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Chapter 15 : The Pho Regulon

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Abstract:

This chapter focuses on genes expressed during the phosphate deficiency response, with special emphasis on genes of the Pho regulon that are directly regulated by the PhoP-PhoR two-component systems. The study of phosphate metabolism in species in general and in in particular has been complicated by several factors that reflect the developmental complexity of the organism. PhoP or the N-terminal PhoP domain is a dimer in solution independent of its phosphorylation state. Although both PhoP and PhoP~P can bind to Pho regulon promoters, only PhoP~P is able to stimulate transcription initiation at any promoter tested. The regulatory coupling of the PhoP-PhoR and ResD-ResE signal transduction systems is illustrated in a working model consistent with current data. The Pho regulon of is directly regulated by PhoB (RR) and PhoR (HK). The signal transduction network emphasizes the importance of regulation upstream of PhoP and PhoR such that decreased Pi is not sufficient for Pho induction in certain mutant backgrounds or in certain growth conditions. The long linker region of over 180 aa in PhoR may include a second domain in addition to a PAS domain next to the catalytic domain. Although the catalytic domain of PhoR () has been shown to be sufficient for Pi-limited Pho induction and subsequent repression, it cannot be supposed that the N-terminal 248 aa of PhoR have no function. More likely, there is redundant regulation controlling the Pho regulon.

Citation: Hulett F. 2002. The Pho Regulon, p 193-201. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch15

Key Concept Ranking

Transcription Start Site
0.56077343
Operon Components
0.45476508
Cell Wall Components
0.43614388
Core Promoter
0.42314225
Upstream Promoter
0.40707758
0.56077343
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Figures

Image of FIGURE 1
FIGURE 1

(A) PhoP core binding region found between bp −20 and −60 in promoters activated by PhoP∼P. The core contains four repeats of conserved 6-bp sequence that is believed to bind two dimers based largely on mutagenesis of the PhoD promoter. (B) Determination of the conserved sequence for PhoP binding site repeats. The TTAACA-like sequences from 11 Pho regulon promoters were aligned. The tabulated numbers represent the number of times a specific nucleotide appears at that position. The boldface number identifies the most frequent nucleotide at that position. The promoters and the number of consensus repeats used from each included tu&A (8 consensus repeats) ( ), (6 repeats) ( ), (4 repeats) ( ), pfioB (4 repeats) ( ), tagA (4 repeats) ( ), tagD (2 repeats) ( ), (6 repeats) ( ), resA (2 repeats) ( ), (2 repeats) ( ), (4 repeats) ( ), and (4 repeats) ( ). (C) Tally of the frequency at which the assigned consensus nucleotide appears at each position in the 46 repeats.

Citation: Hulett F. 2002. The Pho Regulon, p 193-201. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch15
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Image of FIGURE 2
FIGURE 2

Insertion and/or deletion mutagenesis of promoter. (A) The wild-type promoter. Solid rectangles represent 1 1 1 ACA-like sequences at approximately −25, −35, −45, −55, −185, and −195 relative to the transcription start site. A straight arrow (→ or ←) shows the 5′ to 3′ direction of two consensus repeats (two solid rectangles separated by nonconserved sequence) believed to bind one PhoP dimer. Two dimer-binding sites separated by approximately five nonconserved bp make up the PhoP core binding region. Diagonal lines (//) indicates that the distance between upstream binding site and core binding region is not to scale. The bent arrow indicates the start of the PhoD coding sequence. Percent of transcription activity is designated 100% for the wild-type promoter. (B) Insertion mutation between consensus repeats in a putative dimer-binding site. Triangle (Δ) indicates the point of insertion of 5 or 10 bp. (C) Insertion between two dimer binding sites (Δ). (D) Insertion between core binding region and upstream secondary binding site (Δ). (E) Deletion of upstream secondary PhoP binding site. (F) Inverted orientation of secondary 5′ PhoP dimer binding site (↔). The effect of each promoter mutation (B, C., D, E, and F) is given as percent transcription activity compared with the wild-type promoter. Where two numbers are given, the first number reports results for a 5-bp insertion that would change the face of the helix, and the second number reports results for a 10-bp insertion that should restore the face of the helix, albeit with a 10-bp distance change.

Citation: Hulett F. 2002. The Pho Regulon, p 193-201. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch15
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Image of FIGURE 3
FIGURE 3

Model depicting the signal transduction network leading to Pho induction in a phosphate deficiency response. Proteins are indicated by ovals, and genes/operons are symbolized by rectangles. Solid lines indicate that direct interaction has been demonstrated. Dashed lines are utilized for interactions that could either be direct or indirect. Positive regulation is labeled with an arrow and a plus sign (+), while repression is noted by an arrow and a minus sign (−). Two-component system members are labeled as either the histidine kinase (HK) or response regulator (RR).

Citation: Hulett F. 2002. The Pho Regulon, p 193-201. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch15
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Image of FIGURE 4
FIGURE 4

The PhoR protein. The domains and the predicted topology of wild-type PhoR protein. Numbers indicate the approximate boundaries of each domain. Solid boxes represent the transmembrane sequence. The hatched box represents the conserved catalytic domain. TM1, the first transmembrane sequence; P, periplasmic or extracytoplasmic domain; TM2, the second transmembrane sequence; C2, the cytoplasmic linking domain containing a putative PAS domain adjacent to the catalytic domain; diagonal-striped box, the conserved catalytic domain; H360, the conserved histidine residue; O, outside of membrane; I, inside cytoplasmic membrane.

Citation: Hulett F. 2002. The Pho Regulon, p 193-201. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch15
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Tables

Generic image for table
TABLE 1

Pho regulon genes/operons

In vivo transcript was dependent on PhoP and/or PhoR during phosphate deprivation.

PhoP and/or PhoP∼P footprint within the promoter region.

PhoP-P was required for activation or repression of in vitro transcription with σ RNP.

Citation: Hulett F. 2002. The Pho Regulon, p 193-201. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch15
Generic image for table
TABLE 2

Mutational analysis determining interactions among regulatory genes

% change in APase expression, either reduced or hyperinduced, compared with the parental strain, JH642.

% change in expression, either reduced or hyperinduced, compared with the parental strain, JH642.

Spontaneous-compensatory mutation.

does not map to res, or locus; under investigation.

Citation: Hulett F. 2002. The Pho Regulon, p 193-201. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch15
Generic image for table
TABLE 3

Percent identity matrices

Citation: Hulett F. 2002. The Pho Regulon, p 193-201. In Sonenshein A, Losick R, Hoch J (ed), and Its Closest Relatives. ASM Press, Washington, DC. doi: 10.1128/9781555817992.ch15

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