Article
Multidisciplinary Sciences
Luana G. Morao, Livia R. Manzine, Livia Oliveira D. Clementino, Carsten Wrenger, Alessandro S. Nascimento
Summary: Structural biology projects rely on the large-scale expression of soluble proteins, usually achieved through heterologous expression in bacteria or yeast. This study evaluated a scalable approach for screening host cells/strains for maximum yield of soluble heterologous protein expression. The Arctic Express (DE3) strain showed better yields compared to other strains tested, suggesting its suitability for high-throughput structural biology pipelines.
Article
Multidisciplinary Sciences
Atieh Hashemi, Majid Basafa, Aidin Behravan
Summary: This study modeled and optimized the soluble production of antibodies using artificial neural network (ANN) and response surface methodology (RSM). The results showed that the ANN model had higher accuracy in predicting the experimental results compared to the RSM model.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Constantina Bianca Vulpe, Mariana Adina Matica, Renata Kovacevic, Daniela Dascalu, Zoran Stevanovic, Adriana Isvoran, Vasile Ostafe, Gheorghita Menghiu
Summary: The aim of this research was to investigate the bioremediation conditions of copper in synthetic water. Various genetically modified strains of Saccharomyces cerevisiae, Pichia pastoris, and Escherichia coli were used to determine the copper ions accumulation efficiency. The E. coli BL21 RIL strain had the best copper accumulation efficiency, which was 1250 times more efficient than the control strain.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Multidisciplinary
Jian Zha, Zhiqiang Liu, Runcong Sun, Guoli Gong, Jonathan S. Dordick, Xia Wu
Summary: An improved programmable autolytic E. coli platform has been developed for efficient cell lysis through engineering of peptide sequence and copy number, allowing for high recovery yield of recombinant proteins. This system demonstrates potential for large-scale microbial production of proteins and other biopolymers.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemical Research Methods
Eleni Vasilopoulou, Artemis Giannakopoulou, Charalampos Kapsalis, Myrsini Michou, Aristeidis Michoglou-Sergiou, Fragiskos N. Kolisis, Georgios Skretas
Summary: By co-expressing the effector gene rraA, a specialized E.coli strain called SuptoxR can suppress the high toxicity during membrane protein overexpression and enhance the accumulation of properly folded recombinant membrane proteins. The second-generation strains, SuptoxR2.1 and SuptoxR2.2, engineered with improved properties, achieve even higher levels of recombinant membrane protein production. The RraA proteins from Proteus mirabilis and Providencia stuartii are identified as potent enhancers of membrane protein productivity.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Spectroscopy
Saba Bashir, Haq Nawaz, Muhammad Irfan Majeed, Mashkoor Mohsin, Ali Nawaz, Nosheen Rashid, Fatima Batool, Saba Akbar, Muhammad Abubakar, Shamsheer Ahmad, Saqib Ali, Muhammad Kashif
Summary: This study aimed to identify and differentiate tigecycline-resistant E. coli (TREC) from tigecycline-sensitive E. coli (TSEC) using Surface-enhanced Raman Spectroscopy (SERS). Statistical analyses including PCA, HCA, and PLS-DA were employed to assess the diagnostic potential of SERS. Qualitative identification and differentiation between resistant and sensitive strains were efficiently done using PCA and HCA. PLS-DA successfully discriminated among TREC and TSEC at the strain level with 98% area under the ROC curve, 100% sensitivity, 98.7% specificity, and 100% accuracy.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Biochemistry & Molecular Biology
Haixiu Wang, Eric Cox, Bert Devriendt
Summary: Enterotoxigenic Escherichia coli (ETEC) strains recognize and respond to factors secreted by gut epithelial cells, leading to transcriptional modulation of key ETEC virulence genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agriculture, Dairy & Animal Science
Jonathan J. Lopez-Islas, Estela T. Mendez-Olvera, Daniel Martinez-Gomez, Andres M. Lopez-Perez, Libertad Orozco, Gerardo Suzan, Carlos Eslava
Summary: Emerging diseases pose a constant challenge in public health, and wild carnivores can be carriers of atypical strains of pathogenic microorganisms, highlighting the importance of natural environments in studying emerging diseases.
Article
Microbiology
Kanoknart Lantong, Jirarat Songsri, Sueptrakool Wisessombat, Wanida Mala, Warinda Prommachote, Wilaiwan Senghoi, Manas Kotepui, Jedsada Kaewrakmuk, Treenate Jiranantasak, Apichai Tuanyok, Wiyada Kwanhian Klangbud
Summary: The TssM-IFA method showed high sensitivity, specificity, positive predictive value, negative predictive value, efficiency, and accuracy, with no cross-reactivity. All five IFA methods agreed well with the standard culturing method, while the traditional IHA method had moderate agreement with the culture. This study demonstrated the potential of the TssM-IFA method for melioidosis diagnosis.
Article
Biochemical Research Methods
Guangbao Zhang, Xiaohui Yang, Zhenhua Zhao, Tao Xu, Xiaoqiang Jia
Summary: In this study, three engineered Escherichia coli BL21 strains were constructed with different metabolic modules to form an artificial consortium for PAH degradation. By optimizing degradation conditions and supplementing engineered strains in batches, efficient phenanthrene degradation was achieved.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jun Fan, Hafez El Sayyed, Oliver J. Pambos, Mathew Stracy, Jingwen Kyropoulos, Achillefs N. Kapanidis
Summary: Bacterial transcription by RNA polymerase (RNAP) is spatially organized, with highly expressed genes located in the nucleoid periphery. RNAP clustering has been linked to transcription of rRNA (rrn), but the nature of these clusters and their association with rrn transcription remains unclear. Through single-molecule tracking, this study showed that RNAPs in strains with reduced chromosomal rrn operons redistribute to copies of the remaining rrn operons. In rich medium, the redistribution of RNAPs in these strains minimizes growth defects caused by rrn deletions, but high RNAP densities on rrn genes can lead to genomic instability.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Jiaqi Tu, Lanlan Feng, Yanbin Hong, Qiuyun Liu, Xia Huang, Yin Li
Summary: PEPC is a crucial enzyme in plants functioning in stress responses and osmotic stress. Peanut has 5 isoforms of PEPC, showing differential expression patterns in various plant tissues. AhPEPC3 and AhPEPC4 are correlated with roots, while AhPEPC5 is closely related to flowers.
Article
Biotechnology & Applied Microbiology
Jan Weber, Zhaopeng Li, Ursula Rinas
Summary: Recent research has shown that the production of recombinant proteins in E. coli BL21(DE3) using pET based expression vectors leads to metabolic stress similar to a carbon overfeeding response. Surprisingly, it was found that excessive accumulation of energy and precursor metabolites, rather than limitation, were identified as being connected to the protein production associated metabolic burden. Additionally, it was demonstrated that this phenomenon occurs not only in BL21(DE3) but also in E. coli K12, indicating that energy generation is not a limiting factor for recombinant protein production.
MICROBIAL CELL FACTORIES
(2021)
Article
Spectroscopy
Aqsa Mushtaq, Haq Nawaz, Muhammad Irfan Majeed, Nosheen Rashid, Muhammad Tahir, Muhammad Zaman Nawaz, Kashif Shahzad, Ghulam Dastgir, Rana Zaki Abdul Bari, Anwar ul Haq, Mudassar Saleem, Farwa Akhtar
Summary: Surface-enhanced Raman spectroscopy (SERS) was used to characterize colistin-resistant and susceptible E. coli strains for the development of rapid and cost-effective detection methods. Multivariate data analysis techniques were employed to examine the SERS spectral data and achieved high specificity, accuracy, sensitivity, and AUROC for discriminating resistant and susceptible E. coli strains.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Multidisciplinary Sciences
Misun Yun, Sung-Hwan You, Vu Hong Nguyen, Jaya Prakash, Sarah Glasl, Vipul Gujrati, Hyon E. Choy, Andre C. Stiel, Jung-Joon Min, Vasilis Ntziachristos
Summary: The use of optoacoustics imaging with tyrosinase-expressing E. coli allows for improved visualization of cancer-targeting bacteria through melanin production in the tumor microenvironment, enabling longitudinal monitoring of bacterial growth in tumors using multispectral optoacoustic tomography (MSOT).
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Applied
Siqiang Chen, Qingbo Zhang, Xinya Zhang, Xiaodong Jiang, Haibo Zhang, Yiguang Zhu, Changsheng Zhang, Liping Zhang
Summary: A new cyclo-heptadepsipeptide xanthostatin B was isolated from marine sponge derived Streptomyces sp. SCSIO 40064, along with four other compounds. Their structures were elucidated through spectroscopic data analyses and literature comparison. Compound 5 exhibited inhibitory activity against alpha-glucosidase.
NATURAL PRODUCT RESEARCH
(2022)
Article
Biochemical Research Methods
Abigael J. Kosgei, Mitchell D. Miller, Minakshi Bhardwaj, Weijun Xu, Jon S. Thorson, Steven G. Van Lanen, George N. Phillips
Summary: This paper reports the crystal structure of DynF, a gene product within the biosynthetic gene cluster of dynemicin. DynF is revealed to be a dimeric eight-stranded beta-barrel structure with palmitic acid bound within a cavity. The presence of palmitic acid suggests that DynF may be involved in binding the precursor polyene heptaene, which is central to the synthesis of the ten-membered ring of the enediyne core.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Bin Tan, Qingbo Zhang, Ji Xiao, Chengshan Yuan, Yuchan Chen, Siqiang Chen, Weimin Zhang, Yiguang Zhu, Changsheng Zhang
Summary: In this study, the function of LobP1, a P450 monooxygenase encoded in the LOB biosynthetic gene cluster, was investigated through in vivo deletion and in vitro biochemical assays. LobP1 was shown to have a broad substrate scope, with a preference for substrates with a nitrosugar. The new LOBs derivatives exhibited significant antibacterial and cytotoxic activities against various bacteria and cancer cell lines.
CHINESE JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Xuemin Ding, Weixia Ye, Bin Tan, Qiaoyun Song, Yuchan Chen, Wei Liu, Lili Sun, Wei Tang, Yulei Qiao, Qingbo Zhang, Haibo Zhang, Ying Wang, Weimin Zhang, Changsheng Zhang, Wenjun Zhang
Summary: Three new cytochalasins, talachalasins A-C (1-3), were discovered from a deep-sea-derived fungus called Talaromyces muroii sp. SCSIO 40439. The structures and absolute configurations of 1-3 were determined using various analytical techniques. Talachalasins A-C (1-3) are unique cytochalasans with a 168-methyl group, which distinguishes them from over 500 known CYTs. Talachalasin C (3) is a novel 20,21-seco-cytochalasans with a 2-oxabicyclo-[3.3.1]nonan-3-one unit. Talachalasin A (1) exhibited moderate cytotoxic activity against four tumor cell lines (IC50: 3.40-10.02 μM). Talachalasin B (2) demonstrated comparable anti-RSV and HSV-1 activities (IC50: 12.5 p.M or IC50: 20.0 μM).
CHINESE JOURNAL OF CHEMISTRY
(2023)
Article
Plant Sciences
Bin Tan, Qingbo Zhang, Jieyi Li, Yiguang Zhu, Liping Zhang, Wenjun Zhang, Haibo Zhang, Yang Chen, Changsheng Zhang
Summary: The installation of halogen atoms into aromatic and less activated polyketide substrates by halogenases is a powerful strategy to tune the bioactivity, bioavailability, and reactivity of compounds. In this study, the halogenase TotH was confirmed to catalyze the C-4 chlorination in the biosynthetic pathway of totopotensamide A (1), leading to the formation of ClMeDPG. Six new deschloro totopotensamide (TPM) congeners TPMs H2-H7 (5-10) were isolated and their structures were elucidated. Additionally, the cytotoxicity of compounds 5, 6, 8, and 9 against several cell lines was evaluated.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Biochemistry & Molecular Biology
Ziqian Cheng, Qingbo Zhang, Jing Peng, Xiaoyang Zhao, Liang Ma, Changsheng Zhang, Yiguang Zhu
Summary: In this study, a benzoxazole alkaloid-encoding biosynthetic gene cluster (mich BGC) was identified in the marine-derived actinomycete Micromonospora sp. SCSIO 07395 and heterologously expressed in Streptomyces albus. This led to the discovery of five new benzoxazole alkaloids microechmycin A-E (1-5) and a previously synthesized compound 6. Their structures were elucidated using HRESIMS and 1D and 2D NMR data. Microechmycin A (1) exhibited moderate antibacterial activity against Micrococcus luteus SCSIO ML01 with a minimal inhibitory concentration (MIC) value of 8 μg/mL.
Article
Chemistry, Multidisciplinary
Bin Tan, Liping Zhang, Qingbo Zhang, Siqiang Chen, Weiliang Xiong, Yiguang Zhu, Changsheng Zhang
Summary: This study identified a new environmental resistance determinant, the lobophorin (LOB) resistance-related glycosidase KijX, which has an unexpected correlation with the host-dependent chemical diversity of LOBs. KijX homologues are widely found among bacteria, archaea, and fungi, and they encode the same glycohydrolytic activity on LOBs. The crystal structure of a KijX homologue, AcvX, revealed its ability to accommodate and deglycosylate LOBs. This study highlights the importance of KijX-related glycosidases as preexisting resistance determinants and provides insight into the integration of resistance genes into natural product assembly.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Plant Sciences
Lijuan Wang, Mengyi Zhu, Qingbo Zhang, Shilan Zhai, Yiguang Zhu, Haibo Zhang, Changsheng Zhang
Summary: In this study, an alternative biological route to produce structurally diverse fidaxomicin aglycones was developed by refactoring the promoter and expressing it in a different host. The resulting titers of the five fidaxomicin aglycones ranged from 4.9 to 15.0 mg L-1. Overall, these findings demonstrate the potential of using a biological strategy to construct and diversify fidaxomicin aglycones.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Plant Sciences
Jucelia Iantas, Daiani Cristina Savi, Larissa V. Ponomareva, Jon S. Thorson, Juergen Rohr, Chirlei Glienke, Khaled A. Shaaban
Summary: Chemical investigation of the endophyte Pseudofusicoccum stromaticum CMRP4328 isolated from the medicinal plant Stryphnodendron adstringens resulted in the discovery of ten compounds, including two new dihydrochromones. The study found that four of these compounds exhibited antifungal activity against the citrus pathogen Phyllosticta citricarpa, and the development of citrus black spot symptoms in citrus fruits was also inhibited by two of the compounds. These findings suggest that further research on the strain CMRP4328 of P. stromaticum and its metabolites is warranted for the control of citrus black spot disease.
Article
Biochemical Research Methods
Mengyi Zhu, Lijuan Wang, Haibo Zhang, Liping Zhang, Bin Tan, Qi Huang, Yiguang Zhu, Changsheng Zhang
Summary: Ribosome-targeting oligosaccharides, everninomicins (EVNs), are promising drug leads with a unique mode of action. By duplicating the biosynthetic gene cluster (BGC) in Micromonospora sp. SCSIO 07395, the production of EVNs was enhanced, allowing for bioactivity evaluation. EVNs showed significant inhibition against multidrug-resistant bacteria, with potency comparable or superior to vancomycin, linezolid, and daptomycin. The BGC duplication strategy successfully increased the titer of bioactive EVN M from trace amounts to 98.6 mg L-1, demonstrating the utility of a bioengineering approach for enhanced production and chemical diversification of EVNs.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Peng Jiang, Hongbo Jin, Guangtao Zhang, Wenjun Zhang, Wei Liu, Yiguang Zhu, Changsheng Zhang, Liping Zhang
Summary: This study provides mechanistic understanding of the functional differences between the homologous cytochrome P450 enzymes IkaD and CftA, which catalyze multiple C-H oxidations on the same substrate with distinct regio- and chemoselectivity. The crystal structures reveal that the differences in the conformation of the F/G region in IkaD and CftA control the substrate orientation and determine their binding patterns with polar moieties. Fine-tuning the polar subpocket of IkaD can alter its regioselectivity.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemistry & Molecular Biology
Thaddeus Q. Paulsel, Gavin J. Williams
Summary: Polyketide natural products have great potential as pharmaceutical targets and molecular tools for human health and disease research. Despite the well-understood biosynthetic logic of polyketide synthases, the synthesis of designer polyketides remains challenging due to various issues. Chemical enzymatic synthesis of PKSs has provided valuable insights into enzymatic promiscuity and mechanistic activity and has successfully yielded natural product derivatives. Combining chemical synthesis and enzymology can further improve polyketide synthetic biology approaches.
Article
Plant Sciences
Xiaoyang Zhao, Youzhe Chen, Ting Long, Zhiying Liu, Qingbo Zhang, Haibo Zhang, Yan Yan, Changsheng Zhang, Yiguang Zhu
Summary: In this study, a depsidone encoding gene cluster from Ovatospora sp. SCSIO SY280D was heterologously reconstituted in Aspergillus nidulans A1145, resulting in the production of mollicellins, a representative family of depsidones. Furthermore, a bifunctional P450 monooxygenase that catalyzes both ether formation and hydroxylation in the biosynthesis of the mollicellins was discovered. The functions of a decarboxylase and an aromatic prenyltransferase were also characterized to understand the tailoring modification steps. This work provides important insights into the biosynthesis of mollicellins.
JOURNAL OF NATURAL PRODUCTS
(2023)
Article
Chemistry, Organic
Zhuangjie Fang, Qingbo Zhang, Weiliang Xiong, Lili Sun, Bin Tan, Mengyi Zhu, Liang Ma, Liping Zhang, Yiguang Zhu, Changsheng Zhang
Summary: In this study, four new tetronate antibiotics called kongjuemycins (KJMs) were discovered from a coral-associated actinomycete. The biosynthetic gene cluster responsible for KJMs production was identified and characterized through various experiments. It was found that KJM biosynthesis utilizes diverse precursors from primary metabolism.
Correction
Multidisciplinary Sciences
Minakshi Bhardwaj, Zheng Cui, Erome Daniel Hankore, Faruk H. Moonschi, Hoda Saghaeiannejad Esfahani, Edward Kalkreuter, Chun Gui, Dong Yang, George N. Phillips, Jon S. Thorson, Ben Shen, Steven G. Van Lanen
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
