Biology subjects

Chou, H.-H. D.

Publications and source records attributed to Chou, H.-H. D..

4 recordsLinked to original sources

bioRxiv2026

GBactPro: cross-species bacterial promoter prediction using element-resolved promoter definitions

Accurate bacterial promoter prediction remains challenging across species, partly because conventional models often use fixed-length promoter windows that do not explicitly account for promoter architecture. Using promoter annotations derived from the Promoter Architecture Scanner (PAS), we found that training on sequences comprising the -35 element, spacer, and -10 element improved cross-species prediction compared with fixed-length promoter windows. Based on this element-resolved promoter definition, we developed GBactPro, a convolutional neural network-bidirectional long short-term memory (CNN-BiLSTM) model jointly trained on curated promoter data from 43 bacterial species. The jointly trained model achieved a mean AUROC of 0.9943 on held-out test sequences. Under matched-length benchmarking, GBactPro outperformed Promotech, iPro-MP, Prompt, and iPro-WAEL by 0.066-0.314 in mean AUROC. Genome-wide scanning of Escherichia coli achieved an AUROC of 0.979 and an AUPRC of 0.160 under stringent one-to-one promoter-site matching, increasing to 0.997 and 0.323, respectively, with a 100-bp positional tolerance. Unmatched predictions were enriched for H-NS binding, and independent H-NS-knockout data further supported the possibility that some predicted promoter-like regions are transcriptionally repressed. Together, these findings highlight the importance of promoter-sequence definition for cross-species prediction and demonstrate the potential of GBactPro for genome-wide promoter identification and biological interpretation.

genomics↗

bioRxiv2026

Data coverage and model formulation reshape quantitative interpretations of bacterial transcriptional regulation

Thermodynamic models quantitatively describe interactions between transcription machinery and bacterial promoters. Contrary to conventional understanding, model analysis by Parisutham et al. (2025) attributes transcriptional inhibition by repressors to overstabilization of the RNA polymerase-promoter complex rather than prevention of its formation. Moreover, it suggests an inverse scaling relationship between basal promoter strength and transcriptional fold change, applicable to both repressor- and activator-mediated regulation. To reevaluate findings from this study, we systematically analyze empirical data and compare its framework with conventional thermodynamic models. In contrast to the inverse scaling relationship, data across multiple sources exhibit a peaked tradeoff between basal promoter strength and fold change, underscoring the importance of broad data coverage in revealing the full pattern required for reliable model inference. Furthermore, we identify the model assumption responsible for the apparent inverse scaling and misinterpretation of regulatory mechanisms. Relaxing this assumption enables the model to capture the peaked tradeoff and yield inferences consistent with established mechanisms of transcriptional repression and activation. We further derive a mathematical solution that connects basal expression to fold change for both repressor- and activator-regulated promoters. Our results underscore the importance of broad data coverage to avoid a blind-men-and-elephant interpretation and establish basal promoter strength as a key design parameter governing transcriptional regulation.

systems biology↗

bioRxiv2025

Core elements play distinct roles in promoter birth and transcriptional regulation

Gene expression shapes phenotypes and evolution. However, studies of gene regulation focus on transcription factors, overlooking core promoters. To investigate how promoters emerge and regulate transcription, we determined the sequence-function landscapes of core elements, -35 and -10, in constitutive and transcription factor-regulated promoters in Escherichia coli. Characterization of in vivo transcriptional landscapes and in vitro RNA polymerase-promoter interactions showed the -10 element as essential for promoter evolution from random sequences. In contrast, the -35 element, though broadly conserved, is dispensable for promoter birth. Instead, it exerts greater impact on gene regulation via coordinated interactions with transcription activators and RNA polymerase. We further showed that evolution fine-tunes the -35 and -10 sequences of transcription factor-regulated promoters to achieve near-maximal fold changes by lowering basal while elevating induced expression. A notable exception is PluxI, whose leaky expression provides a crucial baseline for initiating quorum sensing. These findings elucidate promoter design principles and underscore the interdependence and coevolution of core elements, RNA polymerase, and transcription factors.

systems biology↗

bioRxiv2025

Unravel the start element and promoter architecture across the domain Bacteria

Core promoters comprise multiple elements whose interaction with RNA polymerase initiates transcription. Despite decades of research, substantial sequence and length variation of promoter elements has hindered efforts to elucidate their function and the evolutionary diversity of transcriptional regulation. Combining massively parallel assays, biophysical modeling, and functional validation, we systematically dissected the promoter architecture upstream of experimentally determined transcription start sites in 49 phylogenetically diverse bacterial genomes (GC content: 27.8-72.1%). We identified a conserved 3-bp promoter element, termed start, that dictates transcription start site selection and enhances transcription. We uncovered a four-region organization within the variable spacer element, whose sequence composition modulates transcription by up to 600-fold. We showed that the discriminator element is conserved in Terrabacteria but diverse in Gracilicutes, the two major bacterial clades. High discriminator sequence diversity in Gracilicutes likely reflects diversifying evolution, enabling promoter-encoded regulation to orchestrate global gene expression in response to growth rate changes. Together, our findings reveal broad conservation of bacterial promoter organization while highlighting regulatory divergence of promoter elements and RNA polymerase between Terrabacteria and Gracilicutes. Sequence and functional similarities between bacterial promoter elements and their archaeal and eukaryotic counterparts further suggest a shared evolutionary origin of promoter architecture.

microbiology↗