Examples of plant-released molecules that are recognized as signals for induction of specific responses in various plant-associated bacteria. Luteolin (A) and genistein (B) are flavonoids that induce the transcription of nodulation genes in various rhizobia. Stachydrine (C) and trigonelline (D) are nonflavonoids that induce nod genes in S. meliloti. Tetronic acid (E) and erytronic acid (F) activate nod expression in S. meliloti, M. loti, and R. lupini. Acetosyringone (G) and ferulate (H) are phenolic compounds that induce virulence genes in A. tumefaciens. Shikimate (I) and quinate (J) induce coronatine biosynthetic genes in P. syringae pv. tomato DC3000. Quercetin (K) and arbutin (L) are phenolic glycosides that activate the production of syringomycin in P. syringae pv. syringae.

Structure of CbnR, a LysR-type regulator homologous to NodD and OccR. (A) Schematic drawing of a subunit of a CbnR tetramer. The subunit can be divided into two domains, the DNA binding domain (DBD) and the regulatory domain (RD), which are connected by the 29 amino acid residues of the linker helix α4. Cylinders and arrows represent α-helices and β-sheets, respectively. (B) Ribbon drawing of a CbnR dimer. The two CbnR subunits, shown in red and blue, are dimerized through the α4 linker helix of each subunit. In the dimer, the two subunits adopt different conformations, such that the two DNA binding domains and the two α4-helices show a two-fold rotational symmetry (blue arrow), while the two regulatory domains are related to each other by a 112° rotation around an axis between them (dotted red arrow). The two axes ofthe rotation lie at approximately a 50° angle to each other. (C) Model structure of the CbnR tetramer in complex with bent DNA. The tetramer, which is thought to be the DNA-bound form of CbnR, can be regarded as a dimer of dimers, which are related to each other by a two-fold axis but are each composed of two subunits in different conformations. This unique subunit composition of the tetramer enables the arrangement of the DNA binding domains in a linear fashion, which is required to interact with the long DNA binding sites that are bound by LysR-type proteins. DNA bending seems to be caused by the curved arrangement of the four DNA binding domains in the tetramer. Adapted from reference 342 with permission of the publisher.

Structure of the oxygen-sensing two-component kinase FixL, and regulation of rhizobial nitrogen fixation genes. (A) Hydropathy profile of FixL of S. meliloti. The hydropathy plot was constructed with the amino acid sequence of the complete FixL protein (SmFixL), which contains four hydrophobic stretches that serve to anchor the protein to the membrane. The periplasmic and membrane-spanning residues are not required for the function of this protein, since a truncated FixL lacking this region is fully functional (SmFixL*). FixL of B. japonicum (BjFixL) lacks the membrane-spanning domain. (B) Detection of oxygen by the PAS domain of BjFixL. (Reprinted in part from reference 194 with permission of the publisher). Panel I shows a ribbon diagram of the BjFixL PAS domain complexed with carbon monoxide (CO-BjFixLH). The PAS domain has a glove-like fold consisting of a central β-sheet with flanking α-helices. The heme cofactor lies in the palm of the glove. Panel II shows the BjFixL heme-binding pocket for deoxy-BjFixLH and oxy-BjFixLH. In the unliganded (on) state, the FG loop (residues Thr209 to Arg220) moves close to the heme pocket, while in the oxygen-bound state, the loop is shifted away from the heme pocket. This FG loop shift presumably induces a global conformational change in the full-length protein, which in turn inhibits the kinase activity of the protein. (C) Regulation of nitrogen fixation genes of S. meliloti in response to oxygen. Dashed blocked lines represent inhibition of FixL and NifA activity under aerobic conditions. Solid arrows represent transcriptional activation, and blocked solid lines represent transcriptional repression, under microaerobic conditions.

Structures of rhizopines produced and released by bacteroids of S. meliloti and R. leguminosarum and of conjugal opines released from tumors induced by A. tumefaciens. (A and B) Rhizopines 3-O-MSI (B) and SI (A) are released from nodules infected by S. meliloti and R. leguminosarum. (C to G) Agrocinopines A and B, agrocinopines C and D, and octopine are the conjugal opines of nopaline-, chrysopine-, and octopine-type A. tumefaciens strains. (H) Nopaline and agrocinopines A and B serve as conjugal opines in A. rhizogenes.

Regulation of A. tumefaciens virulence genes by plant-released signals. (A) The vir-gene regulatory cascade involving the VirA-VirG two-component system and ChvE sugar binding protein. VirA is a transmembrane histidine kinase that detects plant-released phenolics, sugars, and acidity and phosphorylates the DNA binding response regulator VirG. Acidic pH and phenolics are detected by the linker domain of VirA, while sugars are detected by the chromosomally encoded ChvE protein. ChvE is a periplasmic sugar binding protein that makes contacts with the VirA periplasmic domain, enhancing the phenolic-induced activity of VirA. The phosphorylated VirG activates the transcription of vir genes and of the repABC operon, which is required for replication of the pTi plasmid. (B) Model for regulation of kinase activity of a VirA dimer. VirA histidine kinase is a dimer in its native form (368). Each of its subunits is composed of the periplasmic, linker, kinase, and receiver domains. Each kinase domain is further divided into the phospho-donor subdomain, which contains the ATP binding site, and the phospho-acceptor subdomain, which contains the conserved His residue that is the site of autophosphorylation. Within a VirA dimer, the phospho-donor subdomain of each VirA subunit interacts with the phospho-acceptor domain of the opposite subunit. Environmental signals are transmitted from the periplasmic and linker domains of one subunit to a complex containing the phospho-donor subdomain of the same subunit and the phospho-acceptor domain of the opposite subunit. Similarly, the receiver domain of each subunit inhibits the complex composed of the phospho-donor subdomain of the same subunit and the phospho-acceptor domain of the opposite subunit. Adapted from reference 51 with permission of the publisher.

Regulation and organization of conjugal opine-regulated operons in different types of Ti plasmids. (A) Model for OccR activation of the occQ promoter. In the absence of octopine, OccR binds four nonconsecutive major grooves (sites 1, 2, 4, and 5), resulting in a 60-nucleotide footprint and a high-angle DNA bend. Octopine (represented by black dots) causes one dimer to shift position by one helical turn (from sites 1 and 2 to sites 2 and 3), shortening the footprint and relaxing the DNA bend. This conformation allows stimulatory contacts with RNA polymerase that are not permitted by the elongated conformation. OccR binds at all times to the high-affinity subsite (sites 4 and 5). (B) Location of traR in the opine-regulated operons on different Agrobacterium Ti plasmids. For octopine-type Ti plasmids, the occ operons of pTiR10, pTiA6, pAch5, and pTi15955 are regulated by octopine via a LysR-type regulator OccR. traR is the last gene of this 14-gene operon. Gene organization and designations are as described in reference 152. For nopaline-type Ti plasmids, the acc and arc operons of pTiC58 are regulated by agrocinopines A and B via the repressor AccR. traR is the fourth gene of the arc operon (386). For chrysopine-type Ti plasmids, the arc operon and a putative acc region of pTiChry5 are presumably regulated by the product of accR_Chry5, which, based on the incomplete sequence, could code for a protein related to AccR of pTiC58. traR_Chry5 is part of a two-gene arc operon (364). For plasmid pAtK84, the nox and arc operons of pAtK84b are regulated by nopaline and agrocinopines A and B, respectively. traR_noc and traR_acc lie within the nox and arc operons, respectively (365).

Regulation of the production of pectinolytic (Pel) exoenzymes in soft rot erwinias. (A) Signals and regulatory proteins involved in regulation of expression of pectinolytic enzymes in E. chrysanthemi. Several environmental signals such as pH, temperature, and osmolarity affect the expression of the exoenzyme genes; however, it is unknown how these signals are recognized and integrated. PecT and PecS are transcriptional regulators of exoenzyme genes, but the signals to which they respond are unknown. See the text for details. (B) Interaction between KdgR repressor and global regulatory system ExpS-ExpA in regulation of exoenzyme production in E. carotovora. Synthesis of extracellular enzymes in E. carotovora is under the control of a global regulatory two-component system, ExpS-ExpA, which is homologous to the GacS-GacA systems found in various proteobacteria. Based on the current model (211, 247), activation of the sensor kinase ExpS by unknown signals triggers a phosphorelay, activating the response regulator ExpA. By an unknown mechanism, phosphorylated ExpA positively controls the transcription of regulatory RNA species RsmB, which sequester the translational repressor RsmA and thereby render the mRNAs of pectinolytic exoenzymes accessible for translation. The ExpS-ExpA system also induces production of AHLs, and there is evidence that AHLs control the production of E. carotovora virulence factors through RsmA and RsmB (72). Expression of extracellular enzymes is also controlled by KdgR, which, in the absence of pectate, represses the transcription of exoenzyme genes. Repression is relieved by pectate and its intracellular metabolites KDG, DKI, and DKII. KdgR also regulates the expression of rsmA and rsmB; it induces the transcription of rsmA and represses the expression of rsmB (234, 292). E. carotovora pel genes are also regulated by several other regulators, which are described in the text.

Models of the hrp gene regulatory cascades in P. syringae, E. amylovora, and R. solanacearum. Based on differences in regulation, hrp genes can be divided into two groups. Group I hrp clusters are found in P. syringae, Erwinia, and Pantoea spp., where hrp genes are activated by a member of the ECF subfamily of sigma factors, called HrpL (150, 520, 537, 538). (A) In P. syringae, expression of hrpL requires the products of the hrpRS operon, which are 60% identical to each other and belong to the NtrC family of two-component response regulators. There is some controversy regarding the mechanism by which HrpR and HrpS regulate the hrpL promoter. It has been proposed by one group that hrpL transcription is induced by an HrpR-HrpS heterodimer (229). Another group reported that HrpR functions as a transcriptional activator of hrpS expression and that HrpS acts independently of HrpR to activate expression of hrpL (data not shown) (182). (B) In E. amylovora, expression of HrpL is activated by HrpS, which is highly similar to HrpS of P. syringae (520). In E. amylovora, a two-component system, HrpX-HrpY, is also involved in the hrpL regulation. Transcription of hrpRS in P. syringae and hrpS in E. amylovora is upregulated in the plant apoplast and in hrp-inducing minimal medium. HrpL and HrpS are conserved in all members of this group and are shaded in gray in panels A and B. (C) Group II hrp operons are found in X. campestris and R. solanacearum, where an OmpR-like transcriptional regulator HrpG induces the transcription of hrpB, whose product is a member of the AraC family of regulators and induces transcription of the rest of the hrp and hrc genes. HrpG and HrpB are conserved in all members of this group and are shaded in gray. In R. solanacearum, an outer membrane protein, PrhA, is involved in detection of a plant signal, which appears to be a nondiffusible component of the plant cell wall and whose detection was proposed to require a physical bacterium-plant cell contact. Based on a proposed model (55), the signal detected by PrhA is transmitted to the membrane protein PrhR, which activates an ECF sigma factor, PrhI. PrhI induces the transcription of a gene encoding a transcriptional regulator, PrhJ, leading to expression of hrpG. HrpG activates the expression of hrpB, resulting in induction of the remaining hrp genes. OM, outer membrane; IM, inner membrane.