Biology subjects

Zhou, K.

Publications and source records attributed to Zhou, K..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

vClassifier: a toolkit for species-level classification of prokaryotic viruses

As the most abundant and diverse biological entities, prokaryotic viruses play pivotal roles in ecological systems. Their taxonomic classification has been instrumental in elucidating their diversity and ecological functions. However, determination of viral taxonomy remains a considerable challenge. Recently developed approaches succeed in assignment of viral taxonomy at higher ranks, such as at the family level and above, but struggle at the subfamily level and below to the genus and species resolutions. Here, we describe the vClassifier toolkit, a phylogeny-informed methodology to provide species-level taxonomic assignments of viruses. We used single-copy marker genes relevant to specific taxa and reference phylogenetic trees for these groups which facilitates direct comparisons with the taxonomic framework of the International Committee on Taxonomy of Viruses (ICTV). Our method demonstrated significant congruence with the ICTV taxonomy, showing 84-91% alignment at the subfamily and genus levels. For species-level classification, our strategy was integrated with average nucleotide identity, yielding a high congruence rate of over 92% with the taxonomic data from the NCBI Virus database. Benchmarking comparisons revealed that vClassifier matches or surpasses other available tools regarding precision and classification success rates. By achieving objectivity and high levels of consistency, vClassifier streamlines the taxonomic categorization of prokaryotic viral genomes. Accurate assignments at the subfamily, genus, and species levels will significantly refine the taxonomic resolution of viruses, fostering a deeper understanding of viral diversity in microbiomes and ecosystems.

evolutionary biology↗

bioRxiv2024

ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction

The prediction of protein-protein interactions (PPIs) is crucial for understanding biological functions and diseases. Previous machine learning approaches to PPI prediction mainly focus on direct physical interactions, ignoring the broader context of nonphysical connections through intermediate proteins, thus limiting their effectiveness. The emergence of Large Language Models (LLMs) provides a new opportunity for addressing this complex biological challenge. By transforming structured data into natural language prompts, we can map the relationships between proteins into texts. This approach allows LLMs to identify indirect connections between proteins, tracing the path from upstream to downstream. Therefore, we propose a novel framework ProLLM that employs an LLM tailored for PPI for the first time. Specifically, we propose Protein Chain of Thought (ProCoT), which replicates the biological mechanism of signaling pathways as natural language prompts. ProCoT considers a signaling pathway as a protein reasoning process, which starts from upstream proteins and passes through several intermediate proteins to transmit biological signals to downstream proteins. Thus, we can use ProCoT to predict the interaction between upstream proteins and downstream proteins. The training of ProLLM employs the ProCoT format, which enhances the models understanding of complex biological problems. In addition to ProCoT, this paper also contributes to the exploration of embedding replacement of protein sites in natural language prompts, and instruction fine-tuning in protein knowledge datasets. We demonstrate the efficacy of ProLLM through rigorous validation against benchmark datasets, showing significant improvement over existing methods in terms of prediction accuracy and generalizability. Our results highlight the potential of LLMs to transform the field of PPI, serving as a robust potential tool for various categories of biological and medical research. The code is available at: https://github.com/MingyuJ666/ProLLM.

bioinformatics↗

bioRxiv2023

ARHGAP32 as a novel RhoGAP interacting with desmoplakin is required for desmosomal organization and assembly

Desmosomes are specialized cell-cell junctions that play a critical role in maintaining tissue barrier integrity, particularly in mechanically stressed tissues. The assembly of desmosomes is regulated by the cytoskeleton and its regulators, and desmosomes also function as a central hub for regulating F-actin. However, the specific mechanisms underlying the crosstalk between desmosomes and F-actin, particularly involving RhoGAP or RhoGEF proteins, remain unclear. In our study, we identified that ARHGAP32, a Rho GTPase-activating protein, is located in desmosomes through its interaction with DSP via its GAB2-interacting domain. Using CRISPR-Cas9 gene knockout system, we confirmed that ARHGAP32 is required for proper desmosomal organization, maturation, and length regulation. Notably, the loss of ARHGAP32 resulted in increased formation of F-actin stress fibers and phosphorylation of MYOSIN at T18/S19, indicating enhanced actomyosin contractility. Furthermore, inhibition of ROCK1 kinase activity using Y27632 effectively restored desmosomal organization. Moreover, we demonstrated that the regulation of desmosomes by ARHGAP32 is crucial for maintaining the integrity of epithelial cell sheets. Collectively, our study unveils ARHGAP32 as a RhoGAP present at desmosomes, potentially facilitating the crosstalk between desmosomes and F-actin. Its presence is indispensable for desmosomal assembly and the preservation of epithelial cell sheet integrity by regulating actomyosin contractility.

cell biology↗

bioRxiv2023

Artificial intelligence-assisted stimulated Raman molecular cytology enables accurate and rapid intraoperative assessment of the surgical margin in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a highly mortal cancer whose only potentially curative treatment is surgical resection. Intraoperative assessment of its surgical margins is vital for patient survival. Frozen-section biopsy is routinely performed for this purpose. However, its high dependence on pathologists experience frequently poses diagnostic discrepancies. The essential invasiveness of PDAC also causes sampling errors. This study developed an intelligent molecular cytology approach with improved diagnostic objectivity and broader sampling coverage. Our method, Multi-Instance Cytology with Learned Raman Embedding (MICLEAR), is characterized by compositional information provided by label-free Raman imaging. First, 4085 cells were brushed off from the pancreases of 41 patients and imaged using stimulated Raman scattering microscopy. Then, a contrastive learning-based cell embedding model was developed to compress each cells morphological and compositional information into a compact cell vector. Finally, a multi-instance learning-based diagnosis model using cell vectors was employed to predict the likelihood of a patients margin being positive. MICLEAR achieved 80% sensitivity, 94.1% specificity, and an AUC of 0.86 on 27 patients for validation, comprising 10 with positive margins and 17 with negative ones, within approximately 8 minutes per patient. It may hold promises for more efficient and accurate intraoperative assessment of PDAC surgical margins.

biophysics↗

bioRxiv2023

Paternal genomic resources from the YanHuang cohort suggested a Weakly-Differentiated Multi-source Admixture model for the formation of Hans founding ancestral lineages

The large-scale human genome revolution and rapidly advanced statistical innovation have updated our understanding of the fine-scale and complex genetic structure, the entire landscape of genetic diversity and the evolutionary trajectories of spatiotemporally different ancients and ethnolinguistically diverse modern populations. Recent ancient DNA research provided a detailed and complex admixture picture of ancient Europeans but limited insights into East Asians as the few available genomes. Y-chromosome variations in the male-specific regions, served as molecular archaeological tool, have unique evolutionary features that can be utilized to reconstruct the origin and subsequent interaction of ancient East Asian paternal lineages. We launched the YanHuang cohort using our designed highest-resolution capture sequencing panel to explore the detailed evolutionary trajectory of the Han Chinese, one of the largest ethnic groups in the world. We reported one of the largest uniparental genomic resources and observed multiple founding paternal lineages dominant in ancient western Eurasian, Siberian and East Asian participating in the formation of the gene pool of the Han Chinese. We identified fine-scale paternal genetic structure correlated with different patterns of ancient population interaction and geographical mountain barriers (Qinling-Huaihe line and Nanling Mountains), suggesting isolation-enhanced and admixture-introduced genetic differentiation enhanced the complexity of the Han Chinese genomic diversity. We observed a strong direct correlation between the frequency of multiple founding lineages of the Han Chinese and the proportion of subsistence-related ancestry sources related to western pastoralists, Holocene Mongolian Plateau people and ancient East Asians, reflecting the ancient migration events contributed to our identified patterns of Chinese paternal genomic diversity. We finally provided one novel and the most plausible admixture-by-admixture model, the Weakly-Differentiated Multi-Source Admixture model, as the major genetic mechanism to illuminate our observed pattern of complex interactions of multiple ancestral sources and landscape of the Han Chinese paternal genetic diversity. Generally, we presented one large-scale uniparental genomic resource from the YanHuang cohort, portrayed one novel admixture formation model and presented the entire genomic landscape with multiple ancestral sources related to ancient herders, hunter-gatherers and farmers who participated in the ancestral formation of the Han Chinese.

evolutionary biology↗

bioRxiv2023

Ancient farmer and steppe pastoralist-related founding lineages contributed to the complex landscape of episodes in the diversification of Chinese paternal lineages

Ancient DNA advances have reported the complex genetic history of Eurasians, but how the knowledge of ancient subsistence strategy shifts and population movements influenced the fine-scale paternal genetic structure in East Asia has not been assessed. Here, we reported one integrated Y-chromosome genomic database of 15,530 people, including 1753 ancient people and newly-reported 919 individuals genotyped using our recently-developed targeted sequencing YHSeqY3000 panel, to explore Chinese genomic diversity, population evolutionary tracts and their genetic formation mechanism. We identified four major ancient technological innovations and population movements that shaped the landscape of Chinese paternal lineages. First, the expansion of millet farmers and early East Asians from the Yellow River Basin carrying the major O2/D subclades promoted the formation of the Sino-Tibetan peoples major composition and accelerated the Tibetan Plateaus permanent occupation. Second, rice farmers dispersal from the Yangtze River Valley carrying O1 and some sublineages of O2 contributed significantly to Tai-Kadai, Austronesian, Hmong-Mien, Austroasiatic people and southern Han Chinese. Third, Siberian-related paternal lineages of Q and C originated and boomed from Neolithic hunter-gatherers from the Mongolian Plateau and the Amur River Basin and significantly influenced the gene pools of northern Chinese. Fourth, western Eurasian-derived J, G and R lineages initially spread with Yamnaya steppe pastoralists and other proto-Indo-European people and further widely dispersed via the trans-Eurasian cultural communication along the Eurasian Steppe and the ancient Silk Road, remaining genetic trajectories in northwestern Chinese. Our work provided comprehensive modern and ancient genetic evidence to illuminate the impact of population interaction from the ancient farmer or herder-based societies on the genetic diversity patterns of modern people, revised our understandings of ancestral sources of Chinese paternal lineages, underscored the scientific imperative of the large-scale genomic resources of dense spatiotemporal underrepresented sampling populations to understand human evolutionary history.

genetics↗

bioRxiv2023

Shared and distinct neural signatures of feature and spatial attention

The debate on whether feature attention (FA) and spatial attention (SA) share a common neural mechanism remains unresolved. Previous neuroimaging studies have identified fronto-parietal-temporal attention-related regions that exhibited consistent activation during various visual attention tasks. However, these studies have been limited by small sample sizes and methodological constraints inherent in univariate analysis. Here, we utilized a between-subject whole-brain machine learning approach with a large sample size (N = 235) to investigate the neural signatures of FA (FAS) and SA (SAS). Both FAS and SAS showed cross-task predictive capabilities, though inter-task prediction was weaker than intra-task prediction, suggesting both shared and distinct mechanisms. Specifically, the frontoparietal network exhibited the highest predictive performance for FA, while the visual network excelled in predicting SA, highlighting their respective prominence in the two attention processes. Moreover, both signatures demonstrated distributed representations across large-scale brain networks, as each cluster within the signatures was sufficient for predicting FA and SA, but none of them were deemed necessary for either FA or SA. Our study challenges traditional network-centric models of attention, emphasizing distributed brain functioning in attention, and provides comprehensive evidence for shared and distinct neural mechanisms underlying FA and SA.

neuroscience↗

bioRxiv2023

DNA Nanostructure-Guided Assembly of Proteins into Programmable Shapes

The development of methods to synthesize protein oligomers with precisely controlled number and configuration of components will enable artificial protein complexes and nanostructures with diverse biological and medical applications. Using DNA hybridization to link protein-DNA conjugates provides for a programmability that can be difficult to achieve with other methods, such as engineering multiple orthogonal protein-protein interfaces. However, it is still difficult to construct well-defined protein assemblies, and the challenge is magnified if only a single type of building block is used. To overcome this hurdle, we use a DNA origami as an "assembler" to guide the linking of protein-DNA conjugates using a series of oligonucleotide hybridization and displacement operations. We constructed several isomeric protein nanostructures on a DNA origami platform by using a C3-symmetric building block comprised of a protein trimer modified with DNA handles. By changing the number of protein-DNA building blocks attached to the origami, and the sequence of the linking and displacement strands added, we were able to produce dimers, two types of trimer structures, and three types of tetramer assemblies. Our approach expands the scope for the precise design and assembly of protein-based nanostructures, and will enable the formulation of functional protein complexes with stoichiometric and geometric control.

bioengineering↗

bioRxiv2023

The effect of circulation rate on the water quality of container-type recirculation aquaculture system under different feeding rates of Schizothorax wangchiachii

As an experimental fish, juvenile Schizothorax wangchiachii were fed different dosages (100, 300, or 500 g), and the changes in water quality in the inlet and outlet of the biofilter and in the aquaculture buckets were measured under different circulation rates (1.5, 3, or 4.5 m3/h; water samples were collected every 2 hours). With 100 g of feed and different circulation rates (1.5, 3, or 4.5 m3/h), the average removal rates of ammonia nitrogen and nitroso nitrogen by the biofilter were 40.4, 36.8, and 27.7% and 43.9, 36.9, and 29.8%, respectively. With 300 g of feed, the average removal rates of ammonia nitrogen and nitroso nitrogen were 42.3, 37.9, and 33.6% and 45.8, 32.7, and 21.7%, respectively. With 500 g of feed, the average removal rates of ammonia nitrogen and nitroso nitrogen by biofilters with different circulation rates were 53.5, 42.6, and 35.7% and 40.3, 26.5, and 18.1%, respectively. Therefore, when the feeding amounts were 100, 300, and 500 g, respectively, the optimal circulation rates were 1.5, 1.5, or 4.5 m3/h, which allowed the best management and reduction in energy consumption of the circulating aquaculture system. This research conclusion provides a reliable scientific reference for the promotion of a low-cost new model of industrial circular water aquaculture.

animal behavior and cognition↗

bioRxiv2023

The TRIP6/LATS1 complex constitutes the tension sensor of α-catenin/vinculin at both bicellular and tricellular junctions

Cell-cell mechanotransduction regulates tissue development and homeostasis. -catenin, the core component of adherens junctions, functions as a tension sensor and transducer by recruiting vinculin and transducing the signals to influence cell behaviors. However, little is known about the components, distributions, and dynamics of the -catenin based tension sensors at the cell junctions. Here, we uncovered the TRIP6/LATS1 complex locates at the tension sites where -catenin/vinculin is at both the bicellular junctions (BCJs) and tricellular junctions (TCJs). Vinculin/TRIP6/LATS1 are prone to form as puncta in the cytoplasm without -catenin participation. Furthermore, the tension sensing complex distributed stronger at TCJs and exhibited a discontinuously button-like pattern on BCJs. The -catenin/vinculin BiFC-based mechanosensor further proved the discontinuous distribution of the tension at BCJs, and was more motile than the TCJs. In summary, our study revealed that TRIP6 and LATS1 are novel compositions of the tension sensor, together with the core complex of -catenin/vinculin, at both the BCJs and TCJs. This work gives insights and improvements in exploring the molecular mechanism that mediates cell-cell mechanotransduction at cell junctions.

cell biology↗

bioRxiv2023

Leading Basic Modes of Spontaneous Activity Drive Individual Functional Connectivity Organization in the Resting Human Brain

Spontaneous activity of the human brain provides a window to explore intrinsic principles of functional organization. However, most studies have focused on interregional functional connectivity. The principles underlying rich repertoires of instantaneous activity remain largely unknown. We apply a novel eigen-microstate analysis to three resting-state functional MRI datasets to identify basic modes that represent fundamental activity patterns that coexist over time. We identify a few (i.e., five) leading basic modes that dominate activity fluctuations. Each of these modes exhibits a distinct functional system-dependent coactivation pattern and corresponds to specific cognitive profiles. In particular, the spatial pattern of the first leading basis mode shows the separation of activity between the default-mode and primary and attention regions. We further reconstruct individual functional connectivity as the weighted contribution of these leading basic modes based on theoretical modelling. Moreover, these leading basic modes capture sleep deprivation-induced changes in brain activity and interregional connectivity, primarily involving the default-mode and task-positive regions. Our findings reveal a dominant set of basic modes of spontaneous activity that reflect multiplexed interregional coordination and drive conventional functional connectivity, furthering the understanding of the functional significance of spontaneous brain activity.

neuroscience↗

bioRxiv2023

Chromosome-level genome assembly provides insights into adaptive evolution of chromosome and important traits in the gecko Gekko japonicus

Gekko japonicus possess excellent flexible climbing and detoxification ability under insectivorous habits, and its chromosomes and the genetic evolutionary mechanisms behind these traits are still unclarified. Here, we assembled a chromosome-level genome of G. japonicus with a total size of 2.53 Gb contained in 19 pairs of chromosomes. The evolutionary breakpoint regions (EBRs) are significantly enriched for some repetitive elements compared to the rest of genome and the genes located in the EBRs are enriched in defense response pathway. G. japonicus specific gene families, expanded gene families and positively selected genes are mainly enriched in some pathways related to the immune, sensory and nervous systems. These results from comprehensive comparative genomics and evolutionary genomics analyses indicated that bitter taste receptor type 2 (T2Rs) expanded in different lineages by tandem gene duplication. The expansion and independent duplication events of T2Rs and positively selected branches were predominantly present in insectivorous species, suggests that T2Rs are associate with clearance of bitter toxins in gekkotans. Detoxification genes in detox and biosynthetic cytochrome P450 of G. japonicas have frequent duplication and loss events, suggests that they undergo more birth and death processes compared to biosynthesis type genes. Pro, Cys, Gly and Ser are the most abundant amino acids in 66 epidermis formation corneous beta proteins (CBPs) of G. japonicas, the abundance of Gly and Cys in CBPs implying significant effects on the flexibility and setae adhesiveness of gekkotans. Some thermosensitive thermoregulatory transient receptor potential channels under relaxed purifying selection or positive selection in G. japonicus, implying that one of the important factors improve the ability to adapt to climate change.

genomics↗

bioRxiv2023

Conserved Chamber-Specific Polyploidy Maintains Heart Function in Drosophila

Developmentally programmed polyploidy (whole-genome-duplication) of cardiomyocytes is common across evolution. Functions of such polyploidy are essentially unknown. Here, we reveal roles for precise polyploidy levels in cardiac tissue. We highlight a conserved asymmetry in polyploidy level between cardiac chambers in Drosophila larvae and humans. In Drosophila, differential Insulin Receptor (InR) sensitivity leads the heart chamber to reach a higher ploidy/cell size relative to the aorta chamber. Cardiac ploidy-reduced animals exhibit reduced heart chamber size, stroke volume, cardiac output, and acceleration of circulating hemocytes. These Drosophila phenotypes mimic systemic human heart failure. Using human donor hearts, we reveal asymmetry in nuclear volume (ploidy) and insulin signaling between the left ventricle and atrium. Our results identify productive and likely conserved roles for polyploidy in cardiac chambers and suggest precise ploidy levels sculpt many developing tissues. These findings of productive cardiomyocyte polyploidy impact efforts to block developmental polyploidy to improve heart injury recovery.

developmental biology↗

bioRxiv2023

Engineering Escherichia coli to produce aromatic chemicals from ethylene glycol

Microbial overproduction of aromatic chemicals has gained considerable industrial interest and various metabolic engineering approaches have been employed in recent years to address the associated challenges. So far, most studies have used sugars (mostly glucose) or glycerol as the primary carbon source. In this study, we used ethylene glycol (EG) as the main carbon substrate. EG could be obtained from the degradation of plastic and cellulosic wastes. As a proof of concept, Escherichia coli was engineered to transform EG into L-tyrosine, a valuable aromatic amino acid. Under the best fermentation condition, the strain produced 2 g/L L-tyrosine from 10 g/L EG at approximately 50% of the theoretical yield, outperforming glucose (the most common sugar feedstock) in the same experimental conditions. To prove the concept that EG can be converted into different aromatic chemicals, E. coli was further engineered with a similar approach to synthesize other valuable aromatic chemicals, L-phenylalanine and p-coumaric acid. Finally, waste polyethylene terephthalate (PET) bottles were degraded using acid hydrolysis and the resulting monomer EG was transformed into L-tyrosine using the engineered E. coli, yielding a comparable titer to that obtained using commercial EG. The strains developed in this study should be valuable to the community for producing valuable aromatics from EG.

bioengineering↗

bioRxiv2023

Accurate and Rapid Detection of Peritoneal Metastasis from Gastric Cancer by AI-assisted Stimulated Raman Cytology

Peritoneal metastasis (PM) is the most common form of distant metastasis and one of the leading causes of death in gastric cancer (GC). For locally advanced GC, clinical guidelines recommend peritoneal lavage cytology for intraoperative PM detection. Unfortunately, current peritoneal lavage cytology is limited by low sensitivity (<60%). Here we established the stimulated Raman cytology (SRC), a chemical microscopy-based intelligent cytology. By taking advantages of stimulated Raman scattering in label-free, high-speed, and high-resolution chemical imaging, we firstly imaged 53951 exfoliated cells in ascites obtained from 80 GC patients (27 PM positive, 53 PM negative), at the Raman bands corresponding to DNA, protein, and lipid, respectively. Then, we revealed 12 single cell features of morphology and composition that were significantly different between PM positive and negative specimens, including cellular area, lipid protein ratio, etc. Importantly, we developed a single cell phenotyping algorithm to further transform the above raw features to feature matrix. Such matrix was crucial to identify the significant marker cell cluster, the divergence of which was finally used to differentiate the PM positive and negative. Compared with histopathology, the gold standard of PM detection, our SRC method assisted by machine learning classifiers could reach 81.5% sensitivity, 84.9% specificity, and the area under receiver operating characteristic curve of 0.85, within 20 minutes for each patient. Such remarkable improvement in detection accuracy is largely owing to incorporation of the single-cell composition features in SRC. Together, our SRC method shows great potential for accurate and rapid detection of PM from GC.

biophysics↗

bioRxiv2022

MC1R drives cutaneous repair by promoting angiogenesis and lymphangiogenesis

Cutaneous healing results in scarring with significant functional and psychological sequelae, while chronic non-healing wounds represent repair failure often with devastating consequences, including amputation and death. Due to a lack of effective therapies, novel interventions addressing scarring and chronic wounds are urgently needed. Here, we demonstrate that harnessing melanocortin 1 receptor with a selective agonist (MC1R-Ag) confers multifaceted benefits to wound repair. MC1R-Ag accelerates wound closure and re-epithelialization while improving wound bed perfusion and lymphatic drainage by promoting angiogenesis and lymphangiogenesis. Concomitant reductions in oxidative stress, inflammation and scarring were also observed. To evaluate the therapeutic potential of targeting MC1R in pathological healing, we established a novel murine model that recapitulates the hallmarks of human non-healing wounds. This model combines advanced age and locally elevated oxidative stress. Remarkably, topical application of MC1R-Ag restored repair, whereas disrupting MC1R signalling exacerbated the chronic wound phenotype. Our study highlights MC1R agonism as a promising therapeutic approach for scarring and non-healing wound pathologies, and our chronic wound model as a valuable tool for elucidating ulcer development mechanisms.

pathology↗

bioRxiv2022

Quartet metabolite reference materials for assessing inter-laboratory reliability and data integration of metabolomic profiling

Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets. As part of the Quartet Project, we established a publicly available suite of four metabolite reference materials derived from B-lymphoblastoid cell lines from a family quartet of parents and monozygotic twin daughters. We generated comprehensive LC-MS based metabolomic data from the Quartet reference materials using targeted and untargeted strategies in different laboratories. High variabilities in the qualitative and quantitative metabolomic measurements were observed across laboratories. Moreover, the Quartet multi-sample-based quality metrics were developed for objectively assessing the reliability of metabolomic profiling in detecting intrinsic biological differences among difference groups of samples. Importantly, the ratio-based metabolomic profiling, by scaling the absolute values of a study sample relative to those of a universal reference sample, enables data integration in long-term measurements across difference laboratories or platforms. Thus, we constructed the ratio-based high-confidence reference datasets between two reference samples, providing "ground truth" for inter-laboratory proficiency test, which enables objective assessment of various metabolomic methods. Our study provided the community with rich resources and best practice for objective assessment of inter-laboratory measurements and data integration, ensuring reliable large-scale and longitudinal metabolomic profiling.

systems biology↗

bioRxiv2022

DNA looping mediates cooperative transcription activation

Transcription factors respond to multi-level stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by [~]50{o}, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a DNA looping mechanism of cooperative transcription activation in bacteria.

molecular biology↗