A Structural Code for Discriminating between Transcription Signals Revealed by the Feast/Famine Regulatory Protein DM1 in Complex with Ligands

Abstract

Feast/famine regulatory proteins (FFRPs) comprise the largest group of archaeal transcription factors. Crystal structures of an FFRP, DM1 from Pyrococcus, were determined in complex with isoleucine, which increases the association state of DM1 to form octamers, and with selenomethionine, which decreases it to maintain dimers under some conditions. Asp39 and Thr/Ser at 69-71 were identified as being important for interaction with the ligand main chain. By analyzing residues surrounding the ligand side chain, partner ligands were identified for various FFRPs from Pyrococcus, e.g., lysine facilitates homo-octamerization of FL11, and arginine facilitates hetero-octamerization of FL11 and DM1. Transcription of the fl11 gene and lysine synthesis are regulated by shifting the equilibrium between association states of FL11 and by shifting the equilibrium toward association with DM1, in response to amino acid availability. With FFRPs also appearing in eubacteria, the origin of such regulation can be traced back to the common ancestor of all extant organisms, serving as a prototype of transcription regulations, now highly diverged.

Transcription Regulation by Feast/Famine Regulatory Proteins, FFRPs, in Archaea and Eubacteria

“…Although several FFRPs from archaea and eubacteria have been crystallized (Table 1), [7][8][9][10][11][12][13][14][15] FL11 remains as the single FFRP whose structure has been determined in complex with its target DNA. 7) A DNA duplex was included when crystallizing Lrp, but the DNA was disordered and not traced.…”

“…8) Another FFRP from P. OT3, DM1 (pot1216151), was crystallized in complexes with two respective ligands that have different effects on the association state of this FFRP; isoleucine increases the association state to form octamers, and methionine has more dissociating effects to keep dimers under some conditions. 9) Another FFRP, NMB0573 from the eubacterium Neisseria meningitidis has been co-crystallized with isoleucine and with methionine, although the effects of interactions have not been characterized well. 10) These crystal structures have enabled us to study the molecular basis of regulation by FFRPs.…”

“…1). 9,14) FFRPs of this type are referred to as demi (DM-) FFRPs (Table 1). 12,16) Higher-order structures are formed by assembling dimers (Fig.…”

“…2). In the crystal structures, octameric disks formed by four dimers were frequently observed ( 9,17) A decameric disk was formed in the crystal by five dimers of TTHA0845.…”

“…9 7,18) Changing any base in TGAAA/ TTTCA weakens the interaction. 7) Although any combinations of W bases are tolerated at the central 3 bps, replacing these by G:C severely weakens the interaction.…”