U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights


Finding “Small” Proteins and Discovering How They Affect Plant Biomass Growth
Published: March 21, 2011
Posted: April 06, 2011

Proteins less than 200 amino acids in length are commonly called “small proteins.” They have recently been found to have important roles in regulating biological processes such as stress response, flowering, and cell-to-cell communication in plants. However, identification of short open reading frames (sORFs), the genes that encode small proteins, has been a problem because their small size makes accurate prediction difficult. Researchers at Oak Ridge National Laboratory, working with scientists at the DOE BioEnergy Research Center, have applied computational biology to gene expression and protein data to discover sORFs encoding small proteins in the promising bioenergy feedstock Populus deltoids (poplar). Using the capacity of the DOE Joint Genome Institute for deep RNA sequencing, they reconstructed high-quality, full-length genes directly from the set of genes expressed in poplar (transcriptome), thus avoiding the uncertainty of prediction from genome sequence. The team then applied three computational filters to enrich for protein-encoding sORFs: prediction based on known protein sequences, evolutionary conservation between poplar and other plants, and protein family clustering. The results demonstrated the efficacy of this strategy in discovering candidate sORFs in sequenced as well as yet unannotated genomes. This method will greatly enhance understanding of the regulatory mechanisms underlying processes such as growth and stress response, features important to the development of high-yielding, sustainable bioenergy feedstocks.

Reference: Yang, X., T. J. Tschaplinski, G. B. Hurst, S. Jawdy, P. E. Abraham, P. K. Lankford, R. M. Adams, M. B. Shah, R. L. Hettich, E. Lindquist, U. C. Kalluri, L. E. Gunter, C. Pennacchio, and G. A. Tuskan. 2011. “Discovery and Annotation of Small Proteins Using Genomics, Proteomics, and Computational Approaches,” Genome Research doi:10.1101/gr.109280.110. Published online March 2, 2011.

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Plant Systems and Feedstocks, Plant-Microbe Interactions
  • Research Area: DOE Joint Genome Institute (JGI)
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: DOE Bioenergy Research Centers (BRC)
  • Research Area: Computational Biology, Bioinformatics, Modeling

Division: SC-23.2 Biological Systems Science Division, BER

 

BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

May 10, 2019
Quantifying Decision Uncertainty in Water Management via a Coupled Agent-Based Model
Considering risk perception can improve the representation of human decision-making processes in age [more...]

May 09, 2019
Projecting Global Urban Area Growth Through 2100 Based on Historical Time Series Data and Future Scenarios
Study provides country-specific urban area growth models and the first dataset on country-level urba [more...]

May 05, 2019
Calibrating Building Energy Demand Models to Refine Long-Term Energy Planning
A new, flexible calibration approach improved model accuracy in capturing year-to-year changes in bu [more...]

May 03, 2019
Calibration and Uncertainty Analysis of Demeter for Better Downscaling of Global Land Use and Land Cover Projections
Researchers improved the Demeter model’s performance by calibrating key parameters and establi [more...]

Apr 22, 2019
Representation of U.S. Warm Temperature Extremes in Global Climate Model Ensembles
Representation of warm temperature events varies considerably among global climate models, which has [more...]

List all highlights (possible long download time)