Resurrection science: How plant proteomics could safeguard Africa's food future

In Sub-Saharan Africa, crop yields are projected to decline by 5-17% by 2050, especially in major staples, partly due to climate change. How can farmers protect and enhance their yields to meet the nutritional needs of a growing population? In the face of the climate crisis, plant scientists are turning to proteomics, the largescale study of proteins, to understand and enhance drought-resilience in local crops.

After losing up to 95% of its water content, the sub-Saharan African shrub Xerophyta schlechter can green and unfurl its long grassy leaves within hours of rainfall. Aptly named a resurrection plant, X. schlechter is one of the stars of the University of Cape Town’s Plant Stress lab run by plant scientist Jill Farrant. For Farrant and her team, X. schlechter and other resurrection plants hold the molecular key to unlocking climate change resilience in local crops and safeguarding our food security.

Proteomics and other ‘omics’ technologies enable researchers to compare proteins, DNA and metabolites to identify why and how plants like X. schlechteri respond to stressors the way they do. Because proteins drive all biological processes, proteomics – the large-scale study of proteins – is critical for understanding plants’ responses. A proteome is a set of all expressed proteins in a cell, tissue, or organism.  Unlike the genome, which acts as a blueprint for how the plant operates, the proteome is dynamic. It behaves like a skilled military unit, taking commands from above but adapting its tactics in response to conditions on the ground. 

Liam Bell, a proteomics coordinator at Diplomics, explains the significance of a proteomics approach to understanding plants’ responses. “At a genomics level, you might look at what genes are present in one plant that are not present in another, and you would hypothesise that those genes are doing something to make [drought or heat tolerance] happen,” Bell says. “At the protein level, you’re actually seeing the physical response – the plant’s workforce in action in response to these conditions.”

A plant superpower

To find out how X. schlechteri survived desiccation (extreme drying), Farrant’s team subjected it to drought conditions and analysed the number and type of proteins expressed at each stage.

Their proteomic analysis revealed various protective compounds in X. schlechteri that prevent cellular damage, including proteins found in seeds (known as late embryogenesis abundant proteins), heat shock proteins, antioxidants, and specific sugars. Interestingly, these compounds are common across the plant kingdom. However, most plants only use them during their seed phase, when they may need to endure long periods of drought or cold before sprouting in warmer conditions.  

‘Arguably, vegetative desiccation tolerance is an evolutionary rewiring of seed desiccation tolerance that has occurred in several independent events across Angiosperm taxa [flowering plants],’ Farrant writes with her colleague Henk Hilhorst. Although the genetic code for this already exists in crops, it is suppressed. The researchers’ ultimate goal is to devise a ‘molecular switch’ from resurrection plants to trigger this dormant ability in staple crops like maize.

Other efforts to produce drought-tolerant crops focus on breeding more resilient crops using traditional breeding methods or gene editing technologies. Groups such as Maize for Africa are using omics technologies to develop more resilient maize stains.  Proteomic and genomic studies identified genes and proteins associated with disease resistance in African bananas, enabling research groups to breed disease-resistant banana varieties. Omics studies can also investigate sustainable farming practices – for instance, interspersing crops among other plants (intercropping) to improve soil health and boost yields.

Local is lekker

As global temperatures rise, studies predict declining yields of maize, rice, and corn, staples that account for 60% of Africa’s total calorie intake.

 However, these staples are just three of 30,000 known edible plant species on the continent. Tafadzwa Mabhaudbi of the London School of Hygiene and Tropical Medicine is among a growing community of advocates for commercialising and promoting indigenous crops. Local crops are adapted to local weather conditions, resistant to pests and diseases and can grow on semi-arable land. Unlike introduced starchy staples, they also tend to be nutrient-dense.

In 2017, Mabhaudbi and colleagues devised a roadmap to commercialising local crops in South Africa. They selected 13 promising indigenous crops based on their nutritional profiles and heat and drought tolerance. Limited available resources should focus on developing these ‘priority crops’, which include the Ethiopian grain tef, sorghum, the Bambara groundnut, the cowpea, amadumbe (taro), wild mustard, and the leafy green vegetable amaranth.

Although they have an edge on major crops when it comes to resilience, indigenous crops tend to be low-yielding, particularly under drought conditions. Proteomics analysis and other biotechnology can inform the kind of breeding programmes that historically resulted in the high yields of the major crops. Proteomic research can also fill in knowledge gaps about the priority crops’ nutritional profiles, optimise desirable traits, and develop their suitability for cultivation in arid and semi-arid areas. Promoting the cultivation of local crops can make nutritious food more accessible and enhance communities’ resilience to climate change.

Protein fingerprints

Proteins can help plants adapt to a changing climate and guide the development of climate-smart crops. At the other end of the food supply chain, researchers use proteomics techniques to detect food fraud – the deliberate alteration of food products for profit. Although research is lacking, reports suggest that food fraud is widespread across sub-Saharan Africa. As the weather warms, interruptions to the supply chain are likely to incentivise fraudulent practises to meet demand.

Food fraud might take the shape of bleaching cassava-derived products with chlorine, ripening plantains with unsafe levels of plant hormones, or knowingly selling contaminated foods. Major crops in sub-Saharan Africa are particularly prone to mycotoxin contamination – toxins produced by fungi growth. Contaminated and altered foods pose significant health risks, from allergic reactions and acute poisoning to cancer and other long-term complications.

Although traditional methods of detecting food fraud are expensive and time-consuming, fraudulent food practices often leave molecular fingerprints that can be detected with proteomics technologies. Mass spectrometer instruments measure the number and quantity of proteins in a sample, and can be used to detect cheap meat substitutes or proteins associated with mycotoxins. Alongside traditional laboratory techniques, such technologies may one day help to safeguard local food supplies.

Addressing food insecurity is a complex social, political and economic problem that extends beyond simply producing enough food. However, ensuring adequate, accessible and nutritious fresh produce is a positive first step. Developing local biotechnology capacity is critical to driving sustainable agriculture, supporting small-scale farmers, and reducing the consumption of adulterated and contaminated food.