title: Reference gene selection in Carnobacterium maltaromaticum, Lactobacillus curvatus, and Listeria innocua subjected to temperature and salt stress.
abstract: Eight putative consistently expressed genes in Carnobacterium maltaromaticum and Lactobacillus curvatus, and nine in Listeria innocua, were examined for their potential as references for the normalization of gene expression. Expression stability of candidate reference genes was evaluated under growth conditions of low (5 °C) and moderately high (40-42.5 °C) temperatures, and high salt (≥3 % NaCl) using the geNormplus and NormFinder algorithms. Under temperature stress, both algorithms ranked elongation factor Tu (Tuf) as the most stably expressed gene in C. maltaromaticum. In L. curvatus, at similar conditions, geNormplus identified Tuf and 6-phosphogluconate dehydrogenase (6PGDH) as suitable for normalization, while NormFinder identified phenylalanyl-tRNA synthase and recombinase A as the best pair. In L. innocua grown under the same temperatures, geNormplus ranked 6PGDH, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and Tuf as the top three most stable references, whereas NormFinder identified GAPDH and 6PGDH as suitable for normalization, with Tuf ranked as number six. There was less consistency between algorithms in the salt stress experiment. No gene was identified that exhibited such a constant level of expression as to outperform the other candidates under both experimental conditions. This study underlines the need for normalizing bacterial gene expression using multiple carefully selected references.
authors.affiliation: Department of Process Technology, Nofima AS, 4068, Stavanger, Norway, trond.lovdal@nofima.no.
authors.forename: Trond
authors.initials: T
authors.lastname: Løvdal
authors.forename: Aparna
authors.initials: A
authors.lastname: Saha
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000378:metabolism*; D056573:Carnobacterium / Q000145:classification / Q000235:genetics* / Q000502:physiology; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D007778:Lactobacillus / Q000145:classification / Q000235:genetics* / Q000502:physiology; D008087:Listeria / Q000145:classification / Q000235:genetics* / Q000502:physiology; D013312:Stress, Physiological
chemical_list: D001426:Bacterial Proteins
references.citation: Appl Environ Microbiol. 1993 Apr;59(4):1247-50
references.pmid: 8489233
references.citation: Science. 2001 Oct 26;294(5543):849-52
references.pmid: 11679669
references.citation: Food Microbiol. 2008 May;25(3):529-33
references.pmid: 18355678
references.citation: Anal Biochem. 2009 Apr 15;387(2):238-42
references.pmid: 19454243
references.citation: Int J Food Microbiol. 2010 Jul 31;141 Suppl 1:S60-8
references.pmid: 20206397
references.citation: Syst Appl Microbiol. 2005 Mar;28(2):151-64
references.pmid: 15830808
references.citation: Int J Dev Biol. 2006;50(7):627-35
references.pmid: 16892176
references.citation: J Appl Microbiol. 2008 Feb;104(2):587-94
references.pmid: 18081777
references.citation: Biotechniques. 2000 Aug;29(2):332-7
references.pmid: 10948434
references.citation: J Biotechnol. 1999 Oct 8;75(2-3):291-5
references.pmid: 10617337
references.citation: Foodborne Pathog Dis. 2009 Jul-Aug;6(6):669-80
references.pmid: 19580450
references.citation: J Med Microbiol. 2003 May;52(Pt 5):403-408
references.pmid: 12721316
references.citation: Plant Cell. 2008 Jul;20(7):1734-5
references.pmid: 18664615
references.citation: Cancer Res. 2004 Aug 1;64(15):5245-50
references.pmid: 15289330
references.citation: Genome Biol. 2002 Jun 18;3(7):RESEARCH0034
references.pmid: 12184808
references.citation: Food Microbiol. 2010 Sep;27(6):698-709
references.pmid: 20630312
references.citation: J Microbiol Methods. 2011 Aug;86(2):210-7
references.pmid: 21620905
references.citation: Curr Microbiol. 2001 Oct;43(4):227-31
references.pmid: 11683354
references.citation: Int J Food Microbiol. 2009 Aug 31;134(1-2):140-6
references.pmid: 19403190
references.citation: Microbiol Rev. 1991 Sep;55(3):476-511
references.pmid: 1943998
references.citation: Syst Appl Microbiol. 2005 Jan;28(1):1-18
references.pmid: 15709360
references.citation: J Bacteriol. 2001 Dec;183(24):7094-101
references.pmid: 11717267
references.citation: Bacteriol Rev. 1966 Jun;30(2):309-82
references.pmid: 4956900
references.citation: Nat Protoc. 2006;1(3):1559-82
references.pmid: 17406449
references.citation: Genome Biol. 2007;8(2):R19
references.pmid: 17291332
references.citation: BMC Plant Biol. 2007 Sep 21;7:50
references.pmid: 17888160
references.citation: J Microbiol Methods. 2007 Aug;70(2):355-62
references.pmid: 17590462
references.citation: Plant Biotechnol J. 2008 Aug;6(6):609-18
references.pmid: 18433420
references.citation: Methods. 2010 Apr;50(4):262-70
references.pmid: 20060046
references.citation: Anaerobe. 2010 Aug;16(4):439-43
references.pmid: 20599622
references.citation: Biotechniques. 2008 Apr;44(5):619-26
references.pmid: 18474036
references.citation: Mol Microbiol. 2003 Mar;47(6):1613-25
references.pmid: 12622816
references.citation: J Microbiol Methods. 2004 Dec;59(3):363-70
references.pmid: 15488279
references.citation: Int J Food Microbiol. 2012 Jan 16;152(3):107-15
references.pmid: 21704418
references.citation: FEMS Microbiol Lett. 2007 Apr;269(2):265-72
references.pmid: 17263845
references.citation: Mol Microbiol. 1996 Feb;19(3):483-93
references.pmid: 8830239
references.citation: J Microbiol Methods. 2011 Jan;84(1):61-6
references.pmid: 21047531
references.citation: J Bacteriol. 2012 Jan;194(2):538-9
references.pmid: 22207745
references.citation: Appl Microbiol Biotechnol. 2007 Oct;76(6):1403-11
references.pmid: 17690878
references.citation: J Ind Microbiol Biotechnol. 2011 Sep;38(9):1279-86
references.pmid: 21104423
references.citation: BMC Mol Biol. 2010 Sep 21;11:74
references.pmid: 20858237