Andrey L. Karamyshev, Ph.D.
Molecular Mechanisms of Translational Regulation, RNA/Protein Quality Control and Protein Interactions in Health and Disease. Protein Synthesis, Targeting, Folding and Transport. Mechanisms of Protein Misfolding in Neurodegenerative Diseases.
Regulation of Aberrant Protein Production in Health and Disease.
This project is based on our recent discovery of the novel pathway of translational regulation and protein quality control known as RAPP (Regulation of Aberrant Protein Production) (see Cell, 2014, 156, 146-157 for details) (Fig. 1). This pathway monitors the status of nascent chain interactions during translation and transfers the signal to the mRNA degradation machinery to prevent the synthesis of proteins that lost these natural interactions. During protein synthesis the nascent chains that emerge from the ribosomal tunnel interact with multiple factors for proper folding, targeting and modifications. These interactions are critical for normal protein biogenesis. As we demonstrated, the synthesis of the aberrant secretory proteins that are not able to interact with the targeting factor SRP (Signal Recognition Particle) leads to the activation of the RAPP pathway and the destruction of the defective protein’s mRNA. While the existence of the RAPP pathway is well documented, its mechanism is practically unknown. Currently, we identified only one component of the RAPP pathway, Ago2. Ago2 is a key element of the RAPP process and Ago2 triggers mRNA degradation. There are many questions that remain to be answered. What are the other components of the RAPP machinary? What are signals for mRNA degradation? Has mRNA cleavage happened at the ribosome? Which enzyme cleaves mRNA? How is the signal about aberrant nascent chain transmitted to mRNA degradation machinery? To answer these questions we use complex approaches as in vivo (cultured human cells, immunofluorescence, microscopy, RNAi, overexpression, etc.), as well as in vitro (protein translation systems, incorporation of unnatural amino acids by suppressor tRNAs, site-specific photo-crosslinking (Fig. 2), recently developed by us method for the identification of Proteins Interacting with Nascent Chains (iPINCH) (Fig. 3), and many others). The future directions of our research are focused on the elucidation of the RAPP mechanism, its involvement in mRNA/protein quality control of different types of aberrant proteins, and the role of RAPP in human diseases. Our data demonstrate that RAPP may be a molecular basis for various human diseases. It opens up the opportunity for the identification of new pharmacological targets for treatment of the diseases.
Mechanisms of Protein Misfolding in Neurodegenerative Diseases.
Numerous neurodegenerative diseases are associated with the accumulation of protein aggregates and the death of neurons. Alzheimer’s, Parkinson’s and Huntington’s diseases, amyotrophic lateral sclerosis and others are caused by the aggregation of aberrant proteins. This project takes our view at these proteins during the first steps in their synthesis. Normally, during translation, the proteins interact with their partners that assist in correct folding. We propose that the loss of these early interactions leads to protein aggregation and disease. We use site-specific photo-crosslinking (Fig. 2) and recently developed iPINCH (Fig. 3) to identify nascent chain interactions during translation in health and in neurodegenerative diseases. This project is directed at establishing a new and currently under-examined area of neurodegenerative research — co-translational interactions of proteins and their roles in the disease state. The interacting partners may serve as modulators of protein folding and aggregation. Potentially this project will lead to the discoveries of novel therapeutics for the treatment of neurodegenerative disease.
(From 31 publications)
- Vetter,* A. J., Karamyshev,* A. L., Patrick, A. E., Hudson, H., Thomas, P. J. (2016) N-alpha-acetyltransferases and regulation of CFTR expression. PLoS ONE 11(5): e0155430. *These authors contributed equally to this work. PubMed
- Nilsson, I., Lara, P., Hessa T., Johnson, A. E., von Heijne, G., Karamyshev, A. L. (2015) The code for directing proteins for translocation across ER membrane: SRP cotranslationally recognizes specific features of a signal sequence. J. Mol. Biol., 427, 1191-1201. PubMed
- Karamyshev,* A. L., Patrick, A. E., Karamysheva, Z. N., Griesemer, D. S., Hudson, H., Tjon-Kon-Sang, S, Nilsson, I., Otto, H., Liu, Q., Rospert, S., von Heijne, G., Johnson, A. E., Thomas,* P. J. (2014) Inefficient SRP Interaction with a Nascent Chain Triggers a mRNA Quality Control Pathway. Cell, 156, 146-157. (* = co-corresponding authors). Spotlight about this paper was published in TIBS: Popp, M. W.-L. and Maquat L. E. (2014) Defective secretory-protein mRNAs take the RAPP, Trends in Biochemical Sciences, 39(4), 154-156. Highlighted in Nature Reviews Genetics: Research highlights: Novel mRNA quality control mechanism. Nature Reviews Genetics (2014), 15(3), 144. The article has been recommended by Faculty of 1000 - selected for F1000Prime. PubMed
- Patrick A. E., Karamyshev A. L., Millen L., Thomas P. J. (2011) Alteration of CFTR transmembrane span integration by disease-causing mutations. Mol. Biol. Cell, 22(23), 4461-4471. PubMed
- Karamyshev, A. L., Kelleher, D. J., Gilmore, R., Johnson, A. E., von Heijne, G., Nilsson, I. (2005) Mapping the interaction of the STT3 subunit of the oligosaccharyl transferase complex with nascent polypeptide chains. J. Biol. Chem., 280, 49, 40489-40493. PubMed
- Karamyshev, A. L., Johnson, A. E. (2005) Selective SecA association with signal sequences in ribosome-bound nascent chains: A potential role for SecA in ribosome targeting to the bacterial membrane. J. Biol. Chem., 280, 45, 37930-37940. The article has been recommended by Faculty of 1000 - selected for F1000Prime. PubMed
- Karamyshev, A. L., Karamysheva, Z. N., Yamami, T., Ito, K., Nakamura, Y. (2004) Transient idling of posttermination ribosomes ready to reinitiate protein synthesis. Biochimie, 86(12), 933-938. PubMed
- Karamysheva, Z. N., Karamyshev, A. L., Ito, K., Yokogawa, T., Nishikawa, K., Nakamura, Y., Matsufuji, S. (2003) Antizyme frameshifting as a functional probe of eukaryotic translational termination. Nucleic Acids Res., 31(20), 5949-5956. The article has been recommended by Faculty of 1000 - selected for F1000Prime. PubMed
- Ito, K., Frolova, L., Seit-Nebi, A., Karamyshev, A., Kisselev, L., Nakamura, Y. (2002) Omnipotent decoding potential resides in eukaryotic translation termination factor eRF1 of variant-code organisms and is modulated by the interactions of amino acid sequences within domain 1. Proc. Natl. Acad. Sci. USA, 99(13), 8494-8499. PubMed
- Kervestin, S., Garnier, O. A., Karamyshev, A. L., Ito, K., Nakamura, Y., Meyer, E., Jean-Jean, O. (2002) Isolation and expression of two genes encoding eukaryotic release factor 1 from Paramecium tetraurelia. J. Eukaryot. Microbiol., 49(5), 374-382. PubMed
- Karamyshev, A. L., Ito, K., Nakamura, Y. (1999) Polypeptide release factor eRF1 from Tetrahymena thermophila: cDNA cloning, purification and complex formation with yeast eRF3. FEBS Lett., 457(3), 483-488. PubMed
- Karamyshev, A. L., Karamysheva, Z. N., Kajava, A. V., Ksenzenko, V. N., Nesmeyanova, M. A. (1998) Processing of Escherichia coli alkaline phosphatase: role of the primary structure of the signal peptide cleavage region. J. Mol. Biol., 277(4), 859-870. PubMed
- Nesmeyanova, M. A., Karamyshev, A. L., Karamysheva, Z. N., Kalinin, A. E., Ksenzenko, V. N., Kajava A. V. (1997) Positively charged lysine at the N-terminus of the signal peptide of the Escherichia coli alkaline phosphatase provides the secretion efficiency and is involved in the interaction with anionic phospholipids. FEBS Lett., 403, 203-207.