title: Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells.
abstract: Acinetobacterbaumannii has emerged as a dangerous opportunistic pathogen, with many strains able to form biofilms and thus cause persistent infections. The aim of the present study was to use high-throughput sequencing techniques to establish complete transcriptome profiles of planktonic (free-living) and sessile (biofilm) forms of A. baumannii ATCC 17978 and thereby identify differences in their gene expression patterns. Collections of mRNA from planktonic (both exponential and stationary phase cultures) and sessile (biofilm) cells were sequenced. Six mRNA libraries were prepared following the mRNA-Seq protocols from Illumina. Reads were obtained in a HiScanSQ platform and mapped against the complete genome to describe the complete mRNA transcriptomes of planktonic and sessile cells. The results showed that the gene expression pattern of A. baumannii biofilm cells was distinct from that of planktonic cells, including 1621 genes over-expressed in biofilms relative to stationary phase cells and 55 genes expressed only in biofilms. These differences suggested important changes in amino acid and fatty acid metabolism, motility, active transport, DNA-methylation, iron acquisition, transcriptional regulation, and quorum sensing, among other processes. Disruption or deletion of five of these genes caused a significant decrease in biofilm formation ability in the corresponding mutant strains. Among the genes over-expressed in biofilm cells were those in an operon involved in quorum sensing. One of them, encoding an acyl carrier protein, was shown to be involved in biofilm formation as demonstrated by the significant decrease in biofilm formation by the corresponding knockout strain. The present work serves as a basis for future studies examining the complex network systems that regulate bacterial biofilm formation and maintenance.
authors.affiliation: Department of Microbiology, Biomedical Research Institute, University Hospital, A Coruña, Spain.
authors.forename: Soraya
authors.initials: S
authors.lastname: Rumbo-Feal
authors.forename: Manuel J
authors.initials: MJ
authors.lastname: Gómez
authors.forename: Carmen
authors.initials: C
authors.lastname: Gayoso
authors.forename: Laura
authors.initials: L
authors.lastname: Álvarez-Fraga
authors.forename: María P
authors.initials: MP
authors.lastname: Cabral
authors.forename: Ana M
authors.initials: AM
authors.lastname: Aransay
authors.forename: Naiara
authors.initials: N
authors.lastname: Rodríguez-Ezpeleta
authors.forename: Ane
authors.initials: A
authors.lastname: Fullaondo
authors.forename: Jaione
authors.initials: J
authors.lastname: Valle
authors.forename: María
authors.initials: M
authors.lastname: Tomás
authors.forename: Germán
authors.initials: G
authors.lastname: Bou
authors.forename: Margarita
authors.initials: M
authors.lastname: Poza
mesh_terms: D015107:4-Butyrolactone / Q000031:analogs & derivatives / Q000096:biosynthesis; D040981:Acinetobacter baumannii / Q000166:cytology* / Q000235:genetics* / Q000254:growth & development / Q000502:physiology; D018441:Biofilms; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D055786:Gene Knockout Techniques; D005798:Genes, Bacterial; D009154:Mutation / Q000235:genetics; D010933:Plankton / Q000166:cytology / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics; D015854:Up-Regulation / Q000235:genetics
chemical_list: D012333:RNA, Messenger; C088386:homoserine lactone; D015107:4-Butyrolactone
references.citation: Antimicrob Agents Chemother. 2002 Jun;46(6):1946-52
references.pmid: 12019113
references.citation: PLoS One. 2012;7(7):e36696
references.pmid: 22815678
references.citation: Gene. 2009 Feb 1;430(1-2):123-31
references.pmid: 19010402
references.citation: Nature. 2009 Jun 18;459(7249):950-6
references.pmid: 19448609
references.citation: Respirology. 2009 Nov;14(8):1200-5
references.pmid: 19909464
references.citation: FEMS Microbiol Rev. 2013 Mar;37(2):130-55
references.pmid: 22568581
references.citation: Biomaterials. 2011 Apr;32(11):2689-94
references.pmid: 21295343
references.citation: PLoS One. 2011;6(10):e26030
references.pmid: 22046254
references.citation: Science. 2010 Apr 30;328(5978):627-9
references.pmid: 20431016
references.citation: J Antimicrob Chemother. 2010 Feb;65(2):233-8
references.pmid: 19996144
references.citation: Science. 1996 Jun 14;272(5268):1655-8
references.pmid: 8658141
references.citation: Clin Microbiol Infect. 2008 Mar;14(3):276-8
references.pmid: 18190568
references.citation: Genes Dev. 2007 Mar 1;21(5):601-14
references.pmid: 17344419
references.citation: J Mol Microbiol Biotechnol. 2010;18(1):24-36
references.pmid: 20068355
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5354-9
references.pmid: 17374723
references.citation: Nature. 2010 Mar 11;464(7286):250-5
references.pmid: 20164839
references.citation: Res Microbiol. 2009 Apr;160(3):213-8
references.pmid: 19530313
references.citation: Microbiology (Reading). 2008 Nov;154(Pt 11):3398-3409
references.pmid: 18957593
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: BMC Genomics. 2011 Feb 23;12:126
references.pmid: 21342532
references.citation: Clin Microbiol Infect. 2000 Dec;6(12):635-43
references.pmid: 11284921
references.citation: Microbiology (Reading). 2011 Sep;157(Pt 9):2534-2544
references.pmid: 21700662
references.citation: J Microbiol. 2011 Apr;49(2):243-50
references.pmid: 21538245
references.citation: PLoS One. 2012;7(2):e31092
references.pmid: 22319605
references.citation: Environ Microbiol. 2007 Feb;9(2):332-46
references.pmid: 17222132
references.citation: J Biotechnol. 2008 Aug 31;136(1-2):3-10
references.pmid: 18616967
references.citation: J Proteome Res. 2010 Apr 5;9(4):1951-64
references.pmid: 20108952
references.citation: J Clin Microbiol. 2000 Nov;38(11):4086-95
references.pmid: 11060073
references.citation: Nucleic Acids Res. 2008 Jun;36(10):3420-35
references.pmid: 18445632
references.citation: Clin Microbiol Infect. 2008 Jan;14(1):49-54
references.pmid: 18005176
references.citation: BMC Genomics. 2009 Dec 11;10:599
references.pmid: 20003355
references.citation: Antimicrob Agents Chemother. 2009 Sep;53(9):4013-4
references.pmid: 19581458
references.citation: J Hosp Infect. 2012 Jan;80(1):56-60
references.pmid: 21975219
references.citation: Infect Immun. 2009 Aug;77(8):3150-60
references.pmid: 19470746
references.citation: Antimicrob Agents Chemother. 2009 Dec;53(12):5312-6
references.pmid: 19770280
references.citation: PLoS One. 2012;7(9):e45758
references.pmid: 23029226
references.citation: J Bacteriol. 2008 Jan;190(1):264-74
references.pmid: 17981982
references.citation: PLoS Pathog. 2009 Nov;5(11):e1000668
references.pmid: 19936057
references.citation: J Microbiol Immunol Infect. 2014 Aug;47(4):275-81
references.pmid: 23453128
references.citation: Nucleic Acids Res. 2009 Apr;37(6):e46
references.pmid: 19223322
references.citation: PLoS Pathog. 2010 Apr 01;6(4):e1000834
references.pmid: 20368969
references.citation: J Bacteriol. 2008 May;190(9):3386-92
references.pmid: 18281398
references.citation: BMC Genomics. 2010 Jun 24;11:404
references.pmid: 20576116
references.citation: Ann Clin Microbiol Antimicrob. 2004 Jul 29;3:14
references.pmid: 15283864
references.citation: Int J Antimicrob Agents. 2010 Mar;35(3):219-26
references.pmid: 20047818
references.citation: PLoS Genet. 2008 Aug 22;4(8):e1000163
references.pmid: 18725932
references.citation: Genome Biol. 2010;11(10):R106
references.pmid: 20979621
references.citation: Science. 2006 Feb 24;311(5764):1113-6
references.pmid: 16497924
references.citation: J Proteome Res. 2011 Aug 5;10(8):3399-417
references.pmid: 21612302
references.citation: Antimicrob Agents Chemother. 2010 Jan;54(1):333-40
references.pmid: 19884373
references.citation: BMC Microbiol. 2010 Nov 09;10:279
references.pmid: 21062436
references.citation: PLoS One. 2009 Nov 04;4(11):e7660
references.pmid: 19888459
references.citation: Nat Rev Microbiol. 2007 Dec;5(12):939-51
references.pmid: 18007677
references.citation: J Bacteriol. 2006 Jul;188(13):4737-48
references.pmid: 16788183
references.citation: Microbiology (Reading). 2003 Dec;149(Pt 12):3473-3484
references.pmid: 14663080
references.citation: BMC Res Notes. 2011 Jan 11;4:5
references.pmid: 21223561
references.citation: Future Microbiol. 2009 Apr;4(3):273-8
references.pmid: 19327114
references.citation: J Antimicrob Chemother. 2003 Mar;51(3):565-74
references.pmid: 12615856
references.citation: Microbios. 1996;86(346):49-58
references.pmid: 8771775
references.citation: Antimicrob Agents Chemother. 2013 Apr;57(4):1926-9
references.pmid: 23318804
references.citation: Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21878-82
references.pmid: 19996181
references.citation: Mol Microbiol. 2011 Aug;81(3):767-83
references.pmid: 21696457
references.citation: Infect Immun. 2004 Oct;72(10):6032-9
references.pmid: 15385507
references.citation: Clin Microbiol Infect. 2005 Jul;11(7):540-6
references.pmid: 15966971
references.citation: Antimicrob Agents Chemother. 2010 Mar;54(3):1029-41
references.pmid: 20028819
references.citation: J Bacteriol. 2010 May;192(9):2359-72
references.pmid: 20190049
references.citation: Science. 1999 May 21;284(5418):1318-22
references.pmid: 10334980
references.citation: BMC Microbiol. 2008 May 02;8:72
references.pmid: 18454850
references.citation: Antimicrob Agents Chemother. 2005 Aug;49(8):3198-202
references.pmid: 16048925
references.citation: J Bacteriol. 2008 Feb;190(3):1036-44
references.pmid: 18024522
references.citation: Nature. 2001 Oct 25;413(6858):860-4
references.pmid: 11677611
references.citation: J Antimicrob Chemother. 2010 Feb;65(2):228-32
references.pmid: 20008046