Cooperativity of Negative Autoregulation Confers Increased Mutational Robustness

High-throughput assays to assess variant effects on disease

Interpreting the wealth of rare genetic variants discovered in population-scale sequencing efforts and deciphering their associations with human health and disease present a critical challenge due to the lack of sufficient clinical case reports. One promising avenue to overcome this problem is deep mutational scanning (DMS), a method of introducing and evaluating large-scale genetic variants in model cell lines. DMS allows unbiased investigation of variants, including those that are not found in clinical reports, thus improving rare disease diagnostics. Currently, the main obstacle limiting the full potential of DMS is the availability of functional assays that are specific to disease mechanisms. Thus, we explore high-throughput functional methodologies suitable to examine broad disease mechanisms. We specifically focus on methods that do not require robotics or automation but instead use well-designed molecular tools to transform biological mechanisms into easily detectable signals, such as cell survival rate, fluorescence or drug resistance. Here, we aim to bridge the gap between disease-relevant assays and their integration into the DMS framework.

A double-negative feedback loop between NtrBC and a small RNA rewires nitrogen metabolism in legume symbionts

IMPORTANCE

Root nodule endosymbioses between diazotrophic rhizobia and legumes provide the largest input of combined N to the biosphere, thus representing an alternative to harmful chemical fertilizers for sustainable crop production. Rhizobia have evolved intricate strategies to coordinate N assimilation for their own benefit with N2 fixation to sustain plant growth. The rhizobial N status is transduced by the NtrBC two-component system, the seemingly ubiquitous form of N signal transduction in Proteobacteria. Here, we show that the regulatory sRNA NfeR1 (nodule formation efficiency RNA) of the alfalfa symbiont Sinorhizobium meliloti is transcribed from a complex promoter repressed by NtrC in a N-dependent manner and feedback silences ntrBC by complementary base-pairing. These findings unveil a more prominent role of NtrC as a transcriptional repressor than hitherto anticipated and a novel RNA-based mechanism for NtrBC regulation. The NtrBC-NfeR1 double-negative feedback loop accurately rewires symbiotic S. meliloti N metabolism and is likely conserved in α-rhizobia.

Effect of caldesmon mutations in the development of zebrafish embryos

Cancer is a profound medical concern and better treatments are needed for cancer patients. Therefore, new cancer targets are constantly being studied. These targets need not only be relevant for cancer progression, but their modulation needs to be tolerated reasonably well by the host. Caldesmon is one of these proposed novel targets for cancer therapy. Therefore, we analyzed effects of caldesmon mutations in normal development using genetically modified zebrafish embryos. We analyzed mutations in both zebrafish caldesmon genes, cald1a and cald1b and analyzed effects of either mutation alone or as in combination in double homozygous embryos using molecular, morphological and functional analyses. The effects of caldesmon mutations were mild and the gross development of zebrafish embryos was normal. The caldesmon mutant embryos had, however, alterations in response to light-stimulus in behavioural assays. Taken together, the effects of caldesmon mutations in the development of zebrafish embryos were reasonably well tolerated and did not indicate significant concerns for caldesmon being a potential target for cancer therapy.

The Parameter-Fitness Landscape of lexA Autoregulation in Escherichia coli

Feedback mechanisms are critical to control physiological responses. In gene regulation, one important example, termed negative autoregulation (NAR), occurs when a transcription factor (TF) inhibits its own production. NAR is common across the tree of life, enabling rapid homeostatic control of gene expression. NAR behavior can be described in accordance with its core biochemical parameters, but how constrained these parameters are by evolution is unclear. Here, we describe a model genetic network controlled by an NAR circuit within the bacterium Escherichia coli and elucidate these constraints by experimentally changing a key parameter and measuring its effect on circuit response and fitness. This analysis yielded a parameter-fitness landscape representing the genetic network, providing a window into what gene-environment conditions favor evolution of this regulatory strategy.

Feedback mechanisms are fundamental to the control of physiological responses. One important example in gene regulation, termed negative autoregulation (NAR), occurs when a transcription factor (TF) inhibits its own production through transcriptional repression. This enables more-rapid homeostatic control of gene expression. NAR circuits presumably evolve to limit the fitness costs of gratuitous gene expression. The key biochemical reactions of NAR can be parameterized using a mathematical model of promoter activity; however, this model of NAR has been studied mostly in the context of synthetic NAR circuits that are disconnected from the target genes of the TFs. Thus, it remains unclear how constrained NAR parameters are in a native circuit context, where the TF target genes can have fitness effects on the cell. To quantify these constraints, we created a panel of Escherichia coli strains with different lexA-NAR circuit parameters and analyzed the effect on SOS response function and bacterial fitness. Using a mathematical model for NAR, these experimental data were used to calculate NAR parameter values and derive a parameter-fitness landscape. Without feedback, survival of DNA damage was decreased due to high LexA concentrations and slower SOS “turn-on” kinetics. However, we show that, even in the absence of DNA damage, the lexA promoter is strong enough that, without feedback, high levels of lexA expression result in a fitness cost to the cell. Conversely, hyperfeedback can mimic lexA deletion, which is also costly. This work elucidates the lexA-NAR parameter values capable of balancing the cell’s requirement for rapid SOS response activation with limiting its toxicity.

IMPORTANCE Feedback mechanisms are critical to control physiological responses. In gene regulation, one important example, termed negative autoregulation (NAR), occurs when a transcription factor (TF) inhibits its own production. NAR is common across the tree of life, enabling rapid homeostatic control of gene expression. NAR behavior can be described in accordance with its core biochemical parameters, but how constrained these parameters are by evolution is unclear. Here, we describe a model genetic network controlled by an NAR circuit within the bacterium Escherichia coli and elucidate these constraints by experimentally changing a key parameter and measuring its effect on circuit response and fitness. This analysis yielded a parameter-fitness landscape representing the genetic network, providing a window into what gene-environment conditions favor evolution of this regulatory strategy.

NRF2-Driven KEAP1 Transcription in Human Lung Cancer

Constitutive NRF2 activation by disrupted KEAP1-NRF2 interaction has been reported in a variety of human cancers. However, studies focusing on NRF2-driven KEAP1 expression under human cancer contexts are still uncommon. We examined mRNA expression correlation between NRF2 and KEAP1 in multiple human cancers. We measured KEAP1 mRNA and protein alterations in response to the activation or silencing of NRF2. We queried chromatin immunoprecipitation sequencing (ChIP-seq) datasets to identify NRF2 binding to KEAP1 promoters in human cells. We used reporter assay and CRISPR editing to assess KEAP1 promoter activity and mRNA abundance change. To determine specimen implication of the feedback pattern, we used gene expression ratio to predict NRF2 signal disruption as well as patients' prognosis. Correlation analysis showed KEAP1 mRNA expression was in positive association with NRF2 in multiple squamous cell cancers. The positive correlations were consistent across all squamous cell lung cancer cohorts, but not in adenocarcinomas. In human lung cells, NRF2 interventions significantly altered KEAP1 mRNA and protein expressions. ChIP-quantitative PCR (ChIP-qPCR) and sequencing data demonstrated consistent NRF2 occupancy to KEAP1 promoter. Deleting NRF2 binding site significantly reduced baseline and inducible KEAP1 promoter activity and KEAP1 mRNA expression. By incorporating tumor tissue KEAP1 mRNA expressions in estimating NRF2 signaling disruptions, we found increased TXN/KEAP1 mRNA ratio in cases with NRF2 gain or KEAP1 loss and decreased NRF2/KEAP1 mRNA ratio in cases with NRF2-KEAP1 somatic mutations. In TCGA PanCancer datasets, we also identified that cases with loss-of-function mutations in NRF2 pathway recurrently appeared above the NRF2-KEAP1 mRNA expression regression lines. Moreover, compared with previous NRF2 signatures, the ratio-based strategy showed better predictive performance in survival analysis with multiple squamous cell lung cancer cohort validations. IMPLICATIONS: NRF2-driven KEAP1 transcription is a crucial component of NRF2 signaling modulation. This hidden circuit will provide in-depth insight into novel cancer prevention and therapeutic strategies.

The MtDMI2-MtPUB2 Negative Feedback Loop Plays a Role in Nodulation Homeostasis

DOES NOT MAKE INFECTION 2 (MtDMI2) is a Leu rich repeat-type receptor kinase required for signal transduction in the Medicago truncatula/Sinorhizobium meliloti symbiosis pathway. However, the mechanisms through which MtDMI2 participates in nodulation homeostasis are poorly understood. In this study, we identified MtPUB2-a novel plant U-box (PUB)-type E3 ligase-and showed that it interacts with MtDMI2. MtDMI2 and MtPUB2 accumulation were shown to be similar in various tissues. Roots of plants in which MtPUB2 was silenced by RNAi (MtPUB2-RNAi plants) exhibited impaired infection threads, fewer nodules, and shorter primary root lengths compared to those of control plants transformed with empty vector. Using liquid chromatography-tandem mass spectrometry, we showed that MtDMI2 phosphorylates MtPUB2 at Ser-316, Ser-421, and Thr-488 residues. When MtPUB2-RNAi plants were transformed with MtPUB2^S421D , which mimics the phosphorylated state, MtDMI2 was persistently ubiquitinated and degraded by MtPUB2^S421D, resulting in fewer nodules than observed in MtPUB2/MtPUB2-RNAi-complemented plants. However, MtPUB2^S421A /MtPUB2-RNAi-complemented plants showed no MtPUB2 ubiquitination activity, and their nodulation phenotype was similar to that of MtPUB2-RNAi plants transformed with empty vector. Further studies demonstrated that these proteins form a negative feedback loop of the prey (MtDMI2)-predator (MtPUB2) type. Our results suggest that the MtDMI2-MtPUB2 negative feedback loop, which displays crosstalk with the long-distance autoregulation of nodulation via MtNIN, plays an important role in nodulation homeostasis.