The TrmB family: a versatile group of transcriptional regulators in Archaea

Abstract

Microbes are organisms which are well adapted to their habitat. Their survival depends on the regulation of gene expression levels in response to environmental signals. The most important step in regulation of gene expression takes place at the transcriptional level. This regulation is intriguing in Archaea because the eu-karyotic-like transcription apparatus is modulated by bacterial-like transcription regulators. The transcriptional regulator of mal operon (TrmB) family is well known as a very large group of regulators in Archaea with more than 250 members to date. One special feature of these regulators is that some of them can act as repressor, some as activator and others as both repressor and activator. This review gives a short updated overview of the TrmB family and their regulatory patterns in different Archaea as a lot of new data have been published on this topic since the last review from 2008.

Fig. 1

The gene clusters of the trehalose/maltose (TM) and the maltodextrin (MD) operon. a The TM gene cluster encoding the binding protein-dependent ABC transporter for trehalose/maltose, a trehalose synthase and TrmB is shown. The red lines mark the palindromic binding sequence of TrmB (TACTN₃AGTA) at the promoter region of malE (green). (b) The MD gene cluster encoding the binding protein-dependent ABC transporter for maltodextrin and an amylopullulanase is shown. A separate regulator is missing in the MD operon. The red line tags the first half of the binding sequence palindrome (TACT) (modified after Lee et al. 2008)

Fig. 2

Binding sites of Pfu TrmB at the first genes of the TM (malE, a) and MD (mdxE, b) operon. The binding sites are shown in bold letters. +1 represents the transcription start site. The promoter region of the malE gene includes a perfect palindrome (underlined), whereas the promoter region of mdxE just contains the first half of the palindrome. The B recognition element (BRE) and the TATA-box are shown in green boxes. The Thermococcales glycolytic motif (TGM, van de Werken et al. 2006), just present in the mdxE promoter, is in a blue box (modified after Lee et al. 2008)

Fig. 3

Models of the regulation mechanism of P. furiosus TrmB (a and b) and TrmBL1 (a–d), T. littoralis TrmB (a and b), T. kodakarensis Tgr (a–d) and H. salinarum VNG1451C (a–d) for genes where the proteins are acting as repressor and/or as activator. All binding motifs are palindromic inverted repeats with cis-regulatory sequences in front of the BRE/TATA box or at the transcription start site (+1). The binding motif for Pfu TrmB and Tli TrmB at the TM promoter is TACT-N₃-AGTA, at the MD operon of P. furiosus it is just the TACT sequence. Pfu TrmBL1 and Tk Tgr bind to TATCAC-N₅-GTGATA (TGM), the binding motif in H. salinarum is TACT-N_7-8-GAGTA. TBP, TATA binding protein; TFB, transcription factor II B; RNAP, RNA polymerase (modified after Lee et al. and Kanai et al. 2007)

Fig. 4

The structure of Pyrococcus furiosus TrmB with bound sucrose in yellow wireframe (ribbon presentation). The N-terminal DNA-binding domain (DBD) consists of a winged helix-turn-helix motif. Helix α4 represents the DNA recognition helix. The wing and the recognition helix are colored yellow. Helices (α) and strands (β) are consecutively numbered. Helix α5 (CC) and a short linker connect the DBD to the sugar/effector binding domain (EBD) harboring sucrose (in yellow) (taken from Krug et al. with permission from the authors and the publisher)

Fig. 5

a Structure of the Pyrococcus furiosus TrmB dimer in ribbon presentation and bound sucrose in yellow wireframe. The structure represents the dimer created by -X, Y-X, 2/3-Z crystallographic symmetry operation. One monomer is colored grey, the other mauve. The protein presumably builds a dimer by forming a coiled coil of the CC helices of the two monomers. The dimer can be considered as a result of domain swapping of the DBDs between two copies of an ancestral protein consisting of the EBD and the DBD with the CC helices as a hinge loop. The distances between the two recognition helices (α4) are indicated. b Zooming of the coiled-coil formed by two crystallographic counterparts of CC in ribbon presentation with side chains in stick representation. The hydrophobic residues Phe₈₁/Ile_91′, Phe₈₄/Leu_88′, Leu₈₈/Phe_84′ and Ile₉₁/Phe_81′ are represented in a zipper-like arrangement (taken from Krug et al. with permission from the authors and the publisher)

Fig. 6

The sugar binding domain (EBD) of Pyrococcus furiosus TrmB in complex with sucrose. The TrmB residues which interact with sucrose as well as the distances of potential hydrogen bonds in Å units are indicated. The omit electron density map of sucrose is shown at the 5 σ level (taken from Krug et al. with permission from the authors and the publisher)

Fig. 7

Sequence alignment of the discussed TrmB homologs. The boxes represent conserved protein domains. Dashes indicate gaps in the alignment. Highly conserved amino acids are represented via asterisks. Dots represent conserved amino acids. Strongly conserved amino acids with special function are highlighted in bold letters. The seven sugar binding amino acids of Pfu TrmB are shown in pink letters. Organism abbreviations are as follows: Pfu, Pyrococcus furiosus; Tli, Thermococcus litoralis; Tk, Thermococcus kodakaraensis; Hs, Halobacterium salinarum; Ma, Methanosarcina acetivorans; Sa, Sulfolobus acidocaldarius

Fig. 8

AFM images of a 3-kbp linear DNA of Escherichia coli (plasmid Bluescript II linearized by HindIII digestion). Image (a) shows the DNA without protein. Image (b) illustrates the DNA incubated with recombinant TK0471/TrmBL2 at a protein-to-DNA ratio of 10:1 (wt/wt) (taken from Maruyama et al. with permission from the authors and the publisher)