Transcription by RNA polymerase III: insights into mechanism and regulation

Abstract

The highly abundant, small stable RNAs that are synthesized by RNA polymerase III (RNAPIII) have key functional roles, particularly in the protein synthesis apparatus. Their expression is metabolically demanding, and is therefore coupled to changing demands for protein synthesis during cell growth and division. Here, we review the regulatory mechanisms that control the levels of RNAPIII transcripts and discuss their potential physiological relevance. Recent analyses have revealed differential regulation of tRNA expression at all steps on its biogenesis, with significant deregulation of mature tRNAs in cancer cells.

Keywords: RNA polymerase III; tRNA; transcription elongation; transcription factors.

Figure 1.

The RNAPIII transcription cycle. (A) RNAPIII transcription initiation on tRNA genes. (i and ii) The internal box A and B elements present within tRNA genes (tDNA) are bound by the multiprotein TFIIIC complex. (iii) This recruits the TFIIB complex and the RNA-binding protein Nab2 facilitates this interaction. (iv) RNAPIII is recruited and transcription initiates. (B) RNAPIII transcription cycle on tRNA genes. (i) During transcription elongation, Nab2 remains associated with RNAPIII and/or the nascent transcript. (ii and iii) TFIIIC remains associated with the tDNA, possibly because it is not simultaneously displaced from both the A and B boxes. (iv) In canonical termination, RNAPIII terminates following transcription of an oligo(U) tract. (v) In noncanonical termination, RNAPIII continues further downstream generating a readthrough product. (vi) This typically terminates in a U-rich region. (C) Pre-tRNA surveillance factors. (i) Readthrough transcripts are cleaved at the 3′-end of the mature tRNA, liberating a tRNA extension fragment, or can be trimmed on the 3′-end by the exosome complex. (ii) Released fragment of tRNA extension can be 5′ degraded by the 5′-exonuclease Rat1 (Xrn2 in humans) or 3′ degraded by the exosome complex. Nab2 may also participate in surveillance of 3′ extended pre-tRNAs.

Figure 2.

Regulated steps in RNAPIII transcription. The activity of the major transcription repressor Maf1 is regulated by cycles of phosphorylation and dephosphorylation, coupled with nuclear-cytoplasmic transport. These allow the integration RNPIII activity with nutrient availability and stress. See text for further details.

Figure 3.. Changes in tRNA synthesis and maturation can affect protein production.

The rate of pre-tRNA synthesis can be altered by changes in transcription rate, with a subset of ‘housekeeping’ tRNAs showing limited responses to environmental stress. In addition, tRNA abundance can be affected by changes in pre-tRNA processing, nuclear export and reimport, or surveillance activities. Different mRNAs show distinct patterns of codon bias, so changes in the relative tRNA abundances can alter protein expression levels.