Evolutionary analyses of NIN-like proteins in plants and their roles in nitrate signaling

Mu, Xiaohuan; Luo, Jie

doi:10.1007/s00018-019-03164-8

Cited by 74 publications

(63 citation statements)

References 111 publications

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“…Auxin is the master regulator of adventitious root (AR) formation [102], and other signaling pathways also can mount auxin to shape root architecture, such as nitrate [103]. Numerous studies have demonstrated that early auxin accumulation is a critical signal to initiate cell fate transition of the root founder cells, which is essential for vegetative propagation of plants [104][105][106].…”

Section: Root Developmentmentioning

confidence: 99%

The Roles of Auxin Biosynthesis YUCCA Gene Family in Plants

Cao

Yang

Shang

et al. 2019

IJMS

152

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Auxin plays essential roles in plant normal growth and development. The auxin signaling pathway relies on the auxin gradient within tissues and cells, which is facilitated by both local auxin biosynthesis and polar auxin transport (PAT). The TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA)/YUCCA (YUC) pathway is the most important and well-characterized pathway that plants deploy to produce auxin. YUCs function as flavin-containing monooxygenases (FMO) catalyzing the rate-limiting irreversible oxidative decarboxylation of indole-3-pyruvate acid (IPyA) to form indole-3-acetic acid (IAA). The spatiotemporal dynamic expression of different YUC gene members finely tunes the local auxin biosynthesis in plants, which contributes to plant development as well as environmental responses. In this review, the recent advances in the identification, evolution, molecular structures, and functions in plant development and stress response regarding the YUC gene family are addressed.

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Section: Root Developmentmentioning

confidence: 99%

The Roles of Auxin Biosynthesis YUCCA Gene Family in Plants

Cao

Yang

Shang

et al. 2019

IJMS

152

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“…Moreover, it is unclear how many PB1 domain-containing gene families are present in other kingdoms. Deep evolution has been relatively well studied for ARF and Aux/IAA gene families [26] and to a certain extent for NLPs [27], but the presence and the evolution of other PB1 domains, if any, in plants and unicellular eukaryotes is obscure. Hence, the current study is designed to address several important questions related to the distribution and ancestry of PB1 domains in the eukaryotic tree of life: (1) How many PB1 domain-containing gene families are present in the kingdoms Protozoa, Chromista, Fungi and Plantae?…”

Section: Introductionmentioning

confidence: 99%

Deep Evolutionary History of the Phox and Bem1 (PB1) Domain Across Eukaryotes

Mutte

Weijers

2020

Preprint

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6 7 Sumanth Kumar Mutte: Sumanth.mutte@wur.nl 8 * Corresponding author (Dolf Weijers): dolf.weijers@wur.nl ABSTRACT 21Protein oligomerization is a fundamental process to build complex functional modules. 22 Domains that facilitate the oligomerization process are diverse and widespread in nature 23 across all kingdoms of life. One such domain is the Phox and Bem1 (PB1) domain, which is 24 functionally (relatively) well understood in the animal kingdom. However, beyond animals, 25 neither the origin nor the evolutionary patterns of PB1-containing proteins are understood. 26 While PB1 domain proteins have been found in other kingdoms, including plants, it is unclear 27 how these relate to animal PB1 proteins. 28 To address this question, we utilized large transcriptome datasets along with the proteomes of 29 a broad range of species. We discovered eight PB1 domain-containing protein families in 30 plants, along with three each in Protozoa and Chromista and four families in Fungi. Studying 31 the deep evolutionary history of PB1 domains throughout eukaryotes revealed the presence of 32 at least two, but likely three, ancestral PB1 copies in the Last Eukaryotic Common Ancestor 33 (LECA). These three ancestral copies gave rise to multiple orthologues later in evolution. 34 Tertiary structural models of these plant PB1 families, combined with Random Forest based 35 classification, indicated family-specific differences attributed to the length of PB1 domain 36 and the proportion of β-sheets. 37 This study identifies novel PB1 families and reveals considerable complexity in the protein 38 oligomerization potential at the origin of eukaryotes. The newly identified relationships 39 provide an evolutionary basis to understand the diverse functional interactions of key 40 regulatory proteins carrying PB1 domains across eukaryotic life. 41 42 43 44 3 KEYWORDS 45 Phylogeny, protein oligomerization, plants, animals, homology modeling, random forest 46 47 BACKGROUND 48Protein-protein interaction is a basic and important mechanism that brings proteins 49 together in a functional module and thus allows the development of higher-order 50 functionalities. One of the versatile interaction domains that brings this modularity through 51 either dimerization or oligomerization is the PB1 domain. Initially, the two animal proteins, 52 p40 Phox and p67 Phox , were shown to interact through a novel motif that contains a stretch of 53 negatively charged amino acids [1]. In the same study, it was also shown that the yeast CELL 54 DIVISION CONTROL 24 (Cdc24) protein contains the same motif as found in p40 Phox , and 55 hence named as PC motif (for p40 Phox and Cdc24; Nakamura et al. 1998). Later, the BUD 56 EMERGENCE 1 (Bem1) protein in yeast was also found to have this motif, after which it has 57 been renamed as PB1 domain (for Phox and Bem1). The PB1 domain of Bem1 in yeast is 58 required for the interaction with Cdc24 to maintain cell polarity [2]. Later, in mammals, 59 many protein families were identified that contain a ...

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“…The Arabidopsis genome contains nine NIN-like Proteins (NLPs), with all of them comprising the RWP-RK motif, enabling DNA binding and transcriptional activation, and an additional PB-domain (Protein Binding) (Chardin et al, 2014). In addition, NLPs comprise a highly conserved nitrate-responsive domain (NRD), which determines nitrate perception and signaling transmission (Mu & Luo, 2019). In Arabidopsis, the characterization of NLP function is described for AtNLP8 and AtNLP6/AtNLP7 complex.…”

Section: Introductionmentioning

confidence: 99%

“…One of the central transcriptional regulators is the Nodule-INception protein (NIN), which was originally identified in Lotus japonicus (Schauser et al, 1999). Different to other NLPs, the Nitrate-responsive domain of legume NINs is only partially conserved, which could explain the loss of direct nitrate responsiveness of NIN and thus may represent an evolutional adaptation of legumes (Mu & Luo, 2019) to maintain this mutualistic interaction. However, it should be noted that the functionality of root-nodule symbiosis is strictly regulated by the availability of nitrate via NLP function as exemplified by the Nitrate unResponsive SYMbiosis 1 (NRSYM1) in Lotus japonicus (Nishida et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

Integration of A Nitrate-Related Signaling Pathway in Rhizobia-Induced Responses During Interactions with Non-Legume Host Arabidopsis thaliana

Schenk

Lichtenberg

Keller

et al. 2020

Preprint

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Nitrogen (N) is an essential macronutrient and a key cellular messenger. Plants have evolved refined molecular systems to sense the cellular nitrogen status. Exemplified by the root nodule symbiosis between legumes and symbiotic rhizobia, where external nitrate availability inhibits the interaction. However, nitrate also functions as a metabolic messenger, resulting in nitrate signaling cascades which intensively cross-talk with other physiological pathways. NIN (NODULE INCEPTION)-LIKE PROTEINS (NLPs) are key players in nitrate signaling and regulate nitrate-dependent transcription. Nevertheless, the coordinated interplay between nitrate signaling pathways and rhizobacteria-induced responses remains to be elucidated. In our study, we investigate rhizobia-induced changes in the root system architecture of the non-legume host Arabidopsis in dependence of different nitrate conditions. We demonstrate that rhizobia induce lateral root growth, and increase root hair length and density in a nitrate-dependent manner. These processes are regulated by AtNLP4 and AtNLP5 as well as nitrate transceptor NRT1.1, as the corresponding mutants fail to respond to rhizobia. On a cellular level, NLP4 and NLP5 control a rhizobia-induced decrease in cell elongation rates, while additional cell divisions occurred independent of NLP4. In summary, our data suggest that root morphological responses to rhizobia, dependent on a nutritional signaling pathway that is evolutionary related to regulatory circuits described in legumes.

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Evolutionary analyses of NIN-like proteins in plants and their roles in nitrate signaling

Cited by 74 publications

References 111 publications

The Roles of Auxin Biosynthesis YUCCA Gene Family in Plants

The Roles of Auxin Biosynthesis YUCCA Gene Family in Plants

Deep Evolutionary History of the Phox and Bem1 (PB1) Domain Across Eukaryotes

Integration of A Nitrate-Related Signaling Pathway in Rhizobia-Induced Responses During Interactions with Non-Legume Host Arabidopsis thaliana

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