'Moonlighting' Molecules Discovered

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'Moonlighting' Molecules Discovered

http://www.medicalnewstoday.com/articles/169224.php

Since the completion of the human genome sequence, a question has baffled

researchers studying gene control: How is it that humans, being far more complex

than the lowly yeast, do not proportionally contain in our genome significantly

more gene-control proteins?

Now, a collaborative effort at the s Hopkins School of Medicine to examine

protein-DNA interactions across the whole genome has uncovered more than 300

proteins that appear to control genes, a newly discovered function for all of

these proteins previously known to play other roles in cells. The results, which

appear in the October 30 issue of Cell, provide a partial explanation for human

complexity over yeast but also throw a curve ball in what we previously

understood about protein functions.

" Everyone knows that transcription factors bind to DNA and everyone knows that

they bind in a sequence-specific manner, " says Heng Zhu, Ph.D., an assistant

professor in pharmacology and molecular sciences and a member of the High

Throughput Biology Center. " But you only find what you look for, so we looked

beyond and discovered proteins that essentially moonlight as transcription

factors. "

The team suspects that many more proteins encoded by the human genome might also

be moonlighting to control genes, which brings researchers to the paradox that

less complex organisms, such as plants, appear to have more transcription

factors than humans. " Maybe most of our genes are doing double, triple or

quadruple the work, " says Zhu. " This may be a widespread phenomenon in humans

and the key to how we can be so complex without significantly more genes than

organisms like plants. "

The team set out to figure out which proteins encoded by the genome bind to

which DNA sequences. It had been predicted by examining the human genome

sequence that about 1,400 to 1,700 of encoded proteins are so-called

transcription factors - proteins that bind to specific sequences in DNA to turn

a gene on or off. The researchers also included in their study, in addition to

these proteins, other types that are known to maintain chromosome structure and

bind to structurally different RNA. Also included were proteins that normally

relay information within a cell and are not thought to directly come in contact

with DNA. In total, they collected nearly 4,200 human proteins together on a

protein microarray, or protein " chip. "

To identify proteins on that chip that bound DNA directly, the group first

reviewed previously published scientific literature and catalogued 460

different, short sequences of DNA that are known or predicted to bind proteins.

One at a time, the team tested each of the 460 DNA sequences against the 4,200

protein-containing chip. In addition to finding many protein-DNA interactions

for transcription factors, some confirming previously known interactions, the

team found 367 new unconventional DNA binding proteins-proteins known to do

other cellular jobs.

" This nearly doubled the number of known protein-DNA interactions, " says Jiang

Qian, Ph.D., an assistant professor of ophthalmology at Hopkins. " But we only

looked at about a fifth of all the proteins in the human genome - there could be

hundreds, even thousands more of these unconventional transcription factors that

we don't yet know about. "

One of the unconventional transcription factors discovered was the protein MAP

Kinase 1, also known as ERK2, a protein long studied for its ability to control

cell growth and development via its ability to add phosphate groups to other

molecules.

" It's one of the best studied proteins out there, but no one ever thought ERK2

could directly regulate gene expression by actually binding to DNA, " says Seth

Blackshaw, Ph.D., an assistant professor of neuroscience and a member of the

High Throughput Biology Center and the Neuroregeneration Program at the

Institute for Cell Engineering.

To be certain that ERK2 really does bind DNA and control genes in living cells,

the team tested the protein in human cells. They found that ERK2 mutated to no

longer bind DNA causes specific genes to be turned on, while both normal ERK2

and ERK2 that's no longer able to chemically modify proteins turn off those same

genes. " It clearly acts to repress specific genes, " says Blackshaw. " Maybe this

will help clear up some of the puzzles that have arisen in ERK2 experiments over

the years. "

A central question in understanding how genes are controlled is hich of the

20,000 proteins encoded by our genome act on which segments of DNA. " It's not

possible to predict this a priori, " Blackshaw says. " Someone has to do the

experiment - because we just don't know enough about how proteins bind to DNA -

patterns have surfaced in this field's 45 year history, but not enough yet to

establish any rules. "

This study was funded by the National Institutes of Health, a National Eye

Institute Vision Core grant, a W. M. Keck Foundation Distinguished Young

Investigator in Medical Research Award, a grant from the Ruth and Milton

Steinbach Fund and a generous gift from Mr. and Mrs. and Clarice

Authors on the paper are Shaohui Hu, Zhi Xie, Akishi Onishi, Xueping Yu, Lizhi

Jiang, Jimmy Lin, Hee-Sool Rho, Crystal Woodard, Hong Wang, Jun-Seop Jeong,

Shunyou Long, Xiaofei He, Herschel Wade, Blackshaw, Qian, and Zhu, all of s

Hopkins.