YEAST PROTEIN NHP6A BINDS WITH SHORT GC-RICH GENES

Nhp6A is a small non-histone chromosomal yeast protein that binds DNA nonspecifically. This protein is present at many promoters and transcribed regions of genome and is involved in regulation of transcription. Recently, Nhp6A was shown to participate in destabilization of the nucleosomal structure. This may explain its location in regulatory sites, but its function in the coding regions remains unknown. In the present work, in order to reveal the mechanism of action of Nhp6A, we have studied genes associated with the protein along the entire length, including the open reading frame. We have shown that Nhp6A predominantly binds to the coding regions of short GC-rich yeast genes. The observed interaction is not associated directly with the high content of GC-pairs in these DNA loci, so we can propose a specific regulatory mechanism involving Nhp6A for this group. Since a part of genes retain features of the ancestral bacterial genome, we suggest this group as an “ancient”. Presumably, this genomic distribution of Nhp6 is related to the mechanisms of regulation of gene transcription that appeared early in the course of evolution.

1. Kornberg R.D., Thomas J.O. Chromatin structure; oligomers of the histones // Science. 1974. Vol. 184. N 4139. P. 865–868.

2. Reeves R. HMG nuclear proteins: linking chromatin structure to cellular phenotype // Biochim. Biophys. Acta. 2010. Vol. 1799. N 1–2. P. 3–14.

3. Stillman D.J. Nhp6: a small but powerful effector of chromatin structure in Saccharomyces cerevisiae // Biochim. Biophys. Acta. 2010. Vol. 1799. N 1–2. P. 175–180.

4. Ruone S., Rhoades A.R., Formosa T. Multiple Nhp6 molecules are required to recruit Spt16-Pob3 to form yFACT complexes and to reorganize nucleosomes // J. Biol. Chem. 2003. Vol. 278. N 46. P. 45288–45295.

5. Allain F.H., Yen Y.M., Masse J.E., Schultze P., Dieckmann T., Johnson R.C., Feigon J. Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding // EMBO J. 1999. Vol. 18. N 9. P. 2563–2579.

6. Coats J.E., Lin Y., Rueter E., Maher L.J., III, Rasnik I. Single-molecule FRET analysis of DNA binding and bending by yeast HMGB protein Nhp6A // Nucleic Acids Res. 2013. Vol. 41. N 2. P. 1372–1381.

7. Masse J.E., Wong B., Yen Y.M., Allain F.H., Johnson R.C., Feigon J. The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding // J. Mol. Biol. 2002. Vol. 323. N 2. P. 263–284.

8. Bustin M. Revised nomenclature for high mobility group (HMG) chromosomal proteins // Trends Biochem. Sci. 2001. Vol. 26. N 3. P. 152–153.

9. Costigan C., Kolodrubetz D., Snyder M. NHP6A and NHP6B, which encode HMG1-like proteins, are candidates for downstream components of the yeast SLT2 mitogen-activated protein kinase pathway // Mol. Cell Biol. 1994. Vol. 14. N 4. P. 2391–2403.

10. Yu Y., Eriksson P., Stillman D.J. Architectural transcription factors and the SAGA complex function in parallel pathways to activate transcription // Mol. Cell Biol. 2000. Vol. 20. N 7. P. 2350–2357.

11. Dowell N.L., Sperling A.S., Mason M.J., Johnson R.C. Chromatin-dependent binding of the S. cerevisiae HMGB protein Nhp6A affects nucleosome dynamics and transcription // Genes Dev. 2010. Vol. 24. N 18. P. 2031–2042.

12. Xin H., Takahata S., Blanksma M., McCullough L., Stillman D.J., Formosa T. yFACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement // Mol. Cell. 2009. Vol. 35. N 3. P. 365–376.

13. Hsieh F.K., Kozlova A.L., Gerasimova N.S., Kotova E.Yu., Formosa T., Studitsky V.M. Role of the Nhp6 protein in in vitro transcription through the nucleosome // Moscow Univ. Biol. Sci. Bull. 2017. Vol. 72. N 4. P. 218–221.

14. Prat Y., Fromer M., Linial N., Linial M. Codon usage is associated with the evolutionary age of genes in metazoan genomes // BMC Evol. Biol. 2009. Vol. 9:285.

15. Wolfe K.H., Shields D.C. Molecular evidence for an ancient duplication of the entire yeast genome // Nature. 1997. Vol. 387. N 6634. P. 708–713.