1

Transcriptional Regulation in

As is often the case, epoch-makingideas carry with them implicit,unanalyzed assumptions thatultimately impede scientific progressuntil they are recognized for what theyare. So it is with the prokaryote-eukaryote distinction. Our failure tounderstand its true nature set thestage for the sudden shattering of theconcept when a �third form of life was discovered in the late 1970s, adiscovery that actually left many biologists incredulous. Archaebateria, as athird form has come to be known, have revolutionized our notion of theprokaryote, have altered and refined the way in which we think about therelationship between prokaryotes and eukaryotes� and will influencestrongly the view we develop of the ancestor that gave rise to all extant life.

- C. Woese and R. S. Wolfe (1985)

ArchaebacteriaYellowstone Archaeal Transcription

Archaea

Bacteria

Eucarya

Universal Phylogentic TreeArchaeaBacteria Eucarya

Thermophile

Halophiles

Hypothermophiles

Thermophiles

Archaea: life at the extremes

Methanogen(rumen)

Brock (1996)Biology ofMicroorganisms,Prince-Hall, Inc..

Methanogens are responsible forthe production of methane.

Volta�s experiment in 1776showing �combustible air�produced at the bottom oflakes.

Archaeaphiles at the University of FloridaDepartment of Microbiology & Cell Science

Dr. MadelineRasche Dr. Thomas Bobik

Dr. Julie Maupin-Furlow

Biochemistry and physiology ofmethane-producingmicroorganisms; investigation ofmetalloenzyme structure andfunction using kinetic analysis,molecular genetics, and biophysicalspectroscopy.

Microbial physiologist andbiochemist with an interest inregulation of cells by proteolyticenzymes and a specialization inproteasomes from the methanogenicand halophilic archaea. Interests alsoinclude metabolic engineering ofbacteria for optimization of theof pyruvate decarboxylase inorganisms growing at hightemperature and low pH.

Collaborating with Dr. Raschestudying the biochemistry ofmethane production inmethanogens. Other studies arerelated to encasement of vitaminB12-dependent enzymes withinpolyhedral organelles inSalmonella.

Photo of Thiobacillus kindly provided by Dr. Henry Aldrich

2

Archaeal factors

1) TATA binding protein (TBP): 30 kDa2) TFB (homolog to TFIIB)

N-

View from +1back upstream atTBP bound atTATAAA

C-TBP

Archaeal Transcription

Fig. 5

Red = Pyrococcalgreen = yeast

TBPs in Archaeabacteriaare nearly identical to those in eucaryotes. Many Archaeahave multiple TBPs.

Tsai et al. In: Cold Spring Harbor Symposiavol. LXIII, pp. 53-61

Archaeal TranscriptionFig. 1

Yeast TBP Pyrococcal TBPThe peptide repeats of TBP aremore symmetrical in their contactwith TATAAA. Only 60/40% pre-ference for TATAAA over TTTATA.

TTTATA orTATAAA

Tsai et al. In: Cold Spring Harbor Symposiavol. LXIII, pp. 53-61

Archaeal Transcription

TATAAA inr

+1-30

DPE

-110BRE

Typical eucaryotic promoter:

Polarity of transcription is determined by1) TATAAA2) BRE3) inr (initiation region or initiator)4) DPE (downstream promoter element)

Upstream elements

Note: onlyTATAAA isknown in plants

Inr = Py-Py-A+1-N-T/A-Py-Py (mammals) T-C-A +1 -G/T-T-T/C (Drosophila)

DPE = A/G-G-A/T-CGTG (Drosophila)

+28-+34

spacing important

BRE = 5�-G/C-G/C-G/A-CGCC-3� (metazoan)

Archaeal Transcription

TATAAA

+1-30-110BRE

BRE = 5�-c-A/G-n-a-A-n-T-T-T-A-A/T-A-t-r-3�

Typical Archaeal promoter:

Polarity of transcription is determined by1) TATAAA2) BRE

3) inr; weakly conserved; Py-Pu+1

Upstream elements

?????

TTTATAor

Inr?

Basal factorsTFIIB/TBP/DNA complex

TBP

TFIIB

TFIIBconserved coredomain has tworepeat structures(R1 & R2).

R2

R1