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Table 1 List of genes identified as potentially being phase variable in N. gonorrhoeae – excluding the opa and pilC genes.

From: Strain-specific differences in Neisseria gonorrhoeae associated with the phase variable gene repertoire

XNG# †

TRACT ‡

CANDIDACY *

FUNCTIONAL ROLE

GENE

ANNOTATED FUNCTION

XNG0023

GGGGCGG -

L

Other

 

prolyl oligopeptidase family protein

XNG0060

C(G)6 -

S

Surface sugar biosynthesis

wbpC / pglI

putative LPS biosynthesis or pilin glycosylation protein

XNG0075

(C)7 -

L

Hypothetical protein

 

hypothetical protein

XNG0080

(C)10 -

S

Hypothetical protein

pglH

pilin glycosylation protein

XNG0081

A(C)7 -

S

Surface sugar biosynthesis

pglG

pilin glycosylation protein

XNG0112

(A)6 p

S

Hypothetical protein

 

hypothetical protein

XNG0115

(C)4 -

L

Other

cvaA

putative colicin V secretion protein

XNG0158

(C)5 degenerate

L

Hypothetical protein

 

hypothetical protein

XNG0188

AA(C)5 -

L

Other

potD-2

spermidine/putrescine ABC transporter,

XNG0189

(CAAACAC)4 -

K

Surface sugar biosynthesis

pglE

pilin glycosylation protein

XNG0245

degenerate

S

Iron acquisition

lbpA

lactoferrin-binding protein A

XNG0388

(G)7 +

S

R-M Systems

hsdS||

type I restriction enzyme S protein

XNG0412

(G)7 +

S

Hypothetical protein

 

hypothetical protein

XNG0470

(G)7 +

S

Hypothetical protein

 

hypothetical protein ††

XNG0473

(T)9 +

S

Hypothetical protein

 

hypothetical protein

XNG0503a

(C)6A(C)9 +

S

Hypothetical protein

 

hypothetical protein

XNG0508

AACCGGCAAACA -

L / M

Hypothetical protein

 

hypothetical protein

XNG0520

(CCCAA)12 -

S

R-M Systems

 

type III restriction system methylase

XNG0552

(C)5 degenerate

L

Hypothetical protein

 

hypothetical protein

XNG0608

CCACACCC -

M

Other

nifS

aminotransferase

XNG0610

(G)7 -

L

Other

lldD

L-lactate dehydrogenase

XNG0612

(GCCA)37 -

S

R-M Systems

 

putative restriction system methylase

XNG0644

(A)9 -

L

R-M Systems

 

modification methylase NlaIV

XNG0663

CCCCTCC +

L

Hypothetical protein

 

hypothetical protein

XNG0703

(C)7 -

L

Other

dnaX

DNA polymerase III, subunits gamma and tau

XNG0714

GGAAGG -

L

Other

mobA

molybdopterin-guanine dinucleotide biosynthesis

XNG0832

(T)11C(G)6 p

K

Surface associated proteins

porA

outer membrane protein

XNG0887

(AAGC)4 -

S

Hypothetical protein

 

hypothetical protein

XNG0905

(AAGC)3 +

S

Surface associated proteins

virG

AIDA related protein

XNG0954

(C)7 -

L

Other

ppx

exopolyphosphatase

XNG0973

(C)6 -

L

Hypothetical protein

 

hypothetical protein

XNG0986

(C)6 degenerate

S

Other

aspA

putative serotype-1-specific antigen

XNG1000

(G)7 +

S

Hypothetical protein

 

hypothetical protein

XNG1041

piv-Nm1B inserted

S

Surface sugar biosynthesis

 

putative glycosyl transferase

XNG1207a

(G)8 +

S

Hypothetical protein

 

hypothetical protein **

XNG1216

GGCGGCCAA

K

Iron acquisition

hmbR

hemoglobin receptor

XNG1268

(AT)5 -

L

Other

fixP

cytochrome c oxidase, subunit III

XNG1281

G(A)7 -

S

Hypothetical protein

 

hypothetical protein

XNG1341

(CAAG)20

S

Surface associated proteins

 

adhesin

XNG1356

CCCTGCACC p

M

Other

pntA

NAD(P) transhydrogenase alpha subunit

XNG1384

TCCGCCC -

L

Other

amiC

N-acetylmuramoyl-L-alanine amidase

XNG1423

TGTGGGGG -

S

Other

dca

competence-associated protein

XNG1460

(C)7 -

L

Hypothetical protein

 

hypothetical protein

XNG1511

(G)8 +

S

Hypothetical protein

 

hypothetical protein

XNG1563

(AAGC)3 +

S

Surface associated proteins

vapA

virulence associated protein

XNG1577

(G)8 +

S

Hypothetical protein

 

hypothetical protein **

XNG1589

(C)4TCC -

L

Other

dinG

probable ATP-dependent helicase

XNG1644

(G)11 -

K

Surface sugar biosynthesis

pgtA

pilin glycosylation protein

XNG1733

(G)8 -

M

Hypothetical protein

 

hypothetical protein

XNG1740

(C)7 -

L

Other

rplK

50S ribosomal protein L11

XNG1788

(G)8 +

M

Hypothetical protein

 

hypothetical protein **

XNG1834

(C)8 -

M

Hypothetical protein

 

hypothetical protein

XNG1856

(TA)5 -

L

Hypothetical protein

 

hypothetical protein

XNG1858

(G)5 -

L

Surface associated proteins

mafA-3

putative adhesin

XNG1868

(C)7 +

L

Other

map

methionine aminopeptidase

XNG1934

(A)9 p

S

Other

 

putative lipoprotein

XNG1942/41

(C)6 +

S

Other

 

putative hydrolase

XNG1968

(C)11 -

K

Surface sugar biosynthesis

lgtG

lipopolysaccharide glycosyl transferase

XNG1989

(C)13 p

K

Iron acquisition

frpB / fetA

iron-regulated outer membrane protein

XNG2004

(G)9 +

K

Iron acquisition

hpuA

hemoglobin-haptoglobin utilization protein

XNG2045

(G)11 +

K

Surface sugar biosynthesis

lgtA

acto-N-neotetraose biosynthesis glycosyl transferase

XNG2047

(G)14 +

K

Surface sugar biosynthesis

lgtC

LPS biosynthesis protein

XNG2048

(G)14 -

K

Surface sugar biosynthesis

lgtD

LPS biosynthesis protein

XNG2061

(TTCC)3 -

L

Other

plsX

fatty acid-phospholipid synthesis protein

  1. † CDS designation numbers come from our own annotation of the N. gonorrhoeae strain FA1090 genome sequence.
  2. ‡ The known or potential phase variable repeat tract from N. gonorrhoeae strain FA1090. The equivalent sequence is identified for genes without a repeat tract that are phase variable candidates from the meningococci. Following the sequence a - or + signifies if the CDS is in-frame or frame-shifted, respectively. Repeats in promoter or predicted promoter locations are indicated with a p. Degenerate indicates a gene with multiple frame-shifts or in-frame termination conditions.
  3. * The predicted likelihood of phase variability. K indicates a known phase variable gene; S indicates a strong candidate for phase variation; M indicates a moderate candidate; L indicates a low candidate. See text for details of these thresholds.
  4. †† XNG0470 is a homologue of XNG1014, and XNG1513 which have a (G)6 and are not frame-shifted.
  5. ** XNG1207a, XNG1577, and XNG1788 are homologues of each other.
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BMC Microbiology

ISSN: 1471-2180

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