Introduction

Using KnetMiner, we search for ten genes identified by a machine learning analysis performed on the first 15 plant spaceflight response transcriptomes compiled by Barker et al. (2023) as part of the NASA OSDR Plant AWG.

The resulting network shows intricate molecular, biochemical, and physiological connections among these genes, revealing their roles in processes like aspartate phosphorylation, cell elongation, and plant stress responses. This network aids in understanding plant adaptive responses to spaceflight, linking gene functions to physiological processes and highlighting the potential for genetic manipulation to enhance future crop resilience in astro-agro-ecosystems.

The Question

How do the key genes interact under spaceflight conditions to regulate biological processes crucial to Arabidopsis thaliana?

To answer this, we break the root question into smaller, manageable parts:

• What are the specific roles of the 10 identified genes in Arabidopsis thaliana?

• Which publications detail the functional implications of these loci in relation to germination, secretion, or physiological processes like root or leaf growth?

• How do these genes interact with each other?

• Do any of these interactions suggest potential targets for genetic manipulation?

The Method

Enhanced Transparency and Resource Management

To begin, we run a Search in KnetMiner. Since Arabidopsis is a model organism, it is included in many of our resources. Here, we use Cereals Premium, as Arabidopsis shares strong links with neighboring cereal crops like wheat and rice.

We then take the ten genes extracted as part of NASA OSDR Plant AWG’s upstream machine learning analysis:

AT1G64940, AT3G02020, AT1G11570, AT5G57420, AT1G02220, AT2G38530, AT2G26400, AT3G18260, AT5G07190, AT2G41610

1. Paste this list into the KnetMiner Gene List Search.

2. Without applying an optional keyword filter, hit Search.

3. The results confirm that all ten genes are present in KnetMiner, with significant linked evidence.

4. To explore a network using all ten genes, tick the ‘Select all’ checkbox beside Accession in the table header and click Create Network.

Further Results

Examining the various publications connected throughout the graph allows us to answer our first question:

• Almost every gene has text-mined evidence (dotted lines) or has been published in one or more articles.

• Clicking on the NTL gene in the local Graph Explorer shows 14 directly linked publications—indicating it is a well-studied gene.

• Clicking on a publication within the graph opens the Info Box, where we learn:

• NAC transcription factors regulate gene expression by modulating the RNA GTP nuclear import system, a component of the retrograde signaling system.

• This system enables plants to adapt to endoplasmic reticulum-associated degradation (ERAD), which is part of the unfolded protein response (UPR), potentially removing unwanted denatured proteins.

Other gene functions can be confirmed similarly using the literature linked via the network.

To address the second question:

1. Use the “Search network” button in Network View and search for germination.

2. Two currently hidden publications appear in the subgraph.

3. Select their checkboxes and click Show in Graph.

4. Both publications are linked to the NTL gene via text-mined evidence, supporting its role in plant development and ABA response on Earth.

Exploring Further Gene Interactions

• Clicking on the NAC003 gene in the local Graph Explorer, we add the Cellular Component node to the graph.

• This reveals that ARD3 and NAC003 are located in the Plasma Membrane.

• Similar connections are visible in the network or can be added using the Graph Explorer.

Conclusion

Analysis of these connections reveals:

• NAC003 regulates vascular meristem activity, balancing xylem formation and cambial cell division.

• Spaceflight missions have reported alterations in plant cell walls (Choi et al., 2019).

• The data suggests links between:

• Plant cellulose content

• Phospholipid transfer to membranes

• Cutin-based cuticle development

• Leaf length regulation via LTPI, a lipid transfer protein traveling through the ER to the extracellular matrix.

• ATS3 interacts with NAC003 via protein interaction and plays a role in callus induction, found in literature.

• Callus induction is influenced by changes in auxin/cytokinin ratios, suggesting a potential hormonal shift in spaceflight environments.

In this use case, we focused on Arabidopsis, but the figure also links evidence to other species, such as Rice and Maize.

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The network uncovers a web of molecular interactions involving:

IAA33, ARD3, NAC003, CYP89A6, ATS3, AK3, RTNLB9, DICE1, NTL, and LP2.

These connections highlight gene roles in:

• Salicylic acid-dependent systemic resistance

• Nuclear transport

• Aspartate phosphorylation

These processes likely affect cellular elongation, enhancing our understanding of plant adaptation to stress and paving the way for genetic improvements for future astro-agro-ecosystems.

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Testimonial from Use Case Co-Author at NASA GeneLab‍

“KnetMiner has been a game-changer for our research. Its intuitive interface made it easy to uncover complex gene interactions we never knew existed. These insights have accelerated our ability to translate fundamental discoveries in Arabidopsis into practical tools for crop improvement. By identifying key genetic markers involved in plant response to spaceflight, this will significantly advance humanity’s marker-assisted breeding programs and lay the groundwork for more efficient genetic engineering efforts to tailor crops for built environments in low Earth orbit and beyond.”

Dr. Richard Barker

Project Scientist @ NASA GeneLab

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