The Modular Adaptive Ribosome.
The ribosome is an ancient machine, performing the same function across organisms. Although functionally unitary, recent experiments suggest specialized roles for some ribosomal proteins. Our central thesis is that ribosomal proteins function in a modular fashion to decode genetic information in a context dependent manner. We show through large data analyses that although many ribosomal proteins are essential with consistent effect on growth in different conditions in yeast and similar expression across cell and tissue types in mice and humans, some ribosomal proteins are used in an environment specific manner. The latter set of variable ribosomal proteins further function in a coordinated manner forming modules, which are adapted to different environmental cues in different organisms. We show that these environment specific modules of ribosomal proteins in yeast have differential genetic interactions with other pathways and their 5'UTRs show differential signatures of selection in yeast strains, presumably to facilitate adaptation. Similarly, we show that in higher metazoans such as mice and humans, different modules of ribosomal proteins are expressed in different cell types and tissues. A clear example is nervous tissue that uses a ribosomal protein module distinct from the rest of the tissues in both mice and humans. Our results suggest a novel stratification of ribosomal proteins that could have played a role in adaptation, presumably to optimize translation for adaptation to diverse ecological niches and tissue microenvironments.
Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India.
Anupama
A
Yadav
Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India.
Aparna
A
Radhakrishnan
Department of Physics, Rutgers University, Piscataway, New Jersey 08854, United States of America.
Anshuman
A
Panda
Department of Physics, Rutgers University, Piscataway, New Jersey 08854, United States of America.
Amartya
A
Singh
Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India.|Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India.|Initiative for Biological Systems Engineering, Indian Institute of Technology Madras, Chennai 600036, India.
Himanshu
H
Sinha
Department of Physics, Rutgers University, Piscataway, New Jersey 08854, United States of America.|Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, United States of America.|The Cancer Institute of New Jersey, New Brunswick, New Jersey 08903, United States of America.
Gyan
G
Bhanot
D000818:Animals; D019143:Evolution, Molecular; D006801:Humans; D051379:Mice; D010641:Phenotype; D012269:Ribosomal Proteins / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000235:genetics / Q000378:metabolism
D012269:Ribosomal Proteins