Molecular paleontology: a biochemical model of the ancestral ribosome.
Ancient components of the ribosome, inferred from a consensus of previous work, were constructed in silico, in vitro and in vivo. The resulting model of the ancestral ribosome presented here incorporates ∼20% of the extant 23S rRNA and fragments of five ribosomal proteins. We test hypotheses that ancestral rRNA can: (i) assume canonical 23S rRNA-like secondary structure, (ii) assume canonical tertiary structure and (iii) form native complexes with ribosomal protein fragments. Footprinting experiments support formation of predicted secondary and tertiary structure. Gel shift, spectroscopic and yeast three-hybrid assays show specific interactions between ancestral rRNA and ribosomal protein fragments, independent of other, more recent, components of the ribosome. This robustness suggests that the catalytic core of the ribosome is an ancient construct that has survived billions of years of evolution without major changes in structure. Collectively, the data here support a model in which ancestors of the large and small subunits originated and evolved independently of each other, with autonomous functionalities.
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.
Chiaolong
C
Hsiao
Timothy K
TK
Lenz
Jessica K
JK
Peters
Po-Yu
PY
Fang
Dana M
DM
Schneider
Eric J
EJ
Anderson
Thanawadee
T
Preeprem
Jessica C
JC
Bowman
Eric B
EB
O'Neill
Lively
L
Lie
Shreyas S
SS
Athavale
J Jared
JJ
Gossett
Catherine
C
Trippe
Jason
J
Murray
Anton S
AS
Petrov
Roger M
RM
Wartell
Stephen C
SC
Harvey
Nicholas V
NV
Hud
Loren Dean
LD
Williams
D019143:Evolution, Molecular; D008274:Magnesium / Q000737:chemistry; D008957:Models, Genetic; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010446:Peptide Fragments / Q000737:chemistry; D011485:Protein Binding; D059367:RNA Cleavage; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012338:RNA, Ribosomal, 23S / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016914:Ribonuclease H / Q000737:chemistry; D012269:Ribosomal Proteins / Q000737:chemistry / Q000378:metabolism; D012270:Ribosomes / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D016963:Thermus thermophilus / Q000235:genetics
D010446:Peptide Fragments; D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; D012269:Ribosomal Proteins; D016914:Ribonuclease H; D008274:Magnesium