ArticleProceedings of the National Academy of Sciences of the United States of America2012
Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers.
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Who cites it
168 citing papers in PubMed, 454 citations in OpenAlex.
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- Quantitative Dissection of Agrobacterium Virulence to Generate a Synthetic Ti Plasmid.ACS synthetic biology · 2026Article
- Predicting compatibility between ferredoxins and the Fe protein of nitrogenase using in silico protein modeling.Protein science : a publication of the Protein Society · 2026Article
- Enhancement of Nitrogenase Activity in Recombinant Escherichia coli by Replacing Upstream Region of nif Operon from Paenibacillus Species.Chembiochem : a European journal of chemical biology · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Microbial Biotechnology in Agriculture.Progress in molecular and subcellular biology · 2026Review
- Unlocking associative nitrogen fixation in Poaceae: molecular mechanisms, regulatory constraints, and pathways to sustainable productivity.Frontiers in microbiology · 2026Review
- Intraspecific microbiome dynamics across the life cycle of the milkweed bugMicrobial genomics · 2026Article
- Iterative SCRaMbLE for engineering synthetic genome modules and chromosomes.Nature communications · 2025Article
- Be a GEM: Biocontained, environmentally applied, genetically engineered microbes.Advanced drug delivery reviews · 2025Review
- The design and engineering of synthetic genomes.Nature reviews. Genetics · 2025Review
- AACS synthetic biology · 2025Article
- Investigation of themBio · 2025Article
- Article
- Synthetic biology and artificial intelligence in crop improvement.Plant communications · 2025Review
- Directed evolution of an orthogonal transcription engine for programmable gene expression in eukaryotes.iScience · 2025Article
- Regulation of Rhizobial Nodulation Genes by Flavonoid-Independent NodD Supports Nitrogen-Fixing Symbioses With Legumes.Environmental microbiology · 2025Article
- Directed evolution of an orthogonal transcription engine for programmable gene expression in eukaryotes.bioRxiv : the preprint server for biology · 2024Article
- Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists.Nature communications · 2024Review
108 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacterial genes associated with a single trait are often grouped in a contiguous unit of the genome known as a gene cluster. It is difficult to genetically manipulate many gene clusters because of complex, redundant, and integrated host regulation. We have developed a systematic approach to completely specify the genetics of a gene cluster by rebuilding it from the bottom up using only synthetic, well-characterized parts. This process removes all native regulation, including that which is undiscovered. First, all noncoding DNA, regulatory proteins, and nonessential genes are removed. The codons of essential genes are changed to create a DNA sequence as divergent as possible from the wild-type (WT) gene. Recoded genes are computationally scanned to eliminate internal regulation. They are organized into operons and placed under the control of synthetic parts (promoters, ribosome binding sites, and terminators) that are functionally separated by spacer parts. Finally, a controller consisting of genetic sensors and circuits regulates the conditions and dynamics of gene expression. We applied this approach to an agriculturally relevant gene cluster from Klebsiella oxytoca encoding the nitrogen fixation pathway for converting atmospheric N(2) to ammonia. The native gene cluster consists of 20 genes in seven operons and is encoded in 23.5 kb of DNA. We constructed a "refactored" gene cluster that shares little DNA sequence identity with WT and for which the function of every genetic part is defined. This work demonstrates the potential for synthetic biology tools to rewrite the genetics encoding complex biological functions to facilitate access, engineering, and transferability.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.