Santa Cruz,
CA (9/25/99)- The first complete images of a ribosome in action should
open new vistas in many fields of biological research, from studies of antibiotic
resistance to those involving the origins of life, report researchers at the
University of California, Santa Cruz.
left:
The bacterial ribosome is composed of three different RNA molecules and more
than 50 different proteins arranged in two major subunits, which join together
to form the complete ribosome. During protein synthesis, the ribosome binds
transfer RNA molecules in three different sites. In this image of the ribosome,
with transfer RNAs in all three binding sites, the large subunit is gray,
the small subunit is violet, and the three transfer RNAs are green, blue,
and red. Credit: Cate et al
The new X-ray crystallography images obtained by UCSC researchers show not
only the structure of bacterial ribosomes they also indicate how different
parts of the ribosome interact with one another and how the ribosome interacts
with molecules involved in protein synthesis. It is an achievement representing
many decades of research.
"What we have at present are a few snapshots, and ultimately what we would
like is a movie of the ribosome in action," said Harry Noller, Sinsheimer
Professor of Molecular Biology at UC Santa Cruz.
Most research has focused on bacterial ribosomes, which are a bit smaller
than those in higher organisms. Even bacterial ribosomes are extraordinarily
complex. They are composed of three different RNA molecules and more than
50 different proteins arranged in two major subunits, which join together
to form the complete ribosome.
Dr. Noller's group utilized x-ray crystallography to obtain the images.
This complicated process involves growing crystals of purified ribosomes,
shining a focused beam of x-rays through the crystals, and analyzing the resulting
diffraction pattern. The complete ribosome is the largest molecular structure
ever solved by x-ray crystallography. Noller collaborated with scientists
at the crystallography facility at Lawrence Berkeley National Laboratory,
one of a handful of sites with a synchrotron capable of producing the high-energy
x-rays needed for crystallography of a structure as large as the ribosome.
The research is detailed in several articles in the journal Science. In one
paper, the researchers describe the structure of the complete ribosome with
several of the molecules involved in protein synthesis bound to it. A crystallographic
analysis, performed by postdoctoral researchers Jamie Cate, now on the faculty
of the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts,
yielded a medium-resolution structure, not detailed enough to show the location
of every atom but sufficient to provide valuable insights into the ribosome's
mechanism of action.
The ribosome resembles a miniature factory where proteins are made on an
assembly line, says Cate: "To a large extent it has been a mystery how this
assembly line is laid out, and these papers show where different pieces of
equipment are on the shop floor."
Biologists have known the basic outlines of protein synthesis for decades.
The instructions for making a protein are carried to the ribosome by a messenger
RNA molecule, which has copied the instructions from chromosomal DNA, the
storehouse of genetic information carried in every cell. The building blocks
of proteins are carried to the ribosome by transfer RNA molecules. On the
ribosome, the transfer RNAs recognize specific sequences of genetic code on
the messenger RNA, and the protein building blocks are then joined together
in the proper order.
There are three distinct binding sites for transfer RNAs on the ribosome,
and the new images show how the transfer RNAs are positioned in each of those
binding sites. During protein synthesis, the transfer RNAs pass sequentially
through the three binding sites, which are located at the interface between
the two subunits of the ribosome.
"The transfer RNAs come through as if on a conveyor belt, and we can see
how the ribosome holds the transfer RNA differently in each of the binding
sites," Cate said.
The new imaging research also led to the recognition of what appears to
be a molecular relay mechanism that may be part of a communication pathway
between the large subunit and the small subunit. One of the elements of this
pathway is a coil of RNA previously identified by other researchers as a molecular
"switch" that can move between two different conformations.
"The ribosome appears to be a dynamic molecular machine with moving parts
and a very complicated mechanism of action," Dr. Noller said.
The journal articles also present additional details of the connections
between the two subunits of the ribosome. They describes a molecular bridge
in which a loop of ribosomal RNA projects from the large subunit and interacts
with a protein component of the smaller subunit.
"Understanding how the subunits interact is critical to understanding how
the ribosome works, and for the first time we've been able to identify the
protein and RNA components of a bridge between the two subunits," said Gloria
Culver, an assistant professor at Iowa State University, who performed a series
of biochemical studies to characterize the components of the bridge.
The potential applications of this research cover a broad range, from understanding
the origins of life to developing more effective antibiotics, Noller said.
Ribosomes are ancient structures that show little variation among different
forms of life. Inside every living cell, tens of thousands of ribosomes churn
out proteins with mind-boggling speed and precision.
The current research also reflects an ongoing 'horse race' in the imaging
field. Other researchers have been trying for decades to unravel the mysteries
of the ribosome using another imaging technique called cryo-electron microscopy
(cryo-EM). Four years ago some of those researchers published structures resolved
to about 25 angstroms, putting them ahead in the race. The new research puts
the X-ray crystallographers in the lead, at least for now.
The articles appear in the September 24, 1999 issue of Science.
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