Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli - PubMed (original) (raw)
Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli
Ludovic Pelosi et al. Genetics. 2006 Aug.
Abstract
Twelve populations of Escherichia coli evolved in and adapted to a glucose-limited environment from a common ancestor. We used two-dimensional protein electrophoresis to compare two evolved clones, isolated from independently derived populations after 20,000 generations. Exceptional parallelism was detected. We compared the observed changes in protein expression profiles with previously characterized global transcription profiles of the same clones; this is the first time such a comparison has been made in an evolutionary context where these changes are often quite subtle. The two methodologies exhibited some remarkable similarities that highlighted two different levels of parallel regulatory changes that were beneficial during the evolution experiment. First, at the higher level, both methods revealed extensive parallel changes in the same global regulatory network, reflecting the involvement of beneficial mutations in genes that control the ppGpp regulon. Second, both methods detected expression changes of identical gene sets that reflected parallel changes at a lower level of gene regulation. The protein profiles led to the discovery of beneficial mutations affecting the malT gene, with strong genetic parallelism across independently evolved populations. Functional and evolutionary analyses of these mutations revealed parallel phenotypic decreases in the maltose regulon expression and a high level of polymorphism at this locus in the evolved populations.
Figures
Figure 1.—
Two-dimensional protein gel electrophoresis of the ancestor and an evolved clone. Protein extracts were prepared from cultures grown in DM250 medium for 24 hr at 37°. Laboratory-made dry strips (18 cm, pH range from 4 to 8) were hydrated in 500-μg protein samples from the ancestral strain (A) and from an evolved clone isolated at generation 20,000 from population Ara + 1 (B). The steady-state isoelectrofocalization patterns were analyzed by 12% acrylamide-bis SDS–PAGE and Coomassie blue staining. Protein spots numbered M1 and M2 did not show any variation among the three genotypes analyzed but are shown as internal standards (□) (see Table 1). (○) Protein spots modified in both evolved clones. Spots decreasing or disappearing in both evolved clones are marked on the ancestral protein pattern (A); spots increasing or appearing in both evolved clones are marked on the evolved protein pattern (B). (▵) Protein spots modified only in the Ara + 1 evolved clone. (▿) Protein spots showing decreased intensity only in the Ara − 1 evolved clone. The insets show enlarged parts of each gel with the maltoporin LamB and the maltose-binding protein MalE (open arrowheads). Mw, molecular weight; pI, isoelectric point.
Figure 2.—
Schematic structure of the MalT protein and location of evolved mutant alleles. The protein is composed of four domains (D
anot
2001; R
ichet
et al. 2005): DT1 (residues 1–241), DT2 (residues 250–436), DT3 (residues 437–806), and DT4 (residues 807–901). DT1 binds ATP and contains surface determinants involved in the binding of repressor proteins, including Aes, MalK, and MalY. DT2 and DT3 are involved in maltotriose binding and represent putative multimerization domains. DT4 corresponds to the DNA-binding domain and presumably recruits RNA polymerase. The malT gene was sequenced in one clone isolated at 20,000 generations from each of the 12 populations designated Ara − 1–Ara − 6 and Ara + 1–Ara + 6. Amino-acid substitutions deduced from the mutations identified in the evolved clones are indicated using the one-letter code, and the residue number refers to its position in the MalT polypeptide. In both the Ara + 1 and Ara + 2 populations, small internal deletions were found in malT (their size and position relative to the malT translational start codon are shown).
Figure 3.—
Phenotypic tests of MalT activity. The ancestral strain is labeled 606. One evolved clone was isolated at 20,000 generations from each of the 12 populations designated Ara − 1–Ara-6 and Ara + 1–Ara + 6. A malT_-deleted strain (Δ_malT) served as a control. (A) Growth ability in DM250 maltose at 37°. +, Growth after 8 hr; −, no growth even after 24 hr. (B) Relative level of LamB protein. Cellular extracts were prepared from all strains after overnight culture in DM250 medium. Each sample contained 20 μg of total protein and was subjected to 12% SDS–PAGE and immunoblot analysis with polyclonal antibodies against LamB (anti-LamB) or RpoA (anti-RpoA) as a control. (C) The number of mutations identified in malT in each population is indicated. Δ, deletion allele; Anc, ancestral state.
Figure 4.—
Fitness effects of two evolved malT mutations and a mutation with upregulated expression of malT, all moved into the ancestral genetic background. Competitions were performed in the same medium used in the long-term evolution experiment. Error bars are 95% confidence intervals based on six replicate competition assays for each genotype. From left to right, the four genotypes are as follows: 606 is the ancestral strain with the ancestral malT allele; malTAra+1 and malTAra−1 are alleles that evolved in the focal populations Ara + 1 and Ara − 1, respectively, which were then moved into the ancestral chromosome; and malTup is an upregulated allele also moved into the ancestral chromosome.
Similar articles
- The landscape of transcriptional and translational changes over 22 years of bacterial adaptation.
Favate JS, Liang S, Cope AL, Yadavalli SS, Shah P. Favate JS, et al. Elife. 2022 Oct 10;11:e81979. doi: 10.7554/eLife.81979. Elife. 2022. PMID: 36214449 Free PMC article. - Expression profiles reveal parallel evolution of epistatic interactions involving the CRP regulon in Escherichia coli.
Cooper TF, Remold SK, Lenski RE, Schneider D. Cooper TF, et al. PLoS Genet. 2008 Feb;4(2):e35. doi: 10.1371/journal.pgen.0040035. PLoS Genet. 2008. PMID: 18282111 Free PMC article. - Adaptive laboratory evolution of Escherichia coli under acid stress.
Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Gao Y, Hefner Y, Feist AM, Palsson BO. Du B, et al. Microbiology (Reading). 2020 Feb;166(2):141-148. doi: 10.1099/mic.0.000867. Epub 2019 Oct 18. Microbiology (Reading). 2020. PMID: 31625833 Free PMC article. - Evolution of global regulatory networks during a long-term experiment with Escherichia coli.
Philippe N, Crozat E, Lenski RE, Schneider D. Philippe N, et al. Bioessays. 2007 Sep;29(9):846-60. doi: 10.1002/bies.20629. Bioessays. 2007. PMID: 17691099 Review. - Evolution of competitive fitness in experimental populations of E. coli: what makes one genotype a better competitor than another?
Lenski RE, Mongold JA, Sniegowski PD, Travisano M, Vasi F, Gerrish PJ, Schmidt TM. Lenski RE, et al. Antonie Van Leeuwenhoek. 1998 Jan;73(1):35-47. doi: 10.1023/a:1000675521611. Antonie Van Leeuwenhoek. 1998. PMID: 9602277 Review.
Cited by
- Proteome partitioning constraints in long-term laboratory evolution.
Mori M, Patsalo V, Euler C, Williamson JR, Scott M. Mori M, et al. Nat Commun. 2024 May 14;15(1):4087. doi: 10.1038/s41467-024-48447-2. Nat Commun. 2024. PMID: 38744842 Free PMC article. - Linking genotypic and phenotypic changes in the E. coli long-term evolution experiment using metabolomics.
Favate JS, Skalenko KS, Chiles E, Su X, Yadavalli SS, Shah P. Favate JS, et al. Elife. 2023 Nov 22;12:RP87039. doi: 10.7554/eLife.87039. Elife. 2023. PMID: 37991493 Free PMC article. - Evolution of a cross-feeding interaction following a key innovation in a long-term evolution experiment with Escherichia coli.
Turner CB, Blount ZD, Mitchell DH, Lenski RE. Turner CB, et al. Microbiology (Reading). 2023 Aug;169(8):001390. doi: 10.1099/mic.0.001390. Microbiology (Reading). 2023. PMID: 37650867 Free PMC article. - The landscape of transcriptional and translational changes over 22 years of bacterial adaptation.
Favate JS, Liang S, Cope AL, Yadavalli SS, Shah P. Favate JS, et al. Elife. 2022 Oct 10;11:e81979. doi: 10.7554/eLife.81979. Elife. 2022. PMID: 36214449 Free PMC article. - Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria.
Ali F, Seshasayee ASN. Ali F, et al. Nucleic Acids Res. 2020 May 7;48(8):4100-4114. doi: 10.1093/nar/gkaa162. Nucleic Acids Res. 2020. PMID: 32182360 Free PMC article.
References
- Boos, W., and A. Böhm, 2000. Learning new tricks from an old dog: MalT of the Escherichia coli maltose system is part of a complex regulatory network. Trends Genet. 16: 404–409. - PubMed
- Cashel, M., V. J. Gentry, V. J. Hernandez and D. Vinella, 1996. The stringent response, pp. 1458–1496 in Escherichia coli and Salmonella: Cellular and Molecular Biology, edited by F. C. Neidhardt. American Society of Microbiology, Washington, DC.
- Colosimo, P. F., K. E. Hosemann, S. Balabhadra, G. Villarreal, Jr., M. Dickson et al., 2005. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307: 1928–1933. - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources