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Xerobranching, a temporary suppression of root branching when water is limiting, is controlled by the plant hormone abscisic acid (ABA). A recently published study reveals how root branching is dynamically controlled by redistribution in opposite directions of ABA and auxin., Competing Interests: Declaration of interests P.N.B. is the co-founder and Chair of the Scientific Advisory Board of Hi Fidelity Genetics, Inc., a company that works on crop root growth., (Copyright © 2022 Elsevier Inc. All rights reserved.)

The development of lateral roots requires multiple mechanisms that act together for accurate spatiotemporal emergence of the new organ. A new paper shows how cell death in overlying endodermis cells contributes to the formation of new lateral root primordia., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Plant developmental plasticity relies on the activities of meristems, regions where stem cells continuously produce new cells [1]. The lateral root cap (LRC) is the outermost tissue of the root meristem [1], and it is known to play an important role during root development [2-6]. In particular, it has been shown that mechanical or genetic ablation of LRC cells affect meristem size [7, 8]; however, the molecular mechanisms involved are unknown. Root meristem size and, consequently, root growth depend on the position of the transition zone (TZ), a boundary that separates dividing from differentiating cells [9, 10]. The interaction of two phytohormones, cytokinin and auxin, is fundamental in controlling the position of the TZ [9, 10]. Cytokinin via the ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) control auxin distribution within the meristem, generating an instructive auxin minimum that positions the TZ [10]. We identify a cytokinin-dependent molecular mechanism that acts in the LRC to control the position of the TZ and meristem size. We show that auxin levels within the LRC cells depends on PIN-FORMED 5 (PIN5), a cytokinin-activated intracellular transporter that pumps auxin from the cytoplasm into the endoplasmic reticulum, and on irreversible auxin conjugation mediated by the IAA-amino synthase GRETCHEN HAGEN 3.17 (GH3.17). By titrating auxin in the LRC, the PIN5 and the GH3.17 genes control auxin levels in the entire root meristem. Overall, our results indicate that the LRC serves as an auxin sink that, under the control of cytokinin, regulates meristem size and root growth., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Signaling centers within developing organs regulate morphogenesis in both plants and animals. The putative transcription factor SHORT-ROOT (SHR) is an organizing signal regulating the division of specific stem cells in the Arabidopsis root. Comparison of gene transcription with protein localization indicates that SHR moves in a highly specific manner from the cells of the stele in which it is synthesized outward. Here, we provide evidence that SHR intercellular trafficking is both regulated and targeted. First, we show that subcellular localization of SHR in the stele is intrinsic to the SHR protein. Next, we show that SHR must be present in the cytoplasm to move, providing evidence that SHR movement is regulated. Finally, we describe an informative new shr allele, in which the protein is present in the cytoplasm yet does not move. Thus, in contrast to proteins that move by a process resembling diffusion, a cytoplasmic pool of SHR is not sufficient for movement.

The function of unknown genes is often inferred from comparisons to well-characterized homologs. In this paper, we show that, even if all of the homologs of a gene are unannotated, its function may be deduced through phylogenetic profiling. We have designed a series of algorithms that make functional predictions of genes based on orthology and set theory, but our approach to predicting gene function requires no previous knowledge of homolog function. With this technique, we successfully identified 94% of the clusters of orthologous groups that are known to be involved in flagella development or function. As a test, we removed the function of three putative flagellar genes that had been previously uncharacterized in Bacillus subtilis. We observed a motility phenotype for two of these three genes. Thus, these algorithms allow for high-throughput functional prediction of genes beyond that provided by simple orthology-based annotation endeavors.

How does auxin affect so many different aspects of plant growth and development? Recent evidence from localization of auxin efflux carriers and the effects of auxin on degradation of transcription factors has begun to reveal a possible mechanism for auxin action.

Homologous genes have recently been shown to regulate stem cell maintenance in animals and plants. This discovery should facilitate elucidation of the poorly understood factors that control stem cell maintenance and differentiation.