Comparative genomics hints at dispensability of multiple essential genes in two Escherichia coli L-form strains.
Bacterial cell wall
Essential genes
Genome sequence
L-form
Mutation
Journal
Bioscience reports
ISSN: 1573-4935
Titre abrégé: Biosci Rep
Pays: England
ID NLM: 8102797
Informations de publication
Date de publication:
31 10 2023
31 10 2023
Historique:
received:
11
07
2023
revised:
09
10
2023
accepted:
11
10
2023
medline:
26
10
2023
pubmed:
11
10
2023
entrez:
11
10
2023
Statut:
ppublish
Résumé
Despite the critical role of bacterial cell walls in maintaining cell shapes, certain environmental stressors can induce the transition of many bacterial species into a wall-deficient state called L-form. Long-term induced Escherichia coli L-forms lose their rod shape and usually hold significant mutations that affect cell division and growth. Besides this, the genetic background of L-form bacteria is still poorly understood. In the present study, the genomes of two stable L-form strains of E. coli (NC-7 and LWF+) were sequenced and their gene mutation status was determined and compared with their parental strains. Comparative genomic analysis between two L-forms reveals both unique adaptions and common mutated genes, many of which belong to essential gene categories not involved in cell wall biosynthesis, indicating that L-form genetic adaptation impacts crucial metabolic pathways. Missense variants from L-forms and Lenski's long-term evolution experiment (LTEE) were analyzed in parallel using an optimized DeepSequence pipeline to investigate predicted mutation effects (α) on protein functions. We report that the two L-form strains analyzed display a frequency of 6-10% (0% for LTEE) in mutated essential genes where the missense variants have substantial impact on protein functions (α<0.5). This indicates the emergence of different survival strategies in L-forms through changes in essential genes during adaptions to cell wall deficiency. Collectively, our results shed light on the detailed genetic background of two E. coli L-forms and pave the way for further investigations of the gene functions in L-form bacterial models.
Identifiants
pubmed: 37819245
pii: 233611
doi: 10.1042/BSR20231227
pmc: PMC10600066
pii:
doi:
Substances chimiques
Escherichia coli Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2023 The Author(s).
Références
Nature. 2009 Feb 12;457(7231):849-53
pubmed: 19212404
Nucleic Acids Res. 2014 Jan;42(Database issue):D574-80
pubmed: 24243843
Biochem Soc Trans. 2017 Apr 15;45(2):287-295
pubmed: 28408469
Mol Gen Genet. 1980;180(1):185-91
pubmed: 7003307
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Z Allg Mikrobiol. 1969;9(4):297-313
pubmed: 4903940
Nat Microbiol. 2019 Oct;4(10):1716-1726
pubmed: 31285586
Mol Microbiol. 1999 Oct;34(2):350-64
pubmed: 10564478
Appl Environ Microbiol. 2002 Feb;68(2):525-31
pubmed: 11823186
Nat Commun. 2019 Oct 2;10(1):4463
pubmed: 31578326
Mol Biol Evol. 2021 Jul 29;38(8):3144-3152
pubmed: 33749796
Nature. 2014 Jan 16;505(7483):372-7
pubmed: 24402227
Nat Microbiol. 2021 Mar;6(3):301-312
pubmed: 33462433
Bioessays. 2012 Dec;34(12):1078-84
pubmed: 23108858
Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):425-30
pubmed: 16407165
PLoS One. 2012;7(6):e38514
pubmed: 22701656
Science. 2016 Mar 25;351(6280):aad6253
pubmed: 27013737
Annu Rev Biochem. 1993;62:749-95
pubmed: 8394684
Microbiology (Reading). 2000 Jul;146 ( Pt 7):1547-1553
pubmed: 10878119
Nat Commun. 2021 May 13;12(1):2775
pubmed: 33986273
J Bacteriol. 1998 Dec;180(23):6429-32
pubmed: 9829961
J Biol Chem. 2012 Apr 20;287(17):13666-73
pubmed: 22378793
J Bacteriol. 1993 Mar;175(6):1841-3
pubmed: 8449890
Proc Natl Acad Sci U S A. 1977 Jul;74(7):2976-9
pubmed: 331322
FEMS Microbiol Rev. 2008 Mar;32(2):168-207
pubmed: 18266853
Genetics. 2000 Jun;155(2):487-97
pubmed: 10835375
Mol Syst Biol. 2006;2:2006.0008
pubmed: 16738554
OMICS. 2012 May;16(5):284-7
pubmed: 22455463
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Biochemistry. 1997 Aug 12;36(32):9747-58
pubmed: 9245406
Nature. 1998 Aug 6;394(6693):531-2
pubmed: 9707111
Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14391-5
pubmed: 8962061
J Biol Chem. 1985 Oct 25;260(24):12987-92
pubmed: 2997151
J Biol Chem. 1990 Jul 5;265(19):11185-92
pubmed: 2162835
Nat Microbiol. 2016 Jun 27;1(8):16091
pubmed: 27573111
Elife. 2014 Oct 30;3:
pubmed: 25358088
Cell. 2021 Apr 29;184(9):2430-2440.e16
pubmed: 33784496
FEMS Microbiol Lett. 2007 Apr;269(2):229-33
pubmed: 17250759
PLoS One. 2009 Oct 06;4(10):e7316
pubmed: 19806199
J Bacteriol. 2000 Mar;182(5):1419-22
pubmed: 10671467
Mol Syst Biol. 2011 Aug 30;7:528
pubmed: 21878915
Z Allg Mikrobiol. 1971;11(1):19-33
pubmed: 4933935
Elife. 2019 Jan 18;8:
pubmed: 30657448
J Mol Biol. 2011 Nov 18;414(1):75-85
pubmed: 21983341
Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):E2774-83
pubmed: 22991466
Eur J Biochem. 1996 Dec 15;242(3):689-94
pubmed: 9022698
Nat Methods. 2018 Oct;15(10):816-822
pubmed: 30250057
Z Allg Mikrobiol. 1974;14(8):675-90
pubmed: 4619519
Mol Microbiol. 2009 Jul;73(2):306-22
pubmed: 19555455
FEMS Microbiol Rev. 2008 Mar;32(2):234-58
pubmed: 18266856
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Mol Syst Biol. 2017 May 10;13(5):931
pubmed: 28490437
Proc Natl Acad Sci U S A. 1989 Nov;86(22):8877-81
pubmed: 2682664
Mol Gen Genet. 1981;184(1):33-9
pubmed: 6278247
Microbiology (Reading). 1995 May;141 ( Pt 5):1085-1092
pubmed: 7773404
Curr Biol. 2015 Jun 15;25(12):1613-8
pubmed: 26051891
Eur J Biochem. 1995 Jun 1;230(2):538-48
pubmed: 7607227
Nat Genet. 2011 May;43(5):491-8
pubmed: 21478889
mBio. 2012 Aug 31;3(4):
pubmed: 22911967
Science. 2020 May 29;368(6494):973-980
pubmed: 32467386
Infect Immun. 1974 Oct;10(4):915-27
pubmed: 4214786
J Mol Biol. 1999 Aug 13;291(2):393-415
pubmed: 10438628
Mutat Res. 1991 Jan;254(1):1-12
pubmed: 1986271
FEMS Microbiol Lett. 2006 May;258(2):305-11
pubmed: 16640589
Microbiology (Reading). 2019 Aug;165(8):842-851
pubmed: 30958258
Nat Commun. 2018 Sep 3;9(1):3562
pubmed: 30177705
PLoS One. 2017 Jul 11;12(7):e0180800
pubmed: 28700629
Nat Microbiol. 2022 Oct;7(10):1580-1592
pubmed: 36097170
Bioinformatics. 2011 Nov 1;27(21):2987-93
pubmed: 21903627
Mol Microbiol. 2001 Sep;41(5):1101-11
pubmed: 11555290
Front Microbiol. 2021 Jul 28;12:711077
pubmed: 34394059
PLoS One. 2014 May 29;9(5):e98042
pubmed: 24875494
Science. 1996 Nov 15;274(5290):1208-11
pubmed: 8895473
mBio. 2018 Feb 20;9(1):
pubmed: 29463657
Nature. 1990 Sep 13;347(6289):203-6
pubmed: 2203971
Fly (Austin). 2012 Apr-Jun;6(2):80-92
pubmed: 22728672
J Bacteriol. 1980 Dec;144(3):1190-2
pubmed: 7002911
PLoS Biol. 2007 Jan;5(1):e7
pubmed: 17194213
PLoS Genet. 2018 Nov 7;14(11):e1007749
pubmed: 30403660
Philos Trans R Soc Lond B Biol Sci. 2010 Apr 27;365(1544):1177-86
pubmed: 20308092
Nucleic Acids Res. 2021 Jan 8;49(D1):D412-D419
pubmed: 33125078
Mol Biosyst. 2009 Dec;5(12):1672-8
pubmed: 19452048
J Biol Chem. 2006 Mar 17;281(11):7309-16
pubmed: 16407191
Proc Natl Acad Sci U S A. 2019 May 14;116(20):10072-10080
pubmed: 31036669
J Bacteriol. 1996 Dec;178(24):7167-72
pubmed: 8955398
J Bacteriol. 1989 Jan;171(1):303-7
pubmed: 2536658
Trends Microbiol. 2009 Oct;17(10):433-8
pubmed: 19765999
Nat Biotechnol. 2011 Jan;29(1):24-6
pubmed: 21221095
Nature. 1992 Jan 16;355(6357):273-5
pubmed: 1309939
Nat Commun. 2016 Nov 23;7:13631
pubmed: 27876798
FEBS Lett. 1977 Jul 15;79(2):374-8
pubmed: 330236
Biochem Biophys Res Commun. 1980 Nov 17;97(1):287-93
pubmed: 7006606
J Biol Chem. 2009 Oct 23;284(43):29836-46
pubmed: 19710024
Cell. 2013 Feb 28;152(5):997-1007
pubmed: 23452849
J Gen Microbiol. 1987 Mar;133(3):527-34
pubmed: 3309159
Mol Gen Genet. 1985;200(2):272-7
pubmed: 2993822
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nat Commun. 2019 Sep 26;10(1):4379
pubmed: 31558767
Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):7022-5
pubmed: 1495996
Mol Microbiol. 1997 Aug;25(4):671-81
pubmed: 9379897
Adv Microb Physiol. 2019;74:97-141
pubmed: 31126537
Proc Natl Acad Sci U S A. 2009 Feb 24;106(8):2607-11
pubmed: 19196991
DNA Repair (Amst). 2003 Feb 3;2(2):159-73
pubmed: 12531387
Nature. 2009 Oct 29;461(7268):1243-7
pubmed: 19838166
Mutat Res. 2000 Mar 14;448(1):47-55
pubmed: 10751622
PLoS One. 2015 Nov 11;10(11):e0142870
pubmed: 26560897
Proc Natl Acad Sci U S A. 2023 Feb 7;120(6):e2216244120
pubmed: 36716373
Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6
pubmed: 18940858