TFS and Spt4/5 accelerate transcription through archaeal histone‐based chromatin. Issue 3 (1st February 2019)

• Record Type: Journal Article
• Authors: Sanders, Travis J.; Lammers, Marshall; Marshall, Craig J.; Walker, Julie E.; Lynch, Erin R.; Santangelo, Thomas J.
• Is Part Of: Molecular microbiology. Volume 111:Issue 3(2019)
• Page Start: 784
• Page End: 797
• Publication Date: 2019-02-01
• Subjects: Molecular microbiology -- Periodicals; 572.829
• DOI: 10.1111/mmi.14191
• Languages: English
• ISSNs: 0950-382X

Abstract

Summary: RNA polymerase must surmount translocation barriers for continued transcription. In Eukarya and most Archaea, DNA‐bound histone proteins represent the most common and troublesome barrier to transcription elongation. Eukaryotes encode a plethora of chromatin‐remodeling complexes, histone‐modification enzymes and transcription elongation factors to aid transcription through nucleosomes, while archaea seemingly lack machinery to remodel/modify histone‐based chromatin and thus must rely on elongation factors to accelerate transcription through chromatin‐barriers. TFS (TFIIS in Eukarya) and the Spt4–Spt5 complex are universally encoded in archaeal genomes, and here we demonstrate that both elongation factors, via different mechanisms, can accelerate transcription through archaeal histone‐based chromatin. Histone proteins in Thermococcus kodakarensis are sufficiently abundant to completely wrap all genomic DNA, resulting in a consistent protein barrier to transcription elongation. TFS‐enhanced cleavage of RNAs in backtracked transcription complexes reactivates stalled RNAPs and dramatically accelerates transcription through histone‐barriers, while Spt4–Spt5 changes to clamp‐domain dynamics play a lesser‐role in stabilizing transcription. Repeated attempts to delete TFS, Spt4 and Spt5 from the T. kodakarensis genome were not successful, and the essentiality of both conserved transcription elongation factors suggests that both conserved elongation factors play important roles in transcription regulation in vivo, including mechanisms to accelerate transcription through downstream protein barriers. Abstract : Archaeal genomes are often organized into histone‐based chromatin structures that obstruct recognition of promoter elements and hinder progression of RNA polymerase during transcription elongation. Archaeal genomes do not encode chromatin remodeling complexes nor histone‐modification machinery, implying that the archaeal RNA polymerase must rely on conserved transcription factors to surmount chromatin barriers to elongation. Our results detail the mechanistic activities of the conserved transcription factors Spt4‐Spt5 and TFS that promote continued elongation through chromatin barriers.