FPMD-FUNGAL PROMOTER MOTIF DATABASE: A DATABASE FOR THE OF THE PROMOTER MOTIFS REGIONS IN FUNGAL GENOMES

Fungal promoter motif database is the collection of promoter motifs from fully sequenced fungal genomes. Promoter sequences and its frequency are analyzed by the positions of nucleotide sequence and its repetition. The fungal promoter motif database holds the promoter sequence motifs identified by genome wide motif discovery, similarity studies and clustering. These data sets are typically 6 to 10 bp long, that have been extracted from the promoter regions. These promoter regions extend from 1.5 kb upstream to 200bp downstream of a transcription start site. We believe that the availability of these promoter motifs will be a valuable resource for researchers for comparative sequence analysis and evolutionary studies.

Mediator Subunits MED16, MED14, and MED2 Are Required for Activation of ABRE-Dependent Transcription in Arabidopsis

The Mediator complex controls transcription of most eukaryotic genes with individual subunits required for the control of particular gene regulons in response to various perturbations. In this study, we reveal the roles of the plant Mediator subunits MED16, MED14, and MED2 in regulating transcription in response to the phytohormone abscisic acid (ABA) and we determine which cis elements are under their control. Using synthetic promoter reporters we established an effective system for testing relationships between subunits and specific cis-acting motifs in protoplasts. Our results demonstrate that MED16, MED14, and MED2 are required for the full transcriptional activation by ABA of promoters containing both the ABRE (ABA-responsive element) and DRE (drought-responsive element). Using synthetic promoter motif concatamers, we showed that ABA-responsive activation of the ABRE but not the DRE motif was dependent on these three Mediator subunits. Furthermore, the three subunits were required for the control of water loss from leaves but played no role in ABA-dependent growth inhibition, highlighting specificity in their functions. Our results identify new roles for three Mediator subunits, provide a direct demonstration of their function and highlight that our experimental approach can be utilized to identify the function of subunits of plant transcriptional regulators.

Conservation and discreteness of the atromentin gene cluster in fungi

The atromentin synthetase gene cluster is responsible for catalyzing the precursor pigment atromentin, which is further catalyzed into hundreds of different pigments that span different taxa in the Basidiomycota and is a distinguished feature of Boletales. Previous work identified co-transcription of the two essential clustered atromentin genes (the atromentin synthetase (NPS) and the aminotransferase) by inducible pigment conditions and also conserved genetic elements in the promoter regions (motifs). For this work, we found that the NPS and its promoter motif appeared to follow the same evolutionary path as the mushrooms’. The NPS appears to predate Boletales and originate in Agaricomycetes, and with convergent/parallel evolution that allowed ascomycetes to produce atromentin. Additionally, a consensus of the intron-exon gene structure for basidiomycetous, atromentin-catalyzing NPSs was identified whereby a significant deviation occurred in the paraphyletic group, Paxillaceae. This gene structure was not present in NPSs in Aspergilli. Lastly, we found a putative TATA box adjacent to the palindromic motif of NPS, indicating (co-)transcriptional control by a TATA(-like) binding transcription factor. Combined with previous decades’ worth of research, our results support that not only can atromentin derivatives be used for chemo-taxonomy, but also atromentin’s genetic basis. Future work using the putative promoter motif will provide new insight into which (co-)transcription factor may be responsible for the transcriptional control of atromentin synthetases.

A TetR-family protein activates transcription from a new promoter motif associated with essential genes for autotrophic growth in acetogens

Acetogens can fix carbon (CO or CO2) into acetyl-CoA via the Wood-Ljungdahl pathway (WLP) that also makes them attractive cell factories for the production of fuels and chemicals from waste feedstocks. Although most biochemical details of the WLP are well understood and systems-level characterisation of acetogen metabolism has recently improved, key transcriptional features such as promoter motifs and transcriptional regulators are still unknown in acetogens. Here, we use differential RNA-sequencing to identify a previously undescribed promoter motif associated with essential genes for autotrophic growth of the model-acetogen Clostridium autoethanogenum. RNA polymerase was shown to bind to the new promoter motif using a DNA-binding protein assay and proteomics enabled the discovery of four candidates to potentially function directly in control of transcription of the WLP and other key genes of C1 fixation metabolism. Next, in vivo experiments showed that a TetR-family transcriptional regulator (CAETHG_0459) and the housekeeping sigma factor (σA) activate expression of a reporter protein (GFP) in-frame with the new promoter motif from a fusion vector in E. coli. Lastly, a protein-protein interaction assay with the RNA polymerase (RNAP) shows that CAETHG_0459 directly binds to the RNAP. Together, the data presented here advance the fundamental understanding of transcriptional regulation of C1 fixation in acetogens and provide a strategy for improving the performance of gas-fermenting bacteria by genetic engineering.