{PDOC00592}
{PS00715; SIGMA70_1}
{PS00716; SIGMA70_2}
{BEGIN}
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* Sigma-70 factors family signatures *
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Sigma factors [1] are bacterial transcription initiation factors  that promote
the attachment of the core RNA polymerase to specific initiation sites and are
then released.  They  alter  the  specificity  of  promoter  recognition. Most
bacteria express a multiplicity of sigma factors. Two of these factors, sigma-
70 (gene  rpoD),  generally  known  as the major or primary sigma factor,  and
sigma-54 (gene  rpoN  or  ntrA)  direct the transcription of a wide variety of
genes. The    other  sigma  factors,  known  as alternative sigma factors, are
required for the transcription of specific subsets of genes.

With regard  to  sequence  similarity,  sigma  factors can be grouped into two
classes: the  sigma-54 and sigma-70 families. The sigma-70 family includes, in
addition to the primary sigma factor, a wide variety of sigma factors, some of
which are listed below:

 - Bacillus  sigma  factors  involved  in  the control of sporulation-specific
   genes: sigma-E  (sigE or spoIIGB), sigma-F (sigF or spoIIAC), sigma-G (sigG
   or spoIIIG),      sigma-H      (sigH   or   spo0C)  and  sigma-K  (sigK  or
   spoIVCB/spoIIIC).
 - Escherichia coli and related bacteria sigma-32 (gene rpoH or htpR) involved
   in the expression of heat shock genes.
 - Escherichia coli  and  related   bacteria  sigma-27 (gene fliA) involved in
   the expression of the flagellin gene.
 - Escherichia  coli   sigma-S (gene rpoS or katF)  which seems to be involved
   in the  expression  of  genes  required  for  protection  against  external
   stresses.
 - Myxococcus xanthus sigma-B  (sigB)  which  is  essential for the late-stage
   differentiation of that bacteria.

Alignments of the sigma-70 family permit the identification of four regions of
high conservation [2,3].  Each of these four regions can in turn be subdivided
into a number of sub-regions. We developed signature patterns based on the two
best conserved sub-regions.  The  first pattern corresponds to sub-region 2.2;
the exact  function of  this sub-region is  not  known  although  it could  be
involved in the binding of  the sigma factor to  the core RNA polymerase.  The
second pattern corresponds  to  sub-region  4.2  which seems to harbor  a DNA-
binding 'helix-turn-helix'    motif    involved  in  binding the conserved -35
region of  promoters recognized by the major sigma factors. The second pattern
starts one  residue  before  the  N-terminal  extremity  of the HTH region and
ends six residues after its C-terminal extremity.

-Consensus pattern: [DE]-[LIVMF](2)-[HEQS]-x-G-x-[LIVMFA]-G-L-[LIVMFYE]-x-
                    [GSAM]-[LIVMAP]
-Sequences known to belong to this class detected by the pattern: ALL,  except
 for Bacillus subtilis sigma-B and Vibrio parahaemolyticus flaS.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Consensus pattern: [STN]-x(2)-[DENQ]-[LIVMT]-[GAS]-x(4)-[LIVMF]-[PSTG]-x(3)-
                    [LIVMA]-x-[NQR]-[LIVMA]-[EQH]-x(3)-[LIVMFWK]-x(2)-[LIVM]
-Sequences known to belong to this class detected by the pattern:  Almost  all
 of them, with a few exceptions.
-Other sequence(s) detected in Swiss-Prot: 1.

-Note: The  sigma-70  factor  family  also includes a divergent subfamily that
 regulates gene  encoding  for  proteins  with  extracytoplasmic function [4].
 These sigma  factors,  collectively  known  as  ECF, are not picked up by the
 above patterns. A separate entry (see <PDOC00814>) has been developed to deal
 with them.

-Last update: December 2004 / Pattern and text revised.

[ 1] Helmann J.D., Chamberlin M.J.
     "Structure and function of bacterial sigma factors."
     Annu. Rev. Biochem. 57:839-872(1988).
     PubMed=3052291; DOI=10.1146/annurev.bi.57.070188.004203
[ 2] Gribskov M., Burgess R.R.
     "Sigma factors from E. coli, B. subtilis, phage SP01, and phage T4 are
     homologous proteins."
     Nucleic Acids Res. 14:6745-6763(1986).
     PubMed=3092189
[ 3] Lonetto M.A., Gribskov M., Gross C.A.
     "The sigma 70 family: sequence conservation and evolutionary
     relationships."
     J. Bacteriol. 174:3843-3849(1992).
     PubMed=1597408
[ 4] Lonetto M.A., Brown K.L., Rudd K.E., Buttner M.J.
     "Analysis of the Streptomyces coelicolor sigE gene reveals the
     existence of a subfamily of eubacterial RNA polymerase sigma factors
     involved in the regulation of extracytoplasmic functions."
     Proc. Natl. Acad. Sci. U.S.A. 91:7573-7577(1994).
     PubMed=8052622

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