Biology subjects

Sheng, J.

Publications and source records attributed to Sheng, J..

53 records · Page 3Linked to original sources

bioRxiv2020

The role of cation diffusion facilitator CDF-1 in lipid metabolism in Caenorhabditis elegans

Zinc is one of the most important trace elements that plays a vital role in many biological processes, and aberrant zinc metabolism has been implicated in lipid-related metabolic diseases. Previously, we showed that zinc antagonizes iron to regulate sterol regulatory element-binding proteins and stearoyl-CoA desaturase (SREBP-SCD) pathway in lipid metabolism in model organism Caenorhabditis elegans. Here, we further identified another cation diffusion facilitator CDF-1 in addition to SUR-7 in response to zinc to regulate lipid metabolism. Inactivation of SBP-1, the only homolog of SREBPs, leads to increased zinc level but decreased lipid accumulation reversely. However, either cdf-1(n2527) or sur-7(tm6523) mutation could successfully restore the altered fatty acid profile, fat content and zinc level of sbp-1(ep79) mutant. Furthermore, we found that CDF-1/SUR-7 may function bypass SBP-1 to directly affect the conversion activity of SCD in the biosynthesis of unsaturated fatty acids and lipid accumulation. Collectively, these results consistently support the link between zinc homeostasis and lipid metabolism via SREBP-SCD axis by cation diffusion facilitators CDF-1 and SUR-7.

zoology↗

bioRxiv2020

A chemiluminescent protease probe for rapid, sensitive, and inexpensive detection of live Mycobacterium tuberculosis

Tuberculosis (TB) is a top-ten cause of death worldwide. Successful treatment is often limited by insufficient diagnostic capabilities, especially at the point of care in low-resource settings. The ideal diagnostic must be fast, cheap, and require minimal clinical resources while providing high sensitivity, selectivity, and the ability to differentiate live from dead bacteria. We describe here the development of a Fast, Luminescent, and Affordable Sensor of Hip1 (FLASH) for the diagnosis and monitoring of drug sensitivity of Mycobacterium tuberculosis (Mtb). FLASH is a selective chemiluminescent substrate for the Mtb protease Hip1 that when processed, produces visible light that can be measured with a high signal to noise ratio using inexpensive sensors. FLASH is sensitive to fmol of recombinant Hip1 enzyme in vitro and can detect as few as thousands of Mtb cells in culture or in human sputum samples within minutes. The probe is highly selective for Mtb compared to other non-tuberculous mycobacteria and can distinguish live from dead cells. Importantly, FLASH can be used to measure antibiotic killing of Mtb in culture with greatly accelerated timelines compared to traditional protocols. Overall, FLASH has the potential to enhance both TB diagnostics and drug resistance monitoring in resource-limited settings. One Sentence SummaryA luminescent probe enables sensitive detection of Mycobacterium tuberculosis for diagnostics, treatment monitoring, and drug susceptibility testing.

microbiology↗

bioRxiv2020

Base Pairing and Functional Insights into N3-methylcytidine (m3C) in RNA

N3-methylcytidine (m3C) is present in both eukaryotic tRNA and mRNA and plays critical roles in many biological processes. We report the synthesis of the m3C phosphoramidite building block and its containing RNA oligonucleotides. The base-pairing stability and specificity studies show that the m3C modification significantly disrupts the stability of the Watson-Crick C:G pair. Further m3C decreases the base pairing discrimination between C:G and the other mismatched C:A, C:U, and C:C pairs. Our molecular dynamic simulation study further reveals the detailed structural insights into the m3C:G base pairing pattern in an RNA duplex. More importantly, the biochemical investigation of m3C using reverse transcription shows that N3-methylation specifies the C:A pair and induces a G to A mutation using HIV-1-RT, MMLV-RT and MutiScribe-RT enzymes, all with relatively low replication fidelity. For other reverse transcriptases with higher fidelity like AMV-RT, the methylation could completely shut down DNA synthesis.

biochemistry↗

bioRxiv2020

Conflict Processing in Schizophrenia: Dissociable Neural Mechanisms Revealed by the N2 and Frontal Midline Theta

Deficits in executive control have long been regarded as one of the hallmark cognitive characteristics in people with schizophrenia (SZ), and current neurocognitive models of SZ generally regard the dysfunctional anterior cingulate cortex (ACC) as the possible neural mechanism. This however, contrasts with recent studies showing that conflict processing, a key component of executive functions that relies on ACC, remains relatively intact in SZ. The current study aimed to investigate this issue through two well-known electrophysiological signatures of conflict processing that have been suggested to origin from ACC, i.e., the N2 component of event-related potentials (ERPs) and frontal midline theta (FM{theta}) oscillations. We recorded 64-channel scalp electroencephalography from 29 SZ (17 women; mean age: 30.4 years) and 31 healthy control subjects (HC; 17 women; mean age: 29.1 years) performing a modified flanker task. Behavioral data revealed no significant differences in flanker conflict effects (lower accuracy and longer reaction time in incongruent trials than in congruent trials) between HC and SZ. Trial-averaged ERP and spectral analysis suggested that both N2 and FM{theta} were significantly impaired in SZ relative to HC. Furthermore, by sorting incongruent trials according to their reaction times within individual subjects, we found that the trial-by-trial modulation of N2 (larger amplitude and longer latency in slower trials) which was observed and localized in ACC in HC was totally absent in SZ. By contrast, the trial-by-trial modulation of FM{theta} (larger power in slower trials) was observed and localized in ACC in both groups, despite a relatively smaller magnitude in SZ. Notably, such trial-by-trial FM{theta} modulation was only present in incongruent trials that demanded conflict processing. Taken together, our results not only support the idea that FM{theta}, not N2, serves as the neural substrate of conflict processing in SZ, but also provide novel insights into the functional roles of ACC during executive control, enriching the current neurocognitive models of SZ.

neuroscience↗

bioRxiv2020

Transcriptome profiling reveals the mechanism of ripening and epidermal senescence in passionfruit (Passiflora edulia Sims)

Passion fruit (Passiflora edulia Sims), an important tropical and sub-tropical species, is classified as a respiration climacteric fruit, the quality deteriorates rapidly after harvest. To reveal the mechanisms involved in ripening and rapidly fruit senescence, the phytochemical characteristics and RNA sequencing were conducted in the purple passion fruits with different (1-MCP and PF) treatment. Comprehensive functional annotation and KEGG enrichment analysis showed that the starch and sucrose metabolism, plant hormone signal transduction, phenylpropanoid biosynthesis, flavonid biosynthesis, carotenoid biosynthesis were involved in fruit ripening. Applying with PF and 1-MCP significantly affected transcript levels of passion fruit after harvest storage. A large number of differently expressed unigenes (DEGs) were identified significantly enrichen in starch and sucrose metabolism, plant hormone signal transduction and phenylpropanoid biosynthesis at postharvest stage. The preservative film (PF) and 1-Methylcyclopropene (1-MCP) treatments increased superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) gene expression and enzyme activities, accelerated the lignin accumulation, decline {beta}-galactosidase ({beta}-Gal), polygalacturonase (PG) and cellulose activities and gene expression to delay cell wall degradation during fruit senescence. The RNA sequencing data of cell wall metabolism and hormone signal transduction pathway related unigenes were verified by RT-qPCR. The results indicated that the cell wall metabolism and hormone signal pathways were notably related to passion fruit ripening. PF and 1-MCP treatment might inhibited ethylene signaling and regulated cell wall metabolism pathways to inhibited cell wall degradation. Our results reveal ripening and senescence related networks during passion fruit ripening, which can provide a foundation for understanding the molecular mechanisms underlying PF and 1-MCP treatment on fruit ripening.

plant biology↗

bioRxiv2020

Single species RNA purification with DNA nanoswitches

We report a novel method to purify individual RNA species using programmable DNA nanoswitches to facilitate RNA capture, release, and isolation. We validate sequence-based purification of microRNA, rRNA, and an mRNA fragment from total RNA, demonstrate multiplexing with two different RNA species, and show an application with downstream LC/MS analysis to identify RNA modifications. The simplicity, low cost, and low sample requirements of our method make it suitable for easy adoption.Competing Interest StatementLZ, ARC, and KH have intellectual property related to DNA nanoswitches. All other authors declare no competing interests.View Full Text

molecular biology↗

bioRxiv2020

Biodegradation of polyester polyurethane by Aspergillus flavus G10

Polyurethanes (PU) are integral to many aspects of our daily lives. Due to the extensive use of and difficulties in recycling or reusing PU, it mostly accumulates as waste. Various bacteria and fungi have been reported to degrade PU. We examined the fungus Aspergillus flavus G10 in that regard, after isolating it from the guts of Gryllus bimaculatus, a common cricket species. We observed surficial and chemical changes of PU with atomic force microscopy, scanning electron microscopy, and attenuated total reflectance Fourier-transform infrared spectroscopy. We measured physical changes as loss in tensile stress, stretching force, and weight of PU after incubations. Fungal hydrolysis of urethane bonds in the polymer backbone was demonstrated by detecting the formation of methylene di-aniline during incubations. Trapped CO2 during incubations equaled 52.6% of PU carbon. Biodegradation of PU was maximal by fungi cultured on a malt extract medium at 25 °C, pH 12, and 14:10 hrs light to dark ratio. Pretreating PU films with UV light or 1% FeSO4 or NaCl solutions further enhanced the rate of biodegradation. A range of techniques are needed to fully characterize the degradation of PU or other plastic polymers and to optimize conditions for their microbial degradation.View Full Text

bioengineering↗

bioRxiv2020

Comparative transcriptome analysis reveals the intensive early-stage responses of host cells to SARS-CoV-2 infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a widespread outbreak of highly pathogenic COVID-19. It is therefore important and timely to characterize interactions between the virus and host cell at the molecular level to understand its disease pathogenesis. To gain insights, we performed high-throughput sequencing that generated time-series data simultaneously for bioinformatics analysis of virus genomes and host transcriptomes implicated in SARS-CoV-2 infection. Our analysis results showed that the rapid growth of the virus was accompanied by an early intensive response of host genes. We also systematically compared the molecular footprints of the host cells in response to SARS-CoV-2, SARS-CoV and MERS-CoV. Upon infection, SARS-CoV-2 induced hundreds of up-regulated host genes hallmarked by a significant cytokine production followed by virus-specific host antiviral responses. While the cytokine and antiviral responses triggered by SARS-CoV and MERS-CoV were only observed during the late stage of infection, the host antiviral responses during the SARS-CoV-2 infection were gradually enhanced lagging behind the production of cytokine. The early rapid host responses were potentially attributed to the high efficiency of SARS-CoV-2 entry into host cells, underscored by evidence of a remarkably up-regulated gene expression of TPRMSS2 soon after infection. Taken together, our findings provide novel molecular insights into the mechanisms underlying the infectivity and pathogenicity of SARS-CoV-2.

microbiology↗

bioRxiv2020

Abortion and various associated risk factors in dairy cow and sheep in Ili, China

We studied livestock abortion and various associated risk factors in the Ili region of northwest China. Livestock abortion prevalence was estimated and correlated with infections (Brucellosis, Salmonellosis, Mycoplasma and Chlamydia seropositivity) and management (farming type and contact with other herds/flocks) risk factors. The prevalence of cow and sheep abortion induced by Brucella was 76.8% (P<0.0001) and 84.1% (P<0.0001), and Mycoplasma caused an estimated 15.5% (P=0.025) and 17.6% (P<0.001) abortions, respectively. Abortion-related risk factors included mixed farming (cow P=0.001, sheep P<0.001), contact with other flocks (cow P=0.007, sheep P=0.003), brucellosis positivity (cow P<0.001, sheep P<0.001) and Mycoplasma positivity (cow P=0.031, sheep P<0.001). A total of 2996 serum samples (1402 cow, 1594 sheep) were identified by RBPT (Rose Bengal Plate Test), and they showed the seroprevalence of brucellosis in X county was cow 7.1%, sheep 9.1%; in H county was cow 11.7%, sheep 10.7%; and in Q county was cow 4.2%, sheep 9.1%. The seroprevalence of Mycoplasma in X county was cow 3.4%, sheep 7.9%; in H county was cow 5.3%, sheep 9.9%; and in Q county was cow 2.1%, sheep 4.3%. A total of 54 samples, including aborted cow (22), sheep (30) fetuses and milk samples (2), were identified as Brucella melitensis (B. melitensis) positive. A total of 38 Brucella were isolated from 16 aborted cow, 20 sheep fetuses and 2 milk samples. All of these isolates were identified, and confirmed, as B. melitensis. A phylogenetic tree showed that the Brucella isolates closely matched the B. melitensis biovar 3 isolated in Inner Mongolia, China, and B. melitensis isolated from Norway and India. These results suggest that B. melitensis biovar 3 is the main pathogen responsible for cow and sheep abortion and also pose a human health risk. Additionally, livestock reproduction can also be influenced by Mycoplasma infection and managerial factors (farming type and contact with other herds/flocks), especially in remote areas.View Full Text

zoology↗

bioRxiv2020

Cryo-EM structure of C9ORF72-SMCR8-WDR41 reveals the role as a GAP for Rab8a and Rab11a

A massive intronic hexanucleotide repeat (GGGGCC) expansion in C9ORF72 is a genetic origin of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recently, C9ORF72, together with SMCR8 and WDR41, has been shown to regulate autophagy and function as Rab GEF. However, the precise function of C9ORF72 remains unclear. Here, we report the cryo-EM structure of the human C9ORF72-SMCR8-WDR41 complex at a resolution of 3.2 [A]. The structure reveals the dimeric assembly of a heterotrimer of C9ORF72-SMCR8-WDR41. Notably, the C-terminal tail of C9ORF72 and the DENN domain of SMCR8 play critical roles in the dimerization of the two protomers of the C9ORF72-SMCR8-WDR41 complex. In the protomer, C9ORF72 and WDR41 are joined by SMCR8 without direct interaction. WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix. Interestingly, the prominent structural feature of C9ORF72-SMCR8 resembles that of the FLNC-FNIP2 complex, the GTPase activating protein (GAP) of RagC/D. Structural comparison and sequence alignment revealed that Arg147 of SMCR8 is conserved and corresponds to the arginine finger of FLCN, and biochemical analysis indicated that the Arg147 of SMCR8 is critical to the stimulatory effect of the C9ORF72-SMCR8 complex on Rab8a and Rab11a. Our study not only illustrates the basis of C9ORF72-SMCR8-WDR41 complex assembly but also reveals the GAP activity of the C9ORF72-SMCR8 complex. Significance StatementC9ORF72, together with SMCR8 and WDR41, has been shown to form a stable complex that participates in the regulation of membrane trafficking. We report the cryo-EM structure of the C9ORF72-SMCR8-WDR41 complex at atomic resolution. Notably, the stoichiometry of the three subunits in the C9ORF72-SMCR8-WDR41 complex is 2:2:2. Interestingly, the C-termini of C9ORF72 and the DENN domain of SMCR8 mediate the dimerization of the two C9ORF72-SMCR8-WDR41 protomers in the complex. Moreover, WDR41 binds to the DENN domain of SMCR8 by the C-terminal helix without direct contact with C9ORF72. Most importantly, the C9ORF72-SMCR8 complex works as a GAP for Rab8a and Rab11a in vitro, and the Arg147 of SMCR8 is the arginine finger.

biochemistry↗

bioRxiv2020

DeepDigest: prediction of protein proteolytic digestion with deep learning

In shotgun proteomics, it is essential to accurately determine the proteolytic products of each protein in the sample for subsequent identification and quantification, because these proteolytic products are usually taken as the surrogates of their parent proteins in the further data analysis. However, systematical studies about the commonly used proteases in proteomics research are insufficient, and there is a lack of easy-to-use tools to predict the digestibilities of these proteolytic products. Here, we propose a novel sequence-based deep learning model - DeepDigest, which integrates convolutional neural networks and long-short term memory networks for digestibility prediction of peptides. DeepDigest can predict the proteolytic cleavage sites for eight popular proteases including trypsin, ArgC, chymotrypsin, GluC, LysC, AspN, LysN and LysargiNase. Compared with traditional machine learning algorithms, DeepDigest showed superior performance for all the eight proteases on a variety of datasets. Besides, some interesting characteristics of different proteases were revealed and discussed.

bioinformatics↗

bioRxiv2020

Single-cell RNA-seq reveals endoimmune cells in zebrafish

Endothelial cells (ECs) constitute a monolayer that covers the interior surface of blood vessels and participates in various processes. Although vascular ECs share certain common properties, they differ in both structure and function. So far, the transcriptome profile and heterogeneity of the full repertoire of ECs in vertebrates remain poorly understood. The relatively small size of zebrafish embryos and larvae allows a feasible analysis of the broad spectrum of ECs within every tissue and organ of a whole organism. ECs have been suggested to be conditional innate immune cells. Whether ECs possess the comparable capacity of involvement in immune response is so far undetermined. Currently, through single-cell RNA sequencing analysis of total ECs of zebrafish we identified a fraction of endothelial cells expressing the marker genes of innate immune cells, named "endoimmune cells". We found the percentage of these cells gradually increased along with the embryonic development. Then, we observed the patrolling mCherry+ cells displayed the morphology alike to the macrophages and neutrophils. Furthermore, we revealed that some of the kdrl:ras-mCherry ECs were labelled with coro1a:EGFP as well. In addition, we demonstrated that the mCherry+ EC from intersegmental vessel could gradually present the expression of GFP in Tg(kdrl:ras-mCherry::coro1a:GFP) line, suggesting the endoimmune cells are derived from ECs. Importantly, we showed the endoimmune cells are responsive to the inflammation in zebrafish. Taken together, these data suggested the existence of endoimmune cells, a novel type of subpopulations of ECs. It will provide novel insights for understanding endothelial roles in both normal physiological function and human diseases and enable endoimmune cells-based target therapies.

cell biology↗

bioRxiv2019

Chromosome level draft genomes of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), an alien invasive pest in China

The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a severely destructive pest native to the Americas, but has now become an alien invasive pest in China, and causes significant economic loss. Therefore, in order to make effective management strategies, it is highly essential to understand genomic architecture and its genetic background. In this study, we assembled two chromosome scale genomes of the fall armyworm, representing one male and one female individual procured from Yunnan province of China. The genome sizes were identified as 542.42 Mb with N50 of 14.16 Mb, and 530.77 Mb with N50 of 14.89 Mb for the male and female FAW, respectively. We predicted about 22,201 genes in the male genome. We found the expansion of cytochrome P450 and glutathione s-transferase gene families, which are functionally related to the intensified detoxification and pesticides tolerance. Further population analyses of corn strain (C strain) and rice strain (R strain) revealed that the Chinese fall armyworm was most likely invaded from Africa. These strain information, genome features and possible invasion source described in this study will be extremely important for making effective strategies to manage the fall armyworms.

genomics↗

bioRxiv2019

Extensive genetic diversity of bat-borne polyomaviruses reveals inter-family host-switching events

Polyomaviruses (PyVs) are small, double-stranded DNA tumor viruses carried by diverse vertebrates. PyVs have previously been considered highly host restricted in mammalian hosts, with host-switching events thought rare or nonexistent. Prior investigations have revealed short-range host-switching events of PyVs in two different African bat species within the horseshoe bat genus Rhinolophus. Herein, we have conducted a systematic investigation of PyVs in 1,083 archived bat samples collected from five provinces across China, and identified 192 PyVs from 186 bats from 15 host species within 6 families (Rhinolophidae, Vespertilionidae, Hipposideridae, Emballonuridae, Miniopteridae and Pteropodidae) representing 28 newly-described PyVs, indicative of extensive genetic diversity of bat PyVs. Surprisingly, two PyVs were identified in multiple bat species from different families, and another PyV clustered phylogenetically with PyVs carried by bats from a different host family, indicative of three inter-family PyV host-switching events. The time to most recent common ancestor (tMRCA) of the three events was estimated at 0.02-11.6 million years ago (MYA), which is inconsistent with the estimated tMRCA of their respective bat hosts (36.3-66.7 MYA), and is most parsimoniously explained by host-switching events. PyVs identified from geographically separated Chinese horseshoe bat species in the present study showed close genetic identities, and clustered with each other and with PyVs from African horseshoe bats, allowing assessment of the effects of positive selection in VP1 within the horseshoe bat family Rhinolophidae. Correlation analysis indicated that co-evolution with their hosts contributed much more to evolutionary divergence of PyV than geographic distance. In conclusion, our findings provide the first evidence of inter-family host-switching events of PyV in mammals and challenge the prevailing evolutionary paradigm for strict host restriction of mammalian PyVs.\n\nAuthor summarySince the discovery of murine polyomavirus in the 1950s, polyomaviruses (PyVs) have been considered both genetically stable and highly host-restricted in their mammalian hosts. In this study, we have identified multiple cases of host-switching events of PyVs by large scale surveillance in diverse bat species collected in China. These host-switching events occurred between bat families living in the same colony, indicating that a large population with frequent contacts between different bat species may represent an ecological niche facilitating PyV host-switching. The cases studied involved members of bats from several families, including horseshoe bats, which were previously found to harbor a number of highly virulent viruses to both humans and domestic animals. Our findings have provided evidence that even highly host-specific DNA viruses can transmit between bats of different species and indicate an increased propensity for spillover events involving horseshoe bats. We propose an evolutionary scheme for bat-borne PyVs in which intra-host divergence and host-switching has generated the diverse PyVs in present day bats. This scheme provides a useful model to study the evolution of PyVs in other hosts and, potentially, the modeling of bat zoonoses and the transmission of other DNA viruses in other mammals, including humans.

microbiology↗

bioRxiv2018

Molecular basis for the acid initiated uncoating of human enterovirus D68

Enterovirus D68 (EV-D68) belongs to a group of enteroviruses that contain a single positive-sense RNA genome surrounded by an icosahedral capsid. Like common cold viruses, EV-D68 mainly causes respiratory infections and is acid labile. The molecular mechanism by which the acid sensitive EV-D68 virions uncoat and deliver their genome into a host cell is unknown. Using cryo-electron microscopy (cryo-EM), we have determined the structures of the full native virion and an uncoating intermediate (the A(altered)-particle) of EV-D68 at 2.2 [A] and 2.7 [A] resolution. These structures showed that acid treatment of EV-D68 leads to particle expansion, externalization of the viral protein VP1 N-termini from the capsid interior, and formation of pores around the icosahedral two-fold axes through which the viral RNA can exit. Moreover, because of the low stability of EV-D68 at neutral pH, cryo-EM analyses of a mixed population of particles demonstrated the involvement of multiple structural intermediates during virus uncoating. Among these, a previously undescribed state, the expanded (\"E1\") particle, shows a majority of internal regions (e.g, the VP1 N-termini) to be ordered as in the full native virion. Thus, the E1 particle acts as an intermediate in the transition from full native virions to A-particles. Molecular determinants, including a histidine-histidine pair near the two-fold axes, were identified that facilitate this transition under acidic conditions. Thus, the present work delineates the pathway of EV-D68 uncoating and provides the molecular basis for the acid lability of EV-D68 and of the related common cold viruses.\n\nSignificance StatementEnterovirus D68 (EV-D68) is an emerging pathogen that primarily causes childhood respiratory infections and is linked to neurological diseases. It was unclear how the virus uncoats and delivers its genome into a host cell to establish viral replication. Using high resolution cryo-electron microscopy, we showed that acid induces structural rearrangements of EV-D68 to initiate genome release from the virus. Structural analyses delineated a viral uncoating pathway that involves multiple distinct conformational states. Particularly, the structure of a previously unknown uncoating intermediate enabled the identification of molecular determinants that facilitate EV-D68 uncoating in an acidic environment. These results advance the knowledge of cell entry of EV-D68 and open up possibilities for developing antiviral therapeutics that impede structural rearrangements of the virus.

microbiology↗

bioRxiv2018

An Optically Decodable Bead Array for Linking Imaging and Sequencing with Single-Cell Resolution

Optically decodable beads link the identity of an analyte or sample to a measurement through an optical barcode, enabling libraries of biomolecules to be captured on beads in solution and decoded by fluorescence. This approach has been foundational to microarray, sequencing, and flow-based expression profiling technologies. We have combined microfluidics with optically decodable beads to link phenotypic analysis of living cells to sequencing. As a proof-of-concept, we applied this to demonstrate an accurate and scalable tool for connecting live cell imaging to single-cell RNA-Seq called Single Cell Optical Phenotyping and Expression (SCOPE-Seq).

systems biology↗

bioRxiv2017

Data-Driven Prediction of CRISPR-Based Transcription Regulation for Programmable Control of Metabolic Flux

Multiplex and multi-directional control of metabolic pathways is crucial for metabolic engineering to improve product yield of fuels, chemicals, and pharmaceuticals. To achieve this goal, artificial transcriptional regulators such as CRISPR-based transcription regulators have been developed to specifically activate or repress genes of interest. Here, we found that by deploying guide RNAs to target on DNA sites at different locations of genetic cassettes, we could use just one synthetic CRISPR-based transcriptional regulator to simultaneously activate and repress gene expressions. By using the pairwise datasets of guide RNAs and gene expressions, we developed a data-driven predictive model to rationally design this system for fine-tuning expression of target genes. We demonstrated that this system could achieve programmable control of metabolic fluxes when using yeast to produce versatile chemicals. We anticipate that this master CRISPR-based transcription regulator will be a valuable addition to the synthetic biology toolkit for metabolic engineering, speeding up the \"design-build-test\" cycle in industrial biomanufacturing as well as generating new biological insights on the fates of eukaryotic cells.

synthetic biology↗