Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum.
Anaerobic degradation
Aromatic compounds
Complete genome
Desulfonema limicola
Desulfonema magnum
Differential proteomics
Metabolism
Physiology
Stress response
Sulfate reduction
Journal
Microbial physiology
ISSN: 2673-1673
Titre abrégé: Microb Physiol
Pays: Switzerland
ID NLM: 101758692
Informations de publication
Date de publication:
19 Feb 2021
19 Feb 2021
Historique:
received:
24
09
2020
accepted:
19
11
2020
entrez:
21
2
2021
pubmed:
22
2
2021
medline:
22
2
2021
Statut:
aheadofprint
Résumé
The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69-96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.
Identifiants
pubmed: 33611323
pii: 000513383
doi: 10.1159/000513383
pmc: PMC8315694
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
1-20Informations de copyright
© 2021 The Author(s) Published by S. Karger AG, Basel.
Références
Proteomics. 2013 Oct;13(18-19):2851-68
pubmed: 23613352
Science. 2014 May 23;344(6186):889-91
pubmed: 24812207
Appl Environ Microbiol. 1998 Aug;64(8):2943-51
pubmed: 9687455
FEMS Microbiol Ecol. 2020 Feb 1;96(2):
pubmed: 31841144
Appl Environ Microbiol. 2003 Sep;69(9):5609-21
pubmed: 12957951
Nat Rev Microbiol. 2008 Jun;6(6):441-54
pubmed: 18461075
Annu Rev Microbiol. 2011;65:215-38
pubmed: 21663439
J Bacteriol. 2001 Jan;183(1):101-8
pubmed: 11114906
Sci Rep. 2015 Oct 26;5:15607
pubmed: 26499760
Chembiochem. 2002 May 03;3(5):384-97
pubmed: 12007171
Nat Rev Microbiol. 2006 May;4(5):383-94
pubmed: 16715050
Mar Geol. 1993;113:27-40
pubmed: 11539842
Nucleic Acids Res. 2015 Jul 1;43(W1):W104-8
pubmed: 25916842
BMC Bioinformatics. 2007 Jun 18;8:209
pubmed: 17577412
Nat Rev Microbiol. 2016 Apr;14(5):305-19
pubmed: 27040757
Nucleic Acids Res. 1999 Dec 1;27(23):4636-41
pubmed: 10556321
Nucleic Acids Res. 2015 Jan;43(Database issue):D261-9
pubmed: 25428365
Electrophoresis. 1988 Jun;9(6):255-62
pubmed: 2466658
Appl Environ Microbiol. 1999 Oct;65(10):4659-65
pubmed: 10508103
J Bacteriol. 1989 Dec;171(12):6689-95
pubmed: 2480344
Nucleic Acids Res. 1997 Mar 1;25(5):955-64
pubmed: 9023104
PLoS Genet. 2009 Sep;5(9):e1000651
pubmed: 19763168
J Mol Microbiol Biotechnol. 2017;27(3):199-212
pubmed: 28850952
Appl Environ Microbiol. 2000 Nov;66(11):5005-12
pubmed: 11055956
Appl Environ Microbiol. 1992 Jan;58(1):70-7
pubmed: 16348641
Nat Biotechnol. 2004 May;22(5):554-9
pubmed: 15077118
Mol Microbiol. 2010 Oct;78(1):13-34
pubmed: 20923416
Front Microbiol. 2019 Feb 19;10:227
pubmed: 30837965
Proteomics. 2016 Mar;16(6):973-88
pubmed: 26792001
J Mol Microbiol Biotechnol. 2016;26(1-3):119-37
pubmed: 26959374
EMBO J. 2010 Jan 20;29(2):327-39
pubmed: 19959992
Nucleic Acids Res. 2019 Jan 8;47(D1):D351-D360
pubmed: 30398656
Nat Rev Microbiol. 2018 Apr;16(4):187-201
pubmed: 29355854
Science. 2010 Jan 8;327(5962):167-70
pubmed: 20056882
Appl Environ Microbiol. 1993 May;59(5):1444-51
pubmed: 7686000
Arch Microbiol. 1998 Jun;169(6):509-16
pubmed: 9575237
J Bacteriol. 2019 Oct 4;201(21):
pubmed: 31405915
Nat Commun. 2017 Oct 10;8(1):841
pubmed: 29018197
Annu Rev Microbiol. 2000;54:827-48
pubmed: 11018146
Cell. 1999 Apr 30;97(3):339-47
pubmed: 10319814
Nucleic Acids Res. 2000 Jan 1;28(1):45-8
pubmed: 10592178
Nucleic Acids Res. 2016 Jul 8;44(W1):W16-21
pubmed: 27141966
Proteomics. 2013 Oct;13(18-19):2743-60
pubmed: 23907795
Environ Microbiol. 2013 May;15(5):1334-55
pubmed: 23088741
J Mol Microbiol Biotechnol. 2010;18(2):92-101
pubmed: 20185932
Annu Rev Biochem. 2018 Jun 20;87:677-696
pubmed: 29648875
Arch Microbiol. 1998 Oct;170(5):319-30
pubmed: 9818351
J Mol Microbiol Biotechnol. 2010;18(2):74-84
pubmed: 20110731
Appl Environ Microbiol. 2004 Aug;70(8):4440-8
pubmed: 15294771
Microbiol Mol Biol Rev. 2008 Sep;72(3):545-54
pubmed: 18772288
Microb Ecol. 2008 Jul;56(1):90-100
pubmed: 17952491
Nat Rev Microbiol. 2008 Jun;6(6):466-76
pubmed: 18461074
Adv Microb Physiol. 2015;66:55-321
pubmed: 26210106
FEMS Microbiol Ecol. 2001 Jul;36(2-3):175-183
pubmed: 11451522
Curr Protoc Bioinformatics. 2003 Aug;Chapter 11:Unit11.2
pubmed: 18428695
Appl Environ Microbiol. 2018 Oct 1;84(20):
pubmed: 30097444
FEMS Microbiol Ecol. 2009 May;68(2):164-72
pubmed: 19573198
Chem Rec. 2010 Aug;10(4):217-29
pubmed: 20607761
Proteomics. 2016 Nov;16(22):2878-2893
pubmed: 27701823
Bioinformatics. 2000 Oct;16(10):944-5
pubmed: 11120685
Appl Microbiol Biotechnol. 2014 Apr;98(8):3371-88
pubmed: 24493567
Arch Microbiol. 2005 Jan;183(1):27-36
pubmed: 15551059
Environ Microbiol. 2009 May;11(5):1038-55
pubmed: 19187283
BMC Genomics. 2016 Nov 15;17(1):918
pubmed: 27846794
Proteomics. 2012 May;12(9):1402-13
pubmed: 22589189
Arch Microbiol. 1999 Oct;172(4):193-203
pubmed: 10525735
Nucleic Acids Res. 2007;35(9):3100-8
pubmed: 17452365
Cell Mol Life Sci. 2019 Nov;76(21):4245-4273
pubmed: 31317204
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610
Appl Environ Microbiol. 2008 Apr;74(8):2267-74
pubmed: 18263750