Article
Biochemical Research Methods
Tyll Stocker, Lena Altrogge, Caroline Marcon, Yan Naing Win, Frank Hochholdinger, Heiko Schoof
Summary: Insertional mutagenesis is a powerful tool for creating loss-of-function mutations on a genome-wide scale. MuWU is an automated Mutant-seq workflow utility that efficiently identifies insertion sites and handles complex bioinformatic tasks, making it a valuable resource for functional genomics studies.
Article
Microbiology
Wonsik Lee
Summary: Transposon mutant libraries are valuable resources for studying bacterial metabolism and pathogenesis. By analyzing the fitness of mutants in libraries under different growth conditions, important insights into the physiology and biogenesis of structural components of bacterial cells can be gained. Transposon sequencing (Tn-seq) allows for high-throughput genome profiling and synthetic lethality analysis, and has been used to identify essential genes and study the mode of action of antibacterials.
JOURNAL OF MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Cristina Cheng, Mi Zhou, Qiwen Su, Alexandra Steigmeyer, Jia Niu
Summary: The generation of a library of variant genes is necessary for directed evolution, and efficient library diversification in living cells is essential for in vivo technologies. Recent advancements in using genome editors allow for precise mutagenesis focused on specific genes, higher mutational density, and reduced occurrence of cheater mutations.
CELL CHEMICAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Limei Chen, Xiumin Liu, Chaofeng Li, Hanchen Li, Wuxi Chen, Demao Li
Summary: This study investigated the mechanism of high DHA production in Schizochytrium limacinum LD11 and found that certain genes were upregulated, leading to increased synthesis of acetyl-CoA and triacylglycerol. The study also revealed that genes involved in β-oxidation were upregulated and downregulated, resulting in a significant increase in DHA content.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Biochemistry & Molecular Biology
Yanhui Li, Neil Molyneaux, Haitao Zhang, Gang Zhou, Carly Kerr, Mark D. Adams, Kathleen L. Berkner, Kurt W. Runge
Summary: In this study, we developed an efficient method to construct a library of barcoded insertion mutants with a wider range of phenotypes. By leveraging sequence information, we were able to identify the barcode sequences and DNA insertion sites of 4391 Schizosaccharomyces pombe insertion mutations with only 40 sequencing preparations.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Dongzhi Wang, Yongpeng Li, Haojie Wang, Yongxin Xu, Yiman Yang, Yuxin Zhou, Zhongxu Chen, Yuqing Zhou, Lixuan Gui, Yi Guo, Chunjiang Zhou, Wenqiang Tang, Shuzhi Zheng, Lei Wang, Xiulin Guo, Yingjun Zhang, Fa Cui, Xuelei Lin, Yuling Jiao, Yuehui He, Junming Li, Fei He, Xigang Liu, Jun Xiao
Summary: In this study, a library for the popular wheat variety KN9204 was created using EMS mutagenesis, providing a comprehensive understanding of its genome, transcriptome, and epigenome. Exome capture sequencing revealed a high mutation rate in coding genes, with an average of 1383 EMS-type SNPs per line. New allelic variations for important agronomic trait-related genes were identified, and altered sensitivity to drought and salinity stress was observed in certain NAC transcription factors. This research provides valuable resources for functional genomics research and genetic manipulation of wheat.
PLANT COMMUNICATIONS
(2023)
Article
Microbiology
Melanie M. Pearson, Sapna Pahil, Valerie S. Forsyth, Allyson E. Shea, Harry L. T. Mobley
Summary: Ordered transposon libraries are a valuable resource for studying bacterial species, especially those with difficult methods for targeted genetic mutations. In this study, we constructed an ordered transposon library for the bacterial urinary tract pathogen Proteus mirabilis strain HI4320. The library enables large-scale screens and facilitates the study of P. mirabilis biology. However, the library's coverage of predicted genes was lower than expected due to unmapped insertions and a high proportion of mixed clones and multiple transposon insertion events. Future library construction can be improved by addressing these challenges.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Venkata H. Bhavana, Gideon H. Hillebrand, Kathyayini P. Gopalakrishna, Rebekah A. Rapp, Adam J. Ratner, Herve Tettelin, Thomas A. Hooven
Summary: In this study, a large-scale GBS indexed library was created and validated, providing a useful genetic tool for GBS researchers. The library contains interruptions of 878 genes and 253 intergenic regions, covering multiple functional categories including metabolism, structure, and virulence.
MICROBIOLOGY SPECTRUM
(2023)
Review
Agronomy
Wenjun Xia, Peipei Zhang, Xinyang Wu, Mingxuan Li, Ting Sun, Pingping Fang, Arun K. Pandey, Pei Xu
Summary: This review provides information on mutant library resources and mutant screening technologies in legume crops. Traditional hybrid breeding and gene editing technologies are difficult to apply in legumes, but mutation technologies can accelerate breeding and facilitate functional genomic studies.
Article
Plant Sciences
Mengxi Bi, Zhijun Wang, Keyan Cheng, Yiqing Cui, Yi He, Jian Ma, Mingfang Qi
Summary: This study successfully applied the CRISPR/Cas9 large-scale screening strategy in tomato and constructed a CRISPR/Cas9 mutant library. The study found that homozygous and biallelic mutations occurred at higher frequencies in the mutant population. Additionally, a small-scale CRISPR/Cas9 library enhanced the efficacy of single sgRNA recognition in positive plants.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Biology
Heidi A. Arjes, Jiawei Sun, Hualan Liu, Taylor H. Nguyen, Rebecca N. Culver, Arianna I. Celis, Sophie Jean Walton, Kimberly S. Vasquez, Feiqiao Brian Yu, Katherine S. S. Xue, Daniel Newton, Ricardo Zermeno, Meredith Weglarz, Adam Deutschbauer, Kerwyn Casey Huang, Anthony L. Shiver
Summary: In this study, we assembled a genome-scale ordered collection of transposon-insertion mutants in Bacteroides thetaiotaomicron VPI-5482. By using flow cytometry and barcode sequencing strategies, we created a condensed collection with single-insertion strains covering over 2500 genes. We demonstrated the potential of this collection for phenotypic screening by analyzing growth dynamics and cell morphology. In addition, we analyzed the process of assembling the collection and identified areas for improvement in future efforts to assemble ordered mutant collections for gut microbiota members.
Article
Environmental Sciences
Chenshuo Lin, Fu-Yi Huang, Shu-Yi-Dan Zhou, Hu Li, Xian Zhang, Jian-Qiang Su
Summary: This study developed a high-throughput library construction chip for profiling environmental microbial communities and evaluated its performance. The chip showed high conformity with conventional methods and demonstrated advantages in accuracy, high-throughput, cost-efficiency, and broad practicability. Additionally, the study found that bacteria tend to impose competitive pressures, resulting in a more connected network under certain conditions.
ENVIRONMENTAL RESEARCH
(2022)
Article
Chemistry, Physical
Yutaka Saito, Misaki Oikawa, Takumi Sato, Hikaru Nakazawa, Tomoyuki Ito, Tomoshi Kameda, Koji Tsuda, Mitsuo Umetsu
Summary: The study shows that machine learning is a useful tool in designing proteins with desired functions in protein engineering. Depending on the presence or absence of highly positive variants in the training data, machine learning-guided directed evolution can lead to improved variants in different regions of sequence space.
Article
Horticulture
Lijuan Yin, Yinjie Hou, Xiaoyao Chen, Xin Huang, Mengjiao Feng, Chunxia Wang, Zhongyuan Wang, Zhen Yue, Yong Zhang, Jianxiang Ma, Hao Li, Jianqiang Yang, Xian Zhang, Rong Yu, Chunhua Wei
Summary: This study created mutant libraries of watermelon through mutagenesis, resulting in several mutants with desirable horticultural characteristics. Some of these mutations showed stable inheritance. These results are significant for genetic breeding and exploration of functional genes in watermelon.
Article
Environmental Sciences
Fanna Kong, Jiqiang Yin, Xinzi Yu, Junhao Wang, Bin Sun, Yunxiang Mao, Jang Kyun Kim, Hongzhong Ren, Huijie Yue, Chenggong Yu, Xinping Miao, Ying Sun
Summary: With the development of the laver industry, the lack of germplasm resources has become a serious problem. In order to increase genetic diversity and develop more germplasm sources, a mutant library was constructed using ethyl methanesulfonate (EMS)-mutagenized archeospores. The mutant library consisted of 1860 haploid thalli, which were evaluated for their phenotypic traits. This research not only provides a practical reference for the construction of mutant libraries for other seaweeds but also serves as a valuable resource for functional genomics research and laver breeding.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Diego Duchi, Kristofer Gryte, Nicole C. Robb, Zakia Morichaud, Carol Sheppard, Konstantin Brodolin, Sivaramesh Wigneshweraraj, Achillefs N. Kapanidis
NUCLEIC ACIDS RESEARCH
(2018)
Article
Chemistry, Multidisciplinary
Bing Liu, Zhihao Wang, Ling Lan, Qianfan Yang, Peipei Zhang, Lei Shi, Yunhe Lang, Aline Tabib-Salazar, Sivaramesh Wigneshweraraj, Jiye Zhang, Yawen Wang, Yalin Tang, Steve Matthews, Xiufeng Zhang
CHEMISTRY-A EUROPEAN JOURNAL
(2018)
Article
Microbiology
Amy Switzer, Dimitrios Evangelopoulos, Rita Figueira, Luiz Pedro S. de Carvalho, Daniel R. Brown, Sivaramesh Wigneshweraraj
Article
Microbiology
Aishwarya Krishna, Matthew T. G. Holden, Sharon J. Peacock, Andrew M. Edwards, Sivaramesh Wigneshweraraj
Article
Multidisciplinary Sciences
Aline Tabib-Salazar, Bing Liu, Declan Barker, Lynn Burchell, Udi Qimron, Steve J. Matthews, Sivaramesh Wigneshwerararj
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Review
Biochemistry & Molecular Biology
Amy Switzer, Daniel R. Brown, Sivaramesh Wigneshweraraj
BIOCHEMICAL SOCIETY TRANSACTIONS
(2018)
Article
Biochemistry & Molecular Biology
Nancy Mulvenna, Ingo Hantke, Lynn Burchell, Sophie Nicod, David Bell, Kuersad Turgay, Sivaramesh Wigneshweraraj
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Microbiology
Aishwarya Krishna, Bing Liu, Sharon J. Peacock, Sivaramesh Wigneshweraraj
Article
Microbiology
Amy Switzer, Lynn Burchell, Josh McQuail, Sivaramesh Wigneshweraraj
JOURNAL OF BACTERIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Josh McQuail, Amy Switzer, Lynn Burchell, Sivaramesh Wigneshweraraj
JOURNAL OF BIOLOGICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Josh McQuail, Agamemnon J. Carpousis, Sivaramesh Wigneshweraraj
Summary: Under nutrient adversity, bacteria minimize cellular energy usage by adjusting metabolism through controlling RNA synthesis and degradation. RNA degradosome components RNase E and Hfq co-localize in a single focus, known as the H-body, in long-term nitrogen starved E. coli, suggesting a subcellular compartmentalization of RNA management in stressed bacteria.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jovana Bakovic, Bess Yi Kun Yu, Daniel Silva, Maria Baczynska, Sew Yeu Peak-Chew, Amy Switzer, Lynn Burchell, Sivaramesh Wigneshweraraj, Muralidharan Vandanashree, Balasubramanian Gopal, Valeriy Filonenko, Mark Skehel, Ivan Gout
Summary: S. aureus AgrA is modified by covalent binding of CoA in response to oxidative or metabolic stress, leading to decreased DNA-binding activity.
Correction
Microbiology
Amy Switzer, Lynn Burchell, Josh McQuail, Sivaramesh Wigneshweraraj
JOURNAL OF BACTERIOLOGY
(2022)
Article
Microbiology
Amy Switzer, Lynn Burchell, Panagiotis Mitsidis, Teresa Thurston, Sivaramesh Wigneshweraraj
Summary: The canonical function of sigma factor is to determine the gene specificity of RNA polymerase. Sigma(54) uniquely confers distinct functional and regulatory properties on RNAP in various bacterial species. The absence of sigma(54) in uropathogenic E. coli results in different colony sizes appearing at different times, suggesting a non-canonical function of sigma(54) in regulating genetic information flow.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Emma Bartram, Masanori Asai, Philippe Gabant, Sivaramesh Wigneshweraraj
Summary: This study retrofitted probiotic Escherichia coli bacteria to overproduce heterologous bacteriocins and found that strains producing the lowest amount of bacteriocins displayed the highest antibacterial efficacy with minimal impact on their fitness, highlighting important considerations for retrofitting probiotic bacteria.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)