Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth

Axillary bud outgrowth determines shoot architecture and is under the control of endogenous hormones and a fine-tuned gene-expression network, which probably includes small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets within axillary buds are largely unknown. Here, we employed sRNA next-generation sequencing as well as computational and gene-expression analysis to identify and quantify sRNAs and their targets in vegetative axillary buds of the biofuel crop sugarcane (Saccharum spp.). Computational analysis allowed the identification of 26 conserved miRNA families and two putative novel miRNAs, as well as a number of trans-acting small interfering RNAs. sRNAs associated with transposable elements and protein-encoding genes were similarly represented in both inactive and developing bud libraries. Conversely, sequencing and quantitative reverse transcription-PCR results revealed that specific miRNAs were differentially expressed in developing buds, and some correlated negatively with the expression of their targets at specific stages of axillary bud development. For instance, the expression patterns of miR159 and its target GAMYB suggested that they may play roles in regulating abscisic acid-signalling pathways during sugarcane bud outgrowth. Our work reveals, for the first time, differences in the composition and expression profiles of diverse sRNAs and targets between inactive and developing vegetative buds that, together with the endogenous balance of specific hormones, may be important in regulating axillary bud outgrowth

It takes two to tango : molecular links between plant immunity and brassinosteroid signalling

In response to the invasion of microorganisms, plants actively balance their resources for growth and defence, thus ensuring their survival. The regulatory mechanisms underlying plant immunity and growth operate through complex networks, in which the brassinosteroid phytohormone is one of the central players. In the past decades, a growing number of studies have revealed a multi-layered crosstalk between brassinosteroid-mediated growth and plant immunity. In this Review, by means of the tango metaphor, we immerse ourselves into the intimate relationship between brassinosteroid and plant immune signalling pathways that is tailored by the lifestyle of the pathogen and modulated by other phytohormones. The plasma membrane is the unique stage where brassinosteroid and immune signals are dynamically integrated and where compartmentalization into nanodomains that host distinct protein consortia is crucial for the dance. Shared downstream signalling components and transcription factors relay the tango play to the nucleus to activate the plant defence response and other phytohormonal signalling pathways for the finale. Understanding how brassinosteroid and immune signalling pathways are integrated in plants will help develop strategies to minimize the growth-defence trade-off, a key challenge for crop improvement

Dinâmica subcelular do peptídeo endógeno AtPep1 e seus receptores em Arabidopsis: implicações na imunidade de plantas

This work investigated the subcellular dynamics of the plant elicitor peptide AtPep1 and its interplay with plant defense responses. First, an introduction of the plant innate immunity system is provided with emphasis on pattern trigger immunity (PTI), which is based on the recognition of \"non-self\" and \"self\" elicitor molecules by surface-localized patternrecognition receptors (PRRs). Then, the Arabidopsis endogenous peptides that act as selfelicitor molecules are presented, with details on AtPep1 and its PEPR receptors. Plant endomembrane trafficking is described, encompassing endocytic pathways, clathrin mediated endocytosis (CME) and receptor-mediated endocytosis (RME). In the next chapter, we explored strategies for the in vivo study of the subcellular behavior of AtPep1; to this end, we fused the precursor protein of AtPep1 (PROPEP1) to GFP and assessed its localization. We found that PROPEP1 was associated with the tonoplast and accumulated in the vacuole, suggesting that this organelle could work as the station where PROPEP1 is stored and later released, only in a danger situation, hence initiating AtPep1. Moreover, we generated AtPep1 versions labeled with fluorescent dyes and demonstrated that this peptide could be fluorescently tagged without loss of its biological activity. In chapter 3, we combined classical and chemical genetics with life imaging to study the behavior of a bioactive fluorescently labeled AtPep1 in the Arabidopsis root meristem. We discovered that the labeled AtPep1 was able to bind the plasma membrane very quickly in a receptor-dependent manner. Subsequently, the PEPR-AtPep1 complex was internalized via CME and transported to the lytic vacuole, passing through early and late endosomal compartments. Impairment of CME compromised the AtPep1 responses. Our findings provide for the first time an in vivo visualization of a signaling peptide in plant cells, thus giving insights into its intracellular fate and dynamics. The role of the coregulatory receptor BRI1-associated kinase 1 (BAK1) in AtPep1-responses was also investigated (chapter 4). Our results confirmed that BAK1 interacts with PEPRs in a ligand-dependent manner and indicate that BAK1 modulates AtPep1 signaling and endocytosis, but that, when absent, it might be replaced by homologous SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) proteins that could have additional functions during the AtPep1 signaling. Furthermore, phosphorylation events after the formation of PEPR-BAK1 complexes seem to dictate the molecular bases of AtPep1 internalization and signaling. Finally, we discussed our findings in a more general perspective, highlighting the important findings for the plant endomembrane trafficking field, the potential use of fluorescently labeled ligands as a tool to study ligand-receptors pairs, the availability of AtPep1-PEPRs as an excellent model to study endocytosis and its interplay with signaling, and the future challenges in the field.Neste trabalho, foi investigada a dinâmica subcelular do peptídeo elicitor de planta AtPep1 e suas implicações nas respostas de defesa. Primeiramente, é fornecida uma introdução do sistema imune inato de plantas com ênfase na imunidade ativada por moléculas elicitoras derivadas de organismos invasores ou da mesma planta, após seu reconhecimento por receptores localizados na membrana plasmática (PTI responses). Peptídeos endógenos que têm sido reportados em Arabidopsis como ativadores de PTI são descritos, dando especial destaque para o peptídeo AtPep1 e seus receptores PEPRs. O tráfego de endomembranas em plantas é introduzido, abrangendo as vias de internalização, endocitose mediada por proteínas clathrinas (CME) e endocitose mediada por receptor (RME). No capítulo seguinte, foram avaliadas estratégias para o estudo in vivo da dinâmica subcelular do AtPep1. Para isso a proteína precursora do AtPep1 (PROPEP1) foi fusionada a GFP e sua localização visualizada, encontrando que PROPEP1 é associado com o tonoplasto e acumula dentro do vacúolo, fato que sugere uma função de armazenamento do PROPEP1 para esta organela, desde onde é liberado em caso de uma situação de perigo dando origem ao AtPep1. Adicionalmente, foram produzidas versões biologicamente ativas do AtPep1 marcado com fluróforos. No capítulo três foram combinados genética clássica e genética química com visualizações in vivo para estudar o comportamento de um AtPep1 bioativo e marcado fluorescentemente na células meristemática da ponta da raiz de Arabidopsis, sendo encontrado que AtPep1 se liga rapidamente na membrana plasmática numa forma dependente de receptor. Em seguida, o complexo AtPep1-PEPR foi internalizado via CME e transportado para o vacúolo, passando através do endossomo primário e secundário. Quando o funcionamento da CME foi comprometido, as respostas ao AtPep1 também foram afetadas. Estes resultados fornecem a primeira visualização in vivo de um peptídeo de sinalização em plantas, mostrando sua dinâmica e destino intracelular. O papel regulatório durante as respostas induzidas pelo AtPep1 do co-receptor BRI1-associated kinase 1 (BAK1) foram investigadas (Capítulo quatro). Nossos resultados confirmaram que BAK1 interage com PEPRs numa forma dependente do ligante e indicam que BAK1 modula sinalização e endocitose do AtPep1, no entanto quando ausente, BAK1 pode ser substituído por seus homólogos SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE os quais poderiam ter funções adicionais durante as repostas induzidas pelo AtPep1. Eventos de fosforilação após a formação do complexo PEPR-BAK1 parecem ditar as bases moleculares da internalização e sinalização do AtPep1. Finalmente, são discutidos os resultados encontrados nesta pesquisa numa perspectiva geral, destacando a relevância destas descobertas na área de pesquisa em que estão inseridos, o potencial que representa o uso de ligantes marcados fluorescentemente como ferramenta para o estudo de complexos entre ligante-receptor, a disponibilidade do sistema AtPep1-PEPRs como modelo de estudo da endocitose em plantas e sua relação com sinalização, e os futuros desafios na área

It takes two to tango – molecular links between plant immunity and brassinosteroid signalling

ABSTRACT In response to the invasion of microorganisms, plants actively balance their resources for growth and defence, thus ensuring their survival. The regulatory mechanisms underlying plant immunity and growth operate through complex networks, in which the brassinosteroid phytohormone is one of the central players. In the past decades, a growing number of studies have revealed a multi-layered crosstalk between brassinosteroid-mediated growth and plant immunity. In this Review, by means of the tango metaphor, we immerse ourselves into the intimate relationship between brassinosteroid and plant immune signalling pathways that is tailored by the lifestyle of the pathogen and modulated by other phytohormones. The plasma membrane is the unique stage where brassinosteroid and immune signals are dynamically integrated and where compartmentalization into nanodomains that host distinct protein consortia is crucial for the dance. Shared downstream signalling components and transcription factors relay the tango play to the nucleus to activate the plant defence response and other phytohormonal signalling pathways for the finale. Understanding how brassinosteroid and immune signalling pathways are integrated in plants will help develop strategies to minimize the growth–defence trade-off, a key challenge for crop improvement.</jats:p

Dimensions of social and political capital in interventions to improve household well-being: Implications for coffee-growing areas in southern Colombia

This paper studies the influence of community capitals on well-being through a Community Capital Index (CCI) within coffee-growing families in southern Colombia. Our results show different farm typologies, with different levels of capital endowment translated into well-being that, in our case, were represented in the CCI. Specifically, social and political capitals positively affect coffee-growing families’ decisions in terms of life strategies. The results of this study increase our understanding of welfare enhancement and its relationship with capital endowment according to the type of coffee producer, having implications for the planning of more effective programs towards the improvement of quality of life.</jats:p

Dimensions of social and political capital in interventions to improve household well-being: Implications for coffee-growing areas in southern Colombia.

This paper studies the influence of community capitals on well-being through a Community Capital Index (CCI) within coffee-growing families in southern Colombia. Our results show different farm typologies, with different levels of capital endowment translated into well-being that, in our case, were represented in the CCI. Specifically, social and political capitals positively affect coffee-growing families' decisions in terms of life strategies. The results of this study increase our understanding of welfare enhancement and its relationship with capital endowment according to the type of coffee producer, having implications for the planning of more effective programs towards the improvement of quality of life

Silvopastoral Systems Enhance Soil Health in the Amazon Region

Silvopastoral systems (SPS), an integrated farming system in which tropical grasses are combined with trees and shrubs, have been implemented in the last years in the Amazon region in order to mitigate the impacts generated by the traditional cattle ranching system. However, despite the multiple SPS’s benefits to soil and ecosystem, there is a paucity of comprehensive studies revealing the potential soil health (SH) restoration through SPS. Here, by developing an overall SH index using local native vegetation (Amazon rainforest) as a reference, we aimed to assess SH changes induced by the land transition from the traditional livestock production system to the SPS in the Colombian Amazon region. A chronosequence conformed by three areas: (i) native vegetation, (ii) traditional pasture and (iii) silvopastoral system was established in two study sites located in the Colombian Amazon, specifically in Caquetá State, the second hotspot of deforestation in the Amazon Basin. The results indicated high soil compaction and loss of macrofauna diversity and richness due to pasture management, causing a loss of 9% of soil capacity to function. In contrast, by integrating 31 soil indicators, our SH assessment revealed that SPS was an effective strategy for the recovery of SH, impacting positively multiple soil functions related to nutrient dynamics, water retention and supply, and biological activity.</jats:p