title: Transcription, translation, and the evolution of specialists and generalists.
abstract: We used DNA microarrays to measure transcription and iTRAQ 2D liquid chromatography-mass spectrometry/mass spectrometry (a mass-tag labeling proteomic technique) to measure protein expression in 14 strains of Escherichia coli adapted for hundreds of generations to growth-limiting concentrations of either lactulose, methylgalactoside, or a 72:28 mixture of the two. The two ancestors, TD2 and TD10, differ only in their lac operons and have similar transcription and protein expression profiles. Changes in transcription and protein expression are observed at 30-250 genes depending on the evolved strain. Lactulose specialists carry duplications of the lac operon and show increased transcription and translation at lac. Methylgalactoside specialists are galS(-) and so constitutively transcribe and translate mgl, which encodes a transporter of methylgalactoside. However, there are two strains that carry lac duplications, are galS(-), and show increased transcription and translation at both operons. One is a generalist, the other a lactulose specialist. The generalist fails to sweep to fixation because its lac(+), galS(+) competitor expresses the csg adhesin and sticks to the chemostat wall, thereby preventing complete washout. Transcription and translation are sometimes decoupled. Lactulose-adapted strains show increased protein expression at fru, a fructose transporter, without evidence of increased transcription. This suggests that fructose, produced by the action of beta-galactosidase on lactulose, may leach from cells before being recouped. Reduced expression, at "late" flagella genes and the constitutive gat operon, is an adaptation to starvation. A comparison with two other long-term evolution experiments suggests that certain aspects of adaptation are predictable, some are characteristic of an experimental system, whereas others seem erratic.
authors.affiliation: Department of Plant Pathology, North Dakota State University, North Dakota, USA.
authors.forename: Shaobin
authors.initials: S
authors.lastname: Zhong
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Miller
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Dykhuizen
authors.forename: Antony M
authors.initials: AM
authors.lastname: Dean
mesh_terms: D000595:Amino Acid Sequence; D000704:Analysis of Variance; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D005075:Biological Evolution; D016000:Cluster Analysis; D004926:Escherichia coli / Q000145:classification* / Q000187:drug effects / Q000235:genetics*; D018628:Gene Dosage / Q000187:drug effects; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D005798:Genes, Bacterial / Q000235:genetics; D007553:Isotope Labeling; D007792:Lactulose / Q000494:pharmacology; D008756:Methylgalactosides / Q000494:pharmacology; D008969:Molecular Sequence Data; D009068:Movement / Q000187:drug effects; D009876:Operon / Q000235:genetics; D010455:Peptides / Q000737:chemistry; D010802:Phylogeny; D014176:Protein Biosynthesis / Q000187:drug effects / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D014158:Transcription, Genetic / Q000187:drug effects; D001616:beta-Galactosidase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D008756:Methylgalactosides; D010455:Peptides; D012333:RNA, Messenger; D007792:Lactulose; D001616:beta-Galactosidase
references.citation: Nat Rev Genet. 2003 Jun;4(6):457-69
references.pmid: 12776215
references.citation: J Bacteriol. 2001 May;183(9):2834-41
references.pmid: 11292803
references.citation: PLoS Genet. 2008 Aug 22;4(8):e1000163
references.pmid: 18725932
references.citation: Environ Microbiol. 1999 Feb;1(1):45-52
references.pmid: 11207717
references.citation: Mol Microbiol. 2005 Jul;57(1):1-8
references.pmid: 15948944
references.citation: Mol Ecol. 2008 Apr;17(7):1850-70
references.pmid: 18312278
references.citation: Proc Natl Acad Sci U S A. 2003 Feb 4;100(3):1072-7
references.pmid: 12538876
references.citation: Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8649-54
references.pmid: 17494741
references.citation: Genetics. 1989 Sep;123(1):19-28
references.pmid: 2680755
references.citation: Genetics. 1963 Feb;48:157-69
references.pmid: 13954911
references.citation: Physiol Biochem Zool. 2005 May-Jun;78(3):299-315
references.pmid: 15887077
references.citation: Proc Natl Acad Sci U S A. 1999 Aug 17;96(17):9721-6
references.pmid: 10449761
references.citation: Microbiology (Reading). 2008 Sep;154(Pt 9):2887-2895
references.pmid: 18757823
references.citation: Genetics. 2008 Feb;178(2):1049-60
references.pmid: 18245349
references.citation: J Biol Chem. 2003 Nov 21;278(47):46446-51
references.pmid: 12963713
references.citation: Cold Spring Harb Symp Quant Biol. 1961;26:239-45
references.pmid: 14480575
references.citation: Biochim Biophys Acta. 1962 Jan 22;55:152-63
references.pmid: 14448925
references.citation: Mol Microbiol. 1995 Nov;18(4):661-70
references.pmid: 8817489
references.citation: Mol Biol Evol. 2008 Jan;25(1):101-10
references.pmid: 17998255
references.citation: Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12170-5
references.pmid: 11027315
references.citation: Genetics. 1989 Nov;123(3):441-54
references.pmid: 2513251
references.citation: Evolution. 1993 Feb;47(1):1-12
references.pmid: 28568084
references.citation: Nature. 2000 Oct 12;407(6805):736-9
references.pmid: 11048718
references.citation: Nature. 1998 Jul 2;394(6688):69-72
references.pmid: 9665128
references.citation: Proc Natl Acad Sci U S A. 2004 Aug 10;101(32):11719-24
references.pmid: 15289609
references.citation: Genetics. 1995 Jan;139(1):19-33
references.pmid: 7705623
references.citation: J Bacteriol. 1994 Aug;176(16):5101-7
references.pmid: 8051023
references.citation: Genome Biol. 2003;4(9):117
references.pmid: 12952525
references.citation: Mol Cell Proteomics. 2004 Dec;3(12):1154-69
references.pmid: 15385600
references.citation: Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8
references.pmid: 9843981
references.citation: Mol Cell Proteomics. 2002 Apr;1(4):323-33
references.pmid: 12096114
references.citation: Adv Microb Physiol. 2008;53:169-229
references.pmid: 17707145
references.citation: Genetics. 2004 Aug;167(4):2015-26
references.pmid: 15342537
references.citation: Crit Rev Biochem Mol Biol. 2005 Mar-Apr;40(2):93-113
references.pmid: 15814430
references.citation: Mol Biol Evol. 1998 Jul;15(7):789-97
references.pmid: 9656481
references.citation: Mol Microbiol. 1996 May;20(3):467-73
references.pmid: 8736526
references.citation: Proteomics. 2005 Oct;5(15):4012-24
references.pmid: 16130168
references.citation: Microbiol Rev. 1985 Sep;49(3):270-97
references.pmid: 3930934
references.citation: Methods Mol Biol. 2003;224:61-78
references.pmid: 12710666
references.citation: Genetics. 2008 Mar;178(3):1653-60
references.pmid: 18245823
references.citation: Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):17004-9
references.pmid: 17942681
references.citation: Nucleic Acids Res. 2006 Jan 05;34(1):1-9
references.pmid: 16397293
references.citation: Genetics. 1991 May;128(1):23-7
references.pmid: 1829427
references.citation: Genetics. 1994 Aug;137(4):903-17
references.pmid: 7982572
references.citation: RNA. 2008 Sep;14(9):1907-17
references.pmid: 18658123
references.citation: Annu Rev Genet. 1992;26:131-58
references.pmid: 1482109
references.citation: PLoS One. 2008 Jun 11;3(6):e2397
references.pmid: 18545680
references.citation: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9232-7
references.pmid: 12878731
references.citation: Microbiology (Reading). 2005 Jul;151(Pt 7):2487-2497
references.pmid: 16000739
references.citation: Heredity (Edinb). 2008 May;100(5):471-7
references.pmid: 18449959
references.citation: Genetics. 2002 Sep;162(1):485-99
references.pmid: 12242256
references.citation: Nature. 2006 Mar 9;440(7081):242-5
references.pmid: 16525476
references.citation: Trends Microbiol. 2003 Oct;11(10):457-61
references.pmid: 14557028
references.citation: J Exp Bot. 2006;57(7):1501-8
references.pmid: 16574745
references.citation: Proc Biol Sci. 2003 Aug 7;270(1524):1645-50
references.pmid: 12908987
references.citation: Genome Biol. 2008 Apr 10;9(4):R72
references.pmid: 18402659