Functional in vivo verification in E. coli of promoter activities from the rDNA/tDNA(Val)(GAC) leader region of Zea mays chloroplasts

Potentiation of the activity of Escherichia coli chaperone DnaJ by tailing hyper-acidic minipeptides

The chaperone network plays an essential role in cellular protein homeostasis. However, some core components often coaggregate with misfolded proteins for sequestration and dysfunction, leading to abnormal cell proteostasis, aggregation-associated disorders, and poor solubility of overexpressed recombinant proteins. Among them, DnaJ or its ortholog, an obligate co-chaperone in the tripartite DnaK-DnaJ-GrpE system, is of more implications, probably due to its intrinsic propensity for aggregation. Herein, we potentiated the activity of Escherichia coli DnaJ by using hyper-acidified protein fusion strategy. We found DnaJ did possess only a moderate solubility that could be remarkably improved by fusing hyper-acidic minipeptides. Most importantly, we revealed the hyper-acidified DnaJ with a fusion tail could outperform its native form (significantly up to 2.1-fold) to enhance the solubility of target proteins and meanwhile appropriately impart them an elevated activity. These results suggest the hyper-acidified DnaJs can chaperone target proteins with correct folding into a truly soluble and active form. Moreover, we showed these hyper-acidified DnaJ variants could surpass its prototype to confer E. coli or yeast an enhanced heat tolerance, and DnaJ itself could be solubilized by its hyper-acidified fusion cognates. Finally, we discussed the overall mechanism for DnaJ activity potentiation mediated by hyper-acidic tailing fusion.

Regulation of rDNA transcription in chloroplasts: promoter exclusion by constitutive repression

Spinach chloroplasts contain two types of RNA polymerases. One is multimeric and Escherichia coli-like. The other one is not E. coli-like and might represent a monomeric enzyme of 110 kD. The quantitative relation of the two polymerases changes during plant development. This raises the question, how are plastid genes transcribed that contain E. coli-like and non-E. coli-like promoter elements during developmental phases when both enzymes are present? Transcription of the spinach plastid rrn operon promoter is initiated at three sites: P1, PC, and P2. P1 and P2 are preceded by E. coli-like promoter elements that are recognized by E. coli RNA polymerase in vitro. However, in vivo, transcription starts exclusively at PC. We analyzed different promoter constructions using in vitro transcription and gel mobility-shift studies to understand why P1 and P2 are not used in vivo. Our results suggest that the sequence-specific DNA-binding factor CDF2 functions as a repressor for transcription initiation of the E. coli-like enzyme at P1 and P2. We propose a mechanism of constitutive repression to keep the rrn operon in all developmental phases under the transcriptional control of the non-E. coli-like RNA polymerase.

In vitro analysis of the pea chloroplast 16S rRNA gene promoter

A cloned pea chloroplast 16S rRNA gene promoter has been characterized in detail by use of a homologous in vitro transcription system that contains a highly purified chloroplast RNA polymerase. The in vivo and in vitro 16S rRNA transcriptional start site has been identified to be a T on the plus strand, 158 bases upstream of the mature 5' end of the gene. BAL 31 deletions of the 16S rRNA leader region demonstrated that the bases between -66 to +30 relative to the transcriptional start site (+1) are necessary for specific 16S transcription. Disruption of canonical TTGACA or TATAAT elements within this region caused complete transcriptional inactivation and prevented protein binding. The topological requirement for 16S transcription was examined by using a construct that synthesized a transcript from the 16S promoter and released it from a pea plastid putative terminator sequence. This minigene was relaxed in vitro with a topoisomerase I from pea chloroplast. It was shown that the 16S promoter was most active when the minigene plasmid was supercoiled.

In vitro analysis of the pea chloroplast 16S rRNA gene promoter

A cloned pea chloroplast 16S rRNA gene promoter has been characterized in detail by use of a homologous in vitro transcription system that contains a highly purified chloroplast RNA polymerase. The in vivo and in vitro 16S rRNA transcriptional start site has been identified to be a T on the plus strand, 158 bases upstream of the mature 5' end of the gene. BAL 31 deletions of the 16S rRNA leader region demonstrated that the bases between -66 to +30 relative to the transcriptional start site (+1) are necessary for specific 16S transcription. Disruption of canonical TTGACA or TATAAT elements within this region caused complete transcriptional inactivation and prevented protein binding. The topological requirement for 16S transcription was examined by using a construct that synthesized a transcript from the 16S promoter and released it from a pea plastid putative terminator sequence. This minigene was relaxed in vitro with a topoisomerase I from pea chloroplast. It was shown that the 16S promoter was most active when the minigene plasmid was supercoiled.

Evidence for a translation-mediated attenuation of a spinach chloroplast rDNA operon

The presence of potential hairpin structures H1, H2, H3 in the leader region of a spinach rDNA operon led us to postulate that this operon is regulated by premature termination. The mechanism would be controlled by the presence or absence of ribosomes translating a leader peptide. In vitro synchronized transcription by E. coli RNA polymerase shows that pauses do occur in the leader region. By their sizes, the transient transcripts could correspond to pauses on H1 and H2 as predicted by the model in the absence of ribosomes. The complete leader sequence (pKOPH) and the leader sequence with the hairpin structures deleted (pKOP) have been used to the GalK gene in the pK01 plasmid. The resulting plasmids have been used to transform a GalK- E. coli strain. Measurements of GalK expression show that the promoter region of spinach chloroplast rDNA is neither subjected to the growth rate nor to the stringent control. However, under growth conditions leading to an excess of free ribosomes, the expression of GalK gene appears systematically to be reduced in pKOPH when compared with that of pKOP. These results are consistent with a role of the leader region in a translation-mediated attenuation of the chloroplast rDNA expression.