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Article ; Online: Anomalies of the anaerobic tricarboxylic acid cycle in Shewanella oneidensis revealed by Tn-seq.

Brutinel, Evan D / Gralnick, Jeffrey A

2012 Volume 86, Issue 2, Page(s) 273–283

Abstract: The availability of increasingly inexpensive sequencing combined with an ever-expanding molecular biology toolbox has transported classical bacterial genetics into the 21st century. Whole genome genetic fitness analysis using transposon mutagenesis ... ...

Abstract	The availability of increasingly inexpensive sequencing combined with an ever-expanding molecular biology toolbox has transported classical bacterial genetics into the 21st century. Whole genome genetic fitness analysis using transposon mutagenesis combined with next-generation high-throughput sequencing (Tn-seq) promises to revolutionize systems level analysis of microbial metabolism. Tn-seq measures the frequency of actual members of a heterogeneous mutant pool undergoing purifying selection to determine the contribution of every non-essential gene in the genome to the fitness of an organism under a given condition. Here we use Tn-seq to assess gene function in the Gram negative γ-proteobacterium Shewanella oneidensis strain MR-1. In addition to being a model environmental organism, there is considerable interest in using S. oneidensis as a platform organism for bioremediation and biotechnology, necessitating a complete understanding of the metabolic pathways that may be utilized. Our analysis reveals unique aspects of S. oneidensis metabolism overlooked by over 30 years of classical genetic and systems level analysis. We report the utilization of an alternative citrate synthase and describe a dynamic branching of the S. oneidensis anaerobic tricarboxylic acid cycle, unreported in any other organism, which may be a widespread strategy for microbes adept at dissipating reducing equivalents via anaerobic respiration.
MeSH term(s)	Anaerobiosis ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Citric Acid Cycle ; Gene Expression Regulation, Bacterial ; High-Throughput Nucleotide Sequencing ; Mutation ; Shewanella/genetics ; Shewanella/metabolism
Chemical Substances	Bacterial Proteins
Language	English
Publishing date	2012-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/j.1365-2958.2012.08196.x
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Article ; Online: Shuttling happens: soluble flavin mediators of extracellular electron transfer in Shewanella.

Brutinel, Evan D / Gralnick, Jeffrey A

Applied microbiology and biotechnology

2012 Volume 93, Issue 1, Page(s) 41–48

Abstract: The genus Shewanella contains Gram negative γ-proteobacteria capable of reducing a wide range of substrates, including insoluble metals and carbon electrodes. The utilization of insoluble respiratory substrates by bacteria requires a strategy that is ... ...

Abstract	The genus Shewanella contains Gram negative γ-proteobacteria capable of reducing a wide range of substrates, including insoluble metals and carbon electrodes. The utilization of insoluble respiratory substrates by bacteria requires a strategy that is quite different from a traditional respiratory strategy because the cell cannot take up the substrate. Electrons generated by cellular metabolism instead must be transported outside the cell, and perhaps beyond, in order to reduce an insoluble substrate. The primary focus of research in model organisms such as Shewanella has been the mechanisms underlying respiration of insoluble substrates. Electrons travel from the menaquinone pool in the cytoplasmic membrane to the surface of the bacterial cell through a series of proteins collectively described as the Mtr pathway. This review will focus on respiratory electron transfer from the surface of the bacterial cell to extracellular substrates. Shewanella sp. secrete redox-active flavin compounds able to transfer electrons between the cell surface and substrate in a cyclic fashion-a process termed electron shuttling. The production and secretion of flavins as well as the mechanisms of cell-mediated reduction will be discussed with emphasis on the experimental evidence for a shuttle-based mechanism. The ability to reduce extracellular substrates has sparked interest in using Shewanella sp. for applications in bioremediation, bioenergy, and synthetic biology.
MeSH term(s)	Electrons ; Flavins/metabolism ; Oxidation-Reduction ; Shewanella/metabolism ; Vitamin K 2/metabolism
Chemical Substances	Flavins ; Vitamin K 2 (11032-49-8)
Language	English
Publishing date	2012-01
Publishing country	Germany
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-011-3653-0
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Article ; Online: Preferential utilization of D-lactate by Shewanella oneidensis.

Brutinel, Evan D / Gralnick, Jeffrey A

Applied and environmental microbiology

2012 Volume 78, Issue 23, Page(s) 8474–8476

Abstract: Shewanella oneidensis couples oxidation of lactate to respiration of many substrates. Here we report that llpR (L-lactate-positive regulator, SO_3460) encodes a positive regulator of L-lactate utilization distinct from previously studied regulators. We ... ...

Abstract	Shewanella oneidensis couples oxidation of lactate to respiration of many substrates. Here we report that llpR (L-lactate-positive regulator, SO_3460) encodes a positive regulator of L-lactate utilization distinct from previously studied regulators. We also demonstrate D-lactate inhibition of L-lactate utilization in S. oneidensis, resulting in preferential utilization of the D isomer.
MeSH term(s)	Gene Expression Regulation, Bacterial ; Gene Expression Regulation, Enzymologic ; Lactic Acid/chemistry ; Lactic Acid/metabolism ; Oxidation-Reduction ; Shewanella/metabolism ; Stereoisomerism ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors ; Lactic Acid (33X04XA5AT)
Language	English
Publishing date	2012-09-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.02183-12
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Article ; Online: A Ferrous Iron Exporter Mediates Iron Resistance in Shewanella oneidensis MR-1.

Bennett, Brittany D / Brutinel, Evan D / Gralnick, Jeffrey A

Applied and environmental microbiology

2015 Volume 81, Issue 22, Page(s) 7938–7944

Abstract: Shewanella oneidensis strain MR-1 is a dissimilatory metal-reducing bacterium frequently found in aquatic sediments. In the absence of oxygen, S. oneidensis can respire extracellular, insoluble oxidized metals, such as iron (hydr)oxides, making it ... ...

Abstract	Shewanella oneidensis strain MR-1 is a dissimilatory metal-reducing bacterium frequently found in aquatic sediments. In the absence of oxygen, S. oneidensis can respire extracellular, insoluble oxidized metals, such as iron (hydr)oxides, making it intimately involved in environmental metal and nutrient cycling. The reduction of ferric iron (Fe(3+)) results in the production of ferrous iron (Fe(2+)) ions, which remain soluble under certain conditions and are toxic to cells at higher concentrations. We have identified an inner membrane protein in S. oneidensis, encoded by the gene SO_4475 and here called FeoE, which is important for survival during anaerobic iron respiration. FeoE, a member of the cation diffusion facilitator (CDF) protein family, functions to export excess Fe(2+) from the MR-1 cytoplasm. Mutants lacking feoE exhibit an increased sensitivity to Fe(2+). The export function of FeoE is specific for Fe(2+), as an feoE mutant is equally sensitive to other metal ions known to be substrates of other CDF proteins (Cd(2+), Co(2+), Cu(2+), Mn(2+), Ni(2+), or Zn(2+)). The substrate specificity of FeoE differs from that of FieF, the Escherichia coli homolog of FeoE, which has been reported to be a Cd(2+)/Zn(2+) or Fe(2+)/Zn(2+) exporter. A complemented feoE mutant has an increased growth rate in the presence of excess Fe(2+) compared to that of the ΔfeoE mutant complemented with fieF. It is possible that FeoE has evolved to become an efficient and specific Fe(2+) exporter in response to the high levels of iron often present in the types of environmental niches in which Shewanella species can be found.
MeSH term(s)	Bacterial Outer Membrane Proteins/genetics ; Bacterial Outer Membrane Proteins/metabolism ; Ferrous Compounds/metabolism ; Iron/metabolism ; Oxidation-Reduction ; Shewanella/genetics ; Shewanella/metabolism
Chemical Substances	Bacterial Outer Membrane Proteins ; Ferrous Compounds ; Iron (E1UOL152H7)
Language	English
Publishing date	2015-09-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.02835-15
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Article ; Online: Global Regulatory Pathways Converge To Control Expression of Pseudomonas aeruginosa Type IV Pili.

Coggan, Kimberly A / Higgs, Matthew G / Brutinel, Evan D / Marden, Jeremiah N / Intile, Peter J / Winther-Larsen, Hanne C / Koomey, Michael / Yahr, Timothy L / Wolfgang, Matthew C

mBio

2022 Volume 13, Issue 1, Page(s) e0369621

Abstract: The opportunistic pathogen Pseudomonas aeruginosa relies upon type IV pili (Tfp) for host colonization and virulence. Tfp are retractile surface appendages that promote adherence to host tissue and mediate twitching motility, a form of surface-associated ...

Abstract	The opportunistic pathogen Pseudomonas aeruginosa relies upon type IV pili (Tfp) for host colonization and virulence. Tfp are retractile surface appendages that promote adherence to host tissue and mediate twitching motility, a form of surface-associated translocation. Tfp are composed of a major structural pilin protein (PilA), several less abundant, fiber-associated pilin-like proteins (FimU, PilV, PilW, PilX, and PilE), and a pilus-associated tip adhesin and surface sensor (PilY1). Several proteins critical for Tfp biogenesis and surface sensing are encoded by the
MeSH term(s)	Fimbriae Proteins/genetics ; Pseudomonas aeruginosa/genetics ; Bacterial Proteins/metabolism ; Fimbriae, Bacterial/genetics ; Virulence Factors/metabolism
Chemical Substances	Fimbriae Proteins (147680-16-8) ; Bacterial Proteins ; Virulence Factors
Language	English
Publishing date	2022-01-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.03696-21
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Article ; Online: Description of a riboflavin biosynthetic gene variant prevalent in the phylum Proteobacteria.

Brutinel, Evan D / Dean, Antony M / Gralnick, Jeffrey A

Journal of bacteriology

2013 Volume 195, Issue 24, Page(s) 5479–5486

Abstract: Riboflavin (vitamin B2) is the precursor of flavin mononucleotide and flavin adenine dinucleotide, which are cofactors essential for a host of intracellular redox reactions. Microorganisms synthesize flavins de novo to fulfill nutritional requirements, ... ...

Abstract	Riboflavin (vitamin B2) is the precursor of flavin mononucleotide and flavin adenine dinucleotide, which are cofactors essential for a host of intracellular redox reactions. Microorganisms synthesize flavins de novo to fulfill nutritional requirements, but it is becoming increasingly clear that flavins play a wider role in cellular physiology than was previously appreciated. Flavins mediate diverse processes beyond the cytoplasmic membrane, including iron acquisition, extracellular respiration, and interspecies interactions. While investigating the regulation of flavin electron shuttle biosynthesis in the Gram-negative gammaproteobacterium Shewanella oneidensis, we discovered that a riboflavin biosynthetic gene (ribBA) annotated as encoding a bifunctional 3,4-dihydroxy-2-butanone 4-phosphate (DHBP) synthase/GTP cyclohydrolase II does not possess both functions. The novel gene, renamed ribBX here, encodes an amino-terminal DHBP synthase domain. The carboxy-terminal end of RibBX not only lacks GTP cyclohydrolase II activity but also has evolved a different function altogether in S. oneidensis, regulating the activity of the DHBP synthase domain. Phylogenetic analysis revealed that the misannotation of ribBX as ribBA is rampant throughout the phylum Proteobacteria (40% of 2,173 annotated ribBA genes) and that ribBX emerged early in the evolution of this group of microorganisms. We examined the functionality of representative ribBX genes from Beta-, Gamma-, and Epsilonproteobacteria and found that, consistent with sequence-based predictions, the encoded GTP cyclohydrolase II domains lack catalytic activity. The persistence of ribBX in the genomes of so many phylogenetically divergent bacterial species lends weight to the argument that ribBX has evolved a function which lends a selective advantage to the host.
MeSH term(s)	Biosynthetic Pathways/genetics ; Evolution, Molecular ; Intramolecular Transferases/genetics ; Intramolecular Transferases/metabolism ; Phylogeny ; Protein Structure, Tertiary ; Proteobacteria/enzymology ; Proteobacteria/genetics ; Riboflavin/biosynthesis ; Sequence Homology, Amino Acid
Chemical Substances	Intramolecular Transferases (EC 5.4.-) ; L-3,4-dihydroxy-2-butanone-4-phosphate synthase (EC 5.4.-) ; Riboflavin (TLM2976OFR)
Language	English
Publishing date	2013-10-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00651-13
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Article: Control of gene expression by type III secretory activity.

Brutinel, Evan D / Yahr, Timothy L

Current opinion in microbiology

2008 Volume 11, Issue 2, Page(s) 128–133

Abstract: The bacterial flagellum and the highly related injectisome (or needle complex) are among the most complicated multi-protein structures found in Gram-negative microorganisms. The assembly of both structures is dependent upon a type III secretion system. ... ...

Abstract	The bacterial flagellum and the highly related injectisome (or needle complex) are among the most complicated multi-protein structures found in Gram-negative microorganisms. The assembly of both structures is dependent upon a type III secretion system. An interesting regulatory feature unique to these systems is the coordination of gene expression with type III secretory activity. This means of regulation ensures that secretion substrates are expressed only when required during the assembly process or upon completion of the fully functional structure. Prominent within the regulatory scheme are secreted proteins and type III secretion chaperones that exert effects on gene expression at the transcriptional and post-transcriptional levels. Although the major structural components of the flagellum and injectisome systems are highly conserved, recent studies reveal diversity in the mechanisms used by secretion substrates and chaperones to control gene expression.
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Flagella/metabolism ; Gene Expression Regulation, Bacterial ; Gram-Negative Bacteria/genetics ; Gram-Negative Bacteria/metabolism ; Molecular Chaperones/genetics ; Molecular Chaperones/metabolism
Chemical Substances	Bacterial Proteins ; Molecular Chaperones
Language	English
Publishing date	2008-04-08
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1418474-6
ISSN	1879-0364 ; 1369-5274
ISSN (online)	1879-0364
ISSN	1369-5274
DOI	10.1016/j.mib.2008.02.010
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Article: Shuttling happens: soluble flavin mediators of extracellular electron transfer in Shewanella

Brutinel, Evan D / Gralnick, Jeffrey A

Applied microbiology and biotechnology.. 2012 Jan., v. 93, no. 1

2012

Abstract	The genus Shewanella contains Gram negative γ-proteobacteria capable of reducing a wide range of substrates, including insoluble metals and carbon electrodes. The utilization of insoluble respiratory substrates by bacteria requires a strategy that is quite different from a traditional respiratory strategy because the cell cannot take up the substrate. Electrons generated by cellular metabolism instead must be transported outside the cell, and perhaps beyond, in order to reduce an insoluble substrate. The primary focus of research in model organisms such as Shewanella has been the mechanisms underlying respiration of insoluble substrates. Electrons travel from the menaquinone pool in the cytoplasmic membrane to the surface of the bacterial cell through a series of proteins collectively described as the Mtr pathway. This review will focus on respiratory electron transfer from the surface of the bacterial cell to extracellular substrates. Shewanella sp. secrete redox-active flavin compounds able to transfer electrons between the cell surface and substrate in a cyclic fashion—a process termed electron shuttling. The production and secretion of flavins as well as the mechanisms of cell-mediated reduction will be discussed with emphasis on the experimental evidence for a shuttle-based mechanism. The ability to reduce extracellular substrates has sparked interest in using Shewanella sp. for applications in bioremediation, bioenergy, and synthetic biology.
Keywords	Shewanella ; bacteria ; bioenergy ; bioremediation ; carbon ; cell membranes ; electrodes ; electron transfer ; electrons ; flavins ; metabolism ; metals ; proteins ; secretion ; synthetic biology
Language	English
Dates of publication	2012-01
Size	p. 41-48.
Publishing place	Springer-Verlag
Document type	Article
ZDB-ID	392453-1
ISSN	1432-0614 ; 0171-1741 ; 0175-7598
ISSN (online)	1432-0614
ISSN	0171-1741 ; 0175-7598
DOI	10.1007/s00253-011-3653-0
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Article ; Online: ExsA recruits RNA polymerase to an extended -10 promoter by contacting region 4.2 of sigma-70.

Vakulskas, Christopher A / Brutinel, Evan D / Yahr, Timothy L

Journal of bacteriology

2010 Volume 192, Issue 14, Page(s) 3597–3607

Abstract: ExsA is a member of the AraC family of transcriptional activators and is required for expression of the Pseudomonas aeruginosa type III secretion system (T3SS). ExsA-dependent promoters consist of two binding sites for monomeric ExsA located ... ...

Abstract	ExsA is a member of the AraC family of transcriptional activators and is required for expression of the Pseudomonas aeruginosa type III secretion system (T3SS). ExsA-dependent promoters consist of two binding sites for monomeric ExsA located approximately 50 bp upstream of the transcription start sites. Binding to both sites is required for recruitment of sigma(70)-RNA polymerase (RNAP) to the promoter. ExsA-dependent promoters also contain putative -35 hexamers that closely match the sigma(70) consensus but are atypically spaced 21 or 22 bp from the -10 hexamer. Because several nucleotides located within the putative -35 region are required for ExsA binding, it is unclear whether the putative -35 region makes an additional contribution to transcription initiation. In the present study we demonstrate that the putative -35 hexamer is dispensable for ExsA-independent transcription from the P(exsC) promoter and that deletion of sigma(70) region 4.2, which contacts the -35 hexamer, has no effect on ExsA-independent transcription from P(exsC). Region 4.2 of sigma(70), however, is required for ExsA-dependent activation of the P(exsC) and P(exsD) promoters. Genetic data suggest that ExsA directly contacts region 4.2 of sigma(70), and several amino acids were found to contribute to the interaction. In vitro transcription assays demonstrate that an extended -10 element located in the P(exsC) promoter is important for overall promoter activity. Our collective data suggest a model in which ExsA compensates for the lack of a -35 hexamer by interacting with region 4.2 of sigma(70) to recruit RNAP to the promoter.
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Base Sequence ; DNA, Bacterial ; DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Gene Expression Regulation, Bacterial/physiology ; Molecular Sequence Data ; Promoter Regions, Genetic ; Protein Subunits/genetics ; Protein Subunits/metabolism ; Pseudomonas aeruginosa/genetics ; Pseudomonas aeruginosa/metabolism ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Sigma Factor/genetics ; Sigma Factor/metabolism ; Trans-Activators/genetics ; Trans-Activators/metabolism ; Transcription, Genetic
Chemical Substances	Bacterial Proteins ; DNA, Bacterial ; ExsA protein, Pseudomonas aeruginosa ; Protein Subunits ; Recombinant Fusion Proteins ; Sigma Factor ; Trans-Activators ; RNA polymerase sigma 70 (EC 2.7.7.-) ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
Language	English
Publishing date	2010-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00129-10
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Article ; Online: The distal ExsA-binding site in Pseudomonas aeruginosa type III secretion system promoters is the primary determinant for promoter-specific properties.

Brutinel, Evan D / King, Jessica M / Marsden, Anne E / Yahr, Timothy L

Journal of bacteriology

2012 Volume 194, Issue 10, Page(s) 2564–2572

Abstract: Transcription of the Pseudomonas aeruginosa type III secretion system is controlled by ExsA, a member of the AraC/XylS family of regulators. Each ExsA-dependent promoter contains two adjacent binding sites for monomeric ExsA. The promoter-proximal site ( ... ...

Abstract	Transcription of the Pseudomonas aeruginosa type III secretion system is controlled by ExsA, a member of the AraC/XylS family of regulators. Each ExsA-dependent promoter contains two adjacent binding sites for monomeric ExsA. The promoter-proximal site (binding site 1) consists of highly conserved GnC and TGnnA sequences that are individually recognized by the two helix-turn-helix (HTH) DNA-binding motifs of an ExsA monomer. While the GnC and TGnnA sequences are important for binding to site 1, the promoter-distal binding sites (site 2) lack obvious similarity among themselves or with binding site 1. In the present study, we demonstrate that site 2 in the P(exsC) promoter region contains a GnC sequence that is functionally equivalent to the GnC in site 1 and recognized by the first HTH motif of an ExsA monomer. Likewise, the second HTH interacts with an adenine residue in binding site 2. Although several candidate GnC sequences are also present in site 2 of the P(exsD), P(exoT), and P(pcrG) promoters, the GnC sequences were not required for ExsA-dependent transcription or ExsA binding. A comparison of hybrid promoters composed of binding site 2 from one promoter fused to binding site 1 derived from another promoter indicates that ExsA-binding affinity, promoter strength, and the degree of promoter bending are properties that are largely determined by binding site 2. Based on these data, we propose that the manner in which ExsA interacts with binding site 2 at the P(exsC) promoter is distinct from the interactions occurring at other promoters.
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Base Sequence ; Binding Sites ; DNA, Bacterial ; Gene Expression Regulation, Bacterial/physiology ; Mutagenesis ; Mutation ; Promoter Regions, Genetic/genetics ; Protein Binding ; Pseudomonas aeruginosa/genetics ; Pseudomonas aeruginosa/metabolism ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Trans-Activators/genetics ; Trans-Activators/metabolism
Chemical Substances	Bacterial Proteins ; DNA, Bacterial ; ExsA protein, Pseudomonas aeruginosa ; Recombinant Fusion Proteins ; Trans-Activators
Language	English
Publishing date	2012-03-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00106-12
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