title: Genome dynamics of short oligonucleotides: the example of bacterial DNA uptake enhancing sequences.
abstract: Among the many bacteria naturally competent for transformation by DNA uptake-a phenomenon with significant clinical and financial implications- Pasteurellaceae and Neisseriaceae species preferentially take up DNA containing specific short sequences. The genomic overrepresentation of these DNA uptake enhancing sequences (DUES) causes preferential uptake of conspecific DNA, but the function(s) behind this overrepresentation and its evolution are still a matter for discovery. Here I analyze DUES genome dynamics and evolution and test the validity of the results to other selectively constrained oligonucleotides. I use statistical methods and computer simulations to examine DUESs accumulation in Haemophilus influenzae and Neisseria gonorrhoeae genomes. I analyze DUESs sequence and nucleotide frequencies, as well as those of all their mismatched forms, and prove the dependence of DUESs genomic overrepresentation on their preferential uptake by quantifying and correlating both characteristics. I then argue that mutation, uptake bias, and weak selection against DUESs in less constrained parts of the genome combined are sufficient enough to cause DUESs accumulation in susceptible parts of the genome with no need for other DUES function. The distribution of overrepresentation values across sequences with different mismatch loads compared to the DUES suggests a gradual yet not linear molecular drive of DNA sequences depending on their similarity to the DUES. Other genomically overrepresented sequences, both pro- and eukaryotic, show similar distribution of frequencies suggesting that the molecular drive reported above applies to other frequent oligonucleotides. Rare oligonucleotides, however, seem to be gradually drawn to genomic underrepresentation, thus, suggesting a molecular drag. To my knowledge this work provides the first clear evidence of the gradual evolution of selectively constrained oligonucleotides, including repeated, palindromic and protein/transcription factor-binding DNAs.
authors: Institute of Genetics, Queen's Medical Center, University of Nottingham, Nottingham, United Kingdom. mbakkali@gmail.com
authors: Mohammed
authors: M
authors: Bakkali
mesh_terms: D001483:Base Sequence; D003198:Computer Simulation; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D006193:Haemophilus influenzae / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009344:Neisseria gonorrhoeae / Q000235:genetics* / Q000378:metabolism; D009841:Oligonucleotides / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D009841:Oligonucleotides
references: Proc Natl Acad Sci U S A. 1992 Feb 15;89(4):1358-62
references: 1741388
references: Nucleic Acids Res. 1992 Mar 25;20(6):1363-70
references: 1313968
references: J Hered. 1993 Sep-Oct;84(5):400-4
references: 8409360
references: Infect Immun. 1994 Nov;62(11):4922-8
references: 7927773
references: Microbiol Rev. 1994 Sep;58(3):563-602
references: 7968924
references: Nature. 1995 Jan 26;373(6512):357-9
references: 7830772
references: Nucleic Acids Res. 1995 Mar 11;23(5):729-35
references: 7708486
references: Science. 1995 Jul 28;269(5223):538-40
references: 7542802
references: Mol Gen Genet. 1984;193(2):358-63
references: 6607396
references: J Bacteriol. 1984 Mar;157(3):785-8
references: 6365892
references: Proc Natl Acad Sci U S A. 1988 Sep;85(18):6982-6
references: 3137581
references: J Bacteriol. 1990 Oct;172(10):5924-8
references: 2170331
references: Nucleic Acids Res. 1990 Oct 25;18(20):6097-100
references: 2172928
references: EMBO J. 1991 Feb;10(2):477-88
references: 1671354
references: J Bacteriol. 1991 Jun;173(12):3911-3
references: 1904861
references: Nature. 1991 Jul 4;352(6330):25-6
references: 2062373
references: Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):7986-90
references: 7644525
references: Mol Microbiol. 1994 Aug;13(4):673-84
references: 7997179
references: Proc Natl Acad Sci U S A. 1996 Oct 15;93(21):11913-8
references: 8876237
references: Microbiology. 1996 Oct;142 ( Pt 10):2839-45
references: 8885400
references: Trends Genet. 1996 Apr;12(4):150-5
references: 8901420
references: Nucleic Acids Res. 1996 Nov 1;24(21):4263-72
references: 8932382
references: J Bacteriol. 1997 Jun;179(12):3899-913
references: 9190805
references: Proc Natl Acad Sci U S A. 1997 Jun 24;94(13):6706-11
references: 9192629
references: J Bacteriol. 1997 Jul;179(13):4227-31
references: 9209037
references: Infect Immun. 1997 Aug;65(8):2997-3002
references: 9234745
references: Rev Biol Trop. 1997 Jun;45(2):753-71
references: 9458988
references: Trends Biochem Sci. 1998 Mar;23(3):109-13
references: 9581503
references: J Bacteriol. 1998 Aug;180(16):4116-22
references: 9696758
references: Annu Rev Genet. 1998;32:185-225
references: 9928479
references: J Gen Physiol. 1961 Jul;44:1201-27
references: 13707010
references: Genome Biol. 2005;6(2):R18
references: 15693947
references: Vet Microbiol. 2005 Feb 25;105(3-4):223-8
references: 15708819
references: BMC Biol. 2005;3:6
references: 15752428
references: Artif Life. 2005 Summer;11(3):317-38
references: 16053573
references: Science. 2005 Dec 2;310(5753):1456-60
references: 16322448
references: J Theor Biol. 2006 Jan 7;238(1):157-66
references: 16023142
references: J Bacteriol. 2006 Jun;188(11):3902-10
references: 16707682
references: Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W124-7
references: 16844974
references: J Bacteriol. 2006 Oct;188(20):7257-66
references: 17015664
references: Philos Trans R Soc Lond B Biol Sci. 2006 Nov 29;361(1475):1929-40
references: 17062412
references: BMC Evol Biol. 2006;6:82
references: 17038178
references: Microbiology. 2006 Nov;152(Pt 11):3319-25
references: 17074902
references: Annu Rev Microbiol. 1999;53:217-44
references: 10547691
references: Res Microbiol. 1999 Nov-Dec;150(9-10):603-16
references: 10673000
references: Science. 2000 Mar 10;287(5459):1809-15
references: 10710307
references: Nature. 2000 Mar 30;404(6777):502-6
references: 10761919
references: Nat Rev Genet. 2001 Aug;2(8):634-9
references: 11483988
references: J Bacteriol. 2001 Nov;183(21):6288-93
references: 11591672
references: Appl Environ Microbiol. 2002 Jan;68(1):440-3
references: 11772660
references: Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2072-7
references: 11854503
references: J Bacteriol. 2002 Jul;184(13):3442-9
references: 12057937
references: Syst Biol. 2001 Aug;50(4):513-24
references: 12116650
references: Annu Rev Microbiol. 2002;56:457-87
references: 12142474
references: J Mol Evol. 2002 Oct;55(4):386-400
references: 12355260
references: Methods Mol Med. 2003;71:57-70
references: 12374031
references: Nucleic Acids Res. 2002 Dec 15;30(24):5549-60
references: 12490723
references: Front Biosci. 2003 May 1;8:s544-56
references: 12700070
references: J Bacteriol. 1974 May;118(2):369-73
references: 4597440
references: J Bacteriol. 1977 Feb;129(2):983-92
references: 14116
references: J Bacteriol. 1981 Jan;145(1):638-40
references: 6780524
references: Nucleic Acids Res. 1981 Oct 24;9(20):5383-97
references: 7301590
references: Proc Natl Acad Sci U S A. 1982 Apr;79(7):2393-7
references: 6285382
references: J Gen Microbiol. 1982 May;128(5):1159-61
references: 6809888
references: J Bacteriol. 1982 Dec;152(3):1071-7
references: 6292160
references: Annu Rev Genet. 1982;16:169-92
references: 6297373
references: Nucleic Acids Res. 2003 Jul 1;31(13):3586-8
references: 12824371
references: Nucleic Acids Res. 2004;32(3):1050-8
references: 14960717
references: Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4513-8
references: 15070749
references: Nat Rev Microbiol. 2004 Mar;2(3):241-9
references: 15083159
references: Genome Res. 2004 Jun;14(6):1188-90
references: 15173120
references: J Bacteriol. 1970 Feb;101(2):517-24
references: 5308771