Structure of a yeast spliceosome at 3.6 Å resolution
Structures of individual RNA components in the spliceosome
Spliceosome structure and pre-mRNA splicing unveiled by Chinese scientist Yigong SHI's team at Tsinghua University
【LWBS 2015 08 24 A】(SpringRain Edited from Tsinghua University News）
Chinese scientists recently unveiled the structure of yeast spliceosome, and had the related two essays published on Science, the international top academic magazine.
On August 21st, the research team led by Prof. Yigong SHI from School of Life Sciences, Tsinghua University published two side-by-side research articles in Science, reporting the long-sought-after structure of a yeast spliceosome at 3.6 angstrom resolution determined by single particle cryo-electron microscopy (cryo-EM), and the molecular mechanism of pre-messenger RNA splicing.
Gene expression is the basic principle of all living cells. During the process known as the Central Dogma, the genomic information stored in genome DNA sequences is delivered to pre-mRNAs by transcription and finally to functional proteins by translation. In eukaryotes, pre-mRNAs are intervened by coding sequences containing exons and untranslated introns. The excision of introns and ligation of exons is named as pre-mRNA splicing, and executed by spliceosome. This macromolecular machinery consists of five small nuclear ribonucleoprotein particles (snRNPs), nineteen complex (NTC), NTC related (NTR), and a number of associated enzymes and cofactors. In total, more than 100 proteins and at least 5 RNAs were identified to be the core and auxiliary components of spliceosome. The involved proteins and RNAs assemble into and dissociate from spliceosome in a strict order during splicing, endowing extreme dynamics and flexibility of the spliceosome. These features guarantee the accomplishment of the complex splicing reaction, but at the same time tangling the structural investigations of spliceosome.
"The pre-messenger RNA, which has different amounts of so-called introns, cannot be transformed into protein. Exons contain protein information. It is spliceosome's work to join the pre-messenger RNA and exons together and turn them into messenger RNA that contains rich protein information," said Shi.
Spliceosome was found for the first time in 1977, but scientists have made no breakthrough in the analysis of its structure until Shi's team discovered it recently, after six year's investigation.
"The spliceosome is a huge dynamic molecular machine. So naturally, we can see how each protein in the spliceosome functions, and how the sequences inside introns are identified. Therefore, we can imagine that if there is some problem that leads to disease, how is the problem formed," Shi said.
Besides the basic biological importance of spliceosome, numerous diseases are related to the dysfunction of spliceosomal regulation or the splicing mistakes. Almost 35 percent of genetic disorder is resulted from wrong splicing, exemplified by unusual expression of alternative splicing that leads to frontotemporal dementia driven by tau mis-splicing. The mutation of key spliceosomal proteins like Brr2 or Prp8 can lead to the Autosomal Dominant retinitis pigmentosa. Some cancer is also associated with abnormal splicing.
"We have the structure of the spliceosome from this leading group in China. It puts Chinese science in a very big way on the international stage," said Dinshaw J. Patel, an American structural biologist.
The history and current situation of spliceosome research
In 1977, Richard Roberts and Philip Sharp was first discovered gene splicing phenomenon. In 1983, Joan Steitz was first isolated complexes composed of spliced subunits. In the same year, Philip Sharp and Walter Keller used nuclear extracts to test splicing activity in vitro.
However, due to the shape changing and complex composition, structural analysis of spliceosome has been recognized as a major problem in the world in the field of structural biology. In addition, there have been no proper research techniques, although scientist from various counties never stopped research, only the crystal structures of partial important components and various electron microscopy density maps with low resolution have been obtained from 1983 to 2014.
Before Shi Yigong’s results released, the latest development in international structure biology is an academic paper from KiyoShi Nagai study group at the British MRC Laboratory of Molecular Biology, which was online published on Nature on June 24 this year, improving the resolution of a complex structure of three small nuclear ribonucleoprotein (tri-snRNP) involved in the spliceosome assembly process to 5.9 Å, which once aroused international academic sensation. Before that, the resolution of spliceosome that people recognized was only 29 Å. Nagai's latest work has been a qualitative leap than before, but still cannot see the details of amino acid composition of proteins.
The results that Yigong SHI’s team obtained, not only improved the resolution from 5.9 Å to 3.6 Å so that you can clearly see the details of amino acids, but also its analysis target is truly spliceosome instead of Nagai team’s components involved in spliceosome assembly complex process, which is the first time to see the details of the spliceosome with a resolution at near atomic level.
It is known that there are many international teams are currently studying spliceosome, those at the most cutting-edge including Germany's Reinhard Lührmann team, Melissa Moore team at Massachusetts Medical School, Robin Reed team at Harvard University, Kathleen Gould team at Vanderbilt University, KiyoShi Nagai team at the British MRC Laboratory of Molecular Biology, Jean Beggs team at University of Edinburgh, and Soo-Chen Cheng team at Taiwan Yangming University of China.
About Yigong Shi
Yigong Shi, born in 1967 in Henan Province, graduated from Johns Hopkins University with PhD degree at Biophysics, Academician of Chinese Academy of Sciences, new vice president of Tsinghua University, dean of School of Life Sciences and Graduate School of Life Science and Medicine Research.
Recently, Yigong SHI’s team repeatedly published papers in the top international journals. August 21, 2015, the team simultaneously online published two research articles on Science to report analysis of three-dimensional structure of spliceosome and describes basic molecular structure basis of RNA splicing. The peers believe that this work is a significant milestone.
A few days ago on August 18, the team online published an article entitled "An atomic structure of human γ-secretase" on Nature to reveal the electron microscopy structure of human γ- secretase, providing an important basis for understanding the pathogenesis of Alzheimer's disease.
In 2008, Shi Yigong abandoned the position of tenured professor at Princeton University and return back to China, becoming the first member of the Chinese "thousands of people plan". After returning, Yigong SHI’ team at Tsinghua University has yielded fruitful results. In 2009, the achievements of his research team at Tsinghua have exceeded those of his team at Princeton during the peak period of 2006.
In academic circles, the experience of Yigong SHI is legendary. During his school years at Tsinghua University, he was always the first in the class year after year, and not only graduated one year ahead of graduation but also received a Bachelor of Mathematics; he was hired as the youngest full professor of the Department of Molecular Biology at Princeton University in history at 36-year-old; and got lifelong ProfessorShip at 40 year-old; has been elected as a foreign member of the American Academy of Arts and Sciences, the National Academy of Sciences, Chinese Academy of Sciences. In Tsinghua, he was known as "Daniel (means ‘big guy’)".
In 2011, Yigong SHI was unsuccessful for academician co-opted, once sparked heated debate.
In addition to academic research, Yigong Shi is currently held various executive positions, including Vice-President of Tsinghua University, Dean of School of Life Sciences and Life Sciences and Medical Research Institute. Yigong Shi has said publicly that the time spent on heavy administrative duties is worthy, and he wished to be able to change the soft mechanism of life science research at Tsinghua for reference by other domestic institutions.
In the graduation ceremony speech at Tsinghua University School of Life Sciences in 2015, Yigong Shi expected the students to take on social responsibility, he said, "Life is an experience, since you will experience only once, why not do the best?”