Synthetic and Systems Biotechnology最新文献

{"title":"Highly efficient synthesis of the natural product β-himachalene in yeast and its potential as a novel anti-HSV-1 therapeutic agent","authors":"Qian Yang ,&nbsp;Yutong Zhang ,&nbsp;Pan Feng ,&nbsp;Hui Zhang ,&nbsp;Kai Wang ,&nbsp;Biqiang Chen ,&nbsp;Tianwei Tan","doi":"10.1016/j.synbio.2025.05.007","DOIUrl":"10.1016/j.synbio.2025.05.007","url":null,"abstract":"<div><div>Terpenoids, a high-value natural product family in nature, have garnered significant attention due to their diverse pharmaceutical activities. However, the current supply of most structurally complex terpenoids relies predominantly on plant extraction, and supply insufficiency has become a critical challenge. In this study, targeting the sesquiterpene synthase <em>Po</em>TPS01 from <em>Platycladus orientalis</em>i, we screened efficient expression cassettes through promoter engineering and achieved, for the first time, the biosynthesis of β-himachalene in <em>Saccharomyces cerevisiae</em>, with an initial titer of 1.11 mg/L. To further enhance production, we employed strategies including utilizing a fusion protein expression approach and optimizing fermentation conditions, ultimately increasing the β-himachalene titer to 2.12 g/L. Furthermore, we conducted an in-depth investigation into the bioactivity of β-himachalene and discovered its significant antiviral activity against Herpes Simplex Virus type 1 (HSV-1). β-himachalene effectively inhibited the viral titer of both wild-type and acyclovir-resistant HSV-1 strains, exerting its inhibitory effect during the early stages of viral replication. This research not only provides a novel strategy for the biosynthesis of other high-value plant natural products but also paves new avenues for the development of novel drugs based on sesquiterpenoids.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 1002-1013"},"PeriodicalIF":4.4,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144123149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From reactants to products: computational methods for biosynthetic pathway design","authors":"Shaozhen Ding ,&nbsp;Dongliang Liu ,&nbsp;Yu Tian ,&nbsp;Dachuan Zhang ,&nbsp;HuaDong Xing ,&nbsp;Junni Chen ,&nbsp;Zhiguo Liu ,&nbsp;Qian-Nan Hu","doi":"10.1016/j.synbio.2025.05.005","DOIUrl":"10.1016/j.synbio.2025.05.005","url":null,"abstract":"<div><div>One of the main goals in synthetic biology is to produce value-added compounds from available precursors using enzymatic approaches. The construction of biosynthetic pathways for synthesizing target molecules plays a crucial role in this process. However, it is challenging and time-consuming for researchers to design efficient pathways manually. In recent decades, pathway design has advanced through data- and algorithm-driven approaches. In this article, we review key computational tools involved in biosynthetic pathway design, covering: 1) Biological Big-Data including compounds, reactions/pathways and enzymes. 2) Retrosynthesis methods leveraging multi-dimensional biosynthesis data to predict potential pathways for target compounds synthesis. 3) Enzyme engineering relying on data mining to identify/de novo design enzymes with desired functions. Integrating these three key components can significantly enhance the efficiency and accuracy of biosynthetic pathway design in synthetic biology.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 1038-1049"},"PeriodicalIF":4.4,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168021","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolic reprogramming and computation-aided protein engineering for high-level de novo biosynthesis for 2-phenylethanol in Pichia pastoris","authors":"Lijing Sun ,&nbsp;Suyun Liu ,&nbsp;Renjie Sun ,&nbsp;Jinshan Li ,&nbsp;Aiqun Yu ,&nbsp;Adison Wong ,&nbsp;Liangcai Lin ,&nbsp;Cuiying Zhang","doi":"10.1016/j.synbio.2025.05.004","DOIUrl":"10.1016/j.synbio.2025.05.004","url":null,"abstract":"<div><div>2-Phenylethanol (2-PE), an aromatic compound with a characteristic rose fragrance, is extensively used in the food and cosmetic industries as a flavoring and fragrance agent. Due to limitations in obtaining 2-PE from natural plant sources, microbial cell factories offer a promising alternative for sustainable biosynthesis. In this study, <em>Pichia pastoris</em> was engineered to efficiently synthesize 2-PE. Using computer-assisted predictions of interactions between the key phenylpyruvate decarboxylase KDC2 and its substrates or products, an optimal enzyme variant was rationally designed to boost 2-PE production. Additionally, the shikimic acid pathway was enhanced, and a dynamic regulation promoter was employed to reduce competition from alternative pathways. These strategies significantly increased metabolic flux toward 2-PE production, achieving a titer of 2.81 g/L and 45.8-fold improvement over the non-engineered strain. By integrating controlled carbon feeding and in situ extraction to alleviate acetic acid inhibition and product toxicity, the recombinant strain achieved a final 2-PE titer of 7.10 g/L and a yield of 0.14 g/g glucose, the highest reported microbial production to date. This study highlights the significant potential of <em>P. pastoris</em> as a versatile cell factory for the green biosynthesis of 2-PE and other natural products.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 1027-1037"},"PeriodicalIF":4.4,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144154586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biosynthesis of lanosterol in Escherichia coli","authors":"Wenjie Sun ,&nbsp;Yun Chen ,&nbsp;Syed Bilal Shah ,&nbsp;Yanfen Bai ,&nbsp;Zaigao Tan","doi":"10.1016/j.synbio.2025.05.006","DOIUrl":"10.1016/j.synbio.2025.05.006","url":null,"abstract":"<div><div>Lipid composition represents a significant differentiator across the three domains (eukaryotes, bacteria, and archaea) of cellular life. Eukaryotes possess distinct lipids, such as sterols and sphingolipids, generally, these are not commonly found in typical bacteria and archaea. Sterols play a pivotal role in eukaryotic cellular functions, lanosterol, a key precursor for animal and fungal steroids, has well established functions in eukaryotes, while its potential functions in bacteria remain largely uninvestigated. In this study, we genetically engineered <em>Escherichia coli</em> (<em>E. coli</em>) to reconstruct the biosynthesis of lanosterol, and successfully developed a novel <em>E. coli</em> strain capable of synthesizing lanosterol, although its specific location, such as whether it is incorporated into the cell membrane, remains to be further determined. Comprehensive characterization of the observed phenotypic changes has unveiled that, despite an unaltered growth rate under normal condition, the engineered <em>E. coli</em> strain displayed notably enhanced tolerance to various stresses. Subsequent analysis has indicated that lanosterol plays a role in preserving membrane integrity, fluidity, hydrophobicity, and ATP production, mirroring the functions of sterols in eukaryotes. This study unveils the unexpected capacity of <em>E. coli</em> to synthesize sterols, not only underscores the importance of lanosterol as a precursor for essential cellular lipids but also offers fresh insights into the potential functions of sterols within bacterial systems.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 993-1001"},"PeriodicalIF":4.4,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144083930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Robust production of N-acetyl-glucosamine in engineered Escherichia coli from glycerol-glucose mixture","authors":"Wenchao Sun ,&nbsp;Yulin Tang ,&nbsp;Yahao Tian ,&nbsp;Zhengkai Liu ,&nbsp;Wenwen Xiong ,&nbsp;Hengshuai Zhang ,&nbsp;Liang Chen ,&nbsp;Heyun Wu ,&nbsp;Qian Ma ,&nbsp;Xixian Xie","doi":"10.1016/j.synbio.2025.05.003","DOIUrl":"10.1016/j.synbio.2025.05.003","url":null,"abstract":"<div><div>Achieving a balanced cell growth and biosynthesis of target products is a pivotal challenge confronted in the realm of green biomanufacturing of chemicals, and it holds the promise of significantly enhancing the titer/yield/productivity of the target products. The co-utilization of carbon sources has emerged as a proven approach for the precise regulation of cell growth and biosynthesis processes, thereby serving as a potent strategy to expedite the production of chemicals. In our previous study, we successfully demonstrated the efficient production of N-acetyl-glucosamine in engineered <em>Escherichia coli</em> by leveraging an appropriate catabolic division of labor, utilizing a mixture of glycerol and glucose as the carbon source. In this study, we further refined the division of labor between these two carbon sources by meticulously regulating the expression of the <em>zwf</em> gene, which encodes glucose-6-phosphate dehydrogenase and is crucial in diverting carbon source to the pentose phosphate pathway (PPP). After comparing three strategies for balancing cell growth and production, the engineered strain NAG-1 with <em>zwf</em> knocked out aided by the optimization of the glycerol-to-glucose ratio and the feeding mode of carbon sources resulted in robust production of N-acetyl-glucosamine. Remarkable production in a 5 L bioreactor was achieved, obtaining 249 g/L of N-acetyl-glucosamine with a yield of 0.684 g/g of total carbon sources (specifically, 0.791 g/g of glucose) and a productivity of 3.46 g/L/h. These results establish NAG-1 as the most efficient microbial cell factory reported thus far for the bioproduction of N-acetyl-glucosamine. The robust production of N-acetyl-glucosamine in <em>E. coli</em> using a mixture of glycerol and glucose suggests the immense potential of mixed carbon sources in the industrial green biomanufacturing of chemicals.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 1014-1026"},"PeriodicalIF":4.4,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144134773","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-yield production and characterization of functional Kir2.1 ion channel using E. coli cell-free protein synthesis system","authors":"Tianqi Zhou ,&nbsp;Zitong Zhao ,&nbsp;Huizi Zhang ,&nbsp;Yunyang Song ,&nbsp;Yifeng Yin ,&nbsp;Fanghui Wu ,&nbsp;Yanli Liu ,&nbsp;Dan Xu","doi":"10.1016/j.synbio.2025.05.002","DOIUrl":"10.1016/j.synbio.2025.05.002","url":null,"abstract":"<div><div>A family of inwardly-rectifying potassium (Kir) channels plays a key role in the regulation of cellular potassium (K⁺) balance, affecting muscle, nerve and immune function. Kir channels are comprised of either homologous or heterologous tetramer of Kir subunits, each of which contains two-transmembrane domains. The challenges associated with the precise biophysical characterization of Kir channels have limited our understanding of this important class of molecules. Moreover, the complex multi-transmembrane domains inherent to Kir channels present significant obstacles in producing sufficient quantities for accurate characterization, further constraining our knowledge about these channels. In this study, we selected Kir2.1 as a model molecule and utilized an <em>Escherichia coli</em> cell-free protein expression system (CFPS) to synthesize Kir2.1 in the presence of peptide surfactant A₆K, which aids in promoting the soluble production, achieving α-helical conformations, and stabilizing membrane proteins (MPs). Ni-NTA affinity chromatography column was employed to purify Kir2.1, achieving a yield of approximately 1.5 mg/mL. Circular dichroism spectroscopy (CD) measurements confirmed that the purified Kir2.1 exhibited typical α-helix structures. Microscale thermophoresis (MST) assays demonstrated the binding capability of Kir2.1 with Hydrocinnamic Acid and ML133 hydrochloride, Kir2 channel selection inhibitory. Recombinant Kir2.1-liposomes exhibited specific channel activity to K⁺ using the voltage-sensitive fluorescent dye Oxonol VI to monitor the concentration gradient-driven potassium influx. This work contributes to enhancing both the efficiency of preparation, characterization and drug high-throughput screening of ion channels.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 973-982"},"PeriodicalIF":4.4,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144068099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification, characterization, and application of an NADPH-dependent carbonyl reductase in Saccharomyces cerevisiae AS2.346 for improving production of (13R,17S)-ethyl secol","authors":"Qixin Liang,&nbsp;Wanqing Guo,&nbsp;Xiaoshuang Sun,&nbsp;Xianpu Ni,&nbsp;Huanzhang Xia","doi":"10.1016/j.synbio.2025.04.016","DOIUrl":"10.1016/j.synbio.2025.04.016","url":null,"abstract":"<div><div>Levonorgestrel is currently the most widely used contraceptive, with advantages that include rapid oral absorption and high bioavailability. Among the various synthetic methods employed in its production, <em>Saccharomyces cerevisiae</em> AS2.346 was first introduced by the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, in 1976, successfully catalyzing the conversion of ethyl secodione to (13R,17S)-ethyl secol. Presently, <em>Saccharomyces cerevisiae</em> AS2.346 whole-cell catalysis is still used in levonorgestrel industrial production. To identify the enzyme responsible for catalyzing the conversion of ethyl secodione to (13R,17S)-ethyl secol, we isolated two genes, As<em>sdr1</em> and As<em>sdr2</em>, both encoding carbonyl reductases. The biochemical characterization of AsSDR1 and AsSDR2 showed that they had high activity for ethyl secodione. Functional analysis demonstrated that the deletion of As<em>sdr</em>1 almost completely abolished the production of (13R,17S)-ethyl secol, while the deletion of As<em>sdr</em>2 had little to no effect on the production, indicating that As<em>sdr1</em> plays a pivotal role in the biosynthesis of (13R,17S)-ethyl secol. The reason for the difference in the function of AsSDR1 and AsSDR2 <em>in vivo</em> may be attributed to their different cellular localizations, with AsSDR1 located outside the mitochondria and AsSDR2 in the mitochondria. A metabolomics analysis of As<em>sdr</em>1 knockout strains revealed that AsSDR1 may act as a pterin reductase. Overexpression of the newly isolated gene As<em>sdr</em>1 led to an average 47.88 % higher (13R,17S)-ethyl secol yield compared to that of the wild-type strain. Furthermore, engineering the metabolism of the NADPH cofactor by overexpressing the truncated gene <em>pos</em>5Δ17 encoding mitochondrial NADH kinase produced a 111.25 % higher (13R,17S)-ethyl secol yield compared to that of the wild-type strain. These findings not only elucidate the key enzymatic players involved in the synthesis of (13R,17S)-ethyl secol but also provide a framework for optimizing the industrial biotransformation process for levonorgestrel production.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 983-992"},"PeriodicalIF":4.4,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144083931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CgAS, a gene encoding anthranilic acid synthase, contributes to tryptophan biosynthesis and enhanced chaetoglobosin A production in Chaetomium globosum W7","authors":"Shanshan Zhao ,&nbsp;Zefei Wang ,&nbsp;Liyan Tian ,&nbsp;Kejing Li ,&nbsp;Shiwei Sun ,&nbsp;Gen Chen ,&nbsp;Daoqiong Zheng","doi":"10.1016/j.synbio.2025.05.001","DOIUrl":"10.1016/j.synbio.2025.05.001","url":null,"abstract":"<div><div>Chaetoglobosin A (cheA) is a complex indole alkaloid exhibiting preferential cytotoxicity against plant pathogens, parasites, and tumor cells. However, the limited production and high synthesis costs of cheA impede its widespread application. Tryptophan serves as a precursor for cheA biosynthesis, and strategic modification of the expression of key genes represents a novel approach to enhance the target yield. Herein, <em>CgAS</em>, a gene encoding anthranilic acid synthase involved in tryptophan synthesis, was identified through bioinformatics analysis and overexpressed via a promoter optimization strategy in <em>Chaetomium globosum</em> W7. The AS1 and AS3 mutants, in which the <em>CgAS</em> gene was constitutively overexpressed under the control of promoter <em>oliC</em>, presented a significant increase in tryptophan accumulation. <em>CgAS</em> overexpression caused a dramatic increase in cheA production, reaching a maximum yield of 217.81 mg/L during the stationary phase, which was 3.73-fold higher than that noted in the wild-type strain. Interestingly, AS1 and AS3 mutants exhibited a substantial upregulation in the transcription levels of critical genes involved in cheA biosynthesis. Phenotypic characterization and metabolomic analysis indicated that tryptophan accumulation strengthened microbial nitrogen metabolism, which not only provided sufficient precursors for secondary metabolism, but also functioned as an essential energy source to accelerate fungal development and sporulation. These findings illustrate the impact of precursor accumulation on indole alkaloid biosynthesis and provide novel insights for optimizing the production of biopesticides and clinical drugs.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 936-949"},"PeriodicalIF":4.4,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143929211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering the cytochrome P450 to enhance parthenolide production in Saccharomyces cerevisiae","authors":"Tongqing Yang ,&nbsp;Yixun Jiang ,&nbsp;Tianyu Dong ,&nbsp;Haoyu Liu ,&nbsp;Ying Wang ,&nbsp;Wenhai Xiao ,&nbsp;Mingdong Yao","doi":"10.1016/j.synbio.2025.04.006","DOIUrl":"10.1016/j.synbio.2025.04.006","url":null,"abstract":"<div><div>Parthenolide is confirmed to be an important component of the anticancer drug—ACT001. However, parthenolide biosynthesis in <em>Saccharomyces cerevisiae</em> (<em>S. cerevisiae</em>) was greatly hindered by the low conversion rate of its precursor, costunolide. In this study, the Position Specific Scoring Matrix (PSSM) was used to analyze the sequence evolutionary information of parthenolide synthase from <em>Tanacetum parthenium</em> (TpPTS), and a series of mutants were designed and validated. Notably, when the mutant of TpPTS—Y22G was introduced in <em>S. cerevisiae</em>, the parthenolide titer increased by 110 % compared to that of the TpPTS wild-type. Considering TpPTS as an endoplasmic reticulum-localized cytochrome P450 and the importance of heme supply, endoplasmic-associated molecular chaperone HRD1 (hydroxymethyl glutaryl-coenzyme A reductase degradation protein 1) and heme biosynthesis gene HEM2 (aminolevulinate dehydratase) were overexpressed in <em>S. cerevisiae</em> to improve TpPTS expression and catalytic activity. As a result, a titer of 27.08 mg/L parthenolide was achieved in a shake flask, which was further increased by 209 %. Additionally, the conversion rate of costunolide to parthenolide increased from 20.4 % to 51.8 % compared to the initial strain yYTQ001. Eventually, a parthenolide titer of 99.71 mg/L was achieved in a 5-L bioreactor. Our research provides effective strategies and valuable references for engineering rate-limiting cytochrome P450 enzymes to improve sesquiterpenes production in <em>S. cerevisiae</em>.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 950-958"},"PeriodicalIF":4.4,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143934860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA-CTMF: Reconstruct high quality image from lossy DNA storage via Pixel-Base codebook and median filter","authors":"Qi Xu,&nbsp;Ying Zhou,&nbsp;Qingjiang Sun,&nbsp;Xiangwei Zhao,&nbsp;Zuhong Lu,&nbsp;Kun Bi","doi":"10.1016/j.synbio.2025.04.015","DOIUrl":"10.1016/j.synbio.2025.04.015","url":null,"abstract":"<div><div>Limited by uncertain base errors in DNA storage, additional correction measures may introduce redundancy or even expand errors, resulting in poor reconstructed image. DNA-CTMF is proposed to reconstruct high quality images at high errors and indels. Firstly, Pixel-Base codebook and chaotic system ensure DNA sequences meet biological constraints. Then, codebook adjusts offset base-groups affected by indels to their original position. Finally, median filter removes salt-and-pepper noise caused by base errors. Simulated experiments show reconstructed images by DNA-CTMF exhibit high quality with minimal variation at different error compositions. Even at 5 % error rate and indels accounting for 2/3, DNA-CTMF reconstruct high quality images with PSNR approximately 23 and MS-SSIM exceeding 0.9. Tests on 4000 images demonstrate DNA-CTMF's superiority on multiple images. Wet experiments proves that DNA-CTMF can reconstruct images close to original at low error rate, which is consistent with the results of simulated experiments. Different from researches which adopted error correction codes, DNA-CTMF addresses base errors by image processing technology, providing a new interdisciplinary solution and perspective for storing images into DNA.</div></div>","PeriodicalId":22148,"journal":{"name":"Synthetic and Systems Biotechnology","volume":"10 3","pages":"Pages 925-935"},"PeriodicalIF":4.4,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143923627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}