Arabidopsis thaliana

Using KnetMiner, we search for ten genes identified by a machine learning analysis performed on the first 15 plant spaceflight response transcriptomes that were 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, thereby linking gene functions to physiological processes and highlighting potential for genetic manipulation to enhance future crop resilience in astro-agro-ecosystems.

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THE QUESTION
How do the key genes interact under spaceflight conditions to regulate biological processes crucial to Arabidopsis Thaliana?
Let’s start by breaking up the root question, as answering smaller sets of questions can be simpler.
  • 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 start answering our questions, we need to run a Search in KnetMiner. Since Arabidopsis is a Model organism, it’s included in many of our resources. In this case, let’s use Cereals Premium, as Arabidopsis has many strong links to neighbouring cereal crops, like Wheat and Rice. We then take the ten genes extracted as part of NASA OSDR Plant AWG upstream machine learning analysis:

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

We paste this list into the KnetMiner Gene List Search. Without using an optional Keyword filter, we hit search. A moment later, we see that all ten genes are present in KnetMiner; all with a significant amount of evidence linked to them. To explore a network using all ten, we tick the ‘Select all’ checkbox at the top left, beside Accession in the table header, and click Create Network.
Further Results
Taking a closer look into the various publications connected throughout the graph, we can easily answer our first question, as almost every gene has either text-mined evidence (dotted lines) or was published in one or more articles. Clicking on the NTL gene we can see in the local Graph Explorer that it has a total of 14 directly linked publications - a well studied gene! Clicking on one of the publications in the graph, we can read more about it in the Info Box. One example tells us that NAC transcription factors regulate genome expression is by modulating the RNA GTP nuclear import system which is part of the retrograde signalling system that allows plants to adapt to endoplasmic reticulum associated degradation (ERAD), a system which is part of the unfolded protein response (UPR) system, which is potentially removing unwanted denatured proteins.

Other gene functions can also be confirmed in the same way using the literature linked to via the network.

To answer the second question, we can use the “Search network” button on the top right in Network View, and search for germination. Two currently hidden publications are found in the subgraph, which can be added by selecting their checkboxes and clicking Show in Graph. Both publications are linked to the NTL gene with text-mined evidence - which makes sense as we previously learnt that NTL helps regulate plant development and on Earth its expression is increased in response to ABA or in response to pathogen elicitor detection.

By further navigating the network, we can navigate off the NAC003 gene, clicking it to enable the local Graph Explorer - from here we add the Cellular Component node to the graph, and see both ARD3 and NAC003 are located in the Plasma Membrane. Similar connections are already visible in the network, or can be added using the Graph Explorer.
Conclusion
Analysis of these connections reveals NAC003 is involved in the control of the balance of xylem formation and cambial cell divisions by regulating vascular meristem activity. Alteration to cell walls related components have previously been reported in space flight missions (Choi, et al., 2019); these analysis reveal links between the plant cellulose content, phospholipid transfer to membrane, cutin based cuticle development and leaf length regulated by LTPI (a lipid transfer protein that travels through the ER to extracellular matrix). These loci also associate in the network with ATS3 via protein interaction and a role in callus induction found within the literature. As callus induction can be achieved by changing the ratio of auxin and cytokinin in the plants, perhaps these connections are indicative of changing in plant hormone signalling in the spaceflight environment that influencing NAC003 expression in meristem, nitrogen-associated metabolism and potentially influences cell wall structure in concert with change in LTPI.
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In this use case we only explored evidence within Arabidopsis, but as seen in the figure, the search also linked evidence to other species within the dataset, like 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 the diverse roles these genes play in salicylic acid-dependent systemic resistance, nuclear transport and aspartate phosphorylation which are likely to alter cellular elongation. Understanding these interactions not only deepens our knowledge of plant adaptation to stress but also paves the way for genetic enhancements designed to enhance plant resilience for growth in future astro-agro-ecosystems.

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 that are involved in plant response to spaceflight, this will significantly advanced humanities 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

We’ve worked on these updates alongside the experts who use them most and believe they make KnetMiner a more powerful, user-friendly tool, tailored for those who need results fast.
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‍We welcome any and all positive feedback as we begin rolling out the all New KnetMiner.

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