Evidence map›Paper›PMID 25419741›Full record

ArticleNature biotechnology2014

Functional optimization of gene clusters by combinatorial design and assembly.

Michael J Smanski, Swapnil Bhatia, Dehua Zhao, YongJin Park, Lauren B A Woodruff, Georgia Giannoukos, Dawn Ciulla, Michele Busby, Johnathan Calderon, Robert Nicol and 3 more

Abstract read
PubMed Publisher
In one paragraph

Article in Nature biotechnology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers.

0numbers the graph read from it
0cells of the map it votes in
158citing papers in PubMed
21.9field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

158 citing papers in PubMed, 351 citations in OpenAlex.

  1. Article
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  4. Multi-Targeting Non-Specific Genome Engineering in Bacteria.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026
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98 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors at 3 institutions in 1 country.

Michael J SmanskiSynthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Swapnil BhatiaElectrical and Computer Engineering Department, Boston University, Boston, Massachusetts, USA.
Dehua ZhaoSynthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
YongJin ParkSynthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Lauren B A Woodruff1] Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Broad Technology Labs, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Georgia GiannoukosBroad Technology Labs, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Dawn CiullaBroad Technology Labs, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Michele BusbyBroad Technology Labs, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Johnathan CalderonSynthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Robert NicolBroad Technology Labs, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
D Benjamin Gordon1] Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Broad Technology Labs, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Douglas DensmoreElectrical and Computer Engineering Department, Boston University, Boston, Massachusetts, USA.
Christopher A Voigt1] Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Broad Technology Labs, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Massachusetts Institute of Technology · USBroad Institute · USBoston University · US

Funding

Howard Hughes Medical Institute
6 · The paper itself

Abstract

Large microbial gene clusters encode useful functions, including energy utilization and natural product biosynthesis, but genetic manipulation of such systems is slow, difficult and complicated by complex regulation. We exploit the modularity of a refactored Klebsiella oxytoca nitrogen fixation (nif) gene cluster (16 genes, 103 parts) to build genetic permutations that could not be achieved by starting from the wild-type cluster. Constraint-based combinatorial design and DNA assembly are used to build libraries of radically different cluster architectures by varying part choice, gene order, gene orientation and operon occupancy. We construct 84 variants of the nifUSVWZM operon, 145 variants of the nifHDKY operon, 155 variants of the nifHDKYENJ operon and 122 variants of the complete 16-gene pathway. The performance and behavior of these variants are characterized by nitrogenase assay and strand-specific RNA sequencing (RNA-seq), and the results are incorporated into subsequent design cycles. We have produced a fully synthetic cluster that recovers 57% of wild-type activity. Our approach allows the performance of genetic parts to be quantified simultaneously in hundreds of genetic contexts. This parallelized design-build-test-learn cycle, which can access previously unattainable regions of genetic space, should provide a useful, fast tool for genetic optimization and hypothesis testing.

Indexed as

Multigene FamilyHigh-Throughput Nucleotide SequencingKlebsiella oxytocaNitrogenaseNitrogen FixationOperonPromoter Regions, GeneticTranscription, GeneticNitrogenase

Identifiers

PMID25419741
OpenAlexW1967382476

What OpenQuestion holds

Textmetadata
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Registered trials

None linked

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.