Table 1 Possible role for uncharacterized TFs in S. aureus USA300

SAUSA300_0063

Crp

Present in the ACME element

[9]

SAUSA300_0093

LysR

YwqM (30.2%) and GltR (27.9%), in B. subtilis. The latter appears to be involved in glutamate synthase expression.

[10]

SAUSA300_0095

LysR

PtxR of Pseudomonas aeruginosa PAO1 (41.5%) and Yersinia pestis (38.7%). Activates the expression of exotoxins and represses the expression of quorum sensing related genes.

[11, 12]

SAUSA300_0104

AraC

Btr (24.5%) from B. subtilis. One-component regulator that controls siderophore transport

[13]

SAUSA300_0137

GntR

TreR (37%), involved in the regulation of trehalose related genes in B. subtilis. It is encoded divergent to purine synthesis genes.

[14]

SAUSA300_0217

TCS-RR

YesN (38.4%) and DegU (35.8%) from B. subtilis. The latter is involved in the expression of proteases and biofilm.

[15]

SAUSA300_0238

BglG

MnaR (25%) from B. subtilis

SAUSA300_0258

GntR

LutR (44.4%), involved in regulation of lactate and biofilm in B. subtilis. It has a UbiC transcription regulator-associated (UTRA) domain.

[16]

SAUSA300_0333

BglG

LicR (28.5%) from B. subtilis. Regulates the transport and degradation of oligomeric beta-glucosides

[17]

SAUSA300_0350

Xre

YgzD (46%) B. subtilis

SAUSA300_0373

Xre

No identity to characterized proteins

SAUSA300_0503

GntR

YdeL (36%) and GabR (32.3%) both from B. subtilis. GabR regulates the expression of GABA synthesis genes. It also has some identity to S. aureus NorG (23%). It has a pyridoxal phosphate (PLP)-dependent aspartate aminotransferase domain.

[18]

SAUSA300_0577

GntR

This is the first gene in a putative operon with a pyridine nucleotide-disulphide oxidoreductase.

SAUSA300_0658

LysR

E. coli OxyR (29.4%), positive regulator for a hydrogen peroxide-inducible regulon. Possible CcpC homolog, involved in regulation of TCA.

[19]

SAUSA300_0683

GntR

IolR (30.9%), repressor or the myo-inositol operon in B. subtilis. Its genomic context shows that it may regulate genes involved in fructose metabolism.

[20]

SAUSA300_0803

Xre

Toxin-antitoxin systems. These systems may contribute to the preservation of plasmids and genetic islands, however the role of many of them is still unknown

[21]

SAUSA300_0804

Xre

Toxin-antitoxin system

[21]

SAUSA300_0878

LysR

CytR (25%), regulator of the citrate synthase genes in B. subtilis. In S. aureus it is divergent to isopropylmalate synthase involved in Leu and pyruvate metabolism.

[22]

SAUSA300_0858

Rps1

B. subtilis YabR (42%), putative polyribonucleotide nucleotidyl transferase

SAUSA300_0928

ComK

B. subtilis ComK (33.9%), required for genetic competence

[23]

SAUSA300_0954

MarR

YdgJ (35.4%), B. subtilis

SAUSA300_0998

Xre

Rpc (33.7%) from B. subtilis bacteriophage phi 105. Involved in the regulation of lysogeny.

SAUSA300_1170

GntR

YmfC (34.3%), B. subtilis. It has a UbiC transcription regulator-associated (UTRA) domain.

SAUSA300_1174

GntR

YmfK (65%), B. subtilis

SAUSA300_1175

GntR

YmfM (31.25%) B. subtilis

SAUSA300_1204

Xre

No identity to characterized proteins

SAUSA300_1220

TCS-RR

LuxR-like protein with identity to DesR (43.2%), responsible for thermosensing and signal transduction at low temperatures in B. subtilis. Also has identity to YvfU (45%) from B. subtilis

[24]

SAUSA300_1424

Unknown

No identity to characterized proteins

SAUSA300_1433

Xre

No identity to characterized proteins

SAUSA300_1434

Xre

Toxin-antitoxin system

[21]

SAUSA300_1455

AraC

AarP (30.8%), involved in regulation of 2'-N-acetyltransferase in Providencia stuartii.

[25]

SAUSA300_1469

ArgR

28% identity with S.aureus ArgR. In operon with a DNA repair protein

SAUSA300_1914

GltR

B. subtilis YtrA (39.45%), possible repressor of an operon for a putative ATP-binding cassette transport system involved in acetoin utilization. YtrA is an additional regulator of cell envelope stress responses in B. subtilis.

[26, 27]

SAUSA300_1946

RinB

RinB (76%) from phage 11. Activates int gene expression

[28]

SAUSA300_1968

Xre

No identity to characterized proteins

SAUSA300_1969

Xre

LexA (28%), SOS regulator in E. coli

SAUSA300_2077

HxlR

B. subtilis YodB (38.46%), regulation of yocJ (azoR1) after exposure to thiol-reactive compounds. A similar gene in B. subtilis regulates formaldehyde detoxification via hxlAB. In S. aureus it is not close to these genes, even though they are present in the genome.

[29]

SAUSA300_2106

BglG

ManR_(23.6%), mannose utilization in B. subtilis

[30]

SAUSA300_2160

MerR

AdhR (38%) B. subtilis. Transcriptional regulator involved in the response to aldehyde stress.

[31]

SAUSA300_2216

MarR

YwoH (31.6%) from B. subtilis

SAUSA300_2248

AraC

E. coli YijO (28.6%), might be involved in the regulation of genes encoding enzymes related to PTS systems

[32]

SAUSA300_2261

GntR

No identity to characterized proteins

SAUSA300_2300

TetR

No identity to characterized proteins. Divergent to 2 multidrug transport proteins (emrAB homologs)

SAUSA300_2310

LytTr

Bears a LytTR domain, which is an only recently characterized family.

SAUSA300_2322

TetR

B. subtilis YxbF (42.4%). In S. aureus it is in an operon with a CorA Mg transporter

SAUSA300_2336

MerR

CueR (42.8%), involved in copper induction in B. subtilis.

[33]

SAUSA300_2445

MerR

36% identical to BltR, B. subtilis, and MerR (31%), S. aureus. The former is involved in response to structurally dissimilar drugs, while the latter is on a plasmid specifying resistance for mercurial compounds.

[34, 35]

SAUSA300_2547

Unknown

B. subtilis YuaC (55.4%)

SAUSA300_2452

MarR

Similar to B. subtilis YvnA (35.8%), (29%) and AdcR from Streptococcus pneumoniae. AdcR is able to sense metals for the regulation of zinc uptake proteins related genes encoding cell-surface zinc-binding pneumococcal histidine triad proteins and AdcAII (laminin binding). Also has a 33% identity to SarZ

[36]

SAUSA300_2459

MarR

MhqR (41.5%) regulates multiple dioxygenases/glyoxalases and an azoreductase that confer resistance to 2-methylhydroquinone and catechol in B. subtilis

[37]

SAUSA300_2490

LysR

No identities to characterized proteins. Divergent to operon encoding mmpL (transporter) and Feo iron dependent transporters

SAUSA300_2509

TetR

B. subtilis YxbF (31.6%).

SAUSA300_2515

TetR

SlmA (26.2%) in Vibrio parahaemolyticus. SlmA proteins are involved in nucleoid occlusion systems in E. coli. In S. aureus it is in an operon with genes encoding an oxidoreductase, an amidohyrolase and a hydrolase.

[38]

SAUSA300_2530

TetR

No identity to characterized proteins.

SAUSA300_2563

MarR

PetP, (33.06%), necessary for photosynthetic and respiratory growth in Rhodobacter capsulatus

[39]

SAUSA300_2575

BglG

No identity to characterized proteins.

SAUSA300_2640

Xre

ImmR (46% identity), involved in mobilization of the genetic element ICEB1 in B. subtilis

[40, 41]

SAUSA300_2625

PadR

PadR (37.5%), repressor of phenolic acid response genes in B. subtilis

[42]