genes and 83 RNA genes. Similarly, the genome of GM4792 Lac- consists of a 4,621,656-bp chromosome containing 4,043 protein-coding genes and 74 RNA genes. Genome comparison analysis reveals that the differences between GM4792 Lac+ and GM4792 Lac- are minimal and limited to only the targeted lac region. Moreover, a previous study on competitive experimentation indicates the two strains are identical or nearly identical in survivability except for lactose utilization in a nitrogen-limited environment. Therefore, at both a genetic and a phenotypic level, GM4792 Lac+ and GM4792 Lac-, with opposite neutral markers, are ideal systems for future experimental evolution studies.
The microbial experimental evolution systems, with the ability to generate a ‘fossil’ record for later study and the design of replicate populations to test the predictability of evolution, offer a chance to ‘replay’ the evolutionary process, ‘watch’ evolution in action  and measure the fitness of evolved lines under the relevant environmental conditions . However, the lack of obvious differences in phenotypic characteristics makes microbes difficult to observe. Fortunately, some neutral genetic markers help distinguish evolved lines by differences in colony color . Typically, when a derived strain with an opposite marker relative to its progenitor is required, one can be selected using specific culture media . Subsequently, the degree of neutrality for this marker is evaluated by comparing the fitness of the two strains containing opposite markers under the culture conditions used in the study . The lactose marker is one such marker. For the lac operon, a previous study has been performed utilizing its mutations between strains with opposite lactose markers via target sequencing .
Since the publication of the K-12 genome in 1977 , Escherichia coli has been thoroughly studied with regard to its genetics [7–9], biochemistry [10–12], metabolic reconstruction , pathway inference , genomics [14–16] and metabolic . E. coli strain K-12 GM4792, a laboratory strain, contains the chromosomal lacI33::lacZ allele and is unable to utilize lactose . GM4792 was a derivative of the parent strain P90C [ara-600 del(gpt-lac)5 LAM- relA1 spoT1 thiE1] [19–21] by homogenizing a Pro+ Lac+/F' lacI33::lacZ and then curing the episome with acridine orange  (M. G. Marinus, personal communication). A previous study  resulted in two closely related strains, GM4792 Lac- and GM4792 Lac+ that carry opposite lactose markers and plasmids are knocked out for further studies on experimental evolution. Here, Lac+ refers to the ability of the strain to utilize lactose and Lac- refers to the inability to utilize lactose. These strains were chosen as ancestors for our ongoing studies of the experimental evolution of E. coli in a nitrogen-limited environment. In this study, we summarize the classification and features of E. coli GM4792 Lac+ and GM4792 Lac-, together with a description of the genome sequencing and annotation. This work provides a foundation for future variant analysis of evolved lines at the genomic scale. To compare GM4792 Lac+ and GM4792 Lac-, we used the breseq pipeline v0.20  to detect initial variants and subsequently applied a series of filters to eliminate false positives. Using this method, two significant variants were detected, including a synonymous single nucleotide polymorphism, and a 1-bp deletion responsible for lactose metabolism. A previous study on competitive experimentation  has shown that these two strains are identical or nearly identical in survivability, except for lactose utilization in a nitrogen-limited environment. Thus, both genetically and phenotypically, GM4792 Lac+ and GM4792 Lac- carry neutral markers and are appropriate for future experimental evolution studies.
Classification and features
GM4792 is a strain of E. coli K-12. It is asexual (F-), carries lacI33::lacZ allele and cannot metabolize lactose . This laboratory strain was a generous gift from M. G. Marinus (University of Massachusetts Medical School). We obtained it on October 7, 2007. Firstly, GM4792 was transferred to Luria-Bertani (LB) liquid medium for 24 h with shaking at 150 rpm. Subsequently, strains were streaked on LB solid medium. Twenty-four hours later, a single colony was transferred to LB liquid medium, with shaking for 24 h. The inoculated medium was mixed 1:1 with glycerol saline and stored in a –40 °C freezer. Thus, a monoclonal GM4792 Lac- strain was obtained. The monoclonal GM4792 Lac- colonies were grown in LB liquid medium, collected by centrifugation, and washed with the culture solution. Then, approximately 109 cells were plated on Davis minimal media  containing only lactose as the carbon source. Following a 4-day incubation period, the colonies began to utilize the lactose in the medium. One colony was selected and amplified in LB liquid medium, then stored at –40 °C. Thus, GM4792 Lac+ strain was obtained with the ability to metabolize lactose. The genome of each strain is a single circular chromosome with knockout plasmids; so, genetic variants between them could arise only from de novo mutations. Like most strains of E. coli , the cells of GM4792 are rod-shaped (Fig. 1, Additional file 1: Figure S1), Gram-negative, motile with peritrichous flagella, non-pigmented, chemo-organotrophic and facultative anaerobes. As GM4792 does not ferment sucrose or salicin, the strain belongs to E. coli “var. communis” . As previously described, GM4792 can grow at temperatures between 10 °C and 45 °C, with an optimum growth temperature of 37 °C, and pH 5.5-8.0 [25, 26]. Strain characteristics of E. coli K-12 GM4792 are shown in Table 1.
As a model organism, the molecular structure and chemical composition of the cell wall of E. coli have been thoroughly studied. This is described in detail by Scheutz and Strockbine . Similar to other strains of E. coli , GM4792 has a single peptidoglycan layer within the periplasm, consisting of D-glutamic acid, D-alanine, mesodiaminopimelic acid, N-acetyglucosamine and N-acetylmuramic acid linked to the tetrapeptide L-alanine. The cells stain Gram-negative and contain an outer membrane, with a lipopolysaccharide layer containing lipid A, the core region of the phosphorylated nonrepeating oligosaccharides and the O-antigen polymer [7, 25, 26].
Genome sequencing information
Genome project history
The two closely related E. coli lab strains K-12 GM4792 Lac+ and GM4792 Lac- were selected for genome sequencing for subsequent use in experimental evolution studies. The genomes were sequenced in the year 2012. The genome project is deposited at the Genome OnLine Database  and the NCBI BioProject database. The finished genome sequences are deposited at GenBank with the accession numbers CP011342 and CP011343. A summary of the project information is shown in Table 2.
Growth conditions and genomic DNA preparation
After receiving the laboratory strain GM4792 from M. G. Marinus, a single clone was randomly selected as a Lac- strain. A single Lac+ clone was obtained after the Lac- strain had been incubated for 4 days under selection conditions for lactose metabolism. Strains stored at –40 °C were thawed at room temperature. Each strain was streaked on LB solid medium with an inoculation needle and incubated for 24 h at 37 °C. Distinctive monoclonal colonies grew, and a single colony was selected and inoculated into 5 ml LB liquid medium and grown at 37 °C with shaking for 24 h. Total genomic DNA was extracted using the TIANamp Bacteria DNA Kit (Code:DP302, TIANGEN BIOTECH, Beijing, China), according to the manufacturer’s instructions. Additional RNaseA (Code:RT405-12, TIANGEN BIOTECH CO, Beijing, China) was added, following the manufacturer’s instruction. The quality and quantity of the genomic DNA was evaluated using agarose gel electrophoresis and the λ-Hind III digest DNA Marker (Code:D3403A, TaKaRa, China). For each sample, approximately 3 μg DNA with a concentration of 100 ng/μl was obtained.
Genome sequencing and assembly
Whole-genome sequencing was performed using the Illumina HiSeq 2000 by generating paired-end and mate-pair libraries with an average insert size of 180 bp, 380 bp, 2 kbp and 6 kbp. The length of reads for each library was 100 bp. Duplicate paired reads were filtered out from each library with FastUniq v1.1 , and reads that were contaminated by Illumina adapter were removed with the cutadapt tool . Subsequently, reads with ~370×/~330×, ~100×, ~100× and ~100× coverage from each library, respectively, were used to perform the assembly. ALLPATHS-LG Release 42411  was applied to assemble the genomes, which begins by correcting sequencing errors. The GapCloser version 1.12  program was used on the resulting scaffolds to close gaps. After that, ICORN  was used to perform corrections on the assembly. Finally, six remaining gaps were completely closed by additional PCR experiments. More details are shown in Additional file 2.
As the GM4792 strains are very closed to the strain MG1655, the annotations of GM4792 strains were firstly transferred from MG1655 using RATT . And then, de novo annotation was performed on both those regions with imperfectly transferred annotations and the insertions with respect to the stain MG1655. tRNA and rRNA were identified using tRNAscan-SE v1.3.1  and RNAmmer v1.2 , respectively. Coding sequences (CDSs) were identified using Prodigal v2.5 . CDSs were translated and analyzed using the NCBI nonredundant database, UniProt (released 2012-10) , InterPro v40 , TIGRFAMs , Pfam , and COG  databases for functional annotation. Genes with signal peptides and transmembrane helices were predicted with TMHMM v2.0  and SignalP v4.0 , respectively. Clustered regularly interspaced short palindromic repeats (CRISPR) were identified with CRT v1.2 . Transcription factors were identified based on the results of domain identification and the DBD database v2.0 . Gene ontology term assignment was performed using the GO database (released 2013-3-30)  and Blast2Go Pipeline v2.5.0 . Metabolic pathways were constructed based on the KEGG database (Release 76.0)  and KAAS . The complete sets of input parameters used for each program are shown in Table S7 of Additional file 1.
GM4792 Lac+ genome contains a 4,622,342 bp long chromosome with 50.81 % G + C content. GM4792 Lac- genome has one circular chromosome of 4,621,656 bp with a G + C content of 50.80 %. Totally 4,144 genes were predicted for GM4792 Lac+, including 4,061 protein-coding genes and 83 RNA genes (tRNA and rRNA). Similarly, GM4792 Lac- is composed of 4,117 genes (4,043 protein-coding genes and 74 RNA genes). The majority of protein-coding genes, for both GM4792 Lac+ and GM4792 Lac-, were assigned a putative function (94.64 % and 94.73 %, respectively) and the remaining genes were annotated as hypothetical proteins. The properties and statistics of the two GM4792 strains are summarized in Tables 3 and 4, and the circular maps of the chromosome are shown in Fig. 2 and Figure S3 of the Additional file 1. As GM4792 belongs to K-12 strain, all fully assembled K-12 strains were used for phylogenetic analysis. The other groups may add any further information. All completely assembled and well-annotated K-12 strains were downloaded on 10 October 2015. In order to better characterize the phylogenetic relationships for K-12 strains, Escherichia albertii KF1 was included as outgroup. Totally, 45 genomes including 44 Escherichia coli K-12 strains were analyzed (Additional file 1: Table S6). According to phylogenetic analysis based on whole-genome sequences, the two GM4792 strains cluster together and are next to E. coli RV308 with a high support value (Fig. 3), a similar pattern also supported using a concatenation of single copy protein sequences (Additional file 1: Figure S2).
Insights from the genome sequence
The paired-end reads with an insert size of 380 bp of Lac+ and the scaffolds of Lac- were analyzed using the breseq pipeline v0.20  to identify mutations based on read alignments. Six types of variants, including single-base substitution, multiple-base substitution, insertion, deletion, mobile element insertion, and sequence amplification, could be identified. All mutations containing a variant within the adjacent 20 base pairs were removed. Then, mutations that persisted when mapping the reads of Lac- to the genome of Lac- were removed. All of the retained mutations were manually reviewed using the graphical output of the mapping results. After filtering, only two significant variants were left: one 1-bp deletion in lacI and one synonymous SNP outside of the lac operon (Additional file 1: Table S1). We performed a multiple sequence alignment of the three DNA segments containing the lacI and lac operons from the MG1655, Lac- and Lac+ strains using the CLUSTALW program . We detected a 212-bp deletion, which consisted of the last 16 bp of lacI, all of the lac promoter and operator, and the first 74 bp of lacZ, in both the Lac- and Lac+ genomes compared to MG1655. In the Lac- strain, an insertion of a C at bp 961 generates a stop codon at bp 1281. Lacking the promoter and operator, the lac operon cannot be transcribed. Therefore, the Lac- strain could not utilize lactose. In Lac+, the reverse occurred: a 1-bp deletion in this region. The frameshift mutation 1-bp deletion in lacI led to the loss of the stop codon, and thus, lacI was fused to the lac operon, and consequently, the fused protein was transcribed via the lacI promoter (Additional file 1: Figure S4). Thus, GM4792 Lac+ could catabolize lactose. This transition is in agreement with previous studies [5, 18, 51]. In addition, the GM4792 strains were compared to MG1655 on the whole-genome scale with Mauve version snapshot_2015-02-25 . For GM4792 Lac+, 450 SNPs and 112 indels were identified compared to the MG1655. As to GM4792 Lac-, there were totally 441 SNPs and 109 indels compared to the MG1655. More details are shown in Additional file 1: Tables S2–S5.
Phenotypic analysis revealed that the lactose marker was neutral under the conditions used in our studies of experimental evolution of E. coli in a nitrogen-limited environment; the ratio of fitness between GM4792 Lac- and GM4792 Lac+ was 1.00 (0.994 ~ 1.036, 95 % confidence interval) . Therefore, at both the genotypic and phenotypic levels, these two strains differ only by their ability to utilize lactose, indicating that GM4792 Lac+ and GM4792 Lac- are a good system for studies of population evolution and adaption.
This study presents two closely related genomes, E. coli lab strains K-12 GM4792 Lac+ and GM4792 Lac-, which lay a solid foundation for future variant analysis of evolved lines at the genome scale in evolutionary experiments. A whole-genome comparison of GM4792 Lac+ and GM4792 Lac- reveals that the extent of genome-wide differences between GM4792 Lac+ and GM4792 Lac- are not significant and are isolated to the loci related to the utilization of lactose. Only two significant variants have been detected. One is a synonymous SNP, and the other is 1-bp deletion that is responsible for lactose utilization in GM4792 Lac+. Moreover, phenotypic analysis also showed that GM4792 Lac+ and GM4792 Lac- are nearly identical regarding survivability, except for lactose utilization, in a nitrogen-limited environment. All of the results indicate that GM4792 Lac+ and GM4792 Lac- with neutral markers are ideal systems for future experimental evolution studies.
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We thank two anonymous reviewers for their invaluable comments and suggestions. The authors gratefully acknowledge the generous help of M. G. Marinus for providing us GM4792. We also thank Hong-Tao Song for useful comments on the manuscript. This work was supported by the National Natural Science Foundation of China (Grant No. 31421063) and the State Key Laboratory of Earth Surface Processes and Resource Ecology (Grant No. 2013-ZY-10).
The authors declare that they have no competing interests.
KL and D-YZ designed and coordinated the study. Y-CZ, YZ and EP performed the bioinformatics analyses and wrote the manuscript, and KL assisted in writing the manuscript. B-WZ, B-RZ and CN performed the experiment. YH performed the electron micrograph scanning. All authors commented on the manuscript prior to submission. All authors read and approved the final manuscript.
Supplementary Tables and Figures. Table S1. Genomic differences between E. coli GM4792 Lac+ and Lac- detected via reads mapping with breseq pipeline. Table S2. Structural variations (insertions, deletions) of GM4792 Lac+ compared to MG1655 obtained with Mauve. Table S3. Structural variations (insertions, deletions) of GM4792 Lac- compared to MG1655 obtained with Mauve. Table S4. Nonsynonymous changes in protein sequence of GM4792 Lac+ compared to MG1655 obtained with Mauve. Table S5. Nonsynonymous changes in protein sequence of GM4792 Lac- compared to MG1655 obtained with Mauve. Table S6. 45 complete genomes used in this study. Table S7. The complete set of input parameters used for programs. Figure S1. Scanning-electron micrograph of strain E. coli GM4792 Lac-. Figure S2. Phylogenetic tree inferred from the supermatrix of proteome sequences under the Maximum-likelihood (ML) criterion. Figure S3. Graphical circular map of the chromosome of Escherichia coli K-12 GM4792 Lac-. Figure S4. Mutations related to lactose utilization. (PDF 4042 kb)
PCR experiment description. Table S8. The primer sequences for two GM4792 strains. Figure S5. The primer design for the large gap (~2,900 bps) in GM4792 Lac-. (PDF 124 kb)
Title of data: A document containing missing key taxonomic references. (PDF 96 kb)