Arabidopsis plant architecture. (A) Representative image of a whole plant. (B) Upon transition from the vegetative phase to the reproductive phase, the shoot apical meristem (SAM), which produces a leaf at its flank, becomes an inflorescence meristem and produces a flower at its flank. The organizing center (OC) and the central zone (CZ) within in the SAM constitute the stem cell niche (SCN). (C) Inset depicts an immature heart-shaped embryo within the silique (fruit). (D) Inset displays the cross section of the inflorescence stem showing different tissues. (E) Inset shows the leaf with mid vein, lateral vein and petiole. (F) Inset depicts lateral root emergence. (G) Inset depicts the root tip showing different tissues. The QC and its surrounding cells form the SCN within the RAM. Abbreviations: CZ, central zone; OC, organizing center; PZ, peripheral zone; RZ, rib zone; LP, leaf primordia; FM, floral meristem; FP, floral primordia.

Tissue culture-induced regeneration. (A) Summary of the sequential events that occur during tissue culture-mediated root (top) and shoot (bottom) regeneration. Explants of different developmental origins first form a pluripotent callus. They then undergo self-organization and, if cultured in the presence of shoot inductive cues, form shoot progenitor cells, ultimately culminating in the formation of a shoot (bottom). Note that not all shoot progenitors convert into shoots. If explants are cultured in root inductive cues, root formation occurs (top) (B) The graph depicts the relative abundance of root stem cell regulators and shoot fate determinants (y-axis) against the days (x- axis) explants were incubated on callus induction medium (CIM) or shoot induction medium (SIM). Root stem cell regulators (blue) are transiently upregulated throughout the callus while it is incubated on CIM, ensuring its acquisition of pluripotency, and are downregulated following transfer of the callus onto SIM. In response to shoot inductive cues, shoot fate determinants (red) get activated in the pluripotent callus, and their expression peaks by the time the callus undergoes shoot progenitor regeneration and self-assembly (denoted by broad red dots) leading to the formation of an entire shoot de novo. (C) Regulatory module indicating the sequential events during regeneration of shoot system de novo.

⇒ https://journals. dev/article/148 /6/dev195347/ 237860/Model -systems-for- regeneration- Arabidopsis

de novo shoot regeneration in response to external inductive cues i.e., by modulating the ratio of two major plant hormones auxin/cytokinin has been used for decades in plant tissue culture for the large-scale vegetative propagation of plants. However, the molecular mechanism underlying the cellular reprogramming events leading to the de novo formation of fertile plants remained elusive. One of the challenges in studying regeneration in plants and animals is the difficulty in uncoupling the intermediate developmental phases during the course of regeneration. Our study elucidated a two-step mechanism driving de novo shoot regeneration in Arabidopsis. Using plt3,plt5-2,plt7 triple mutant and a series of careful genetic reconstitutions with key cell fate determinants, the study dissected the intermediate steps of shoot regeneration. Kareem et al., revealed that in the first step of the mechanism, PLETHORA genes namely, PLT3, PLT5 and PLT7 activate root stem cell regulators PLT1 and PLT2 to generate a pluripotent callus mass. The timely expression of root specific factors specifically during the callus induction phase makes the callus competent to produce shoot progenitors later in response to shoot inductive cues. However, the second step of shoot outgrowth can only be accomplished when PLT genes upregulate the shoot promoting factor, CUC2. Thus, using a combination of genetics and dynamic live imaging, the study uncouples the acquisition of competence to regenerate shoot progenitor cells from completion of shoot formation, indicating a two-step mechanism of de novo shoot regeneration that operates in all explants irrespective of their developmental origin.

⇒ https://www.cell .com/current- biology/ references/ S0960-9822 (15)00161-X
⇒ https://www. /science/ article/pii /S136952661730095X

Mechanical injury-induced regeneration at root tip. (A) The concentration of PLETHORA 2 (PLT2), a TF that is expressed as a gradient along the root meristem, instructs the boundary for root tip restoration. The root tip is restored when excision is within the region of meristem expressing high levels of PLT2 (top) but restoration fails when the tip is excised in a region expressing low PLT2 levels (bottom). (B) A schematic depicting the importance of the PLT2-autoregulatory loop in regeneration and how it distinguishes growth of the root meristem from its regeneration potential.

⇒ https://journals dev/article/148/ 6/dev195347 /237860/Model -systems-for -regeneration -Arabidopsis

All organisms display varying levels of regenerative responses ranging from healing in the form of local cell proliferation to complete restoration of the lost organ. Although healing can be ubiquitious, the organ restoration ability is not uniformly distributed along the organ axis. The mechanism dictating the variation in regenerative ability along the organ axis remained unresolved for years. Here, Durgaprasad et al, unravels the mechanistic basis of organ restoration using excision of Arabidopsis root tip as a model. By tracking the PLT2 expression real time in its inducible knock down and inducible mis expression in the background of multiple mutant combinations, the study demonstrated that dosage of a gradient expressed Transcription Factor PLT2, instructs the boundary for organ restoration potential. The study uncovered the correlation between root tip restoration ability with high PLT2 levels where, transient downregulation of PLT2 ceased root tip restoration in otherwise restoration competent zone, while forced expression of PLT2 triggered endogenous PLT2 transcription and conferred root tip restoration in otherwise restoration non competence zone and even from the differentiating cells. Surprisingly, sustained expression of PLT2 beyond a threshold abolished root tip restoration from competence zone, but lead to a longer meristem in growing root. The threshold sensitive PLT2 autoregulatory loop therefore distinguishes the regeneration potential of an organ from its growth during normal development.

⇒ https://www. /science/article /pii/S22111 24719311611
⇒ https://www. science/article /pii/S1369526 619301220

Mechanical injury-induced regeneration. (A) Incision of the inflorescence stem (top inset) disrupts vascular tissue continuity and induces cell proliferation to seal the gap between the disconnected tissues. Subsequently, vascular continuity is re-instated by the vascular stands regenerating around the wounded area. By contrast, surface abrasion of the inflorescence stem (bottom inset) induces only local cell proliferation to heal the injury. (B) Excision of the distal end of a growing leaf (left inset) does not initiate regeneration to replace the lost part. By contrast, incision of the leaf mid vein (right inset) disrupts vascular continuity. The regenerating vasculature circumvents the wounded area to re-establish vascular continuity in the growing leaf. (C) Schematic depicting the PLT-CUC2 regulatory module involved in vascular regeneration in aerial organs.

⇒ https://journals dev/article/148/ 6/dev195347/2 37860/Model- systems-for- regeneration -Arabidopsis

Aerial organs of plants are highly susceptible to injuries caused by environmental factors. Due to their remarkable developmental plasticity plants are capable of regenerating and repairing lost and damaged organs. Until recently the mechanism mediating the regeneration responses in aerial organs remained poorly understood. In this study, Radhakrishnan et al., mimicked naturally occurring mechanical damages in growing aerial organs such as leaves and stem of Arabidopsis plants to dissect the regulatory module driving vascular regeneration and tissue repair. In the process we have established a new system to study the recognition, communication and re-union of two physically separated tissues in leaf. Using a combination of mutants, transient pulse of overexpression lines of key cell fate determinants as well as by tracking the expression of early vascular identity marker ATHB8 and polar auxin transporter PIN1 in real time, we revealed the unprecedented role of PLETHORA (PLT) genes in vascular regeneration and wound repair. Additionally, we showed that AINTEGUMENTA (ANT) transcription factor also contributes to vascular regeneration in injured leaves. We reveal that upon damage, PLT protein binds to the CUC2 promoter and directly activate its transcription. PLT and CUC2 act in a coherent feed forward loop to upregulate local auxin biosynthesis thereby guiding the regenerating vascular stand to its destination. The study elucidates that PLT- CUC2 axis is required for proper cell polarisation and fate determination during vascular regeneration. We show that the PLT-CUC2 regulatory axis is required for vascular tissue regeneration but is dispensable for its formation during normal development, thereby distinguishing the ability of the tissue to regenerate from its normal growth during development.

⇒ https://dev. /content/147 /6/dev185710
⇒ https://www. /science/article /pii/S13695 26619301220

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Recent Publications

● Shanmukhan AP, Mathew MM, Aiyaz M, Varaparambathu V, Kareem A, Radhakrishnan D, Prasad K*, (2021) Regulation of touch-stimulated de novo root regeneration from Arabidopsis leaves, Plant Physiology, 187 (1), 52-58. (Selected as Plant Physiology Article of the Week by American Society of Plant Biologists (ASPB))

● Radhakrishnan D, Shanmukhan AP, Kareem A, Aiyaz M, Varapparambathu V, Toms A, Kerstens M, Valsakumar D, Landge AN, Shaji A, Mathew MK, Sawchuk MG, Scarpella E, Krizek BA, Efroni I, Mähönen AP, Willemsen V, Scheres B, Prasad K*. (2020) A coherent feed-forward loop drives vascular regeneration in damaged aerial organs of plants growing in a normal developmental context. Development. 147(6):dev185710. doi:10.1242/dev.185710 (Selected for highlights of the issue and Featured on Cover)

● Shanmukhan AP, Mathew MM, Radhakrishnan D, Aiyaz M, Prasad K*. (2020) Regrowing the damaged or lost body parts. Current Opinion in Plant Biology. 53:117‐127. doi:10.1016/j.pbi.2019.12.007

● Durgaprasad K, Roy MV, Venugopal MA, Kareem A, Raj K, Willemsen V, Mähönen AP, Scheres B, Prasad K*. Gradient Expression of Transcription Factor Imposes a Boundary on Organ Regeneration Potential in Plants.
Cell Reports. 2019;29(2):453‐463.e3. doi:10.1016/j.celrep.2019.08.099 (Recommended by F1000 and Featured on Cover)

● Radhakrishnan D, Kareem A, Durgaprasad K, Sreeraj E, Sugimoto K, Prasad K*. (2018) Shoot regeneration: a journey from acquisition of competence to completion. Current Opinion Plant Biology. 41:23‐31. doi:10.1016/j.pbi.2017.08.001

● Kareem A, Durgaprasad K, Sugimoto K, Du Y, Pulianmackal AJ, Trivedi ZB, Abhayadev PV, Pinon V, Meyerowitz EM, Scheres B, Prasad K*. (2015) PLETHORA Genes Control Regeneration by a Two-Step Mechanism. Current Biology. 25(8):1017‐1030. doi:10.1016/j.cub.2015.02.022 (Featured on Cover)

● Santuari L, Sanchez-Perez GF, Luijten M, Rutjens B, Terpstra I, Berke L, Gorte M, Prasad K, Bao D, Timmermans-Hereijgers JLPM, Maeo K, Nakamura K, Shimotohno A, Pencik A, Novak O, Ljung K, Heesch SV, de Bruijn E, Cuppen E, Willemsen V, Mähönen AP, Lukowitz W, Snel B, de Ridder D, Scheres B, Heidstra R (2016) The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots. Plant Cell. 28(12):2937‐2951. doi:10.1105/tpc.16.00656 (Featured on Cover)

● Mähönen AP, Ten Tusscher K, Siligato R, Smetana O, Díaz-Triviño S, Salojärvi J, Wachsman G, Prasad K, Heidstra R, Scheres B. (2014) PLETHORA gradient formation mechanism separates auxin responses. Nature. 515(7525):125‐129. doi:10.1038/nature13663


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