Evidence map›Paper›PMID 40355701›Full record

ArticleNature plants2025

Quantitative dissection of Agrobacterium T-DNA expression in single plant cells reveals density-dependent synergy and antagonism.

Simon Alamos, Matthew J Szarzanowicz, Mitchell G Thompson, Danielle M Stevens, Liam D Kirkpatrick, Amanda Dee, Hamreet Pannu, Ruoming Cui, Shuying Liu, Monikaben Nimavat and 3 more

Abstract read
In one paragraph

Article in Nature plants, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing papers in PubMed
–field-weighted citation impact
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

9 citing papers in PubMed.

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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.

Simon Alamos *Joint BioEnergy Institute, Emeryville, CA, USA. simon.alamos@berkeley.edu.ORCID 0000-0003-2867-3840
Matthew J Szarzanowicz *Joint BioEnergy Institute, Emeryville, CA, USA.ORCID 0009-0003-4398-5196
Mitchell G Thompson *Joint BioEnergy Institute, Emeryville, CA, USA.ORCID 0000-0002-1490-8074
Danielle M StevensDepartment of Plant and Microbial Biology, University of California, Berkeley, CA, USA.ORCID 0000-0001-5630-137X
Liam D KirkpatrickJoint BioEnergy Institute, Emeryville, CA, USA.ORCID 0000-0002-2744-9102
Amanda DeeJoint BioEnergy Institute, Emeryville, CA, USA.ORCID 0009-0008-6312-4058
Hamreet PannuJoint BioEnergy Institute, Emeryville, CA, USA.
Ruoming CuiJoint BioEnergy Institute, Emeryville, CA, USA.
Shuying LiuJoint BioEnergy Institute, Emeryville, CA, USA.
Monikaben NimavatJoint BioEnergy Institute, Emeryville, CA, USA.ORCID 0009-0000-2190-6512
Ksenia KrasilevaDepartment of Plant and Microbial Biology, University of California, Berkeley, CA, USA.ORCID 0000-0002-1679-0700
Edward E K BaidooJoint BioEnergy Institute, Emeryville, CA, USA.
Patrick M ShihJoint BioEnergy Institute, Emeryville, CA, USA. pmshih@berkeley.edu.ORCID 0000-0002-2119-3345

Funding

Cross-kingdom health: evolution of innate immune receptors and their targetsDP2AT011967 · NCCIH · UNIVERSITY OF CALIFORNIA BERKELEY · PI KRASILEVA, KSENIA V · 2021 to 2024
$2.2M
NCCIH NIH HHS DP2 AT011967
6 · The paper itself

Abstract

Agrobacterium pathogenesis, which involves transferring T-DNA into plant cells, is the cornerstone of plant genetic engineering. As the applications that rely on Agrobacterium increase in sophistication, it becomes critical to achieve a quantitative and predictive understanding of T-DNA expression at the level of single plant cells. Here we examine if a classic Poisson model of interactions between pathogens and host cells holds true for Agrobacterium infecting Nicotiana benthamiana. Systematically challenging this model revealed antagonistic and synergistic density-dependent interactions between bacteria that do not require quorum sensing. Using various approaches, we studied the molecular basis of these interactions. To overcome the engineering constraints imposed by antagonism, we created a dual binary vector system termed 'BiBi', which can improve the efficiency of a reconstituted complex metabolic pathway in a predictive fashion. Our findings illustrate how combining theoretical models with quantitative experiments can reveal new principles of bacterial pathogenesis, impacting both fundamental and applied plant biology.

Indexed as

AgrobacteriumAgrobacterium tumefaciensDNA, BacterialNicotianaPlant CellsPlant DiseasesDNA, BacterialT-DNA

Identifiers

PMID40355701
PMCPMC12095076

What OpenQuestion holds

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Registered trials

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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.