B Br ri id dg ge e h he el li ix x a an nd d t tr ri ig gg ge er r l lo oo op p p pe er rt tu ur rb ba at ti io on ns s g ge en ne er ra at te e s su up pe er ra ac ct ti iv ve e R RN NA A p po ol ly ym me er ra as se es s A Ab bs st tr ra ac ct t B Ba ac ck kg gr ro ou un nd d: : Cellular RNA polymerases are highly conserved enzymes that undergo complex conformational changes to coordinate the processing of nucleic acid substrates through the active site. Two domains in particular, the bridge helix and the trigger loop, play a key role in this mechanism by adopting different conformations at various stages of the nucleotide addition cycle. The functional relevance of these structural changes has been difficult to assess from the relatively small number of static crystal structures currently available. R Re es su ul lt ts s: : Using a novel robotic approach we characterized the functional properties of 367 site-directed mutants of the Methanocaldococcus jannaschii RNA polymerase A′ subunit, revealing a wide spectrum of in vitro phenotypes. We show that a surprisingly large number of single amino acid substitutions in the bridge helix, including a kink-inducing proline substitution, increase the specific activity of RNA polymerase. Other 'superactivating' substitutions are located in the adjacent base helices of the trigger loop. C Co on nc cl lu us si io on ns s: : The results support the hypothesis that the nucleotide addition cycle involves a kinked bridge helix conformation. The active center of RNA polymerase seems to be constrained by a network of functional interactions between the bridge helix and trigger loop that controls fundamental parameters of RNA synthesis.B Ba ac ck kg gr ro ou un nd d RNA polymerases (RNAPs) are central components of the cellular transcriptional machineries that are targeted by numerous regulatory proteins to fine-tune the expression of genomes in a highly controlled manner. It is therefore important to study the functional properties of RNAPs in order to understand how these are modulated during the various stages of the transcription cycle.Combined insights from biochemical, genetic and structural studies have led to the unambiguous identification of several structural motifs that participate in the key enzymatic

The in-depth structure/function analysis of large protein complexes, such as RNA polymerases (RNAPs), requires an experimental platform capable of assembling variants of such enzymes in large numbers in a reproducible manner under defined in vitro conditions. Here we describe a streamlined and integrated protocol for assembling recombinant archaeal RNAPs in a high-throughput 96-well format. All aspects of the procedure including construction of redesigned expression plasmids, development of automated protein extraction/in vitro assembly methods and activity assays were specifically adapted for implementation on robotic platforms. The optimized strategy allows the parallel assembly and activity assay of 96 recombinant RNAPs (including wild-type and mutant variants) with little or no human intervention within 24 h. We demonstrate the high-throughput potential of this system by evaluating the side-chain requirements of a single amino acid position of the RNAP Bridge Helix using saturation mutagenesis.

Mast cells play an important role at the early stages of immunological response to bacterial infections and parasite infestations. One of the major mast cell proinflammatory mediators is TNF‐α. Mast cells are considered the only cells capable of storing TNF‐α in cytoplasmic granules and rapidly releasing it upon activation. To determine what pathway is utilized to direct TNF‐α to cytoplasmic granules and what motifs are responsible for the sorting process, we constructed a fusion protein covering the full sequence of TNF‐α, N‐terminally fused to enhanced green fluorescent protein (EGFP). In rodent mast cells, such protein was sorted to secretory granules, and this process was inhibited by both brefeldin A and monensin. Considering the relationship between lysosomes and secretory granules and following TNF‐α sequence analysis, it was determined whether TNF‐α is sorted through the mannose‐6‐phosphate receptor (MPR)‐dependent pathway. We observed that ammonium chloride and tunicamycin blocked TNF‐α‐EGFP fusion protein delivery to secretory granules. In situ mutagenesis experiments confirmed the necessity of N‐linked glycosylation for efficient sorting of TNF‐α into rodent mast cell granules. In this work we established that TNF‐α travels from the ER to mast cell granules via a brefeldin A‐ and monensin‐sensitive route, utilizing the MPR‐dependent pathway, although this dependency does not seem to be absolute.

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