Researchers at the University
of California, Berkeley, have for the first time captured elusive nanoscale
movements of ribosomes at work, shedding light on how these cellular factories
take in genetic instructions and amino acids to churn out proteins.
 | | Shown is an entire ribosome with its changes in position color-coded -- ranging from blue, indicating no movement, to red, indicating large movements. Credit: Courtesy of Cate Research Group, UC Berkeley |
Ribosomes, which number in the millions in a single human cell, have long been
considered the "black boxes" in molecular biology. "We know what
goes in and what comes out of ribosomes, but we're only beginning to learn about
what is going on in between," said the study's principal investigator,
Jamie Cate, UC Berkeley associate professor in chemistry and molecular and cell
biology, and a faculty scientist at Lawrence Berkeley National Laboratory.
The achievement, described in the Aug. 21 issue of the journal Science, could
eventually lead to significant advances in the fight against human disease,
the researchers said.
They point out that many infectious diseases involve ribosomal warfare between
humans and our bacterial or viral invaders. Important antibiotic drugs, like
spectinomycin, capreomycin and aminoglycosides, exploit the structural differences
between human and bacterial ribosomes to selectively attack the bacteria. Some
viruses, like polio and hepatitis C, hijack human ribosomes, forcing them to
pump out proteins that are beneficial for the viruses.
"Inside the ribosome, antibiotics and viruses are using chemistry to
either fight or promote disease," said Cate, who conducted the work with
research specialist Wen Zhang and graduate student Jack Dunkle, both co-lead
authors of the study, in his lab at UC Berkeley. "But what sort of chemistry?
The short answer is that we have a lot still to learn. Once we find out, that
knowledge could lead to more effective antibiotics, or new treatments against
devastating diseases like hepatitis C."
In the protein manufacturing process, the genetic code - or instruction manual
- for making proteins lies inside a cell's double-stranded DNA. When the cell
needs to produce more proteins, the DNA unzips into two separate strands, exposing
the protein code so it can be duplicated by single-stranded messenger RNA (mRNA).
The mRNA dutifully delivers that code to the ribosome, which somehow reads the
instructions, or "data tape," as each amino acid is added to a growing
protein chain.
At the same time, other RNA molecules, called transfer RNA (tRNA), bring to
the ribosome amino acids, the raw building blocks needed for protein construction.
To help elucidate the ribosome's movements as it interacts with mRNA and tRNA,
the researchers used X-ray crystallography to obtain a highly detailed picture
of the ribosome - a mere 21 nanometers wide - from an Escherichia coli bacterium.
In addition to revealing atomic level detail, the technique allowed the researchers
to capture the ribosome mid-action, a challenge because it acts fast, adding
20 new amino acids to a protein chain every second.
"Scientists used to think that the ribosome made a simple two-stage ratcheting
motion by rotating back and forth as it interacts with mRNA and tRNA,"
said Cate, who is also a member of the California Institute for Quantitative
Biomedical Research (QB3) at UC Berkeley. "What we captured were images
of the ribosome in intermediate stages between the rotations, showing that there
are at least four steps in this ratcheting mechanism."
"We suspect that the ribosome changes its conformation in so many steps
to allow it to interact with relatively big tRNAs while keeping the two segments
of the ribosome from flying apart," said Cate. "It's much more complicated
than the simple ratcheting mechanism in a socket wrench."
Cate said that while this study marked a major accomplishment in cracking open
the "black box" of ribosomal function, there are far more details
yet to be revealed. Advances in imaging techniques over the next decade should
allow researchers to go beyond the snapshots taken in this study to high-resolution
movies of a ribosome's movements, he said.
"I'm looking forward to producing a movie of a ribosome with enough resolution
and enough frames per millisecond that we can see what is happening at a molecular
level," said Cate. "It would be great to watch and really understand
how the ribosome makes a protein, how antibiotics interfere with a bacterial
ribosome, or why a strand of genetic code in a hepatitis C virus is so effective
at hijacking a human ribosome. We still have a long way to go, but we're working
hard."
Posted August 21st, 2009
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