The African continent has considerable potential to reap the benefits associated with modern agricultural biotechnology. Plant biotechnology and breeding represent an invaluable toolbox to face the challenges of African agriculture, such as food and nutrition security, environment protection, soil fertility, and crop adaptation to new climatic conditions. As Africa has only relatively recently adopted agricultural biotechnology, it has the opportunity to harness the immense knowledge gathered over the last two decades while avoiding some of the difficulties experienced by early adopters. High-level research and education systems together with a specific regulatory framework are critical elements in the development of sustainable biotechnology-based agriculture and industry. The more actors that are involved in Research & Development applied to nutritionally and important local crops, the faster Africa will generate its future African innovators. Here, we discuss the contribution of plant biotechnology to a transformative African agriculture that combines intensification of land productivity and environmental sustainability. KEY WORDS: PLANT BIOTECHNOLOGY, AFRICA, YIELD POTENTIAL, NUTRITION SECURITY, ENVIRONMENTAL MITIGATION

Genetically modified (GM) crops are cultivated globally on more than 185 million hectares, but the use of GM crops in Europe and Africa is very limited. Politicians are reluctant to allow such crops because they fear negative public reaction. The political hostility in the EU towards GM crops also has a significant impact on how African policy makers form their opinions for accepting GM crops in their own countries. However, studies reveal that specific types of GM food are welcomed by consumers and that few Europeans avoid GM labels when buying food. Similarly, African farmers and consumers are generally positive about GM crops. Policy makers should take these results into account when a decision needs to be made on whether or not to allow GM crop cultivation in their country.

MAIN CONCLUSION:Although grass pea is an environmentally successful robust legume with major traits of interest for food and nutrition security, the genetic potential of this orphan crop has long been neglected. Grass pea (Lathyrus sativus L.) is a Neolithic plant that has survived millennia of cultivation and has spread over three continents. It is a robust legume crop that is considered one of the most resilient to climate changes and to be survival food during drought-triggered famines. The hardy penetrating root system allows the cultivation of grass pea in various soil types, including marginal ones. As an efficient nitrogen fixer, it meets its own nitrogen requirements and positively benefits subsequent crops. However, already in ancient India and Greece, overconsumption of the seeds and a crippling neurological disorder, later coined neurolathyrism, had been linked. Overemphasis of their suspected toxic properties has led to disregard the plant's exceptionally positive agronomic properties and dietary advantages. In normal socio-economic and environmental situations, in which grass pea is part of a balanced diet, neurolathyrism is virtually non-existent. The etiology of neurolathyrism has been oversimplified and the deficiency in methionine in the diet has been overlooked. In view of the global climate change, this very adaptable and nutritious orphan crop deserves more attention. Grass pea can become a wonder crop if the double stigma on its reputation as a toxic plant and as food of the poor can be disregarded. Additionally, recent research has exposed the potential of grass pea as a health-promoting nutraceutical. Development of varieties with an improved balance in essential amino acids and diet may be relevant to enhance the nutritional value without jeopardizing the multiple stress tolerance of this promising crop.

More than 20 years ago, the first genetically modified (GM) plants entered the seed market. The patents covering the first GM plants have begun to expire and these can now be considered as Off-Patent Events. Here we describe the challenges that will be faced by a Secondary Party by further use and development of these Off-Patent Events. Indeed, the conditions for Off-Patent Events are not available yet to form the basis for a new viable industry similar to the generic manufacturers of agrochemicals or pharmaceutical products, primarily because of (i) unharmonized global regulatory requirements for GM organisms, (ii) inaccessibility of regulatory submissions and data, and (iii) potential difficulties to obtain seeds and genetic material of the unique genotypes used to generate regulatory data. We propose certain adaptations by comparing what has been done in the agrochemical and pharmaceutical markets to facilitate the development of generics. Finally, we present opportunities that still exist for further development of Off-Patent Events in collaboration with Proprietary Regulatory Property Holders in emerging markets, provided (i) various countries approve these events without additional regulatory burdens (i.e., acceptance of the concept of data transportability), and (ii) local breeders agree to meet product stewardship requirements.

To transform developing and least developing countries into industrialised ones, biotechnology could be deployed along the value chain, to provide support to the development of the bio-based industries in such a way to ensure sustainability of the sector and to reduce negative environmental impacts that might otherwise occur. In agribusiness development, for instance, interventions could start from inputs and agricultural mechanization, modern processing technologies, packaging of perishable products, the promotion of food safety in the processing and regulatory environment; and interventions to improve competitiveness and productivity. Worth over USD 300 billion in revenue, the role of the biotechnology goes beyond industrial growth, since it provides opportunities for progress towards many of the UN sustainable development goals (SDGs). This paper reviews the status of industrial biotechnology as it relates to inclusive and sustainable industrial development.

Ultraviolet-B radiation (UV-B) is an intrinsic part of sunlight that is accompanied by significant biological effects. Plants are able to perceive UV-B using the UV-B photoreceptor UVR8 which is linked to a specific molecular signaling pathway and leads to UV-B acclimation. Herein we review the biological process in plants from initial UV-B perception and signal transduction through to the known UV-B responses that promote survival in sunlight. The UVR8 UV-B photoreceptor exists as a homodimer that instantly monomerises upon UV-B absorption via specific intrinsic tryptophans which act as UV-B chromophores. The UVR8 monomer interacts with COP1, an E3 ubiquitin ligase, initiating a molecular signaling pathway that leads to gene expression changes. This signaling output leads to UVR8-dependent responses including UV-B-induced photomorphogenesis and the accumulation of UV-B-absorbing flavonols. Negative feedback regulation of the pathway is provided by the WD40-repeat proteins RUP1 and RUP2, which facilitate UVR8 redimerization, disrupting the UVR8-COP1 interaction. Despite rapid advancements in the field of recent years, [...] TILBROOK, Kimberley, et al. The UVR8 UV-B Photoreceptor: Perception, Signaling and Response. Arabidopsis Book, 2013, vol. 11, p. e0164 DOI : 10.1199/tab.0164

Plants require the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) for acclimation and survival in sunlight. Upon UV-B perception, UVR8 switches instantaneously from a homodimeric to monomeric configuration, which leads to interaction with the key signaling protein CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and induction of UV-B-protective responses. Here, we show that UVR8 monomerization is reversible in vivo, restoring the homodimeric ground state. We also demonstrate that the UVR8-interacting proteins REPRESSOR OF UV-B PHOTOMORPHOGENESIS (RUP) 1 and RUP2 mediate UVR8 redimerization independently of COP1. UVR8 redimerization consequently disrupts the UVR8-COP1 interaction, which halts signaling. Our results identify a key role of RUP1- and RUP2-mediated UVR8 redimerization in photoreceptor inactivation, a crucial process that regenerates reactivatable UVR8 homodimers.

Arabidopsis thaliana UV RESISTANCE LOCUS 8 (UVR8) is a UV-B photoreceptor that initiates photomorphogenic responses underlying acclimation and UV-B tolerance in plants. UVR8 is a homodimer in its ground state, and UV-B exposure results in its instantaneous monomerization followed by interaction with CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1), a major factor in UV-B signaling. UV-B photoreception by UVR8 is based on intrinsic tryptophan aromatic amino acid residues, with tryptophan-285 as the main chromophore. We generated transgenic plants expressing UVR8 with a single amino acid change of tryptophan-285 to alanine. UVR8(W285A) appears monomeric and shows UV-B-independent interaction with COP1. Phenotypically, the plants expressing UVR8(W285A) exhibit constitutive photomorphogenesis associated with constitutive activation of target genes, elevated levels of anthocyanins, and enhanced, acclimation-independent UV-B tolerance. Moreover, we have identified COP1, REPRESSOR OF UV-B PHOTOMORPHOGENESIS 1 and 2 (RUP1 and RUP2), and the SUPPRESSOR OF PHYA-105 (SPA) family as proteins copurifying with UVR8(W285A). Whereas COP1, RUP1, and RUP2 are known to directly interact with UVR8, we show that SPA1 interacts with UVR8 indirectly through COP1. We conclude that UVR8(W285A) is a constitutively active UVR8 photoreceptor variant in Arabidopsis, as is consistent with the crucial importance of monomer formation and COP1 binding for UVR8 activity.

Ultraviolet-B radiation (UV-B) is an intrinsic part of sunlight that is accompanied by significant biological effects. Plants are able to perceive UV-B using the UV-B photoreceptor UVR8 which is linked to a specific molecular signaling pathway and leads to UV-B acclimation. Herein we review the biological process in plants from initial UV-B perception and signal transduction through to the known UV-B responses that promote survival in sunlight. The UVR8 UV-B photoreceptor exists as a homodimer that instantly monomerises upon UV-B absorption via specific intrinsic tryptophans which act as UV-B chromophores. The UVR8 monomer interacts with COP1, an E3 ubiquitin ligase, initiating a molecular signaling pathway that leads to gene expression changes. This signaling output leads to UVR8-dependent responses including UV-B-induced photomorphogenesis and the accumulation of UV-B-absorbing flavonols. Negative feedback regulation of the pathway is provided by the WD40-repeat proteins RUP1 and RUP2, which facilitate UVR8 redimerization, disrupting the UVR8-COP1 interaction. Despite rapid advancements in the field of recent years, further components of UVR8 UV-B signaling are constantly emerging, and the precise interplay of these and the established players UVR8, COP1, RUP1, RUP2 and HY5 needs to be defined. UVR8 UV-B signaling represents our further understanding of how plants are able to sense their light environment and adjust their growth accordingly.

Ultraviolet-B radiation (UV-B) is a key environmental signal that is specifically perceived by plants to promote UV acclimation and survival in sunlight. Whereas the plant photoreceptors for visible light are rather well characterised, the UV-B photoreceptor UVR8 was only recently described at the molecular level. Here, we review the current understanding of the UVR8 photoreceptor-mediated pathway in the context of UV-B perception mechanism, early signalling components and physiological responses. We further outline the commonalities in UV-B and visible light signalling as well as highlight differences between these pathways.

Cryptochromes and photolyases are homologous flavoproteins either involved in photosensory functions or in the photorepair of UV-damaged DNA. We report on the presence, nature and ultrafast photoinduced dynamics of a photoantenna in two recently discovered cryptochrome/photolyase proteins (OtCPF1, a (6-4) photolyase, and OtCPF2, a cryptochrome-DASH), coming from the green alga Ostreococcus tauri . Whereas OtCPF1 does not show any apparent photoantenna after purification, OtCPF2 is found to bind the folate MTHF. Resonance energy transfer, from MTHF to the flavin cofactor (FAD) of OtCPF2, was studied by femtosecond transient absorption spectroscopy. It takes place in 15 ps when FAD is oxidized and 100 ps when it is fully reduced. The intrinsic photophysics of MTHF in acidic solution was studied for comparison. Two decays in the sub-100 ps regime were tentatively attributed to the presence of two conformers or to a quenching mechanism involving large-amplitude motions of the 1,2,3,4-tetrahydropyraxine ring. On the other hand, the nature of the missing photoantenna of OtCFP1 was questioned by means of sequence alignment and homology modeling. We propose that the deazaflavin 8-HDF could be the photoantenna of OtCFP1 in vivo .

Phytochrome A (phyA) is the dominant photoreceptor of far-red light sensing in Arabidopsis thaliana. phyA accumulates at high levels in the cytoplasm of etiolated seedlings, and light-induced phyA signaling is mediated by a complex regulatory network. This includes light- and FHY1/FHL protein-dependent translocation of native phyA into the nucleus in vivo. It has also been shown that a short N-terminal fragment of phyA (PHYA406) is sufficient to phenocopy this highly regulated cellular process in vitro. To test the biological activity of this N-terminal fragment of phyA in planta, we produced transgenic phyA-201 plants expressing the PHYA406-YFP (YELLOW FLUORESCENT PROTEIN)-DD, PHYA406-YFP-DD-NLS (nuclear localization signal), and PHYA406-YFP-DD-NES (nuclear export signal) fusion proteins. Here, we report that PHYA406-YFP-DD is imported into the nucleus and this process is partially light-dependent whereas PHYA406-YFP-DD-NLS and PHYA406-YFP-DD-NES display the expected constitutive localization patterns. Our results show that these truncated phyA proteins are light-stable, they trigger a constitutive photomorphogenic-like response when localized in the nuclei, and neither of them induces proper phyA signaling. We demonstrate that in vitro and in vivo PHYA406 Pfr and Pr bind COP1, a general repressor of photomorphogenesis, and co-localize with it in nuclear bodies. Thus, we conclude that, in planta, the truncated PHYA406 proteins inactivate COM in the nuclei in a light-independent fashion.

Author(s): Bowler, Chris; Allen, Andrew E.; Badger, Jonathan H.; Grimwood, Jane; Jabbari, Kamel; Kuo, Alan; Maheswari, Uma; Martens, Cindy; Maumus, Florian; Otillar, Robert P.; Rayko, Edda; Salamov, Asaf; Vandepoele, Klaas; Beszteri, Bank; Gruber, Ansgar; Heijde, Marc; Katinka, Michael; Mock, Thomas; Valentin, Klaus; Verret, Frederic; Berges, John A.; Brownlee, Colin; Cadoret, Jean-Paul; Chiovitti, Anthony; Choi, Chang Jae; Coesel, Sacha; Martino, Alessandra De; Detter, J. Chris; Durkin, Colleen; Falciatore, Angela; Fournet, Jerome; Haruta, Miyoshi; Huysman, Marie; Jenkins, Bethany D.; Jiroutova, Katerina; Jorgensen, Richard E.; Joubert, Yolaine; Kaplan, Aaron; Kroeger, Nils; Kroth, Peter; Roche, Julie La; Lindquist, Erica; Lommer, Markus; Martin-Jezequel, Veronique; Lopez, Pascal J.; Lucas, Susan; Mangogna, Manuela; McGinnis, Karen; Medlin, Linda K.; Montsant, Anton; Secq, Marie-Pierre Oudot-Le; Napoli, Carolyn; Obornik, Miroslav; Petit, Jean-Louis; Porcel, Betina M.; Poulsen, Nicole; Robison, Matthew; Rychlewski, Leszek; Rynearson, Tatiana A.; Schmutz, Jeremy; Parker, Micaela Schnitzler; Shapiro, Harris; Siaut, Magali; Stanley, Michele; Sussman, Michael J.; Taylor, Alison; Vardi, Assaf; Dassow, Peter von; Vyverman, Wim; Willis, Anusuya; Wyrwicz, Lucjan S.; Rokhsar, Daniel S.; Weissenbach, Jean; Armbrust, E. Virginia; Green, Beverley R.; Peer, Yves Van de; Grigoriev, Igor V. | Abstract: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (40percent) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.

Background: Despite the enormous importance of diatoms in aquatic ecosystems and their broad industrial potential, little is known about their life cycle control. Diatoms typically inhabit rapidly changing and unstable environments, suggesting that cell cycle regulation in diatoms must have evolved to adequately integrate various environmental signals. The recent genome sequencing of Thalassiosira pseudonana and Phaeodactylum tricornutum allows us to explore the molecular conservation of cell cycle regulation in diatoms.Results: By profile-based annotation of cell cycle genes, counterparts of conserved as well as new regulators were identified in T. pseudonana and P. tricornutum. In particular, the cyclin gene family was found to be expanded extensively compared to that of other eukaryotes and a novel type of cyclins was discovered, the diatom-specific cyclins. We established a synchronization method for P. tricornutum that enabled assignment of the different annotated genes to specific cell cycle phase transitions. The diatom-specific cyclins are predominantly expressed at the G1-to-S transition and some respond to phosphate availability, hinting at a role in connecting cell division to environmental stimuli.Conclusion: The discovery of highly conserved and new cell cycle regulators suggests the evolution of unique control mechanisms for diatom cell division, probably contributing to their ability to adapt and survive under highly fluctuating environmental conditions.

Plants respond to low levels of UV-B radiation with a coordinated photomorphogenic response that allows acclimation to this environmental stress factor. The key players in this UV-B response are COP1 (an E3 ubiquitin ligase), UVR8 (a β-propeller protein), and HY5 (a bZIP transcription factor). We have shown previously that an elevated UV-B–specific response is associated with dwarf growth, indicating the importance of balancing UV-B–specific signaling. Negative regulators of this pathway are not known, however. Here, we describe two highly related WD40-repeat proteins, REPRESSOR OF UV-B PHOTOMORPHOGENESIS 1 (RUP1) and RUP2, that interact directly with UVR8 as potent repressors of UV-B signaling. Both genes were transcriptionally activated by UV-B in a COP1-, UVR8-, and HY5-dependent manner. rup1 rup2 double mutants showed an enhanced response to UV-B and elevated UV-B tolerance after acclimation. Overexpression of RUP2 resulted in reduced UV-B–induced photomorphogenesis and impaired acclimation, leading to hypersensitivity to UV-B stress. These results are consistent with an important regulatory role for RUP1 and RUP2, which act downstream of UVR8–COP1 in a negative feedback loop impinging on UVR8 function, balancing UV-B defense measures and plant growth.

The photoactivation dynamics of two new flavoproteins (OtCPF1 and OtCPF2) of the cryptochrome photolyase family (CPF), belonging to the green alga Ostreococcus tauri , was studied by broadband UV-vis femtosecond absorption spectroscopy. Upon excitation of the protein chromophoric cofactor, flavin adenine dinucleotide in its oxidized form (FAD(ox)), we observed in both cases the ultrafast photoreduction of FAD(ox): in 390 fs for OtCPF1 and 590 fs for OtCPF2. Although such ultrafast electron transfer has already been reported for other flavoproteins and CPF members, the present result is the first demonstration with full spectral characterization of the mechanism. Analysis of the photoproduct spectra allowed identifying tryptophan as the primary electron donor. This residue is found to be oxidized to its protonated radical cation form (WH(*+)), while FAD(ox) is reduced to FAD(*-). Subsequent kinetics were observed in the picosecond and subnanosecond regime, mostly described by a biexponential partial decay of the photoproduct transient signal (9 and 81 ps for OtCPF1, and 13 and 340 ps for OtCPF2), with reduced spectral changes, while a long-lived photoproduct remains in the nanosecond time scale. We interpret these observations within the model proposed by the groups of Brettel and Vos, which describes the photoreduction of FADH(*) within E. coli CPD photolyase (EcCPD) as a sequential electron transfer along a chain of three tryptophan residues, although in that case the rate limiting step was the primary photoreduction in 30 ps. In the present study, excitation of FAD(ox) permitted to reveal the following steps and spectroscopically assign them to the hole-hopping process along the tryptophan chain, accompanied by partial charge recombination at each step. In addition, structural analysis performed by homology modeling allowed us to propose a tentative structure of the relative orientations of FAD and the conserved tryptophan triad. The results of preliminary transient anisotropy measurements performed on OtCPF2 finally showed good compatibility with the oxidation of the distal tryptophan residue (WH(351)) in 340 ps, hence, with the overall Brettel-Vos mechanism.

Background: Despite the enormous importance of diatoms in aquatic ecosystems and their broad industrial potential, little is known about their life cycle control. Diatoms typically inhabit rapidly changing and unstable environments, suggesting that cell cycle regulation in diatoms must have evolved to adequately integrate various environmental signals. The recent genome sequencing of Thalassiosira pseudonana and Phaeodactylum tricornutum allows us to explore the molecular conservation of cell cycle regulation in diatoms. Results: By profile-based annotation of cell cycle genes, counterparts of conserved as well as new regulators were identified in T. pseudonana and P. tricornutum. In particular, the cyclin gene family was found to be expanded extensively compared to that of other eukaryotes and a novel type of cyclins was discovered, the diatom-specific cyclins. We established a synchronization method for P. tricornutum that enabled assignment of the different annotated genes to specific cell cycle phase transitions. The diatom-specific cyclins are predominantly expressed at the G1-to-S transition and some respond to phosphate availability, hinting at a role in connecting cell division to environmental stimuli. Conclusion: The discovery of highly conserved and new cell cycle regulators suggests the evolution of unique control mechanisms for diatom cell division, probably contributing to their ability to adapt and survive under highly fluctuating environmental conditions.

Cryptochromes (Crys) are blue light receptors believed to have evolved from the DNA photolyase protein family, implying that light control and light protection share a common ancient origin. In this paper, we report the identification of five genes of the Cry/photolyase family (CPF) in two green algae of the Ostreococcus genus. Phylogenetic analyses were used to confidently assign three of these sequences to cyclobutane pyrimidine dimer (CPD) photolyases, one of them to a DASH-type Cry, and a third CPF gene has high homology with the recently described diatom CPF1 that displays a bifunctional activity. Both purified OtCPF1 and OtCPF2 proteins show non-covalent binding to flavin adenine dinucleotide (FAD), and additionally to 5,10-methenyl-tetrahydrofolate (MTHF) for OtCPF2. Expression analyses revealed that all five CPF members of Ostreococcus tauri are regulated by light. Furthermore, we show that OtCPF1 and OtCPF2 display photolyase activity and that OtCPF1 is able to interact with the CLOCK:BMAL heterodimer, transcription factors regulating circadian clock function in other organisms. Finally, we provide evidence for the involvement of OtCPF1 in the maintenance of the Ostreococcus circadian clock. This work improves our understanding of the evolutionary transition between photolyases and Crys.

Background: Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes.Results: We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity.Conclusions: The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.