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.

There’s a plant for that

South Africa’s indigenous medicinal plants

Under the unblinking gaze of the autumn sun, the colour drains from the woody shrubs (myrothamnus flabellifolia) growing on the bare rock of the mountain slopes. Some almost as tall as a human in summer, they shrink as the days shorten. Their fan-shaped leaves curl and close. As winter arrives, life quietly departs. 

Or does it? The isiZulu name for the shrub is ‘uvukwabafile’ – ‘wakes from the dead’. Within hours of the first summer rains that release the heat from the earth, the extensive roots of the uvukwabafile plants begin to stir, intercepting the water collecting in rocky crevices. The apparently lifeless leaves unfold. When the sun next rises, the shrubs stand tall and green once again, restored to their original glory. These miraculous resurrections occur every year in the mountains across South Africa, Botswana, Zimbabwe, Mozambique, Malawi, Tanzania and Kenya. The shrub can survive losing up to 95% of its water content and recover almost instantly when it rains. (For comparison, most plants can tolerate losing 10-20% of their water content before experiencing significant stress.)  

For centuries, the indigenous peoples of Southern Africa have used uvukwabafile – also known as the resurrection plant – to restore health to the sick or injured. Smoked or prepared as a tea or tonic, it is used to treat mood disorders, infectious diseases, respiratory issues, inflammation, and kidney ailments, among others. Research has found that the plant contains a wide and varied collection of essential oils and bioactive ingredients. A 2020 literature review, led by Joseph Erhabor of the University of the Free State, found that these include compounds with anticancer, anti-inflammation, antimicrobial, antioxidant, antimicrobial and antiviral properties. 

The resurrection plant is one of an estimated 3,400 medicinal plants in Southern Africa. According to Sibusiso Xego, a traditional health practitioner and researcher at Cape Town University of Technology, indigenous medicinal plants are a cornerstone of spiritual and physical wellbeing in South Africa. “If we trace back to ancient times, our grandmothers and grandfathers used medicinal plants as the main form of medicine. It’s part of everyday life.” 

Sustainable harvesting 

Despite their medical and cultural importance, many of South Africa’s medicinal plants are endangered. With their natural habitat shrinking due to urban development, agricultural expansion, and climate change, the plants are particularly vulnerable to overharvesting.  To reduce pressure on remaining wild populations, some researchers and traditional health practitioners are looking for ways to propagate indigenous medicinal plants.  

This is more challenging than it may seem. 

For some traditional healers, the medicinal properties of the plants are bound up in their wild state. Research shows that some wild and cultivated plants may indeed have different medicinal profiles. That’s because some of the plants’ medicinal compounds are a response to external conditions like drought or insect attacks – conditions that farmed plants wouldn’t typically experience. Xego’s research involves comparing the active compounds of cultivated plants with wild varieties, and exploring how to adjust growing conditions to maintain the medicinal properties that the plant would have in the wild.

“In my research that I've done with wild ginger I saw that there is not much difference [in the medicinal compounds] when you cultivate the plants [hydroponically] and when they grow in their natural habitat,” she says. In fact, propagated plants may have the edge because they are protected from adverse conditions linked to climate change. 

Wild ginger, or African ginger (Siphonochilus aethiopicus) is a forest dwelling plant with elegant sage-green leaves and pale pink, tissue-paper blooms. Long used to treat coughs, allergies and inflammation, wild ginger contains compounds with studied antimicrobial, anti-asthmatic, anti-inflammatory, and antimalarial activities. Naturally occurring from tropical Africa to southern Africa, African ginger has all but disappeared from the wild in South Africa today. That’s partly because, as striking as the plant is, its most valued parts are its roots.

However, Xego’s research has found that the bioactive ingredients of wild ginger are also found in the leaves, which makes room for sustainable harvesting practices. Xebo is working with other traditional healers to share her findings and to increase the acceptability of propagated plants in traditional medicine.

 “When we talk about sustainability, we are talking about the ability to maintain our natural resources,” she says. Maintaining our natural resources requires us to be adaptive, she adds. We need to use technologies to find ways of growing traditional medical plants faster than usual –   without changing their medicinal properties. 

Something to chew on

Traditionally, medicinal plants in South Africa have been the guardians of spiritual and psychological wellbeing as well as physical health. Kanna (sceletium tortuosum) or kougoed (‘chew(able) things), for instance, has long been psychological aid among the San and Khoikhoi peoples. An unassuming ground-cover succulent, kanna occurs naturally in semi-arid regions of the Eastern and western Cape. In spring, it produces flowers with lemon-yellow centres and white petals so fine they could almost be eyelashes.  

Hunters and pastoralists in Namaqualand and the Karoo reportedly chewed fermented kanna during prolonged hunts to relieve stress and fatigue, and at other times for social relaxation. One of kanna’s active compounds is a mood-booster called mesmerine, which is unique to sceletium succulents. Like some antidepressants, mesmerine works by increasing the availability of the feel-good neurotransmitter serotonin in the brain. Kanna is also reported to improve concentration and cognitive function. In the upswelling of interest in the therapeutic potential of psychoactive drugs, kanna has come under a global spotlight for its mood-boosting effects, and can be purchased online in tea and supplement form.  A patented extract of Kanna, dubbed Zembrin®, has also reached the shelves.  

While the commercial potential of South Africa’s medicinal plants could in theory benefit local communities, in practice, commercial operations often don’t follow fair benefit-sharing practices. Despite the cultural and historical value of the plants, traditional knowledge holders are rarely compensated fairly for the knowledge that gave rise to the product. 

In South Africa, traditional health practitioners are also not recognised in the healthcare system. Many South Africans will consult both traditional healers and doctors, who operate in different domains and may provide contradictory advice.

Xego argues that bridging the gap between traditional practitioners and doctors, and combining knowledge, could have significant benefits for patients. Collaboration could enable traditional healers to refer patients to doctors for diagnoses, for instance, while doctors could refer patients to traditional healers when plant medicines would be beneficial. This kind of integration of Western medicine and traditional medicine is already taking place in other African countries, including Ghana, Botswana, Zimbabwe, Liberia, Sierra Leone.

 Closer collaborations between traditional healers, researchers, and conservationists may also yield effective strategies for conserving South Africa’s medicinal flora. The work of Xego and others to conserve South Africa’s medicinal plant heritage offers hope that the fragrance of wild ginger flowers will one day return to our forests, and that the resurrection plant will continue to shrug off death for centuries to come.

One shot, better defence against cervical cancer

Photo: cottonbro studio, Pexels

Women have a better shot at avoiding cervical cancer thanks to the single-dose human papillomavirus (HPV) vaccination, which has now been approved in South Africa.

The much-anticipated transition from the current two-vaccination strategy aligns with recent evidence-based World Health Organisation (WHO) recommendations.

Health experts who participated in a recent “Women Up To Know Good” webinar, titled “HPV at your cervix” emphasised the effectiveness and affordability of the single-dose strategy in low- and middle-income countries.

HPV vaccinations are the most effective available tool for preventing cervical cancer. Usually administered to girls under the age of 15, the vaccine triggers an immune response that later protects against strains of HPV – the virus responsible for the development of virtually all cervical cancer cases.

Comprehensive roll-out of the single-dose vaccine is one part of a multifaceted approach to eliminating cervical cancer in Africa. To eliminate cervical cancer globally, the WHO set the following goals for 2030:  90% of girls vaccinated by age 15; 70% of women screened for HPV (by a high-performance test) by age 35, and again at 45; and 90% of women with cervical cancer receiving treatment.

However, resource constraints have seen low- and middle-income countries moving slowly to reach these targets. The success of South Africa’s school-based programme, initiated in 2014, illustrates how targeted interventions can help low- and middle-income countries (LMICs) to reach vaccination targets.

Clearing cost hurdles

At the GIFT webinar, leading cervical cancer expert Professor Lynette Denny of the University of Cape Town, Dr Zizipho Mbulawa of the National Health Laboratory Services and Walter Sisulu University, and physician scientist Dr Ruanne Barnabas of Harvard University discussed ways of increasing the accessibility and uptake of vaccinations and cervical cancer screenings.

Barnabas shared findings from research she and her colleagues conducted in Kenya that provided the evidence for the WHO policy change recommending the one-dose vaccine. The study showed a 98% vaccine efficacy against HPV 16/18 – the strains that are most strongly linked to cervical cancer.

 “After three years, single-dose HPV vaccine efficacy remained high and durable,” Barnabas said, adding that the vaccine also provided protection against other HPV strains.

Journeying with turtles

The impact of South Africa’s marine protected areas

Following months of rehabilitation, a rescued baby loggerhead turtle surfaces in its tank at the Two Oceans Aquarium, just days away from its release into the wild, 19 January 2024.

The ocean glints metallic blue under the evening sky. Gulls huddle together as the December light fades, and ghost crabs run lightly over white sand. It’s a peaceful scene for a human. But for baby loggerhead turtles, the KwaZulu-Natal beach is perilous.

For days after hatching, they stayed hidden under the sand, waiting for their shells to harden. Now, they must make a break for the water. They clamber as fast as their flippers can carry them, but they’re easy pickings for gulls, crabs and mongooses.

 The few that make it into the surf must get as far out as quickly as possible. Weighing just 20g, the hatchlings drift with the current. “They’re being attacked by everything bigger than them – which is everything,” says Talitha Noble, a conservation manager at the Two Oceans Foundation. 

Those lucky enough to avoid predators drift for about 1600km down the coast with the warm Agulhas current towards Cape Town. Here, the turtles face a new danger: cold. While some manage to stick to the Agulhas and return to the safety of the warm Indian Ocean, others are ejected into the cool coastal waters of the Cape. In March 2023, one such hatchling, #60 – barnacle-adorned and large-eyed – washed up on De Hoop Beach, cold and in shock. 

“We don’t have nesting grounds in the Western Cape,” Noble explains. “What that means is that any turtles on the [Cape] beaches have arrived at the point where they’re going to die because they aren’t able to control their movements anymore.”  

That’s when Cape Town’s turtle rescue network springs into action. Each year, around a thousand volunteers rescue dozens from the beaches of Cape Town during ‘stranding season’: last year’s intake was 79, including little #60. By December 2023, just before her release, she is unrecognisable: barnacle-free, noticeably bigger and paddling energetically in a tank in the two oceans aquarium. Around her are dozens of other baby turtles, each in their own small tank, and each ready to take on the ocean once more. 

Protected nesting sites

Loggerhead turtles were once critically endangered in South Africa. But the establishment and later expansion of marine protected areas off the KwaZulu Natal coast has seen the population rebound. In the early 1960s, fewer than 250 loggerhead turtles nested annually in the iSimangaliso Wetland Park.

“From the starting point, our nesting turtles are given a good opportunity, a safe space that’s being monitored and protected and where poaching is much more under control than it is across the border into Mozambique,” Noble says.

But what about when the hatchlings leave the relative safety of the coastal waters for the deep sea? Equipped with an internal type of ‘GPS’ that allows them to sense the strength and inclination of the earth’s magnetic field, turtles migrate up to 10 000 km a year. But, because satellite tags have historically been too heavy for baby turtles to carry, where they go during the first decade of their lives – before returning to nest on the beaches of their birth – remains largely a mystery.

Source: Jack Journal, with data from https://www.marineprotectedareas.org.za/

South Africa’s marine protected areas

The waters off South Africa’s mainland are rich and diverse; the confluence of the warm Agulhas and cool Benguela current creates the conditions for abundant life. Undersea ecosystems are as varied as those on land: in the cold Cape waters, seals weave between golden kelp; in the north-east, vibrant fishes dance among coral reefs. For centuries, these marine ecosystems have supported human communities living along South Africa’s coastline. Now, they’re under threat from pollution, habitat destruction and unsustainable fishing systems. 

Marine protected areas are widely considered one of the most powerful ways to address these challenges and increase resilience to climate change. South Africa has 41 protected areas around its mainland. An expansion in 2019 increased the total area from 0.43% to 5.4% of these waters – better than many places on the planet. Resource extraction in MPAs is either restricted (no-take zones) or controlled (permissible only with permits). 

Led by Steven Kirkman of the Department of Forestries and Fisheries, a group of researchers reviewed the research on the ecological effectiveness of our MPAs. They found that the country’s MPAs now provide some protection to all ecoregions (large geographic areas with similar physical and ecological characteristics) and to 87% of ecosystem types (habitats such as coral reefs). Most of the reviewed studies reported benefits to marine life, such as greater abundance, size or reproductive success. .The few that assessed the impacts on adjacent fisheries recorded healthier fishing populations, underscoring the importance of MPAs to sustainable fishing.

However, the team found that conservation gaps remain in the West Coast, estuaries and the deep sea. Enforcement is lacking, and many MPAs could be improved through expansion or by increasing the size and number of ‘no-take’ zones. They also recommend more research to understand the ecological connectivity of protected areas. Despite room for improvement, “there’s always a sense of relief when [tagged turtles] enter an MPA,” Noble says. 

Community involvement 

Part of the success of iSimangaliso MPA and the turtle monitoring programme is active community involvement. This is not typical of conserved areas; an enduring criticism of South Africa’s MPAs is a lack of community consultation and buy-in. A recent analysis led by Two Oceans Aquarium Foundation’s Judy Mann-Lang found that MPAs declared in 2019, unlike older areas, include some social and economic objectives. These include conserving culturally significant areas, boosting nature-based tourism, and improving commercially important fish stocks.

However, the study found that knowledge of the social and economic effects of MPAs is still lacking. In addition to disadvantaging local communities and small-scale fishers, a failure to consider the needs of local communities alongside ecological goals ultimately undermines conservation efforts.  

Improved communication is another way of drawing attention to MPAs and inspiring people to take action for the ocean. Through its education and conservation efforts, the Two Oceans Aquarium Foundation helps to illuminate our vast undersea worlds, and the necessity of conserving them. 

In January 2024, Nobel and her team released the remaining 14 baby loggerheads. These youngsters are fitted with lightweight, solar-powered satellite tags: a first in South Africa. After having rehabilitated and released a thousand loggerhead turtles on faith, the researchers will now find out what becomes of some of the rescues. Since #60 and her peers washed up onto the shore, the ocean has not become any safer. But, with months of good nutrition under their carapaces, they have a chance at survival. And, unbeknown them, a great many humans are rooting for them.

Weighing only 9g, the solar-powered tags are attached to the turtles’ shells with silicone, which can expand as the turtles grow. According to Talitha Noble of the Two Oceans Aquarium Foundation, they’re expected to last between 6 and 9 months and do not hinder the animals’ movements.